identifier: METPO:1000639 label: chemolithotrophic definition: A trophic type characterized by the use of inorganic chemical compounds as electron donors and carbon dioxide as the primary carbon source for energy generation and biosynthesis. 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: chemolithotroph synonym_type: RELATED_SYNONYM source: metpo.owl created_by: Anthea Guo evidence: - reference: DOI:10.1016/B978-0-12-378630-2.00219-X snippet: chemolithotrophic bacteria and archaea notes: Review supports inorganic compound oxidation as chemolithotrophic growth. - reference: DOI:10.1146/annurev.micro.55.1.485 snippet: Chemolitho-autotrophic ammonia-oxidizing bacteria notes: Review supports ammonia oxidation as an example chemolithoautotrophic process. - reference: PMID:12700255 snippet: Nitrosomonas europaea notes: 'Organism example: Nitrosomonas europaea is the model chemolithotrophic ammonia-oxidizing bacterium, conserving energy from NH3 → NO2- oxidation (Chain et al. 2003, J Bacteriol, complete genome).' canonical_examples: - taxon_id: NCBITaxon:915 taxon_label: Nitrosomonas europaea note: "ammonia-oxidising chemolithotroph" reference: PMID:12700255 - taxon_id: NCBITaxon:36861 taxon_label: Thiobacillus denitrificans note: "sulfur-oxidising chemolithotroph" reference: PMID:16452431 causal_graphs: - graph_id: chemolithotrophic_inorganic_oxidation title: Chemolithotrophic inorganic chemical oxidation description: DOI-backed graph for inorganic chemical electron donors, representative ammonia and sulfur oxidation, and respiratory energy conservation. nodes: - node_id: chemolithotrophic_trait label: chemolithotrophic node_type: TRAIT grounding: METPO:1000639 description: Trophic type using inorganic chemicals for energy generation. - node_id: inorganic_chemical_donor label: inorganic chemical electron donor node_type: CHEMICAL description: Reduced inorganic chemical substrate. - node_id: ammonia label: ammonia node_type: CHEMICAL grounding: CHEBI:16134 description: Representative reduced nitrogen electron donor. - node_id: ammonia_monooxygenase label: ammonia monooxygenase node_type: GENE_OR_PROTEIN description: Enzyme initiating aerobic ammonia oxidation. grounding: UniProtKB:A0A059V4Z9 - node_id: hydroxylamine label: hydroxylamine node_type: CHEMICAL description: Intermediate formed from ammonia oxidation. grounding: CHEBI:15429 - node_id: nitrite label: nitrite node_type: CHEMICAL grounding: CHEBI:16301 description: Oxidized nitrogen product of ammonia oxidation. - node_id: sox_enzyme_system label: Sox enzyme system node_type: GENE_OR_PROTEIN description: Sulfur-oxidizing multienzyme system. - node_id: thiosulfate label: thiosulfate node_type: CHEMICAL description: Representative reduced sulfur donor. grounding: CHEBI:16094 - node_id: respiratory_chain label: respiratory chain node_type: PATHWAY description: Electron-transfer system conserving energy from donor oxidation. grounding: GO:0022904 - node_id: atp label: ATP node_type: CHEMICAL grounding: CHEBI:30616 description: Energy carrier produced by respiratory energy conservation. - node_id: calvin_benson_bassham_cycle label: Calvin-Benson-Bassham cycle node_type: PATHWAY grounding: GO:0015977 description: Reductive pentose phosphate carbon-fixation pathway. - node_id: carbon_dioxide label: carbon dioxide node_type: CHEMICAL grounding: CHEBI:16526 description: Inorganic carbon source fixed during chemolithoautotrophy. - node_id: acidification label: acidification node_type: ENVIRONMENTAL_FACTOR description: Decrease in environmental pH. - node_id: nitrification_rate label: nitrification rate node_type: BIOLOGICAL_PROCESS description: Rate of microbial oxidation of ammonia to nitrate. - node_id: nitrous_oxide label: nitrous oxide node_type: CHEMICAL description: N2O byproduct generated during nitrification. grounding: CHEBI:17045 edges: - subject: chemolithotrophic_trait predicate: uses electron donor object: inorganic_chemical_donor description: Chemolithotrophy uses inorganic chemicals as electron donors. evidence: - reference: DOI:10.1016/B978-0-12-378630-2.00219-X snippet: oxidize inorganic atoms or molecules notes: Supports inorganic chemical oxidation as chemolithotrophy. predicate_id: METPO:2000009 - subject: ammonia_monooxygenase predicate: oxidizes object: ammonia description: Ammonia monooxygenase initiates ammonia oxidation. evidence: - reference: DOI:10.1146/annurev.micro.55.1.485 snippet: ammonia-oxidizing bacteria notes: Supports ammonia oxidation as a chemolithoautotrophic process. predicate_id: METPO:2000016 - subject: ammonia predicate: oxidized to object: hydroxylamine description: Ammonia oxidation proceeds through hydroxylamine. evidence: - reference: DOI:10.1007/s00775-020-01820-0 snippet: convert ammonia to hydroxylamine notes: Supports AMO-catalyzed ammonia-to-hydroxylamine conversion. predicate_id: METPO:2007405 - subject: hydroxylamine predicate: oxidized to object: nitrite description: Hydroxylamine oxidation yields nitrite in ammonia oxidizers. evidence: - reference: DOI:10.3389/fmicb.2012.00210 snippet: oxidation of hydroxylamine to nitrite notes: Supports hydroxylamine oxidation as the next nitrification step. predicate_id: METPO:2007405 - subject: sox_enzyme_system predicate: oxidizes object: thiosulfate description: Sox proteins mediate oxidation of reduced sulfur compounds such as thiosulfate. evidence: - reference: DOI:10.1111/j.1574-6976.2009.00187.x snippet: oxidation of thiosulfate notes: Supports the Sox multienzyme system in lithotrophic sulfur oxidation. predicate_id: METPO:2000016 - subject: inorganic_chemical_donor predicate: feeds electrons into object: respiratory_chain description: Oxidation of inorganic donors feeds electrons into respiratory chains. evidence: - reference: DOI:10.1016/j.bbabio.2008.09.008 snippet: membrane-bound electron transport chain notes: Supports respiratory chains as energy-conserving redox systems. predicate_id: METPO:2007402 - subject: respiratory_chain predicate: produces object: atp description: Respiratory energy conservation produces ATP. evidence: - reference: DOI:10.1016/j.bbabio.2008.09.008 snippet: drives ATP synthesis notes: Supports ATP synthesis from the respiratory ion gradient. predicate_id: METPO:2000202 - subject: calvin_benson_bassham_cycle predicate: mediates fixation of object: carbon_dioxide description: Chemolithoautotrophs fix CO2 via the Calvin-Benson-Bassham cycle. evidence: - reference: DOI:10.3390/microorganisms12030590 notes: fixes atmospheric CO2 via the Calvin-Benson-Bassham (CBB) cycle - subject: acidification predicate: decreases object: nitrification_rate description: Environmental acidification reduces nitrification rates. evidence: - reference: DOI:10.1038/s41467-023-37104-9 notes: a 5.8-18.1% drop and ~11.1-34.1% decline when pCO2 was doubled predicate_id: RO:0002212 - subject: acidification predicate: stimulates generation of object: nitrous_oxide description: Acidification stimulates N2O byproduct generation during nitrification. evidence: - reference: DOI:10.1038/s41467-023-37104-9 notes: Acidification also stimulate[s] generation of byproduct nitrous oxide (N2O) curation_history: - timestamp: '2026-05-05T01:35:46.871549+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 chemical electron donors, ammonia oxidation, sulfur oxidation, respiratory energy conservation, and ATP synthesis. llm_assisted: true - timestamp: '2026-05-16T05:00:00-07:00' curator: claude action: ADDED_ORGANISM_EXAMPLE changes: Added Nitrosomonas europaea organism example with PMID-backed evidence. llm_assisted: true - timestamp: '2026-05-20T03:35:31Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000016×2, METPO:2000009×1, METPO:2000202×1). llm_assisted: true - timestamp: '2026-05-23T21:30:07Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007405×2, METPO:2007402×1). llm_assisted: true - timestamp: '2026-05-24T04:38:01Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0022904×1). llm_assisted: true - timestamp: '2026-05-24T05:05:15Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A059V4Z9×1). 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 (CHEBI:33542×1). llm_assisted: true - timestamp: '2026-06-14T05:51:47Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:15429×1). llm_assisted: true - timestamp: '2026-06-15T07:19:09Z' curator: claude action: FIX_NODE_GROUNDING_CURIE changes: Overwrote 1 causal-node grounding(s) to corrected CURIEs (phase-2 id-label fix; verified vs OAK). llm_assisted: true - timestamp: '2026-06-23T00:00:00Z' curator: claude action: ENRICH_CAUSAL_GRAPH changes: Added 3 evidence-backed generic edges (5 new nodes) from the deep-research report. llm_assisted: true - timestamp: '2026-06-24T17:21:14Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212×1). 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:17045×1). llm_assisted: true