]> Lead Creator: Carrine E. Blank, University of Montana, fall 2013 through spring 2016. Co-contributors and advisors: Hong Cui (University of Arizona), Lisa Moore (University of Southern Maine), and Ramona Walls (University of Arizona). Many thanks to Chris Mungall (LBNL), Elvis Hsin-Hui Wu (University of Arizona), Gail Gasparich (Towson University), and Gordon Burleigh (University of Florida) for comments and/or assistance with ontology construction and compilation of taxonomic descriptions and term definitions. Thanks to Oliver He (University of Michigan) for technical assistance with OntoBee and OntoFox, and Gareth Owen (ChEBI project leader, head curator) and other curators at ChEBI for assistance in the incorporation of microbial-specific chemical terms and synonyms into ChEBI. Thanks also to the instructors (Melissa Haendel, Matt Yoder, Jim Baihoff) and students of the 2013 NESCent Ontologies for Evolutionary Biology workshop, and to Karen Cranston (NESCent director) and the support staff at NESCent. This work was supported by a grant from the National Science Foundation Assembling the Tree of Life Program (DBI-1208534), and by a travel grant to attend the 2013 NESCent Ontologies for Evolutionary Biology workshop. MicrO (An Ontology of Prokaryotic Phenotypic and Metabolic Characters). Version 1.3 released 3/23/2016. Includes terms and term synonyms extracted from > 1500 prokaryotic taxonomic descriptions, collected from a large number of taxonomic descriptions from Archaea, Cyanobacteria, Bacteroidetes, Firmicutes and Mollicutes. The ontology and the synonym lists were developed to facilitate the automated extraction of phenotypic data and character states from prokaryotic taxonomic descriptions using a natural language processing algorithm (MicroPIE). MicroPIE is currently being developed by Hong Cui, Elvis Hsin-Hui Wu, and Jin Mao (University of Arizona) in collaboration with Carrine E. Blank (University of Montana) and Lisa R. Moore (University of Southern Maine). A description and link to MicroPIE can be found at http://avatol.org/ngp/nlp/overview-2/. The most current version of MicrO can be downloaded from https://github.com/carrineblank/MicrO. Note regarding term synonyms: Some synonyms listed in this ontology are synonyms for terms and classes as they were used in published microbiological taxonomic descriptions. Thus, the synonyms are not necessarily applicable to the wider world. If the term synonyms could not be classified as broad, exact, or narrow synonyms, they were labeled as related synonyms. The synonym lists were developed to facilitate the automated extraction of phenotypic data and character states from prokaryotic taxonomic descriptions using a natural language processing algorithm (MicroPIE). is an assay for the metabolic substrate Carrine Blank Relationship between an assay (x) and a chemical entity (y), where the chemical entity is a metabolic substrate used in the designated process (generally a metabolic process deriving from a combination of enzymatic processes). is the enzymatic activity assayed by Carrine Blank A relationship between a molecular function (x), namely the enzymatic activity being tested and an assay (y), namely an analytical investigation/test for the presence of an enzymatic activity. biosynthetic production is assayed by Carrine Blank A relationship between a chemical entity (x), which is a biosynthetic product, that is assayed by an assay (y). Differentiated from 'is metabolic production of' which has the same domain and ranges, but is where an assay is used to detect a product of metabolism (i.e. energy generation). uses electron donor Relationship between a prokaryotic metabolically differentiated cell or prokaryotic metabolic process (x) and a chemical entity (y), where the chemical entity is a electron donor. Carrine Blank uses electron acceptor Carrine Blank Relationship between a prokaryotic metabolically differentiated cell or prokaryotic metabolic process (x) and a chemical entity (y), where the chemical entity is an electron acceptor. is an assay using the culture medium Relationship between an assay (x) and a microbiological culture medium (y), where the medium is needed to carry out the assay. Carrine Blank has shape Relationship between a cellular component, prokaryotic cell or prokaryotic colony (x) and a shape (y). Carrine Blank has position Carrine Blank Relationship between a cellular component, prokaryotic cell or prokaryotic colony (x) and a position quality (y). has structure Carrine Blank Relationship between a cellular component, prokaryotic cell or prokaryotic colony (x) and a structure (y). has morphology Relationship between a cellular component, prokaryotic cell or prokaryotic colony (x) and a morphology (y). Carrine Blank has angle Relationship between two connected entities that are connected and have a spatial relationship defined by an angle that exists between the two connected entities. Carrine Blank is an assay using the chemical reagent Relationship between an assay (x) and a chemical entity (y), where the chemical entity is used as a chemical reagent or substance used to carry out the assay. Carrine Blank has size Relationship between a cellular component, prokaryotic cell or prokaryotic colony (x) and a size (y). Carrine Blank has physical quality Carrine Blank Relationship between a cellular component, prokaryotic cell or prokaryotic colony (x) and a physical quality (y). has texture Relationship between a cellular component, prokaryotic cell or prokaryotic colony (x) and a texture (y). Carrine Blank has organismal quality Carrine Blank Relationship between a cellular component, prokaryotic cell or prokaryotic colony (x) and an organismal quality (y). has physical object quality Relationship between a cellular component, prokaryotic cell or prokaryotic colony (x) and a physical object quality (y). Carrine Blank is an enzymatic hydrolytic extract derived from Relationship between a material entity (x) and a cellular organism or environmental material (y) where the material entity is created as a result of a chemical extraction procedure performed via the process of enzymatic hydrolysis. Carrine Blank is an acid hydrolytic extract derived from Carrine Blank Relationship between a material entity (x) and a cellular organism or environmental material (y) where the material entity is created as a result of a chemical extraction procedure performed via the process of acid hydrolysis. is the quality assayed by Relationship between a quality (x) and an assay (y). Carrine Blank is culture medium used by Relationship between a microbiological culture medium (x) and a cellular organism (y) where the culture medium is used to support the growth of cellular organism y. Carrine Blank is an extract derived from Carrine Blank Relationship between a material entity (x) and a cellular organism or environmental material (y) where the material entity is created as a result of a chemical or physical extraction procedure. Carrine Blank is an oleaginous extract derived from Carrine Blank Relationship between an oleoginous (oily) material entity (x) and a cellular organism or environmental material (y) where the material entity is created as a result of a chemical extraction procedure performed from material derived from the organism. Carrine Blank is an aqueous extract derived from Carrine Blank Relationship between a material entity (x) and a cellular organism or environmental material (y) where the material entity is created as a result of a chemical extraction procedure performed via the process of an aqueous extraction (an extraction with water). Carrine Blank is an assay for the quality Carrine Blank Relationship between an assay (x) and a quality (y). uses chemical entity Relationship between a prokaryotic metabolically differentiated cell or prokaryotic metabolic process (x) and a chemical entity (y). Carrine Blank is an assay for the enzymatic substrate Carrine Blank Relationship between an assay (x) and a chemical entity (y), where the chemical entity used is a chemical enzymatic reactant in the designated process (namely a chemical reaction catalyzed by an enzyme). is an assay for the enzymatic product Carrine Blank Relationship between an assay (x) and a chemical entity (y), where the chemical entity is a chemical enzymatic product of the designated process (namely a chemical reaction catalyzed by an enzyme). is an assay for the metabolic substrate Carrine Blank Relationship between an assay (x) and a chemical entity (y), where the chemical entity is a metabolic substrate used in the designated process (generally a metabolic process deriving from a combination of enzymatic processes). is an assay for the metabolic product Carrine Blank Relationship between an assay (x) and a chemical entity (y), where the chemical entity is a metabolic product in the designated process (generally a metabolic process deriving from a combination of enzymatic processes). is metabolic substrate assayed by Carrine Blank Relationship between a chemical entity (x) and an assay (y), where the chemical entity is a metabolic substrate (generally a metabolic process deriving from a combination of enzymatic processes) assayed by the diagnostic assay. is enzymatic substrate assayed by Relationship between a chemical entity (x) and an assay (y), where the chemical entity is a chemical enzymatic reactant (namely a chemical reaction catalyzed by an enzyme) being assayed in the diagnostic assay. Carrine Blank is metabolic product assayed by Relationship between a chemical entity (x) and an assay (y), where the chemical entity is a metabolic product of the process (a metabolic process deriving from a combination of enzymatic processes) which is being assayed by the diagnostic assay. Carrine Blank is enzymatic product assayed by Relationship between a chemical entity (x) and an assay (y), where the chemical entity is a chemical enzymatic product of the enzymatic process (a chemical reaction catalyzed by an enzyme) assayed by the diagnostic assay. Carrine Blank is the enzymatic activity assayed by Carrine Blank A relationship between a molecular function (x), namely the enzymatic activity being tested and an assay (y), namely an analytical investigation/test for the presence of an enzymatic activity. is an assay for the enzymatic activity of Carrine Blank A relationship between an assay (x), namely an analytical investigation/test for the presence of an enzymatic activity, and a molecular function (y), namely the enzymatic activity being tested. is an assay for the fermentation substrate Relationship between an assay (x) and a chemical entity (y), where the chemical entity used is a fermentation substrate in the designated process (generally a metabolic fermentation process deriving from a combination of enzymatic processes). Carrine Blank is fermentation product assayed by Relationship between a chemical entity (x) and an assay (y), where the chemical entity is a fermentation product (generally a metabolic fermentation process deriving from a combination of enzymatic processes) assayed by the diagnostic assay. Carrine Blank is fermentation substrate assayed by Relationship between a chemical entity (x) and an assay (y), where the chemical entity is a fermentation substrate (generally a metabolic fermentation process deriving from a combination of enzymatic processes) being assayed by the diagnostic assay. Carrine Blank is assayed by A relationship between a process, quality, cellular component, molecular function, or a chemical entity (x) and an assay (y). Carrine Blank is an assay for Carrine Blank A relationship between a microbiological diagnostic test (x) and a biological process, quality, cellular component, molecular function, or a chemical entity (y). is an assay for the biological process of Carrine Blank A relationship between an assay (x), namely an analytical investigation/test for the presence of a physical biological process, and a biological process (y). is the biological process assayed by Carrine Blank A relationship between a biological process (x), and an assay (y) which is an analytical investigation/test for the presence of a physical biological process. is an assay for the biosynthetic production of Carrine Blank A relationship between a n assay (x), namely an analytical investigation/test for the presence of a metabolic product, and a chemical entity (y). biosynthetic production is assayed by Carrine Blank A relationship between a chemical entity (x), which is a biosynthetic product, that is assayed by an assay (y). Differentiated from 'is metabolic production of' which has the same domain and ranges, but is where an assay is used to detect a product of metabolism (i.e. energy generation). is prokaryotic physiological quality of Carrine Blank A relationship between a prokaryotic physiological quality (x) and a prokaryotic physiologically differentiated cell (y). Carrine Blank is an assay for the cellular component Carrine Blank A relationship between an assay (x), namely an analytical investigation/test for the presence of a physical cellular component, and a cellular component (y). is the cellular component assayed by A relationship between a cellular component (x), and an assay (y) which is an analytical investigation/test for the presence of a cellular component. Carrine Blank has ingredient Relationship between a material entity (x), which is a man-made material entity such as a chemical solution or a culture medium, and a chemical entity (y), where the chemical entity forms part of a mixture of chemicals that make up the material entity. Carrine Blank Wikipedia:ingredient An ingredient is a substance that forms part of a mixture (in a general sense). For example, in cooking, recipes specify which ingredients are used to prepare a specific dish. Many commercial products contain a secret ingredient that is purported to make them better than competing products. In the pharmaceutical industry, an active ingredient is that part of a formulation that yields the effect required by the customer. National laws usually require prepared food products to display a list of ingredients, and specifically require that certain additives be listed. In most developed countries, the law requires that ingredients be listed according to their relative weight[1] in the product. If an ingredient itself consists of more than one ingredient (such as the cookie pieces which are a part of "cookies and cream" flavor ice cream), then that ingredient is listed by what percentage of the total product it occupies, with its own ingredients displayed next to it in brackets. The term constituent is often chosen when referring to the substances that constitute the tissue of living beings such as plants and people, because the word ingredient in many minds connotes a sense of human agency (that is, something that a person combines with other substances), whereas the natural products present in living beings were not added by any human agency but rather occurred naturally ("a plant doesn't have ingredients"). Thus all ingredients are constituents, but not all constituents are ingredients. is an ingredient of Relationship between a chemical entity (x) and a mixture, culture medium, or chemical solution (y), where y is artificial created by human activity. Carrine Blank has susceptibility towards the chemical Carrine Blank Relationship between a prokaryotic cell or cellular component (x) and a chemical solution or chemical entity (y). develops into Relationship between an independent continuant (x) and another independent continuant (y), where x develops (or transforms) into y through a developmental process. Carrine Blank has salinity Carrine Blank Relationship between a microbiological culture medium (x) and a salinity quality (y). has pH Carrine Blank Relationship between a microbiological culture medium (x) and a pH quality (y). has redox Carrine Blank Relationship between a microbiological culture medium (x) and a redox quality (y). Carrine Blank culture medium has quality Carrine Blank Relationship between a microbiological culture medium (x) and a quality (y). has chemical composition Relationship between a material entity (x) and a material entity (y), where the material entity is a natural substance (such as a chemical entity) that has a mixture of chemical substances in it. Carrine Blank is an assay using the material entity Relationship between an assay (x) and a material entity (y), where the material entity is needed to carry out the assay. Carrine Blank is quality of the culture medium Carrine Blank Relationship between a quality (x), such as a pH quality, redox quality, or salinity quality, and a microbiological culture medium (y) which is an independent continuant. Relationship between a material entity (x) and a cellular organism or environmental material (y) where the material entity is derived from the starting complex entity y. is chemical entity derived from Carrine Blank has cell wall Carrine Blank Relationship between a particular cellular organism (x) and an external encapuslating structure (y). is an assay using the cellular organism Relationship between an assay (x) and cellular organisms (y), where the organism(s) is needed to carry out the assay. Carrine Blank uses carbon source Carrine Blank Relationship between a prokaryotic metabolically differentiated cell or prokaryotic metabolic process (x) and a chemical entity (y), where the chemical entity is a carbon source. uses energy source Relationship between a prokaryotic metabolically differentiated cell or prokaryotic metabolic process (x) and a chemical entity or sunlight (y), where the chemical entity or sunlight is a energy source. Carrine Blank uses electron donor Relationship between a prokaryotic metabolically differentiated cell or prokaryotic metabolic process (x) and a chemical entity (y), where the chemical entity is a electron donor. Carrine Blank uses electron acceptor Carrine Blank Relationship between a prokaryotic metabolically differentiated cell or prokaryotic metabolic process (x) and a chemical entity (y), where the chemical entity is an electron acceptor. working-temp obj props Carrine Blank has symmetry Relationship between a cellular component, prokaryotic cell or prokaryotic colony (x) and a symmetry quality (y). Carrine Blank has spatial pattern Relationship between a cellular component, prokaryotic cell or prokaryotic colony (x) and a spatial position quality (y). Carrine Blank contains prokaryotic metabolic process Carrine Blank Relationship between a prokaryotic metabolically differentiated cell (x) and a prokaryotic metabolic process (y). has prokaryotic physiological quality A relationship between a prokaryotic physiologically differentiated cell (x) and a prokaryotic physiological quality (y). Carrine Blank has measurement Carrine Blank xxxx is prokaryotic metabolic process carried out in the presence of Carrine Blank A relationship between a prokaryotic metabolic process (x) and an inorganic molecular entity, an organic molecular entity or sunlight (y). is prokaryotic metabolic process occuring in Relationship between a prokaryotic metabolic process (x) and a prokaryotic metabolically differentiated cell (y). Carrine Blank has prokaryotic metabolic quality Carrine Blank Relationship between a prokaryotic metabolically differentiated cell (x) and a prokaryotic metabolic quality (y). is prokaryotic metabolic quality of Relationship between a prokaryotic metabolic quality (x) and a prokaryotic metabolically differentiated cell (y) which is an independent continuant. Carrine Blank is prokaryotic metabolic quality of a cell carrying out the process A relationship between a prokaryotic metabolic quality (x) and a prokaryotic metabolic process (y). Carrine Blank is prokaryotic metabolic process which makes a cell Carrine Blank Relationship between a prokaryotic metabolic process (x) and a prokaryotic metabolic quality (y). has colony margin symmetry Relationship between a prokaryotic colony (x) and a symmetry quality (y), pertaining specifically to the symmetry of the prokaryotic colony margin. Carrine Blank contains biological process A relationship between a prokaryotic differentiated cell (x) and a biological process (y). Carrine Blank is an assay for the fermentation product Carrine Blank Relationship between an assay (x) and a chemical entity (y), where the chemical entity is a fermentation product in the designated process (generally a metabolic fermentation process deriving from a combination of enzymatic processes). has sodium chloride percentage of Carrine Blank Describes the percentage of sodium chloride concentration in which an organism is capable of growth. has cell width has pH value Carrine Blank Describes the pH (hydrogen ion concentration) in which an organism is capable of growth. zzzz Note that there is an error with this class (sulfate can't be used as an electron donor) flagellar quality Prokaryotic cell quality where a cell has either a bacterial-type flagellum (or flagella) or a periplasmic flagellum. Carrine Blank branch perpendicular to trichome Filament branch angle, where the angle between the cylindrical cells of the branching filament and the cylindrical cells of the main trichome is perpendicular. lateral branches branches perpendicular to trichome Carrine Blank branches lateral branches perpendicular to the long trichome axis filament branch size Carrine Blank branch length Filament branch morphological quality relating to the size (length, and hence the number of cells in the branch, and thickness) of a filament branch, relative to the size of the main trichome. branch size morphologically differentiated branches Carrine Blank branching morphology Filament branch physical object quality defining the morphology (shape, size, length) of branches in relationship to the main filament. straight filament branch filament branch straight Carrine Blank branches straight The nature of branches in a microbial filament to be straight (i.e. not curved). arcuate filament branch branches later curve to the direction of the original trichome Carrine Blank branches arcuate filament branch arcuate The nature of branches in a microbial filament to be arcuate (curved). solitary branches irregularly branched branches solitary Filament branch spatial pattern where the filament exhibits branching (either false or true branching). Filaments occur singularly (solitary), and do not occur in pairs (are offset from one another). Carrine Blank filaments irregularly branched paired branches Carrine Blank branches paired Filament branch spatial pattern where the filament exhibits branching (either false or true branching). Filaments occur paired, opposite from one another. heterocyte position relative to branches Carrine Blank Differentiated filament branching relating the distribution of heterocytes in the filament and their spatial relationship to the branches. branches thinner than main filament branches thinner secondary filaments thinner secondary lateral branches generally thinner thinner branches Filament branch size where the diameter of cylindrical cells in the filament branches are thicker than the diameter of cylindrical cells in the main trichome. Carrine Blank branches usually slightly thinner heterocytes basal in branches The physical relationship of branches in a microbial filament to heterocytes, being physically adjacent to heterocytes wherein branches initiate at the heterocytes. branches initiating at the heterocytes branches initiate at heterocytes Carrine Blank lateral branches initiating at the heterocytes branches initiate usually at originally intercalary heterocytes heterocytes apical in branches branches terminated by heterocytes The physical relationship of branches in a microbial filament to heterocytes, where heterocytes are located at the end of branches. Carrine Blank heterocytes not in branches branches distant from heterocytes branches distant from heterocytes distant from the heterocytes Heterocyte position where the heterocyte is not located in the filament branch. Carrine Blank heterocytes in branches Carrine Blank Heterocyte position where the heterocyte is located in the filament branch. Heterocyte location within the filament branch has apical-basal polarity. paired false branching binary false branched Carrine Blank double false branching Paired filament branches where the filament exhibits false branching. paired true branching paired true branching Paired filament branches where the filament exhibits true branching. Carrine Blank solitary false branching Solitary filament branches where the filament exhibits false branching. single false branching Carrine Blank solitary true branching Carrine Blank Solitary filament branches where the filament exhibits true branching. differentiated apical cell Filament differentiation quality, relating to the morphology and differentiation of the apical cell in the filament. Carrine Blank sub-apical cell A trichome cell that is located subterminally in a trichome, and which has undergone differentation. Found in trichomes with apical-basal polarity. Carrine Blank short filament branch Carrine Blank branches short Filament branch length where the branches are short and contain few cells (relative to the length and number of cells in the main filament). long filament branch Carrine Blank Filament branch length where the branches are long and contain many cells (relative to the length and number of cells in the main filament). branches many-celled branches long prokaryotic nucleobase quality The molar percentage of nucleobases in the DNA of a prokaryotic chromosome and/or plasmid. Carrine Blank bacilloid cell Carrine Blank bacilloid A prokaryotic cell that is bacillus-like (some variation of cylindrical). amphilophotrichous cell 2 bipolar polytrichous flagella tufts of polar flagella Flagellated cell where the cell has multiple flagella, located in two tufts at both ends (poles) of the cell. Carrine Blank polar tufts of flagella prokaryotic acidic environment acidic Carrine Blank An acidic environment that is the environment inhabited by a prokaryotic cell. prokaryotic alkaline environment An alkaline environment that is the environment inhabited by a prokaryotic cell. Carrine Blank alkaline optical quality assay An assay to determine macroscopic or microscopic optical quality of a prokaryotic cell, or aggregation of prokaryotic cells. Carrine Blank fermentation product Prokaryotic metabolite where fermentation produces are produced as a result of fermentation. cyanobacterial filament A type of filament only found in some filamentous cyanobacterial taxa. Is comprised by a trichome and an extracellular sheath. May or may not have branches. Carrine Blank isopolar symmetric An isopolar trichome morphology quality where heterocysts are only present at the poles, or terminals, of the trichome such that the trichome morphology is symmetric. Carrine Blank isopolar metameric An isopolar trichome morphology quality where heterocysts are regularly dispersed along the length of the trichome such that the trichome morphology is symmetric. Carrine Blank differentiated isopolar trichome Carrine Blank Trichome differentiation quality of isopolar trichomes with respect to the location of heterocytes and the symmetrical arrangement of the heterocytes. meristematic zone A part of a trichome where rapid cell division occurs. Meristematic zones, which arise terminally or subterminally, are found in the trichomes of Scytonemataceae, Rivulariaceae, and Microchaetaceae. Zone involves several cells along the trichome. Carrine Blank diffluent sheath A sheath that is easily dissolving and indistinct (unlocalized). Carrine Blank casein agar https://catalog.hardydiagnostics.com/cp_prod/Content/hugo/CaseinAgar.html FORMULA Ingredients per liter of deionized water:* Dry Milk, Instant Nonfat 50.0gm Pancreatic Digest of Casein 5.0gm Yeast Extract 2.5gm Glucose 1.0gm Agar 12.5gm Final pH 6.8 +/- 0.3 at 25 degrees C. An organic-rich, solid microbiological culture medium that contains nonfat dry milk, pancreatic digest of casein (casitone), yeast extract, glucose, and agar. Used for the differentiation of prokaryotes based on their ability to degrade casein. Carrine Blank cell filament trichomous filaments filament A group of prokaryotic cells where the cells are attached to one another end-to-end, forming long threads. Formed when cell division occurs in a single plane (at right angles to the filament axis) and when cells do not detach from one another. Carrine Blank chains filamentous mycelium-like filament-forming true branch Carrine Blank A trichome part formed when there is transient cell division in another plane other than crosswise to the length of the trichome axis. This results in the formation of a branch at right angles to the axis of the length of the trichome. Found only in the Stigonematales (Cyanobacteria). false branch A trichome part formed when there is interruption of the axis of a trichome. Are initiated when necritic cells form, breaking the trichome. Or are initiated at heterocytes. At first both ends of the interrupted trichome grow aside one another, later on the two new trichome ends grow in different directions. Occurs in the Oscillatoriales, Nostocales, and Stigonematales (Cyanobacteria). Carrine Blank filament branch A filament part formed when a new trichome begins to grow at an angle to the axis of the original length of the filament, also enclosed in sheath. Carrine Blank firm sheath A sheath that is firm and distinct (localized, not easily dissolving and not indistinct). Carrine Blank sheath having distinctive spatial pattern Carrine Blank Morphologically differentiated filament part, where the sheath has a distinctive spatial pattern. thylakoid-containing cell Carrine Blank A prokaryotic cell containing thylakoids membranes. epilithic environment Carrine Blank An environment that exists on the surface of a rock (or a rocky substrate). epilithic epipelic environment epipelic Carrine Blank A submerged environment consisting of a rocky substrate comprised of sediments, clays, or silt, colonized by a microorganisms or a microbial community. submerged stones epiphytic environment Wikipedia: Epiphyte An epiphyte is a plant that grows harmlessly upon another plant (such as a tree) and derives its moisture and nutrients from the air, rain, and sometimes from debris accumulating around it. Epiphytes differ from parasites in that epiphytes grow on other plants for physical support and do not necessarily negatively affect the host. An epiphytic organism that is not a plant is called an epibiont.[1] Epiphytes are usually found in the temperate zone (e.g., many mosses, liverworts, lichens, and algae) or in the tropics (e.g., many ferns, cacti, orchids, and bromeliads).[2] Many houseplants are epiphyte species due to their minimal water and soil requirements. Epiphytes provide a rich and diverse habitat for other organisms including animals, fungi, bacteria, and myxomycetes.[3] Carrine Blank An environment that exists on a terrestrial plant (Embryophyte). epiphytic endophytic environment An environment that exists within a plant (Embryophyte). Carrine Blank endophytic Wikipedia: Endophyte An endophyte is an endosymbiont, often a bacterium or fungus, that lives within a plant for at least part of its life cycle without causing apparent disease.[1][2][3][4] Endophytes are ubiquitous and have been found in all species of plants studied to date; however, most of these endophyte/plant relationships are not well understood.[5][6] Endophytes are also known to occur within lichens[7] and algae. Many economically important grasses (e.g., Festuca spp. and Lolium spp. ) carry fungal endophytes in genus Epichloë,[8] some of which may enhance host growth[9] and may improve the plant's ability to tolerate abiotic stresses, such as drought, and enhance resistance to insects, plant pathogens and mammalian herbivores.[10][11][12][13] lives inside a plant periphytic environment periphytic Carrine Blank periphytically An environmental system that is submerged, and attached to submerged rocks, plants, animals, or other objects. calyptra Modified apical cell, having a thickened or enlarged morphology. Has a hood-like, lid-like, or cap-like form. Little is known about the role, although presence is environmentally influenced. Not all trichomes in a natural population will exhibit a calyptra. Found in the Oscillatoriales and Nostocales. Carrine Blank end cells aways with calyptra http://huey.colorado.edu/cyanobacteria/taxa/calyptra.php Definition of Calyptra Thickened or enlarged tip of a cyanobacterial filament, a hoodlike, lidlike, or caplike structure. morphologically distinct colony A prokaryotic colony that has a distinct morphology (size, shape, texture, or structure). Carrine Blank tapered by apical and basal widening trichomes narrowed in the middle part and clearly widened at the ends Carrine Blank branches dilated terminal portions Tapered trichome quality where the trichome is wider at the apical and basal ends, and narrower toward the center of the trichome (hour-glass shaped). prokaryotic cell part quality Prokaryotic quality (morphology, symmetry, position) relating to a cell part or cellular component. Carrine Blank tapered by apical and basal narrowing attenuated trichome ends trichomes attenuated towards the ends trichomes attenuated toward both ends continually attenuated to the ends trichomes attenuated at the ends of developed trichomes Carrine Blank tapering to the ends cells narrowed at both ends trichomes narrowed to the ends attenuated toward the ends Tapered trichome quality where the trichome is narrower at the apical and basal ends, and widened toward the center of the trichome (fusiform-shaped). trichomes narrows towards the ends trichomes attenuated to the ends widened spaces between thylakoids Carrine Blank intrathylakoidal spaces Thylakoid-containing cell where there are widened spaces between the thylakoid membranes. Function is not clear and are likely influenced by environmental factors. Frequency and location are taxa-specific. susceptibility to lysis by detergent Carrine Blank Prokaryotic cell wall lysis susceptibility that defines how susceptible the cell wall is to lysis when the cell is placed in the presence of an environment with an altered chemical composition (detergent). Berkefeld N filter A gravity-driven water filter made by the British Berkefeld® company, with an intermediate pore size N (for Normal). Pore sizes average 0.43 microns in diameter. Carrine Blank 216L marine medium An organic rich, liquid marine microbiological culture medium containing acetate, tryptone, yeast extract, citrate, ammonium nitrate, with a seawater base. Used for the cultivation of Marispirillum. From: Lai, Q., Yuan, J., Gu, L. & Shao, Z. (2009). Marispirillum indicum gen. nov., sp. nov., isolated from a deep-sea environment. Int J Syst Evol Microbiol 59, 1278–1281. Recipe: sodium acetate, 1.0 g Tryptone, 10.0 g yeast extract, 2.0 g sodium citrate, 0.5 g NH4NO3, 0.2 g seawater, 1L pH 7.5 Carrine Blank 216L 216L broth 216L marine agar From: Lai, Q., Yuan, J., Gu, L. & Shao, Z. (2009). Marispirillum indicum gen. nov., sp. nov., isolated from a deep-sea environment. Int J Syst Evol Microbiol 59, 1278–1281. Recipe: sodium acetate, 1.0 g Tryptone, 10.0 g yeast extract, 2.0 g sodium citrate, 0.5 g NH4NO3, 0.2 g seawater, 1L pH 7.5 Agar is added to the medium to solidify. Carrine Blank 216L agar An organic rich, solid marine microbiological culture medium containing acetate, tryptone, yeast extract, citrate, ammonium nitrate, with a seawater base. Used for the cultivation of Marispirillum. ZoBell marine medium ZoBell 2216e broth ZoBell 2216e ZoBell medium MA2216 Zobell's medium Marine broth 2216 An organic-rich, mineral-salts, liquid microbiological culture medium containing peptones and yeast extract in a base of artificial sea water. Used for the cultivation of heterotrophic marine microorganisms. ZoBell broth From: http://himedialabs.com/TD/M384.pdf Zobell Marine Agar 2216 Zobell Marine Agar 2216 is recommended for cultivation, isolation and enumeration of heterotrophic marine bacteria. Composition Ingredients (Gms/Litre) Peptic digest of animal tissue 5.000 Yeast extract 1.000 Ferric citrate 0.1000 Sodium chloride 19.450 Magnesium chloride 8.800 Sodium sulfate 3.240 Calcium chloride 1.800 Potassium chloride 0.550 Sodium bicarbonate 0.160 Potassium bromide 0.080 Strontium chloride 0.034 Boric acid 0.022 Sodium silicate 0.004 Sodium fluorate 0.0024 Ammonium nitrate 0.0016 Disodium phosphate 0.008 Final pH (25˚C) 7.6+/-0.2 MB Carrine Blank ZoBell's microbiological culture medium A culture medium used to select for, grow, and maintain prokaryotic microorganisms. Can be in either liquid (broth) or solidified (e.g. with agar) forms. growth medium growth media culture media Carrine Blank media medium defined microbiological culture medium defined mineral medium defined medium Carrine Blank A chemically defined microbiological culture medium where all chemicals used are known. Does not contain any plant, animal, or microbiological cell extracts. mineral media defined media mineral medium liquid microbiological culture medium liquid media broth A microbiological culture medium that is liquid. Carrine Blank liquid medium solid microbiological culture medium solid medium solid media Carrine Blank A microbiological culture medium that is solidified with a gelling agent, such as agar, agarose, gelatin, or pectin. agar medium undefined microbiological culture medium basal media complex medium basal medium complex media A microbiological culture medium that has components that are chemically heterogeneous, unknown, or uncharacterized mixtures or cellular extracts. Carrine Blank Balch medium 1 pH is not noted in the original publication. However, pH of the medium is reported to be 7.0 in The Prokaryotes: Vol 3: Archaea. Bacteria: Firmicutes, Actinomycetes, p. 213, copyrighted 2006. mineral medium and H2 + CO2 A mineral-salts liquid microbiological culture medium containing acetate, formate, yeast extract, trypticase, cysteine and sulfide with H2 and CO2 in the headspace gas mixture. Used for the growth of methanogenic archaea. A mineral-salts, liquid microbiological culture medium containing acetate, formate, yeast extract, trypticase, cysteine and sulfide with hydrogen and carbon dioxide in the headspace gas mixture. Used for the growth of methanogenic archaea. Carrine Blank mineral medium with H2-CO2 From: Balch WE et al, 1979. Methanogens: reevaluation of a unique biological group. Microbiol Rev 43(2):260. Ingredients are added to distilled water to give a final volume of 1L. Cysteine and Na2S are added after boiling the medium under an 80% N2-20% CO2 gas mixture, the final gas phase of tubed medium being an 80% H2-CO2 gas mixture at two atmospheres of pressure. 50 mL mineral 1 solution (6 g K2HPO4 per liter) 50 mL mineral 2 solution (per liter: KH2PO4, 6 g; (NH4)2SO4, 6 g, NaCl, 12 g; MgSO4x7H2O, 2.6 g; CaCl2x2H2O, 0.16 g) 10 mL trace minerals (pH to 7.0 with KOH; per liter: nitrilotriacetic acid, 1.5 g; MgSO4x7H2O, 3.0 g; MnSO2x2H2O, 0.5 g; NaCl, 1.0 g; FeSO4x7H2O, 0.1g; CoSO4 or CoCl2, 0.1 g; CaCl2x2H2O, 0.1 g; ZnSO4, 0.1 g; CuSO4x5H2O, 0.01 g; AlK(SO4)2, 0.01 g; H3BO3, 0.01 g; Na2MoO4x2H2O, 0.01g); dissolve nitrilotriacetic acid with KOH to pH 6.5 then proceed to add minerals) 10 mL trace vitamines (contains in milligrams per liter: biotin, 2; folic acid, 2; pyridoxine hydrochloride, 10; thiamine hydrochloride, 5; riboflavin, 5; nicotinic acid, 5; DL-calcium pantothenate, 5; vitamin B12, 0.1; p-aminobenzoic acid, 5; lipoic acid, 5) 0.002 g FeSO4x7H2O 5.0 g NaHCO3 2.5g sodium acetate 2.5 g sodium formate 2.0 g yeast extract 2.0 g trypticase (BBL) 0.5 g L-Cysteine hydrochloridexH2O 0.5 g Na2Sx9H2O minerals salts-H2/CO2 medium artificial kinneret water medium artificial kinneret water A dilute, mineral-salts liquid microbiological culture medium formulated to mimic Lake Kinneret (Sea of Galilee) water. Used to cultivate freshwater autotrophic microorganisms. Could not find in any references the pH of AKW, however the pH of Lake Kinneret varies from about 8.6 at the surface to 7.8 at depth. http://kinneret.ocean.org.il/ar_grp.aspx artificial lake kinneret water AKW AKW media Carrine Blank From Table 1 in: Sherr BF, Sherr EB, Berman T. 1983. Grazing, growth, and ammonium excretion rates of a heterotrophic microflagellate fed with four species of bacteria. Appl Environ Microbiol 45(4):1196-1201. Salt Amt (mg L-1 of distilled water) NaHCO3 197 NaCl 155 CaCl2 130 MgCl2 124 MgSO4 65 KCl 13 CaSO4 9.5 Total salts, 693.5 mg L-1. Total solids in Lake Kinneret water range from 640 to 714 mg L-1. Gram stain quality Carrine Blank Prokaryotic cell part quality, describing the nature of the cell wall. Determined from the results of the Gram stain assay. MGM medium MGM liquid medium A hypersaline, liquid microbiological culture medium that contains mineral salts, peptone, and yeast extract. Used for the cultivation of Haloarchaeobium iranensis. Carrine Blank MGM broth From:Makhdoumi-Kakhki et al 2011. Haloarchaeobium iranensis gen.nov., sp. nov., an extremeley halophilic archaeon isolated from the saline lake Aran-Bidgol, Iran. Int J. Syst. Evol. MIcrobiol. doi:10.1099/ijs.0.033167-0 and Dyall-Smith. 2009. Halohandbook. http://www.haloarchaea.com/resources/halohandbook/ Add the following to a large beaker: Salt water (30% stock), 767 Pure water, 200 Peptone (Oxoid), 5 yeast extract, 1 Stir to dissolve, adjust pH up to 7.5 with 1M Tris pH 7.5, using 5 mL per liter. Adjust to 1L with pure water. For solid medium add 15g Difco Bacto-agar. 30% Salt water stock solution (the CaCl2 is not added until just before pouring plates and some TrisHCl pH 7.5 is added): per liter: H2O, 850 mL NaCl, 240 g MgCl2x6H2O, 30g KCl, 7g 1M TrisHCL pH 7.5, 20 mL modified 9K medium From: Zhou H et al. 2008. Isolation and characterization of Ferroplasma thermophilum sp. nov., a novel extremely acidophilic, moderately thermophilic archaeon and its role in bioleaching of chalcopyrite. J Appl Microbiol 105:591. Modified 9K medium contained (per litre): 3.0 g (NH4)2SO4, 0.5 g KH2PO4, 0.1 g KCl, 0.5 g MgSO4x7H2O, 0.01 g Ca(NO3)2. Trace elements (per litre) comprised: 11.0 mg FeCl3x6H2O, 0.5 mg CuSO4x5H2O, 50 mg Na2SO4, 2.0 mg H3BO3, 2.0 mg MnSO4, 0.8 mg Na2MoO4x2H2O, 0.6 mg CoCl2x6H2O, 0.9 mg ZnSO4x7H2O and 0.1 mg Na2SeO4. The pH of the medium was adjusted to 1.0 by adding 50% (v ⁄ v) H2SO4, was autoclaved, and then filter-sterilized (0.2 um filter paper) trace elements and FeSO4x7H2O were added in the medium. Carrine Blank An acidic, liquid, mineral-salts microbiological culture medium, high in ferrous iron. Used for the cultivation of Ferroplasma thermophilum. NOM-1 medium NOM-1 liquid medium From: Heng-Lin Cui, Xin-Yi Li, Xia Gao, Xue-Wei Xu, Yu-Guang Zhou, Hong-Can Liu, Aharon Oren and Pei-Jin Zhou. 2010. Halopelagius inordinatus gen. nov., sp. nov., a new member of the family Halobacteriaceae isolated from a marine solar saltern. IJSEM 60:2089-2093. per liter: yeast extract, 0.2 g fish peptone, 0.2 g sodium pyruvate, 2.0 g sodium lactate, 2.0 g KCl, 5.4 g K2HPO4, 0.3 g NH4Cl, 0.5 g MgSO4x7H2O, 20.0 g NaCl, 200.0 g pH 7.0-7.2. neutral oligotrophic haloarchaeal medium A hypersaline, liquid microbiological culture medium containing mineral-salts, magnesium sulfate, pyruvate, lactate, peptone, and yeast extract. Used for the cultivation of Halopelagius inordinatus. Carrine Blank modified R2A medium A hypersaline, liquid microbiological culture medium containing mineral-salts, magnesium sulfate, pyruvate, glucose, glutamate, citrate, and peptones. Used for the cultivation of Halogranum rubrum and Halosarcina limi. CM2 medium CM2 liquid medium From: Cui H-L, et al. 2010. Halogranum rubrum gen. nov., sp. nov., a halophilic archaeon isolated from a marine solar saltern. Int J Syst Evol Microbiol 60:1366. Modified R2A medium: Contains the following ingredients per liter: Casamino acids 0.5g yeast extract, 0.5g sodium pyruvate, 0.5 g fish peptone, 0.5g glucose, 0.5g sodium glutamate, 0.5g trisodium citrate, 3.0g KCl, 2.0g K2HPO4, 0.3g CaCl2, 0.5g MgSO4x7H2O, 20.0g NaCl, 200.0 g pH 7.0-7.2 Carrine Blank MR2A From: Cui H-L et al. 2010. Halosarcina limi sp. nov., a halophilic archaeon from a marine solar saltern, and emended description of the genus Halosarcina. Int J. Syst. Evol. Microbiol. 60:2462. CM2 Recipe: Per liter: Casamino acids (Difco), 0.5 g yeast extract (Difco), 0.5 g sodium pyruvate, 0.5 g fish peptone, 0.5 g glucose, 5.0 g sodium glutamate, 0.5 g trisodium citrate, 3.0 g KCl, 2.0 g K2HPO4, 0.3 g CaCl2, 0.5 g MgSO4x7H2O, 20 g NaCl, 230.0 g pH 7.0–7.2 MR2A liquid medium defined inorganic chemical mixture Inorganic compounds or mixtures of inorganic compounds added to culture media to support growth or metabolism of a microorganism. Because the exact composition of the mixture is known, it is referred to as "defined". Carrine Blank DSMZ Medium 954 Halococcus dombrowskii medium DSM strains: 19505 Haladaptatus cibarius 18796 Halalkalicoccus jeotgali B3 14522 Halococcus dombrowskii 19504 Halorubrum cibi 18794 Haloterrigena jeotgali A29 18795 Natronococcus jeotgali DSM 18795 Medium for Halococcus dombrowskii Carrine Blank From: http://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium954.pdf 954. Medium for Halococcus dombrowskii. Casamino acids 5.00 g Yeast extract 5.00 g TRIS 12.10 g KCl 2.00 g MgCl2x6H2O 20.00 g CaCl2x2H2O 0.20 g NaCl 200.00 g Agar 20.00 g Distilled water 1000.00 mL Adjust pH to 7.4. Add the agar after dissolving all ingredients in the water and adjustment of pH. © 2007 DSMZ GmbH - All rights reserved A hypersaline, organic-rich, solid microbiological culture medium containing mineral-salts, tris, casamino acids, and yeast extract. Used to cultivate Halococcus dombrowskii (DSM 14522). Hayflick medium From:http://www.atcc.org/~/media/B61DC4844DBE4D51867A06D49DE22564.ashx ATCC Medium: 2820 HAYFLICK Medium Yeast Extract…………………………………..19.6 g PPLO…………………………………………...17.7 g Phenol Red……………………………………24 mg DNA sodium salt (Sigma, D1501)………...…0.24 g Horse serum (aseptically add)……………….157 ml DI Water………………………………………..843 ml Combine all ingredients except for the horse serum. Adjust pH to 7.8 +/- 0.2. Autoclave at 121C and let medium cool to 55C. Aseptically add horse serum and dispense as required. Carrine Blank An organic-rich, liquid microbiological culture medium containing beef heart infusion, peptone, and sodium chloride. Developed for the growth of Mycoplasma pneumoniae. nutrient broth From: Nutrient Broth (Becton-Dickinson Difco and BBL Manual of Microbiological Culture Media, 2nd edition): Nutrient Broth has the formula originally designed for use in the Standard Methods for the Examination of Water and Wastewater. It is not a recommended bacteriological medium in later editions of this publication. It is one of several nonselective media recommended for use in the Most Probable Number (MPN) technique of estimating the density of viable organisms in food samples1 and is useful in routine cultivation of microorganisms. Principles of the Procedure This relatively simple formulation supports the growth of nonfastidious microorganisms due to its content of peptone and beef extract. Formula Difco™ Nutrient Broth Approximate Formula* Per Liter Beef Extract.................................................................. 3.0 g Peptone....................................................................... 5.0 g *Adjusted and/or supplemented as required to meet performance criteria. pH 6.8 ± 0.2 Carrine Blank nutrient medium NB An organic-rich, liquid culture medium comprised of beef extract and peptone. nutrient broth nutrient broth media ZoBell phytagel From: http://himedialabs.com/TD/M384.pdf Zobell Marine Agar 2216 Zobell Marine Agar 2216 is recommended for cultivation, isolation and enumeration of heterotrophic marine bacteria. Composition Ingredients (Gms/Litre) Peptic digest of animal tissue 5.000 Yeast extract 1.000 Ferric citrate 0.1000 Sodium chloride 19.450 Magnesium chloride 8.800 Sodium sulfate 3.240 Calcium chloride 1.800 Potassium chloride 0.550 Sodium bicarbonate 0.160 Potassium bromide 0.080 Strontium chloride 0.034 Boric acid 0.022 Sodium silicate 0.004 Sodium fluorate 0.0024 Ammonium nitrate 0.0016 Disodium phosphate 0.008 Final pH (25˚C) 7.6+/-0.2 Barbeyron T, L'Haridon S, Corre E, Kloareg B & Potin P. 2001. Zobellia galactanovorans gen. nov., sp. nov., a marine species of Flavobacteriaceae isolated from a red alga, and classification of [Cytophaga] uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Zobellia uliginosa gen. nov., comb. nov. IJSEM 51:985-997.: When it was desirable to avoid attack of the substratum, strains were grown on ZoBell solidified with 0.7% (w/v) Phytagel (a gellan gum; Sigma). Carrine Blank An organic-rich, mineral-salts, liquid microbiological culture medium containing peptones and yeast extract in a base of artificial sea water. Solidified using Phytagel (gellan gum) instead of agar. Used for the cultivation of heterotrophic marine microorganisms capable of degrading agar. ZoBell phytagel plates ZoBell phytagel agar medium containing ruminal fluid Carrine Blank A microbiological culture medium that contains bovine rumen fluid (or ruminal fluid), used for the culture of microorganisms that live in the rumen. Sehgal and Gibbons medium Sehgal and Gibbons, 1960, Effect of some metal ions on the growth of Halobacterium cutirubrum. Can J Microbiol 6:165. A hypersaline, organic-rich liquid medium containing casamino acids, yeast extract, and salts. Used for the growth of Halobacterium cutirubrum. Original citation: Sehgal SN, Gibbons NE (1960) Effect of some metal ions on the growth of Halobacterium cutirubrum. Can J Microbiol 6:165–169. The routine medium contained 7.5 g casamino acids (Difco), 10 g yeast extract (Difco), 3 g trisodium citrate, 2 g potassium chloride, 20 g magnesium sulphate heptahydrate, 250 g sodium chloride, aid distilled water to 1 liter. The ingredients were dissolved in 800 ml water, the pH adjusted to 7.5-7.8 with N potassium hydroxide, and the medium autoclaved 5 minutes at 120˚C. It was then filterecl to remove the precipitate, the pH mas adjusted to 7.4 with N hydrochloric acid, and the medium made up to final volume. S-G medium From: Schneegurt MA, Chapter 2, Media and conditions for the growth of halophilic and halotolerant bacteria and archaea. pg. 39, Table 2.1. In Vreeland RH (ed) Advances in Understanding the Biology of Halophilic Microorganisms. DOI 10.1007/978-94-007-5539-0_2 Medium composition in grams per liter: NaCl, 250 MgSO4x7H2O, 20 FeCl2, 0.023 Na-citrate, 3 Casamino acids, 7.5 yeast extract, 10 Carrine Blank Brucella agar with sheep blood From: Brucella Agar with 5% Sheep Blood, Hemin and Vitamin K1 (Becton-Dickinson Difco and BBL Manual of Microbiological Culture Media, 2nd edition): Intended Use Brucella Agar with 5% Sheep Blood, Hemin and Vitamin K1 is used for the isolation and cultivation of fastidious, obligately anaerobic microorganisms. BRU Carrine Blank An organic-rich, solid microbiological culture medium, containing peptones, yeast extract, glucose, and sodium bisulfite as a reducing agent. Supplemented with 5% sheep blood, hemin, and vitamin K. Used for the growth of Brucella. Zobell phytagel starch Starch phytagel plates Carrine Blank Zobell phytagel starch agar An organic-rich, mineral-salts, liquid microbiological culture medium containing peptones and yeast extract in a base of artificial sea water. Solidified using Phytagel instead of agar. Supplemented with starch. Used for the cultivation of heterotrophic marine microorganisms capable of degrading agar. Barbeyron T, L'Haridon S, Corre E, Kloareg B & Potin P. 2001. Zobellia galactanovorans gen. nov., sp. nov., a marine species of Flavobacteriaceae isolated from a red alga, and classification of [Cytophaga] uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Zobellia uliginosa gen. nov., comb. nov. IJSEM 51:985-997. The strain was assayed for amylase activity using starch at a concentration of 0.2 % (w/v) in ZoBell agar or in ZoBell Phytagel plates. BRN medium Balch et al. 1979. Methanogens: reevaluation of a unique biological group. Microbiol Rev 43(2):260. A liquid, mineral-salts microbiological culture medium containing acetate, formate, yeast extract, trypticase, cysteine and sulfide with H2 and CO2 in the headspace gas mixture. Supplemented with additional 0.1% NH4Cl, 10% rumen fluid, 2% agar, and with clindamycin and cephalotin (cefalotin). Used for the growth of Methanobrevibacter from feces. Miller, 2001. In Bergey's Manual of Systematic Bacteriology, v. 1, 2nd ed. p.219. Carrine Blank Miller TL et al, 1982. Isolation of Methanobrevibacter smithii from human feces. Appl Environ Microbiol 43(1):227. MGM agar From:Makhdoumi-Kakhki et al 2011. Haloarchaeobium iranensis gen.nov., sp. nov., an extremeley halophilic archaeon isolated from the saline lake Aran-Bidgol, Iran. Int J. Syst. Evol. MIcrobiol. doi:10.1099/ijs.0.033167-0 and Dyall-Smith. 2009. Halohandbook. http://www.haloarchaea.com/resources/halohandbook/ Add the following to a large beaker: Salt water (30% stock), 767 Pure water, 200 Peptone (Oxoid), 5 yeast extract, 1 Stir to dissolve, adjust pH up to 7.5 with 1M Tris pH 7.5, using 5 mL per liter. Adjust to 1L with pure water. For solid medium add 15g Difco Bacto-agar. 30% Salt water stock solution (the CaCl2 is not added until just before pouring plates and some TrisHCl pH 7.5 is added): per liter: H2O, 850 mL NaCl, 240 g MgCl2x6H2O, 30g KCl, 7g 1M TrisHCL pH 7.5, 20 mL A hypersaline, organic-rich, solid microbiological culture medium that contains mineral-salts, tris, peptone, and yeast extract. Used for the cultivation of Haloarchaeobium iranensis. Carrine Blank microbiological culture medium containing blood blood agar BAP Blood agar plates A microbiological culture medium that contains blood, treated blood, lysed blood cells, blood serum, or treated blood serum. Carrine Blank citrated blood Carrine Blank From: https://catalog.hardydiagnostics.com/cp_prod/Content/hugo/AnimalBloodProd.htm Animal Blood, Citrated is blood that has been washed and treated with sodium citrate as the anticoagulant. It serves as a source of erythrocytes for serological procedures. Blood medium ingredient comprised of animal blood where citrate has been added to prevent coagulation. Used in the cultivation of microorganisms. equine serum-containing microbiological culture medium Carrine Blank media containing 1% serum fraction A liquid microbiological culture medium that contains horse (equine) serum. horse serum containing agar media containing 20% horse serum microbiological culture medium, containing procine serum Carrine Blank A microbiological culture medium (a blood serum agar), made with porcine (pig) blood serum. PPLO medium PPLO serum fraction PPLO media PPLO broth An organic-rich, liquid microbiological culture medium containing various peptones and sodium chloride. Developed for the growth of mycoplasmas. From: PPLO Media (Mycoplasma Media) (Becton-Dickinson Difco and BBL Manual of Microbiological Culture Media, 2nd edition): Intended Use PPLO (Mycoplasma) agars and broths, when supplemented with nutritive enrichments, are used for isolating and cultivating Mycoplasma. Mycoplasma Broth Base (Frey) is used for the cultivation of avian mycoplasmas. Principles of the Procedure Meat digests, peptones, beef extract and yeast extract provide the nitrogen, vitamins, amino acids and carbon in these media. Sodium chloride maintains the osmotic balance of these formulations. Agar, the solidifying agent, is used in PPLO (Mycoplasma) Agar at a concentration slightly reduced from usual to ensure formation of the largest possible colonies because the organisms grow into the agar with only slight surface growth.13 The base media are supplemented with Mycoplasma Supplement or Mycoplasma Enrichment w/o Penicillin because Mycoplasma spp. are fastidious in their growth requirements. 14 Mycoplasma Supplement contains fresh yeast extract and horse serum. Yeast extract provides the preformed nucleic acid precursors that are required by Mycoplasma spp.14 Horse serum supplies cholesterol, a growth stimulant.14 Mycoplasma Enrichment without Penicillin is a selective enrichment containing the inhibitor thallium acetate, to which a penicillin of choice (penicillin G or a broad-spectrum semisynthetic penicillin) can be added at the time of use to make it selective against gram-positive and gram-negative bacteria. Formulae Difco™ PPLO Agar Approximate Formula* Per Liter Beef Heart, Infusion from 50 g..................................... 6.0 g Peptone..................................................................... 10.0 g Sodium Chloride.......................................................... 5.0 g Agar.......................................................................... 14.0 g Difco™ PPLO Broth Consists of the the same ingredients without the agar. pH 7.8 ± 0.2 BBL™ Mycoplasma Agar Base (PPLO Agar Base) Approximate Formula* Per Liter Beef Heart, Infusion from (solids).................................. 2.0 g Pancreatic Digest of Casein.......................................... 7.0 g Beef Extract.................................................................. 3.0 g Yeast Extract................................................................ 3.0 g Sodium Chloride.......................................................... 5.0 g Agar.......................................................................... 14.0 g pH 7.8 ± 0.2 BBL™ Mycoplasma Broth Base (PPLO Broth Base) Consists of the same ingredients without the agar. BBL™ Mycoplasma Broth Base (Frey) Approximate Formula* Per Liter Pancreatic Digest of Casein.......................................... 7.5 g Papaic Digest of Soybean Meal..................................... 2.5 g Yeast Extract................................................................ 5.0 g Sodium Chloride.......................................................... 5.0 g Potassium Chloride...................................................... 0.4 g Magnesium Sulfate...................................................... 0.2 g Disodium Phosphate.................................................... 1.6 g Monopotassium Phosphate.......................................... 0.1 g pH 7.7 ± 0.2 Difco™ Mycoplasma Supplement Approximate Formula* Per 30 mL Vial Yeast Extract................................................................ 0.09 g Horse Serum.............................................................. 22.8 mL BBL™ Mycoplasma Enrichment without Penicillin Approximate Formula* Per 30 mL Vial Horse Serum.............................................................. 20.0 mL Yeast Extract (fresh autolysate)................................... 10.0 mL Thallium Acetate........................................................ 50.0 mg *Adjusted and/or supplemented as required to meet performance criteria. Carrine Blank SP-4 medium An organic-rich, liquid microbiological culture medium containing pancreatic digests of casein and gelatin, PPLO broth (without CV, i.e. without crystal violet), fetal bovine serum (fetal calf serum), CMRL 1066 medium (a mixture of amino acids, vitamins, co-factors, and organic micronutrients), yeast extract, and polymyxin B, Amphotericin B, and penicillin. Used for the growth of mycoplasmas. Carrine Blank SP-4 media From: https://catalog.hardydiagnostics.com/cp_prod/Content/hugo/SP4Media.htm SP4 Broth, Plain**: Pancreatic Digest of Casein 10.0gm Pancreatic Digest of Gelatin 5.0gm PPLO Broth without CV 3.5gm Polymyxin B 50.0mg Amphotericin B 5.0mg Fetal Bovine Serum 170.0ml CMRL 1066 Medium (10X) 50.0ml Yeast Extract 35.0ml Yeastolate 10% 20.0ml Penicillin 1,000,000U Final pH at 25 degrees C.: SP4 Broth, Plain SP4 Broth with Arginine 7.0 +/- 0.2 horse blood agar Carrine Blank A solid microbiological culture medium (a blood agar), containing horse blood. horse blood agar slant culture medium A slant culture is where liquified (melted) solid medium has been added to a sterile test tube and allowed to solidify (cool) at an angle with respect to the horizontal, such that the solid medium surface is at an angle with respect to the sides of the test tube. The slant culture allows for a larger surface of the agar to be exposed to oxygen. blue green medium blue-green medium Carrine Blank BG media A mineral-salts, marine, liquid microbiological culture medium containing soil extract. Used for the growth of photoautotrophic microorganisms. http://www-cyanosite.bio.purdue.edu/media/table/bg.html From: Moss,B. 1972. The influence of environmental factors on the distribution of freshwater algae: an experimental study. J. Ecol. 60:917-932. Blue-Green (BG) Medium This medium is made up in 2 parts. Autoclave parts 1 and 2 separately at 15 psi, allow to cool them then mix aseptically. For agar plates, add 15 g non-nutrient agar per L. Part 1: Tricine 0.50 g Soil extract (SE1) 25.00 mL Extra nutrient salts 3.75 mL Filtered natural seawater to 1.0 L Adjust pH to 7.6-7.8 with 1M NaOH or HCl. Part 2: NaNO3 1.500 g K2HPO4x3H2O 0.040 g MgSO4x7H2O 0.075 g CaCl2x2H2O 0.036 g Citric acid 0.006 g Ammonium ferric citrate green 0.006 g EDTANa2 0.001 g Na2CO3 0.020 g Trace metal solution 1.00 mL Distilled water to 1.0 L Adjust pH to 7.4. Extra nutrient salts: NaNO3 3.00 g Na2HPO4 0.12 g K2HPO4 0.10 g Distilled water to 100.0 mL Trace metal solution: H3BO3 0.286 g MnCl2x4H2O 0.022 g Na2MoO4x2H2O 0.039 g CuSO4x5H2O 0.008 g Co(NO3)2x6H2O 0.005 g Distilled water to 100 mL BG medium Lindstrom medium L-medium No. 16 Lindstrom media A mineral-salts, liquid microbiological culture medium comprised mainly of sodium bicarbonate. Used to cultivate autotrophic microorganisms from lakes. L 16 Carrine Blank From: Lindstrom, K. 1983. Selenium as a growth factor for plankton algae in laboratory experiments and in some Swedish lakes. Hydrobiologia 101:35-48. Macronutrients (all values mg per L) NaHCO3 84.00 NaNO3 12.75 CaCl2x2H2O 14.70 MgSO4x7H2O 12.32 K2HPO4 1.74 Na2SiO3x9H2O 1.14 Micronutrients FeCl3x6H2O 0.108 Na2MoO4x2H2O 0.048 ZnCl2 0.027 MnCl2x4H2O 0.010 CoCl2x6H2O 0.0096 Na2SeO3x5H2O 0.000184 EDTA 0.558 pH 8.1 Aa medium A mineral-salts, liquid microbiological culture medium containing sodium acetate, potassium phosphate, sodium carbonate, ammonium sulfate, cysteine hydrochloride, sodium sulfide, magnesium sulfate, calcium chloride, sodium chloride, ferrous sulfate, nitrilotriacetic acid, manganese sulfate, cobalt chloride, zinc sulfate, resazurin, copper sulfate, potassium aluminum sulfate, boric acid, sodium molybdate, pyridoxine hydrochloride, thiamine hydrochloride, riboflavin, nicotinic acid, p-aminobenzoic acid (4-aminobenzoic acid), lipoic acid, biotin, folic acid, and vitamin B12 (cobalamin). Prepared under an atmosphere of dinitrogen and carbon dioxide. Used for the growth of Methanosaeta concillii. Carrine Blank From: Patel GB. 1984. Characterization and nutritional properties of Methanothrix concilii sp. nov., a mesophilic, aceticlastic methanogen. Can J Microbiol 30:1383-1396. The composition of the Aa medium used for isolation and stock culture maintenance was as follows (in milligrams per litre): CH3COONa·3H2O, 6800; K2HPO4, 2190; KH2PO4, 1500; Na2CO3, 480; (NH4)2SO4, 450; cysteine-HCl, 125; Na2S·9H2O, 125; MgSO4·7H2O, 120; CaCl2·2H2O, 60; NaCl, 54; FeSO4 ·7H2O, 21; nitrilotriacetic acid, 15; MnSO4 · 2H2O, 5; CoCl2-6H2O, 1; ZnSO4·7H2O, I; resazurin, I; CuSO4·5H2O, 0.1; AIK(SO4)2- 12H2O, 0.1; H3BO3, 0.1; Na2Mo04·2H2O, 0.1; pyridoxine-HCl, 0.1; thiamine-HCl, riboflavin, nicotinic acid, p-aminobenzoic acid, lipoic acid, each 0.05; biotin and folic acid, each 0.02; vitamin B-12, 0.005. The Aa medium ingredients, except Na2CO3 and cysteine- Na2S, were 'mixed and adjusted to pH 7.8. The medium was then reduced with cysteine- Na2S, and Na2CO3 was added, using the Hungate (1950) technique. The reduced medium was dispensed in 10-mL aliquots into 60-mL serum vials (Miller and Wolin 1974) under 80% N2: 20% CO2 gas phase. The postautoclave (121°C, 15 min) pH was 7.2 ± 0.1. If the same medium contained 10000 mg/L of CH3COONa·3H20, it was referred to as AA medium. prokaryotic quality Carrine Blank Quality that inheres in a prokaryotic cell, group of cells, prokaryotic colony, or part of a prokaryotic cell. subaerial prokaryote habitat subaerial Carrine Blank aerophytic subaerophytic water filter A filter with a specified pore size that filters solid material above the specified pore size out of a liquid medium. Carrine Blank Berkefeld filter candle A gravity-driven water filter made by the British Berkefeld® company. Carrine Blank prokaryotic cell quality Physical object quality of a prokaryotic cell. Carrine Blank trichome pole Carrine Blank A trichome part, refering to the poles (terminal ends) of a prokaryotic trichome. May involve one cell or multiple cells along the trichome. mesophilic Carrine Blank Temperature optimum quality, where growth rates at moderate temperatures (20-40˚C) are higher than growth rates at other temperatures. ZoBell marine agar MA From: http://himedialabs.com/TD/M384.pdf Zobell Marine Agar 2216 Zobell Marine Agar 2216 is recommended for cultivation, isolation and enumeration of heterotrophic marine bacteria. Composition Ingredients (Gms/Litre) Peptic digest of animal tissue 5.000 Yeast extract 1.000 Ferric citrate 0.1000 Sodium chloride 19.450 Magnesium chloride 8.800 Sodium sulfate 3.240 Calcium chloride 1.800 Potassium chloride 0.550 Sodium bicarbonate 0.160 Potassium bromide 0.080 Strontium chloride 0.034 Boric acid 0.022 Sodium silicate 0.004 Sodium fluorate 0.0024 Ammonium nitrate 0.0016 Disodium phosphate 0.008 Final pH (25˚C) 7.6+/-0.2 MA2216 agar MA plates ZMA MA solid medium An organic-rich, mineral-salts, solid microbiological culture medium containing peptones and yeast extract in a base of artificial sea water. Used for the cultivation of heterotrophic marine microorganisms. Carrine Blank Marine agar MA medium marine agar 2216 Marine 2216 agar Zobell marine agar Zobell 2216E agar tryptic soy broth Trypticase soy broth From: Bacto™ Tryptic Soy Broth/Trypticase™ Soy Broth (Becton-Dickinson Difco and BBL Manual of Microbiological Culture Media, 2nd edition): Intended Use Tryptic (Trypticase) Soy Broth (Soybean-Casein Digest Medium) is a general purpose medium used in qualitative procedures for the cultivation of fastidious and nonfastidious microorganisms from a variety of clinical and nonclinical specimens. Principles of the Procedure Enzymatic digests of casein and soybean provide amino acids and other complex nitrogenous substances. Dextrose is an energy source. Sodium chloride maintains the osmotic equilibrium. Dibasic potassium phosphate acts as a buffer to control pH. The addition of 6.5% sodium chloride to Trypticase Soy Broth permits the differentiation of salt-tolerant enterococci, which are resistant to the high salt content, from the salt-intolerant S. bovis group and other streptococcal species. At this concentration, the sodium chloride is a selective agent that interferes with membrane permeability and osmotic and electrokinetic equilibria.4 Fildes Enrichment is a peptic digest of sheep blood that supplies the X (hemin) and V (nicotinamide adenine dinucleotide, NAD) factors necessary for the growth of H. influenzae. Dextrose is omitted from the formula for Tryptic Soy Broth without Dextrose to permit use of the medium in fermentation studies. The carbohydrate concentration used most frequently in fermentation reactions is 0.5% or 1%. Tryptic Soy Broth and Trypticase Soy Broth are provided as prepared media in a variety of bottle styles. In addition, Tryptic Soy Broth is provided as a Sterile Pack Bottle; i.e., the bottle has been terminally sterilized inside of autoclavable double-bags. All varieties of bottled TSB conform with requirements for Ready- To-Use Media as described in the USP. Formulae Bacto™ Tryptic Soy Broth (Soybean-Casein Digest Medium) Approximate Formula* Per Liter Pancreatic Digest of Casein........................................ 17.0 g Papaic Digest of Soybean............................................. 3.0 g Dextrose...................................................................... 2.5 g Sodium Chloride.......................................................... 5.0 g Dipotassium Phosphate................................................ 2.5 g pH 7.3 ± 0.2 BBL™ Trypticase™ Soy Broth (Soybean-Casein Digest Broth) Approximate Formula* Per Liter Pancreatic Digest of Casein........................................ 17.0 g Papaic Digest of Soybean............................................. 3.0 g Sodium Chloride.......................................................... 5.0 g Dipotassium Phosphate................................................ 2.5 g Dextrose...................................................................... 2.5 g pH 7.3 ± 0.2 Bacto™ Tryptic Soy Broth without Dextrose Approximate Formula* Per Liter Pancreatic Digest of Casein........................................ 17.0 g Enzymatic Digest of Soybean Meal............................... 3.0 g Sodium Chloride.......................................................... 5.0 g Dipotassium Phosphate................................................ 2.5 g *Adjusted and/or supplemented as required to meet performance criteria. pH 7.3 ± 0.2 Soya broth media Tryptone soya broth An organic-rich, liquid culture medium comprised of pancreatic digest of casein (casitone), papaic digest of soybean (soy peptone), dextrose (D-glucose), sodium chloride, and dipotassium phosphate (potassium dibasic phosphate). Tryptic soy broth Wikipedia:Tryptic_soy_broth Tryptic soy broth (frequently abbreviated as TSB) is used in microbiology laboratories as a culture broth to grow aerobic bacteria. It is frequently used in commercial diagnostics in conjunction with the additive Thio which promotes growth of anaerobes. Soya broth tryptic soy medium TSB Carrine Blank tryptic soy agar TSBA plates Tryptone soy agar TSA Tryptone Soya Agar TSA agar Tryptic soy broth agar Trypticase soy broth agar Trypticase soy agar TSBA Tryptic soy agar Trypticase-Soy agar An organic-rich, solid medium containing casitone (pancreatic digest of casein), Phytone peptone (papaic digest of soybean), and sodium chloride. Used for the cultivation of aerobic heterotrophic microorganisms. From: Tryptic Soy Agar/Trypticase™ Soy Agar (Becton-Dickinson Difco and BBL Manual of Microbiological Culture Media, 2nd edition): Intended Use Tryptic (Trypticase) Soy Agar (TSA) is used for the isolation and cultivation of nonfastidious and fastidious microorganisms. It is not the medium of choice for anaerobes. Principles of the Procedure The combination of casein and soy peptones in TSA renders the medium highly nutritious by supplying organic nitrogen, particularly amino acids and longer-chained peptides. The sodium chloride maintains osmotic equilibrium. Agar is the solidifying agent. Haemophilus species may be differentiated by their requirements for X and V factors. Paper strips impregnated with these factors are placed on the surface of the medium after inoculation with the test organism. Following incubation, a zone of growth around the strip indicates a requirement for the factor(s). Formulae Difco™ Tryptic Soy Agar Approximate Formula* Per Liter Pancreatic Digest of Casein........................................ 15.0 g Papaic Digest of Soybean............................................. 5.0 g Sodium Chloride.......................................................... 5.0 g Agar.......................................................................... 15.0 g pH 7.3 ± 0.2 BBL™ Trypticase™ Soy Agar Approximate Formula* Per Liter Pancreatic Digest of Casein........................................ 15.0 g Papaic Digest of Soybean............................................. 5.0 g Sodium Chloride.......................................................... 5.0 g Agar.......................................................................... 15.0 g *Adjusted and/or supplemented as required to meet performance criteria. Carrine Blank prokaryotic metabolic process Carrine Blank A single-organism metabolic process that is present in a prokaryotic metabolically differentiated cell. chemical mixture, serving as microbiological medium ingredients Carrine Blank A solid or liquid mixture of chemicals which are used as ingredients in microbiological culture media used to grow and propogate prokaryotic microorganisms. sub-cylindrical A flattened prokaryotic cell where the shape is partially spherical. sub-cylindrical thermophilic Carrine Blank Temperature optimum quality, where growth rates at elevated temperatures (40-85˚C) are higher than growth rates at ambient temperatures. filament septation Carrine Blank A filament of prokaryotic cells relating to the presence or absence of septa separating the individual cells that make up the filament. cyanobacterial filament part Carrine Blank Cell part of a cyanobacterial filament. filamentous distinctively shaped filament Carrine Blank A cell filament that has a distinctive shape. spatially differentiated filaments A filament morphological quality where the filaments have a particular spatial orientation with respect to a substrate or surface. Carrine Blank scytonematoid-branched filaments loop-formation loop formation Scytonema-like false branching filaments in loop-like formations common lateral loops Scytonema-type false scytonematoid branching S-type scytonematoid false branching False-branched filaments, where branches initiate at a necridic cell. Branches often appear as pairs. Carrine Blank filaments make sometimes typical loop-like lateral formations tolypothrixoid-branched filaments False-branched filaments, where branches initiate at a heterocyte. Branches only sometimes appear as pairs. tolypotrichoid branched Tolypothrix-type false branching Tolypothrix-like false branching Carrine Blank Tolypothrix-type Tolypothrix-like false branched T-type X-branched filaments X-branching Carrine Blank Chlorogloeopsis-type branching True-branched filaments, where the cells divide irregularly in different planes and form clusters of cells. The cells remain physiologically attached. irregular clustering T-branched filaments T-type branching Carrine Blank perpendicular branching true branching lateral (usually unilateral) laterally true branched T-type of branching branching type "T" type of branching: T-type branching of T-type erect true branches develop usually unilaterally after the lengthwise cell division true branching lateral Westiella-type lateral T-branching irregularly lateral true branched lateral T-type branching lateral Hapalosiphon-type branching lateral (T-type) Stigonema-type Fischerella-type zzzz 'inheres in' some (Stigonema or Fischerella or Hapalosiphon or Westiella) Westiella is in NCBI Tax browser, but not in OntoFox. True-branched filaments, where a cell in the trichome divides longitudinally (parallel to the axis of the filament) and the trichome branch starts to grow perpendicular to one side of the main trichome. T-branching V-branched filaments pseudodichotomous branches arise by longitudinal division of the apical cells Hyphomorpha-type branching type "V" Loriella-type pseudodichotomously true branched pseudodichotomously divaricated branches Carrine Blank zzzz 'inheres in' some (Hyphomorpha or Pulvinularia or Colteronema or Loriella or Mastigocoleopsis) - no NCBI entries. pseudodichotomously branched pseudodichotomously divaricated at the ends V-branching Mastigocoleopsis-type pseudodichotomous branchings pseudodichotomously divaricated V-type V-type of branching pseudodichotomous V-type True-branched filaments, where an apical cell divides longitudinally, from which grows obliquely two equivalent branches. branching lateral (V-type) pseudodichotomously divaricated free filaments pseudodichotomous reverse Y-branched filaments Carrine Blank reverse Y-like branching Y-type True-branched filaments, where branches arise in the intercalary (medial) cells after oblique cell division at an intercalary (medial cell). reverse Y-type Y-branching zzzz 'inheres in' some (Scytonema or Brachytrichia or Mastigocladus) Brachytrichia is in NCBI Tax Browser, but not in OntoFox. reverse Y-branching biseriate filament 2 2 Filament with one trichome in the sheath, where the trichome is two cells in width. Arises as a result of cell division occuring in two planes,one perpendicular to the axis of the trichome and one parallel to the axis of the trichome. bi-seriate Carrine Blank with 2 cells aside extracellular sheath An extracellular sheath in cyanobacteria is typically a laminated (lamellated, laminar), fibrillar, extracellular structure made of polysaccharides (glycan). It plays a role in desiccation tolerance and often contains pigments (such as scytonemin) which protect from photodamage caused by uv light. It also has proteins (including water stress proteins, pectases). Often multilayered and colored. Carrine Blank sheath trichome Wikipedia: trichome Algal trichomes Certain, usually filamentous, algae have the terminal cell produced into an elongate hair-like structure called a trichome. The same term is applied to such structures in some cyanobacteria, such as Spirulina and Oscillatoria. Cyanobacteria trichomes may be unsheathed, as in Oscillatoria, or sheathed, as in Calothrix.[1] These structures play an important role in preventing soil erosion, particularly in cold desert climates.[citation needed] The filamentous sheaths form a persistent sticky network that helps maintain soil structure. Carrine Blank A prokaryotic filament part, comprised of a chain of cells that has undergone binary fission in a single plane, where the cells remain attached after cell division. Found in the Nostocales and Stigonematales (Cyanobacteria). isopolar trichome apical cells not differentiated A prokaryotic trichome where the two poles of the trichome have the cell diameter (i.e., are symmetrical and not tapered). Caused by the development of a basal heterocyte. trichomes isopolar morphologically not diversified in "main" filaments and branches simple trichomes trichomes not distinctly diversified filaments simple Carrine Blank simple filaments apical cells morphologically not different from other cells heteropolar trichome filaments polarized A prokaryotic trichome where the two poles of the trichome have different cell diameters (i.e. trichomes are tapered on end end and asymmetrical). Caused by the development of a basal heterocyte. trichomes heteropolar filaments differentiated into basal and apical parts trichomes, oriented by their bases with heterocytes to their substrate and by their apical hir-like parts to the surface Carrine Blank free apical end filaments distinctly divided into basal end with a heterocyte and the apical end differentiating into basal and apical parts apical cell Carrine Blank free apical end A trichome cell that is located terminally in a trichome, and which has undergone differentiation. Found in trichomes with apical-basal polarity. susceptibility to lysis by hypotonic solution Prokaryotic cell wall lysis susceptibility that defines how susceptible the cell wall is to lysis when the cell is placed in the presence of an environment with an altered chemical composition (hypotonic solution). Carrine Blank basal prostrate filaments Filament orientation quality where erect filaments and prostrate filaments are present, refers to the basal filaments that are prostrate to the substrate. Carrine Blank necritic cell nectrotic cells Carrine Blank trichomes disintegrating in separated cells within filaments trichomes often disintegrate soon after heterocyte formation between heterocytes A trichome cell comprised of a cell that has undergone differentiation such that it is dead (nectritic). chroococcoid cell cluster old trichomes change often in chroococcoid stages chroococcoid stage chroococcoid clusters of cells chroococcoidal known chroococcal stages chroococcoid cell clusters arise Carrine Blank Cell clusters, where the cells are chroococcoid (spherical). differentiated meristematic zone not all cells capable of dividing not all cells capable to divide distinct merstematic zones Filament differentiation quality with respect to the positioning of the meristematic zone along the length of the trichome. not all cells capable of division Carrine Blank tapered trichome trichomes variable width Carrine Blank trichomes tapered Heteropolar trichome where the width of the trichome varies such that the trichome is tapered. trichome tapering hair cell apical hairs An apical cell or cells in a heteropolar filament that is differentiated to form an elongated hair-like extension. long tapering to the hair-like ends hair-like apical ends long hairs hair-like ends terminal hairs hyaline hairs in the apical part narrowed in elongated, cellular hair elongated hyaline cells hair formation hyaline cells cellular hair hairs Carrine Blank trichomes elongated in cellular hair-like ends apical hair-like ends hair-cells vacuolized apical cell vacuolized cells at the ends apical cells vacuolated vacuolized apical cells terminal cells vacuolized end cells sometimes vacuolated Carrine Blank Apical cell that is vacuolized (has gas vacuoles). morphologically distinctive apical cell Cyanobacterial filament part, where the apical cell is morphologically distinctive. Carrine Blank conical-rounded apical cell end cells conical-rounded rounded-conical apical cells Carrine Blank apical cells conical-rounded Apical cell that is conical-rounded (conical-blunt). conical apical cell apical cells conical end cells conical terminal cells conical Apical cell that is conical. terminal cells are conical Carrine Blank pointed apical cell pointed at the ends apical cells pointed Apical cell that is pointed (tapered). Carrine Blank pointed terminal cells rounded apical cell club-shaped ends of trichomes and branches end cells spherical terminal cells are rounded rounded apical cells rounded at the ends rounded terminal cell end cells rounded terminal cells rounded apical cells rounded Apical cell that is rounded (blunt). Carrine Blank rounded at the apex rounded end cells rounded apical cell end cells widely spherical end cells widely rounded end cells widened-rounded end cells rounded at apex elongated apical cell Apical cell that is elongated. apical cells long apical cells cylindrical terminal cells elongated apical cells elongated end cells cylindrical apical part elongated Carrine Blank narrowed apical cell apical cells narrowed terminal cells are narrowed end cells narrowed Carrine Blank apical part narrowed Apical cell that is narrowed (has decreased width). terminal cells narrow apical cell develops into nanocytes terminal cells of branches divide often repeatedly in nanocytes Apical cell quality related the developmental transformation of the apical cell into nanocytes. Carrine Blank transforms into nanocytes hyaline apical cell apical cells hyaline Apical cell that is hyaline (spindle-shaped). Carrine Blank elongated-rounded apical cell Apical cell that is elongated-rounded (elongated-blunt). Carrine Blank terminal cells elongated-rounded bluntly pointed apical cell Carrine Blank Pointed apical cell that is bluntly pointed (attenuate). end cells bluntly pointed terminal cells are bluntly pointed apical cells bluntly pointed sharply pointed apical cell apical cells acuminate apical cells sharply pointed Pointed apical cell that is sharply pointed (acuminate). Carrine Blank vacuolized sub-apical cell vacuolized subapical cells Carrine Blank Sub-apical cell quality where the sub-apical cell is vacuolized (has gas vacuoles). subterminal meristematic zones subapical meristematic zones Carrine Blank apical cells are not able to divide Meristematic zone position quality where the position is subterminal. terminal meristematic zones in the apical part sometimes with meristematic zones meristematic zons near the ends of branches Meristematic zone position quality where the position is terminal. Carrine Blank meristematic (mainly apical) zones tapered by apical widening branches dilated terminal portions end cells enlarged trichomes sometimes with slightly widened apical parts end cells widened-rounded end cells widened Tapered trichome quality where the trichome is wider at the apical end, and narrower at the basal end (cuneate-shaped). apical cell is larger than the other ones Carrine Blank tapered by apical narrowing apical cells attenuated Tapered trichome quality where the trichome is narrower at the apical end, and wider at the basal end (attenuate-shaped). trichomes widened at the base Carrine Blank trace elements solution TES Carrine Blank From: Irgens RL. 1977. Meniscus, a new genus of aerotolerant, gas-vacuolated bacteria. Int J Syst Bacteriol 27(1):38-43. The TES, modified from Pfennig’s formula (personal communication), contained (per liter): ZnSO4x7H2O, 0.10 g; MnCl2x4H2O, 0.03 g; H3BO3, 0.3 g; CoCl2x6H20, 0.2 g; CuCl2x2H2O,0.01 g ; NiCl2x6H2O, 0.02 g; Na2MoO4x 2H2O, 0.03g; pH3 to 4. A trace elements solution containing zinc sulfate, manganese chloride, boric acid, cobalt chloride, copper chloride, nickel chloride, and sodium molybdate. Balch vitamin solution Carrine Blank From: Balch WE et al, 1979. Methanogens: reevaluation of a unique biological group. Microbiol Rev 43(2):260. Trace vitamines (contains in milligrams per liter: biotin, 2; folic acid, 2; pyridoxine hydrochloride, 10; thiamine hydrochloride, 5; riboflavin, 5; nicotinic acid, 5; DL-calcium pantothenate, 5; vitamin B12, 0.1; p-aminobenzoic acid, 5; lipoic acid, 5) Also reported in Wolin EA, Wolin MJ, Wolfe RS. 1963. Formation of methane by bacterial extracts. J Biol Chem 238(8):2882-2886. A solution of vitamins containing biotin, folic acid, pyridoxine, thiamine, riboflavin, nicotinic acid, calcium pantothenate, cobalamin (vitamin B12), 4-aminobenzoic acid (p-aminobenzoic acid), and lipoic acid. Used to support growth of methanogenic archaea. Balch trace vitamines prokaryotic metabolite Carrine Blank A chemical entity produced by a prokaryotic cell, as a result of metabolism. organic chemical mixture Carrine Blank Organic compounds or mixtures of organic compounds added to culture media to support growth or metabolism of a microorganism. methane produced by methanogenesis methane production formation of methane methane formed Prokaryotic metabolite where methane is produced as a result of methanogenesis. CH4 formation CH4 formed forming CH4 produce methane CH4 as the product CH4 production methane generated methane as the product methanogens formation of CH4 production of CH4 CH4 generated methane formation Wikipedia:methanogenesis Methanogenesis or biomethanation is the formation of methane by microbes known as methanogens. Organisms capable of producing methane have been identified only from the domain Archaea, a group phylogenetically distinct from both eukaryotes and bacteria, although many live in close association with anaerobic bacteria. The production of methane is an important and widespread form of microbial metabolism. In most environments, it is the final step in the decomposition of biomass. methanogenic CO2 reduction to methane produces CH4 CO2 reduction to CH4 methane as the end product CH4 as the end product methanogenesis produce CH4 methane produced CH4 produced Carrine Blank forming methane production of methane produces methane obligate methanogen Prokaryotic metabolically differentiated cell, specialized for the production of methane. Found only in the archaeal domain of life. obligately methanogenic Carrine Blank undefined organic chemical mixture Carrine Blank A mixture of dry or liquid organic compounds added to culture media to support growth or metabolism of a microorganism. Because the exact composition of the mixture is unknown or uncharacterized, it is referred to as "undefined". tetrathionate reduction Carrine Blank The process in which tetrathionate is reduced to sulfide. microbiological medium ingredient, derived from aqueous extracts of animal tissues or fluids Undefined mixture of complex organic compounds deriving from the aqueous extraction (an extraction using water, such as hot water or steam) of animal organs, animal tissues, or animal secretions. Used in the cultivation of microorganisms. Carrine Blank microbiological medium ingredient, derived from extracts of microbial organisms Undefined mixtures of complex organic compounds deriving from the aqueous extraction (an extraction using water, such as hot water or steam) of microbial (prokaryotic or microbial eukaryotic) cells. Used in the cultivation of microorganisms. Carrine Blank microbiological medium ingredient, derived from oil Undefined mixtures of complex organic compounds derived from hydrophobic substances including lipids, fatty acids, and triacylglycerols, derived from the chemical or physical extraction of oil from an organism, the part of an organism, or a naturally occurring substance (such as crude oil). Carrine Blank microbiological medium ingredient, derived from extracts of proteinaceous material An undefined mixture of complex organic compounds (peptides, sometimes with additional undefined vitamins and cofactors) derived from enzymatic, acid, or base digests of protein from plant or animal sources. Used in the cultivation of microorganisms. Carrine Blank microbiological medium ingredient, derived from chemical hydrolysis of protein Undefined mixtures of complex organic compounds derived (typically amino acids) from the acid hydrolysis of animal or plant protein added to culture media. Carrine Blank microbiological medium ingredient, derived from enzymatic hydrolysis of protein BD Bionutrients Technical Manual (3rd edition revised). Carrine Blank Protein hydrolysates, also called peptones, are the result of the enzymatic hydrolysis of protein. Trypticase peptone Biotrypticase Trademarked commercial name for pancreatic digest of casein (milk protein from cow's milk, Bos taurus), used for the culturing of microorganisms. Reference for Bio-trypticase: "Rapport de Mission au Centre National de l'Elevage et de Recherches Veterinaires de Nouakchott du 12/07 au 02/08/1999"; Institute Senegalais de Recherches Agricoles. Retired name for "peptone pancreatique du caseine"; produced by Bio-Merieux (www.biomerieux.com) or Oxoid (www.remel.com/Microbiology). From BD Bionutrients Technical Manual (3rd edition revised): BBL™ Trypticase™ Peptone is a pancreatic digest of casein and is the primary nitrogen source in Trypticase Soy Broth and Agar. Ash content is 5.7% NaCl content is 0.1% Carrine Blank TrypticaseTM Peptone bio-trypticase Trypticase meat peptone An enzymatic hydrolysis of meat (muscle tissue) proteins from mixed animal (mammalian) sources, used for the culturing of microorganisms. From BD Bionutrients Technical Manual (3rd edition revised): Meat peptones are proteins from animal sources that have been hydrolyzed, or broken down into amino acids and peptides, to provide nitrogen for microorganisms. Meat peptones can be tailored to specific nutritive needs of microorganisms by controlling the quality and origin of the protein, the quality and source of the enzyme used to digest the protein, and the methods used for hydrolysis, concentration and drying the peptone. Peptone manufacture methods are discussed in the section titled Hydrolysis to Hydrolysate. Sources of animal protein include meat from muscle tissue or offal (waste parts, entrails) and gelatin. Muscular tissue and offal are utilized fresh, frozen or dried. Gelatin is extracted by boiling collagen, the fibrous protein found in connective tissue, bone and cartilage. A variety of proteolytic enzymes, or proteases, may be used to accomplish enzymatic hydrolysis of animal protein. Pepsin and trypsin are widely used for animal peptone manufacture. Pepsin is isolated from porcine or other animal stomach. Trypsin, along with chymotrypsin, carboxypeptidase A, carboxypeptidase B, and elastase, are enzymes isolated from animal pancreas. Carrine Blank neopeptone Carrine Blank From BD Bionutrients Technical Manual (3rd edition revised): Bacto™ Neopeptone is an enzymatic digest of protein. Neopeptone contains a wide variety of peptide sizes in combination with vitamins, nucleotides and minerals. Ash content is 6.9% NaCl content is 1.4% An enzymatic digest of meat, used for the culturing of microorganisms. peptone An enzymatic digest of animal (mammalian) protein (of unspecified orgin), used for the culturing of microorganisms. From BD Bionutrients Technical Manual (3rd edition revised).: Bacto™ Peptone is an enzymatic digest of animal protein. Bacto Peptone was first introduced in 1914 and became the standard Peptone for the preparation of bacteriological culture media. The nutritive value of Bacto Peptone is largely dependent on the amino acid content that supplies essential nitrogen. Bacto Peptone contains only a negligible quantity of proteoses and more complex constituents. Ash content is 6.9% NaCl content is 1.7% Carrine Blank Bacto-peptone Bacto Peptone polypeptone Carrine Blank A mixture of peptones (pancreatic digest of casein and peptic digest of animal/mammalian tissue - meat), used for the culturing of microorganisms. From BD Bionutrients Technical Manual (3rd edition revised).: BBL™ Polypeptone™ Peptone is a mixture of peptones made up of equal parts of pancreatic digest of casein and peptic digest of animal tissue. Polypeptone Peptone includes the high content of amino acids and small polypeptides characteristic of pancreatic digest of casein and the larger polypeptides characteristic of peptic digest of animal tissue. Ash content is 9.7% NaCl content is 2.7% Proteose Peptone From BD Bionutrients Technical Manual (3rd edition revised). The Bacto™ Proteose Peptones are enzymatic digests of protein. Studies of peptic digests of animal tissue prepared under varying digestion parameters led to the development of Proteose Peptone, Proteose Peptone No. 2 and Proteose Peptone No. 3. Data accumulated during these studies demonstrated that no one peptone is the most suitable nitrogen source for every microbiological application. Bacto Proteose Peptone No. 4 is a spray-dried version of Bacto Proteose Peptone. BiTek™ Proteose Peptone and BiTek Proteose Peptone No. 3 are enzymatic digests of protein, developed to offer alternatives to the Bacto Proteose Peptones for scale-up to production applications. Ash content is 7.8% NaCl content is 4.9% Peptic digest of animal tissue A peptic digest of protein derived from animal (mammalian) tissue, used for the culturing of microorganisms. meat peptic digest Carrine Blank Bacto(TM) Proteose Peptone soy peptone A mixed enzymatic digest of flour made of the seed of the soybean (Hordeum vulgare), used for the culturing of microorganisms. Bacto™ Soytone papaic digest of soybean soytone Carrine Blank From BD Bionutrients Technical Manual (3rd edition revised): Enzymeatic digests of soy flour. Soy contains several heat labile protease inhibitors. The most common way of eliminating these factors is to heat or toast the defatted soy beans in a processing plant under controlled conditions. Soy flour, the principle substrate in a soy peptone, is rich in high-quality protein, carbohydrates, calcium and B vitamins. The enzymes used in the digestion of soy flour are typically from animal-free sources or from microorganisms that have been grown in animal-free media. Ash content is 12% NaCl content is 0.2% tryptone Proteose Tryptone Bacto-Tryptone From: Wikipedia:Tryptone Tryptone is the assortment of peptides formed by the digestion of casein by the protease trypsin. An enzymatic hydrolysate of casein (a milk protein from cow's milk, Bos taurus) made using the hydrolytic enzyme trypsin, used for the culturing of microorganisms. Carrine Blank From BD Bionutrients(TM) Techical Manual (3rd edition, revised): Bacto™ Tryptone is a pancreatic digest of casein. It was developed by Difco Laboratories while investigating a peptone particularly suitable for the elaboration of indole by bacteria. It is also notable for the absence of detectable levels of carbohydrates. Ash content is 6.6% NaCl content is 0.0% Bacto Tryptone tryptose From BD Bionutrients Technical Manual (3rd edition revised).: Bacto™ Tryptose is a mixed enzymatic hydrolysate with distinctive nutritional properties. The digestive process of Tryptose results in assorted peptides of higher molecular weight suitable for long-chain amino acid requirements. Ash content is 8.8% NaCl content is 3.2% Carrine Blank A mixed enzymatic hydrolysate of protein (animal meat of unspecified origin), used for the cultivation of microorganisms. casamino acids From BD Bionutrients Technical Manual (3rd edition revised): Bacto™ Casamino Acids is an acid hydrolysate of casein, prepared according to the method described by Mueller and Miller. The method described, reduces the sodium chloride and iron content of the hydrolyzed casein. This hydrolyzed casein, supplemented with inorganic salts, growth factors, cystine, maltose and an optimum amount of iron was used by Mueller and Miller to prepare diptheria toxin. Bacto Casamino Acids duplicate this specially treated hydrolyzed casein. Ash content is 18.3% NaCl content is 12.1% Casein Hydrolysate acid digest of casein Carrine Blank An acid hydrolysate of casein (milk protein from cow's milk, Bos taurus), used for the culturing of microorganisms. crude oil A complex mixture of unrefined petrolium hydrocarbons, pumped from subsurface geologic formations, used in the cultivation of microorganisms. Carrine Blank egg yolk oil Carrine Blank From Wikipedia: Yolk: The yolk of one large egg (50 g total, 17 g yolk) contains approximately: 2.7 g protein, 210 mg cholesterol, 0.61 g carbohydrates, and 4.51 g total fat. All of the fat-soluble vitamins (A, D, E, and K) are found in the egg yolk. Egg yolk is one of the few foods naturally containing vitamin D. The composition (by weight) of the most prevalent fatty acids in egg yolk is typically as follows: Unsaturated fatty acids: Oleic acid, 47% Linoleic acid, 16% Palmitoleic acid, 5% Linolenic acid, 2% Saturated fatty acids: Palmitic acid, 23% Stearic acid, 4% Myristic acid, 1% Oil extracted from yolk of chicken eggs, used in the cultivation of microorganisms. disproportionation of thiosulfate The process by which thiosulfate undergoes disproportionation to sulfate and hydrogen sulfide. Carrine Blank olive oil Carrine Blank Oil extracted from olives (the fruit of Olea europaea), used in the cultivation of microorganisms. From Wikipedia:Olive_oil: Olive oil is a fat obtained from the olive (the fruit of Olea europaea; family Oleaceae), a traditional tree crop of the Mediterranean Basin. The oil is produced by pressing whole olives. Olive oil is composed mainly of the mixed triglyceride esters of oleic acid and palmitic acid and of other fatty acids, along with traces of squalene (up to 0.7%) and sterols (about 0.2% phytosterol and tocosterols). xxxx Carrine Blank archaea cell extract An extract made from archaeal cells, used for culturing microorganisms. Carrine Blank bacterial cell extract An extract made from bacterial cells, used for culturing microorganisms. Carrine Blank beef heart infusion From http://www.oxoid.com/UK/blue/prod_detail/prod_detail.asp?pr=CM1032&cat=&sec=1: Heart Infusion Broth has been developed to give the same performance characteristics as Brain Heart Infusion (BHI) Broth. However, as bovine brain is a specified risk material, the exclusion of it from the Heart Infusion Broth means that the regulatory requirements when using it are lower. The medium has been developed to give equivalent performance to Brain Heart Infusion but the exclusion of calf brain infusion means that Heart Infusion Broth carries a lower regulatory burden. Simple additions may be made to the medium to make it suitable for the cultivation of yeasts and moulds and for use in blood culture. A highly nutritious infusion medium recommended for the cultivation of streptococci, pneumococci, meningococci and other fastidious organisms. heart infusion Carrine Blank A water extract of bovine (Bos taurus) heart, used in the cultivation of microorganisms. bovine heart infusion brain heart infusion From Wikipedia:Brain_heart_infusion_broth: Brain-heart infusion broth (BHI broth or BHIB) is a highly nutritious general-purpose growth medium for culturing fastidious and nonfastidious microorganisms, such as streptococci, pneumococci and meningococci. It is made by boiling cow or porcine hearts and brains. Boiling releases soluble factors into the broth. The broth can then be turned into powder for easy distribution. BHI broth contains sodium chloride which is used to differentiate enterococci from nonenterococcal group D streptococci. BHI broth is often used in food safety, water safety, and antibiotic sensitivity tests. Carrine Blank Hot water extract of bovine (Bos taurus) or porcine (Sus scrofa) hearts and brains, used in the cultivation of microorganisms. Chlorella cell extract Carrine Blank An extract made from cellular paste from the culture of Chlorella spp., used for the culturing of microorganisms. Chlorella is a microscopic green alga in the Trebouxiophyceae. fecal extract From "Materials and Methods in the Study of Protozoa", pg. 21, by Harold Kirby, University of California Press, 1950: "One part of caecal contents is mixed with 9 parts of Ringer solution, and the mixture strained through a sieve and then through a funnel with a thick pad of absorbent cotten." Carrine Blank A water extract of fecal material derived from some animal (mammal), used in the cultivation of microorganisms. malt extract From BD Bionutrients Technical Manual (3rd edition revised): Bacto™ Malt Extract is the water-soluble portion of malted barley. The extraction process breaks down the polysaccharides into simple sugars. After the malting process is complete, the extract is prepared from the malted barley by cracking the grain in a mill and then extracting the grain with a warm liquor. The resulting “wort” is filtered and evaporated or dried under vacuum. Ash content is 0.3% NaCl content is 0.2% Water-soluble extract of malted (i.e. germinated) seeds of barley (Hordeum vulgare), used for the culturing of microorganisms. Prepared by malting the seed, cracking it (grinding) using a mill, heating it in water, then filtering the extract and drying it. Carrine Blank horse manure extract Carrine Blank manure extract A water extract of horse (Equus caballus) manure, used for the culturing of microorganisms. From "Report of the New York State College of Agriculture at Cornell University, Ithaca, and of the Cornell University Agricultural Experiment Station", v. 25, Part 1, 1913, pg. 431: Manure extract agar. - Prepared as follows: To 100 grams of well-rotted horse manure was added 500 cc. of distilled water. This was allowed to stand for twenty-four hours at room temperature and then filtered. The filtrate was used as a stock solution. meat extract A water extract of animal (mammalian) meat, used for the culturing of microorganisms. From Wikipedia:Meat_extract: Meat extract is highly concentrated meat stock, usually made from beef. Carrine Blank pine needle extract From Jeaon, J-R & Kim, J-Y. 2006. Effects of pine needle extract on differentiation of 3T3-L1 preadipocytes and obesity in high-fat diet fed rats. Biol. Pharm. Bull. 29(10):2111-2115: Pine needles were collected from Kyungbook Province, Republic of Korea, and were extracted using 20 kg of water for 2 h at 80 °C. The extract was filtered, and was then freeze-dried at 40 °C. Pine needle water extract (PNE) was stored at 4 °C until use. A hot water extract of pine needles (the adult leaves of Pinus spp.), used for the culturing of microorganisms. Formed as result of heating pine needles in warm water, filtering the extract and then drying it. Carrine Blank soya extract From Roubos-van den Hil, Dalmas, Nout & Abee. 2009. Soya bean tempe extracts show antibacterial activity against Bacillus cerus cells and spores. J. Appl. MIcrobiol. 109(1):137-145: Fermented soya beans (tempe) and cooked soya beans, were freeze-dried and grounded passing through a 0·5-mm sieve (Ultra Centrifugal Mill ZM 200, Retsch GmbH, Haan, Germany) and were stored at −20°C until further processing. Freeze-dried products were suspended in distilled water (60 g l−1) and stirred with a magnetic stirrer for 3 h at room temperature. The pH was continually checked and adjusted to pH 8·0 with 1 mol l−1 NaOH. To obtain clear supernatants, the soluble extract was obtained by three consecutive centrifugation steps (10 min, 10 000 g, 20°C). Supernatants were freeze-dried and soluble dry matter was stored at −20°C and used as soya bean soluble dry matter in experiments. A water extract of ground beans (the seed) of soya (Glycine max), used for the culturing of microorganisms. Formed by fermenting the beans, heating (cooking) them, filtering the material and freeze dyring it. Next, the material is hydrated, treated with sodium hydroxide, centrifuged and freeze-dried. Soybean extract Soy extract Soya bean extract Carrine Blank yeast extract Yeast extrakt From www.SigmaAldrich.com: A water soluble extract of autolyzed yeast cells. Yeast extract is a mixture of amino acids, peptides, water soluble vitamins and carbohydrates and can be used as additive for culture media. A water-soluble extract of autolyzed yeast (Saccharomyces cerevisiae), used for the culturing of microorganisms. Carrine Blank From BD Bionutrients Technical Manual (3rd edition revised): Bacto™ Yeast Extract is one of the most complete and versatile fermentation bionutrients available. It is an important ingredient for the microbiological assay of vitamins. Yeast extract is also of value in the assay of antibiotics. B factor, a growth substance necessary for the production of rifampin in a Nocardia sp., can be isolated from yeast extract Ash content is 11.2% NaCl content is 0.1% Yeastrel beef extract A water extract of beef (Bos taurus) protein, used for the culturing of microorganisms. beef infusion Carrine Blank From BD Bionutrients Technical Manual (3rd edition revised).: Beef Extract is derived from infusion of beef and provides an undefined source of nutrients. Beef Extract is not exposed to the harsh treatment used for protein hydrolysis, so it can provide some of the nutrients lost during peptone manufacture. Beef Extract is a mixture of peptides and amino acids, nucleotide fractions, organic acids, minerals and some vitamins. “Its function can therefore be described as complementing the nutritive properties of peptone by contributing minerals, phosphates, energy sources and those essential factors missing from peptone.” Beef Extract Powder is a meat extract dried to powder form. Bacto™ Beef Extract, Desiccated, is the dried form of Beef Extract paste. Ash content is 9.3% NaCl content is 0.3% Gram stain assay Cell staining assay where a cell staining assay, performed by staining a smear of prokaryotic cells with two stains (Crystal Violet or Safranin). Delineates prokaryotes into two major groups (Gram positive and Gram negative, although results can be ambiguous in some taxa) that results from the different staining of cell wall types. Wikipedia:Gram_staining Gram staining, also called Gram's method, is a method of differentiating bacterial species into two large groups (gram-positive and gram-negative). The name comes from the Danish bacteriologist Hans Christian Gram, who developed the technique. Gram staining differentiates bacteria by the chemical and physical properties of their cell walls by detecting peptidoglycan, which is present in a thick layer in gram-positive bacteria.[1] In a Gram stain test, gram-positive bacteria retain the crystal violet dye, while a counterstain (commonly safranin or fuchsine) added after the crystal violet gives all Gram-negative bacteria a red or pink coloring. Carrine Blank zzzz has_participant some [ChEBI] safranin - Safranin is not in ChEBI yet. morphologically distinct prokaryotic cell A prokaryotic cell, or group of cells, having a distinct morphology (shape or size). Carrine Blank prokaryotic colony quality Carrine Blank Physical object quality of a prokaryotic colony. triple sugar iron agar TSI An organic-rich, liquid microbiological culture medium that contains peptones, three sugars (glucose, lactose, and sucrose), ferric iron, thiosulfate, and phenol red (a pH indicator). If the sugars are fermented, the pH indicator will turn red indicating a lowered pH. If hydrogen sulfide is produced, the ferric iron will be reduced to ferrous sulfide, producing a black color. From: http://www.microbelibrary.org/component/resource/laboratory-test/2842-triple-sugar-iron-agar-protocols RECIPE Pancreatic digest of casein USP (see Note) 10.0 g Peptic digest of animal tissue USP (see Note) 10.0 g Glucose 1.0 g Lactose 10.0 g Sucrose 10.0 g Ferrous sulfate or ferrous ammonium sulfate 0.2 g NaCl 5.0 g Sodium thiosulfate 0.3 g Phenol red 0.024 g Agar 13.0 g Distilled water 1,000 mL Note: The following combination of ingredients can substitute for the first two components listed: beef extract, 3.0 g; yeast extract, 3.0 g; and peptone, 20.0 g. Combine ingredients, and adjust the pH to 7.3. Boil to dissolve the agar, and dispense into tubes. Sterilize by autoclaving at 121°C for 15 min. Cool in a slanted position to give a 2.5-cm butt and a 3.8-cm slant. Carrine Blank triple sugar iron agar TSIA Carrine Blank Triple sugar iron agar An organic-rich, solid microbiological culture medium that contains peptones, three sugars (glucose, lactose, and sucrose), ferric iron, thiosulfate, and phenol red (a pH indicator). If the sugars are fermented, the pH indicator will turn red indicating a lowered pH. If hydrogen sulfide is produced, the ferric iron will be reduced to ferrous sulfide, producing a black color. From:http://www.microbelibrary.org/component/resource/laboratory-test/2842-triple-sugar-iron-agar-protocols RECIPE Pancreatic digest of casein USP (see Note) 10.0 g Peptic digest of animal tissue USP (see Note) 10.0 g Glucose 1.0 g Lactose 10.0 g Sucrose 10.0 g Ferrous sulfate or ferrous ammonium sulfate 0.2 g NaCl 5.0 g Sodium thiosulfate 0.3 g Phenol red 0.024 g Agar 13.0 g Distilled water 1,000 mL Note: The following combination of ingredients can substitute for the first two components listed: beef extract, 3.0 g; yeast extract, 3.0 g; and peptone, 20.0 g. Combine ingredients, and adjust the pH to 7.3. Boil to dissolve the agar, and dispense into tubes. Sterilize by autoclaving at 121°C for 15 min. Cool in a slanted position to give a 2.5-cm butt and a 3.8-cm slant. macroscopic optical quality assay An optical quality assay of a single prokaryotic cell, determined by visualization of a liquid culture of a prokaryotic microorganism (i.e., a clonal liquid suspension in a liquid culture medium). Carrine Blank pigmented cell Carrine Blank A prokaryotic cell that is pigmented (in that it has a color imparted by a chemical pigment compound). N-benzoyl-L-leucine peptidase activity Carrine Blank An aminopeptidase activity which cleaves the chromogenic substrate N-benzoyl-L-leucine-beta-naphthylamide. opalescent turbidity irridescent Carrine Blank irridescence opalescence The optical quality of a liquid culture of clonal prokaryotic organisms, which exhibits opalescent turbidity (refracting different wavelengths of light under white light illumination, or iridescence) after gentle shaking. tyrosine agar Carrine Blank From: http://www.atcc.org/~/media/DF06C418BB3A44189AD1A3CEB59B8D6E.ashx ATCC Medium: 1776 Tyrosine Agar (ISP Medium 7) Glycerol 15.0 g L-Tyrosine 0.5 g L-Asparagine 1.0 g K2HPO4 0.5 g MgSO4x7H2O 0.5 g NaCl 0.5 g FeSO4x7H2O 10.0 mg Trace elemetns solution Ho-Le (see below) 1.0 mL Agar 20.0 g Distilled water 1.0 L Adjust medium for final pH 7.3 +/- 0.1. Autoclave at 121C for 15 minutes. Trace Elements Solution Ho-Le: H3BO3 2.85 g MnCl2x4H2O 1.8g FeSO4 1.36 g Sodium tartrate 1.77 g CuCl2x2H2O 26.9 mg ZnCl2 20.8 mg CoCl2x6H2O 40.4 mg Na2MoO4x2H2O 25.2 mg Distilled water 1.0 L L-tyrosine agar An organic-rich, mineral-salts, solid microbiological culture medium containing glycerol, tyrosine, asparagine, and minerals salts. Used for the growth of Streptoalloteichus. endospore Carrine Blank sporulating spore-forming From Wikipedia:endospore: An endospore is a dormant, tough, and non-reproductive structure produced by certain bacteria from the Firmicute phylum. The name "endospore" is suggestive of a spore or seed-like form (endo means within), but it is not a true spore (i.e., not an offspring). It is a stripped-down, dormant form to which the bacterium can reduce itself. Endospore formation is usually triggered by a lack of nutrients, and usually occurs in Gram-positive bacteria. In endospore formation, the bacterium divides within its cell wall. One side then engulfs the other. Endospores enable bacteria to lie dormant for extended periods, even centuries. Revival of spores millions of years old has been claimed. When the environment becomes more favorable, the endospore can reactivate itself to the vegetative state. Most types of bacteria cannot change to the endospore form. Examples of bacteria that can form endospores include Bacillus and Clostridium. A differentiated prokaryotic cell, found in the Firmicutes, which is specialized for extreme tolerance to desiccation, radiation, and exposure to ultraviolet light. Characterized by thick cell walls. spore-former gas vacuole Wikipedia:bacterial_cell_structure Gas vacuoles are membrane-bound, spindle-shaped vesicles, found in some planktonic bacteria and Cyanobacteria, that provides buoyancy to these cells by decreasing their overall cell density. Positive buoyancy is needed to keep the cells in the upper reaches of the water column, so that they can continue to perform photosynthesis. They are made up of a shell of protein that has a highly hydrophobic inner surface, making it impermeable to water (and stopping water vapour from condensing inside) but permeable to most gases. Because the gas vesicle is a hollow cylinder, it is liable to collapse when the surrounding pressure becomes too great. aerotopes gas vesicles vacuolized gas vacuole gas-vacuolated An intracellular non-membran-bound organelle (cytoplasmic vesicle) made of protein which functions to provide buoyancy to the cell in the water column. Carrine Blank intracellular granule Cytoplasmic part which forms a distinctive granular particle, which may or may not be visible using light microscopy. granule granulated globule granular central granule intracellular globule Wikipedia:granule_(cell biology) In cell biology, a granule is a small particle. It can be any structure barely visible by light microscopy. Carrine Blank granulated magnetosome Wikipedia:magnetosome Magnetosome chains are membranous prokaryotic structures present in magnetotactic bacteria. They contain 15 to 20 magnetite crystals that together act like a compass needle to orient magnetotactic bacteria in geomagnetic fields, thereby simplifying their search for their preferred microaerophilic environments. Each magnetite crystal within a magnetosome is surrounded by a lipid bilayer, and specific soluble and transmembrane proteins are sorted to the membrane. Recent research has shown that magnetosomes are invaginations of the inner membrane and not freestanding vesicles. Magnetite-bearing magnetosomes have also been found in eukaryotic magnetotactic algae, with each cell containing several thousand crystals. Carrine Blank Intracellular membrane-bound organelle that form chains, comprised of magnetic iron minerals that function to orient the cell axis along the Earth's magnetic field lines. Found in magnetotactic prokaryotes. isopolar subsymmetric An isopolar trichome morphology quality where heterocysts are rarely present along the length of the trichome such that the trichome morphology is asymmetric. Carrine Blank xylose minimal medium XeMM From:Humphry DR, George, A, Black GW, Cumming& s SP. 2001. Flavobacterium frigidarium sp. nov., an aerobic, psychrophilic, xylanolytic and laminarinolytic bacterium from Antarctica. IJSEM 51:1235-1243. Minimal medium (MM) containing the following (w/v): 0.02% FeSO4, 0.02% MgSO4, 0.075% KNO3, 0.05% K2HPO4 and 0.004% CaCl2. The pH was adjusted to 7.2 with 1 M NaOH or 1M HCl. A mineral-salts, liquid microbiological culture medium comprised of ferrous sulfate, magnesium sulfate, potassium nitrate, potassium phosphate, and calcium chloride, supplemented with 0.5% w/v xylose. Used for the cultivation of Flavobacterium frigidarium. Carrine Blank dispersed thylakoids irregular thylakoids Thylakoid-containing cell where thylakoids are dispered irregularly (asymmetrically) throughout the interior of the cell. dispersed thylakoids Carrine Blank parietal thylakoids peripherally stacked thylakoid radially arranged thylakoids concentrically arranged thylakoids concentric thylakoid membranes Carrine Blank Thylakoid-containing cell where thylakoids are located around the inside periphery of the interior of the cell. parietal thylakoids radial thylakoids radial thylakoids Carrine Blank Thylakoid-containing cell where thylakoids are distributed throughout the inside of the cell and have a radial (like spokes on a wheel) arrangement. greigite magnetosome Carrine Blank Intracellular membrane-bound organelle that form chains, comprised of magnetic iron minerals made of greigite that function to orient the cell axis along the Earth's magnetic field lines. Found in magnetotactic prokaryotes. Wikipedia:magnetosome Magnetotactic bacteria usually mineralize either iron oxide magnetosomes, which contain crystals of magnetite (Fe3O4), or iron sulfide magnetosomes, which contain crystals of greigite (Fe3S4). magnetite magnetosome Intracellular membrane-bound organelle that form chains, comprised of magnetic iron minerals made of magnetite that function to orient the cell axis along the Earth's magnetic field lines. Found in magnetotactic prokaryotes. Wikipedia:magnetosome Magnetotactic bacteria usually mineralize either iron oxide magnetosomes, which contain crystals of magnetite (Fe3O4), or iron sulfide magnetosomes, which contain crystals of greigite (Fe3S4). Carrine Blank granulated cell Carrine Blank A prokaryotic cell which has intracellular granules. gas vacuole quality A prokaryotic cell part quality that has gas vacuoles (gas vesicles). Carrine Blank intracellular carbon storage granule Carrine Blank An intracellular granule that is specialized for the storage of carbon. intracellular nitrogen storage granule An intracellular granule that is specialized for the storage of nitrogen. Carrine Blank intracellular phosphorus storage granule An intracellular granule that is specialized for the storage of nitrogen. Carrine Blank intracellular sulfur granule intracellular sulfur globule Intracellular granule composed of elemental sulfur. sulfur globule sulphur granule Wikipedia:Chromatiaceae The Chromatiaceae are the main family of purple sulfur bacteria. Many members conduct an anoxygenic photosynthesis. They are distinguished from the Ectothiorhodospiraceae by producing sulfur globules and storing them within their cells. sulphur globule Carrine Blank intracellular sulphur globule cell having small gas vacuole small gas vacuole A gas vacuolated cell, were gas vacuoles are small (decreased) in size. small vesicles Carrine Blank small vacuole cell having large gas vacuole large vacuole A gas vacuolated cell, were gas vacuoles are large (increased) in size. Carrine Blank large vesicles large gas vacuole gas vacuolated cell vacuolated vesicles vaculoes Carrine Blank vesiculated A prokaryotic cell that has gas vacuoles (gas vesicles). polyphosphate granule volutin granule metachromatic granule Intracellular phosphorus storage granule composed of polyphosphate. Wikipedia:volutin_granules Volutin granules are an intracytoplasmic (inside the cytoplasm of a cell) storage form of complexed inorganic polyphosphate, the production of which is used as one of the identifying criteria when attempting to isolate Corynebacterium diphtheriae on Löffler's medium. Polyphosphate granules are called metachromatic granules due to their displaying the metachromatic effect; they appear red or blue when stained with the blue dyes methylene blue or toluidine blue. Carrine Blank cyanophycin granule Wikipedia:cyanophycin Cyanophycin, or multi-L-arginyl-poly (L-aspartic acid), is a non-protein, non-ribosomally produced amino acid polymer composed of an aspartic acid backbone and arginine side groups. Carrine Blank Intracellular carbon and nitrogen storage granule composed of cyanophycin macromolecules. yeast water medium Filippini M, Svercel M, Laczko E, Kaech A, Ziegler U & Bagheri HC. 2011. Fibrella aestuarina gen. nov., sp. nov., a filamentous bacterium of the family Cytophagaceae isolated from a tidal flat, and emended description of the genus Rudanella Weon et al. 2008. IJSEM 61:184-189. 0.5% yeast water Carrine Blank An organic-rich, liquid microbiological culture medium consisting of a solution of yeast extract (0.5%) in water. From: Filippini M, Kaech A, Ziegler U & Bagheri HC. 2011. Fibrisoma limi gen. nov., sp. nov., a filamentous bacterium isolated from tidal flats. IJSEM 61:1418-1424. 0.5% yeast water poly-beta-hydroxyalkanoate granule Carrine Blank Wikipedia:polyhydroxyalkanoates Polyhydroxyalkanoates or PHAs are linear polyesters produced in nature by bacterial fermentation of sugar or lipids. They are produced by the bacteria to store carbon and energy. More than 150 different monomers can be combined within this family to give materials with extremely different properties. These plastics are biodegradeable and are used in the production of bioplastics. PHA polyhydroxyalkanoate Intracellular carbon storage granule composed of poly-beta-hydroxyalkanoate. poly-beta-hydroxybutyric acid granule polyhydroxybutyric acid Intracellular carbon storage granule composed of poly-beta-hydroxybutyrate. Carrine Blank PHB polyhydroxybutyrate poly-beta-hydroxybutyrate Wikipedia:polyhydroxybutyrate Polyhydroxybutyrate (PHB) is a polyhydroxyalkanoate (PHA), a polymer belonging to the polyesters class that are of interest as bio-derived and biodegradable plastics. The poly-3-hydroxybutyrate (P3HB) form of PHB is probably the most common type of polyhydroxyalkanoate, but other polymers of this class are produced by a variety of organisms: these include poly-4-hydroxybutyrate (P4HB), polyhydroxyvalerate (PHV), polyhydroxyhexanoate (PHH), polyhydroxyoctanoate (PHO) and their copolymers. starch granule starch Intracellular carbon storage granule composed of starch. Carrine Blank coursely granulated course granules large granule Carrine Blank Granulated cell, where the granual size is coarse (has an increased size). finely granulated fine granules Carrine Blank Granulated cell, where the granule size is fine (has a decreased size). numerously granulated 2 numerous granules Granulated cell, where there are many granules (an increased number) per cell. Carrine Blank singularly granulated 1 single granule solitary granules Granulated cell, where there are one granule per cell. Carrine Blank singular granule central endospore Carrine Blank An endospore that forms in the middle of the cell. lateral endospore Carrine Blank An eEndospore that forms laterally to the long axis of a cell. subterminal endospore Carrine Blank An endospore that forms near the ends (or the poles) of the cell, but not at the extreme ends of the cell. terminal endospore Carrine Blank An endospore that forms at the pole (end) of the cell. filaments Amorphously described generic term for filament- or pili-like structures. tuft of filaments pili-like structures Carrine Blank akinete Carrine Blank A differentiated prokaryotic cell, found in the Nostocales (Cyanobacteria), which play a role in dormancy (such as overwintering in lake sediments). Characterized by thick cell walls. From Wikipedia:akinete: An akinete is a thick-walled dormant cell derived from the enlargement of a vegetative cell. It serves as a survival structure. It is a resting cell of cyanobacteria and unicellular and filamentous green algae. Under magnification, akinetes appear thick walled with granular-looking cytoplasms. akinete, adjacent to heterocyte akinetes adjacent to heterocysts Rippka, Castenholz & Herdman, 2001, in Bergeys Manual of Systematic Bacteriology, v. 1, 2nd ed., pg 563. An akinete which is proximally located to a heterocyst. paraheterocytic Carrine Blank akinete, distal to heterocyte Carrine Blank apoheterocytic An akinete that isdistally located from the heterocytes. May occur multiply in chains that, in the absence of combined nitrogen, are initiated at a site that is equidistant from two intercalary or terminal heterocysts. akinetes distant from heterocysts Rippka, Castenholz & Herdman, 2001, in Bergeys Manual of Systematic Bacteriology, v. 1, 2nd ed., pg 563. yeast extract tryptone medium Carrine Blank YT YT broth An organic-rich, liquid microbiological culture medium containing pancreatic digest of casein, yeast extract, and sodium chloride. Used for the cultivation of Escherichia coli. From: 2x Yeast Extract Tryptone (2X YT) Medium (Becton-Dickinson Difco and BBL Manual of Microbiological Culture Media, 2nd edition): Intended Use 2x YT Medium is used for cultivating recombinant strains of Escherichia coli. Principles of the Procedure Peptone and yeast extract provide the necessary nutrients and cofactors required for excellent growth of E. coli. Sodium chloride is included to provide a suitable osmotic environment. 2x YT Medium formula per Liter: Pancreatic digest of casein 16.0 g Yeast extract 10.0 g Sodium chloride 5.0 g pH 7.0 ± 0.2 yeast extract tryptone agar Carrine Blank An organic-rich, solid microbiological culture medium containing pancreatic digest of casein, yeast extract, and sodium chloride. Used for the cultivation of Escherichia coli. From: 2x Yeast Extract Tryptone (2X YT) Medium (Becton-Dickinson Difco and BBL Manual of Microbiological Culture Media, 2nd edition): Intended Use 2x YT Medium is used for cultivating recombinant strains of Escherichia coli. Principles of the Procedure Peptone and yeast extract provide the necessary nutrients and cofactors required for excellent growth of E. coli. Sodium chloride is included to provide a suitable osmotic environment. 2x YT Medium formula per Liter: Pancreatic digest of casein 16.0 g Yeast extract 10.0 g Sodium chloride 5.0 g Agar pH 7.0 ± 0.2 YT agar Todd-Hewitt medium Carrine Blank Todd-Hewitt broth Todd Hewitt Broth From: http://www.neogen.com/Acumedia/pdf/ProdInfo/7161_PI.pdf Intended Use Todd Hewitt Browth is used for the cultivation of steptococci and other fastidious microorganisms. Formula / Liter: Heart infusion (dehydrate) 3.1 g Yeast enriched peptone 20 g Dextrose 2 g Sodium chloride 2 g Disodium phosphate 0.4 g Sodium carbonate 2.5 g Final pH: 7.8 +/- 0.2 at 25˚C. Directions: 1. Dissolve 30 g of the medium in one liter of purified water. 2. Heat with frequent agitation to compeltely dissolve the medium. 3. Autoclave at 121 ˚C for 15 minutes. An organic-rich, liquid microbiological culture medium containing heart infusion (beef heart infusion), yeast enriched peptone (Biosate peptone), dextrose (D-glucose), sodium chloride, disodium hydrogenphosphate, and sodium carbonate. Used for the cultivation of Streptococci. sheath sheath Carrine Blank mucilaginous slime mucilage Castenholz, 2001, in Bergey's Manual of Systematic Bacteriology, vol 1, 2nd ed., pg. 474. An "envelope" outside of the outer membrane.... variously called the sheath, glycocalyx, or capsule, or depending on the consistency, may be referred to as gel, mucilage, or slime. Many sheaths show a microfibrillar substructure. The sheaths of cyanobacteria are predominantly composed of polysaccharide, but in some strains >20% of the weight may consist of polypeptides. ... pigments may accumulate and mask the color of the cells. capsule extracellular polymeric material Part of the glycocalyx, or envelope of a prokaryotic cell, that lies outside the outer membrane. gel gelatinous matrix mucous extracellular polymeric substance ensheathed EPS exopolysaccharide laminated sheath layered sheath striated steath lamillated sheath A sheath having a layered, laminated (i.e., laminar) structure. striated sheathed structure Carrine Blank pigmented sheath A sheath that is pigmented (contains pigmented compounds). colored sheath Carrine Blank proteinaceous sheath A sheath comprised largely of protein. Carrine Blank tryptone glucose extract agar Carrine Blank From: Tryptone Glucose Extract Agar (Becton-Dickinson Difco and BBL Manual of Microbiological Culture Media, 2nd edition): Intended Use Tryptone Glucose Extract Agar is used for cultivating and enumerating microorganisms in water and dairy products. Principles of the Procedure Nutrients, including amino acids, carbon compounds, carbohydrates, minerals and trace substances, are supplied by the tryptone, beef extract and dextrose. Agar is the solidifying agent in Tryptone Glucose Extract Agar. Formulae Difco™ Tryptone Glucose Extract Agar Approximate Formula* Per Liter Beef Extract.................................................................. 3.0 g Tryptone...................................................................... 5.0 g Dextrose (Glucose)....................................................... 1.0 g Agar.......................................................................... 15.0 g pH 7.0 ± 0.2 Difco™ m TGE Broth Approximate Formula* Per Liter Beef Extract.................................................................. 6.0 g Tryptone.................................................................... 10.0 g Dextrose (Glucose)....................................................... 2.0 g *Adjusted and/or supplemented as required to meet performance criteria. pH 7.0 ± 0.2 An organic-rich, solid microbiological culture medium containing beef extract, tryptone, and glucose. Used for cultivation of microorganisms from water and dairy products. TGE agar pseudopeptidoglycan-based cell wall pseudomurein Wikipedia:pseudopeptidoglycan Pseudopeptidoglycan (also known as pseudomurein) is a major cell wall component of some archaea that differs from bacterial peptidoglycan in chemical structure, but resembles eubacterial peptidoglycan in morphology, function, and physical structure. The basic components are N-acetylglucosamine and N-acetyltalosaminuronic acid (peptidoglycan has N-acetylmuramic acid instead), which are linked by β-1,3-glycosidic bonds. Lysozyme, a host defense mechanism, is ineffective against organisms with pseudopeptidoglycan cell walls. Lysozyme can break β-1,4-glycosidic bonds to degrade peptidoglycan; however, pseudopeptidoglycan has β-1,3-glycosidic bonds, rendering lysozyme useless. Carrine Blank Cell wall composed a polymer of N-acetylglucosamine and N-acetyltalosaminuronic acid (2-amino-2-deoxy-L-taluronic acid), linked by beta-1,3-glycosidic bonds. Found in the archaeal domain of life. Biosate peptone yeast enriched peptone From BD Bionutrients Technical Manual (3rd edition revised): BBL™ Biosate™ Peptone is a mixed hydrolysate comprised of 65% pancreatic digest of casein and 35% yeast extract. Ash content is 7.7% NaCl content is 0.3% BBL(TM) Biosate(TM) Peptone A mixed hydrolysate of pancreatic digest of casein (65%) and yeast extract (35%). Biosate is a Trademark of BD. Carrine Blank teichoic acid-based cell wall Carrine Blank Wikipedia:teichoic acid Teichoic acids (cf. Greek τεῖχος, teīkhos, "wall", more specifically a fortification wall, as opposed to τοῖχος, toīkhos, a regular wall) are bacterial polysaccharides of glycerol phosphate or ribitol phosphate linked via phosphodiester bonds. Teichoic acids are found within the cell wall of Gram-positive bacteria such as species in the genera Staphylococcus, Streptococcus, Bacillus, Clostridium, Corynebacterium and Listeria, and appear to extend to the surface of the peptidoglycan layer. Teichoic acids are not found in Gram-negative bacteria. They can be covalently linked to N-acetylmuramic acid of the peptidoglycan layer, to the lipids of the cytoplasmic membrane, or to a terminal D-alanine in the tetrapeptide crosslinkage between N-acetylmuramic acid units. Teichoic acids that remain anchored to lipids are referred to as lipoteichoic acids, while teichoic acids that are covalently bound to peptidoglycan are referred to as wall teichoic acids. Cell wall composed of polysaccharides of glycerol phosphate or ribitol phosphate linked via phosphodiester bonds, found in the peptidoglycan cell walls of Gram-positive bacteria. TBBP medium An organic-rich, liquid medium containing animal and plant peptones and sodium chloride. Supplemented with sheep blood, yeast extract, bacitracin, and polymyxin B. Used for the cultivation of Capnocytophaga spp. Carrine Blank From: Mashimo PA, Yamamoto Y, Nakamura M & Slots J. 1983. Selective recovery of oral Capnocytophaga spp. with sheep blood agar containing bacitracin and polymyxin B. J Clin Microbiol 17:187-91. TBBP medium consists of 4% Trypticase soy agar (BBL Microbiology Systems, Coceysville, Md.), 5% sheep blood, 0.1 % yeast extract, 50 micrograms of bacitracin per mL, and 100 micrograms of polymyxin B per mL. TBBP agar Carrine Blank From: Mashimo PA, Yamamoto Y, Nakamura M & Slots J. 1983. Selective recovery of oral Capnocytophaga spp. with sheep blood agar containing bacitracin and polymyxin B. J Clin Microbiol 17:187-91. TBBP medium consists of 4% Trypticase soy agar (BBL Microbiology Systems, Coceysville, Md.), 5% sheep blood, 0.1 % yeast extract, 50 micrograms of bacitracin per mL, and 100 micrograms of polymyxin B per mL. An organic-rich, solid medium containing animal and plant peptones and sodium chloride. Supplemented with sheep blood, yeast extract, bacitracin, and polymyxin B. Used for the cultivation of Capnocytophaga spp. diazocyte Carrine Blank A prokaryotic differentiated cell capable of nitrogen fixation, found in Trichodesmium species (Cyanobacteria). Diazocytes are mostly found in the center cells of Trichodesmium filaments. From Sandh, Xu & Bergman, 2012, Diazocyte development in the marine diazotrophic cyanobacterium Trichodesmium. Microbiology 158:345-352.: The establishment of non-diazotrophic cultures of the filamentous marine cyanobacterium Trichodesmium erythraeum IMS101 enabled the first detailed investigation of the process leading to the development of its unique nitrogen-fixing cell type, the diazocyte. extracellular mineral precipitates Carrine Blank Crystalline, microcystalline, nanocrystalline, or amorphous inorganic chemical precipitates that form outside the cell as a result of the local presence of the cell or the activities of the cell. extracellular iron precipitates Carrine Blank extracellular iron Crystalline, microcystalline, nanocrystalline, or amorphous inorganic chemical precipitates of iron minerals that form outside the cell as a result of the local presence of the cell or the activities of the cell. extracellular sulfur globule Crystalline, microcystalline, nanocrystalline, or amorphous inorganic chemical precipitates of elemental sulfur that forms outside the cell as a result of the local presence of the cell or the activities of the cell. Produced by Ectothiorhodospiraceae. extracellular sulphur granule extracellular sulfur globule Wikipedia:Ectothiorhodospiraceae The Ectothiorhodospiraceae are a family of purple sulfur bacteria, distinguished by producing sulfur globules outside of their cells. Carrine Blank fimbriae Carrine Blank A pilus, that is thin and short. fimbriated Wikipedia:Fimbria_(bacteriology) In bacteriology, a fimbria [(plural fimbriae); also referred to as a pilus (plural pili) by some scientists] is an appendage composed of curlin proteins that can be found on many Gram-negative and some Gram-positive bacteria that is thinner and shorter than a flagellum. This appendage ranges from 3-10 nanometers in diameter and can be up to several micrometers long. Fimbriae are used by bacteria to adhere to one another and to adhere to animal cells and some inanimate objects. A bacterium can have as many as 1,000 fimbriae. Fimbriae are only visible with the use of an electron microscope. They may be straight or flexible. fimbria SWC medium A dilute organic-containing, liquid microbiological culture medium containing tryptone, yeast extract, beef extract, and acetate, in a base of half-strength artifical seawater. From: Irgens Rl, Suzuki I, Staley JT. 1989. Gas vacuolate bacteria obtained from marine waters of Antarctica. Curr Microbiol 18:261-5. SWC contained (per liter of 1/2 strength artificial seawater [ASW]): tryptone, 0.5 g; yeast extract, 0.5 g; beef extract, 0.2 g; sodium acetate, 0.2 g. The pH was adjusted to 7.6 with a dilute solution of NaOH. ASW, 1/2 strength, contained (per liter): NaCl, 12.0 g; MgSO4x7H2O, 3.5 g; MgCl2x6H2O, 2.6 g; CaCl2x2H2O, 0.55 g; KCl, 0.35 g. Carrine Blank tetrazolium reduction assay An assay for the ability of a microorganism to reduce a compound that contains a tetrazoleum moiety. Tetrazolium compounds are redox indicators of microbial oxidation and reduction, and hence microbial respiration. Carrine Blank multiply flagellated 1 Flagellated cell where the cell has more than one flagellum. numerous flagella Carrine Blank polytrichous flagellated cell flagellated Carrine Blank Prokaryotic cell which has either a bacterial-type flagellum (or flagella) or a periplasmic flagellum. singly flagellated 1 Carrine Blank Flagellated cell where the cell has only one flagellum. monotrichous cell http://microbeonline.com/bacterial-flagella-structure-importance-and-examples-of-flagellated-bacteria/ Monotrichous: Single polar flagellum e.g. Vibrio cholerae (Mneomonics: Mono means one) single flagellum single flagella monopolar flagella polar flagellum monopolar flagellum Flagellated cell where the cell has a single flagellum located at the end (pole) of the cell. monotrichous monotrichous flagella Carrine Blank amphitrichous cell 2 Carrine Blank amphitrichous Flagellated cell where the cell has two flagella, each located at the ends (poles) of the cell. http://microbeonline.com/bacterial-flagella-structure-importance-and-examples-of-flagellated-bacteria/ Amphitrichous: Single flagellum at both ends e.g. Alcaligenes faecalis (Mneomonics: Remember: the characteristics of Amphibians: live both in land and water) lophotrichous cell 2 Carrine Blank tuft of polar flagella Flagellated cell where the cell has multiple flagella, located in a tuft at the end (pole) of the cell. bundles of flagella http://microbeonline.com/bacterial-flagella-structure-importance-and-examples-of-flagellated-bacteria/ Lophotrichous: Tuft of flagella at one or both ends e.g. Spirilla polar flagella polar bundle of flagella polar tuft of flagella lophotrichous monopolar polytrichous flagella cell having periplasmic flagella axial fibrils axial filaments periplasmic fibrils Flagellated cell where the cell has multiple flagella, each located in tufts in the periplasmic space. http://microbewiki.kenyon.edu/index.php/Spirochaeta The morphology and cellular structure of Spirochaeta spp. (and most other Spirochetes) is unique among prokaryotes. The cells are helical in shape and consist of an outer membrane, axial filaments (ultrastructurally similar to bacterial flagella), and a protoplasmic cylinder. The outer membrane or the outer sheath surrounds all of the structures including the axial filaments and the protoplasmic cylinder. The protoplasmic cylinder is the cell body of the organism. It is coiled and is composed of the cytoplasm, the nuclear region and the peptidoglycan-cytoplasmic membrane complex. The axial filaments are usually called the periplasmic flagella but are also known as periplasmic fibrils, axial fibrils and endoflagella. Carrine Blank periplasmic flagella endoflagella peritrichous cell 2 peritrichously http://microbeonline.com/bacterial-flagella-structure-importance-and-examples-of-flagellated-bacteria/ Peritrichous: Flagella surrounding the cell, e.g. Typhoid bacilli (Mneomonic: Remember Periphery) Flagellated cell where the cell has multiple flagella, all located at the periphery of the cell. peritrichous Carrine Blank tumbling motility Wikipedia:Listeria Prokaryotic motility that is characterized microscopically by end-over-end tumbling and employs a flagellum. This type of motility is typical of Listeria. Carrine Blank tumbling heterocyte heterocystous heterocytous Carrine Blank heterocysts From Wikipedia:heterocyst: Heterocysts are specialized nitrogen-fixing cells formed during nitrogen starvation by some filamentous cyanobacteria, such as Nostoc punctiforme, Cylindrospermum stagnale, and Anabaena sphaerica. They fix nitrogen from dinitrogen (N2) in the air using the enzyme nitrogenase, in order to provide the cells in the filament with nitrogen for biosynthesis. Nitrogenase is inactivated by oxygen, so the heterocyst must create a microanaerobic environment. A prokaryotic differentiated cell capable of nitrogen fixation, found in the filamentous Nostocales (Cyanobacteria). Heterocytes (which differentiate into heterocysts) have thick cell walls which exclude oxygen in the air and allow nitrogen fixation to occur. Are terminally differentiated cells, incapable of carrying out photosynthesis. intercalary heterocyte bipored heterocyte Carrine Blank A heterocyte which develops at the middle or near the end (but not the end) of a filament (trichome). intercalary heterocyst From Rippka, Castenholz & Herdman, 2001, in Bergeys Manual of Systematic Bacteriology, v. 1, 2nd ed., pg 563.: In the absence of combined nitrogen (ammonium or nitrate), 5-10% of the vegetative cells differentiate into heterocysts. These specialized cells are the sites of aerobic nitrogen fixation and may occupy terminal or intercalary positions in the trichomes. lateral heterocyte terminal heterocyte terminal heterocyst Carrine Blank From Rippka, Castenholz & Herdman, 2001, in Bergeys Manual of Systematic Bacteriology, v. 1, 2nd ed., pg 563.: In the absence of combined nitrogen (ammonium or nitrate), 5-10% of the vegetative cells differentiate into heterocysts. These specialized cells are the sites of aerobic nitrogen fixation and may occupy terminal or intercalary positions in the trichomes. A heterocyte which develops at the end of a filament (trichome). unipored heterocyte hormogonium Prokaryotic differentiated cell specialized for asexual reproduction comprised of short chains of motile filaments, found in the Nostocales, Stigonematales/Stigonemataceae, and Oscillatoriales (Cyanobacteria). Hormogonia are shorter than the typical length of vegetative filaments. Carrine Blank hormogonia From Wikipedia:hormogonium: Hormogonia are motile filaments of cells formed by some cyanobacteria in the order Nostocales and Stigonematales. They are formed during asexual reproduction in unicellular, filamentous cyanobacteria some contain heterocysts and akinetes. SWC-m medium SWCm salts Carrine Blank A dilute organic-containing, liquid microbiological culture medium containing tryptone, yeast extract, beef extract, and acetate, in a base of full-strength artifical seawater. From: Irgens Rl, Suzuki I, Staley JT. 1989. Gas vacuolate bacteria obtained from marine waters of Antarctica. Curr Microbiol 18:261-5. SWC-m contained (per liter of full strength ASW): KH2PO4, 0.01 g; ferric citrate, 0.001 g; NH4Cl, 0.4 g; yeast extract, 0.4 g; beef extract, 0.4 g; tryptone, 0.4 g; vitamins, 10 mL; trace elements solution (TES), 2.0 mL; carbon source, 0.2 g; pH 7.0. The following macromolecular carbon sources were tested for hydrolysis on plates: starch, 1.0%; tributyrin, 1.0%; chitin, 1.0%; casein, 0.5%. xxxxxxx From: Irgens RL. 1977. Meniscus, a new genus of aerotolerant, gas-vacuolated bacteria. Int J Syst Bacteriol 27(1):38-43. The TES, modified from Pfennig’s formula (personal communication), contained (per liter): ZnSO4x7H2O, 0.10 g; MnCl2x4H2O, 0.03 g; H3BO3, 0.3 g; CoCl2x6H20, 0.2 g; CuCl2x2H2O,0.01 g ; NiCl2x6H2O, 0.02 g; Na2MoO4x 2H2O, 0.03g; pH3 to 4. xxxxxxx From: Staley JT. 1981. The genera Prosthecomicrobium and Ancalomicrobium. In: Starr MP, Stolp H, Truper HG, Balows A,Schlegel HG, (eds). The prokaryotes. Berlin: Springer-Verlag. Pg 68. Vitamin Solution B12 0.1 mg Biotin 2 mg Calcium pantothenate 5 mg Folic acid 2 mg nicotinamide 5 mg pyridoxine HCl 10 mg riboflavin 5 mg thiamine HCL 5 mg Add distilled water up to 1 L and sotre in 4˚C in a dark container. conjugative pili Pilus involved in the transfer of DNA from one bacterium (the donor) to another (the recipient). Wikipedia:pilus Conjugative pili allow the transfer of DNA between bacteria, in the process of bacterial conjugation. They are sometimes called "sex pili", in analogy to sexual reproduction, because they allow for the exchange of genes via the formation of "mating pairs". Perhaps the most well-studied is the F pilus of Escherichia coli, encoded by the F plasmid or fertility factor. Carrine Blank SWC-m agar Carrine Blank A dilute organic-containing, liquid microbiological culture medium containing tryptone, yeast extract, beef extract, and acetate, in a base of full-strength artifical seawater. From: Irgens Rl, Suzuki I, Staley JT. 1989. Gas vacuolate bacteria obtained from marine waters of Antarctica. Curr Microbiol 18:261-5. Agar slants containted 1.5 % agar, agar plates contained 2.0 % agar, and soft agar tubes contained 0.2 % agar. SWCM agar From: Irgens Rl, Suzuki I, Staley JT. 1989. Gas vacuolate bacteria obtained from marine waters of Antarctica. Curr Microbiol 18:261-5. SWC-m contained (per liter of full strength ASW): KH2PO4, 0.01 g; ferric citrate, 0.001 g; NH4Cl, 0.4 g; yeast extract, 0.4 g; beef extract, 0.4 g; tryptone, 0.4 g; vitamins, 10 mL; trace elements solution (TES), 2.0 mL; carbon source, 0.2 g; pH 7.0. The following macromolecular carbon sources were tested for hydrolysis on plates: starch, 1.0%; tributyrin, 1.0%; chitin, 1.0%; casein, 0.5%. xxxxxxx From: Irgens RL. 1977. Meniscus, a new genus of aerotolerant, gas-vacuolated bacteria. Int J Syst Bacteriol 27(1):38-43. The TES, modified from Pfennig’s formula (personal communication), contained (per liter): ZnSO4x7H2O, 0.10 g; MnCl2x4H2O, 0.03 g; H3BO3, 0.3 g; CoCl2x6H20, 0.2 g; CuCl2x2H2O,0.01 g ; NiCl2x6H2O, 0.02 g; Na2MoO4x 2H2O, 0.03g; pH3 to 4. xxxxxxx From: Staley JT. 1981. The genera Prosthecomicrobium and Ancalomicrobium. In: Starr MP, Stolp H, Truper HG, Balows A,Schlegel HG, (eds). The prokaryotes. Berlin: Springer-Verlag. Pg 68. Vitamin Solution B12 0.1 mg Biotin 2 mg Calcium pantothenate 5 mg Folic acid 2 mg nicotinamide 5 mg pyridoxine HCl 10 mg riboflavin 5 mg thiamine HCL 5 mg Add distilled water up to 1 L and sotre in 4˚C in a dark container. distinctly shaped colony Carrine Blank http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol elevated A colony that has a distinct morphology manifested in its 2D or 3D shape. physically distinct colony http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol A prokaryotic colony that has distinct physical characteristics (qualities). Carrine Blank colony having distinct spatial pattern A colony having distinct physical quality that manifests in the spatial pattern of the elements of the colony. Carrine Blank colony having distinct optical quality A prokaryotic colony that manifests in how light (visible electromagnetic radiation) passes through the colony. Carrine Blank texturally distinct colony Carrine Blank A colony with a texture that manifests in the appearance of the surface characteristics. satellite colonies Carrine Blank satellite colonies satellite behavior A prokaryotic colony where small colonies surround larger colonies on an agar (or other solid) surface. http://www.yourdictionary.com/satellite#americanheritage Satellite colonies occur when tiny colonies are found to surround a larger central colony. satellites dense center colony Carrine Blank A colony with distinct spatial pattern where the center part of the colony is tight (densely compacted) and the outer part of the colony is sparse (not densely compacted). dense center diffuse center colony dry colony dry colony Carrine Blank A colony having distinct physical quality that is dry (has a brittle, friable texture that breaks apart). friable dry dull colony Carrine Blank not shiny A colony with distinct optical quality that is dull (not shiny, with a low saturation) in its appearance. dull dull colony granular center colony granular center colony A colony with a structure that has a grainy, or granular, appearance in its center. fine granulation granular granular centers Carrine Blank glistening colony moist shiny surface wet shining aspect glistening shiny A colony with distinct EM radiation quality that has a wet appearance. glistening colony Carrine Blank shining glossy mucoid colony http://www.medilexicon.com/medicaldictionary.php?t=19041 Carrine Blank mucoid mucous A colony with a structure that is mucoid (has a sticky appearance due to the presence of exopolysaccharide capsular material). mucoid colony rough colony rough colony A colony with a texture that is rough (i.e. not smooth). Carrine Blank rough surface smooth colony smooth smooth-surfaced smooth colony A colony with a texture that is smooth. Carrine Blank dendritic colony dendritic colony Carrine Blank A colony with a shape that has raised, branching features starting in the center of the colony, with an appearance that resembles veins or branches of a tree. veined dendiritic wrinkled colony rugose A colony with a texture that is wrinkled (has a shriveled appearance). shriveled Carrine Blank wrinkled colony cloudy colony A colony with distinct optical quality that is cloudy (semi-translucent or semi-opaque, whitish in color). semi-translucent cloudy colony cloudy Carrine Blank semi-opaque iridescent colony A colony having a distinct process quality where the colony is iridescent (appears to change color as the angle of illumination changes). iridescent http://en.wikipedia.org/wiki/Iridescence opalescent irridescent colony Carrine Blank pigmented colony A colony with a structure that contains coloration due to the presence of pigment compounds that absorb particular wavelengths of light. coloured colored Carrine Blank pigmented colony opaque colony Carrine Blank opaque colony A colony with distinct optical quality that is opaque (where light does not pass through). opaque bovine albumin Carrine Blank From: https://catalog.hardydiagnostics.com/cp_prod/Content/hugo/AnimalBloodProd.htm Bovine Albumin contains bovine albumin fraction V, 0.2% in 0.85% saline solution. A blood medium ingredient comprised of bovine (Bos taurus) albumin (a mixture of protein derived from blood). Used in the cultivation of microorganisms. translucent colony translucent colony Carrine Blank translucent semi-transparent almost clear A colony with distinct optical quality that is translucent, where much light is able to pass through it without absorption of particular wavelengths of light. transparent colony transparent Carrine Blank clear transparent colony A colony with distinct optical quality that is completely or nearly completely clear or transparent, where nearly all light is able to pass through it. anaerobic respiration, using sulfate as electron acceptor The process of anaerobic respiration, where sulfate is reduced to sulfite, tetrathionate, thiosulfate, elemental sulfur, or hydrogen sulfide. Carrine Blank pyrazinamidase activity A hydrolase activity, which hydrolyzes pyrazinamide (a drug used to treat tuberculosis) into pyrazinoic acid (the active agent against tuberculosis). Pyrazinamidase catalyzes the following reaction: Pyrazinamide + H2O <=> pyrazinoic acid (pyrazine-2-carboxylic acid) + NH3. E.C. 3.5.1.b15 Carrine Blank anaerobic respiration, using elemental sulfur as electron acceptor The process of anaerobic respiration, where elemental sulfur reduced to hydrogen sulfide. Carrine Blank aerobic respiration, using hydrogen sulfide as electron donor The process of aerobic respiration, where hydrogen sulfide is oxidized (using oxygen) to elemental sulfur, thiosulfate, tetrathionate, sulfite, or sulfate. Carrine Blank aerobic respiration, using elemental sulfur as electron donor The process of aerobic respiration, where elemental sulfur is oxidized (using oxygen) to thiosulfate, tetrathionate, sulfite, or sulfate. Carrine Blank anaerobic respiration, using thiosulfate as electron acceptor The process of anaerobic respiration, where thiosulfate is reduced to elemental sulfur or hydrogen sulfide. Carrine Blank anaerobic respiration, using sulfite as electron acceptor Carrine Blank The process of anaerobic respiration, where sulfite is reduced to tetrationate, thiosulfate, elemental sulfur, or hydrogen sulfide. chymotrypsin assay using BTEE Carrine Blank Uses the substrate N-Benzoyl-L-tyrosine ethyl ester (BTEE). Chymotrypsin activity will cleave the substrate, releasing N-Benzoyl-L-tyrosine. The presence of this produce is measured by recording the increase in absorbance at 256 nm. chymotrypsin assay using NA Uses the substrate N-benzoyl-D-L-phenylalanine-2-naphthylamide at pH 7.1. Trypsin activity will cleave the substrate, releasing 2-naphthylamide. When reacted with Fast Blue BB it forms a colored insoluble precipitate that is purple in color. Carrine Blank N-benzoyl-D-L-phenylalanine 2-naphthylamide trypsin assay using NA Uses the substrate N-benzoyl-D-L-arginine 2-naphthylamide at pH 8.5. Trypsin activity will cleave the substrate, releasing 2-naphthylamide. When reacted with Fast Blue BB it forms a colored insoluble precipitate that is orange in color. N-benzoyl-arginine-2-naphthylamide Carrine Blank N-benzoyl-DL-arginine-2-naphthylamide alanyl alanine arylamidase activity Carrine Blank An aminopeptidaseeptidase activity which cleaves the chromogenic substrate L-alanyl-L-alanine-2-naphthylamide. alanyl phenylalanyl proline arylamidase activity An aminopeptidase activity which cleaves the chromogenic substrate L-alanyl-L-phenylalanyl-L-proline-2-naphthylamide. Carrine Blank glutamyl glutamic acid arylamidase activity An aminopeptidase activity which cleaves the chromogenic substrate L-glutamyl-L-glutamic acid-2-naphthylamide. Carrine Blank glutamyl glycine arylamidase activity Carrine Blank An aminopeptidase activity which cleaves the chromogenic substrate L-glutamyl-glycine-2-naphthylamide. glutamyl glycyl arginine arylamidase activity Carrine Blank An aminopeptidase activity which cleaves the chromogenic substrate L-glutamyl-glycyl-L-arginine-2-naphthylamide. glutaryl phenylalanine arylamidase activity Carrine Blank An aminopeptidase activity which cleaves the chromogenic substrate glutaryl-L-phenylalanine-2-naphthylamide. glycyl phenylalanine arylamidase activity An aminopeptidase activity which cleaves the chromogenic substrate glycyl-L-phenylalanine-2-naphthylamide. Carrine Blank glycyl proline arylamidase activity Carrine Blank An aminopeptidase activity which cleaves the chromogenic substrate glycyl-L-proline-2-naphthylamide. glycyl tryptophan arylamidase activity An aminopeptidase activity which cleaves the chromogenic substrate glycyl-L-tryptophan-2-naphthylamide. Carrine Blank glycyl glycine arylamidase activity Carrine Blank An aminopeptidase activity which cleaves the chromogenic substrate glycyl-glycine-2-naphthylamide. leucyl glycine arylamidase activity An aminopeptidase activity which cleaves the chromogenic substrate L-leucyl-L-glycine-2-naphthylamide. Carrine Blank seryl tyrosine arylamidase activity An aminopeptidase activity which cleaves the chromogenic substrate L-seryl-L-tyrosine-2-naphthylamide. Carrine Blank N-carbobenzoyl-glycyl-glycyl-L-arginine peptidase activity An aminopeptidase activity which cleaves the chromogenic substrate N-carbobenzoyl-glycyl-glycyl-arginine-beta-naphthylamide. Carrine Blank irregular cell highly irregular irregular Carrine Blank Prokaryotic cell where the shape is irregular. irregular shape microscopic optical quality assay Carrine Blank An optical quality assay of a single prokaryotic cell, determined by visualization under a microscope. N-benzoyl-L-valyl-glycyl-L-arginine-4-methoxy peptidase activity Carrine Blank An aminopeptidase activity which cleaves the chromogenic substrate N-benzoyl-L-valyl-glycyl-4-methoxy-beta-naphthylamide. asymmetrical colony margin irregular margin irregular form http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol A prokaryote colony where the shape of the colony margin is asymmetrical (i.e. irregular). Carrine Blank irregular edge diffuse colony A colony with distinct spatial pattern where the colony is diffuse (sparse, where the colony is very thin). diffuse colony Carrine Blank diffuse asymmetrical filamentous colony asymmetrical filamentous colony irregular filamentous A filamentous colony with a shape that is fuzzy, or filamentous and where the colony margin is asymmetrical (i.e. irregular). http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol undulate colony undulate margin Carrine Blank A colony with a shape that is undulate (wave-like) and where the colony margin is asymmetrical (i.e. irregular). http://www.microbelibrary.org/component/resource/laboratory-test/3114-colony-morphology?limit=0&limitstart=0 undulate colony http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol undulate symmetrical colony margin A prokaryotic colony where the shape of the colony margin is symmetrical (i.e. regular). regular margin regular edge http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol Carrine Blank symmetrical colony margin curled colony http://www.ehow.com/list_6938999_types-bacteria-colonies.html curled http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol A colony with a shape that has a curled edge, and where the colony margin is symmetrical (i.e. regular). wavy margin Carrine Blank curled colony entire colony Carrine Blank http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol entire colony entire A colony with a shape which is circular (round), and where the colony margin is symmetrical (i.e. is regular). erose colony Carrine Blank http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol erose A colony with a shape which is erose (i.e. has a notched, toothed, or indented appearance) and where the colony margin is symmetrical (i.e. regular). erose colony symmetrical filamentous colony A filamentous colony with a shape that is fuzzy, or filamentous and where the colony margin is symmetrical (i.e. regular). regular filamentous Carrine Blank symmetrical filamentous colony http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol lobed colony lobate margin A colony with a shape that is lobed and where the colony margin is asymmetrical (i.e. irregular). lobel colony http://www.microbelibrary.org/component/resource/laboratory-test/3114-colony-morphology?limit=0&limitstart=0 Carrine Blank http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol circular colony round http://www.microbelibrary.org/component/resource/laboratory-test/3114-colony-morphology?limit=0&limitstart=0 http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol A colony with a shape that is circular (round). circular colony is round circular colony Carrine Blank effuse colony effuse Carrine Blank effuse colony A colony with distinct spatial pattern where the colony is effuse (i.e. thin, unlocalized without defined margins, with a tendancy to spread). filamentous colony http://www.microbelibrary.org/component/resource/laboratory-test/3114-colony-morphology?limit=0&limitstart=0 A colony with a shape that is fuzzy, or filamentous. filamentous colony Carrine Blank http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol fried-egg colony fried-egg colony Fallon RJ. 1967. Mycoplasmas and their role as rodent pathogens. Lab Anim 1:43. DOI: 10.1258/002367767781006794. http://medical-dictionary.thefreedictionary.com/Fried+Egg+Appearance A colony having distinct physical quality that has differential density. The center part of the colony is opaque and granular, while the surrounding perifery is flat and transulcent, giving the colony the appearance of a fried egg. This shape is typical of Mycoplasma species, and is due to colonies having a thicker center than edge. This appearance is typical of older (mature) colonies of Mycoplasma. fried egg fried eggs Carrine Blank colony having distinct electromagnetic (EM) radiation quality Carrine Blank A colony having distinct physical quality that manifests in the electromagnetic (EM) radiation appearance of the colony. mulberry colony mulberry appearance mulberry colony Carrine Blank Fallon RJ. 1967. Mycoplasmas and their role as rodent pathogens. Lab Anim 1:43. DOI: 10.1258/002367767781006794. A colony having distinct physical quality that is shaped like a mulberry (acinar), sunken, and opaque with little or no pale periphery. Is typical of young colonies of Mycoplasma species that will develop into colonies that have a fried egg appearance when more mature. mulberry punctiform colony A colony with a shape that is very tiny, like a point (where colonies may have a diameter of less than 1 mm). punctiforme colony http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol punctiform Carrine Blank rhizoidal colony http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol irregular rhizoid form http://www.microbelibrary.org/component/resource/laboratory-test/3114-colony-morphology?limit=0&limitstart=0 rhizoid colony rhizoid form A colony having distinct physical quality that is rhizoidal (has margins or edges that resemble the roots of a tree, radiating out from the center of the colony). Carrine Blank rhizoidal rhizoid raised rhizoid growth spindle colony A colony with a shape that is spindle-shaped (i.e. is thickest in the middle, tapering to both ends). Carrine Blank http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol spindle colony fusiform spindle-shaped crateriform colony A colony with a shape that has a depression (or crater) in the center of the colony, and thus has a 2D profile that is cup-shaped. cup-shaped crateriform colony crateriform dimpled collapsed center crater-shaped Carrine Blank flat colony A colony with a shape that is flat (has a flat profile). flat colony flat elevation http://www.microbelibrary.org/component/resource/laboratory-test/3114-colony-morphology?limit=0&limitstart=0 Carrine Blank http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol raised colony http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol raised colony Carrine Blank A colony with a shape that is raised, or elevated from the surface of the agar. pulvinate colony pulvinate colony pulvinate elevation Carrine Blank http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol A colony with a shape that is pulvinate (is strongly elevated with a domed profile being shaped like a cushion). pulvinate http://www.microbelibrary.org/component/resource/laboratory-test/3114-colony-morphology?limit=0&limitstart=0 convex colony http://www.microbelibrary.org/component/resource/laboratory-test/3114-colony-morphology?limit=0&limitstart=0 convex Carrine Blank A colony with a shape that has a convex, or domed, profile. convex colony http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol convex elevation domed umbonate colony Carrine Blank raised at the centres raised at the center umbonate colony umbonate elevation A colony having distinct physical quality that is umbonate (having a mushroom-like profile with a higher center and a lower margin). http://www.microbelibrary.org/component/resource/laboratory-test/3136-colony-morphology-protocol http://www.microbelibrary.org/component/resource/laboratory-test/3114-colony-morphology?limit=0&limitstart=0 raised in the center prokaryotic cell autofluorescence The optical assay of a single prokaryotic cell, having the quality of autofluorescence when illuminated with a particular wavelength of light. Carrine Blank blue-green autofluorescence blue-green fluorescence Autofluorescence of a prokaryotic cell that is blue-green in nature, occurring when the cells are illuminated with radiation at 420 nm. Occurs due to the presence of a particular fluorescent compound in the cell (e.g., Factor 420, also known as Coenzyme F420). Carrine Blank lipase C10 activity Carrine Blank A lipase that hydrolyzes C10 compounds. Assayed using the chromogenic substrate 5-bromo-3-indoxyl-caprate (5-bromo-3-indolyl decanoate; blue-caprate). lipase C14 activity A lipase that hydrolyzes C14 compounds. Assayed using the chromogenic substrate 2-naphthyl myristate. Carrine Blank lipase C8 activity A lipase that hydrolyzes C8 compounds. Assayed using the chromogenic substrate 2-naphthyl caprylate. Carrine Blank coccobacillus Carrine Blank coccobacillary coccobacilli sub-coccoidal Wikipedia:Coccobacillus A coccobacillus (plural coccobacilli) is a type of bacterium with a shape that is intermediate between cocci (spherical bacteria) and bacilli (rod-shaped bacteria). Coccobacilli are therefore in essence very short rods which may be mistaken for cocci. Haemophilus influenzae, Gardnerella vaginalis, and Chlamydia trachomatis are coccobacilli. Aggregatibacter actinomycetemcomitans is a gram-negative coccobacillus that is prevalent in subgingival plaques. Acinetobacter strains may grow on solid media as coccobacilli. Bordetella pertussis is a gram-negative coccobacillus responsible for causing whooping cough. A prokaryotic cell, being a bacillus where the long axis of the cell is only slightly longer than the short axis of the cell. ellipsoidal short rods subspherical oval ovoid subcoccoidal coccobacillus spirillum Wikipedia:Spirillum Spirillum in microbiology refers to a bacterium with a cell body that twists like a spiral. It is the third distinct bacterial cell shape type besides coccus and bacillus cells. Carrine Blank A prokaryotic cell, where the long axis of the cell twists in a spiral. spiral coiled helical spirillum helix wavy prokaryotic cell having distinct cell arrangement aggregates Prokaryotic cells and the physical relationships between the cells (whether they are physically attached, or connected, to one another). Carrine Blank aggregations paired cells 2 Carrine Blank doublets diploid A multicellular relationship of prokaryotic cells where two cells are attached to one another in pairs. pairs morphologically differentiated filament part A filament of prokaryotic cells, where the parts of the filament are morphologically differentiated. Carrine Blank sarcina 8 12 16 sarcinae Carrine Blank A multicellular relationship of prokaryotic cells where cells are attached to one another in multiples of four (8,12, or 16). This morphology forms as a result of cell division occurring in three planes. sarcinoid cell cluster cell clusters A multicellular relationship of prokaryotic cells where cells are attached to one another end-to-end and side-to-side to form clumps or sheets after dividing. This morphology forms as a result of cell division taking place in multiple planes. clusters packet-like Carrine Blank packets clumps cell chain Carrine Blank chains A multicellular relationship of prokaryotic cells where cells are attached to one another end-to-end to form chains. Forms when cell division occurs in one plane and cells become detached after cell division takes place. short chains tetrad 4 tetrads Carrine Blank A multicellular prokaryotic morphological quality where cells are attached to one another in multiples of four. Forms when cell division occurs in two planes at right angles to one another. unicellular prokaryote A prokaryotic cellularity where cells are isolated and singular, where the daughter cells detach from one another after cell division and septation occurs. unicellular Carrine Blank singly singular streptobacillus Wikipedia:Streptobacillus Streptobacillus is a genus of aerobic, gram-negative facultative anaerobe bacteria, which grow in culture as rods in chains. A multicellular relationship of prokaryotic cells where the shape of the cell is elongated (forming a bacillus, or short rod) and the cells are attached to one another end-to-end to form chains. streptobacilli Carrine Blank streptococcus Wikipedia:Streptococcus Streptococcus is a genus of spherical Gram-positive bacteria belonging to the phylum Firmicutes and the lactic acid bacteria group. Cellular division occurs along a single axis in these bacteria, and thus they grow in chains or pairs, hence the name—from Greek στρεπτος streptos, meaning easily bent or twisted, like a chain (twisted chain). Contrast this with staphylococci, which divide along multiple axes and generate grape-like clusters of cells. Most streptococci are oxidase- and catalase-negative, and many are facultative anaerobes. streptococci Carrine Blank A multicellular relationship of prokaryotic cells where the shape of the cells is round (forming a coccus) and the cells are attached to one another end-to-end to form chains. staphylococcus A multicellular relationship of prokaryotic cells where the shape of the cells is round (forming a coccus) and the cells are attached to one another end-to-end and side-to-side to form clumps or clusters. staphylococci Wikipedia:Staphylococcus Staphylococcus (from the Greek: σταφυλή, staphylē, "grape" and κόκκος, kókkos, "granule") is a genus of Gram-positive bacteria. Under the microscope, they appear round (cocci), and form in grape-like clusters. Carrine Blank differentiated filament branching branching of filaments Carrine Blank branching branches A differentiated cyanobacterial filament where the filaments are branched. branched filaments false-branched filaments commonly false branched false branched false branching growing usually at first parallel with original trichome, later diverging Carrine Blank false branching Differentiated filament branching, where filaments have "false" branches. Initiated by the interruption of a trichome between two vegetative cells, either at the location of a necridic cell or a heterocyte. Later on, one or both ends of the interrupted trichomes grow aside from the axis of the main trichome. Found in the Oscilaltoriales and Nostocales and Stigonematales. pseudobranched single false branching falsely branched false ramification pseudobranchings lateral false branches http://www.merriam-webster.com/dictionary/false%20branching A branched arrangement of the cells of certain filamentous bacteria and algae resulting from a slipping of the end of one cell past that of another following cell division, from continued growth of the free end of a trichome through the sheath in various blue-green algae, or esp. from continued growth of parts of a filament separated by one or more intervening dead cells or by heterocysts. pseudobranchings adpressed with each other and only in the upper parts divaricate true-branched filaments Differentiated filament branching, where filaments have "true" branches. Formed when one cell occasionally divides longitudinally (with the cell division plane parallel to the plane of the filament axis) or obliquely with respect to the main axis of the filament. Branches remain attached to the main trichome. true branching true-branching true branches true branching Carrine Blank branching true true branched true-branching filaments true branches grow initially perpendicular to the mother trichome true-branched branches arise after lengthwise cell division diplobacillus A multicellular prokaryotic morphological quality where the shape of the cells are elongated (i.e. bacillus or rod-shaped) and two cells are attached to one another in pairs. Carrine Blank http://medical-dictionary.thefreedictionary.com/diplobacillus A short, rod-shaped organism occurring in pairs, joined end-to-end; diplobacterium. diplobacilli diplococcus dumbbell dumbbell-shaped diplococci Wikipedia:Diplococcus A diplococcus (plural diplococci) is a round bacterium (a coccus) that typically occurs in the form of two joined cells. Examples are gram-negative Neisseria sp., and gram-positive Streptococcus sp. and Staphylococcus sp.. Its name comes from diplo, meaning double, and coccus, meaning berry. A multicellular prokaryotic morphological quality where the shape of the cells are round and two cells are attached to one another in pairs. Carrine Blank erect filaments A filament orientation quality where filaments are lying upright (perpendicular) to a substrate or surface. filaments erect Carrine Blank prostrate filaments Carrine Blank filaments prostrate A filament orientation quality where filaments are lying along (parallel to) a substrate or surface. straight filament filaments straight Carrine Blank A filament shape where the filament has a straight appearance (is not bent, curved, coiled, or torulose). trichomes straight curved filament filaments flexous filaments curved Carrine Blank A filament shape where the filament has a curved appearance along a gradual angle (not straight or bent). filaments flexuous branches waved branches arcuated filaments arcuated trichomes curved trichomes arcuate coiled filament Carrine Blank coiled filaments trichomes coiled A filament shape where the filament has a regularly coiled (helical) appearance. filaments coiled bent filament filaments bent filaments crooked filaments bent in the middle A filament shape where the filament has an appearance of being bent at an angle. Carrine Blank torulose filament filaments roughened trichomes torulose A torulose filament shape where the filament has a non-uniformly beaded appearance, where parts of the filament are swollen and constricted. Carrine Blank filaments torulose http://www.thefreedictionary.com/torulose Adj. 1. torulose - of a cylindrical or ellipsoid body; swollen and constricted at intervals moniliform filament Carrine Blank A filament shape where the filament has a uniformly regular, beaded appearance. Wikipedia: Moniliform Having a form resembling a string of beads, where the component parts or segments are more or less uniform in size and are spherical or rounded in shape. filaments resembling a string of beads trichomes moniliform filaments moniliform trichome part Carrine Blank Any consituent part of a prokaryotic heteropolar filament. basal heterocyte A trichome part that is comprised of the terminal (basal) cell in a trichome, which has differentiated to form a heterocyte (heterocyst). Found in trichomes with apical-basal polarity that have an erect positionality. Carrine Blank tight filament coiling filaments forming tight, regular spirals A coiled filament shape where the shape of the coiling is tight, having increased coiling. densely coiled Carrine Blank tight filament coiling loose filament coiling loose filament coiling filaments slightly coiled A coiled filament shape where the shape of the coiling is loose, having decreased coiling. filaments loosely coiled Carrine Blank irregular filament coiling trichomes irregularly coiled irregular filament coiling trichomes irregularly waved trichomes irregularly screw-like or spirally coiled A coiled filament shape where the shape of the coiling is irregular. Carrine Blank irregularly arranged coiled filaments irregularly coiled coils irregular filaments irregularly spirally coiled regular filament coiling Carrine Blank filaments screw-like coiled A coiled filament shape where the shape of the coiling is regular. helical trichomes coils regular regular filament coiling screw-like coiled cyanobacterial thylakoid Carrine Blank Bacterial thylakoid that is present in Cyanobacteria. differentiated cyanobacterial filament part Carrine Blank A cyanobacterial filament part (e.g. apical cell, meristematic zone) which is differentiated. trichome_differentiation distinctively shaped prokaryotic cell Carrine Blank Prokaryotic cell having a distinctive shape. bacillus rod-shaped rod-like bacillus rods Carrine Blank Wikipedia:Bacillus_(shape) The word bacillus (plural bacilli) may be used to describe any rod-shaped bacterium, and such bacilli are found in many different taxonomic groups of bacteria. However, the name Bacillus, capitalized and italicized, refers to a specific genus of bacteria. The name Bacilli, capitalized but not italicized, can also refer to a more specific taxonomic class of bacteria that includes two orders, one of which contains the genus Bacillus. Bacilli are usually solitary, but can combine to form diplobacilli, streptobacilli, and palisades. bacilli rod shaped A prokaryotic cell, where one axis (the long axis, the length) of the cell is longer than the other axis (the short axis, the width) of the cell. coccus Carrine Blank coccoidal strongly lobed spherical polygonal-rounded spheroids isodiametric coccoid sphere-shaped semi-globose Wikipedia:Coccus Coccus (plural cocci or coccuses) can be used to describe any bacterium that has a spherical shape. It is one of the three distinct types of bacteria shapes, the other two being bacillus (rod-shaped) and spirillum (spiral-shaped) cells. Coccus is an English loanword of a Neolatin noun, which in turn stems from the Greek masculine noun kokkos (κόκκος) meaning "berry". lobed multi-lobed coccus globose sphaerical spheroidal lobes spheres A prokaryotic cell that is spherical with no apparent long axis. cocci cylindrical cell Carrine Blank Wikipedia:Cylinder_(geometry) A cylinder (from Greek κύλινδρος – kulindros, "roller, tumbler") is one of the most basic curvilinear geometric shapes, the surface formed by the points at a fixed distance from a given line segment, the axis of the cylinder. The solid enclosed by this surface and by two planes perpendicular to the axis is also called a cylinder. The surface area and the volume of a cylinder have been known since deep antiquity. cylindrical barrel-shaped barreliform A prokaryotic cell, being a bacillus where the long axis of the cell is much longer than the short axis of the cell. discoid disk disk shaped plate-shaped discoidal Carrine Blank disc A flattened prokaryotic cell where the shape is partially spherical. discoid disc-shaped flattened cell flat flattened A prokaryotic cell where one part of the cell has been made flat so that the shape of the cell is asymmetrical or irregular. flattened cell Carrine Blank compressed pear-shaped cell pear shaped flask shaped flask A prokaryotic cell where one end end of the cell are wider than the middle (pear shaped). flask-like pear-like Carrine Blank pearshaped pear-shaped flaskshaped polygonal cell polygonal shape polygonal Carrine Blank A prokaryotic cell where the surface of the cell is not rounded but is polygonal (has angular edges). prosthecate cell Carrine Blank A prokaryotic cell where the cell has appendages or stalks that are extensions of the cell surface (including the cell wall and cell membrane). appendaged stalked prosthecate Wikipedia:Prosthecate_bacteria Prosthecate bacteria are a non-phylogenetically related group of Gram-negative bacteria that possess appendages, termed prosthecae. These cellular appendages are neither pili nor flagella, as they are extensions of the cellular membrane and contain cytosol. One notable group of prosthecates is the genus Caulobacter. cuboidal cell Carrine Blank square A prokaryotic cell where the surface of the cell is polygonal and the angles of the cell meet at right angles forming a box. Wikipedia:Haloquadratum Haloquadratum ("salt square") is a genus of the family Halobacteriaceae. The first species to be identified in this group, Haloquadratum walsbyi, is highly unusual since its cells are shaped like flat, square boxes. cuboidal pyramidal cell Carrine Blank triangles pyramidal A prokaryotic cell where the surface of the cell is polygonal and the angles of the cell meet at angles that are less than 90 degrees giving the cell a triangular or pyramidal appearance. triangular hemispherical Carrine Blank A sub-cylindrical, flattened prokaryotic cell where the shape is hemispherical (flattened on one side of the sphere). hemisphaerical hemispherical nanocytes Prokaryotic cells that are very small formed as a result of rapid cell division. Carrine Blank diphtheroid cell club-shaped shape regularity diptheroid Carrine Blank diphtheroid A prokaryotic cell, being a bacillus where one one end is wider and more rounded than the other end (i.e. being club-shaped, or cudgel-shaped). The cannonical morphology of Corynebacterium diphtheriae. corneform vibrioid cell crooked Carrine Blank Wikipedia:Vibrio Vibrio is a genus of Gram-negative bacteria possessing a curved rod shape (comma shape), several species of which can cause foodborne infection, usually associated with eating undercooked seafood. A prokaryotic cell, being a bacillus where the elongated axis of the cells is curved (but not spiral). vibrioid curved multiseriate filament 2 2 multiserial Seong-Joo L & Golubic S. 1998. Multi-trichomous cyanobacterial microfossils from the Mesoproterozoic Gaoyuzhuang Formation, China: Paleoecological and taxonomic implications. Lethaia 31:169-184. Multi-trichomous filamentous cyanobacteria of the genera Schizothrix and Microcoleus are the most commonly reported constructive elements in modern microbial mat ecosystems. .... A few specimens within the studied assemblage contain two to several parallel rows of evenly spaced internal bodies within a tube (Fig. 5C, D0, corresponding to a multi-trichomous arrangement. Castenholz, 2001, in Bergey's Manual of Systematic Bacteriology, v. 1, 2nd ed., pg. 473. polyseriate filaments with 2-3 joined trichomes multi-seriate multi-trichomous Cyanobacterial filament with one trichome in the sheath, where the trichome is greater than two cells in width. Arises as a result of cell division occuring in two planes,one perpendicular to the axis of the trichome and one parallel to the axis of the trichome. multitrichomous Carrine Blank uniseriate filament 1 1 uniserial trichomes uniseriate Cyanobacterial filament with one trichome in the sheath, where the trichome is one cell in width. Arises as a result of cell division occuring in only one plane. sheaths envelop always only one trichome Carrine Blank sheaths containing a single trichome trichomes in pairs in one sheath Wiktionary:uniseriate Having one line or series; uniserial, unbranched distinctively sized prokaryotic cell Prokaryotic cell having a distinctive size (width). Carrine Blank filterable cell filterable pass through a filter Carrine Blank A distinctively-sized prokaryotic cell, where the size is small enough to pass through a filter with a defined pore size. filterability pass through filters filtered nanophytoplankton Carrine Blank From: Wikipedia: Nanophytoplankton Nanophytoplankton are particularly small phytoplankton with sizes between 2 ­and 20 µm. They are the autotrophic part of nanoplankton. Like other phytoplankton, nanophytoplankton are microscopic organisms that obtain energy through the process of photosynthesis and must therefore live in the upper sunlit layer of ocean or other bodies of water. These microscopic free-floating organisms, including algae, protists, and cyanobacteria, fix large amounts of carbon which would otherwise be released as carbon dioxide. Photosynthetic prokaryotes, or single-celled eukaryotes, that have a cell size between 2 and 20 micrometers in diameter. picoplankton Carrine Blank From: Wikipedia: Picoplankton Picoplankton is the fraction of plankton composed by cells between 0.2 and 2 μm that can be either : Some species can also be mixotrophic. Picoplankton are responsible for the most primary productivity in oligotrophic gyres, and are distinguished from nanoplankton and microplankton. Because they are small, they have a greater surface to volume ratio, enabling them to obtain the scarce nutrients in these ecosystems. Note that the SI prefix pico- is used quite loosely here, as nanoplankton and microplankton are only 10 and 100 times larger, respectively. Prokaryotes or single-celled eukaryotes that have a cell size between 0.2 and 2 micrometers in diameter. heterotrophic picoplankton Prokaryotes or single-celled eukaryotes that have a cell size between 0.2 and 2 micrometers in diameter and that are not photosynthetic, but rather use organic carbon as a source of energy. From: Wikipedia: Heterotrophic_picoplankton Heterotrophic picoplankton is the fraction of plankton composed by cells between 0.2 and 2 μm that do not perform photosynthesis. Carrine Blank photosynthetic picoplankton picophytoplankton From: Wikipedia: Photosynthetic_picoplankton Photosynthetic picoplankton is the fraction of the phytoplankton performing photosynthesis composed by cells between 0.2 and 2 µm (picoplankton). It is especially important in the central oligotrophic regions of the world oceans that have very low concentration of nutrients. Prokaryotes or single-celled eukaryotes that have a cell size between 0.2 and 2 micrometers in diameter and that are photosynthetic (use light as a source of energy). Carrine Blank picocyanobacteria Prokaryotes or single-celled eukaryotes that have a cell size between 0.2 and 2 micrometers in diameter, that are photosynthetic (use light as a source of energy), and that are members of the genus Prochlorococcus and iin some members of the genus Synechococcus (both Cyanobacteria). Carrine Blank From: Scanlan DJ et al. 2009. Ecological genomics of marine picocyanobacteria. Microbiol Mol Biol Rev 73(2):249-299. Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus numerically dominate the picophytoplankton of the world ocean, making a key contribution to global primary production. septate filaments septa septate Carrine Blank Filament septation, where septa separating the individual cells that make up the filament are present. septum multi-trichomous filament 1 1 Cyanobacterial filament one or more than one trichome in the sheath, with the trichomes oriented parallel to one another, where each trichome is one cell in width. Arises as a result of cell division mostly occurring in only one plane, and occasionally occurring in a second plane. filaments contain one or more trichomes placed together and more or less parallel within one sheath filaments composed of one to more parallel arranged trichomes filaments single or many together sheaths enveloping one (rarely 2) trichomes sheaths containing 1 to several trichomes Carrine Blank one or more trichomes per filament tapered trichome taper A heteropolar trichome that is tapered (has a larger cell diameter at one end of the filament than the other). Carrine Blank tapering cells tapered pleomorphic cell A prokaryotic cell that is irregular in shape, where the shapes of the cells are irregular and variable (pleomorphic). Cell shapes may be variable in size and shape, depending on the environmental conditions. pleiomorphic polymorphic pleomorphic polymorphous Carrine Blank ZoBell starch agar