definition
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
PERSON:Daniel Schober
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL
If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.
is a defining property chain axiom where second argument is reflexive
An alternative label for a class or property which has a more general meaning than the preferred name/primary label.
has broad synonym
disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NCIT:C41009"^^xsd:string
An annotation property that links an ontology entity or a statement to a prefixed identifier or URI.
An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.
has exact synonym
An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.
has narrow synonym
is part of
my brain is part of my body (continuant parthood, two material entities)
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
this day is part of this year (occurrent parthood)
a core relation that holds between a part and its whole
Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
part_of
part of
has part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
a core relation that holds between a whole and its part
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
has_part
preceded by
x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
is preceded by
preceded_by
precedes
x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
A relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist through the separation or transformation of a part of the old entity, and the new entity inherits a significant portion of the matter belonging to that part of the old entity.
derives from part of
inheres in
this fragility is a characteristic of this vase
this red color is a characteristic of this apple
a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
inheres_in
Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.
characteristic of
bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
Inverse of characteristic_of
A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
bearer_of
is bearer of
has characteristic
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
has participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
a relation between a process and a continuant, in which the continuant is somehow involved in the process
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
has_participant
this catalysis function is a function of this enzyme
a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
function_of
is function of
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
function of
this red color is a quality of this apple
a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
A quality inheres in its bearer at all times for which the quality exists.
is quality of
quality_of
quality of
this investigator role is a role of this person
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
is role of
role_of
role of
this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
has_function
has function
this apple has quality this red color
a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
has_quality
has quality
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
has_role
has role
a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
has disposition
disposition of
A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.
A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.
By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.
has negative regulatory component activity
A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.
By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.
has positive regulatory component activity
A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.
w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
ends after
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately preceded by
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
immediately precedes
x overlaps y if and only if there exists some z such that x has part z and z part of y
http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
overlaps
w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
has component
p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.
Regulation precludes parthood; the regulatory process may not be within the regulated process.
regulates
p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.
negatively regulates (process to process)
negatively regulates
p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.
positively regulates (process to process)
positively regulates
mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
osteoclast SubClassOf 'capable of' some 'bone resorption'
A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
capable of
c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
capable of part of
Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporally related to
p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
has input
A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.
c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.
A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.
c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.
p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.
holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y
p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.
q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.
Because part_of is transitive, inheres in is a sub-relation of characteristic of part of
characteristic of part of
A mereological relationship or a topological relationship
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
mereotopologically related to
a particular instances of akt-2 enables some instance of protein kinase activity
c enables p iff c is capable of p and c acts to execute p.
This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.
enables
A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
This is a grouping relation that collects relations used for the purpose of connecting structure and function
functionally related to
this relation holds between c and p when c is part of some c', and c' is capable of p.
part of structure that is capable of
c involved_in p if and only if c enables some process p', and p' is part of p
involved in
enabled by
regulated by
negatively regulated by
positively regulated by
input of
causally downstream of
immediately causally downstream of
p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.
indirectly positively regulates
p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.
indirectly negatively regulates
relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causally related to
p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.
causally upstream of
p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.
immediately causally upstream of
p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.
We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
inverse of causally upstream of or within
c involved in regulation of p if c is involved in some p' and p' regulates some p
c involved in regulation of p if c is involved in some p' and p' positively regulates some p
c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p
OWL does not allow defining object properties via a Union
involved in or involved in regulation of
A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.
An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.
An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.
The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.
The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.
directly negatively regulates activity of
The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
directly positively regulates activity of
This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.
helper property (not for use in curation)
A relationship between a material entity and a process where the material entity has some causal role that influences the process
p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.
The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch
molecular interaction relation helper property
The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).
p directly regulates q iff p is immediately causally upstream of q and p regulates q.
gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p
A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
causal relation between material entity and a process
Holds between c and p if and only if c is capable of some activity a, and a regulates p.
Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
renin -> arteriolar smooth muscle contraction
Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.
directly positively regulates (process to process)
p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.
directly negatively regulates (process to process)
Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.
acts upstream of or within, positive effect
acts upstream of or within, negative effect
c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive
c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative
causally upstream of or within, negative effect
causally upstream of or within, positive effect
The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.
p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.
indirectly causally upstream of
p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.
indirectly regulates
A diagnostic testing device utilizes a specimen.
X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.
A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.
See github ticket https://github.com/oborel/obo-relations/issues/497
device utilizes material
A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.
A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C.
A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C.
An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
continuant
An entity that has temporal parts and that happens, unfolds or develops through time.
occurrent
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
independent continuant
p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
process
disposition
A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
realizable entity
quality
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
specifically dependent continuant
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
role
function
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
Elucidation: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
material entity
An environmental system which includes both living and non-living components.
ecosystem
active ecosystem management process
A planned process during which humans access and obtain resources, benefits, or services from a natural or anthropised ecosystem.
planned environmental usage process
A process in which includes the components of an environmental system as participants.
environmental system process
A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.
This is the same as GO molecular function
Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
gene product or complex activity
A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
biological process
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.
curation status specification
The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
PERSON:Bill Bug
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
root node
An active ecosystem management process during which a human employs machines or tools to directly impact an ecosystem and realize some ecosystem management goal.
mechanical ecosystem management process
A mechanical ecosystem management process during which vegetation is removed.
mechanical vegetation removal process
A mechanical vegetation removal process in which a human employs a tool comprising a lever and gripping portion (root wrench).
root wrench removal process
A mechanical vegetation removal process during which plants at ground level are cut and residual stumps are covered with a sun-blocking material (e.g. silage tarp).
cut and cover removal process
A mechanical vegetation removal process in which a human cuts and removes plant material.
cutting removal process
A mechanical vegetation removal process in which a human severs subsoil roots using a spade and pries the plant out of the ground.
spading removal process
A mechanical vegetation removal process in which a human removes trees from a given area with the goal of reducing overall canopy cover thereby increasing light availability for understorey plants.
canopy thinning process
A mechanical vegetation removal process in which a human removes leaf litter from the ground thereby increasing the light availability for soil.
leaf litter removal process
A mechanical ecosystem management process in which a human controls fauna populations.
mechanical fauna control process
A mechanical fauna control process in which a human uses traps to control fauna.
mammal trapping process
A mechanical fauna control process in which a human targets predators for removal from the ecosystem.
predator control process
A mechanical fauna control process in which a human installs fencing to restrict either immigration or emmigration of fauna from a particular area.
fencing process
A mechanical fauna control process in which a human installs an electronic device to deter species from a particular area.
mechanical species deterrent process
A mechanical ecosystem management process during which a human deliberately alters the hydrologic cycle in an area.
mechanical hydrological alteration process
A mechanical hydrological alteration process in which a human constructs some dam to restore a meander sequence to a river or stream.
beaver dam analogue
dam construction process
A mechanical hydrological alteration process in which a human removes some dam with the goal of altering the hydroperiod of surrounding lands and reconnecting rivers.
dam removal process
A mechanical hydrological alteration process in which a human uncovers and collapses subterranean tile drains in situ to reduce drainage on the landscape and restore wetland hydroperiod.
This technique is actively practiced by the Nature Conservancy of Canada, but has not been documented in the literature yet.
tile drain crushing process
A mechanical hydrological alteration process in which a human uncovers and removes subterranean tile drains to reduce drainage on the landscape and restore wetland hydroperiod.
tile drain removal process
A mechanical ecosystem management process in which a human creates sites for fauna to breed, feed and shelter.
nest site creation process
A mechanical ecosystem management process in which a human creates places for birds to perch.
perch creation process
A mechanical ecosystem management process in which a human cultivates strips of flora between landscape features using earthworks and planting processes.
buffer strip creation process
A mechanical ecosystem management process in which a human cultivates strips of flora in the riparian areas of rivers.
riparian buffer strip creation process
A mechanical ecosystem management process in which a human leaves strips of flora untouched when clearing the land for other purposes.
buffer strip retention process
A mechanical ecosystem management process during which the topology of some area is deliberately changed at least at the micro scale (e.g. 1m2).
Difficult to suggest a firm border for scale. I doubt digging out a small hole would be called earthworks but settled on at least 1 m2 of earth moved. See Landscape Microscale Size and its associated scale properties for more nuance: ENVO:03620005; ENVO:03620006; ENVO:03620007; ENVO:03620008
earthworks process
An earthworks process in which earthen barriers (berms) are constructed with the goal of obstructing or slowing floodwaters.
berm creation process
An earthworks process in which a human creates a pond.
pond creation process
An earthworks process in which a human reshapes the banks or basin of a pond.
pond reprofiling process
An earthworks process in which a human alleviates the compaction of soil.
soil decompaction process
An earthworks process in which a human breaks up the soil, and sometimes adds organic matter.
soil ripping process
tilling process
An earthworks process in which a human deeply breaks up and overturns soil and vegetation.
ploughing process
An earthworks process in which a human creates a specific slope.
grading process
An earthworks process in which a human installs inorganic material, usually a mesh, to stabilize a slope.
slope stabilization process
An earthworks process in which a human installs inorganic material, usually in a mesh, to stabilize a slope on the bank of a body of water.
shoreline reinforcement process
An earthworks process in which a human digs pits and creates mounds to reproduce a natural disturbance regime.
pit and mound excavation process
An earthworks process in which a human realigns the channel of a stream by digging out replacement pathways and filling existing ones.
channel realignment process
An earthworks process in which a human realigns the channel of a stream by digging out replacement pathways and filling existing ones with the goal of recreating a natural pool-riffle-pool meander sequence.
natural channel realignment process
An earthworks process in which a human removes the sediment layer of a water body.
dredging process
A mechanical ecosystem management process in which a human creates a crossing (bridge or underpass) to help fauna pass through a barrier such as a road, fence or property.
fauna passage creation process
A mechanical ecosystem management process in which a human removes the topsoil layer.
topsoil removal process
A mechanical ecosystem management process in which a human installs some material to reduce erosion.
erosion control process
An erosion control process in which a human installs a textile.
erosion blanket process
An erosion control process in which a human installs a fence with a geotextile to restrict sediment transport.
erosion fencing process
An erosion control process in which a human interleaves live materials to make short fencing along a slope.
wattle fencing process
A mechanical ecosystem management process in which a human installs semi-permanent lines to supply a controlled amount of water to plants.
irrigation process
A predator control process in which a human installs a mechanical device designed to deter predators from a given area.
deterrence-focused predator control process
A mechanical fauna control process in which a human excludes fauna from a specific area.
fauna exclusion process
A mechanical fauna control process in which a human deters fauna from a specific area.
mechanical fauna deterrent process
A mechanical fauna control process in which a human captures fauna for the purposes of protecting existing organisms from some threat.
fauna capture for conservation
A mechanical ecosystem management process in which a human installs some means of bypassing hazards (e.g. dams) for fish.
fish bypass installation process
A fish bypass installation process in which a human installs a chute consisting of a series of stepped pools to allow fish to move past a dam.
fish ladder installation process
An earthworks process in which a human fills in a drainage ditch to restore the hydroperiod to a given area.
ditch plugging process
An earthworks process in which a human adds sediment to a water body in order to modify the substrate composition.
sediment addition process
A mechanical ecosystem management process in which a human installs a barrier to protect newly planted flora from herbivory.
new plant protection process
These closed-canopy forests are renowned for their complex structure and high primary productivity, which support high functional and taxonomic diversity. At subtropical latitudes they transition to warm temperate forests (T2.4). Bottom-up regulatory processes are fuelled by large autochthonous energy sources that support very high primary productivity, biomass and LAI. The structurally complex, multi-layered, evergreen tree canopy has a large range of leaf sizes (typically macrophyll-notophyll) and high SLA, reflecting rapid growth and turnover. Diverse plant life forms include buttressed trees, bamboos (sometimes abundant), palms, epiphytes, lianas and ferns, but grasses and hydrophytes are absent or rare. Trophic networks are complex and vertically stratified with low exclusivity and diverse representation of herbivorous, frugivorous, and carnivorous vertebrates. Tree canopies support a vast diversity of invertebrate herbivores and their predators. Mammals and birds play critical roles in plant diaspore dispersal and pollination. Growth and reproductive phenology may be seasonal or unseasonal, and reproductive masting is common in trees and regulates diaspore predation. Fungal, microbial, and diverse invertebrate decomposers and detritivores dominate the forest floor and the subsoil. Diversity is high across taxa, especially at the upper taxonomic levels of trees, vertebrates, fungi, and invertebrate fauna. Neutral processes, as well as micro-niche partitioning, may have a role in sustaining high diversity, but evidence is limited. Many plants are in the shade, forming seedling banks that exploit gap-phase dynamics initiated by individual tree-fall or stand-level canopy disruption by tropical storms (e.g. in near-coastal forests). Seed banks regulated by dormancy are uncommon. Many trees exhibit leaf plasticity enabling photosynthetic function and survival in deep shade, dappled light or full sun, even on a single individual. A few species germinate on tree trunks, gaining quicker access to canopy light, while roots absorb microclimatic moisture until they reach the soil.
Definition taken from Ecosystem Properties section of IUCN - needs to be reformatted for ontology.
T1.1 Tropical-subtropical lowland rainforests
TT1.a1
TT1.a1 Tropical Lowland Rainforest
Tropical Lowland Rainforest
Tropical-subtropical lowland rainforests
These closed-canopy forests and thickets have drought-deciduous or semi-deciduous phenology in at least some woody plants (rarely fully evergreen), and thus seasonally high LAI. Strongly seasonal photoautotrophic productivity is limited by a regular annual water deficit/surplus cycle. Diversity is lower across most taxa than T1.1, but tree and vertebrate diversity is high relative to most other forest systems. Plant growth forms and leaf sizes are less diverse than in T1.1. Grasses are rare or absent, except on savanna ecotones, due to canopy shading and/or water competition, while epiphytes, ferns, bryophytes, and forbs are present but limited by seasonal drought. Trophic networks are complex with low exclusivity and diverse representation of herbivorous, frugivorous, and carnivorous vertebrates. Fungi and other microbes are important decomposers of abundant leaf litter and N-fixing plants can be abundant. Many woody plants are dispersed by wind and some by vertebrates. Most nutrient capital is sequestered in vegetation or cycled through the litter layer. Trees typically have thin bark and low fire tolerance and can recruit in shaded microsites, unlike many in savannas. Plants are tolerant of seasonal drought but can exploit moisture when it is seasonally available through high SLA and plastic productivity. Gap-phase dynamics are driven primarily by individual tree-fall and exploited by seedling banks and vines (seedbanks are uncommon). These forests may be involved in fire-regulated stable-state dynamics with savannas.
T1.2 Tropical-subtropical dry forests and thickets
TT1.b1
TT1.b1 Tropical Seasonally Dry Forest & Thicket
Tropical Seasonally Dry Forest & Thicket
Tropical-subtropical dry forests and thickets
Closed-canopy evergreen forests on tropical mountains usually have a single-layer low tree canopy (~5�20m tall) with small leaf sizes (microphyll-notophyll) and moderate-high SLA. They transition to lowland rainforests (T1.1) with decreasing altitude and to warm temperate forests (T2.4) at higher latitudes. Structure and taxonomic diversity become more diminutive and simpler with altitude, culminating in elfinwood forms. Conspicuous epiphytic ferns, bryophytes, lichens, orchids, and bromeliads drape tree branches and exploit atmospheric moisture (cloud stripping), but grasses are rare or absent, except for bamboos in some areas. Moderate productivity fuelled by autochthonous energy is limited by high exposure to UV-B radiation, cool temperatures, and sometimes by shallow soil or wind exposure. Limited energy and sequestration in humic soils may limit N and P uptake. Growth and reproductive phenology is usually seasonal. Plant propagules are dispersed mostly by wind and territorial birds and mammals. Tree diversity is moderate to low, while epiphytes are diverse, but there is often high local endemism at higher altitudes in most groups, especially amphibians, birds, plants, and invertebrates. Gap-phase dynamics are driven by tree-fall, landslides, lightning strikes, or in some areas more rarely by extreme wind storms. Seedling banks are common (seedbanks are uncommon) and most plants are shade tolerant and can recruit in the shade.
T1.3 Tropical-subtropical montane rainforests
TT1.a2
TT1.a2 Tropical Montane Rainforest
Tropical Montane Rainforest
Tropical-subtropical montane rainforests
Structurally simple evergreen forests with high densities of thin stems, closed to open uniform canopies, typically 5�20 m tall and uniform with a moderate to high LAI. Productivity is lower than in other tropical forests, weakly seasonal and limited by nutrient availability and in some cases by soil anoxia, but decomposition is rapid. Plant traits such as insectivory, N-fixing microbial associations and ant mutualisms are well represented, suggesting adaptive responses to nitrogen deficiency. Plant insectivory aside, trophic networks are simple compared to other tropical forests. Diversity of plant and animal taxa is also relatively low, but dominance and endemism are proportionately high. Tree foliage is characterised by small (microphyll-notophyll) leaves with lower SLA than other tropical forests. Leaves are leathery and often ascending vertically, enabling more light penetration to ground level than in other tropical forests. Tree stems are slender (generally <20 cm in diameter), sometimes twisted, and often densely packed and without buttresses. Epiphytes are usually abundant but lianas are rare and ground vegetation is sparse, with the forest floor dominated by insectivorous vascular plants and bryophytes.
T1.4 Tropical heath forests
TT1.a3
TT1.a3 Tropical Heath Forest
Tropical Heath Forest
Tropical heath forests
Evergreen, structurally simple forests and woodlands in cold climates are dominated by needle-leaf conifers and may include a subdominant component of deciduous trees, especially in disturbed sites, accounting for up to two-thirds of stand-level leaf biomass. Boreal forests are generally less diverse, more cold-tolerant and support a more migratory fauna than temperate montane forests. Structure varies from dense forest up to 30 m tall to stunted open woodlands <5 m tall. Large trees engineer habitats of many fungi, non-vascular plants, invertebrates, and vertebrates that depend on rugose bark, coarse woody debris, or large tree canopies. Energy is mainly from autochthonous sources but may include allochthonous subsidies from migratory vertebrates. Primary productivity is limited by seasonal cold and may also be limited by water deficit on coarse textured soils. Forested bogs occupy peaty soils (TF1.6). Seasonal primary productivity may sustain a trophic web with high densities of small and large herbivores (e.g. hare, bear, deer, and insects), with feline, canine, and raptor predators. Browsers are top-down regulators of plant biomass and cyclers of nitrogen, carbon, and nutrients. Forest structure may be disrupted by insect defoliation or fires on multi-decadal cycles. Tree recruitment occurs semi-continuously in gaps or episodically after canopy fires and may be limited by spring frost, desiccation, permafrost fluctuations, herbivory, and surface fires. Plants and animals have strongly seasonal growth and reproductive phenology and possess morphological, behavioural, and ecophysiological traits enabling cold-tolerance and the exploitation of short growing seasons. Plant traits include bud protection, extra-cellular freezing tolerance, hardened evergreen needle leaves with low SLA or deciduous leaves with high SLA, cold-stratification seed dormancy, seasonal geophytic growth forms, and vegetative storage organs. Tracheids in conifers confer resistance to cavitation in drought by compartmentalising water transport tissues. Some large herbivores and most birds migrate to winter habitats from the boreal zone, and thus function as mobile links, dispersing other biota and bringing allochthonous subsidies of energy and nutrients into the system. Hibernation is common among sedentary vertebrates, while insect life cycles have adult phases cued to spring emergence.
Narrow synonym in eIVC
T2.1 Boreal and temperate high montane forests and woodlands
Boreal and temperate high montane forests and woodlands
These structurally simple, winter deciduous forests have high productivity and LAI in summer. Winter dormancy, hibernation and migration are common life histories among plants and animals enabling cold avoidance. Local endemism is comparatively low and there are modest levels of diversity across major taxa. The forest canopy comprises at least two-thirds deciduous broad-leaf foliage (notophylll-mesophyll) with high SLA and up to one-third evergreen (typically needleleaf) cover. As well as deciduous woody forms, annual turnover of above-ground biomass also occurs some in non-woody geophytic and other ground flora, which are insulated from the cold beneath winter snow and flower soon after snowmelt before tree canopy closure. Annual leaf turnover is sustained by fertile substrates and water surplus, with nutrient withdrawal from foliage and storage of starch prior to fall. Tissues are protected from cold by supercooling rather than extra-cellular freeze-tolerance. Dormant buds are insulated from frost by bracts or by burial below the soil in some non-woody plants. Fungal and microbial decomposers play vital roles in cycling carbon and nutrients in the soil surface horizon. Despite highly seasonal primary productivity, the trophic network includes large browsing herbivores (deer), smaller granivores and herbivores (rodents and hares), and mammalian predators (canids and felines). Most invertebrates are seasonally active. Behavioural and life-history traits allow animals to persist through cold winters, including through dense winter fur, food caching, winter foraging, hibernation, dormant life phases, and migration. Migratory animals provide allochthonous subsidies of energy and nutrients and promote incidental dispersal of other biota. Browsing mammals and insects are major consumers of plant biomass and cyclers of nitrogen, carbon, and nutrients. Deciduous trees may be early colonisers of disturbed areas (later replaced by evergreens) but are also stable occupants across large temperate regions. Tree recruitment is limited by spring frost, allelopathy, and herbivory, and occurs semi-continuously in gaps. Herbivores may influence densities of deciduous forest canopies by regulating tree regeneration. Deciduous leaf fall may exert allelopathic control over tree seedlings and seasonal ground flora.
T2.2 Deciduous temperate forests
TT2.b1
TT2.b1 Temperate Deciduous-Mixed Forest & Woodland
Temperate Deciduous-Mixed Forest & Woodland
Deciduous temperate forests
Broadleaf and needleleaf rainforests in cool temperate climates have evergreen or semi-deciduous tree canopies with high LAI and mostly nanophyll-microphyll foliage. Productivity is moderate to high and constrained by strongly seasonal growth and reproductive phenology and moderate levels of frost tolerance. SLA may be high but lower than in T2.2. Evergreen trees typically dominate, but deciduous species become more abundant in sites prone to severe frost and/or with high soil fertility and moisture surplus. The smaller range of leaf sizes and SLA, varied phenology, frost tolerance, broader edaphic association, and wetter, cooler climate distinguish these forests from warm temperate forests (T2.4). Local or regional endemism is significant in many taxa. Nonetheless, energy sources are primarily autochthonous. Trophic networks are less complex than in other cool-temperate or boreal forests (T2.1 and T2.2), with weaker top-down regulation due to the lower diversity and abundance of large herbivores and predators. Tree diversity is low (usually <8�10 spp./ha), with abundant epiphytic and terrestrial bryophytes, pteridophytes, lichens, a modest range of herbs, and conspicuous fungi, which are important decomposers. The vertebrate fauna is mostly sedentary and of low-moderate diversity. Most plants recruit in the shade and some remain in seedling banks until gap-phase dynamics are driven by individual tree-fall, lightning strikes, or by extreme wind storms in some areas. Tree recruitment varies with tree masting events, which strongly influence trophic dynamics, especially of rodents and their predators.
Oceanic Cool Temperate Rainforest
T2.3 Oceanic cool temperate rainforests
TT2.b2
TT2.b2 Oceanic Cool Temperate Rainforest
Oceanic cool temperate rainforests
Relatively productive but structurally simple closed-canopy forests with high LAI occur in humid warm-temperate to subtropical climates. The tree canopies are more uniform than most tropical forests (T1.1 and T1.2) and usually lack large emergents. Their foliage is often leathery and glossy (laurophyll) with intermediate SLA values, notophyll-microphyll sizes, and prodigiously evergreen. Deciduous species are rarely scattered within the forest canopies. These features, and drier, warmer climates and often more acid soils distinguish them from oceanic cool temperate forests (T2.3), while in the subtropics they transition to T1 forests. Autochthonous energy supports relatively high primary productivity, weakly limited by summer drought and sometimes by acid substrates. Forest function is regulated mainly by bottom-up processes related to resource competition rather than top-down trophic processes or disturbance regimes. Trophic structure is simpler than in tropical forests, with moderate levels of diversity and endemism among major taxa (e.g. typically <20 tree spp./ha), but local assemblages of birds, bats, and canopy invertebrates may be abundant and species-rich and play important roles in pollination and seed dispersal. Canopy insects are the major consumers of primary production and a major food source for birds. Decomposers and detritivores such as invertebrates, fungi, and microbes on the forest floor are critical to nutrient cycling. Vertebrate herbivores are relatively uncommon, with low-moderate mammalian diversity. Although epiphytes and lianas are present, plant life-form traits that are typical of tropical forests (T1.1 and T1.2) such as buttress roots, compound leaves, monopodial growth, and cauliflory are uncommon or absent in warm-temperate rainforests. Some trees have ecophysiological tolerance of acid soils (e.g. through aluminium accumulation). Gap-phase dynamics are driven by individual tree-fall and lightning strikes, but many trees are shade-tolerant and recruit slowly in the absence of disturbance. Ground vegetation includes varied growth forms but few grasses.
T2.4 Warm temperate laurophyll forests
TT2.a1
TT2.a1 Warm Temperate Evergreen Forest & Woodland
Warm Temperate Evergreen Forest & Woodland
Warm temperate laurophyll forests
This group includes the tallest forests on earth. They are moist, multi-layered forests in wet-temperate climates with complex spatial structure and very high biomass and LAI. The upper layer is an open canopy of sclerophyllous trees 40�90-m tall with long, usually unbranched trunks. The open canopy structure allows light transmission sufficient for the development of up to three subcanopy layers, consisting mostly of non-sclerophyllous trees and shrubs with higher SLA than the upper canopy species. These forests are highly productive, grow rapidly, draw energy from autochthonous sources and store very large quantities of carbon, both above and below ground. They have complex trophic networks with a diverse invertebrate, reptile, bird, and mammal fauna with assemblages that live primarily in the tree canopy or the forest floor, and some that move regularly between vertical strata. Some species are endemic and have traits associated with large trees, including the use of wood cavities, thick or loose bark, large canopies, woody debris, and deep, moist leaf litter. There is significant diversification of avian foraging methods and hence a high functional and taxonomic diversity of birds. High deposition rates of leaf litter and woody debris sustain diverse fungal decomposers and invertebrate detritivores and provide nesting substrates and refuges for ground mammals and avian insectivores. The shade-tolerant ground flora may include a diversity of ferns forbs, grasses (mostly C3), and bryophytes. The dominant trees are shade-intolerant and depend on tree-fall gaps or periodic fires for regeneration. In cooler climates, trees are killed by canopy fires but may survive surface fires, and canopy seedbanks are crucial to persistence. Epicormic resprouting (i.e. from aerial stems) is more common in warmer climates. Subcanopy and ground layers include both shade-tolerant and shade-intolerant plants, the latter with physically and physiologically dormant seedbanks that cue episodes of mass regeneration to fire. Multi-decadal or century-scale canopy fires consume biomass, liberate resources, and trigger life-history processes in a range of biota. Seedbanks sustain plant diversity through storage effects.
T2.5 Temperate pyric humid forests
TT2.a2
TT2.a2 Temperate Pyric Sclerophyll Forest & Woodland
Temperate Pyric Sclerophyll Forest & Woodland
Temperate pyric humid forests
Forests and woodlands, typically 10�30-m tall with an open evergreen sclerophyllous tree canopy and low-moderate LAI grow in fire-prone temperate landscapes. Productivity is lower than other temperate and tropical forest systems, limited by low nutrient availability and summer water deficits. Abundant light and water (except in peak summer) enable the development of substantial biomass with high C:N ratios. Trees have microphyll foliage with low to very low SLA. Sclerophyll or subsclerophyll shrubs with low to very low SLA foliage form a prominent layer between the trees. A sparse ground layer of C3 and C4 tussock grasses and forbs becomes more prominent on soils of loamy texture. Diversity and local endemism may be high among some taxa including plants, birds, and some invertebrates such as dipterans and hemipterans. Low nutrients and summer droughts limit the diversity and abundance of higher trophic levels. Plant traits (e.g. sclerophylly, stomatal invagination, tubers, and seedbanks) confer tolerance to pronounced but variable summer water deficits. Plants possess traits that promote the efficient capture and retention of nutrients, including specialised root structures, N-fixing bacterial associations, slow leaf turnover, and high allocation of photosynthates to structural tissues and exudates. Consumers have traits that enable the consumption of high-fibre biomass. Mammalian herbivores (e.g. the folivorous koala) can exploit high-fibre content and phenolics. Plants and animals have morphological and behavioural traits that allow tolerance or avoidance of fire and the life-history processes of many taxa are cued to fire (especially plant recruitment). Key fire traits in plants include recovery organs protected by thick bark or burial, serotinous seedbanks (i.e. held in plant canopies), physical and physiological seed dormancy and pyrogenic reproduction. Almost all plants are shade-intolerant and fire is a critical top-down regulator of diversity through storage effects and the periodic disruption of plant competition.
T2.6 Temperate pyric sclerophyll forests and woodlands
TT2.a3
TT2.a3 Temperate Pyric Sclerophyll Forest & Woodland
Temperate pyric sclerophyll forests and woodlands
These moderate-productivity, mostly evergreen shrublands, shrubby grasslands and low, open forests (generally <6-m tall) are limited by nutritional poverty and strong seasonal drought in the tropical winter months. Taxonomic and functional diversity is moderate in most groups but with high local endemism in plants, invertebrates, birds, and other taxa. Vegetation is spatially heterogeneous in a matrix of savannas (T4.2) or tropical dry forests (T1.2) and dominated by sclerophyllous shrubs with small leaf sizes (nanophyll-microphyll) and low SLA. C4 grasses may be conspicuous or co-dominant (unlike in most temperate heathlands, T3.2) but generally do not form a continuous stratum as in savannas (T4). These systems have relatively simple trophic networks fuelled by autochthonous energy sources. Productivity is low to moderate and constrained by seasonal drought and nutritional poverty. Shrubs are the dominant primary producers and show traits promoting the capture and conservation of nutrients (e.g. sclerophylly, cluster roots, carnivorous structures, and microbial and fungal root mutualisms) and tolerance to severe seasonal droughts (e.g. stomatal invagination). Nectarivorous and/or insectivorous birds and reptiles and granivorous small mammals dominate the vertebrate fauna, but vertebrate herbivores are sparse. Recurring fires play a role in the top-down regulation of ecosystem structure and composition.
Seasonally Dry Tropical Shrubland
T3.1 Seasonally dry tropical shrublands
TT3.b1
TT3.b1 Seasonally Dry Tropical Shrubland
Seasonally dry tropical shrublands
Sclerophyllous, evergreen shrublands are distinctive ecosystems of humid and subhumid climates in mid-latitudes. Their low-moderate productivity is fuelled by autochthonous energy sources and is limited by resource constraints and/or recurring disturbance. Vegetation is dominated by shrubs with very low SLA, high C:N ratios, shade-intolerance, and long-lived, small, often ericoid leaves, sometimes with a low, open canopy of sclerophyll trees. The ground layer may include geophytes and sclerophyll graminoids, though less commonly true grasses. Trophic webs are simple, with large mammalian predators scarce or absent, and low densities of vertebrate herbivores. Native browsers may have local effects on vegetation. Diversity and local endemism may be high among vascular plants and invertebrate consumers. Plants and animals have morphological, ecophysiological, and life-history traits that promote persistence under summer droughts, nutrient poverty, and recurring fires, which play a role in top-down regulation. Stomatal regulation and root architecture promote drought tolerance in plants. Cluster roots and acid exudates, mycorrhizae, and insectivory promote nutrient capture, while cellulose, lignin, exudate production, and leaf longevity promote nutrient conservation in plants. Vertebrate herbivores and granivores possess specialised dietary and digestive traits enabling consumption of foliage with low nutrient content and secondary compounds. Slow decomposition rates are slow, allowing litter-fuel accumulation to add to well-aerated fine fuels in shrub canopies. Life-history traits such as recovery organs, serotiny, post-fire seedling recruitment, pyrogenic flowering, and fire-related germination cues promote plant survival, growth, and reproduction under recurring canopy fires. Animals evade fires in burrows or through mobility. Animal pollination syndromes are common (notably dipterans, lepidopterans, birds, and sometimes mammals) and ants may be prominent in seed dispersal.
Mediterranean-Seasonally Dry Heath, Scrub & Grassland
T3.2 Seasonally dry temperate heaths and shrublands
TT4.a1
TT4.a1 Mediterranean-Seasonally Dry Heath, Scrub & Grassland
Seasonally dry temperate heaths and shrublands
These mixed graminoid shrublands are restricted to cool-temperate maritime environments. Typically, the vegetation cover is >70% and mostly less than 1-m tall, dominated by low, semi-sclerophyllous shrubs with ferns and C3 graminoids. Shrub foliage is mostly evergreen and ericoid, with low SLA or reduced to spiny stems. Modular growth forms are common among shrubs and grasses. Diversity and local endemism are low across taxa and the trophic network is relatively simple. Primary productivity is low, based on autochthonous energy sources and limited by cold temperatures and low-fertility acid soils rather than by water deficit (as in other heathlands, T3). Seasonally low light may limit productivity at the highest latitudes. Cool temperatures and low soil oxygen due to periodically wet subsoil limit decomposition by microbes and fungi so that soils accumulate organic matter despite low productivity. Mammalian browsers including cervids, lagomorphs, and camelids (South America) consume local plant biomass but subsidise autochthonous energy with carbon and nutrients consumed in more productive forest or anthropogenic ecosystems adjacent to the heathlands. Browsers and recurring low-intensity fires appear to be important in top-down regulatory processes that prevent the transition to forest, as is anthropogenic fire, grazing, and tree removal. Canids and raptors are the main vertebrate predators. Other characteristic vertebrate fauna include ground-nesting birds and rodents. At least some communities exhibit autogenic cyclical patch dynamics in which shrubs and grasses are alternately dominant, senescent, and regenerating.
Oceanic Cool Temperate Heathland
T3.3 Cool temperate heathlands
TT4.b2
TT4.b2 Oceanic Cool Temperate Heathland
Cool temperate heathlands
Vegetation dominated by cryptogams (lichens, bryophytes) develops on skeletal rocky substrates and may have scattered shrubs with very low LAI. These low-productivity systems are limited by moisture and nutrient scarcity, temperature extremes, and periodic disturbance through mass movement. Diversity and endemism is low across taxa and the trophic structure is simple. Reptiles and ground-nesting birds are among the few resident vertebrates. Lichens and bryophytes may be abundant and perform critical roles in moisture retention, nutrient acquisition, energy capture, surface stabilisation, and proto-soil development, especially through carbon accumulation. N-fixing lichens and cyanobacteria, nurse plants, and other mutualisms are critical to ecosystem development. Rates of ecosystem development are linked to substrate weathering, decomposition, and soil development, which mediate nutrient supply, moisture retention, and temperature amelioration. Vascular plants have nanophyll-microphyll leaves and low SLA. Their cover is sparse and comprises ruderal pioneer species (shrubs, grasses, and forbs) that colonise exposed surfaces and extract moisture from rock crevices. Species composition and vegetation structure are dynamic in response to surface instability and show limited differentiation across environmental gradients and microsites due to successional development, episodes of desiccation, and periodic disturbances that destroy biomass. Rates of vegetation development, soil accumulation, and compositional change display amplified temperature-dependence due to resource-concentration effects. Older rocky systems have greater micro-habitat diversity, more insular biota, and higher endemism and are classified in other functional groups.
T3.4 Young rocky pavements, screes and lava flows
Young rocky pavements, screes and lava flows
These grassy woodlands and grasslands are dominated by C4 grasses with stoloniferous, rhizomatous and tussock growth forms that are kept short by vertebrate grazers. Trophic savannas (relative to pyric savannas, T4.2) have unique plant and animal diversity within a complex trophic structure dominated by abundant mammalian herbivores and predators. These animals are functionally differentiated in body size, mouth morphology, diet, and behaviour. They promote fine-scale vegetation heterogeneity and dominance of short grass species, sustaining the system through positive feedbacks and limiting fire fuels. Trees and grasses possess functional traits that promote tolerance to chronic herbivory as well as seasonal drought. Seasonal high productivity coincides with summer rains. The dry season induces grass drying and leaf fall in deciduous and semi-deciduous woody plants. Trees are shade-intolerant during their establishment and most develop chemical (e.g. phenolics) or physical (e.g. spinescence) herbivory defence traits and an ability to re-sprout as they enter the juvenile phase. Their soft microphyll-notophyll foliage has relatively high SLA and low C:N ratios, as do grasses. Robust root systems and stolons/rhizomes enable characteristic grasses to survive and spread under heavy grazing. As well as vertebrate herbivores and predators, vertebrate scavengers and invertebrate detritivores are key components of the trophic network and carbon cycle. Nitrogen fixation, recycling, and deposition by animals exceeds volatilisation.
T4.1 Trophic savannas
Trophic savannas
Grassy woodlands and grasslands are dominated by C4 tussock grasses, with some C3 grasses in the Americas and variable tree cover. In the tropics, seasonally high productivity coincides with the timing of summer rains and grasses cure in dry winters, promoting flammability. This pattern also occurs in the subtropics but transitions occur with temperate woodlands (T4.4), which have different seasonal phenology, tree and grass dominance, and fire regimes. Tree basal area, abundance of plants with annual semelparous life cycles and abundant grasses with tall tussock growth forms are strongly dependent on mean annual rainfall (i.e. limited by seasonal drought). Local endemism is low across all taxa but regional endemism is high, especially in the Americas and Australasia. Plant traits such as deciduous leaf phenology or deep roots promote tolerance to seasonal drought and rapid resource exploitation. Woody plants have microphyll-notophyll foliage with moderate-high SLA and mostly high C:N ratios. Some C4 grasses nonetheless accumulate high levels of rubisco, which may push down C:N ratios. Nitrogen volatilisation exceeds deposition because fire is the major consumer of biomass. Woody plant species are shade-intolerant during their establishment and develop fire-resistant organs (e.g. thick bark and below-ground bud banks). The contiguous ground layer of erect tussock grasses creates an aerated flammable fuel bed, while grass architecture with tightly clustered culms vent heat away from meristems. Patchy fires promote landscape-scale vegetation heterogeneity (e.g. in tree cover) and maintain the dominance of flammable tussock grasses over shrubs, especially in wetter climates, and hence sustain the system through positive feedbacks. Fires also enhance efficiency of predators. Vertebrate scavengers and invertebrate detritivores are key components of the trophic network and carbon cycle. Mammalian herbivores and predators are present but exert less top-down influence on the diverse trophic structure than fire. Consequently, plant physical defences against herbivores, such as spinescence are less prominent than in T4.1.
T4.2 Pyric tussock savannas
Pyric tussock savannas
These open woodlands are dominated by C4 hummock grasses (C3 and stoloniferous grasses are absent) with sclerophyllous trees and shrubs. Their primary productivity is lower and less regularly seasonal than in other savannas of the subtropics (T4.1 and T4.2), but the seasonal peak nonetheless coincides with summer monsoonal rains. Plant traits promote tolerance to seasonal drought, including reduced leaf surfaces, thick cuticles, sunken stomata, and deep root architecture to access subsoil moisture. Deciduous leaf phenology is less common than in other savannas, likely due to selection pressure for nutrient conservation associated with oligotrophic substrates. A major feature distinguishing this group of savannas from others is its ground layer of slow-growing sclerophyllous, spiny, domed hummock grasses interspersed with bare ground. Woody biomass and LAI decline along rainfall gradients. Sclerophyll shrubs and trees are shade-intolerant during establishment and most possess fire-resistant organs (e.g. thick bark, epicormic meristematic tissues, and below-ground bud banks). Their notophyll foliage and that of hummock grasses have low SLA and mostly high C:N ratios, although N may be elevated in rubisco-enriched C4 grasses. Trophic structure is therefore simpler than in other savannas. Mammalian herbivores and their predators are present in low densities, but fire and invertebrates are the major biomass consumers. Fire promotes landscape-scale vegetation heterogeneity but occurs less frequently than in other savannas due to slow recovery of perennial hummock grass fuels. Nitrogen volatilisation exceeds deposition due to recurring fires.
T4.3 Hummock savannas
Hummock savannas
These structurally simple woodlands are characterised by space between open tree crowns and a ground layer with tussock grasses, interstitial forbs, and a variable shrub component. Grasses with C3 and C4 photosynthetic pathways are common, but C4 grasses may be absent from the coldest and wettest sites or where rain rarely falls in the summer. In any given area, C4 grasses are most abundant in summer or on dry sites or areas with summer-dominant rainfall, while C3 grasses predominate in winter, locally moist sites, cold sites, or areas without summer rainfall. The ground flora also varies inter-annually depending on rainfall. Trees generate spatial heterogeneity in light, water, and nutrients, which underpin a diversity of microhabitats and mediate competitive interactions among plants in the ground layer. Foliage is mostly microphyll and evergreen (but transmitting abundant light) or deciduous in colder climates. Diversity of plant and invertebrate groups may therefore be relatively high at local scales, but local endemism is limited due to long-distance dispersal. Productivity is relatively high as grasses rapidly produce biomass rich in N and other nutrients after rains. This sustains a relatively complex trophic network of invertebrate and vertebrate consumers. Large herbivores and their predators are important top-down regulators. Bioturbation by fossorial mammals influences soil structure, water infiltration, and nutrient cycling. The fauna is less functionally and taxonomically diverse than in most tropical savannas (T4.1 and T4.2), but includes large and small mammals, reptiles, and a high diversity of birds and macro-invertebrates, including grasshoppers, which are major consumers of biomass. Plants and animals tolerate and persist through periodic ground fires that consume cured-grass fuels, but few have specialised traits cued to fire (cf. pyric ecosystems such as T2.6).
T4.4 Temperate woodlands
Temperate woodlands
Structurally simple tussock grasslands with interstitial forbs occur in subhumid temperate climates. Isolated trees or shrubs may be present in very low densities, but are generally excluded by heavy soil texture, summer drought, winter frost, or recurring summer fires. Unlike tropical savannas (T4.1�T4.3), these systems are characterised by a mixture of both C3 and C4 grasses, with C4 grasses most abundant in summer or on dry sites and C3 grasses predominating in winter or locally moist sites. There are also strong latitudinal gradients, with C3 grasses more dominant towards the poles. Diversity of plant and invertebrate groups may be high at small spatial scales, but local endemism is limited due to long-distance dispersal. Productivity is high as grasses rapidly produce biomass rich in N and other nutrients after rains. This sustains a complex trophic network in which large herbivores and their predators are important top-down regulators. Fossorial mammals are important in bioturbation and nutrient cycling. Mammals are less functionally and taxonomically diverse than in most savannas. Taxonomic affinities vary among regions (e.g. ungulates, cervids, macropods, and camelids), but their life history and dietary traits are convergent. Where grazing is not intense and fire occurs infrequently, leaf litter accumulates from the tussocks, creating a thatch that is important habitat for ground-nesting birds, small mammals, reptiles, and macro-invertebrates, including grasshoppers, which are major consumers of plant biomass. Dense thatch limits productivity. Plant competition plays a major role in structuring the ecosystem and its dynamics, with evidence that it is mediated by resource ratios and stress gradients, herbivory, and fire regimes. Large herbivores and fires both interrupt competition and promote coexistence of tussocks and interstitial forbs.
T4.5 Temperate subhumid grasslands
TT4.b1
TT4.b1 Temperate Lowland-Montane Grassland & Shrubland
Temperate Lowland-Montane Grassland & Shrubland
Temperate subhumid grasslands
These mixed semi-deserts are dominated by suffrutescent (i.e. with a woody base) or subsucculent (semi-fleshy) perennial shrubs and tussock grasses. Productivity and biomass are limited by low average precipitation, extreme temperatures and, to a lesser extent, soil nutrients, but vary temporally in response to water availability. Vegetation takes a range of structural forms including open shrublands, mixed shrublands with a tussock grass matrix, prairie-like tall forb grasslands, and very low dwarf shrubs interspersed with forbs or grasses. Total cover varies from 10% to 30% and the balance between shrubs and grasses is mediated by rainfall, herbivory, and soil fertility. Stress-tolerator and ruderal life-history types are strongly represented in flora and fauna. Trait plasticity and nomadism are also common. Traits promoting water capture and conservation in plants include xeromorphy, deep roots, and C4 photosynthesis. Shrubs have small (less than nanophyll), non-sclerophyll, often hairy leaves with moderate SLA. Shrubs act as resource-accumulation sites, promoting heterogeneity over local scales. C3 photosynthesis is represented in short-lived shrubs, forbs, and grasses, enabling them to exploit pulses of winter rain. Consumers include small mammalian and avian granivores, medium-sized mammalian herbivores, and wide-ranging large mammalian and avian predators and scavengers. Abundant detritivores consume dead matter and structure resource availability and habitat characteristics over small scales. Episodic rainfall initiates trophic pulses with rapid responses by granivores and their predators, but less so by herbivores, which show multiple traits promoting water conservation.
T5.1 Semi-desert steppe
Semi-desert steppe
These deserts are characterised by long-lived perennial plants, many with spines and/or succulent stem tissues or leaves. Local endemism is prominent among plants and animals. Productivity is low but relatively consistent through time and limited by precipitation and extreme summer temperatures. Vegetation cover is sparse to moderate (10�30%) and up to several metres tall. Dominant plants are stress-tolerators with slow growth and reproduction, many exhibiting CAM physiology and traits that promote water capture, conservation, and storage. These include deep root systems, suffrutescence, plastic growth and reproduction, succulent stems and/or foliage, thickened cuticles, sunken stomata, and deciduous or reduced foliage. Spinescence in many species is likely a physical defence to protect moist tissues from herbivores. Annuals and geophytes constitute a variable proportion of the flora exhibiting rapid population growth or flowering responses to semi-irregular rainfall events, which stimulate germination of soil seed banks or growth from dormant subterranean organs. Mammalian, reptilian, and invertebrate faunas are diverse, with avian fauna less well represented. Faunal traits adaptive to drought and heat tolerance include physiological mechanisms (e.g. specialised kidney function and reduced metabolic rates) and behavioural characters (e.g. nocturnal habit and burrow dwelling). Many reptiles and invertebrates have ruderal life histories, but fewer mammals and birds do. Larger ungulate fauna exhibit flexible diets and forage over large areas. Predators are present in low densities due to the low productivity of prey populations.
Succulent-Thorny Desert & Semi-desert
T5.2 Succulent or thorny deserts and semi-deserts
TT5.b1 Succulent-Thorny Desert & Semi-desert
Succulent or thorny deserts and semi-deserts
Arid systems dominated by hard-leaved (sclerophyll) vegetation have relatively high diversity and local endemism, notably among plants, reptiles, and small mammals. Large moisture deficits and extremely low levels of soil nutrients limit productivity, however, infrequent episodes of high rainfall drive spikes of productivity and boom-bust ecology. Spatial heterogeneity is also critical in sustaining diversity by promoting niche diversity and resource-rich refuges during �bust� intervals. Stress-tolerator and ruderal life-history types are strongly represented in both flora and fauna. Perennial, long-lived, slow-growing, drought-tolerant, sclerophyll shrubs and hummock (C4) grasses structure the ecosystem by stabilising soils, acting as nutrient-accumulation sites and providing continuously available habitat, shade, and food for fauna. Strong filtering by both nutritional poverty and water deficit promote distinctive scleromorphic and xeromorphic plant traits. They include low SLA, high C:N ratios, reduced foliage, stomatal regulation and encryption, slow growth and reproduction rates, deep root systems, and trait plasticity. Perennial succulents are absent. Episodic rains initiate emergence of a prominent ephemeral flora, with summer and winter rains favouring grasses and forbs, respectively. This productivity �boom� triggers rapid responses by granivores and their predators. Herbivore populations also fluctuate but less so due to ecophysiological traits that promote water conservation. Abundant detritivores support a diverse and abundant resident reptilian and small-mammal fauna. Small mammals and some macro-invertebrates are nocturnal and fossorial, with digging activity contributing to nutrient and carbon cycling, as well as plant recruitment. The abundance and diversity of top predators is low. Nomadism and ground-nesting are well represented in birds. Periodic fires reduce biomass, promote recovery traits in plants (e.g. re-sprouting and fire-cued recruitment) and initiate successional processes in both flora and fauna.
Sclerophyll Hot Desert & Semi-desert
T5.3 Sclerophyll hot deserts and semi-deserts
TT5.b2
TT5.b2 Sclerophyll Hot Desert & Semi-desert
Sclerophyll hot deserts and semi-deserts
In these arid systems, productivity is limited by both low precipitation and cold temperatures but varies spatially in response to soil texture, salinity, and water table depth. Vegetation cover varies with soil conditions from near zero (on extensive areas of heavily salinized soils or mobile dunes) to >50% in upland grasslands and shrublands, but is generally low in stature (<1 m tall). The dominant plants are perennial C3 grasses and xeromorphic suffrutescent or non-sclerophyllous perennial shrubs. Dwarf shrubs, tending to prostrate or cushion forms occur in areas exposed to strong, cold winds. Plant growth occurs mainly during warming spring temperatures after winter soil moisture recharges. Eurasian winter annuals grow rapidly in this period after developing extensive root systems over winter. Diversity and local endemism are low across all taxa relative to other arid ecosystems. Trophic networks are characterised by large nomadic mammalian herbivores. Vertebrate herbivores including antelopes, equines, camelids, and lagomorphs are important mediators of shrub-grass dynamics, with heavy grazing promoting replacement of grasses by N-fixing shrubs. Grasses become dominant with increasing soil fertility or moisture but may be replaced by shrubs as grazing pressure increases. Fossorial lagomorphs and omnivorous rodents contribute to soil perturbation. Predator populations are sparse but taxonomically diverse. They include raptors, snakes, bears, and cats. Bio-crusts with cyanobacteria, mosses, and lichens are prominent on fine-textured substrates and become dominant where it is too cold for vascular plants. They play critical roles in soil stability and water and nutrient availability.
T5.4 Cool deserts and semi-deserts
Cool deserts and semi-deserts
Hyper-arid deserts show extremely low productivity and biomass and are limited by low precipitation and extreme temperatures. Vegetation cover is very sparse (<1%) and low in stature (typically a few centimetres tall), but productivity and biomass may be marginally greater in topographically complex landscapes within patches of rising ground-water or where runoff accumulates or cloud cover intersects. Trophic networks are simple because autochthonous productivity and allochthonous resources are very limited. Rates of decomposition are slow and driven by microbial activity and UV-B photodegradation, both of which decline with precipitation. Microbial biofilms play important decomposition roles in soils and contain virus lineages that are putatively distinct from other ecosystems. Although diversity is low, endemism may be high because of strong selection pressures and insularity resulting from the large extent of these arid regions and limited dispersal abilities of most organisms. Low densities of drought-tolerant perennial plants (xerophytes) characterise these systems. The few perennials present have very slow growth and tissue turnover rates, low fecundity, generally long life spans, and water acquisition and conservation traits (e.g. extensive root systems, thick cuticles, stomatal regulation, and succulent organs). Ephemeral plants with long-lived soil seed banks are well represented in hyper-arid deserts characterised by episodic rainfall, but they are less common in those that are largely reliant on fog or groundwater. Fauna include both ruderal and drought-tolerant species. Thermoregulation is strongly represented in reptiles and invertebrates. Birds and large mammals are sparse and nomadic, except in areas with reliable standing water. Herbivores and granivores have boom-bust population dynamics coincident with episodic rains.
Hyper-arid Desert
T5.5 Hyper-arid deserts
TT5.b3
TT5.b3 Hyper-arid Desert
Hyper-arid deserts
In these icy systems, extreme cold and periodic blizzards limit productivity and diversity to very low levels, and trophic networks are truncated. Wherever surface or interstitial water is available, life is dominated by micro-organisms including viruses, bacteria, protozoa, and algae, which may arrive by Aeolian processes. Bacterial densities vary from 107 to 1011 cells.L-1. On the surface, the main primary producers are snow (mainly Chlamydomonadales) and ice algae (mainly Zygnematales) with contrasting traits. Metabolic activity is generally restricted to summer months at temperatures close to zero and is enabled by exopolymeric substances, cold-adapted enzymes, cold-shock proteins, and other physiological traits. N-fixing cyanobacteria are critical in the N-cycle, especially in late summer. Surface heterogeneity and dynamism create cryoconite holes, rich oases for microbial life (especially cyanobacteria, prokaryotic heterotrophs and viruses) and active biogeochemical cycling. Most vertebrates are migratory birds with only the emperor penguin over-wintering on Antarctic ice. Mass movement and snow burial also places severe constraints on establishment and persistence of life. Snow and ice algae and cyanobacteria on the surface are ecosystem engineers. Their accumulation of organic matter leads to positive feedbacks between melting and microbial activity that discolours snow and reduces albedo. Organic matter produced at the surface can also be transported through the ice to dark subglacial environments, fuelling microbial processes involving heterotrophic and chemoautotrophic prokaryotes and fungi.
Ice Sheet, Glacier & Perennial Snowfield
T6.1 Ice sheets, glaciers and perennial snowfields
TT6.a1
TT6.a1 Ice Sheet, Glacier & Perennial Snowfield
Ice sheets, glaciers and perennial snowfields
Low biomass systems with very low productivity constrained by extreme cold, desiccating winds, skeletal substrates, periodic mass movement, and, in polar regions, by seasonally low light intensity. The dominant lifeforms are freeze-tolerant crustose lichens, mosses, and algae that also tolerate periodic desiccation, invertebrates such as tardigrades, nematodes, and mites, micro-organisms including bacteria and protozoa, and nesting birds that forage primarily in other (mostly marine) ecosystems. Diversity and endemism are low, likely due to intense selection pressures and wide dispersal. Trophic networks are simple and truncated. Physiological traits such as cold-adapted enzymes and cold-shock proteins enable metabolic activity, which is restricted to summer months when temperatures are close to or above zero. Nutrient input occurs primarily through substrate weathering supplemented by guano, which along with cyanobacteria is a major source of N. Mass movement of snow and rock, with accumulation of snow and ice during the intervals between collapse events, promotes disequilibrium ecosystem dynamics.
T6.2 Polar/alpine cliffs, screes, outcrops and lava flows
Polar/alpine cliffs, screes, outcrops and lava flows
These low productivity autotrophic ecosystems are limited by winter dormancy during deep winter snow cover, extreme cold temperatures and frost during spring thaw, short growing seasons, desiccating winds, and seasonally low light intensity. Microbial decomposition rates are slow, promoting accumulation of peaty permafrost substrates in which only the surface horizon thaws seasonally. Vegetation is treeless and dominated by a largely continuous cover of cold-tolerant bryophytes, lichens, C3 grasses, sedges, forbs, and dwarf and prostrate shrubs. Tundra around the world, is delimited by the physiological temperature limits of trees, which are excluded where the growing season (i.e. days >0.9�C) is less than 90-94 days duration, with mean temperatures less than 6.5�C across the growing season. In the coldest and/or driest locations, vascular plants are absent and productivity relies on bryophytes, lichens, cyanobacteria, and allochthonous energy sources such as guano. Aestivating insects (i.e. those that lay dormant in hot or dry seasons) dominate the invertebrate fauna. Vertebrate fauna is dominated by migratory birds, some of which travel seasonal routes exceeding several thousand kilometres. Many of these feed in distant wetlands or open oceans. These are critical mobile links that transfer nutrients and organic matter and disperse the propagules of other organisms, both externally on plumage or feet and endogenously. A few mammals in the Northern Hemisphere are hibernating residents or migratory herbivores. Pinnipeds occur in near-coast tundras and may be locally important marine subsidies of nutrients and energy. Predatory canids and polar bears are nomadic or have large home ranges.
T6.3 Polar tundra and deserts
Polar tundra and deserts
Mountain systems beyond the cold climatic treeline are dominated by grasses, herbs, or low shrubs (typically <1 m tall). Moderate-low and strictly seasonal productivity is limited by deep winter snow cover, extreme cold and frost during spring thaw, short growing seasons, desiccating winds, and, in some cases, by mass movement. Vegetation comprises a typically continuous cover of plants including bryophytes, lichens, C3 grasses, sedges, forbs, and dwarf shrubs including cushion growth forms. However, the cover of vascular plants may be much lower in low-rainfall regions or in sites exposed to strong desiccating winds and often characterised by dwarf shrubs and lichens that grow on rocks (e.g. fjaeldmark). Throughout the world, alpine ecosystems are defined by the physiological temperature limits of trees, which are excluded where the growing season (i.e. days >0.9�C) is less than 90-94 days, with mean temperatures less than 6.5�C across the growing season. Other plants have morphological and ecophysiological traits to protect buds, leaves, and reproductive tissues from extreme cold, including growth forms with many branches, diminutive leaf sizes, sclerophylly, vegetative propagation, and cold-stratification dormancy. The vertebrate fauna includes a few hibernating residents and migratory herbivores and predators that are nomadic or have large home ranges. Aestivating insects include katydids, dipterans, and hemipterans. Local endemism and beta-diversity may be high due to steep elevational gradients, microhabitat heterogeneity, and topographic barriers to dispersal between mountain ranges, with evidence of both facilitation and competition.
T6.4 Temperate alpine grasslands and shrublands
Temperate alpine grasslands and shrublands
Structurally simple, high-productivity pastures are maintained by the intensive anthropogenic supplementation of nutrients (more rarely water) and artificial disturbance regimes (e.g. periodic ploughing,), translocation (e.g. livestock movement and sowing), and harvesting of animals or plants. The magnitude of these inputs distinguish these systems from semi-natural pastures and rangelands in biomes T4 and T5 used for less intense livestock production. They are dominated by one or few selected plant species (C3 and C4 perennial pasture grasses and/or herbaceous legumes) and animal species (usually large mammalian herbivores) for commercial production of food or materials, ornamental displays, or sometimes subsistence. Their composition and structure is maintained by the translocation and/or managed reproduction of target species and the periodic application of herbicides and pesticides and/or culling to exclude competitors, predators, herbivores, or pathogens. Consequently, compared to �natural� rangeland systems and semi-natural pastures, these systems have low functional and taxonomic diversity and little or no local endemism. Target biota are genetically manipulated to promote rapid growth rates, efficient resource capture, enhanced resource allocation to production tissues, and tolerance to harsh environmental conditions, diseases, and predators, . They are harvested by humans continuously or periodically for consumption or maintenance. Typically, at least 40% of net primary productivity is appropriated by humans. Major examples include intensively managed production pastures for livestock or forage (e.g. hay). Livestock pastures may be rotated inter-annually with non-woody crops (T7.1), or they may be managed as mixed silvo-pastoral systems (T7.3). Target biota coexist with native and cosmopolitan ruderal biota that exploits production landscapes through efficient dispersal, rapid establishment, high fecundity, and rapid population turnover. When the ecosystem is abandoned or managed less intensively, non-target biota become dominant and may form a steady, self-maintaining state or a transitional phase to novel ecosystems.
Sown Pasture & Field
T7.2 Sown pastures and fields
TT7.a2
TT7.a2 Sown Pasture & Field
Sown pastures and fields
These moderate to high productivity autotrophic systems are established by the translocation (i.e. planting or seeding) of woody perennial plants. Target biota may be genetically manipulated by selective breeding or molecular engineering to promote rapid growth rates, efficient resource capture, enhanced resource allocation to production tissues, and tolerance of harsh environmental conditions, insect predators, and diseases. The diversity, structure, composition, function, and successional trajectory of the ecosystem depends on the identity, developmental stage, density, and traits (e.g. phenology, physiognomy, and growth rates) of planted species, as well as the subsequent management of plantation development. Most plantations comprise at least two vertical strata (the managed woody species and a ruderal ground layer). Mixed forest plantings may be more complex and host a relatively diverse flora and fauna if managed to promote habitat features. Cyclical harvest may render the habitat periodically unsuitable for some biota. Mixed cropping systems may comprise two vertical strata of woody crops or a woody and herbaceous layer. Secondary successional processes involve colonisation and regeneration, initially of opportunistic biota. Successional feedbacks occur as structural complexity increases, promoting visits or colonisation by vertebrates and the associated dispersal of plants and other organisms. Crop replacement (which may occur on inter-annual or decadal cycles), the intensive management of plantation structure, or the control of non-target species may reset, arrest, or redirect successional processes. Examples with increasing management intervention include: environmental plantations established for wildlife or ecosystem services; agroforestry plantings for subsistence products or livestock benefits; forestry plantations for timber, pulp, fibre, bio-energy, rubber, or oils; and vineyards, orchards, and other perennial food crops (e.g. cassava, coffee, tea, palm oil, and nuts). Secondary (regrowth) forests and shrublands are not included as plantations even where management includes supplementary translocations.
T7.3 Plantations
TT7.a3
TT7.a3 Plantation
Plantations
These systems are structurally complex and highly heterogeneous fine-scale spatial mosaics of diverse patch types that may be recognised in fine-scale land use classifications. These include: a) buildings; b) paved surfaces; c) transport infrastructure: d) treed areas; e) grassed areas; f) gardens; g) mines or quarries; h) bare ground; and i) refuse areas. Patch mosaics are dynamic over decadal time scales and driven by socio-ecological feedbacks and a human population that is highly stratified, functionally, socially and economically. Interactions among patch types and human social behaviours produce emergent properties and complex feedbacks among components within each system and interactions with other ecosystem types. Unlike most other terrestrial ecosystems, the energy, water and nutrient sources of urban/industrial village systems are highly allochthonous and processes within urban systems drive profound and extensive global changes in land use, land cover, biodiversity, hydrology, and climate through both resource consumption and waste discharge. Biotic community structure is characterised by low functional and taxonomic diversity, highly skewed rank-abundance relationships and relict local endemism. Trophic networks are simplified and sparse and each node is dominated by few taxa. Urban/village biota include humans, dependents (e.g. companion animals and cultivars), opportunists and vagrants, and legacy biota whose establishment pre-dates settlement. Many biota have highly plastic realised niches, traits enabling wide dispersal, high fecundity, and short generation times. The persistence of dependent biota is maintained by human-assisted migration, managed reproduction, genetic manipulation, amelioration of temperatures, and intensive supplementation of nutrients, food, and water. Pest biota are controlled by the application of herbicides and pesticides or culling with collateral impacts on non-target biota.
T7.4 Urban and industrial ecosystems
TT7.b1
TT7.b1 Urban & Industrial Land
Urban & Industrial Land
Urban and industrial ecosystems
Extensive �semi-natural� grasslands and open shrublands exist where woody components of vegetation have been removed or greatly modified for agricultural land uses. Hence they have been �derived� from a range of other ecosystems (mostly from biomes T1, T2, T3, T4, a few from T5). Remaining vegetation includes a substantial component of local indigenous species, as well as an introduced exotic element, providing habitat for a mixed indigenous and non-indigenous fauna. Although structurally simpler at site scales than the systems from which they were derived, spatial complexity may be greater in fragmented landscapes and they often harbour appreciable diversity of native organisms, including some no longer present in �natural� ecosystems. Dominant plant growth forms include tussock or stoloniferous grasses and forbs, with or without non-vascular plants, shrubs and scattered trees. These support microbial decomposers and diverse invertebrate groups that function as detritivores, herbivores and predators, as well as vertebrate herbivores and predators characteristic of open habitats. Energy sources are primarily autochthonous, with varying levels of indirect allochthonous subsidies (e.g. via surface water sheet flows), but few managed inputs (cf. T7.2). Productivity can be low or high, depending on climate and substrate, but is generally lower and more stable than more intensive anthropogenic systems (T7.1-T7.3). Trophic networks include all levels, but complexity and diversity depends on the species pool, legacies from antecedent ecosystems, successional stage, and management regimes. These novel ecosystems may persist in a steady self-maintaining state, or undergo passive transformation (e.g. oldfield succession) unless actively maintained in disequilibrium. For example, removal of domestic herbivores may initiate transition to tree-dominated ecosystems.
Derived Fallow & Weed Field
T7.5 Derived semi-natural pastures and oldfields
TT7.c1
TT7.c1 Derived Fallow & Weed Field
Derived semi-natural pastures and oldfields
Dark subterranean air-filled voids support simple, low productivity systems. The trophic network is truncated and dominated by heterotrophs, with no representation of photosynthetic primary producers or herbivores. Diversity is low, comprising detritivores and their pathogens and predators, although there may be a few specialist predators confined to resource-rich hotspots, such as bat latrines or seeps. Biota include invertebrates (notably beetles, springtails, and arachnids), fungi, bacteria, and transient vertebrates, notably bats, which use surface-connected caves as roosts and breeding sites. Bacteria and fungi form biofilms on rock surfaces. Fungi are more abundant in humid microsites. Some are parasites and many are critical food sources for invertebrates and protozoans. Allochthonous energy and nutrients are imported via seepage moisture, tree roots, bats, and other winged animals. This leads to fine-scale spatial heterogeneity in resource distribution, reflected in patterns of biotic diversity and abundance. Autochthonous energy can be produced by chemoautotrophs. For example, chemoautotrophic Proteobacteria are prominent in subterranean caves formed by sulphide springs. They fix carbon through sulphide oxidation, producing sulphuric acid and gypsum residue in snottite draperies (i.e. microbial mats), accelerating chemical corrosion. The majority of biota are obligate subterranean organisms that complete their life cycles below ground. These are generalist detritivores and some are also opportunistic predators, reflecting the selection pressure of food scarcity. Distinctive traits include specialised non-visual sensory organs, reduced eyes, pigmentation and wings, elongated appendages, long lifespans, slow metabolism and growth, and low fecundity. Other cave taxa are temporary below-ground inhabitants, have populations living entirely above- or below-ground, or life cycles necessitating use of both environments. The relative abundance and diversity of temporary inhabitants decline rapidly with distance from the cave entrance. The specialist subterranean taxa belong to relatively few evolutionary lineages that either persisted as relics in caves after the extinction of above-ground relatives or diversified after colonisation by above-ground ancestors. Although diversity is low, local endemism is high, reflecting insularity and limited connectivity between cave systems.
S1.1 Aerobic caves
Aerobic caves
Lithic matrices and their microscopic cracks and cavities host microbial communities. Their very low productivity is constrained by the scarcity of light, nutrients, and water, and sometimes also by high temperatures. Diversity is low and the trophic network is truncated, supporting microscopic bacteria, archaea, viruses, and unicellular eukaryotes. Most are detritivores or lithoautotrophs, which derive energy, oxidants, carbohydrates, and simple organic acids from carbon dioxide, geological sources of hydrogen, and mineral compounds of potassium, iron and sulphur. Some fissures are large enough to support small eukaryotic predators such as nematodes. Photoautotrophs (i.e. cyanobacteria) are present only in the surface layers of exposed rocks. Sampling suggests that these systems harbour 95% of the world�s prokaryote life (bacteria and archaea), with rocks below the deep oceans and continents containing similar densities of cells and potentially accounting for a significant proportion of sequestered carbon. Endolithic microbes are characterised by extremely slow reproductive rates, especially in deep sedimentary rocks, which are the most oligotrophic substrates. At some depth within both terrestrial and marine substrates, microbes are sustained by energy from organic matter that percolates through fissures from surface systems. In deeper or less permeable parts of the crust, however, lithoautotrophic microbes are the primary energy synthesisers that sustain heterotrophs in the food web. Methanogenic archaea and iron-reducing bacteria appear to be important autotrophs in sub-oceanic basalts. All endolithic microbes are characterised by slow metabolism and reproduction rates. At some locations they tolerate extreme pressures, temperatures (up to 125�C) and acidity (pH<2), notably in crustal fluids. Little is currently known of endemism, but it may be expected to be high based on the insularity of these ecosystems.
S1.2 Endolithic systems
Endolithic systems
These low-productivity systems in subterranean air-filled voids are created by excavation. Although similar to Aerobic caves (S1.1), these systems are structurally simpler, younger, more geologically varied, and much less biologically diverse with few evolutionary lineages and no local endemism. Low diversity, low endemism, and opportunistic biotic traits stem from founder effects related to their recent anthropogenic origin (hence few colonisation events and little time for evolutionary divergence), as well as low microhabitat niche diversity due to the simple structure of void walls compared to natural caves. The trophic network is truncated and dominated by heterotrophs, usually with no representation of photosynthetic primary producers or herbivores. Generalist detritivores and their pathogens and predators dominate, although some specialists may be associated with bat dung deposits. Biota include invertebrates (notably beetles, springtails, and arachnids), fungi, bacteria, and transient vertebrates, notably bats, which use the voids as roosts and breeding sites. Bacteria and fungi form biofilms on void surfaces. Many are colonists of human inoculations, with some microbes identified as �human-indicator bacteria� (e.g. E. coli, Staphylococcus aureus, and high-temperature Bacillus spp.). Fungi are most abundant in humid microsites. Some are parasites and many are critical food sources for invertebrates and protozoans. Sources of energy and nutrients are allochthonous, imported by humans, bats, winged invertebrates, other animals, and seepage moisture. Many taxa have long life pans, slow metabolism and growth, and low fecundity, but lack distinctive traits found in the biota of natural caves. Some are temporary below-ground inhabitants, have populations that live entirely above- or below-ground, or have life cycles necessitating the use of both environments.
S2.1 Anthropogenic subterranean voids
Anthropogenic subterranean voids
Subterranean streams, pools, and aquatic voids (flooded caves) are low-productivity systems devoid of light. The taxonomic and functional diversity of these water bodies is low, but they may host local endemics, depending on connectivity with surface waters and between cave systems. The truncated trophic network is entirely heterotrophic, with no photosynthetic primary producers or herbivores. Detritivores and their predators are dominant, although a few specialist predators may be associated with resource-rich hotspots. Microbial mats composed of bacteria and aquatic fungi covering submerged rock surfaces are major food sources for protozoans and invertebrates. Other biota include planktonic bacteria, crustaceans, annelids, molluscs, arachnids, and fish in larger voids. Chemoautotrophic proteobacteria are locally abundant in sulphur-rich waters fed by springs but not widespread. Obligate denizens of subterranean waters complete their life cycles entirely below ground and derive from relatively few evolutionary lineages. These make up a variable portion of the biota, depending on connectivity to surface waters. Most species are generalist detritivores coexisting under weak competitive interactions. Some are also opportunistic predators, reflecting selection pressures of food scarcity. Distinctive traits include the absence of eyes and pigmentation, long lifespans, slow metabolism and growth rates, and low fecundity. Less-specialised biota include taxa that spend part of their life cycles below ground and part above, as well as temporary below-ground inhabitants. Transient vertebrates occur only in waters of larger subterranean voids that are well connected to surface streams with abundant food.
SF1.1 Underground streams and pools
Underground streams and pools
These low-productivity ecosystems are found within or below groundwater (phreatic) zones. They include aquifers (underground layers of water-saturated permeable rock or unconsolidated gravel, sand, or silt) and hyporheic zones beneath rivers and lakes (i.e. where shallow groundwater and surface water mix). Diversity and abundance of biota decline with depth and connectivity to surface waters, as do nutrients (e.g. most meiofauna is limited to 100m depth). Microbial communities are functionally diverse and invertebrate taxa exhibit high local endemism where aquifers are poorly connected. Trophic networks are truncated and comprised almost exclusively of heterotrophic microbes and invertebrates. Chemoautotrophic bacteria are the only source of autochthonous energy. Herbivores only occur where plant material enters groundwater systems (e.g. in well-connected hyporheic zones). Microbes and their protozoan predators dwell on particle surfaces rather than in pore water. They play key roles in weathering and mineral formation, engineer chemically distinctive microhabitats through redox reactions, and are repositories of Carbon, Nitrogen and Phosphorus within the ecosystem. Meio-faunal detritivores and predators transfer Carbon and nutrients from biofilms to larger invertebrate predators such as crustaceans, annelids, nematodes, water mites, and beetles. These larger trophic generalists live in interstitial waters, either browsing on particle biofilms or ingesting sediment grains, digesting their surface microbes, and excreting �cleaned� grains. They have morphological and behavioural traits that equip them for life in dark, resource-scarce groundwater where space is limited. These include slow metabolism and growth, long lifespans without resting stages, low fecundity, lack of pigmentation, reduced eyes, enhanced non-optic sensory organs, and elongated body shapes with enhanced segmentation. Much of the biota belongs to ancient subterranean lineages that have diverged sympatrically within aquifers or allopatrically from repeated colonisations or aquifer fragmentation.
SF1.2 Groundwater ecosystems
Groundwater ecosystems
Constructed subterranean canals and water pipes are dark, low-productivity systems acting as conduits for water, nutrients, and biota between artificial or natural freshwater ecosystems. Energy sources are therefore entirely or almost entirely allochthonous from surface systems. Although similar to underground streams (S2.1), these systems are structurally simpler, younger, and less biologically diverse with few evolutionary lineages and no local endemism. Diversity and abundance are low, often resulting from the accidental transport of biota from source to sink ecosystems. Trophic networks are truncated, with very few or no primary producers and no vertebrate predators except incidental transients. The majority of the resident heterotrophic biota are bacteria, aquatic fungi, and protists living in biofilms covering mostly smooth artificial surfaces or cut rock faces. Biofilms constitute food sources for detritivores and predators, including protozoans and planktonic invertebrates as well as filter feeders such as molluscs. The structure of the biofilm community varies considerably with hydraulic regime, as does the biota in the water column. Transient vertebrates, notably fish, occupy well-connected ecosystems with abundant food and predominantly depend on transported nutrients and prey. A range of organisms may survive in these environments but only some maintain reproductive populations. All biota are capable of surviving under no or low light conditions, at least temporarily while in transit. Other traits vary with hydraulic regimes and hydrochemistry, with physiological tolerance to toxins important in highly eutrophic, slow-flowing drains and tolerance to low nutrients and turbulence typical in high-velocity minerotrophic water pipes.
SF2.1 Water pipes and subterranean canals
Water pipes and subterranean canals
Abandoned and now flooded underground mines frequently contain extensive reservoirs of geothermally warmed groundwater, colonized by stygobitic invertebrates from nearby natural subterranean habitats. A fraction of the biota is likely to have been introduced by mining activities. A lack of light excludes photoautotrophs from these systems and low connectivity limits inputs from allochthonous energy sources. Consequently, overall productivity is low, and is likely to depend on chemoautrophic microbes (e.g. sulfate-reducing bacteria) as sources of energy. Few studies have investigated the ecology of the aquatic biota in quasi-stagnant water within mine workings, but trophic networks are truncated and likely to be simple, with low diversity and abundance at all trophic levels, and no endemism. Most of the resident heterotrophic biota are bacteria, aquatic fungi, and protists living in biofilms on artificial surfaces of abandoned infrastructure, equipment or cut rock faces. Extremophiles are likely to dominate in waters that are highly acidic or with high concentrations of heavy metals or other toxins. Micro-invertebrates are most likely to be the highest-level predators. Some voids may have simple assemblages of macroinverterbates, but few are likely to support vertebrates unless they are connected with surface waters that provide a means of colonization.
SF2.2 Flooded mines and other voids
Flooded mines and other voids
The subterranean tidal biome is a biome that includes coastal pools and subterranean voids with a partially or entirely submerged connection to marine waters where sunlight is absent or too dim to sustain photosynthesis.
Definition taken from IUCN GET. Needs to be reformatted for ontology.
SM1 Subterranean tidal biome
Subterranean tidal biome
Anchialine caves contain bodies of saline or brackish waters with subterranean connections to the sea. Since virtually all anchialine biota are marine in origin, these caves have a larger and more diverse species pool than underground freshwaters. The trophic network is truncated and dominated by heterotrophs (scavenging and filter-feeding detritivores and their predators), with photosynthetic primary producers and herbivores only present where sinkholes connect caves to the surface and sunlight. Productivity is limited by the scarcity of light and food, but less so than in insular freshwater subterranean systems (SF1.1) due to influx of marine detritus and biota. The dominant fauna includes planktonic bacteria, protozoans, annelids, crustaceans, and fish. Anchialine obligates inhabit locations deep within the caves, with marine biota increasing in frequency with proximity to the sea. Caves closely connected with the ocean tend to have stronger tidal currents and biota such as sponges and hydroids commonly associated with sea caves (SM1.3). Distinctive traits of cave obligates that reflect selection under darkness and food scarcity include varying degrees of eye loss and depigmentation, increased tactile and chemical sensitivity, reproduction with few large eggs, long lifespans, and slow metabolism and growth rates. Some anchialine biota are related to deep sea species, including shrimps that retain red pigmentation, while others include relict taxa inhabiting anchialine caves on opposite sides of ocean basins. Characteristic anchialine taxa also occur in isolated water bodies, far within extensive seafloor cave systems.
SM1.1 Anchialine caves
Anchialine caves
Anchialine pools, like anchialine caves (SM1.1), are tidally influenced bodies of brackish water with subterranean connections to the sea and groundwater, but with significant or full exposure to open air and sunlight. They have no surface connection to the ocean or freshwater ecosystems. Younger anchialine pools are exposed to abundant sunlight, characterized by relatively low productivity, and tend to support only benthic microalgae, cyanobacteria, and primary consumers. Older pools with more established biological communities have higher productivity with a wider range of autotrophs, including macroalgae, aquatic monocots, established riparian and canopy vegetation, and primary and secondary consumers. High productivity is attributed to a combination of sunlight exposure, rugose substrates, and relatively high natural concentrations of inorganic nutrients from groundwater. Anchialine pools may support complex benthic microbial communities, primary consumers, filter-feeders, detritivores, scavengers and secondary consumers. These consumers are primarily molluscs and crustaceans, several of which are anchialine obligates. Due to connections with deeper hypogeal habitats, obligate species may display physical and physiological traits similar to anchialine cave species. However, larger predatory fish and birds also utilize anchialine pools for food and habitat. Anchialine pools are ecologically dynamic systems due to their openness, connections with surrounding terrestrial habitats and subterranean hydrologic connections. Consequently, they are inherently sensitive to ecological phase shifts throughout their relatively ephemeral existence, with senescence initiating in as little as 100 years. However, new anchialine pools may form within a few months after basaltic lava flows.
SM1.2 Anchialine pools
Anchialine pools
Sea caves (also known as marine or littoral caves) are usually formed by wave action abrasion in various rock types. In contrast to anchialine caves (SM1.1), sea caves are not isolated from the external marine environment. Thus, the biota in sea caves are mostly stygophiles (typical of dim-light cryptic and deep-water environments outside caves) or stygoxenes (species sheltering in caves during daytime but foraging outside at night). However, numerous taxa (mostly sessile invertebrates) have so far been reported only from sea caves, and thus can be considered as cave-exclusive sensu lato. Visitors often enter sea caves by chance (e.g. carried in by currents), and survive only for short periods. The diverse sea-cave biota is dominated by sessile (e.g. sponges, cnidarians, bryozoans) and mobile invertebrates (e.g. molluscs crustaceans, annelids,) and fish. Photoautotrophs are restricted close to cave openings, while chemoautotrophic bacteria form extensive mats in sea caves with hydrothermal sulphur springs, similar to those in some terrestrial caves (SF1.1) and deep sea vents (M3.7). In semi-dark and dark cave sectors, the main trophic categories are filter-feeders (passive and active), detritivores, carnivores, and omnivores. Decomposers also play important roles. Filter-feeders consume plankton and suspended organic material delivered by tidal currents and waves. Other organisms either feed on the organic material produced by filter-feeders or move outside caves in order to find food. These �migrants�, especially swarm-forming crustaceans and schooling fish, can be significant import pathways for organic matter, mitigating oligotrophy in confined cave sectors.
SM1.3 Sea caves
Sea caves
Closed-canopy forests in tropical swamps and riparian zones have high biomass and LAI, with unseasonal growth and reproductive phenology. The canopy foliage is evergreen, varying in size from mesophyll to notophyll with moderate SLA. Productivity differs markedly between high-nutrient �white water� riparian systems and low-nutrient �black water� systems. In the latter, most of the nutrient capital is sequestered in plant biomass, litter, or peat, whereas in white water systems, soil nutrients are replenished continually by fluvial subsidies. Some trees have specialised traits conferring tolerance to low-oxygen substrates, such as surface root mats, pneumatophores, and stilt roots. Palms (sometimes in pure stands), hydrophytes, pitcher plants, epiphytic mosses, and ferns may be abundant, but lianas and grasses are rare or absent. The recent origin of these forests has allowed limited time for evolutionary divergence from nearby lowland rainforests (T1.1), but strong filtering by saturated soils has resulted in low diversity and some endemism. The biota is spatially structured by local hydrological gradients. Riparian galleries of floodplain forests also occur within savanna matrices. Trophic networks are complex but with less diverse representation of vertebrate consumers and predators than T1.1, although avian frugivores, primates, amphibians, macro-invertebrates, and crocodilian predators are prominent. Plant propagules are dispersed mostly by surface water or vertebrates. Seed dormancy and seedbanks are rare. Gap-phase dynamics are driven by individual treefall, storm events, or floods in riparian forests, but many plants exhibit leaf-form plasticity and can recruit in the shade.
TF1.1
TF1.1 Tropical flooded forests and peat forests
TP1.a1
TP1.a1 Tropical Flooded Forest & Peat Forest
Tropical Flooded Forest & Peat Forest
Tropical flooded forests and peat forests
These hydrophilic forests and thickets have an open to closed tree or shrub canopy, 2�40 m tall, dependent on flood regimes or groundwater lenses. Unlike tropical forests (TF1.1), they typically are dominated by one or very few woody species. Trees engineer fine-scale spatial heterogeneity in resource availability (water, nutrients, and light) and ecosystem structure, which affects the composition, form, and functional traits of understorey plants and fauna. Engineering processes include the alteration of sediments, (e.g. surface micro-topography by the growth of large roots), the deposition of leaf litter and woody debris, canopy shading, creation of desiccation refuges for fauna and the development of foraging or nesting substrates (e.g. tree hollows). Forest understories vary from diverse herbaceous assemblages to simple aquatic macrophyte communities in response to spatial and temporal hydrological gradients, which influence the density and relative abundance of algae, hydrophytes and dryland plants. Primary production varies seasonally and inter-annually and can be periodically high due to the mobilisation of nutrients on floodplains during inundation. Nutrients accumulate on floodplains during low flows, and may drive microbial blooms, leading to aquatic anoxia, and fish kills, which may be extensive when flushing occurs. Plant and animal life histories are closely connected to inundation (e.g. seed-fall, germination fish-spawning and bird breeding are stimulated by flooding). Inundation-phase aquatic food webs are moderately complex. Turtles, frogs, birds and sometimes fish exploit the alternation between aquatic and terrestrial phases. Waterbirds forage extensively on secondary production, stranded as floodplains recede, and breed in the canopies of trees or mid-storey. Forested wetlands are refuges for many vertebrates during droughts. Itinerant mammalian herbivores (e.g. deer and kangaroos) may have locally important impacts on vegetation structure and recruitment.
TF1.2
TF1.2 Subtropical/temperate forested wetlands
TP1.a2
TP1.a2 Temperate-Boreal Forested Wetland
Temperate-Boreal Forested Wetland
Subtropical/temperate forested wetlands
These shallow, permanently inundated freshwater wetlands lack woody vegetation but are dominated instead by emergent macrophytes growing in extensive, often monospecific groves of rhizomatous grasses, sedges, rushes, or reeds in mosaics with patches of open water. These plants, together with phytoplankton, algal mats, epiphytes, floating, and amphibious herbs, sustain high primary productivity and strong bottom-up regulation. Although most of the energy comes from these functionally diverse autotrophs, inflow and seepage from catchments may contribute allochthonous energy and nutrients. Plant traits including aerenchymatous stems and leaf tissues (i.e. with air spaces) enable oxygen transport to roots and rhizomes and into the substrate. Invertebrate and microbial detritivores and decomposers inhabit the water column and substrate. Air-breathing invertebrates are more common than gill-breathers, due to low dissolved oxygen. The activity of microbial decomposers is also limited by low oxygen levels and organic deposition continually exceeds decomposition. Their aquatic predators include invertebrates, turtles, snakes and sometimes small fish. The emergent vegetation supports a complex trophic web including insects with winged adult phases, waterbirds, reptiles, and mammals, which feed in the vegetation and also use it for nesting (e.g. herons, muskrat, and alligators). Waterbirds include herbivores, detritivores, and predators. Many plants and animals disperse widely beyond the marsh through the air, water and zoochory (e.g. birds, mammals). Reproduction and recruitment coincide with resource availability and may be cued to floods. Most macrophytes spread vegetatively with long rhizomes but also produce an abundance of wind- and water-dispersed seeds.
TF1.3 Permanent marshes
Permanent marshes
This group includes high-productivity floodplain wetlands fed regularly by large inputs of allochthonous resources that drive strong bottom-up regulation, and smaller areas of disconnected oligotrophic wetlands. Functionally diverse autotrophs include phytoplankton, algal mats and epiphytes, floating and amphibious herbs and graminoids, and semi-terrestrial woody plants. Interactions of fine-scale spatial gradients in anoxia and desiccation are related to differential flooding. These gradients shape ecosystem assembly by enabling species with diverse life-history traits to exploit different niches, resulting in strong local zonation of vegetation and high patch-level diversity of habitats for consumers. Wetland mosaics include very productive and often extensive grasses, sedges and forbs (sedges dominate oligotrophic systems) that persist through dry seasons largely as dormant seeds or subterranean organs, as well as groves of woody perennials that are less tolerant of prolonged anoxia but access ground water or arrest growth during dry phases. Productive and functionally diverse autotrophs support complex trophic networks with zooplankton, aquatic invertebrates, fish, amphibians, reptiles, aquatic mammals, waterbirds, and terrestrial animals with diverse dietary and foraging strategies. During dry phases, obligate aquatic organisms are confined to wet refugia. Others, including many invertebrates, have dormancy traits allowing persistence during dry phases. Very high abundances and diversities of invertebrates, waterbirds, reptiles, and mammals exploit resource availability, particularly when prey are concentrated during drawdown phases of floods. Reproduction and recruitment, especially of fish, coincide with food availability cued by flood regimes.
TF1.4 Seasonal floodplain marshes
Seasonal floodplain marshes
Highly episodic freshwater floodplains are distinct from, but associated with, adjacent river channels, which provide water and sediment during flooding. These are low-productivity systems during long, dry periods (maybe years), with periodic spikes of very high productivity when first inundated. These floodplains have a high diversity of aquatic and terrestrial biota in complex trophic networks, with ruderal life-history traits enabling the exploitation of transient water and nutrient availability. Primary producers include flood-dependent macrophytes and algae with physiological traits for water conservation or drought avoidance. Lower trophic levels (e.g. algae, invertebrate consumers) avoid desiccation with traits such as dormant life-cycle phases, deposition of resting eggs (e.g. crustaceans and rotifers), and burial in sediments banks (e.g. larvae of cyclopoid copepods). Higher trophic levels (e.g. fish, amphibians, reptiles, and waterbirds) are highly mobile in large numbers or with resting strategies (e.g. burrowing frogs). These taxa can be important mobile links for the movement of biota and resources, but floods are the primary allochthonous sources of energy and nutrients. Floods are important triggers for life-history processes such as seed germination, emergence from larval stages, dispersal, and reproduction. Common lifeforms include detritus-feeding invertebrate collector-gatherers, indicating a reliance on heterotrophic energy pathways.
TF1.5 Episodic arid floodplains
Episodic arid floodplains
These patterned peatlands account for up to 40% of global soil carbon are dominated by a dense cover (high LAI) of hydrophytic mosses, graminoids, and shrubs, sometimes with scattered trees. Positive feedbacks between dense ground vegetation, hydrology, and substrate chemistry promote peat formation through water retention and inhibition of microbial decomposition. Moderate to low primary production is partially broken down at the soil surface by anamorphic fungi and aerobic bacteria. Burial by overgrowth and saturation by the water table promotes anaerobic conditions, limiting subsurface microbial activity, while acidity, nutrient scarcity, and low temperatures enhance the excess of organic deposition over decomposition. Plant diversity is low but fine-scale hydrological gradients structure vegetation mosaics, which may include fens (TF1.7). Mosses (notably Sphagnum spp.) and graminoids with layering growth forms promote peat formation. Their relative abundance influences microbial communities and peat biochemistry. Plant traits such as lacunate stem tissues, aerenchyma, and surface root mats promote oxygen transport into the anaerobic substrate. Woody plant foliage is small (leptophyll-microphyll) and sclerophyllous, reflecting excess carbohydrate production in low-nutrient conditions. Plants and fungi reproduce primarily by cloning, except where disturbances (e.g. fires) initiate gaps enabling recruitment. Pools within the bogs have specialised aquatic food webs underpinned by algal production and allochthonous carbon. Invertebrate larvae are prominent consumers in the trophic network of bog pools, and as adults they are important pollinators and predators. Assemblages of flies, dragonflies, damselflies, caddisflies and other invertebrates vary with the number, size and stability of pools. Carnivorous plants (e.g. sundews) support N cycling. Vertebrates are mostly itinerant but include specialised resident amphibians, reptiles, rodents, and birds. Some regions are rich in locally endemic flora and fauna, particularly in the Southern Hemisphere.
Boreal, Temperate & Montane Peat Bog
TF1.6
TF1.6 Boreal, temperate and montane peat bogs
TP1.c1
TP1.c1 Boreal, Temperate & Montane Peat Bog
Boreal, temperate and montane peat bogs
Fens are peatland ecosystems dominated by hydrophytic grasses, sedges, or forbs. Fens have higher productivity but lower functional diversity than bogs (TF1.6). Productivity is subsidised by inflow of minerotrophic waters and limited by anoxic substrates. Plant diversity is very low where surface hydrology varies temporally from complete saturation to desiccation but can be high in mineral-rich fens with stable near-surface water tables. Some regions are rich in locally endemic flora and fauna. Woody plants are typically scarce or absent, though some boreal forests (T2.1) develop on minerotrophic peats. Sphagnum mosses and hummock-forming sedges are absent from rich fens but �brown mosses� are common. Primary production is partly broken down on soil-surface layers by anamorphic fungi and aerobic bacteria. Anaerobic conditions due to high water tables limit subsurface microbial activity so that organic deposition exceeds decomposition and peat accumulates. Plant traits such as lacunate stem tissues, aerenchyma, and surface root mats promote oxygen transport into the anaerobic substrate. Methanogenic archaea and anaerobic bacteria may occur in the subsoil if N, Fe, and S are sufficient to sustain them. Fens may be spatially homogeneous or form string mosaics with bogs (e.g. aapa mires of Finland) but often display zonation reflecting differences in water chemistry (notably pH) or saturation. Patches of fen and bogs may be juxtaposed within peatland mosaics. Ongoing peat build-up may lead to transition from fen to bog systems. Plants and fungi reproduce locally by cloning, but seed and spore production enables dispersal and the colonisation of new sites. Invertebrates are dominant consumers in the trophic network, including dragonflies, caddisflies, flies, as well as calcareous specialists such as snails. Vertebrates are mostly itinerant but include specialised resident amphibians and birds.
Boreal & Temperate Fen
TF1.7
TF1.7 Boreal and temperate fens
TP1.c2
TP1.c2 Boreal & Temperate Fen
Boreal and temperate fens
These 1st-3rd order streams generally have steep gradients, fast flows, coarse substrates, often with a riffle-pool (shallow and fast vs deeper and slow) sequence of habitats, and periodic (usually seasonal) high-flow events. Many organisms have specialised morphological and behavioural adaptations to high flow-velocity environments. Riparian trees produce copious leaf fall that provide allochthonous subsidies, and support somewhat separate foodwebs to those based on in situ primary production by bryophytes and biofilms. Tree shade conversely light-limits productivity, a trade-off that relaxes seasonally where deciduous trees dominate. Microbes and detritivores (e.g. invertebrate shredders) break down leaf fall and other organic matter. Microbial biofilms comprising algae, fungi and bacteria establish on rocks and process dissolved organic matter. Invertebrates include shredders (consuming coarse particles), grazers (consuming biofilm), collectors and filter feeders (consuming benthic and suspended fine particles, respectively), and predators. Many benthic macroinvertebrates, mostly insects, have aquatic larvae and terrestrial adults. Filter feeders have traits adapted to swift flows, allowing them to hold fast to substrates while capturing resources, while benthic bryophytes provide shelter for other organisms. Fish are typically small predators of aquatic invertebrates and insects on the water surface. Birds typically have specialised foraging behaviours (e.g. dippers and kingfishers). Trophic cascades involving rapid algal growth, invertebrate grazers and fish are common.
F1.1 Permanent upland streams
Permanent upland streams
Small-medium lowland rivers (stream orders 4-9) are productive depositional ecosystems with trophic webs that are less diverse than large lowland rivers (F1.7). Macrophytes rooted in benthos or along the river margins contribute most primary production, but allochthonous inputs from floodplains and upper catchments generally dominate energy flow in the system. The biota tolerates a range of temperatures, which vary with catchment climate. Aquatic biota have physiological, morphological and even behavioural adaptations to lower oxygen concentrations, which may vary seasonally and diurnally. Zooplankton can be abundant in slower deeper rivers. Sessile (e.g. mussels) and scavenging (e.g. crayfish) macroinvertebrates are associated with the hyporheic zone and structurally complex microhabitats in moderate flow environments, including fine sediment and woody debris. Fish communities are diverse and may contribute to complex trophic networks. They include large predatory fish (e.g. sturgeons), smaller predators of invertebrates, herbivores, and detritivores. The feeding activities and movement of piscivorous birds (e.g. cormorants), diadromous fish (seawater-freshwater migrants), mammals (e.g. otters), and reptiles (e.g. turtles) extend trophic network beyond instream waters. Riparian zones vary in complexity from forested banks to shallow areas where emergent, floating and submerged macrophyte vegetation grows. Intermittently connected oxbow lakes or billabongs increase the complexity of associated habitats, providing more lentic waters for a range of aquatic fauna and flora.
F1.2 Permanent lowland rivers
Permanent lowland rivers
In seasonally cold montane and boreal environments, the surfaces of both small streams and large rivers freeze in winter. These systems have relatively simple trophic networks with low functional and taxonomic diversity, but the biota may include local endemics. In small, shallow streams, substrate algae are the principal autotrophs, while phytoplankton occur in larger rivers and benthic macrophytes are rare. All are seasonally inactive or curtailed when temperatures are cold and surface ice reduces light penetration through the water. Bottom-up regulatory processes dominate. Subsidies of dissolved organic carbon and nutrients from spring meltwaters and riparian vegetation along smaller streams are crucial to maintaining the detritivores that dominate the trophic network. Overall decomposition rates of coarse particles are low, but can exceed rates per degree day in warmer climates as the fauna are adapted to cold temperatures. Microbial decomposers often dominate small streams, but in larger rivers, the massive increase in fine organic particles in spring meltwaters can support abundant filter feeders which consume huge quantities of suspended particles and redeposit them within the river bed. Resident invertebrates survive cold temperatures through dormant life stages, extended life cycles and physiological adaptations. Vertebrate habitat specialists (e.g. dippers, small fish, beavers, and otters) tolerate low temperatures with traits such as subcuticular fat, thick hydrophobic, and/or aerated fur or feathers. Many fish disperse from frozen habitat to deeper water refuges during the winter (e.g. deep pools) before foraging in the meltwater streams from spring to autumn. In the larger rivers, fish, and particularly migratory salmonids returning to their natal streams and rivers for breeding, are a food source for itinerant terrestrial predators such as bears. When they die after reproduction, their decomposition in turn provides huge inputs of energy and nutrients to the system.
F1.3 Freeze-thaw rivers and streams
Freeze-thaw rivers and streams
Upland streams (orders 1-4) with highly seasonal flows generally have low to moderate productivity and a simpler trophic structure than lowland rivers. They tend to be shallow, hence benthic algae are major contributors to in-stream food webs and productivity, but riparian zones and catchments both contribute allochthonous energy and organic carbon through leaf fall, which may include an annual deciduous component. Primary production also varies with light availability and flow. Taxonomic diversity varies between streams, but can be lower than permanent streams and relatively high in endemism. Traits that enable biota to persist in narrow and shallow channels with large seasonal variations in flow velocity, episodes of torrential flow, and seasonal desiccation include small body sizes (especially in resident fish), dormant life phases and/or burrowing (crustaceans), omnivorous diets and high dispersal ability, including seasonal migration. Compared to lowland rivers, the trophic structure has a higher representation of algal and omnivorous feeders and low numbers of larger predators. Birds show specialist feeding strategies (e.g. dippers). Diversity and abundance of invertebrates and their predators (e.g. birds) fluctuate in response to seasonal flood regimes.
F1.4 Seasonal upland streams
Seasonal upland streams
These large riverine systems (stream orders 5-9) can be highly productive with trophic structures and processes shaped by seasonal hydrology and linkages to floodplain wetlands. In combination with biophysical heterogeneity, this temporal variability promotes functional diversity in the biota. Although trophic networks are complex due to the diversity of food sources and the extent of omnivory amongst consumers, food chains tend to be short and large mobile predators such as otters, large piscivorous waterbirds, sharks, dolphins, and crocodilians (in the tropics) can have a major impact on the food webs. Benthic algae are key contributors to primary productivity, although macrophytes become more important during the peak and late wet season when they also provide substrate for epiphytic algae. Rivers receive very significant resource subsidies from both algae and macrophytes on adjacent floodplains when they are connected by flows. Enhanced longitudinal hydrological connectivity during the wet season enables fish and other large aquatic consumers to function as mobile links, extending floodplain and estuarine resource subsidies upstream. Life cycle processess including reproduction, recruitment, and dispersal in most biota are tightly cued to seasonally high flow periods, often with floodplain nursery areas for river fish, amphibians and larger invertebrates.
F1.5 Seasonal lowland rivers
Seasonal lowland rivers
Episodic rivers have high temporal variability in flows and resource availability, shaping a low-diversity biota with periodically high abundance of some organisms. Productivity is episodically high and punctuated by longer periods of low productivity (i.e. boom-bust dynamics). The trophic structure can be complex and dominated by autochthonous primary production. Even though riparian vegetation is sparse, allochthonous inputs from connected floodplains may be important. Top-down control of ecosystem structure is evident in some desert streams. Episodic rivers are hotspots of biodiversity and ecological activity in arid landscapes, acting as both evolutionary and ecological refuges. Most biota have ruderal life cycles, dormancy phases, or high mobility enabling them to tolerate or avoid long, dry periods and to exploit short pulses of high resource availability during flooding. During dry periods, many organisms survive as dormant life phases (e.g. eggs or seeds), by reducing metabolism, or by persisting in perennial refugia (e.g. waterholes, shallow aquifers). They may rapidly recolonise the channel network during flow (networkers). Waterbirds survive dry phases by moving elsewhere, returning to breed during flows. The abundance of water, nutrients and food during flows and floods initiates rapid primary production (especially by algae), breeding and recruitment. Zooplankton are abundant in slower reaches during periods of flow. Macroinvertebrates such as sessile filter-feeders (e.g. mussels) and scavengers (e.g. crayfish) may occur in moderate flow environments with complex microhabitats in fine sediment and amongst woody debris. Assemblages of fish and amphibians are dominated by small body sizes. Most fish species use inundated floodplains in larval, juvenile and mature life stages, and produce massive biomass after large floods. Organisms generally tolerate wide ranges of temperature, salinity, and oxygen.
F1.6 Episodic arid rivers
Episodic arid rivers
Large lowland rivers (typically stream orders 8-12) are highly productive environments with complex trophic webs which are supported by very large flow volumes. Primary production is mostly from autochthonous phytoplankton and riparian macrophytes, with allochthonous inputs from floodplains and upper catchments generally dominating energy flow in the system. The fauna includes a significant diversity of pelagic organisms. Zooplankton are abundant, while sessile (e.g. mussels), burrowing (e.g. annelids) and scavenging (e.g. crustaceans) macroinvertebrates occur in the fine sediment and amongst woody debris. Fish communities are diverse and contribute to complex trophic networks. They include large predatory fish (e.g. freshwater sawfish, Pirhana, Alligator Gar) and in some rivers endemic River Dolphins, smaller predators of invertebrates (benthic and pelagic feeders), phytoplankton herbivores, and detritivores. The feeding activities and movement of semi-aquatic piscivorous birds (e.g. cormorants), mammals (e.g. otters), and reptiles (e.g. turtles, crocodilians) connect the trophic network to other ecosystems beyond instream waters. Riparian and large floodplain zones vary in complexity from forested banks, to productive lentic oxbow lakes and extensive and complex flooded areas where emergent and floodplain vegetation grows (e.g. reeds and macrophytes, shrubs, trees). Riparian zones can be complex but have less direct influence on large rivers than on smaller river ecosystems.
F1.7 Large lowland rivers
Large lowland rivers
Large permanent freshwater lakes, generally exceeding 100 km2, are prominent landscape features connected to one or more rivers either terminally or as flow-through systems. Shoreline complexity, depth, bathymetric stratification, and benthic topography promote niche diversity and zonation. High niche diversity and large volumes of permanent water (extensive, stable, connected habitat) support complex trophic webs with high diversity and abundance. High primary productivity may vary seasonally, driving succession, depending on climate, light availability, and nutrient regimes. Autochthonous energy from abundant pelagic algae (mainly diatoms and cyanobacteria) and from benthic macrophytes and algal biofilms (in shallow areas) is supplemented by allochthonous inflows that depend on catchment characteristics, climate, season, and hydrological connectivity. Zooplankton, invertebrate consumers, and herbivorous fish sustain high planktonic turnover and support upper trophic levels with abundant and diverse predatory fish, amphibians, reptiles, waterbirds, and mammals. This bottom-up web is coupled to a microbial loop, which returns dissolved organic matter to the web (rapidly in warm temperatures) via heterotrophic bacteria. Obligate freshwater biota in large lakes, including aquatic macrophytes and macroinvertebrates (e.g. crustaceans) and fish, often display high catchment-level endemism, in part due to long histories of environmental variability in isolation. Marked niche differentiation in life history and behavioural feeding and reproductive traits enables sympatric speciation and characterises the most diverse assemblages of macroinvertebrates and fish (e.g. ~500 cichlid fish species in Lake Victoria). Large predators are critical in top-down regulation of lower trophic levels. Large lake volume buffers against nutrient-mediated change from oligotrophic to eutrophic states. Recruitment of many organisms is strongly influenced by physical processes such as large inflow events. Mobile birds and terrestrial mammals use the lakes as breeding sites and/or sources of drinking water and play key roles in the inter-catchment transfer of nutrients and organic matter and the dispersal of biota.
F2.1 Large permanent freshwater lakes
Large permanent freshwater lakes
Small permanent freshwater lakes, pools or ponds are lentic environments with relatively high perimeter-to-surface area and surface-area-to-volume ratios. Most are <1 km2 in area, but this functional group includes lakes of transitional sizes up to 100 km2, while the largest lakes (>100 km2) are classified in F2.1. Niche diversity increases with lake size. Although less diverse than larger lakes, these lakes may support phytoplankton, zooplankton, shallow-water macrophytes, invertebrates, sedentary and migratory fish, reptiles, waterbirds, and mammals. Primary productivity, dominated by cyanobacteria, algae, and macrophytes, arises from allochthonous and autochthonous energy sources, which vary with lake and catchment features, climate, and hydrological connectivity. Productivity can be highly seasonal, depending on climate, light, and nutrients. Permanent water and connectivity are critical to obligate freshwater biota, such as fish, invertebrates, and aquatic macrophytes. Trophic structure and complexity depend on lake size, depth, location, and connectivity. Littoral zones and benthic pathways are integral to overall production and trophic interactions. Shallow lakes tend to be more productive (by volume and area) than deep lakes because light penetrates to the bottom, establishing competition between benthic macrophytes and phytoplankton, more complex trophic networks and stronger top-down regulation leading to alternative stable states and possible regime shifts between them. Clear lakes in macrophyte-dominated states support higher biodiversity than phytoplankton-dominated eutrophic lakes. Deep lakes are more dependent on planktonic primary production, which supports zooplankton, benthic microbial and invertebrate detritivores. Herbivorous fish and zooplankton regulate the main primary producers (biofilms and phytoplankton). The main predators are fish, macroinvertebrates, amphibians and birds, many of which have specialised feeding traits tied to different habitat niches (e.g. benthic or pelagic), but there are few filter-feeders. In many regions, shallow lakes provide critical breeding habitat for waterbirds, amphibians, and reptiles, while visiting mammals transfer nutrients, organic matter, and biota.
F2.2 Small permanent freshwater lakes
Small permanent freshwater lakes
These small (mostly <5 km2 in area) and shallow (<2 m deep) seasonal freshwater lakes, vernal pools, turloughs, or gnammas (panholes, rock pools), have a seasonal aquatic biota. Hydrological isolation promotes biotic insularity and local endemism, which occurs in some Mediterranean climate regions. Autochthonous energy sources are supplemented by limited allochthonous inputs from small catchments and groundwater. Seasonal variation in biota and productivity outweighs inter-annual variation, unlike in ephemeral lakes (F2.5 and F2.7). Filling induces microbial activity, the germination of seeds and algal spores, hatching and emergence of invertebrates, and growth and reproduction by specialists and opportunistic colonists. Wind-induced mixing oxygenates the water, but eutrophic or unmixed waters may become anoxic and dominated by air-breathers as peak productivity and biomass fuel high biological oxygen demand. Anoxia may be abated diurnally by photosynthetic activity. Resident biota persists through seasonal drying on lake margins or in sediments as desiccation-resistant dormant or quiescent life stages, e.g. crayfish may retreat to burrows that extend to the water table, turtles may aestivate in sediments or fringing vegetation, amphibious perennial plants may persist on lake margins or in seedbanks. Trophic networks and niche diversity are driven by bottom-up processes, especially submerged and emergent macrophytes, and depend on productivity and lake size. Cyanobacteria, algae, and macrophytes are the major primary producers, while annual grasses may colonise dry lake beds. The most diverse lakes exhibit zonation and support phytoplankton, zooplankton, macrophytes, macroinvertebrate consumers, and seasonally resident amphibians (especially juvenile aquatic phases), waterbirds, and mammals. Rock pools have simple trophic structure, based primarily on epilithic algae or macrophytes, and invertebrates, but no fish. Invertebrates and amphibians may reach high diversity and abundance in the absence of fish.
F2.3 Seasonal freshwater lakes
Seasonal freshwater lakes
The majority of the surface of these lakes is frozen for at least a month in most years. Their varied origins (tectonic, riverine, fluvioglacial), size and depth affect composition and function. Allochthonous and autochthonous energy sources vary with lake and catchment features. Productivity is highly seasonal, sustained in winter largely by the metabolism of microbial photoautotrophs, chemautotrophs and zooplankton that remain active under low light, nutrients, and temperatures. Spring thaw initiates a seasonal succession, increasing productivity and re-establishing complex trophic networks, depending on lake area, depth, connectivity, and nutrient availability. Diatoms are usually first to become photosynthetically active, followed by small and motile zooplankton, which respond to increased food availability, and cyanobacteria later in summer when grazing pressure is high. Large lakes with high habitat complexity (e.g. Lake Baikal) support phytoplankton, zooplankton, macrophytes (in shallow waters), invertebrate consumers, migratory fish (in connected lakes), waterbirds, and mammals. Their upper trophic levels are more abundant, diverse, and endemic than in smaller lakes. Herbivorous fish and zooplankton are significant top-down regulators of the main primary producers (i.e. biofilms and phytoplankton). These, in turn, are regulated by predatory fish, which may be limited by prey availability and competition. The biota is spatially structured by seasonally dynamic gradients in cold stratification, light, nutrient levels, and turbulence. Traits such as resting stages, dormancy, freeze-cued spore production in phytoplankton, and the ability of fish to access low oxygen exchange enable persistence through cold winters under the ice and through seasonal patterns of nutrient availability.
F2.4 Freeze-thaw freshwater lakes
Freeze-thaw freshwater lakes
Shallow ephemeral freshwater bodies are also known as depressions, playas, clay pans, or pans. Long periods of low productivity during dry phases are punctuated by episodes of high production after filling. Trophic structure is relatively simple with mostly benthic, filamentous, and planktonic algae, detritivorous and predatory zooplankton (e.g. rotifers and Daphnia), crustaceans, insects, and in some lakes, molluscs. The often high invertebrate biomass provides food for amphibians and itinerant waterbirds. Terrestrial mammals use the lakes to drink and bathe and may transfer nutrients, organic matter, and �hitch-hiking� biota. Diversity may be high in boom phases but there are only a few local endemics (e.g. narrow-ranged charophytes). Specialised and opportunistic biota exploit boom-bust resource availability through life-cycle traits that confer tolerance to desiccation (e.g. desiccation-resistant eggs in crustaceans) and/or enable rapid hatching, development, breeding, and recruitment when water arrives. Much of the biota (e.g. opportunistic insects) have widely dispersing adult phases enabling rapid colonisation and re-colonisation. Filling events initiate succession with spikes of primary production, allowing short temporal windows for consumers to grow and reproduce, and for itinerant predators to aggregate. Drying initiates senescence, dispersal, and dormancy until the next filling event.
F2.5 Ephemeral freshwater lakes
Ephemeral freshwater lakes
Permanent salt lakes have waters with periodically or permanently high sodium chloride concentrations. This group includes lakes with high concentrations of other ions (e.g. carbonate in soda lakes). Unlike in hypersaline lakes, productivity is not suppressed and autotrophs may be abundant, including phytoplankton, cyanobacteria, green algae, and submerged and emergent macrophytes. These, supplemented by allochthonous energy and C inputs from lake catchments, support relatively simple trophic networks characterised by few species in high abundance and some regional endemism. The high biomass of archaeal and bacterial decomposers and phytoplankton in turn supports abundant consumers including brine shrimps, copepods, insects and other invertebrates, fish, and waterbirds (e.g. flamingos). Predators and herbivores that become dominant at low salinity exert top-down control on algae and low-order consumers. Species niches are structured by spatial and temporal salinity gradients. Species in the most saline conditions tend to have broader ranges of salinity tolerance. Increasing salinity generally reduces diversity and the importance of top-down trophic regulation but not necessarily the abundance of organisms, except at hypersaline levels. Many organisms tolerate high salinity through osmotic regulation (at a high metabolic cost), limiting productivity and competitive ability.
F2.6 Permanent salt and soda lakes
Permanent salt and soda lakes
Ephemeral salt lakes or playas have relatively short-lived wet phases and long dry periods of years to decades. During filling phases, inflow dilutes salinity to moderate levels, and allochthonous energy and carbon inputs from lake catchments supplement autochthonous energy produced by abundant phytoplankton, cyanobacteria, diatoms, green algae, submerged and emergent macrophytes, and fringing halophytes. In drying phases, increasing salinity generally reduces diversity and top-down trophic regulation, but not necessarily the abundance of organisms � except at hypersaline levels, which suppress productivity. Trophic networks are simple and characterised by few species that are often highly abundant during wet phases. The high biomass of archaeal and bacterial decomposers and phytoplankton in turn support abundant consumers, including crustaceans (e.g. brine shrimps and copepods), insects and other invertebrates, fish, and specialist waterbirds (e.g. banded stilts, flamingos). Predators and herbivores that dominate at low salinity levels exert top-down control on algae and low-order consumers. Species niches are strongly structured by spatial and temporal salinity gradients and endorheic drainage promotes regional endemism. Species that persist in the most saline conditions tend to have broad salinity tolerance. Many organisms regulate salinity osmotically at a high metabolic cost, limiting productivity and competitive ability. Many specialised opportunists are able to exploit boom-bust resource cycles through life-cycle traits that promote persistence during dry periods (e.g. desiccation-resistant eggs in crustaceans and/or rapid hatching, development, breeding, and recruitment). Much of the biota (e.g. insects and birds) have widely dispersed adult phases enabling rapid colonisation. Filling events drive specialised succession, with short windows of opportunity to grow and reproduce reset by drying until the next filling event.
F2.7 Ephemeral salt lakes
Ephemeral salt lakes
These groundwater-dependent systems are fed by artesian waters that discharge to the surface. They are.surrounded by dry landscapes and receive little surface inflow, being predominantly disconnected from surface-stream networks. Insularity from the broader landscape results in high levels of endemism in sedentary aquatic biota, which are likely descendants of relic species from a wetter past. Springs may be spatially clustered due to their association with geological features such as faults or outcropping aquifers. Even springs in close proximity may have distinct physical and biological differences. Some springs have outflow streams, which may support different assemblages of plants and invertebrates to those in the spring orifice. Artesian springs and oases tend to have simple trophic structures. Autotrophs include aquatic algae and floating vascular plants, with emergent amphibious plants in shallow waters. Terrestrial plants around the perimeter contribute subsidies of organic matter and nutrients through litter fall. Consumers and predators include crustaceans, molluscs, arachnids, insects, and small-bodied fish. Most biota are poorly dispersed and have continuous life cycles and other traits specialised for persistence in hydrologically stable, warm, or hot mineral-rich water. Springs and oases are reliable watering points for wide-ranging birds and mammals, which function as mobile links for resources and promote the dispersal of other biota between isolated wetlands in the dryland matrix.
F2.8 Artesian springs and oases
Artesian springs and oases
These hot springs, geysers, mud pots and associated wetlands result from interactions of deeply circulating groundwater with magma and hot rocks that produce chemically precipitated substrates. They support a specialised but low-diversity biota structured by extreme thermal and geochemical gradients. Energy is almost entirely autochthonous, productivity is low, and trophic networks are very simple. Primary producers include chemoautotrophic bacteria and archaea, as well as photoautotrophic cyanobacteria, diatoms, algae, and macrophytes. Thermophilic and metallophilic microbes dominate the most extreme environments in vent pools, while mat-forming green algae and animal-protists occur in warm acidic waters. Thermophilic blue-green algae reach optimum growth above 45�C. Diatoms occur in less acidic warm waters. Aquatic macrophytes occur on sinter aprons and wetlands with temperatures below 35�C. Herbivores are scarce, allowing thick algal mats to develop. These are inhabited by invertebrate detritivores, notably dipterans and coleopterans, which may tolerate temperatures up to 55�C. Molluscs and crustaceans occupy less extreme microhabitats (notably in hard water hot springs), as do vertebrates such as amphibians, fish, snakes and visiting birds. Microinvertebrates such as rotifers and ostracods are common. Invertebrates, snakes and fish exhibit some endemism due to habitat insularity. Specialised physiological traits enabling metabolic function in extreme temperatures include thermophilic proteins with short amino-acid lengths, chaperone molecules that assist protein folding, branched chain fatty acids and polyamines for membrane stabilisation, DNA repair systems, and upregulated glycolysis providing energy to regulate heat stress. Three mechanisms enable metabolic function in extremely acidic (pH<3) geothermal waters: proton efflux via active transport pumps that counter proton influx, decreased permeability of cell membranes to suppress proton entry into the cytoplasm, and strong protein and DNA repair systems. Similar mechanisms enable metabolic function in waters with high concentrations of metal toxins. A succession of animal and plant communities occur with distance from the spring source as temperatures cool and minerals precipitate.
F2.9 Geothermal pools and wetlands
Geothermal pools and wetlands
Remarkable lacustrine ecosystems occur beneath permanent ice sheets. They are placed within the Lakes biome (F2) due to their relationships with some Freeze-thaw lakes (F2.4), but they share several key features with the Subterranean freshwater biome (SF1). Evidence of their existence first emerged in 1973 from airborne radar-echo sounding imagery, which penetrates the ice cover and shows lakes as uniformly flat structures with high basal reflectivity. The biota of these ecosystems is very poorly known due to technological limitations on access and concerns about the risk of contamination from coring. Only a few shallow lakes up to 1 km beneath ice have been surveyed (e.g. Lake Whillams in West Antarctica and Gr�msv�tn Lake in Iceland). The exclusively microbial trophic web is truncated, with no photoautotrophs and apparently few multi-cellular predators, but taxonomic diversity is high across bacteria and archaea, with some eukaryotes also represented. Chemosynthesis form the base of the trophic web, chemolithoautotrophic species using reduced N, Fe and S and methane in energy-generating metabolic pathways. The abundance of micro-organisms is comparable to that in groundwater (SF1.2) (104 � 105 cells.ml-1), with diverse morphotypes represented including long and short filaments, thin and thick rods, spirals, vibrio, cocci and diplococci. Subglacial lakes share several biotic traits with extremophiles within ice (T6.1), subterranean waters (SF1.1, SF1.2) and deep oceans (e.g. M2.3, M2.4, M3.3), including very low productivity, slow growth rates, large cell sizes and aphotic energy synthesis. Although microbes of the few surveyed subglacial lakes, and from accreted ice which has refrozen from lake water, have DNA profiles similar to those of other contemporary microbes, the biota in deeper disconnected lake waters and associated lake-floor sediments, could be highly relictual if it evolved in stable isolation over millions of years under extreme selection pressures.
F2.10 Subglacial lakes
Subglacial lakes
Rivers are impounded by the construction of dam walls, creating large freshwater reservoirs, mostly 15�250 m deep. Primary productivity is low to moderate and restricted to the euphotic zone (limnetic and littoral zones), varying with turbidity and associated light penetration, nutrient availability, and water temperature. Trophic networks are simple with low species diversity and endemism. Shallow littoral zones have the highest species diversity including benthic algae, macroinvertebrates, fish, waterbirds, aquatic reptiles, aquatic macrophytes, and terrestrial or amphibious vertebrates. Phytoplankton and zooplankton occur through the littoral and limnetic zones. The profundal zone lacks primary producers and, if oxygenated, is dominated by benthic detritivores and microbial decomposers. Fish communities inhabit the limnetic and littoral zones and may be dominated by managed species and opportunists. Reservoirs may undergo eutrophic succession due to inflow from catchments with sustained fertiliser application or other nutrient inputs.
F3.1 Large reservoirs
Large reservoirs
Rice paddies are artificial wetlands with low horizontal and vertical heterogeneity fed by rain or irrigation water diverted from rivers. They are predominantly temporary wetlands, regularly filled and dried, although some are permanently inundated, functioning as simplified marshes. Allochthonous inputs come from water inflow but also include the introduction of rice, other production organisms (e.g. fish and crustaceans), and fertilisers that promote rice growth. Simplified trophic networks are sustained by highly seasonal, deterministic flooding and drying regimes and the agricultural management of harvest crops, weeds, and pests. Cultivated macrophytes dominate primary production, but other autotrophs including archaea, cyanobacteria, phytoplankton, and benthic or epiphytic algae also contribute. During flooded periods, microbial changes produce anoxic soil conditions and emissions by methanogenic archaea. Opportunistic colonists include consumers such as invertebrates, zooplankton, insects, fish, frogs, and waterbirds, as well as other aquatic plants. Often they come from nearby natural wetlands or rivers and may breed within rice paddies. During dry phases, obligate aquatic organisms are confined to wet refugia away from rice paddies. These species possess traits that promote tolerance to low water quality and predator avoidance. Others organisms, including many invertebrates and plants, have rapid life cycles and dormancy traits allowing persistence as eggs or seeds during dry phases.
F3.3 Rice paddies
Rice paddies
Freshwater aquaculture systems are mostly permanent water bodies in either purpose-built ponds, tanks, or enclosed cages within artificial reservoirs (F3.1), canals (F3.5), freshwater lakes (F2.1 and F2.2), or lowland rivers (F1.2). These systems are shaped by large allochthonous inputs of energy and nutrients to promote secondary productivity by one or a few target consumer species (mainly fish or crustaceans), which are harvested as adults and restocked as juveniles on a regular basis. Fish are sometimes raised in mixed production systems within rice paddies (F3.3), but aquaculture ponds may also be co-located with rice paddies, which are centrally located and elevated above the level of the ponds. The enclosed structures exclude predators of the target species, while intensive anthropogenic management of hydrology, oxygenation, toxins, competitors, and pathogens maintains a simplified trophic structure and near-optimal survival and growth conditions for the target species. Intensive management and low niche diversity within the enclosures limit the functional diversity of biota within the system. However, biofilms and phytoplankton contribute low levels of primary production, sustaining zooplankton and other herbivores, while microbial and invertebrate detritivores break down particulate organic matter. Most of these organisms are opportunistic colonists, as are insects, fish, frogs, and waterbirds, as well as aquatic macrophytes. Often these disperse from nearby natural wetlands, rivers, and host waterbodies.
F3.4 Freshwater aquafarms
Freshwater aquafarms
Canals, ditches and storm water drains are artificial streams with low horizontal and vertical heterogeneity. They function as rivers or streams and may have simplified habitat structure and trophic networks, though some older ditches have fringing vegetation, which contributes to structural complexity. The main primary producers are filamentous algae and macrophytes that thrive on allochthonous subsidies of nutrients. Subsidies of organic carbon from urban or rural landscapes support microbial decomposers and mostly small invertebrate detritivores. While earthen banks and linings may support macrophytes and a rich associated fauna, sealed or otherwise uniform substrates limit the diversity and abundance of benthic biota. Fish and crustacean communities, when present, generally exhibit lower diversity and smaller body sizes compared to natural systems, and are often dominated by introduced or invasive species. Waterbirds, when present, typically include a low diversity and density of herbivorous and piscivorous species. Canals, ditches and drains may provide pathways for dispersal or colonisation of native and invasive biota.
F3.5 Canals, ditches and drains
Canals, ditches and drains
Deepwater coastal inlets (e.g. fjords, sea lochs) are semi-confined aquatic systems with many features of open oceans. Strong influences from adjacent freshwater and terrestrial systems produce striking environmental and biotic gradients. Autochthonous energy sources are dominant, but allochthonous sources (e.g. glacial ice discharge, freshwater streams, and seasonal permafrost meltwater) may contribute 10% or more of particulate organic matter. Phytoplankton, notably diatoms, contribute most of the primary production, along with biofilms and macroalgae in the epibenthic layer. Seasonal variation in inflow, temperatures, ice cover, and insolation drives pulses of in situ and imported productivity that generate blooms in diatoms, consumed in turn by jellyfish, micronekton, a hierarchy of fish predators, and marine mammals. Fish are limited by food, density-dependent predation, and cannibalism. As well as driving pelagic trophic networks, seasonal pulses of diatoms shape biogeochemical cycles and the distribution and biomass of benthic biota when they senesce and sink to the bottom, escaping herbivores, which are limited by predators. The vertical flux of diatoms, macrophytes, and terrestrial detritus sustains a diversity and abundance of benthic filter-feeders (e.g. maldanids and oweniids). Environmental and biotic heterogeneity underpins functional and compositional contrasts between inlets and strong gradients within them. Zooplankton, fish, and jellies distribute in response to resource heterogeneity, environmental cues, and interactions with other organisms. Deep inlets sequester more organic carbon into sediments than other estuaries (FM1.2, FM1.3) because steep slopes enable efficient influx of terrestrial carbon and low-oxygen bottom waters abate decay rates. Inlets with warmer water have more complex trophic webs, stronger pelagic-benthic coupling, and utilise a greater fraction of organic carbon, sequestering it in sea-floor sediments at a slower rate than those with cold water.
FM1.1 Deepwater coastal inlets
Deepwater coastal inlets
These coastal water bodies are mosaic systems characterised by high spatial and temporal variabilities in structure and function, which depend on coastal geomorphology, ratios of freshwater inflows to marine waters and tidal volume (hence residence time of saline water), and seasonality of climate. Fringing shoreline systems may include intertidal mangroves (MFT1.2), saltmarshes and reedbeds (MFT1.3), rocky (MT1.1), muddy (MT1.2) or sandy shores (MT1.3), while seagrasses and macrophytes (M1.1), shellfish beds (M1.4) or subtidal rocky reefs (M1.6) may occur in shallow intertidal and subtidal areas. Water-column productivity is typically higher than in nearby marine or freshwater systems due to substantial allochthonous energy and nutrient subsidies from shoreline vegetation and riverine and marine sources. This high productivity supports a complex trophic network with relatively high mosaic-level diversity and an abundance of aquatic organisms. Planktonic and benthic invertebrates (e.g. molluscs and crustaceans) often sustain large fish populations, with fish nursery grounds being a common feature. Waterbirds (e.g. cormorants), seabirds (e.g. gannets), top-order predatory fish, mammals (e.g. dolphins and dugongs), and reptiles (e.g. marine turtles and crocodilians) exploit these locally abundant food sources. Many of these organisms in upper trophic levels are highly mobile and move among different estuaries through connected ocean waters or by flying. Others migrate between different ecosystem types to complete their various life-history phases, although some may remain resident for long periods. Most biota tolerate a broad range of salinity or are spatially structured by gradients. The complex spatial mixes of physical and chemical characteristics, alongside seasonal, inter-annual, and sporadic variability in aquatic conditions, induce correspondingly large spatial-temporal variability in food webs. Low-salinity plumes, usually proportional to river size and discharge, may extend far from the shore, producing tongues of ecologically distinct conditions into the marine environment.
FM1.2 Permanently open riverine estuaries and bays
Permanently open riverine estuaries and bays
These coastal water bodies have high spatial and temporal variability in structure and function, which depends largely on the status of the lagoonal entrance (open or closed). Communities have low species richness compared to those of permanently open estuaries (FM1.2). Lagoonal entrance closure prevents the entry of marine organisms and resident biota must tolerate significant variation in salinity, inundation, dissolved oxygen, and nutrient concentrations. Resident communities are dominated by opportunists with short lifecycles. Trophic networks are generally detritus-based, fuelled by substantial inputs of organic matter from the terrestrial environment and, to a lesser extent, from the sea. As net sinks of organic matter from the land, productivity is often high, and lagoons may serve as nursery habitats for fish. High concentrations of polyphenolic compounds (e.g. tannins) in the water and periods of low nutrient input limit phytoplankton populations. Benthic communities dominate with attached algae, microphytobenthos and micro- and macro-fauna being the dominant groups. The water column supports plankton and small-bodied fish. Emergent and fringing vegetation is a key source of detrital carbon to the food webs, and also provides important structural habitats. Saltmarsh and reedbeds (MFT1.3) can adjoin lagoons while seagrasses (M1.1) occupy sandy bottoms of some lagoons, but mangroves (MFT1.2) are absent unless the entrance opens
FM1.3 Intermittently closed and open lakes and lagoons
Intermittently closed and open lakes and lagoons
Seagrass meadows are important sources of organic matter, much of which is retained by seagrass sediments. Seagrasses are the only subtidal marine flowering plants and underpin the high productivity of these systems. Macroalgae and epiphytic algae, also contribute to productivity, supporting both detritus production and autochthonous trophic structures, but compete with seagrasses for light. The complex three-dimensional structure of the seagrass provides shelter and cover to juvenile fish and invertebrates, binds sediments and, at fine scales, dissipates waves and currents. Seagrass ecosystems support infauna living amongst their roots, epifauna, and epiflora living on their shoots and leaves, as well as nekton in the water column. They have a higher abundance and diversity of flora and fauna compared to surrounding unvegetated soft sediments and comparable species richness and abundances to most other marine biogenic habitats. Mutualisms with lucinid molluscs may influence seagrass persistence. Mesograzers (such as amphipods and gastropods) play an important role in controlling epiphytic algal growth on seagrass. Grazing megafauna such as dugongs, manatees and turtles can contribute to patchy seagrass distributions, although they tend to �garden� rather than deplete seagrass.
M1.1 Seagrass meadows
Seagrass meadows
Kelps are benthic brown macroalgae (Order Laminariales) forming canopies that shape the structure and function of these highly productive, diverse ecosystems. These large (up to 30 m in length), fast-growing (up to 0.5 m/day) autotrophs produce abundant consumable biomass, provide vertical habitat structure, promote niche diversity, alter light-depth gradients, dampen water turbulence, and moderate water temperatures. Traits such as large, flexible photosynthetic organs, rapid growth, and strong benthic holdfasts enable kelps to persist on hard substrates in periodically turbulent waters. These kelps may occur as scattered individuals in other ecosystem types, but other macroalgae (e.g. green and coralline) rarely form canopies with similar function and typically form mixed communities with sessile invertebrates (see M1.5 and M1.6). Some kelps are fully submerged, while others form dense canopies on the water surface, which profoundly affect light, turbulence, and temperature in the water column. Interactions among co-occurring kelps are generally positive or neutral, but competition for space and light is an important evolutionary driver. Kelp canopies host a diverse epiflora and epifauna, with some limpets having unique kelp hosts. Assemblages of benthic invertebrate herbivores and detritivores inhabit the forest floor, notably echinoderms and crustaceans. The structure and diversity of life in kelp canopies provide forage for seabirds and mammals, such as gulls and sea otters, while small fish find refuge from predators among the kelp fronds. Herbivores keep epiphytes in check, but kelp sensitivity to herbivores makes the forests prone to complex trophic cascades when declines in top predators release herbivore populations from top-down regulation. This may drastically reduce the abundance of kelps and dependent biota and lead to replacement of the forests by urchin barrens, which persist as an alternative stable state.
M1.2 Kelp forests
Kelp forests
Coral reefs are biogenic structures that have been built up and continue to grow over decadal timescales as a result of the accumulation of calcium carbonate laid down by hermatypic (scleractinian) corals and other organisms. Reef-building corals are mixotrophic colonies of coral polyps in endosymbiotic relationships with photosynthesizing zooxanthellae that assimilate solar energy and nutrients, providing almost all of the metabolic requirements for their host. The corals develop skeletons by extracting dissolved carbonate from seawater and depositing it as aragonite crystals. Corals reproduce asexually, enabling the growth of colonial structures. They also reproduce sexually, with mostly synchronous spawning related to annual lunar cues. Other sessile organisms including sponges, soft corals, gorgonians, coralline algae, and other algae add to the diversity and structural complexity of coral reef ecosystems. The complex three-dimensional structure provides a high diversity of habitat niches and resources that support a highly diverse and locally endemic marine biota, including crustaceans, polychaetes, holothurians, echinoderms, and other groups, with one-quarter of marine life estimated to depend on reefs for food and/or shelter. Diversity is high at all taxonomic levels relative to all other ecosystems. The trophic network is highly complex, with functional diversity represented on the benthos and in the water column by primary producers, herbivores, detritivores, suspension-feeders, and multiple interacting levels of predators. Coral diseases also play a role in reef dynamics. The vertebrate biota includes fish, snakes, turtles, and mammals. The fish fauna is highly diverse, with herbivores and piscivores displaying a wide diversity of generalist and specialist diets (including parrot fish that consume corals), feeding strategies, schooling and solitary behaviours, and reproductive strategies. The largest vertebrates include marine turtles and sharks.
M1.3 Photic coral reefs
Photic coral reefs
These ecosystems are founded on intertidal or subtidal 3-dimensional biogenic structures formed primarily by high densities of oysters and/or mussels, which provide habitat for a moderate diversity of algae, invertebrates, and fishes, few of which are entirely restricted to oyster reefs. Structural profiles may be high (i.e. reefs) or low (i.e. beds). Shellfish reefs are usually situated on sedimentary or rocky substrates, but pen shells form high-density beds of vertically orientated non-gregarious animals in soft sediments. Sessile filter-feeders dominate these strongly heterotrophic but relatively high-productivity systems. Tides bring in food and carry away waste. Energy and matter in waste is processed by a subsystem of deposit-feeding invertebrates. Predators are a small component of the ecosystem biomass, but are nevertheless important in influencing the recruitment, biomass, and diversity of prey organisms (e.g. seastar predation on mussels). Shellfish beds and reefs may influence adjoining estuaries and coastal waters physically and biologically. Physically, they modify patterns of currents, dampen wave energy and remove suspended particulate matter through filter-feeding. Biologically, they remove phytoplankton and produce abundant oyster biomass. They function in biogeochemical cycling as carbon sinks, by increasing denitrification rates, and through N burial/sequestration. Relatively (or entirely) immobile and thin-shelled juveniles are highly susceptible to benthic predators such as crabs, fish, and birds. Recruitment can depend on protective microhabitats provided either by abiogenic or biogenic structures. In intertidal environments, the survival of shellfish can increase with density due to self-shading and moisture retention.
M1.4 Shellfish beds and reefs
Shellfish beds and reefs
These benthic systems are characterised by high densities of megabenthic, sessile heterotrophic suspension feeders or coralline algae that act as habitat engineers and dominate a subordinate autotrophic biota. Unlike coral reefs and shellfish beds, the major sessile animals in these animal forests include sponges, aphotic corals, hydroids, ascidians, hydrocorals, bryozoans, polychaetes, and bivalves (the latter only dominate in M1.4). Various coralline algae may be present in Marine animal forests, but rhodoliths, are never dominant (cf. M1.10). All these organisms engineer complex three-dimensional biogenic structures, sometimes of a single species or distinct phylogenetic groups. The structural complexity generates environmental heterogeneity and habitat, promoting a high diversity of invertebrate epifauna, with microphytobenthos and fish. Endemism may be high. Low light limits primary productivity especially by macroalgae, although microphytobenthos can be important. Energy flow and depth-related processes distinguish these systems from their deepwater aphotic counterparts (M3.7). Nonetheless, these systems are strongly heterotrophic, relying on benthic-pelagic coupling processes. Consequently, these systems are generally of moderate productivity and are often found near shallower, less photo-limited, high-productivity areas. Complex biogeochemical cycles govern nutrient release, particle retention, and carbon fixation. Biodiversity is enhanced by secondary consumers (i.e. deposit-feeding and filter-feeding invertebrates). Predators may influence the biomass and diversity of epifaunal prey organisms. Recruitment processes in benthic animals can be episodic and highly localised and, together with slow growth rates, limit recovery from disturbance.
M1.5 Photo-limited marine animal forests
Photo-limited marine animal forests
Submerged rocky reefs host trophically complex communities lacking a dense macroalgal canopy (cf. M1.2). Sessile primary producers and invertebrate filter-feeders assimilate autochthonous and allochthonous energy, respectively. Mobile biota occur in the water column. Reef-associated organisms have diverse dispersal modes. Some disperse widely as adults, some have non-dispersing larvae, others with sessile adult phases develop directly on substrates, or have larval stages or spores dispersed widely by currents or turbulence. Sessile plants include green, brown, and red algae. To reduce dislodgement in storms, macroalgae have holdfasts, while smaller species have low-growing �turf� life forms. Many have traits such as air lacunae or bladders that promote buoyancy. Canopy algae are sparse at the depths or levels of wave exposure occupied by this functional group (cf. kelp forests in M1.2). Algal productivity and abundance decline with depth due to diminution of light and are also kept in check by periodic storms and a diversity of herbivorous fish, molluscs, and echinoderms. The latter two groups and some fish are benthic and consume algae primarily in turf form or at its juvenile stage before stipes develop. Sessile invertebrates occur throughout. Some are high-turbulence specialists (e.g. barnacles, ascidians and anemones), while others become dominant at greater depths as the abundance of faster-growing algae diminishes (e.g. sponges and red algae). Fish include both herbivores and predators. Some are specialist bottom-dwellers, while others are more generalist pelagic species. Herbivores promote diversity through top-down regulation, influencing patch dynamics, trophic cascades and regime shifts involving kelp forests in temperate waters (M1.2). Mosaics of algal dominance, sessile invertebrate dominance, and barrens may shift over time. Topographic variation in the rocky substrate promotes habitat diversity and spatial heterogeneity. This provides refuges from predators but also hiding places for ambush predators including crustaceans and fish.
M1.6 Subtidal rocky reefs
Subtidal rocky reefs
Medium to coarse-grained, unvegetated, and soft minerogenic sediments show moderate levels of biological diversity. The trophic network is dominated by consumers with very few in situ primary producers. Interstitial microalgae and planktonic algae are present, but larger benthic primary producers are limited either by substrate instability or light, which diminishes with depth. In shallow waters where light is abundant and soft substrates are relatively stable, this group of systems is replaced by group M1.1, which is dominated by vascular marine plants. In contrast to those autochthonous systems, Subtidal sand beds rely primarily on allochthonous energy, with currents generating strong bottom flows and a horizontal flux of food. Sandy substrates tend to have less organic matter content and lower microbial diversity and abundance than muddy substrates (M1.8). Soft sediments may be dominated by invertebrate detritivores and suspension-feeders including burrowing polychaetes, crustaceans, echinoderms, and molluscs. Suspension-feeders tend to be most abundant in high-energy environments where waves and currents move sandy sediments, detritus, and living organisms. The homogeneity and low structural complexity of the substrate exposes potential prey to predation, especially from pelagic fish. Large bioturbators such as dugongs, stingrays and whales may also be important predators. Consequently, many benthic animals possess specialised traits that enable other means of predator avoidance, such as burrowing, shells, or camouflage.
M1.7 Subtidal sand beds
Subtidal sand beds
The muddy substrates of continental and island shelves support moderately productive ecosystems based on net allochthonous energy sources. In situ primary production is contributed primarily by microphytobenthos, mainly benthic diatoms with green microalgae, as macrophytes are scarce or absent. Both decline with depth as light diminishes. Drift algae can be extensive over muddy sediments, particularly in sheltered waters. Abundant heterotrophic microbes process detritus. The microbial community mediates most of the biogeochemical cycles in muddy sediments, a feature distinguishing these ecosystems from subtidal sand beds (M1.7). Deposit feeders (notably burrowing polychaetes, crustaceans, echinoderms, and molluscs) are important components of the trophic network as the low kinetic energy environment promotes vertical food fluxes, which they are able to exploit more effectively than suspension-feeders. The latter are less abundant on subtidal mud plains than on rocky reefs (M1.6) and Subtidal sand beds (M1.7) where waters are more turbulent and generate stronger lateral food fluxes. Deposit feeders may also constrain the abundance of co-occurring suspension-feeders by disturbing benthic sediment that resettles and smothers their larvae and clogs their filtering structures. Nonetheless, suspension-feeding tube worms may be common over muddy sediments when settlement substrates are available. Although such interference mechanisms may be important, competition is generally weak. In contrast, foraging predators, including demersal fish, may have a major structuring influence on these systems through impacts on the abundance of infauna, particularly on settling larvae and recently settled juveniles, but also adults. Burrowing is a key mechanism of predator avoidance and the associated bioturbation is influential on microhabitat diversity and resource availability within the sediment.
M1.8 Subtidal mud plains
Subtidal mud plains
Upwelled, nutrient-rich water supports very high net autochthonous primary production, usually through diatom blooms. These, in turn, support high biomass of copepods, euphausiids (i.e. krill), pelagic and demersal fish, marine mammals, and birds. Fish biomass tends to be dominated by low- to mid-trophic level species such as sardine, anchovy, and herring. The abundance of these small pelagic fish has been hypothesised to drive ecosystem dynamics through �wasp-waist� trophic control. Small pelagic fish exert top-down control on the copepod and euphausiid plankton groups they feed on and exert bottom-up control on predatory fish, although diel-migrant mesopelagic fish (M2.2) may have important regulatory roles. Abundant species of higher trophic levels include hake and horse mackerel, as well as pinnipeds and seabirds. Highly variable reproductive success of planktivorous fish reflects the fitness of spawners and suitable conditions for concentrating and retaining eggs and larvae inshore prior to maturity.
M1.9 Upwelling zones
Upwelling zones
Benthic carbonate ecosystems dominated by rhodoliths � non-geniculate (non-jointed), free-living, slow-growing, long-lived coralline algae � cover 30-100% of the seafloor within the beds, providing autochthonous energy to the system. Their pigments enable red algae to absorb more green - blue light efficiently, in addition to red-orange light. Rhodolith primary productivity is likely to be lower than in sea grasses (M1.1) and kelp forests (M1.2), although macrophytes add to primary production in shallow waters. They play a role in benthic nutrient cycling and represent significant long-term carbonate stores. Rhodoliths vary from smooth semi-spherical to complex fruticose structures that may form mono- or multi- specific aggregations typically composed of living and dead rhodoliths, as well as calcic sediments produced by breakdown. They can form 3-dimensional biogenic structures that facilitate coexistence of a diversity of benthic and demersal organisms, including algae, ascidians, sponges, macroinvertebrates and fish. Compared to coral reefs (M1.3), shellfish beds (M1.4) or marine animal forests (M1.5), where rhodoliths may be minor components, they are usually less rugose and less stable, due displacement or aggregation by water motion and bioturbators such as fish and macroinvertebrates. Large rhodoliths appear to facilitate deepwater kelp as well as feeding and reproduction in fish and invertebrates, supporting high species richness. High abundance of larval stages in these groups, suggests the intermediate rugosity of the beds is important for age-dependent predator evasion. Macroinvertebrate detritivores and herbivores well represented in rhodolith beds include crustaceans, molluscs, echinoderms and polychaetes. Closely associated microinvertebrates and microbes include small gastropods, ostracods, diatoms, foraminifera and bacteria. Bacterial guilds on rhodolith surfaces include photolithoautotrophs, anoxygenic phototrophs, anaerobic heterotrophs, sulfide oxidizers and methanogens, suggesting important roles in biomineralization. The biotic assemblages of rhodolith beds vary spatially, with depth gradients and temporally over diurnal and seasonal time scales. Fish and sponges that aggregate and agglutinate individual rhodoliths are thought to promote development of reefs from rhodolith beds, counter-balancing slow recovery from disturbance.
M1.10 Rhodolith/Maërl beds
Rhodolith/Maërl beds
The epipelagic or euphotic zone of the open ocean is the uppermost layer that is penetrated by enough light to support photosynthesis. The vast area of the ocean means that autochthonous productivity in the epipelagic layer, largely by diatoms, accounts for around half of all global carbon fixation. This in turn supports a complex trophic network and high biomass of diatoms, copepods (resident and vertical migrants), fish, cephalopods, marine mammals, and seabirds, including fast-swimming visual predators taking advantage of the high-light environment. The suitability of conditions for recruitment and reproduction depends on the characteristics of the water column, which vary spatially and impact productivity rates, species composition, and community size structure. Mid-ocean subtropical gyres, for example, are characteristically oligotrophic, with lower productivity than other parts of the ocean surface. In contrast to the rest of the epipelagic zone, upwelling zones are characterised by specific patterns of water movement that drive high nutrient levels, productivity, and abundant forage fish, and are therefore included in a different functional group (M1.9). Seasonal variation in productivity is greater at high latitudes due to lower light penetration and duration in winter compared to summer. The habitat and lifecycle of some specialised pelagic species (e.g. herbivorous copepods, flying fish) are entirely contained within epipelagic ocean waters, but many commonly occurring crustaceans, fish, and cephalopods undertake either diel or ontogenetic vertical migration between the epipelagic and deeper oceanic layers. These organisms exploit the food available in the productive epipelagic zone either at night (when predation risk is lower) or for the entirety of their less mobile, juvenile life stages. Horizontal migration is also common and some species (e.g. tuna and migratory whales) swim long distances to feed and reproduce. Other species use horizontal currents for passive migration, particularly smaller planktonic organisms or life stages, e.g. copepods and small pelagic fish larvae moving between spawning and feeding grounds. Unconsumed plankton and dead organisms sink from this upper oceanic zone, providing an important particulate source of nutrients to deeper, aphotic zones.
M2.1 Epipelagic ocean waters
Epipelagic ocean waters
The mesopelagic, dysphotic, or �twilight� zone begins below the epipelagic layer and receives enough light to discern diurnal cycles but too little for photosynthesis. The trophic network is therefore dominated by detritivores and predators. The diverse organisms within this layer consume and reprocess allochthonous organic material sinking from the upper, photosynthetic layer. Hence, upper mesopelagic waters include layers of concentrated plankton, bacteria, and other organic matter sinking from the heterogeneous epipelagic zone (M2.1). Consumers of this material including detritivorous copepods deplete oxygen levels in the mesopelagic zone, more so than in other layers where oxygen can be replenished via diffusion and mixing at the surface or photosynthesis (as in the epipelagic zone), or where lower particulate nutrient levels limit biological processes (as in the deeper layers). Many species undertake diel vertical migration into the epipelagic zone during the night to feed when predation risk is lower. These organisms use the mesopelagic zone as a refuge during the day and increase the flow of carbon between ocean layers. Bioluminescence is a common trait present in more than 90% of mesopelagic organisms often with silvery reflective skin (e.g. lantern fish). Fish in the lower mesopelagic zone (>700 m) are less reflective and mobile due to reduced selection pressure from visual predators in low light conditions. These systems are difficult to sample, but advances in estimating fish abundances indicate that biomass is very high, possibly two orders of magnitude larger than global fisheries landings (1 � 1010 t).
M2.2 Mesopelagic ocean waters
Mesopelagic ocean waters
These are deep, open-ocean ecosystems in the water column, generally between 1,000�3,000 m in depth. Energy sources are allochthonous, derived mainly from the fallout of particulate organic matter from the epipelagic horizon (M2.1). Total biomass declines exponentially from an average of 1.45 mgC m-3 at 1,000 m depth to 0.16 mgC m-3 at 3,000 m. Trophic structure is truncated, with no primary producers. Instead, the major components are zooplankton, micro-crustaceans (e.g. shrimps), medusozoans (e.g. jellyfish), cephalopods, and four main guilds of fish (gelativores, zooplanktivores, micronektivores, and generalists). These organisms generally do not migrate vertically, in contrast to those in the mesopelagic zone (M2.2). Larvae often hatch from buoyant egg masses at the surface to take advantage of food sources. Long generation lengths (>20 years in most fish) and low fecundity reflect low energy availability. Fauna typically have low metabolic rates, with bathypelagic fish having rates of oxygen consumption ~10% of that of epipelagic fish. Fish are consequently slow swimmers with high water content in muscles and relatively low red-to-white muscle tissue ratios. They also have low-density bodies, reduced skeletons, and/or specialised buoyancy organs to achieve neutral buoyancy for specific depth ranges. Traits related to the lack of light include reduced eyes, lack of pigmentation, and enhanced vibratory and chemosensory organs. Some planktonic forms, medusas, and fish have internal light organs that produce intrinsic or bacterial bioluminescence to attract prey items or mates or to defend themselves. Most of the biota possess cell membranes with specialised phospholipid composition, intrinsic protein modifications, and protective osmolytes (i.e. organic compounds that influence the properties of biological fluids) to optimise protein function at high pressure.
M2.3 Bathypelagic ocean waters
Bathypelagic ocean waters
These deep, open-ocean ecosystems span depths from 3,000 to 6,000 m. Autotrophs are absent and energy sources are entirely allochthonous. Particulate organic debris is imported principally from epipelagic horizons (M2.1) and the flux of matter diminishing through the mesopelagic zone (M2.2) and bathypelagic zone (M2.3). Food for heterotrophs is therefore very scarce. Due to extreme conditions and limited resources, biodiversity is very low. Total biomass declines exponentially from an average of 0.16 mgC m-3 at 3,000 m in depth to 0.0058 mgC m-3 at 6,000 m. However, there is an order of magnitude variation around the mean due to regional differences in the productivity of surface waters. Truncated trophic networks are dominated by planktonic detritivores, with low densities of gelatinous invertebrates and scavenging and predatory fish. Fauna typically have low metabolic rates and some have internal light organs that produce bioluminescence to attract prey or mates or to defend themselves. Vertebrates typically have reduced skeletons and watery tissues to maintain buoyancy. Most of the biota possesses cell membranes with specialised phospholipid composition, intrinsic protein modifications, and protective osmolytes (i.e. organic compounds that influence the properties of biological fluids) to optimise protein function at high pressure.
M2.4 Abyssopelagic ocean waters
Abyssopelagic ocean waters
The seasonally frozen surface of polar oceans (1�2 m thick in the Antarctic and 2�3 m thick in the Arctic) may be connected to land or permanent ice shelves and is one of the most dynamic ecosystems on earth. Sympagic (i.e. ice-associated) organisms occur in all physical components of the sea-ice system including the surface, the internal matrix and brine channel system, the underside, and nearby waters modified by sea-ice presence. Primary production by microalgal and microbial communities beneath and within sea ice form the base of the food web and waters beneath sea ice develop. The standing stocks produced by these microbes are significantly greater than in ice-free areas despite shading by ice and are grazed by diverse zooplankton including krill. The sea ice underside provides refuge from surface predators and is an important nursery for juvenile krill and fish. Deepwater fish migrate vertically to feed on zooplankton beneath the sea ice. High secondary production (particularly of krill) in sea ice and around its edges supports seals, seabirds, penguins (in the Antarctic), and baleen whales. The highest trophic levels include vertebrate predators such as polar bears (in the Arctic), leopard seals, and toothed whales. Sea ice also provides resting and/or breeding habitats for pinnipeds (seals), polar bears, and penguins. As the sea ice decays annually, it releases biogenic material consumed by grazers and particulate and dissolved organic matter, nutrients, freshwater and iron, which stimulate phytoplankton growth and have important roles in biogeochemical cycling.
M2.5 Sea ice
Sea ice
These aphotic heterotrophic ecosystems fringe the margins of continental plates and islands, extending from the shelf break (~250 m depth) to the abyssal basins (4,000 m). These large sedimentary slopes with localised rocky outcrops are characterised by strong depth gradients in the biota and may be juxtaposed with specialised ecosystems such as submarine canyons (M3.2), deep-water biogenic systems (M3.6), and chemosynthetic seeps (M3.7), as well as landslides and oxygen-minimum zones. Energy sources are derived mostly from lateral advection from the shelf and vertical fallout of organic matter particles through the water column and pelagic fauna impinging on the slopes, which varies seasonally with the productivity of the euphotic layers. Other inputs of organic matter include sporadic pulses of large falls (e.g. whale falls and wood falls). Photoautotrophs and resident herbivores are absent and the trophic network is dominated by microbial decomposers, detritivores, and their predators. Depth-related gradients result in a marked bathymetric zonation of faunal communities, and there is significant basin-scale endemism in many taxa. The taxonomic diversity of these heterotrophs is high and reaches a maximum at middle to lower depths. The biomass of megafauna decreases with depth and the meio-fauna and macro-fauna become relatively more important, but maximum biomass occurs on mid-slopes in some regions. The megafauna is often characterised by sparse populations of detritivores, including echinoderms, crustaceans, and demersal fish, but sessile benthic organisms are scarce and the bottom is typically bare, unconsolidated sediments.
M3.1 Continental and island slopes
Continental and island slopes
Submarine canyons are major geomorphic features that function as dynamic flux routes for resources between continental shelves and ocean basins. As a result, canyons are one of the most productive and biodiverse habitats in the deep sea. Habitat heterogeneity and temporal variability are key features of submarine canyons, with the diversity of topographic and hydrodynamic features and substrate types (e.g. mud, sand, and rocky walls) within and among canyons contributing to their highly diverse heterotrophic faunal assemblages. Photoautotrophs are present only at the heads of some canyons. Canyons are characterised by meio-, macro-, and mega-fauna assemblages with greater abundances and/or biomass than adjacent continental slopes (M3.1) due mainly to the greater quality and quantity of food inside canyon systems. Habitat complexity and high resource availability make canyons important refuges, nurseries, spawning areas, and regional source populations for fish, crustaceans, and other benthic biota. Steep exposed rock and strong currents may facilitate the development of dense communities of sessile predators and filter-feeders such as cold-water corals and sponges, engineering complex three-dimensional habitats. Soft substrates favour high densities of pennatulids and detritivores such as echinoderms. The role of canyons as centres of carbon deposition makes them an extraordinary habitat for deep-sea deposit-feeders, which represent the dominant mobile benthic trophic guild. The high productivity attracts pelagic-associated secondary and tertiary consumers, including cetaceans, which may visit canyons for feeding and breeding.
M3.2 Submarine canyons
Submarine canyons
This is the largest group of benthic marine ecosystems, extending between 3,000 and 6,000 m depth and covered by thick layers (up to thousands of metres) of fine sediment. Less than 1% of the seafloor has been investigated biologically. Tests of giant protozoans and the lebensspuren (i.e. tracks, borrows, and mounds) made by megafauna structure the habitats of smaller organisms. Ecosystem engineering aside, other biotic interactions among large fauna are weak due to the low densities of organisms. Abyssal communities are heterotrophic, with energy sources derived mostly from the fallout of organic matter particles through the water column. Large carrion falls are major local inputs of organic matter and can later become important chemosynthetic environments (M3.7). Seasonal variation in particulate organic matter flux reflects temporal patterns in the productivity of euphotic layers. Input of organic matter can also be through sporadic pulses of large falls (e.g. whale falls and wood falls). Most abyssal plains are food-limited and the quantity and quality of food input to the abyssal seafloor are strong drivers shaping the structure and function of abyssal communities. Abyssal biomass is very low and dominated by meio-fauna and microorganisms that play key roles in the function of benthic communities below 3,000 m depth. The abyssal biota, however, is highly diverse, mostly composed of macro- and meio-fauna with large numbers of species new to science (up to 80% in some regions). Many species have so far been sampled only as singletons (only one specimen per species) or as a few specimens. The megafauna is often characterised by sparse populations of detritivores, notably echinoderms, crustaceans, and demersal fish. Species distribution and major functions such as community respiration and bioturbation are linked to particulate organic carbon flux. These functions modulate the important ecosystem services provided by abyssal plains, including nutrient regeneration and carbon sequestration.
M3.3 Abyssal plains
Abyssal plains
Seamounts, plateaus, and ridges are major geomorphic features of the deep oceanic seafloor, characterised by hard substrates, elevated topography, and often higher productivity than surrounding waters. Topographically modified currents affect geochemical cycles, nutrient mixing processes, and detrital fallout from the euphotic zone that deliver allochthonous energy and nutrients to these heterotroph-dominated systems. Suspension-feeders and their dependents and predators dominate the trophic web, whereas deposit-feeders and mixed-feeders are less abundant than in other deep-sea systems. Autotrophs are generally absent. Summits that reach the euphotic zone are included within functional groups of the Marine shelf biome. Bathymetric gradients and local substrate heterogeneity support marked variation in diversity, composition, and abundance. Rocky walls, for example, may be dominated by sessile suspension-feeders including cnidarians (especially corals), sponges, crinoids, and ascidians. High densities of sessile animals may form deep-water biogenic beds (M3.5), but those systems are not limited to seamounts or ridges. Among the mobile benthic fauna, molluscs and echinoderms can be abundant. Seamounts also support dense aggregations of large fish, attracted by the high secondary productivity of lower trophic levels in the system, as well as spawning and/or nursery habitats. Elevated topography affects the distribution of both benthic and pelagic fauna. Seamounts and ridges tend to act both as stepping stones for the dispersal of slope-dwelling biota and as dispersal barriers between adjacent basins, while insular seamounts may have high endemism.
M3.4 Seamounts, ridges and plateaus
Seamounts, ridges and plateaus
Benthic, sessile suspension-feeders such as aphotic corals, sponges, and bivalves form structurally complex, three-dimensional structures or �animal forests� in the deep oceans. In contrast to their shallow-water counterparts in coastal and shelf systems (M1.5), these ecosystems are aphotic and rely on allochthonous energy sources borne in currents and pelagic fallout. The trophic web is dominated by filter-feeders, decomposers, detritivores, and predators. Primary producers and associated herbivores are only present at the interface with the photic zone (~250 m depth). The biogenic structures are slow growing but critical to local demersal biota in engineering shelter from predators and currents, particularly in shallower, more dynamic waters. They also provide stable substrates and enhance food availability. This habitat heterogeneity becomes more important with depth as stable, complex elevated substrate becomes increasingly limited. These structures and the microenvironments within them support a high diversity of associated species including symbionts, microorganisms in coral biofilm, filter-feeding epifauna, biofilm grazers, mobile predators (e.g. polychaetes and crustaceans), and benthic demersal fish. Diversity is positively related to the size, flexibility, and structural complexity of habitat-forming organisms. Their impact on hydrography and the flow of local currents increases retention of particulate matter, zooplankton, eggs and larvae from the water column. This creates positive conditions for suspension-feeders, which engineer their environment and play important roles in benthic-pelagic coupling, increasing the flux of matter and energy from the water column to the benthic community.
M3.5 Deepwater biogenic beds
Deepwater biogenic beds
Hadal zones are the deepest ocean systems on earth and among the least explored. They are heterotrophic, with energy derived from the fallout of particulate organic matter through the water column, which varies seasonally and geographically and accumulates in the deepest axes of the trenches. Most organic matter reaching hadal depths is nutrient-poor because pelagic organisms use the labile compounds from the particulate organic matter during fallout. Hadal systems are therefore food-limited, but particulate organic matter flux may be boosted by sporadic pulses (e.g. whale falls and wood falls) and sediment transported by advection and seismically induced submarine landslides. Additional energy is contributed by chemosynthetic bacteria that can establish symbiotic relationships with specialised fauna. These are poorly known but more are expected to be discovered in the future. Hadal trophic networks are dominated by scavengers and detritivores, although predators (including through cannibalism) are also represented. Over 400 species are currently known from hadal ecosystems, with most metazoan taxa represented including amphipods, polychaetes, gastropods, bivalves, holothurians, and fish. These species possess physiological adaptations to high hydrostatic pressure, darkness, low temperature, and low food supply. These environmental filters, together with habitat isolation, result in high levels of endemism. Gigantism in amphipods, mysids, and isopods contrasts with the dwarfism in meio-fauna (e.g. nematodes, copepods, and kinorhynchs).
M3.6 Hadal trenches and troughs
Hadal trenches and troughs
Chemosynthetic-based ecosystems (CBEs) include three major types of habitats between bathyal and abyssal depths: 1) hydrothermal vents on mid-ocean ridges, back-arc basins, and active seamounts; 2) cold seeps on active and passive continental margins; and 3) large organic falls of whales or wood. All these systems are characterised by microbial primary productivity through chemoautotrophy, which uses reduced compounds (such as H2S and CH4) as energy sources instead of light. Microbes form bacterial mats and occur in trophic symbiosis with most megafauna. The continuous sources of energy and microbial symbiosis fuel high faunal biomass. However, specific environmental factors (e.g. high temperature gradients at vents, chemical toxicity, and symbiosis dependence) result in a low diversity and high endemism of highly specialised fauna. Habitat structure comprises hard substrate on vent chimneys and mostly biogenic substrate at seeps and food-falls. Most fauna is sessile or with low motility and depends on the fluids emanating at vents and seeps or chemicals produced by microbes on food-falls, and thus is spatially limited. Large tubeworms, shrimps, crabs, bivalves, and gastropods dominate many hydrothermal vents, with marked biogeographic provinces. Tubeworms, mussels, and decapod crustaceans often dominate cold seeps with demersal fish. These are patchy ecosystems where connectivity relies on the dispersal of planktonic larvae.
M3.7 Chemosynthetically-based ecosystems
Chemosynthetically-based ecosystems
These deployments include submerged structures with high vertical relief including ship wrecks, oil and gas infrastructure, and designed artificial reefs, as well as some low-relief structures (e.g. rubble piles). The latter do not differ greatly from adjacent natural reefs, but structures with high vertical relief are distinguished by an abundance of zooplanktivorous fish, as well as reef-associated fishes. Macroalgae are sparse or absent as the ecosystem is fed by currents and ocean swell delivering phytoplankton to sessile invertebrates. Complex surfaces quickly thicken with a biofouling community characterised by an abundance of filter-feeding invertebrates (e.g. sponges, barnacles, bivalves, and ascidians) and their predators (e.g. crabs and flatworms). Invertebrate diversity is high, with representatives from every living Phylum. Structures without complex surfaces, such as the smooth, wide expanse of a hull, may suffer the sporadic loss of all biofouling communities after storm events. This feeds the sandy bottom community, evident as a halo of benthic invertebrates (e.g. polychaetes and amphipods), which also benefit from the plume of waste and detritus drifting from the reef community. Artificial structures also provide a visual focus attracting the occasional pelagic fish and marine mammals, which respond similarly to fish-attraction devices and drift objects.
M4.1 Submerged artificial structures
Submerged artificial structures
These intertidal benthic systems, composed of sessile and mobile species, are highly structured by fine-scale resource and stress gradients, as well as trade-offs among competitive, facilitation, and predatory interactions. Sessile algae and invertebrates form complex three-dimensional habitats that provide microhabitat refugia from desiccation and temperature stress for associated organisms; these weaken competitive interactions. The biota exhibit behavioural and morphological adaptions to minimise exposure to stressors, such as seeking shelter in protective microhabitats at low tide, possessing exoskeletons (e.g. shells), or producing mucous to reduce desiccation. Morphologies, such as small body sizes and small cross-sectional areas to minimise drag, reflect adaptation to a wave-swept environment. Key trophic groups include filter-feeders (which feed on phytoplankton and dissolved organic matter at high tide), grazers (which scrape microphytobenthos and macroalgal spores from rock or consume macroalgal thalli), and resident (e.g. starfish, whelks, and crabs) and transient (e.g. birds and fish) marine and terrestrial predators. Rocky shores display high endemism relative to other coastal systems and frequently display high productivity due to the large amounts of light they receive, although this can vary according to nutrient availability from upwelling.
MS1.a1 Rocky Shoreline
MT1.1
MT1.1 Rocky shorelines
Rocky Shoreline
Rocky shorelines
Highly productive intertidal environments are defined by their fine particle size (dominated by silts) and are fuelled largely by allochthonous production. Benthic diatoms are the key primary producer, although ephemeral intertidal seagrass may occur. Otherwise, macrophytes are generally absent unlike other ecosystems on intertidal mudflats (MFT1.2, MFT1.3). Fauna are dominated by deposit-feeding taxa (consuming organic matter that accumulates in the fine-grained sediments) and detritivores feeding on wrack (i.e. drift algae deposited at the high-water mark) and other sources of macro-detritus. Bioturbating and tube-dwelling taxa are key ecosystem engineers, the former oxygenating and mixing the sediments and the latter providing structure to an otherwise sedimentary habitat. Infauna residing within sediments are protected from high temperatures and desiccation by the surrounding matrix and do not display the same marked patterns of zonation as rocky intertidal communities. Many infaunal taxa are soft-bodied. Nevertheless, competition for food resources carried by incoming tides can lead to intertidal gradients in fauna. Predators include the substantial shorebird populations that forage on infauna at low tide, including migratory species that depend on these systems as stopover sites. Fish, rays, crabs, and resident whelks forage around lugworm bioturbation. Transitions to mangrove (MFT1.2), saltmarsh or reedbed (MFT1.3) ecosystems may occur in response to isostatic or sea level changes, freshwater inputs or changes in currents that promote macrophyte colonisation.
MS1.a2
MS1.a2 Muddy Shoreline
MT1.2
MT1.2 Muddy shorelines
Muddy Shoreline
Muddy shorelines
Sandy shorelines include beaches, sand bars, and spits. These intertidal systems typically lack macrophytes, with their low productivity largely underpinned by detrital subsidies dominated by wrack (i.e. drift seaweed accumulating at the high-water mark) and phytoplankton, particularly in the surf zone of dissipative beaches. Salt- and drought-tolerant primary producers dominate adjacent dune systems (TM1.4). Meio-faunal biomass in many instances exceeds macrofaunal biomass. In the intertidal zone, suspension-feeding is a more common foraging strategy among invertebrates than deposit-feeding, although detritivores may dominate higher on the shore where wrack accumulates. Invertebrate fauna are predominantly interstitial, with bacteria, protozoans, and small metazoans contributing to the trophic network. Sediments are constantly shifting and thus invertebrate fauna are dominated by mobile taxa that display an ability to burrow and/or swash-ride up and down the beach face with the tides. The transitional character of these systems supports marine and terrestrial invertebrates and itinerant vertebrates from marine waters (e.g. egg-laying turtles) and from terrestrial or transitional habitats (e.g. shorebirds foraging on invertebrates or foxes foraging on carrion).
MS1.a3
MS1.a3 Sandy Shoreline
MT1.3
MT1.3 Sandy shorelines
Sandy Shoreline
Sandy shorelines
These low-productivity, net heterotrophic systems are founded on unstable rocky substrates and share some ecological features with sandy beaches (MT1.3) and rocky shores (MT1.1). Traits of the biota reflect responses to regular substrate disturbance by waves and exposure of particles to desiccation and high temperatures. For example, in the high intertidal zone of boulder shores (where temperature and desiccation stress is most pronounced), fauna may be predominantly nocturnal. On cobble beaches, fauna are more abundant on the sub-surface because waves cause cobbles to grind against each other, damaging or killing attached fauna. Conversely, sandy beaches are where most fauna occupy surface sediments. Intermediate frequencies of disturbance lead to the greatest biodiversity. Only species with low tenacity (e.g. top shells) are found in surface sediments because they can detach and temporarily inhabit deeper interstices during disturbance events. High-tenacity species (e.g. limpets) or sessile species (e.g. macroalgae and barnacles) are more readily damaged, hence rare on cobble shores. Large boulders, however, are only disturbed during large storms and have more stable temperatures, so more fauna can persist on their surface. Encrusting organisms may cement boulders on the low shore, further stabilising them in turbulent water. Allochthonous wrack is the major source of organic matter on cobble beaches, but in situ autotrophs include superficial algae and vascular vegetation dominated by halophytic forbs. On some cobble beaches of New England, USA, extensive intertidal beds of the cordgrass Spartina alterniflora stabilise cobbles and provide shade, facilitating establishment of mussels, barnacles, gastropods, amphipods, crabs, and algae. In stabilising cobbles and buffering wave energy, cordgrass may also facilitate plants higher on the intertidal shore.
Boulder & Cobble Shore
MS1.a4
MS1.a4 Boulder & Cobble Shore
MT1.4
MT1.4 Boulder and cobble shores
Boulder and cobble shores
Relatively low productivity grasslands, shrublands, and low forests on exposed coastlines are limited by salt influx, water deficit, and recurring disturbances. Diversity is low across taxa and trophic networks are simple, but virtually all plants and animals have strong dispersal traits and most consumers move between adjacent terrestrial and marine ecosystems. Vegetation and substrates are characterised by strong gradients from sea to land, particularly related to aerosol salt inputs, substrate instability and disturbance associated with sea storms and wave action. Plant traits conferring salt tolerance (e.g. succulent and sub-succulent leaves and salt-excretion organs) are commonly represented. Woody plants with ramulose and/or decumbent growth forms and small (microphyll-nanophyll) leaves reflect mechanisms of persistence under exposure to strong salt-laden winds, while modular and rhizomatous growth forms of woody and non-woody plants promote persistence, regeneration, and expansion under regimes of substrate instability and recurring disturbance. These strong environmental filters promote local adaptation, with specialised genotypes and phenotypes of more widespread taxa commonly represented on the strandline. Fauna are highly mobile, although some taxa such as ground-nesting seabirds may be sedentary for some parts of their lifecycles. Ecosystem dynamics are characterised by disturbance-driven cycles of disruption and renewal, with early phases dominated by colonists and in situ regenerators that often persist during the short intervals between successive disturbances.
Coastal Marine Dune, Cliff & Headland
MS2.a1
MS2.a1 Coastal Marine Dune, Cliff & Headland
MT2.1
MT2.1 Coastal shrublands and grasslands
Coastal shrublands and grasslands
Large seabird and pinniped colonies are localised eutrophic terrestrial ecosystems near the ocean interface that receive massive nutrient subsidies from large concentrations of roosting or nesting seabirds and pinnipeds that function as mobile links between land and sea. The marine-derived subsidies and potentially massive physical disturbance to vegetation and soils distinguish these colonies from otherwise similar ecosystems in MT2.1. Subsidies are greatest where seabird body size is typically larger (e.g. penguins) and breeding seasons are longer, particularly the sub-Antarctic and Antarctic. The waters around these ecosystems may be locally depleted in seabird prey due to prolonged predation. Colonies occupy diverse habitats, from sandy shores to rocky islands and montane forests, with vegetation composition and structure limited by physical disturbance, nutrient input, salt influx and gradient (e.g., sea spray), water deficit, surface and subsurface bioturbation-driven changes in soil condition and pH, avian seed dispersal, unstable substrates, and high exposure, often exhibiting salt tolerance and clonal reproduction. Plant assemblages exist across a gradient, influenced by seabird/pinniped disturbance, nutrient input and climate, whereby high-density colonies can completely suppress plant growth, but where disturbance and nutrient load is lower, vegetation can establish, typically in low richness but high abundance. Trophic networks are characterized high microbial activity and abundant invertebrates in soils which can lead to localised biodiversity hotspots, in contrast to the low richness of plant communities under high nutrient loading. There are typically low densities or a total absence of terrestrial mammalian predators and grazers (limited by dispersal barriers). Vibrant and specialised lichens can be abundant. Plant dispersal linked to bird migration, and nutrient transport between marine foraging areas and terrestrial breeding areas, may occur over long distances.
Large Seabird & Pinniped Colony
MS2.a2
MS2.a2 Large Seabird & Pinniped Colony
MT2.2
MT2.2 Large seabird and pinniped colonies
Large seabird and pinniped colonies
Constructed sea walls, breakwaters, piers, docks, tidal canals, islands and other coastal infrastructure create substrates inhabited by inter-tidal and subtidal, benthic and demersal marine biota around ports, harbours, and other intensively settled coastal areas. Structurally simple, spatially homogeneous substrates support a cosmopolitan biota, with no endemism and generally lower taxonomic and functional diversity than rocky shores (MT1.1). Trophic networks are simple and dominated by filter-feeders (e.g. sea squirts and barnacles) and biofilms of benthic algae and bacteria. Low habitat heterogeneity and the small surface area for attachment that the often vertical substrate provides, regulate community structure by promoting competition and limiting specialised niches (e.g. crevices or pools) and restricting refuges from predators. Small planktivorous fish may dominate temperate harbours and ports. These can provide a trophic link, but overharvest of predatory fish and sharks may destabilise food webs and cause trophic cascades. Much of the biota possess traits that promote opportunistic colonisation, including highly dispersive life stages (e.g. larvae, eggs, and spores), high fecundity, generalist settlement niches and diet, wide ranges of salinity tolerance, and rapid population turnover. These structures typically contain a higher proportion of non-native species than the natural substrates they replace.
Developed Marine Shoreline
MS3.a1
MS3.a1 Developed Marine Shoreline
MT3.1
MT3.1 Artificial shorelines
Artificial shorelines
Coastal river deltas are prograding depositional systems, shaped by freshwater flows and influenced by wave and tidal flow regimes and substrate composition. The biota of these ecosystems reflects strong relationships with terrestrial, freshwater, and marine realms at different spatial scales. Consequently, they typically occur as multi-scale mosaics comprised of unique elements juxtaposed with other functional groups that extend far beyond the deltaic influence, such as floodplain marshes (FT1.2), mangroves (MFT1.2), sandy shorelines (TM1.3), and subtidal muddy plains (M1.8). Gradients of water submergence and salinity structure these mosaics. Allochthonous subsidies from riverine discharge and marine currents supplement autochthonous sources of energy and carbon and contribute to high productivity. Complex, multi-faceted trophic relationships reflect the convergence and integration of three contrasting realms and the resulting niche diversity. Autotrophs include planktonic algae and emergent and submerged aquatic plants, which contribute to trophic networks mostly through organic detritus (rather than herbivory). Soft sediments and flowing water are critical to in-sediment fauna dominated by polychaetes and molluscs. Freshwater, estuarine, and marine fish and zooplankton are diverse and abundant in the water column. These provide food for diverse communities of wading and fishing birds, itinerant marine predators, and terrestrial scavengers and predators (e.g. mammals and reptiles). Virtually all biota have life-history and/or movement traits enabling them to exploit highly dynamic ecosystem structures and disturbance regimes. High rates of turnover in habitat and biota are expressed spatially by large fluctuations in the mosaic of patch types that make up deltaic ecosystems.
Coastal River Delta
MB1.a1
MB1.a1 Coastal River Delta
MFT1.1
MFT1.1 Coastal river deltas
Coastal river deltas
Mangroves are structural engineers and possess traits including pneumatophores, salt excretion glands, vivipary, and propagule buoyancy that promote survival and recruitment in poorly aerated, saline, mobile, and tidally inundated substrates. They are highly efficient in nitrogen use efficiency and nutrient resorption. These systems are among the most productive coastal environments. They produce large amounts of detritus (e.g. leaves, twigs, and bark), which is either buried in waterlogged sediments, consumed by crabs, or more commonly decomposed by fungi and bacteria, mobilising carbon and nutrients to higher trophic levels. These ecosystems are also major blue carbon sinks, incorporating organic matter into sediments and living biomass. Although highly productive, these ecosystems are less speciose than other coastal biogenic systems. Crabs are among the most abundant and important invertebrates. Their burrows oxygenate sediments, enhance groundwater penetration, and provide habitat for other invertebrates such as molluscs and worms. Specialised roots (pneumatophores) provide a complex habitat structure that protects juvenile fish from predators and serves as hard substrate for the attachment of algae as well as sessile and mobile invertebrates (e.g. oysters, mussels, sponges, and gastropods). Mangrove canopies support invertebrate herbivores and other terrestrial biota including invertebrates, reptiles, small mammals, and extensive bird communities. These are highly dynamic systems, with species distributions adjusting to local changes in sediment distribution, tidal regimes, and local inundation and salinity gradients.
MB1.a2
MB1.a2 Mangrove
MFT1.2
MFT1.2 Intertidal forests and shrublands
Mangrove
Intertidal forests and shrublands
Coastal saltmarshes are vegetated by salt-tolerant forbs, grasses, and shrubs, with fine-scale mosaics related to strong local hydrological and salinity gradients, as well as competition and facilitation. Plant traits such as succulence, salt excretion, osmotic regulation, reduced transpiration, C4 photosynthesis (among grasses), modular growth forms, and aerenchymatous tissues confer varied degrees of tolerance to salinity, desiccation, and substrate anoxia. Adjacent marine and terrestrial ecosystems influence the complexity and function of the trophic network, while freshwater inputs mediate resource availability and physiological stress. Angiosperms are structurally dominant autotrophs, but algal mats and phytoplankton imported by tidal waters contribute to primary production. Cyanobacteria and rhizobial bacteria are important N-fixers. Tides and run-off bring subsidies of organic detritus and nutrients (including nitrates) from marine and terrestrial sources, respectively. Nitrogen is imported into saltmarshes mainly as inorganic forms and exported largely as organic forms, providing important subsidies to the trophic networks of adjacent estuarine fish nurseries (FM1.2). Fungi and bacteria decompose dissolved and particulate organic matter, while sulphate-reducing bacteria are important in the decay of substantial biomass in the anaerobic subsoil. Protozoans consume microbial decomposers, while in situ detritivores and herbivores include a range of crustaceans, polychaetes, and molluscs. Many of these ingest a mixture of organic material and sediment, structuring, aerating, and increasing the micro-scale heterogeneity of the substrate with burrows and faecal pellets. Fish move through saltmarsh vegetation at high tide, feeding mainly on algae. They include small-bodied residents and juveniles of larger species that then move offshore. Itinerant terrestrial mammals consume higher plants, regulating competition and vegetation structure. Colonial and solitary shorebirds breed and/or forage in saltmarsh. Migratory species that play important roles in the dispersal of plants, invertebrates, and microbes, while abundant foragers may force top-down transformational change.
Coastal Saltmarsh & Reedbed
MB1.a3
MB1.a3 Coastal Saltmarsh & Reedbed
MFT1.3
MFT1.3 Coastal saltmarshes and reedbeds
Coastal saltmarshes and reedbeds
The tropical-subtropical forests biome is a biome that includes moderate to highly productive ecosystems with closed tree canopies occurring at lower latitudes north and south of the equator, with fragmented occurrences extend to the subtropics in suitable mesoclimates.
Exact synonym with eIVC biome.
T1 Tropical-subtropical forests biome
TT1
TT1 Tropical Forest
Tropical Forest
Tropical-subtropical forests biome
The temperate-boreal forests and woodlands biome is a biome that includes moderate to highly productive tree-dominated systems with a wide range of physiognomic and structural expressions distributed from warm-temperate to boreal latitudes.
T2 Temperate-boreal forests and woodlands biome
TT2
TT2 Temperate-Boreal Forest & Woodland
Temperate-Boreal Forest & Woodland
Temperate-boreal forests and woodlands biome
The shrublands and shrub-dominated woodlands biome is a biome that includes oligotrophic systems occurring on acidic, sandy soils that are often shallow or skeletal, distributed across al llandmasses outside the polar regions.
T3 Shrublands and shrubby woodlands biome
Shrublands and shrubby woodlands biome
The savannas and grasslands biome is a biome that has ecological functions closely linked to a mostly continuous ground layer of grasses that contribute moderate to very high levels of primary productivity driven by strongly seasonal water surplus and deficit cycles.
T4 Savannas and grasslands biome
Savannas and grasslands biome
The deserts and semi-deserts biome is a biome that includes low to very low biomass ecosystems occurring in arid or semi-arid climates, principally associated with the subtropical high-pressure belts and major continental rain shadows.
Desert & Semi-desert
T5 Deserts and semi-deserts biome
TT5
TT5 Desert & Semi-desert
Deserts and semi-deserts biome
the polar/alpine biome is a biome that encompasses the extensive Arctic and Antarctic regions as well as high mountainous areas across all continental land masses, with low or very low primary productivity.
Polar & Alpine
T6 Polar/alpine (cryogenic) biome
TT6
TT6 Polar & Alpine
Polar/alpine (cryogenic) biome
The intensive land-use biome is a biome that includes major anthropogenic enterprises of cropping, pastoralism, plantation farming, and urbanisation. Human intervention is a dominating influence on this biome, also known as the “anthrome”.
Intensive Land Use
T7 Intensive land-use biome
TT7
TT7 Intensive Land Use
Intensive land-use biome
The anthropogenic subterranean voids biome is a biome that includes a single functional group of ecosystems that owe their genesis to excavation by humans. They include underground mines, transport tunnels, tombs, defence and energy installations, and other infrastructure.
S2 Anthropogenic subterranean voids biome
Anthropogenic subterranean voids biome
The subterranean freshwaters biome is a biome that includes streams, small lakes and aquifers beneath the earth’s surface and potentially has the largest volume of water of all the freshwater biomes.
SF1 Subterranean freshwaters biome
Subterranean freshwaters biome
The anthropogenic subterranean freshwaters biome is a biome that includes aquatic systems in underground canals, drains, sewers, water pipes, and flooded mines constructed by humans. These are usually well connected to surface waters.
SF2 Anthropogenic subterranean freshwaters biome
Anthropogenic subterranean freshwaters biome
The palustrine wetlands biome is a biome that includes vegetated floodplains, groundwater seeps, and mires with permanent or intermittent surface water. Although water and light are abundant at least periodically, saturation of the soil may result in oxygen deprivation below the ground. This suppresses microbial activity and, in many systems, production exceeds decomposition, resulting in peat accumulation.
Palustrine Wetland
TF1
TF1 Palustrine wetlands biome
TP1
TP1 Palustrine Wetland
Palustrine wetlands biome
The rivers and streams biome is a biome that includes lotic (running water) ecosystems, flowing from elevated uplands or underground springs to deltas, estuaries, and lakes. They are defined primarily by their linear structure, unidirectional flow regimes, and close interaction with the surrounding landscape.
F1 Rivers and streams biome
Rivers and streams biome
The lakes biome is a biome that includes lentic ecosystems defined by their still waters. They vary in area, depth, water regime, and connectivity to other aquatic systems across a global distribution.
F2 Lakes biome
Lakes biome
The artificial wetlands biome is a biome that includes built structures that hold or transfer water for human use, treatment, or disposal, including large storage reservoirs, farm dams or ponds, recreational and ornamental wetlands, rice paddies, freshwater aquafarms, wastewater storages and treatment ponds, and canals, ditches and drains.
F3 Artificial wetlands biome
Artificial wetlands biome
The semi-confined transitional waters biome is a biome that includes coastal inlets that are influenced by inputs of both fresh and marine water from terrestrial catchments and ocean tides, waves, and currents. They include deep-water coastal inlets or fjords mostly restricted to high latitudes, as well as estuaries, bays, and lagoons, which are scattered around coastlines throughout the world.
FM1 Semi-confined transitional waters biome
Semi-confined transitional waters biome
The marine shelf biome is a biome that is distributed globally between the shoreline and deep sea-floor biomes and is dominated by benthic productivity. It includes ecosystems with biogenic substrates (such as seagrass meadows, kelp forests, oyster beds, and coral reefs) and minerogenic substrates including rocky reefs, sandy bottoms, and muddy bottoms.
M1 Marine shelf biome
Marine shelf biome
The pelagic ocean waters biome is a biome that comprises the open-ocean water column across all latitudes.
M2 Pelagic ocean waters biome
Pelagic ocean waters biome
The deep sea floors biome is a biome that includes the entire oceanic benthos below ~250 m depth, where there is not enough light to support primary productivity through photosynthesis. It extends from the upper bathyal seafloor to the deepest parts of the ocean, at just under 11 km in the Mariana Trench.
M3 Deep sea floors biome
Deep sea floors biome
The anthropogenic marine biome is a biome that includes constructed, deposited or dumped artificial structures in the oceans that either confine managed marine organisms or attract marine biota that would not otherwise occupy such locations.
M4 Anthropogenic marine biome
Anthropogenic marine biome
The shorelines biome is a biome that includes naturally formed, intertidal abiogenic habitats situated at the interface between land and sea. The distribution of the biome spans all latitudes (temperate to polar) at which landmasses are present.
MS1 Marine Shoreline
MT1
MT1 Shorelines biome
Marine Shoreline
Shorelines biome
The supralittoral coastal biome includes the landward extent of the transition from marine to terrestrial biomes. It is elevated above the direct influence of waves and tides (see the Shoreline biome) and beyond the direct influence of freshwater seepage or rivers (see brackish tidal biota). Supratidal coastal ecosystems extend around all the world’s land masses, occupying a fringe from tens of metres to a few kilometres wide and covering the entire extent of many small islands.
MS2
MS2 Supralittoral Marine Coast
MT2
MT2 Supralittoral coast biome
Supralittoral Marine Coast
Supralittoral coast biome
The anthropogenic shorelines biome is a biome that is distributed globally where urbanised and industrial areas adjoin the coast, and includes some more remote structures such as artificial islands. It includes marine interfaces constructed from hard, smooth surfaces, including concrete, timber, lithic blocks, and earthen fill, adjoining, extending or replacing natural shores, or floating in proximity to them.
Anthropogenic Marine Shoreline
MS3
MS3 Anthropogenic Marine Shoreline
MT3
MT3 Anthropogenic shorelines biome
Anthropogenic shorelines biome
The brackish tidal biome is a biome that is associated with prograding depositional shorelines at the interface of terrestrial, freshwater, and marine realms. The relative influences of marine, freshwater, and terrestrial processes vary from strongly fluvial deltas to marine-dominated intertidal forests and terrestrial-dominated coastal saltmarsh.
Brackish Tidal Wetland
MB1
MB1 Brackish Tidal Wetland
MFT1
MFT1 Brackish tidal biome
Brackish tidal biome
Treeless mountain systems dominated by an open to dense cover of cold-tolerant C3 perennial tussock grasses, herbs, small shrubs, and distinctive arborescent rosette or cushion growth forms. Lichens and bryophytes are also common. Productivity is low, dependent on autochthonous energy, and limited by cold temperatures, diurnal freeze-thaw cycles, and desiccating conditions, but not by a short growing season (as in T6.4). Elfin forms of tropical montane forests (T1.3) occupy sheltered gullies and lower elevations. Diversity is low to moderate but endemism is high among some taxa, reflecting steep elevational gradients, microhabitat heterogeneity, and topographic insularity, which restricts dispersal. Solifluction (i.e. the slow flow of saturated soil downslope) restricts seedling establishment to stable microsites. Plants have traits to protect buds, leaves, and reproductive tissues from diurnal cold and transient desiccation stress, including ramulose (i.e. many-branched), cushion, and rosette growth forms, insulation from marcescent (i.e. dead) leaves or pectin fluids, diminutive leaf sizes, leaf pubescence, water storage in stem-pith, and vegetative propagation. Most plants are long-lived and some rosette forms are semelparous. Cuticle and epidermal layers reduce UV-B transmission to photosynthetic tissues. Plant coexistence is mediated by competition, facilitation, herbivory (vertebrate and invertebrate), and fire regimes. Simple trophic networks include itinerant large herbivores and predators from adjacent lowland savannas as well as resident reptiles, small mammals, and macro-invertebrates.
T6.5 Tropical alpine grasslands and shrublands
TT6.c1
TT6.c1 Tropical High Montane Grassland & Herbfield
Tropical High Montane Grassland & Herbfield
Tropical alpine grasslands and herbfields
High-productivity croplands are maintained by the intensive anthropogenic supplementation of nutrients, water, and artificial disturbance regimes (e.g. annual cultivation), translocation (e.g. sowing), and harvesting of annual plants. These systems are typically dominated by one or few shallow-rooted short-lived plant species such as grains (mostly C3 grasses), vegetables, �flowers�, legumes, or fibre species harvested annually by humans for the commercial or subsistence production of food, materials, or ornamental displays. Disequilibrium community structure and composition is maintained by translocations and/or managed reproduction of target species and usually by periodic application of herbicides and pesticides and/or culling to exclude competitors, predators, herbivores, and/or pathogens. Consequently, compared to antecedent �natural� systems, croplands are structurally simple, have low functional, genetic, and taxonomic diversity and no local endemism. Subsistence croplands, including Swidden rotation systems, are typically more diverse than industrial croplands. Productivity is highly sensitive to variations in resource availability. Target biota are genetically manipulated by selective breeding or molecular engineering to promote rapid growth rates, efficient resource capture, enhanced resource allocation to production tissues, and tolerance to harsh environmental conditions, insect predators, and diseases. Typically, at least 40% of net primary productivity is appropriated by humans. Croplands may be rotated inter-annually with livestock pastures or fallow fields (T7.2) or may be integrated into mixed cropping-livestock systems. Target biota coexists with a cosmopolitan ruderal biota (e.g. weedy plants, mice, and starlings) that exploits production landscapes opportunistically through efficient dispersal, itinerant foraging, rapid establishment, high fecundity, and rapid population turnover. Native biota from adjoining non-anthropogenic systems may also interact with croplands. When actively managed systems are abandoned or managed less intensively, these non-target biota, especially non-woody plants, become dominant and may form a steady, self-maintaining state or a transitional phase to novel ecosystems.
Annual Cropland
T7.1 Annual croplands
TT7.a1
TT7.a1 Annual Cropland
Annual croplands
Shallow, open water bodies have been constructed in diverse landscapes and climates. They may be fringed by amphibious vegetation, or else bedrock or bare soil maintained by earthworks or livestock trampling. Emergents rarely extend throughout the water body, but submerged macrophytes are often present. Productivity ranges from very high in wastewater ponds to low in mining and excavation pits, depending on depth, shape, history and management. Taxonomic and functional diversity range from levels comparable to natural lakes to much less, depending on productivity, complexity of aquatic or fringing vegetation, water quality, management and proximity to other waterbodies or vegetation. Trophic structure includes phytoplankton and microbial detritivores, with planktonic and invertebrate predators dominating limnetic zones. Macrophytes may occur in shallow littoral zones or submerged habitats, and some artificial water bodies include higher trophic levels including macroinvertebrates, amphibians, turtles, fish, and waterbirds. Fish may be introduced by people or arrive by flows connected to source populations, where these exist. Endemism is generally low, but these waterbodies may be important refuges for some species now highly depleted in their natural habitats. Life histories often reflect those found in natural waterbodies nearby, but widely dispersed opportunists dominate where water quality is poor. Intermittent water bodies support biota with drought resistance or avoidance traits, while permanently inundated systems provide habitat for mobile species such as waterbirds.
F3.2 Constructed lacustrine wetlands
Constructed lacustrine wetlands
Marine aquafarms (i.e. mariculture) are localised, high-productivity systems within and around enclosures constructed for the breeding, rearing, and harvesting of marine plants and animals, including finfish, molluscs, crustaceans, algae, and other marine plants. Allochthonous energy and nutrient inputs are delivered by humans and by diffusion from surrounding marine waters. Autochthonous inputs are small and produced by pelagic algae or biofilms on the infrastructure, unless the target species are aquatic macrophytes. More commonly, target species are consumers that belong to middle or upper trophic levels. Diversity is low across taxa, and the trophic web is dominated by a super-abundance of target species. Where multiple target species are cultivated, they are selected to ensure neutral or mutualistic interactions with one another (e.g. detritivores that consume the waste of a higher-level consumer). Target biota are harvested periodically to produce food, fish meal, nutrient agar, horticultural products, jewellery, and cosmetics. Their high population densities are maintained by continual inputs of food and regular re-stocking to compensate harvest. Target species may be genetically modified and are often bred in intensive hatcheries and then released into the enclosures. Food and nutrient inputs may promote the abundance of non-target species including opportunistic microalgae, zooplankton, and pathogens and predators of the target species. These pest species or their impacts may be controlled by antibiotics or herbicides or by culling (e.g. pinnipeds around fish farms). The enclosures constitute barriers to the movement of larger organisms, but some cultivated stock may escape, while wild individuals from the surrounding waters may invade the enclosure. Enclosures are generally permeable to small organisms, propagules and waste products of larger organisms, nutrients, and pathogens, enabling the ecosystem to extend beyond the confines of the infrastructure.
M4.2 Marine aquafarms
Marine aquafarms
The subterranean lithic biome is a biome that includes non-aquatic lithic systems beneath the earth’s surface where sunlight is absent or of insufficient intensity to sustain photosynthesis.
S1 Subterranean lithic biome
Subterranean lithic biome
An ecosystem delineated by broad features of structure and common major ecological drivers, typically global in scale.
biome
A biome which contains tropical savannas and shrublands.
Definition still being developed by eIVC team.
TT3 Tropical Savanna & Shrubland
Tropical Savanna & Shrubland Biome
A biome which contains grasslands and shrublands and is located in the temperate-boreal climactic region.
TT4 Temperate-Boreal Grassland & Shrubland
Temperate-Boreal Grassland & Shrubland Biome
A biome which occurs at the coast of a freshwater body of water.
TP2 Freshwater Coast
Freshwater Coast Biome
A biome which occurs at the coast of an anthropogenic body of water.
TP3 Anthropogenic Freshwater Coast
Anthropogenic Freshwater Coast Biome
TT1.a
TT1.a Tropical Rainforest Subbiome
Tropical Rainforest Subbiome
TT1.b
TT1.b Tropical Dry Forest Subbiome
Tropical Dry Forest Subbiome
TT2.a
TT2.a Warm Temperate Forest & Woodland Subbiome
Warm Temperate Forest & Woodland Subbiome
TT2.b
TT2.b Cool Temperate Forest & Woodland Subbiome
Cool Temperate Forest & Woodland Subbiome
TT2.c
TT2.c Boreal Forest & Woodland Subbiome
Boreal Forest & Woodland Subbiome
TT3.a
TT3.a Tropical Savanna Subbiome
Tropical Savanna Subbiome
TT3.b
TT3.b Tropical Shrubland Subbiome
Tropical Shrubland Subbiome
TT3.c
TT3.c Tropical Open Rock Subbiome
Tropical Open Rock Subbiome
TT4.a
TT4.a Mediterranean-Dry Grassland & Shrubland Subbiome
Mediterranean-Dry Grassland & Shrubland Subbiome
TT4.b
TT4.b Temperate Grassland & Shrubland Subbiome
Temperate Grassland & Shrubland Subbiome
TT4.c
TT4.c Continental Boreal Shrubland & Grassland Subbiome
Continental Boreal Shrubland & Grassland Subbiome
TT4.d
TT4.d Temperate-Boreal Open Rock Subbiome
Temperate-Boreal Open Rock Subbiome
TT5.a
TT5.a Cool Semi-desert Subbiome
Cool Semi-desert Subbiome
TT5.b
TT5.b Warm Desert & Semi-desert Subbiome
Warm Desert & Semi-desert Subbiome
TT6.a
TT6.a Polar & Alpine Snow & Ice Subbiome
Polar & Alpine Snow & Ice Subbiome
TT6.b
TT6.b Temperate-Polar Alpine & Tundra Subbiome
Temperate-Polar Alpine & Tundra Subbiome
TT6.c
TT6.c Tropical Alpine Subbiome
Tropical Alpine Subbiome
TT7.a
TT7.a Agricultural Land Subbiome
Agricultural Land Subbiome
TT7.b
TT7.b Developed Land Subbiome
Developed Land Subbiome
No link on NatureServe Explorer.
TT7.c
TT7.c Derived Land Subbiome
Derived Land Subbiome
TP1.a
TP1.a Forested Wetland Subbiome
Forested Wetland Subbiome
TP1.b
TP1.b Emergent Open Wetland Subbiome
Emergent Open Wetland Subbiome
TP1.c
TP1.c Bog & Fen Subbiome
Bog & Fen Subbiome
TP2.a
TP2.a Freshwater Coast Subbiome
Freshwater Coast Subbiome
TP3.a
TP3.a Developed Freshwater Coast Subbiome
Developed Freshwater Coast Subbiome
MB1.a
MB1.a Coastal Brackish Tidal Wetland Subbiome
Coastal Brackish Tidal Wetland Subbiome
MS1.a
MS1.a Marine-Intertidal Shoreline Subbiome
Marine-Intertidal Shoreline Subbiome
MS2.a
MS2.a Supralittoral Marine Coast Subbiome
Supralittoral Marine Coast Subbiome
MS3.a
MS3.a Developed Marine Shoreline Subbiome
Developed Marine Shoreline Subbiome
TT1.b2
TT1.b2 Tropical Thorn Woodland
Tropical Thorn Woodland
TT2.b3
TT2.b3 Temperate Continental Conifer Forest & Woodland
Temperate Continental Conifer Forest & Woodland
TT2.c1
TT2.c1 Boreal Forest & Woodland
Boreal Forest & Woodland
TT3.a1
TT3.a1 Tropical Lowland Savanna
Tropical Lowland Savanna
TT3.c1
TT3.c1 Tropical Cliff & Rock Outcrop
Tropical Cliff & Rock Outcrop
TT4.c1
TT4.c1 Boreal Shrubland & Grassland
Boreal Shrubland & Grassland
TT4.d1
TT4.d1 Temperate-Boreal Cliff & Rock Outcrop
Temperate-Boreal Cliff & Rock Outcrop
TT5.a1
TT5.a1 Cool Desert & Semi-desert Shrub-Steppe
Cool Desert & Semi-desert Shrub-Steppe
Polar Tundra & Desert
TT6.b2
TT6.b2 Temperate Alpine Grassland & Shrubland
Temperate Alpine Grassland & Shrubland
TP1.b1
TP1.b1 Marsh, Wet Meadow & Shrub Wetland
Marsh, Wet Meadow & Shrub Wetland
Episodic Arid floodplain
Inland Salt Marsh
Coastal Freshwater Shore & Dune
TP3.a1
TP3.a1 Developed Freshwater Shoreline
Developed Freshwater Shoreline
An active ecosystem management process in which a human applys or releases a chemical substance to realize some ecological management goal.
chemical ecosystem management process
A chemical ecosystem management process in which a human applies some chemical to an ecosystem.
chemical application process
A chemical application process in which a human applies chemical fertilizer to a given area with the goal of increasing the available carbon, nitrogen or phosphorous.
fertilizer application process
A chemical application process in which a human adds lime to soil or water in order to reduce the pH.
lime application process
A chemical application process in which a human applies herbicide to plants or soil in a given area.
herbicide application process
A herbicide application process in which a human applies the herbicide glyphosate to plants in some area.
glyphosate application process
A chemical application process in which a human introduces an insecticide to some area with the goal of managing an insect population.
insecticide application process
An active ecosystem management process in which a human adds or removes biological material from an area to realize some ecological management goal.
biological ecosystem management process
A biological ecosystem management process in which a human plants flora (defined as at least having sprouted true leaves) in the soil of a given area.
planting process
A planting process in which a human plants flora grown in a plug tray.
plug planting process
A planting process in which a human plants shrubs.
shrub planting process
A planting process in which a human plants trees.
tree planting process
A planting process in which a human plants trees that have been grown in plug trays.
seedling planting process
A planting process in which a human plants trees that have grown to a diameter greater than 5 cm.
caliper tree planting process
A planting process in which a human inserts cut branches of a flora into soil such that that flora will take root and grow.
live staking process
A planting process in which a human plants flora with the goal of assisting the growth of other flora.
nurse plant process
A biological ecosystem management process in which a human sows seeds in a particular area.
seeding process
A seeding process in which a human sows tree seeds.
tree seeding process
A seeding process in which a human sows seeds in lines along a landscape.
line seeding process
A seeding process in which a human uses a drill seeder to sow seeds.
drill seeding process
A seeding process in which a human sows seeds by scattering them through the air.
broadcast seeding process
A seeding process in which a human scatters seeds by hand.
hand broadcast seeding process
A seeding process in which a human applies seed in a slurry of nutrients and fixatives.
hydroseeding process
A biological ecosystem management process in which a human applies a treatment to seed prior to sowing it.
seed treatment process
A seed treatment process in which a human damages the coating of the seed, usually using sandpaper, to enhance germination.
seed scarification process
A seed treatment process in which a human applies heat to some seed in order to enhance germination.
heat seed treatment process
A seed treatment process in which a human applies cold to some seed in order to enhance germination, such as in cold stratification.
chill seed treatment process
A seed treatment process in which a human soaks seeds in order to enhance germination.
soak seed treatment process
A seed treatment process in which light is applied to seeds in order to enhance germination.
light seed treatment process
A seed treatment process in which some chemical is applied to some seed in order to enhance germination.
chemical seed treatment process
A biological ecosystem management process in which a human uses biological means to reduce or increase a population of fauna.
biological fauna control process
A biological ecosystem management process in which a human facilitates the breeding of fauna, rears the young for a period of time and releases them in some environment.
captive breeding and release process
A captive breeding and release process in which a human collects eggs and relocates them to a safe environment, whereupon they are allowed to hatch.
egg relocation and release process
An egg relocation and release process in which a human collects eggs and relocates them into an incubator, whereupon they are allowed to hatch and released into some environment.
egg incubation and release process
A captive breeding and release process in which a human captures young fauna, rears them into adulthood and releases them into some environment.
young capture, rearing and release
A biological ecosystem management process in which a human provides supplemental water to flora or fauna.
supplemental water process
A biological ecosystem management process in which a human provides supplemental food to fauna.
supplemental feeding process
A biological ecosystem management process in which a human transfers plant material from some area to another.
plant material transfer process
A plant material transfer process in which a human restores the hydroperiod of a peatland by blocking drainage ditches or other means and subsequently moves material from the moss layer (top 10 cm) of another peatland onto the one being restored.
moss layer transfer process
A biological ecosystem management process in which a human transfers soil from one area to another.
soil transfer process
A biological fauna control process in which a human renders some fauna sterile in order to reduce their population.
fauna sterilization process
A biological fauna control process in which a human destroys the eggs of some fauna (e.g. oiling goose eggs).
egg destruction process
A biological ecosystem management process in which a human implements measures to deter fauna from establishing nest sites in a given area.
nest establishment deterrence process
A biological ecosystem management process in which a human adds material to a seabed to facilitate nesting.
seabed amendment process
A biological ecosystem management process in which a human adds some material to soil.
soil amendment process
A soil amendment process in which a human adds mulch (i.e. woody debris).
mulch addition process
A soil amendment process in which a human adds peat.
peat addition process
A soil amendment process in which a human adds topsoil.
topsoil addition process
A soil amendment process in which a human adds some composted organic material.
compost addition process
A soil amendment process in which a human adds some manure.
manure addition process
A biological ecosystem management process in which a human creates an artificial reef out of materials with the goal of attracting coral.
artificial reef creation process
A biological ecosystem management process in which a human introduces grazing animals to an area with the goal of recreating a disturbance regime.
intentional grazing
A biological ecosystem management process in which a human adds mycorrhizae spores to some environment.
mycorrhizae addition process
A biological ecosystem management process in which a human alters the hydroperiod of a peatland such that more water is available.
peatland rewetting process
A biological fauna control process in which a human captures injured fauna from some environment, rehabilitates and releases them.
fauna rescue, rehabilitation and release process
A biological fauna control process in which a human reintroduces fauna into some environment where the fauna once existed.
fauna reintroduction process
A biological fauna control process in which a human provides medical care to some fauna.
fauna medical care process
A biological ecosystem management process in which a human translocates some flora or fauna from one area to another.
translocation process
A translocation process in which a human translocates some fauna from one area to another.
fauna translocation process
A translocation process in which a human translocates coral from one area to another.
coral translocation process
An environmental system process in which a human employs social means to realize some ecosystem management goal.
ecosystem-oriented social process
A ecosystem-oriented social process in which a humans collectively implement legislation with pro-environmental goals.
legislation process
A legislation process in which the legislation explicitly protects something from degradation.
legal protection process
A legal protection process in which the legal protection applies to a specific habitat.
legal habitat protection process
A legal protection process in which the legal protection applies to a specific landscape.
legal landscape protection process
A legal protection process in which the legal protection applies to some taxa.
legal species protection process
A legal protection process in which the legal protection applies to some marine area.
legal marine area protection process
A legal protection process in which the legal protection applies to some privately held land.
private land protection process
A private land protection process in which a landowner agrees to conserve a portion of their land in perpetuity.
conservation easement process
A legislation process in which some legislation applies to some area.
area policy process
An area policy process in which some pro-conservation bylaw is established by a local authority.
local bylaw process
A legislation process in which some group passes pro-conservation legislation at the state or province level.
provincial or state legislation process
A legislation process in which some group passes pro-conservation legislation at the national level.
national legislation process
A ecosystem-oriented social process in which a humans collectively agree to measures that protect, conserve and restore biodiversity.
international agreement process
A ecosystem-oriented social process in which a human actively enforces the pro-conservation legislation or policies governing a specific area.
active enforcement process
A ecosystem-oriented social process in which a human implements measures to reduce conflict between fauna and humans.
human-wildlife conflict reduction process
A ecosystem-oriented social process in which a human assists a species in crossing a road.
human-assisted road crossing process
A ecosystem-oriented social process in which a human undertakes a process in order to make others more aware of threats to biodiversity.
awareness-raising process
An awareness-raising process in which a human uses social media to spread messages about threats to biodiversity.
social media campaign process
An awareness-raising process in which a human hosts an event for the community in a given area.
community event creation process
An awareness-raising process in which a human endeavours to improve the knowledge of others vis-a-vis restoration or conservation of biodiversity.
education process
An awareness-raising process in which a humans gather measurements of some ecosystem elements.
citizen science process
An ecosystem-oriented social process in which a humans are engaged in the restoration and conservation of biodiversity.
community engagement process
A ecosystem-oriented social process in which a human endeavours to alter the behaviour of others vis-a-vis the degradation of ecosystems.
pro-environmental behaviour change process
A pro-environmental behaviour change process in which signage is installed to encourage or deter activities in an area.
signage installation process
A pro-environmental behaviour change process in which a human reaches out to people directly to encourage or deter activities in an area.
individual outreach process
A pro-environmental behaviour change process in which a human reaches out to a landowner to encourage or deter activities in an area.
landowner outreach process
A pro-environmental behaviour change process in which a human marks environmentally sensitive features to deter degradation or interference.
sensitive features marking process
A ecosystem-oriented social process in which a human raises funds to support the restoration and conservation of a specific area.
fundraising process
A ecosystem-oriented social process in which financial incentives are offered to a humans in order to take pro-environmental measures.
financial incentive process
A ecosystem-oriented social process in which some authority regulates the usage of environments.
environmental usage regulation process
An environmental usage regulation process in which some authority regulates grazing in a given area.
regulate grazing
An environmental usage regulation process in which some authority prohibits grazing in a given area.
prohibit grazing
An environmental usage regulation process in which some authority regulates fishing in a given area.
regulate fishing
An environmental usage regulation process in which some authority prohibits fishing in a given area.
prohibit fishing
An environmental usage regulation process in which some authority regulates chemical usage in a given area.
regulate chemical usage
An environmental usage regulation process in which some authority prohibits chemical usage in a given area.
prohibit chemical usage
An environmental usage regulation process in which some authority regulates hunting in a given area.
regulate hunting
An environmental usage regulation process in which some authority prohibits hunting in a given area.
prohibit hunting
An environmental usage regulation process in which some authority regulates recreational activities in a given area.
regulate recreational activities
An environmental usage regulation process in which some authority prohibits recreational activities in a given area.
prohibit recreational activities
An environmental usage regulation process in which some authority limits public access to a given area.
limit public access
An environmental usage regulation process in which some authority prohibits public access to a given area.
prohibit public access
An environmental usage regulation process in which some authority regulates dredging in a given area.
regulate dredging
An environmental usage regulation process in which some authority prohibits dredging in a given area.
prohibit dredging
An environmental usage regulation process in which some authority regulates aquaculture in a given area.
regulate aquaculture
An environmental usage regulation process in which some authority prohibits aquaculture in a given area.
prohibit aquaculture
A ecosystem-oriented social process in which a humans undertake shared practices passed down through generations to manage the ecosystem in which they live.
cultural ecosystem management process
A ecosystem-oriented social process in which a humans harvest resources from the environment for shared practices that are passed down through generations.
cultural ecosystem usage process
A ecosystem-oriented social process in which a human alters the way in which some planned process is undertaken.
plan specification change process
A change to the mowing regime in which a human alters the timing of regular mowing with the goal of protecting specific taxa.
alter mowing timing
A plan specification change process in which a human alters the mowing regime (i.e. frequency, height, timing)
alter mowing regime
A change to the mowing regime in which a human alters the height of a mower with the goal of protecting specific taxa.
alter mowing height
A change to the tilling regime in which a human alters the frequency, timing or severity of a regular tilling process.
alter tilling regime
A change to the chemical regime in which a human alters the frequency, timing or severity of a regular chemical application process.
alter chemical regime
A change to the insecticide regime in which a human alters the frequency, timing or severity of a regular insecticide application process.
alter insecticide regime
A change to the fertilizer regime in which a human alters the frequency, timing or severity of a regular fertilizer application process.
alter fertilizer regime
A change to the lighting regime in which a human alters the frequency, timing or intensity of lighting.
alter lighting regime
A change to the grazing regime in which a human alters the frequency, timing or intensity of grazing.
alter grazing regime
A change to the dam regime in which a human alters the frequency, timing or intensity of water released by a dam.
alter dam regime
A change to the herbicide regime in which a human alters the frequency, timing or severity of a regular herbicide application process.
alter herbicide regime
A change to the herbicide regime in which a human ceases some herbicide application process.
cease herbicide usage
A planned environmental usage process in which fishing equipment is modified for conservation (e.g. bycatch deterrent devices are installed)
fishing with equipment modified for conservation
A fishing process in which a human uses a net that has been modified to reduce bycatch or accomplish some other conservation-oriented goal.
fishing with net modified for conservation
A fishing process in which a human uses a hook that has been modified for conservation.
fishing with hook modified for conservation
A fishing process in which a human adds acoustic devices to fishing gear to deter bycatch.
fishing with added acoustic devices for conservation
A fishing process in which a human uses traps modified to deter bycatch.
fishing with modified traps
A fishing process in which a human attaches bait to lines in a way that deters seabird scavenging (i.e. underwater)
fishing with modified line-setting procedure
A planned environmental usage process in which a human engages in aquaculture with modifications for conservation (e.g. disease control measures)
aquaculture process modified for conservation
A planned environmental usage process in which a human installs an underwater turbine modified for conservation.
underwater turbine modified for conservation
A planned environmental usage process in which a human engages in farming with modifications for the conservation of biodiversity.
farming process modified for conservation
A farming process modified for conservation in which a human grows two or more crop varities in close proximity to one another.
farming with intercropping
A farming process modified for conservation in which a human integrates trees and crops or pasture.
agroforestry process
An agroforestry process in which crops are grown in between rows of trees and shrubs.
alley cropping farming process
A farming process modified for conservation in which a human does not disturb the soil in between crop plantings.
no-till farming
A farming process modified for conservation in which a human avoids synthetic or chemical inputs in the farming process. The definition of organic is often the subject of government regulation.
organic farming regime
A farming process modified for conservation in which the crop type is rotated year over year.
crop rotation
A farming process modified for conservation in which a human agrees not to farm some portion of a landscape.
set aside farmland for conservation
A planned environmental usage process in which a human harvests trees in a manner that attempts to ameliorate the impact on the landscape.
forestry process modified for conservation
A forestry process in which a human cuts trees down to the stump, allowing the trees to regenerate from the stump.
coppice process
A forestry process in which a human harvests trees according to their age with the goal of preserving some overall age for a forest stand.
selective harvesting process
A forestry process in which a human removes coarse woody debris after harvesting trees, thereby reducing the risk and intensity of forest fire.
woody debris removal process
A forestry process in which a human leaves coarse woody debris after harvesting, thereby increasing available resources.
leave woody debris
A forestry process in which a human primarily harvests large trees in order to increase light availability for seedling species.
shelterwood cutting process
A planned environmental usage process in which a human modifies the level of wind speed required to spin turbines, thereby preventing avifauna fatalities.
curtailment
regulate wind turbine speed
A chemical ecosystem management process in which poison is introduced to reduce the population of fauna.
fauna poisoning process
Western Australian Mulga Shrublands Ecoregion
Australasia Ecoregion
Southern central Australia Ecoregion
Simpson Desert Region
Pilbara Shrublands Ecoregion
Carnarvon Xeric Shrublands Ecoregion
Central Ranges Xeric Shrub Ecoregion
Gibson Desert Ecoregion
The Great Sandy-Tanami Desert Ecoregion
Great Victoria Desert Ecoregion
Nullarbor Plains Xeric Shrubland Ecoregion
Afrotropical Ecoregion
Southern Africa: Southern Namibia into South Africa
Succulent Karoo Ecoregion
Arabian Peninsula: Yemen and Saudi Arabia
Yemen and Saudi Arabia Ecoregion
Arabian Peninsula: Yemen, Saudi Arabia, and Oman
Yemen, Saudi Arabia, and Oman Ecoregion
Somali montane xeric woodlands ecoregion
Somali Montane Xeric Woodland Ecoregion
Islands east of the Horn of Africa and south of Yemen Ecoregion
Socotran Archipelago Ecoregion
Red Sea Coastal Desert Ecoregion
Namibian Savanna Woodland Ecoregion
Namib Desert Ecoregion
Nama Karoo Ecoregion
Masai Xeric Grasslands and Shrublands Ecoregion
Madagascar Succulent Woodlands Ecoregion
Madagascar Spiny Thickets Ecoregion
Africa: Coastal Namibia and Angola Ecoregion
Kaokoveld Desert Ecoregion
Kalahari Xeric Savanna Ecoregion
Southern Africa: Islands about half-way between southern Madagascar and southern Mozambique Ecoregion
Ile Europa and Bassas da India Ecoregion
Hobyo Grassland and Shrubland Ecoregion
Arabian Peninsula: Oman and United Arab Emirates Ecoregion
Oman and United Arab Emirates Ecoregion
Ethiopian Xeric Grasslands and Shrublands Ecoregion
Eritrean Coastal Desert Ecoregion
North central Africa: Eastern Chad and small area of western Sudan
East Saharan Montane Xeric Woodland Ecoregion
Western Asia: Oman, Yemen, and Saudi Arabia Ecoregion
Oman, Yemen, and Saudi Arabia Ecoregion
Aldabra Island Xeric Scrub Ecoregion
Indo-Malay Ecoregion
Southern Asia: Western India into Pakistan
Thar Desert
Southern Asia: Eastern India and western Pakistan
Northwestern Thorn Scrub Forests
Solar radiation
example to be eventually removed
metadata complete
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
organizational term
The term was created to ease viewing/sorting terms for development purposes, but will not be included in a release.
ready for release
Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
metadata incomplete
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
uncurated
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
pending final vetting
All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
to be replaced with external ontology term
Terms with this status should eventually replaced with a term from another ontology.
Alan Ruttenberg
requires discussion
A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z
GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'
GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'
If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.
inferring direct reg edge from input to regulatory subfunction
inferring direct neg reg edge from input to regulatory subfunction
inferring direct positive reg edge from input to regulatory subfunction
effector input is compound function input
Input of effector is input of its parent MF
if effector directly regulates X, its parent MF directly regulates X
if effector directly positively regulates X, its parent MF directly positively regulates X
if effector directly negatively regulates X, its parent MF directly negatively regulates X
'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).