identifier: METPO:1000463 label: pH range mid3 definition: A pH range phenotype in which the growth-supporting external pH range spans approximately 8–10, characteristic of alkaliphile physiology. definition_source: DOI:10.1038/nrmicro2549 trait_category: ENVIRONMENT term_kind: CLASS mapping_status: REVIEWED parent_traits: - METPO:1000332 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: Facultative acidophile synonym_type: EXACT_SYNONYM source: metpo.owl - synonym_text: pHR_8_to_10 synonym_type: RELATED_SYNONYM source: metpo.owl evidence: - reference: DOI:10.1038/nrmicro2549 snippet: alkaliphiles notes: pH-homeostasis review supports alkaliphile physiology growing across pH 8–10. causal_graphs: - graph_id: ph_range_mid3_alkaliphile_range title: pH-range-mid3 alkaliphile range description: DOI-backed graph linking alkaliphile cytoplasmic pH homeostasis to a pH growth range of approximately 8–10. nodes: - node_id: ph_range_mid3_trait label: pH range mid3 node_type: TRAIT grounding: METPO:1000463 description: pH growth-supporting range approximately 8–10. - node_id: ph_range label: pH range node_type: TRAIT grounding: METPO:1000332 description: Span of external pH values supporting growth. - node_id: alkaliphile_homeostasis label: alkaliphile pH homeostasis node_type: BIOLOGICAL_PROCESS description: Proton re-import via Na+/H+ antiporters maintaining a less alkaline cytoplasm at high external pH. - node_id: mrp_antiporter label: Mrp Na+/H+ antiporter complex node_type: GENE_OR_PROTEIN description: Multi-subunit cation/proton antiporter conserved in many alkaliphiles. - node_id: intracellular_ph_homeostasis label: intracellular pH homeostasis node_type: BIOLOGICAL_PROCESS description: Maintenance of a less-alkaline cytoplasm under alkaline external stress. - node_id: nahplus_antiport_activity label: Na+/H+ antiport activity node_type: MOLECULAR_FUNCTION description: Electrogenic exchange importing protons in exchange for sodium ions. - node_id: cytoplasm_acidification label: cytoplasm acidification during alkaline growth node_type: BIOLOGICAL_PROCESS description: Proton import that acidifies the cytoplasm relative to alkaline medium. - node_id: acidic_cell_wall_polymers label: acidic cell-wall polymers (teichuronic acid) node_type: CHEMICAL description: Negatively charged cell-wall polymers proposed to repel hydroxide and adsorb cations. - node_id: cardiolipin_membrane label: cardiolipin-rich negatively charged membrane node_type: CELLULAR_LOCALIZATION description: Membrane enriched in negatively charged phospholipids including cardiolipin. - node_id: carbonate_buffered_medium label: carbonate-buffered alkaline medium node_type: EXPERIMENTAL_FACTOR description: Sodium carbonate/bicarbonate buffering used to set culture pH around 9.5-10. - node_id: growth_range_observation label: observed growth-supporting pH range ~7.5-10.2 node_type: EXPERIMENTAL_FACTOR description: Primary growth-range measurements spanning pH 7.5 to ~10-11. edges: - subject: alkaliphile_homeostasis predicate: enables object: ph_range_mid3_trait description: Alkaliphile pH-homeostasis enables growth across pH 8–10. evidence: - reference: DOI:10.1038/nrmicro2549 snippet: alkaliphiles notes: Supports alkaliphile cytoplasmic pH homeostasis as the alkaline growth-range mechanism. predicate_id: RO:0002327 - subject: ph_range_mid3_trait predicate: is a object: ph_range description: pH range mid3 is a quantitative bin of the pH-range phenotype. evidence: - reference: DOI:10.1016/j.tim.2007.02.005 snippet: proton motive force notes: Supports the pH 8–10 range as a value within the pH-range distribution. predicate_id: rdfs:subClassOf - subject: mrp_antiporter predicate: maintains object: intracellular_ph_homeostasis description: Mrp Na+/H+ antiporter complex maintains intracellular pH homeostasis under alkaline stress. evidence: - reference: DOI:10.1038/s41467-022-33640-y notes: Mrp antiporters essential for growth of alkaliphilic bacteria under stress, maintaining intracellular pH and sodium homeostasis. - subject: nahplus_antiport_activity predicate: causes object: cytoplasm_acidification description: Na+/H+ antiport activity acidifies the cytoplasm during alkaline growth. evidence: - reference: DOI:10.1007/s13205-021-02938-x notes: Alkaliphiles rely on dedicated Na+/H+ antiporters that import H+ in exchange for Na+, acidifying the cytoplasm for pH homeostasis. predicate_id: biolink:causes - subject: cytoplasm_acidification predicate: contributes to object: intracellular_ph_homeostasis description: Acidification of the cytoplasm contributes to intracellular pH homeostasis at high external pH. evidence: - reference: DOI:10.1007/s13205-021-02938-x notes: Proton import via antiport acidifies cytoplasm, a core alkaliphile pH-homeostasis mechanism. predicate_id: RO:0002326 - subject: acidic_cell_wall_polymers predicate: contributes to object: ph_range_mid3_trait description: Acidic cell-wall polymers (teichuronic acid) contribute to alkaline pH tolerance. evidence: - reference: DOI:10.1007/s13205-021-02938-x notes: Alkaliphilic Bacilli reinforce the cell wall with negatively charged teichuronic acid/acidic polymers, hypothesized to repel OH- and adsorb Na+/H+. predicate_id: RO:0002326 - subject: cardiolipin_membrane predicate: supports object: intracellular_ph_homeostasis description: Cardiolipin-rich negatively charged membranes support pH homeostasis at high pH. evidence: - reference: DOI:10.1007/s13205-021-02938-x notes: Alkaliphiles tend to enrich membranes in negatively charged phospholipids including cardiolipin, noted as especially important for pH homeostasis. - subject: carbonate_buffered_medium predicate: enables observation of object: ph_range_mid3_trait description: Carbonate-buffered alkaline medium enables assay/observation of the alkaliphile growth phenotype. evidence: - reference: DOI:10.1007/s13205-023-03733-6 notes: Alkaliphiles are commonly cultured with sodium carbonate/bicarbonate to set pH around 9.5-10, shaping the measured pH niche. - subject: growth_range_observation predicate: is evidence for object: ph_range_mid3_trait description: Observed growth across pH ~7.5-10.2 is evidence for the pH range mid3 phenotype. evidence: - reference: DOI:10.3389/fmicb.2023.1228266 notes: C. thermarum grows pH 7.5-11; alkaliphilic methanogens grow 7.5-10.0 and 7.7-10.2, delimiting the pH 8-10 trait scope. curation_history: - timestamp: '2026-05-05T01:35:46.832120+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 alkaliphile pH-homeostasis to the pH-range-mid3 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 (RO:0002327×1, rdfs:subClassOf×1). llm_assisted: true - timestamp: '2026-06-23T00:00:00Z' curator: claude action: ENRICH_CAUSAL_GRAPH changes: Added 7 evidence-backed generic edges (8 new nodes) from the deep-research report. llm_assisted: true - timestamp: '2026-06-24T17:21:11Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326×2, biolink:causes×1). llm_assisted: true