identifier: METPO:1000462 label: pH range mid2 definition: A pH range phenotype in which the growth-supporting external pH range spans approximately 7–8, characteristic of neutrophile or mild-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: Facultative acidophile synonym_type: EXACT_SYNONYM source: metpo.owl - synonym_text: Neutrophile synonym_type: EXACT_SYNONYM source: metpo.owl - synonym_text: pHR_7_to_8 synonym_type: RELATED_SYNONYM source: metpo.owl evidence: - reference: DOI:10.1038/nrmicro2549 snippet: pH homeostasis notes: pH-homeostasis review supports modest alkaline-tolerance physiology as the basis of growth across pH 7–8. causal_graphs: - graph_id: ph_range_mid2_mild_alkaline_tolerance title: pH-range-mid2 mild-alkaline-tolerance range description: DOI-backed graph linking modest alkaline pH-homeostasis to a pH growth range of approximately 7–8. nodes: - node_id: ph_range_mid2_trait label: pH range mid2 node_type: TRAIT grounding: METPO:1000462 description: pH growth-supporting range approximately 7–8. - node_id: ph_range label: pH range node_type: TRAIT grounding: METPO:1000332 description: Span of external pH values supporting growth. - node_id: modest_alkaline_tolerance label: modest alkaline-tolerance physiology node_type: BIOLOGICAL_PROCESS description: Mild K+/H+ antiport and cytoplasmic acidification activity enabling growth at slightly basic external pH. - node_id: external_ph_7_8 label: external pH 7-8 node_type: ENVIRONMENTAL_FACTOR description: Mildly alkaline to neutral external pH condition spanning approximately 7-8. - node_id: cytoplasmic_ph_homeostasis label: cytoplasmic pH homeostasis node_type: BIOLOGICAL_PROCESS description: Maintenance of internal pH near 7.0-7.5 despite external pH variation. grounding: GO:0051453 - node_id: cytoplasmic_buffering label: cytoplasmic buffering node_type: BIOLOGICAL_PROCESS description: Inorganic/organic buffers limit pH fluctuation given very low free proton count. - node_id: na_h_antiport_activity label: Na+/H+ antiporter activity node_type: MOLECULAR_FUNCTION description: Coupled Na+/H+ exchange that acidifies the cytoplasm when internal pH rises. - node_id: cytoplasm label: cytoplasm node_type: CELLULAR_LOCALIZATION description: Intracellular compartment whose pH is regulated by antiport activity. grounding: GO:0005737 - node_id: proton_motive_force label: proton motive force node_type: BIOLOGICAL_PROCESS description: Composite electrochemical proton gradient used for energy transduction and transport. - node_id: external_ph_5_8 label: external pH 5-8 node_type: ENVIRONMENTAL_FACTOR description: External pH span across which neutralophiles keep PMF relatively constant. - node_id: dpsi_dph_rebalancing label: membrane potential / ΔpH rebalancing node_type: BIOLOGICAL_PROCESS description: Shifting relative contributions of Δψ and ΔpH with external pH to preserve PMF. - node_id: f0f1_atpase label: F0F1-ATPase node_type: GENE_OR_PROTEIN description: ATP synthase coupling proton re-entry (PMF) to ATP generation. - node_id: atp_synthesis label: ATP synthesis node_type: BIOLOGICAL_PROCESS description: Generation of ATP driven by the proton motive force. grounding: GO:0006754 - node_id: proton_ion_antiporters label: proton:ion antiporters node_type: GENE_OR_PROTEIN description: Antiporters with a direct role in sustaining membrane potential. - node_id: membrane_potential label: membrane potential (Δψ) node_type: BIOLOGICAL_PROCESS description: Transmembrane electrical potential contributing to PMF. edges: - subject: modest_alkaline_tolerance predicate: enables object: ph_range_mid2_trait description: Modest alkaline-tolerance physiology enables growth across pH 7–8. evidence: - reference: DOI:10.1016/j.tim.2007.02.005 snippet: proton motive force notes: Supports balanced proton motive force at slightly alkaline pH as the range mechanism. predicate_id: RO:0002327 - subject: ph_range_mid2_trait predicate: is a object: ph_range description: pH range mid2 is a quantitative bin of the pH-range phenotype. evidence: - reference: DOI:10.1038/nrmicro2549 snippet: cytoplasmic pH notes: Supports the pH 7–8 range as a value within the pH-range distribution. predicate_id: rdfs:subClassOf - subject: external_ph_7_8 predicate: permits maintenance of object: cytoplasmic_ph_homeostasis description: External pH 7-8 permits cells to keep internal pH near 7.0-7.5. evidence: - reference: DOI:10.1093/femsre/fuad033 notes: Internal pH kept within 7.0-7.5 and PMF relatively constant across external pH 5-8. - subject: cytoplasmic_buffering predicate: stabilizes object: cytoplasmic_ph_homeostasis description: Cytoplasmic buffering stabilizes internal pH given very low free proton count. evidence: - reference: DOI:10.1093/femsre/fuad033 notes: A ~1 fL cytoplasm at pH 7.2 contains only ~10 free protons, so buffering is critical. - subject: na_h_antiport_activity predicate: acidifies object: cytoplasm description: Na+/H+ antiporter activity acidifies the cytoplasm when internal pH rises. evidence: - reference: DOI:10.1093/femsre/fuad033 notes: Na+/H+ and K+/H+ antiporters acidify the cytoplasm by exchanging exported cations for H+. - subject: proton_motive_force predicate: remains relatively constant across object: external_ph_5_8 description: Neutralophiles keep PMF relatively constant across external pH ~5-8. evidence: - reference: DOI:10.1093/femsre/fuad033 notes: Neutralophilic bacteria adjust ΔpH vs Δψ so PMF stays relatively constant across external pH ~5-8. - subject: dpsi_dph_rebalancing predicate: maintains object: proton_motive_force description: Rebalancing of ΔpH and Δψ with external pH maintains PMF. evidence: - reference: DOI:10.1093/femsre/fuad033 notes: The relative contribution of ΔpH and Δψ shifts with external pH to preserve PMF. - subject: f0f1_atpase predicate: couples object: atp_synthesis description: F0F1-ATPase couples the proton motive force to ATP synthesis. evidence: - reference: DOI:10.1093/femsre/fuad033 notes: PMF drives ATP synthesis; F0F1 uses ~3-5 H+ per ATP. - subject: proton_ion_antiporters predicate: maintain object: membrane_potential description: Proton:ion antiporters have a direct role in maintaining membrane potential. evidence: - reference: DOI:10.1146/annurev-biophys-030822-032215 notes: Antiporters have a direct role in maintaining membrane potential in E. coli. curation_history: - timestamp: '2026-05-05T01:35:46.831107+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 modest alkaline-tolerance physiology to the pH-range-mid2 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 (12 new nodes) from the deep-research report. llm_assisted: true - timestamp: '2026-06-24T17:21:17Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0051453×1, GO:0005737×1). llm_assisted: true - timestamp: '2026-06-24T17:23:31Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0006754×1). llm_assisted: true