identifier: METPO:1000459
label: pH range very low
definition: A pH range phenotype in which growth extends to external pH at or below
  approximately 4, characteristic of extreme-acidophile physiology.
definition_source: DOI:10.1038/nrmicro2549
trait_category: ENVIRONMENT
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000332
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: pHR_0_to_4
  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 in the pH 1–4 range as the extreme-acidophile
    growth range.
causal_graphs:
- graph_id: ph_range_very_low_extreme_acidophile
  title: pH-range-very-low extreme-acidophile range
  description: DOI-backed graph linking extreme-acidophile proton-exclusion physiology
    to a pH growth range reaching ≤ ~4.
  nodes:
  - node_id: ph_range_very_low_trait
    label: pH range very low
    node_type: TRAIT
    grounding: METPO:1000459
    description: pH growth-supporting range reaching ≤ ~4.
  - node_id: ph_range
    label: pH range
    node_type: TRAIT
    grounding: METPO:1000332
    description: Span of external pH values supporting growth.
  - node_id: extreme_acidophile_envelope
    label: extreme-acidophile envelope barrier
    node_type: BIOLOGICAL_PROCESS
    description: Combined low-permeability membrane and reversed membrane potential
      preventing cytoplasmic acidification at strongly acidic external pH.
  - node_id: potassium_influx
    label: potassium influx / K+ transport
    node_type: BIOLOGICAL_PROCESS
    description: Active influx of cations such as K+ across the cytoplasmic membrane.
  - node_id: reversed_membrane_potential
    label: inside-positive (reversed) membrane potential
    node_type: STATE
    description: Inside-positive transmembrane electrical potential characteristic
      of extreme acidophiles.
  - node_id: proton_influx
    label: passive proton influx
    node_type: BIOLOGICAL_PROCESS
    description: Passive entry of protons/hydronium ions into the cytoplasm down the
      steep pH gradient.
  - node_id: low_proton_permeability
    label: low passive proton permeability
    node_type: QUALITY
    description: Low permeability of the cell envelope to passive proton flux.
  - node_id: near_neutral_cytoplasmic_ph
    label: near-neutral cytoplasmic pH
    node_type: STATE
    description: Maintenance of a near-neutral intracellular pH despite strongly acidic
      external pH.
  - node_id: weak_organic_acids
    label: protonated weak organic acids
    node_type: CHEMICAL
    description: Lipophilic protonated weak organic acids (e.g., acetic acid) that
      can permeate the membrane.
  - node_id: cytoplasm
    label: cytoplasm
    node_type: CELLULAR_LOCALIZATION
    description: Intracellular cytoplasmic compartment.
    grounding: GO:0005737
  - node_id: cytoplasmic_acidification
    label: cytoplasmic acidification
    node_type: BIOLOGICAL_PROCESS
    description: Acidification of the cytoplasm by influx and dissociation of permeant
      protons/acids.
  edges:
  - subject: extreme_acidophile_envelope
    predicate: enables
    object: ph_range_very_low_trait
    description: Extreme-acidophile envelope barriers enable growth at pH ≤ 4.
    evidence:
    - reference: DOI:10.1016/j.tim.2007.02.005
      snippet: reversed membrane potential
      notes: Supports envelope and membrane-potential mechanisms as enablers of growth
        at strongly acidic pH.
    predicate_id: RO:0002327
  - subject: ph_range_very_low_trait
    predicate: is a
    object: ph_range
    description: pH range very low is a quantitative bin of the pH-range phenotype.
    evidence:
    - reference: DOI:10.1038/nrmicro2549
      snippet: growing at pH 1.0-3.0
      notes: Supports a very-low pH range as a value within the pH-range distribution.
    predicate_id: rdfs:subClassOf
  - subject: potassium_influx
    predicate: causes
    object: reversed_membrane_potential
    description: Active influx of cations such as K+ generates an inside-positive
      membrane potential.
    evidence:
    - reference: DOI:10.1128/9781555818821.ch4.3.1
      notes: generate positive (inside) membrane potentials via the active influx
        of cations, such as K+; mechanism general to acidophiles.
    predicate_id: biolink:causes
  - subject: reversed_membrane_potential
    predicate: reduces
    object: proton_influx
    description: The inside-positive (reversed) membrane potential reduces passive
      proton influx, supporting a large ΔpH.
    evidence:
    - reference: DOI:10.1038/nrmicro2549
      notes: maintain a large transmembrane ΔpH supported by a reversed membrane potential
        (inside-positive); links reversed Δψ to reduced proton entry.
    predicate_id: METPO:2000017
  - subject: low_proton_permeability
    predicate: enables maintenance of
    object: near_neutral_cytoplasmic_ph
    description: Low passive proton permeability enables maintenance of a near-neutral
      cytoplasmic pH at acidic external pH.
    evidence:
    - reference: DOI:10.3389/frbis.2023.1338019
      notes: a low passive proton permeability and a near neutral intracellular pH
        can be maintained.
  - subject: weak_organic_acids
    predicate: diffuse into
    object: cytoplasm
    description: Lipophilic protonated weak organic acids can diffuse across the membrane
      into the cytoplasm.
    evidence:
    - reference: DOI:10.1128/9781555818821.ch4.3.1
      notes: lipophilic weak organic acids can diffuse in and acidify the cytoplasm;
        general principle, key boundary condition for acidophily.
  - subject: weak_organic_acids
    predicate: cause
    object: cytoplasmic_acidification
    description: Permeant weak organic acids dissociate inside the cell and acidify
      the cytoplasm.
    evidence:
    - reference: DOI:10.1128/AEM.04031-15
      notes: small organic acids can act as uncouplers and acidify the cytoplasm;
        strong inhibitor edge distinguishing mineral from permeant organic acids.
curation_history:
- timestamp: '2026-05-05T01:35:46.829000+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 extreme-acidophile
    envelope barriers to the pH-range-very-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
    (RO:0002327×1, rdfs:subClassOf×1).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 5 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 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (biolink:causes×1, METPO:2000017×1).
  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:0005737×1).
  llm_assisted: true