identifier: METPO:1000458 label: pH optimum high definition: A pH optimum phenotype with the best-growth external pH above approximately 8, corresponding to alkaliphilic or extreme-alkaliphilic physiology. definition_source: DOI:10.1038/nrmicro2549 trait_category: ENVIRONMENT term_kind: CLASS mapping_status: REVIEWED parent_traits: - METPO:1000331 synonyms: - synonym_text: Alkali Tolerant synonym_type: EXACT_SYNONYM source: metpo.owl - synonym_text: Alkaliphile synonym_type: EXACT_SYNONYM source: metpo.owl - synonym_text: Extreme Alkaliphile synonym_type: EXACT_SYNONYM source: metpo.owl - synonym_text: pHO_8_to_14 synonym_type: RELATED_SYNONYM source: metpo.owl evidence: - reference: DOI:10.1038/nrmicro2549 snippet: alkaliphiles notes: pH-homeostasis review supports alkaliphile and extreme-alkaliphile physiology growing at high external pH. - reference: DOI:10.1016/j.tim.2007.02.005 snippet: proton motive force notes: pH-homeostasis review supports Na+/H+ antiporters re-importing protons as the alkaliphile mechanism sustaining the proton motive force at high external pH. causal_graphs: - graph_id: ph_optimum_high_alkaliphile_setpoint title: pH-optimum-high alkaliphile setpoint description: DOI-backed graph linking alkaliphile cytoplasmic pH homeostasis via Na+/H+ antiporters to a pH-optimum above 8 (alkaliphile / extreme alkaliphile). nodes: - node_id: ph_optimum_high_trait label: pH optimum high node_type: TRAIT grounding: METPO:1000458 description: pH optimum above ~8. - node_id: ph_optimum label: pH optimum node_type: TRAIT grounding: METPO:1000331 description: External pH supporting maximal growth. - node_id: alkaline_external_ph label: alkaline external pH node_type: ENVIRONMENTAL_FACTOR description: External pH > ~8, typical of soda lakes and other alkaline habitats. grounding: PATO:0001430 - node_id: na_h_antiporters label: Na+/H+ antiporters node_type: GENE_OR_PROTEIN description: Membrane antiporters importing H+ in exchange for Na+ to acidify the cytoplasm at high external pH. - node_id: alkaliphile_homeostasis label: alkaliphile cytoplasmic pH homeostasis node_type: BIOLOGICAL_PROCESS description: Maintenance of a less alkaline cytoplasm than the external environment by proton re-import. - node_id: cpa_nha_antiporters label: CPA/Nha family Na+/H+ antiporters node_type: GENE_OR_PROTEIN description: Monovalent cation/proton antiporter family exporting Na+ and importing H+. - node_id: intracellular_na label: intracellular Na+ concentration node_type: CHEMICAL description: Cytoplasmic sodium ion concentration. - node_id: trkah_k_uptake label: TrkAH K+ uptake system node_type: GENE_OR_PROTEIN description: Potassium uptake transport system aiding membrane potential and pH homeostasis. - node_id: rnf_complex label: Rnf complex node_type: GENE_OR_PROTEIN description: Ferredoxin:NAD oxidoreductase that pumps Na+ to build a transmembrane Na+ gradient. - node_id: transmembrane_na_gradient label: transmembrane Na+ gradient node_type: BIOLOGICAL_PROCESS description: Electrochemical sodium ion gradient across the membrane. - node_id: terminal_oxidases label: branched respiratory chain terminal oxidases node_type: GENE_OR_PROTEIN description: Terminal oxidases (aa3/ba3/bb3) that pump protons with differing efficiencies. - node_id: proton_motive_force label: proton motive force node_type: BIOLOGICAL_PROCESS description: Electrochemical proton gradient powering bioenergetics. - node_id: acidic_membrane_polymers label: acidic plasma membrane polymers node_type: CHEMICAL description: Acidic cell-envelope polymers (teichuronopeptide, peptidoglycan, teichuronic acid). - node_id: organic_acid_secretion label: organic acid secretion node_type: BIOLOGICAL_PROCESS description: Secretion of metabolic organic acids that helps counter alkaline stress. - node_id: ph_balance label: pH balance node_type: BIOLOGICAL_PROCESS description: Maintenance of cytoplasmic pH balance under alkaline stress. edges: - subject: alkaline_external_ph predicate: selects for object: alkaliphile_homeostasis description: Alkaline environments select for alkaliphile cytoplasmic pH homeostasis. evidence: - reference: DOI:10.1038/nrmicro2549 snippet: alkaliphiles notes: Supports the alkaliphile regime as the environmental context for high-pH optima. predicate_id: METPO:2007401 - subject: na_h_antiporters predicate: regulates object: alkaliphile_homeostasis description: Na+/H+ antiporters drive proton re-import that acidifies the cytoplasm relative to the alkaline external pH. evidence: - reference: DOI:10.1016/j.tim.2007.02.005 snippet: proton motive force notes: Supports antiporter-driven proton re-import as the alkaliphile mechanism for maintaining the proton motive force. predicate_id: RO:0002211 - subject: alkaliphile_homeostasis predicate: produces object: ph_optimum_high_trait description: Alkaliphile pH homeostasis yields an alkaline pH-optimum setpoint. evidence: - reference: DOI:10.1038/nrmicro2549 snippet: alkaliphiles notes: Supports a high-pH optimum as the alkaliphile / extreme-alkaliphile outcome. predicate_id: METPO:2000202 - subject: ph_optimum_high_trait predicate: is a object: ph_optimum description: pH optimum high is a quantitative bin of the pH-optimum phenotype. evidence: - reference: DOI:10.1038/nrmicro2549 snippet: cytoplasmic pH notes: Supports an alkaline optimum as a value within the pH-optimum distribution. predicate_id: rdfs:subClassOf - subject: cpa_nha_antiporters predicate: decreases object: intracellular_na description: CPA/Nha family Na+/H+ antiporters export Na+, lowering intracellular Na+ as part of pH homeostasis. evidence: - reference: DOI:10.1128/AEM.00145-24 notes: Monovalent cation/proton antiporters import H+ and efflux Na+; Na+/H+ antiporters effectively decrease the intracellular Na+ concentration. predicate_id: RO:0002212 - subject: trkah_k_uptake predicate: maintains object: alkaliphile_homeostasis description: TrkAH K+ uptake supports membrane potential adjustment and cytoplasmic pH homeostasis. evidence: - reference: DOI:10.1128/AEM.00145-24 notes: TrkAH transport system takes up K+ and maintains pH homeostasis, adjusting membrane potential. - subject: rnf_complex predicate: generates object: transmembrane_na_gradient description: Rnf complex expels sodium ions to establish a transmembrane Na+ gradient usable for bioenergetics at high pH. evidence: - reference: DOI:10.1515/hsz-2015-0137 notes: Rnf transfers electrons from reduced ferredoxin to NAD and uses the redox difference to expel sodium, establishing a transmembrane sodium gradient. predicate_id: biolink:produces - subject: terminal_oxidases predicate: produces object: proton_motive_force description: Branched respiratory chain terminal oxidases pump protons (with varying efficiencies) to sustain proton motive force at high pH. evidence: - reference: DOI:10.3389/fmicb.2024.1468929 notes: Cyt. aa3 pumps protons at 0.7 H+/electron; ba3 and bb3 pump at 0.5 H+/electron, supporting usable PMF at high pH. predicate_id: METPO:2000202 - subject: acidic_membrane_polymers predicate: enhances object: proton_motive_force description: Acidic plasma-membrane polymers aid proton retention and enhance proton motive force generation at high external pH. evidence: - reference: DOI:10.3390/min14090861 notes: Alkaliphilic Bacillus enhances proton motive force generation by synthesis of acidic plasma membrane (teichuronopeptide, peptidoglycan, teichuronic acid). - subject: organic_acid_secretion predicate: regulates object: ph_balance description: Secretion of organic acids by alkaliphiles permits cytoplasmic pH balance against alkaline stress. evidence: - reference: DOI:10.3390/min14090861 notes: Secretion of organic acids by alkaliphilic microbes is a crucial metabolic activity that permits pH balance. predicate_id: RO:0002211 curation_history: - timestamp: '2026-05-05T01:35:46.828378+00:00' curator: seed_from_metpo action: SEEDED_FROM_METPO changes: imported from data/raw/metpo.owl (CLASS) llm_assisted: false - timestamp: '2026-05-13T10:00:00-07:00' curator: claude action: CURATED_CAUSAL_GRAPH changes: Added DOI-backed definition and causal graph linking Na+/H+ antiporter-driven alkaliphile pH homeostasis to the alkaliphile / extreme-alkaliphile pH-optimum-high bin. llm_assisted: true - timestamp: '2026-05-20T03:35:30Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202×1, rdfs:subClassOf×1). llm_assisted: true - timestamp: '2026-05-23T21:30:06Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007401×1). llm_assisted: true - timestamp: '2026-05-24T04:13:18Z' curator: claude action: RENAME_PREDICATE_LABELS changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings: drives → regulates ×1.' llm_assisted: true - timestamp: '2026-05-24T04:13:21Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211×1). llm_assisted: true - timestamp: '2026-05-24T08:14:32Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001429×1). llm_assisted: true - timestamp: '2026-06-15T07:21:43Z' curator: claude action: FIX_NODE_GROUNDING_CURIE changes: Overwrote 1 pH causal-node grounding(s) to corrected PATO CURIEs (phase-2; verified vs OAK). llm_assisted: true - timestamp: '2026-06-23T00:00:00Z' curator: claude action: ENRICH_CAUSAL_GRAPH changes: Added 6 evidence-backed generic edges (10 new nodes) from the deep-research report. llm_assisted: true - timestamp: '2026-06-24T17:21:10Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212×1, biolink:produces×1, METPO:2000202×1, RO:0002211×1). llm_assisted: true