identifier: METPO:1000455 label: pH optimum low definition: A pH optimum phenotype with the best-growth external pH at or below approximately 6, corresponding to acidophilic or extreme-acidophilic physiology. definition_source: DOI:10.1038/nrmicro2549 trait_category: ENVIRONMENT term_kind: CLASS mapping_status: REVIEWED parent_traits: - METPO:1000331 synonyms: - synonym_text: Acid Tolerant synonym_type: EXACT_SYNONYM source: metpo.owl - synonym_text: Acidophile synonym_type: EXACT_SYNONYM source: metpo.owl - synonym_text: Extreme Acidophile synonym_type: EXACT_SYNONYM source: metpo.owl - synonym_text: Facultative acidophile synonym_type: EXACT_SYNONYM source: metpo.owl - synonym_text: Obligative acidophile synonym_type: EXACT_SYNONYM source: metpo.owl - synonym_text: pHO_0_to_6 synonym_type: RELATED_SYNONYM source: metpo.owl evidence: - reference: DOI:10.1038/nrmicro2549 snippet: growing at pH 1.0-3.0 notes: pH-homeostasis review supports growth at acidic external pH as the acidophilic / extreme-acidophilic category. causal_graphs: - graph_id: ph_optimum_low_acidophile_setpoint title: pH-optimum-low acidophile setpoint description: DOI-backed graph linking proton-exclusion physiology at acidic external pH to a pH-optimum at or below 6 (acidophile / extreme acidophile). nodes: - node_id: ph_optimum_low_trait label: pH optimum low node_type: TRAIT grounding: METPO:1000455 description: pH optimum at or below ~6. - node_id: ph_optimum label: pH optimum node_type: TRAIT grounding: METPO:1000331 description: External pH supporting maximal growth. - node_id: acidic_external_ph label: acidic external pH node_type: ENVIRONMENTAL_FACTOR description: External pH ≤ ~6, typical of acidic mine drainage and acidic soils. grounding: PATO:0001429 - node_id: acidophile_proton_exclusion label: acidophile proton-exclusion physiology node_type: BIOLOGICAL_PROCESS description: Low-permeability membranes and reversed membrane potential that exclude protons in acidophiles. - node_id: low_external_ph label: low external pH node_type: ENVIRONMENTAL_FACTOR description: Acidic medium external pH below ~3 imposing a steep proton gradient. - node_id: transmembrane_ph_gradient label: large transmembrane pH gradient node_type: BIOLOGICAL_PROCESS description: Steep outside-to-inside proton (delta pH) gradient maintained by acidophiles. - node_id: inside_positive_membrane_potential label: inside-positive membrane potential node_type: BIOLOGICAL_PROCESS description: Reversed (inside-positive) membrane potential creating an electrochemical barrier to proton influx. - node_id: proton_influx label: proton influx node_type: BIOLOGICAL_PROCESS description: Passive entry of protons into the cytoplasm down the pH gradient. - node_id: proton_pumping_respiratory_complexes label: proton-pumping respiratory complexes node_type: GENE_OR_PROTEIN description: Respiratory chain complexes (I, III, IV) that actively extrude cytoplasmic protons. - node_id: cytoplasmic_proton_load label: cytoplasmic proton load node_type: STATE description: Concentration of protons in the cytoplasm threatening near-neutral intracellular pH. - node_id: proton_impermeable_membrane label: rigid proton-impermeable membrane node_type: CELLULAR_LOCALIZATION description: Rigid membrane highly resistant to proton influx, reducing passive proton permeability. - node_id: passive_proton_permeability label: passive proton permeability node_type: QUALITY description: Rate of passive proton leakage across the cell membrane. edges: - subject: acidic_external_ph predicate: selects for object: acidophile_proton_exclusion description: Acidic environments select for proton-exclusion physiology. evidence: - reference: DOI:10.1016/j.tim.2007.02.005 snippet: highly impermeable cell membranes notes: Supports envelope-based proton barriers as the selected acidophile mechanism. predicate_id: METPO:2007401 - subject: acidophile_proton_exclusion predicate: produces object: ph_optimum_low_trait description: Acidophile proton-exclusion physiology yields an acidic pH-optimum setpoint. evidence: - reference: DOI:10.1038/nrmicro2549 snippet: growing at pH 1.0-3.0 notes: Supports growth at strongly acidic pH as the acidophile outcome. predicate_id: METPO:2000202 - subject: ph_optimum_low_trait predicate: is a object: ph_optimum description: pH optimum low is a quantitative bin of the pH-optimum phenotype. evidence: - reference: DOI:10.1038/nrmicro2549 snippet: cytoplasmic pH notes: Supports an acidic optimum as a value within the pH-optimum distribution. predicate_id: rdfs:subClassOf - subject: low_external_ph predicate: drives object: transmembrane_ph_gradient description: Acidic external pH forces acidophiles to sustain a large transmembrane pH gradient. evidence: - reference: DOI:10.1038/nrmicro2549 notes: cytoplasmic pH ~6.0 while growing at external pH <3; broad physiological input edge. - subject: inside_positive_membrane_potential predicate: counteracts object: proton_influx description: A reversed inside-positive membrane potential electrostatically opposes proton entry. evidence: - reference: DOI:10.1038/nrmicro2549 notes: sustain a large delta pH with a reversed inside-positive membrane potential; hallmark of extreme acidophiles. - reference: DOI:10.3389/fmicb.2023.1149903 notes: inside positive membrane potential creates an electrochemical barrier to proton influx. - subject: proton_pumping_respiratory_complexes predicate: removes object: cytoplasmic_proton_load description: Proton-pumping respiratory complexes actively extrude protons to lower cytoplasmic proton load. evidence: - reference: DOI:10.1038/nrmicro2549 notes: increased expression of proton-pumping respiratory chain complexes; broad mechanism, specific complexes vary by lineage. - subject: proton_impermeable_membrane predicate: decreases object: passive_proton_permeability description: A rigid proton-impermeable membrane reduces passive proton leak and the energetic burden of pH homeostasis. evidence: - reference: DOI:10.3389/fmicb.2023.1149903 notes: rigid and impermeable membrane that is highly resistant to the influx of protons; high-level trait edge. predicate_id: RO:0002212 curation_history: - timestamp: '2026-05-05T01:35:46.826407+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 acidophile proton-exclusion physiology to the pH-optimum-low 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: '2026-05-24T08:14:32Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001428×1). 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 4 evidence-backed generic edges (8 new nodes) from the deep-research report. llm_assisted: true - timestamp: '2026-06-24T17:21:10Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212×1). llm_assisted: true