identifier: METPO:1003009 label: alkalotolerant definition: A pH growth preference in which an organism can tolerate alkaline pH but grows optimally at neutral pH. definition_source: DOI:10.1016/j.bbamem.2005.09.010 trait_category: ENVIRONMENT term_kind: CLASS mapping_status: REVIEWED parent_traits: - METPO:1003000 synonyms: - synonym_text: alkalitolerant synonym_type: EXACT_SYNONYM source: metpo.owl evidence: - reference: DOI:10.1016/j.bbamem.2005.09.010 snippet: alkali-tolerant and extremely alkaliphilic bacteria notes: Supports alkaline pH tolerance as a microbial pH-homeostasis phenotype. canonical_examples: - taxon_id: NCBITaxon:86665 taxon_label: Halalkalibacterium halodurans note: "tolerates high pH (ex-Bacillus halodurans)" reference: PMID:11058132 - taxon_id: NCBITaxon:79885 taxon_label: Alkalihalophilus pseudofirmus note: "alkalitolerant" reference: PMID:21951522 causal_graphs: - graph_id: alkalotolerant_alkaline_stress_homeostasis title: Alkalotolerant alkaline-stress pH homeostasis mechanism description: Evidence-backed causal sketch linking alkalotolerance to alkaline exposure, proton retention, and cation/proton antiport. nodes: - node_id: alkalotolerant_trait label: alkalotolerant node_type: TRAIT grounding: METPO:1003009 description: Tolerates alkaline pH while growing optimally near neutral pH. - node_id: alkaline_exposure label: alkaline exposure node_type: ENVIRONMENTAL_FACTOR description: External pH above neutral. - node_id: cytoplasmic_ph_homeostasis label: cytoplasmic pH homeostasis node_type: BIOLOGICAL_PROCESS description: Maintenance of internal pH during alkaline challenge. grounding: GO:0051453 - node_id: proton_retention label: proton retention node_type: BIOLOGICAL_PROCESS description: Retaining or capturing protons at the cell surface or cytoplasm. - node_id: cation_proton_antiporter label: cation/proton antiporter node_type: GENE_OR_PROTEIN description: Antiporter exchanging cations for protons during pH stress. grounding: UniProtKB:A0A0H3JRG4 - node_id: alkaline_external_ph label: alkaline external pH node_type: ENVIRONMENTAL_FACTOR description: Elevated extracellular pH above neutral. grounding: PATO:0001430 - node_id: electrogenic_na_h_antiport label: electrogenic Na+/H+ antiport node_type: MOLECULAR_FUNCTION description: Electrogenic exchange of sodium for protons, important under alkaline pH. - node_id: cell_surface_acidic_polymers label: acidic non-peptidoglycan cell-surface polymers node_type: CHEMICAL description: Negatively charged cell-wall polymers that modulate ion adsorption at the cell surface. - node_id: sodium_ion label: sodium and hydronium ions node_type: CHEMICAL description: Cations (Na+, H3O+) adsorbed at the cell surface. - node_id: hydroxide_ion label: hydroxide ion node_type: CHEMICAL description: Hydroxide ion (OH-) repelled by the negatively charged cell surface. grounding: CHEBI:16234 - node_id: sodium_motive_force label: sodium motive force node_type: BIOLOGICAL_PROCESS description: Transmembrane sodium gradient supporting bioenergetics and pH control. edges: - subject: alkaline_exposure predicate: challenges object: alkalotolerant_trait description: Alkalotolerance reflects capacity to withstand alkaline pH outside the growth optimum. evidence: - reference: DOI:10.1016/j.bbamem.2005.09.010 snippet: alkali-tolerant and extremely alkaliphilic bacteria notes: Review explicitly covers alkali-tolerant bacteria. predicate_id: METPO:2007406 - subject: alkaline_exposure predicate: challenges object: cytoplasmic_ph_homeostasis description: Alkaline pH requires maintenance of a less alkaline cytoplasm. evidence: - reference: DOI:10.1038/nrmicro2549 snippet: grow in environments with external pH values notes: Review supports pH homeostasis for growth outside cytoplasmic pH range. predicate_id: METPO:2007406 - subject: proton_retention predicate: contributes to object: cytoplasmic_ph_homeostasis description: Proton capture and retention support pH homeostasis in alkaline environments. evidence: - reference: DOI:10.1016/j.bbamem.2005.09.010 snippet: promote proton capture and retention notes: Supports proton retention mechanisms during alkaline pH challenge. predicate_id: RO:0002326 - subject: cation_proton_antiporter predicate: contributes to object: cytoplasmic_ph_homeostasis description: Cation/proton antiporters help regulate intracellular pH under alkaline stress. evidence: - reference: DOI:10.3390/ijms21124566 snippet: maintaining ion and pH homeostasis notes: Supports cation/proton antiporters as pH-homeostasis transporters. predicate_id: RO:0002326 - subject: cytoplasmic_ph_homeostasis predicate: enables object: alkalotolerant_trait description: Alkaline tolerance depends on maintaining cytoplasmic pH during alkaline exposure. evidence: - reference: DOI:10.1038/nrmicro2549 snippet: cell-wide physiological process notes: Supports pH homeostasis as a broad enabling process. predicate_id: RO:0002327 - subject: alkaline_external_ph predicate: increases importance of object: electrogenic_na_h_antiport description: Alkaline extracellular pH makes electrogenic Na+/H+ antiport particularly important for proton import. evidence: - reference: DOI:10.3390/ijms23169156 notes: Negative-inside membrane potential drives Na+ extrusion, particularly important when extracellular pH is alkaline (general prokaryotic mechanism). - subject: cell_surface_acidic_polymers predicate: helps maintain object: cytoplasmic_ph_homeostasis description: Acidic non-peptidoglycan polymers create surface negative charges that reduce pH at the cell surface and help keep intracellular pH near neutrality. evidence: - reference: DOI:10.1007/978-4-431-55408-0_4 notes: Acidic non-peptidoglycan polymers create negative charges that reduce pH at the cell surface and help keep intracellular pH controlled. - subject: cell_surface_acidic_polymers predicate: adsorbs object: sodium_ion description: Negatively charged cell-surface polymers adsorb sodium and hydronium ions. evidence: - reference: DOI:10.1128/MMBR.63.4.735-750.1999 notes: Cell surface acidic polymers adsorb sodium and hydronium ions; cell-envelope charge chemistry mechanism. - subject: cell_surface_acidic_polymers predicate: repels object: hydroxide_ion description: Negatively charged cell-surface polymers repel hydroxide ions, mitigating alkaline stress at the surface. evidence: - reference: DOI:10.1128/MMBR.63.4.735-750.1999 notes: Acidic non-peptidoglycan polymers repulse hydroxide ions at the cell surface. - subject: sodium_motive_force predicate: supports object: cytoplasmic_ph_homeostasis description: A sodium motive force mediated by Na+/H+ antiporters and related proteins supports intracellular pH control. evidence: - reference: DOI:10.1007/s11244-024-01919-7 notes: Sodium motive force mediated by Na+/H+ antiporters, Na+ channels or stator proteins supports intracellular pH control (review-level, broad). curation_history: - timestamp: '2026-05-05T01:35:46.941966+00:00' curator: seed_from_metpo action: SEEDED_FROM_METPO changes: imported from data/raw/metpo.owl (CLASS) llm_assisted: false - timestamp: '2026-05-11T00:00:00-07:00' curator: codex action: CURATED_WITH_LITERATURE changes: Reviewed alkalotolerant trait and added DOI-backed evidence and causal graph for alkaline-stress pH homeostasis. llm_assisted: true - timestamp: '2026-05-20T03:35:29Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326×2, RO:0002327×1). llm_assisted: true - timestamp: '2026-05-23T21:30:06Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007406×2). llm_assisted: true - timestamp: '2026-05-24T04:37:59Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0030641×1). llm_assisted: true - timestamp: '2026-05-24T05:05:13Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A0H3JRG4×1). llm_assisted: true - timestamp: '2026-06-15T07:20:36Z' curator: claude action: FIX_NODE_GROUNDING_CURIE changes: Overwrote 1 causal-node grounding(s) (obsolete/wrong GO -> corrected, verified vs OAK). llm_assisted: true - timestamp: '2026-06-23T00:00:00Z' curator: claude action: ENRICH_CAUSAL_GRAPH changes: Added 5 evidence-backed generic edges (6 new nodes) from the deep-research report. llm_assisted: true - timestamp: '2026-06-24T17:21:16Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001430×1). llm_assisted: true - timestamp: '2026-06-24T17:23:30Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:16234×1). llm_assisted: true