identifier: METPO:1000232 label: pH delta definition: A pH phenotype with numerical limits expressing the breadth (maximum minus minimum) of external pH supporting growth of an organism. definition_source: DOI:10.1038/nrmicro2549 trait_category: ENVIRONMENT term_kind: CLASS mapping_status: REVIEWED parent_traits: - METPO:1000531 - METPO:1000534 evidence: - reference: DOI:10.1038/nrmicro2549 snippet: pH homeostasis notes: pH-homeostasis review supports the breadth of the pH-tolerance span as a derived descriptor reflecting overall pH-homeostasis flexibility. - reference: DOI:10.1016/j.tim.2007.02.005 snippet: proton motive force notes: pH-homeostasis review supports the proton motive force as the energetic constraint underlying broad versus narrow pH tolerance. causal_graphs: - graph_id: ph_delta_homeostasis_flexibility title: pH-delta homeostasis flexibility description: DOI-backed graph linking the flexibility of pH-homeostasis machinery to the breadth of the pH growth range (delta = max − min). nodes: - node_id: ph_delta_trait label: pH delta node_type: TRAIT grounding: METPO:1000232 description: Breadth of the growth-supporting external pH range. - node_id: ph_homeostasis_flexibility label: pH-homeostasis flexibility node_type: BIOLOGICAL_PROCESS description: Capacity to remodel proton extrusion, K+/H+ antiport, and envelope buffering across a wide span of external pH. - node_id: tolerance_breadth label: pH tolerance breadth node_type: BIOLOGICAL_PROCESS description: Span between the minimum and maximum growth-supporting external pH. - node_id: ph_homeostasis label: external pH homeostasis node_type: BIOLOGICAL_PROCESS description: Maintenance of intracellular pH within viable bounds across external pH variation. - node_id: proton_motive_force_generation label: proton motive force generation node_type: BIOLOGICAL_PROCESS description: Establishment of the transmembrane electrochemical proton gradient. - node_id: f0f1_atpase_activity label: F0F1-ATPase activity node_type: MOLECULAR_FUNCTION description: F-type H+-transporting ATPase coupling proton flux to ATP synthesis/hydrolysis. - node_id: cation_proton_antiporter_activity label: monovalent cation:H+ antiporter activity node_type: MOLECULAR_FUNCTION description: Exchange of Na+/K+ for H+ to support pH homeostasis, notably under alkaline conditions. - node_id: membrane_lipid_remodeling label: saturated membrane fatty acid remodeling node_type: BIOLOGICAL_PROCESS description: Enrichment of saturated membrane fatty acids that reduces membrane proton permeability. - node_id: proton_permeability label: membrane proton permeability node_type: QUALITY description: Passive permeability of the cell membrane to protons. - node_id: amino_acid_decarboxylase_acid_resistance label: amino-acid decarboxylase acid-resistance system node_type: PATHWAY description: Decarboxylase systems that consume intracellular protons and export amines under acid stress. - node_id: low_ph_tolerance label: low-pH tolerance node_type: CAPACITY description: Capacity to grow and survive under acidic external pH. - node_id: oxidative_phosphorylation label: oxidative phosphorylation node_type: BIOLOGICAL_PROCESS description: Respiratory generation of PMF and proton export contributing to cytoplasmic pH defense. grounding: GO:0006119 edges: - subject: ph_homeostasis_flexibility predicate: enables object: tolerance_breadth description: pH-homeostasis flexibility enables broad pH tolerance. evidence: - reference: DOI:10.1038/nrmicro2549 snippet: pH homeostasis notes: Supports the breadth of pH homeostasis as the basis of broad pH tolerance. predicate_id: RO:0002327 - subject: tolerance_breadth predicate: manifests as object: ph_delta_trait description: The breadth between minimum and maximum growth-supporting external pH manifests the pH-delta phenotype. evidence: - reference: DOI:10.1016/j.tim.2007.02.005 snippet: proton motive force notes: Supports the bounded proton motive force as the determinant of the pH tolerance breadth. predicate_id: METPO:2007400 - subject: ph_homeostasis predicate: enables object: ph_delta_trait description: External pH homeostasis enables a broader external pH growth breadth. evidence: - reference: DOI:10.1093/femsre/fuad033 notes: Na+/H+ and K+/H+ antiporters and proton-pumping systems prevent internal pH from becoming too low, underpinning growth across pH (general bacteria, review). predicate_id: RO:0002327 - subject: proton_motive_force_generation predicate: supports object: ph_homeostasis description: Proton motive force generation supports external pH homeostasis. evidence: - reference: DOI:10.1093/femsre/fuad033 notes: PMF-linked systems regulate internal pH; decarboxylation can store free energy as PMF (general bacteria, review). - subject: f0f1_atpase_activity predicate: supports object: ph_homeostasis description: F0F1-ATPase activity supports external pH homeostasis. evidence: - reference: DOI:10.1093/femsre/fuad033 notes: F0F1-ATPase uses 3-5 protons per ATP and is among systems that prevent internal pH from becoming too low (general bacteria, review). - subject: cation_proton_antiporter_activity predicate: supports object: ph_homeostasis description: Monovalent cation:H+ antiporter activity supports pH homeostasis under alkaline conditions. evidence: - reference: DOI:10.1128/AEM.00569-24 notes: Monovalent antiporters exchange Na+/K+ to facilitate proton entry for alkali tolerance (generic transporter class). - subject: membrane_lipid_remodeling predicate: decreases object: proton_permeability description: Saturated membrane fatty acid remodeling decreases membrane proton permeability. evidence: - reference: DOI:10.3389/fmicb.2022.1034164 notes: Membranes enriched in saturated fatty acids reduce proton permeability, minimizing proton influx in acidic environments (generalizable low-pH mechanism). predicate_id: RO:0002212 - subject: amino_acid_decarboxylase_acid_resistance predicate: increases object: low_ph_tolerance description: Amino-acid decarboxylase acid-resistance systems increase low-pH tolerance. evidence: - reference: DOI:10.3390/microorganisms12091774 notes: Amino-acid decarboxylase systems consume protons and export corresponding amines as a key acid-resistance mechanism (authoritative review). predicate_id: RO:0002213 - subject: oxidative_phosphorylation predicate: supports object: ph_homeostasis description: Oxidative phosphorylation upregulation supports proton export and resistance to cytoplasmic acidification. evidence: - reference: DOI:10.3390/microorganisms12081565 notes: Increased oxidative phosphorylation generates PMF and a higher proton export rate, causally helping cells resist decreases in cytoplasmic pH. curation_history: - timestamp: '2026-05-05T01:35:46.812528+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 causal graph linking pH-homeostasis flexibility and the proton motive force to the pH-delta breadth phenotype. llm_assisted: true - timestamp: '2026-05-20T03:35:30Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327×1). 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:2007400×1). llm_assisted: true - timestamp: '2026-06-23T00:00:00Z' curator: claude action: ENRICH_CAUSAL_GRAPH changes: Added 7 evidence-backed generic edges (9 new nodes) from the deep-research report. llm_assisted: true - timestamp: '2026-06-24T17:21:10Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327×1, RO:0002212×1, RO:0002213×1). llm_assisted: true - timestamp: '2026-06-24T17:21:17Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0006119×1). llm_assisted: true