identifier: METPO:1000649
label: lithotrophic
definition: A trophic type in which an organism uses inorganic compounds as electron
  donors for energy generation.
definition_source: DOI:10.1016/B978-0-12-378630-2.00219-X
trait_category: PHYSIOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000631
synonyms:
- synonym_text: TT_lithotroph
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
- synonym_text: lithotroph
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
created_by: Luke Wang
evidence:
- reference: DOI:10.1016/B978-0-12-378630-2.00219-X
  snippet: oxidize inorganic atoms or molecules
  notes: Encyclopedia review supports inorganic compounds as growth-supporting reductants
    and energy sources.
- reference: DOI:10.1016/j.bbabio.2008.09.008
  snippet: generation of an electrochemical ion gradient
  notes: Review supports respiratory energy conservation through ion gradients and
    ATP synthesis.
canonical_examples:
- taxon_id: NCBITaxon:920
  taxon_label: Acidithiobacillus ferrooxidans
  note: "iron/sulfur lithotroph"
  reference: PMID:19077236
- taxon_id: NCBITaxon:915
  taxon_label: Nitrosomonas europaea
  note: "ammonia lithotroph"
  reference: PMID:12700255
causal_graphs:
- graph_id: lithotrophic_inorganic_donor_energy
  title: Lithotrophic inorganic-donor energy mechanism
  description: DOI-backed graph linking inorganic electron donors to respiratory electron
    transport, proton motive force, and ATP synthesis.
  nodes:
  - node_id: lithotrophic_trait
    label: lithotrophic
    node_type: TRAIT
    grounding: METPO:1000649
    description: Trophic type using inorganic electron donors for energy generation.
  - node_id: inorganic_electron_donor
    label: inorganic electron donor
    node_type: CHEMICAL
    description: Reduced inorganic compound used as a source of electrons.
    grounding: METPO:1007502
  - node_id: hydrogen
    label: molecular hydrogen
    node_type: CHEMICAL
    grounding: CHEBI:18276
    description: Example inorganic electron donor.
  - node_id: reduced_sulfur_compound
    label: reduced sulfur compound
    node_type: CHEMICAL
    description: Example inorganic electron donor class.
  - node_id: membrane_electron_transport_chain
    label: membrane electron transport chain
    node_type: PATHWAY
    description: Redox chain coupling electron flow to ion translocation.
    grounding: GO:0022900
  - node_id: proton_motive_force
    label: proton motive force
    node_type: STATE
    description: Electrochemical ion gradient used for energy conservation.
    grounding: METPO:1007500
  - node_id: atp
    label: ATP
    node_type: CHEMICAL
    grounding: CHEBI:30616
    description: Energy carrier produced from respiratory energy conservation.
  - node_id: thiosulfate
    label: thiosulfate
    node_type: CHEMICAL
    description: Reduced inorganic sulfur compound used as a lithotrophic electron
      donor.
    grounding: CHEBI:16094
  - node_id: sox_multienzyme_system
    label: Sox multienzyme system
    node_type: GENE_OR_PROTEIN
    description: Periplasmic thiosulfate-oxidizing multienzyme complex (soxXA/soxYZ/soxB/soxCD).
  - node_id: sulfite
    label: sulfite
    node_type: CHEMICAL
    description: Inorganic sulfur intermediate oxidized to sulfate during sulfur lithotrophy.
  - node_id: soeabc_sulfite_dehydrogenase
    label: SoeABC sulfite dehydrogenase
    node_type: GENE_OR_PROTEIN
    description: Membrane-bound sulfite dehydrogenase oxidizing sulfite to sulfate.
  - node_id: ammonia
    label: ammonia
    node_type: CHEMICAL
    description: Inorganic nitrogen electron donor for ammonia-oxidizing lithotrophs.
    grounding: CHEBI:16134
  - node_id: ammonia_monooxygenase
    label: ammonia monooxygenase (AMO)
    node_type: GENE_OR_PROTEIN
    description: Enzyme catalyzing the first step of ammonia oxidation (EC 1.14.99.39).
  - node_id: hydroxylamine
    label: hydroxylamine
    node_type: CHEMICAL
    description: Intermediate of ammonia oxidation.
    grounding: CHEBI:15429
  - node_id: hydroxylamine_oxidoreductase
    label: hydroxylamine oxidoreductase (HAO)
    node_type: GENE_OR_PROTEIN
    description: Enzyme oxidizing hydroxylamine during ammonia oxidation (EC 1.7.2.6).
  - node_id: nitrite
    label: nitrite
    node_type: CHEMICAL
    description: Inorganic nitrogen electron donor for nitrite-oxidizing lithotrophs.
    grounding: CHEBI:16301
  - node_id: nitrite_oxidoreductase
    label: nitrite oxidoreductase (NXR)
    node_type: GENE_OR_PROTEIN
    description: Enzyme oxidizing nitrite to nitrate (EC 1.7.5.1).
  - node_id: oxygen
    label: molecular oxygen
    node_type: CHEMICAL
    description: Terminal electron acceptor for aerobic lithotrophic oxidation.
    grounding: CHEBI:15379
  - node_id: sulfur_oxidation_process
    label: sulfur oxidation
    node_type: BIOLOGICAL_PROCESS
    description: Oxidation of reduced sulfur compounds for energy conservation.
    grounding: GO:0019417
  edges:
  - subject: lithotrophic_trait
    predicate: uses electron donor
    object: inorganic_electron_donor
    description: Lithotrophic organisms use inorganic compounds as electron donors.
    evidence:
    - reference: DOI:10.1016/B978-0-12-378630-2.00219-X
      snippet: inorganic atoms or molecules as a growth-supporting reductant
      notes: Supports inorganic electron donors as the defining lithotrophic substrate
        class.
    predicate_id: METPO:2000009
  - subject: hydrogen
    predicate: example of
    object: inorganic_electron_donor
    description: Molecular hydrogen is a representative inorganic electron donor.
    evidence:
    - reference: DOI:10.21775/cimb.006.159
      snippet: oxidation of hydrogen gas
      notes: Supports hydrogen gas as a microbial inorganic electron donor.
    predicate_id: rdfs:subClassOf
  - subject: reduced_sulfur_compound
    predicate: example of
    object: inorganic_electron_donor
    description: Reduced sulfur compounds are representative lithotrophic electron
      donors.
    evidence:
    - reference: DOI:10.1111/j.1574-6976.2009.00187.x
      snippet: lithotrophic sulfur oxidation
      notes: Supports sulfur oxidation as a lithotrophic process.
    predicate_id: rdfs:subClassOf
  - subject: inorganic_electron_donor
    predicate: donates electrons to
    object: membrane_electron_transport_chain
    description: Electrons from inorganic donors enter respiratory electron transport.
    evidence:
    - reference: DOI:10.1016/j.bbabio.2008.09.008
      snippet: membrane-bound electron transport chain
      notes: Supports membrane-bound redox chains as energy-conserving electron-transfer
        systems.
    predicate_id: METPO:2007403
  - subject: membrane_electron_transport_chain
    predicate: generates
    object: proton_motive_force
    description: Respiratory redox reactions are conserved as an electrochemical ion
      gradient.
    evidence:
    - reference: DOI:10.1016/j.bbabio.2008.09.008
      snippet: generation of an electrochemical ion gradient
      notes: Supports proton motive force generation by respiratory electron transport.
    predicate_id: biolink:produces
  - subject: proton_motive_force
    predicate: drives synthesis of
    object: atp
    description: Proton motive force drives ATP synthesis.
    evidence:
    - reference: DOI:10.1016/j.bbabio.2008.09.008
      snippet: gradient ... drives ATP synthesis
      notes: Supports ATP production from the respiratory ion gradient.
    predicate_id: biolink:produces
  - subject: thiosulfate
    predicate: oxidized by
    object: sox_multienzyme_system
    description: Thiosulfate is oxidized by the periplasmic Sox multienzyme system.
    evidence:
    - reference: DOI:10.3390/microorganisms11061436
      notes: 'Review: "The Sox multienzyme system... performs periplasmic thiosulfate
        oxidation."'
  - subject: sulfite
    predicate: oxidized by
    object: soeabc_sulfite_dehydrogenase
    description: Sulfite is oxidized to sulfate by membrane-bound SoeABC sulfite dehydrogenase.
    evidence:
    - reference: DOI:10.3390/microorganisms11061436
      notes: 'Review: "Sulfite produced is oxidized to sulfate by membrane-bound SoeABC."'
  - subject: ammonia
    predicate: oxidized by
    object: ammonia_monooxygenase
    description: Ammonia is oxidized by ammonia monooxygenase (AMO) in ammonia-oxidizing
      lithotrophs.
    evidence:
    - reference: DOI:10.1186/s40168-025-02290-9
      notes: Key NH4+ oxidation enzymes including ammonia monooxygenase (AMO); canonical
        enzyme role.
  - subject: hydroxylamine
    predicate: oxidized by
    object: hydroxylamine_oxidoreductase
    description: Hydroxylamine is oxidized by hydroxylamine oxidoreductase (HAO).
    evidence:
    - reference: DOI:10.1186/s40168-025-02290-9
      notes: Key NH4+ oxidation enzymes including hydroxylamine oxidoreductase (HAO).
  - subject: nitrite
    predicate: oxidized by
    object: nitrite_oxidoreductase
    description: Nitrite is oxidized to nitrate by nitrite oxidoreductase (NXR).
    evidence:
    - reference: DOI:10.1128/mbio.00749-25
      notes: Nitrite further oxidized to nitrate by a nitrite oxidoreductase gene
        (nxr).
  - subject: oxygen
    predicate: serves as terminal acceptor for
    object: sulfur_oxidation_process
    description: Molecular oxygen serves as a terminal electron acceptor for aerobic
      sulfur oxidation.
    evidence:
    - reference: DOI:10.1038/s41579-024-01104-3
      notes: Sulfur oxidation susceptible to oxidation by electron acceptors; aerobic
        sulfur oxidation contexts.
curation_history:
- timestamp: '2026-05-05T01:35:46.875909+00:00'
  curator: seed_from_metpo
  action: SEEDED_FROM_METPO
  changes: imported from data/raw/metpo.owl (CLASS)
  llm_assisted: false
- timestamp: '2026-05-08T00:00:00-07:00'
  curator: codex
  action: ADDED_CAUSAL_GRAPH
  changes: Added DOI-backed causal graph for inorganic electron donors, respiratory
    electron transport, proton motive force, and ATP synthesis.
  llm_assisted: true
- timestamp: '2026-05-20T03:35:31Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2000009×1).
  llm_assisted: true
- timestamp: '2026-05-23T08:21:50Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (rdfs:subClassOf×2, biolink:produces×1).
  llm_assisted: true
- timestamp: '2026-05-24T04:41:04Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv
    (METPO:1007502×1, METPO:1007500×1).
  llm_assisted: true
- timestamp: '2026-05-24T08:14:33Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (GO:0022900×1).
  llm_assisted: true
- timestamp: '2026-05-26T02:30:13Z'
  curator: claude
  action: RETYPE_CAUSAL_NODES
  changes: 'Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum
    semantics: proton motive force: BIOLOGICAL_PROCESS → STATE ×1.'
  llm_assisted: true
- timestamp: '2026-06-13T21:03:27Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (biolink:produces×1).
  llm_assisted: true
- timestamp: '2026-06-14T07:26:20Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2007403×1).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 6 evidence-backed generic edges (12 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:20Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 5 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:16094×1, CHEBI:16134×1, CHEBI:15429×1, CHEBI:15379×1, GO:0019417×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:23:34Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:16301×1).
  llm_assisted: true