identifier: METPO:1003007
label: facultatively acidophilic
definition: A pH growth preference characterized by optimal growth in acidic environments
  (pH below 5.5) with the capacity to also grow at near-neutral pH values.
definition_source: DOI:10.1099/ijs.0.066175-0
trait_category: ENVIRONMENT
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1003000
synonyms:
- synonym_text: facultative acidophile
  synonym_type: EXACT_SYNONYM
  source: metpo.owl
created_by: Jed Dongjin Kim-Ozaeta
evidence:
- reference: DOI:10.1099/ijs.0.066175-0
  snippet: capable of growth at pH 4.0-7.2
  notes: Species-level example supports acidic-to-near-neutral growth capacity in
    a mildly acidophilic bacterium.
causal_graphs:
- graph_id: facultatively_acidophilic_ph_homeostasis
  title: Facultative acidophily pH homeostasis mechanism
  description: Evidence-backed causal sketch linking facultative acidophily to acidic
    growth, near-neutral growth capacity, and inducible pH homeostasis.
  nodes:
  - node_id: facultatively_acidophilic_trait
    label: facultatively acidophilic
    node_type: TRAIT
    grounding: METPO:1003007
    description: Optimal growth occurs under acidic conditions while near-neutral
      growth remains possible.
  - node_id: acidic_external_ph
    label: acidic external pH
    node_type: ENVIRONMENTAL_FACTOR
    description: External pH below neutral that supports acidophilic growth.
    grounding: PATO:0001429
  - node_id: near_neutral_external_ph
    label: near-neutral external pH
    node_type: ENVIRONMENTAL_FACTOR
    description: External pH near neutrality that facultative acidophiles can tolerate
      or grow in.
    grounding: PATO:0001428
  - node_id: proton
    label: proton
    node_type: CHEMICAL
    grounding: CHEBI:15378
    description: Hydrogen ion contributing to low-pH stress.
  - node_id: cytoplasmic_ph_homeostasis
    label: cytoplasmic pH homeostasis
    node_type: BIOLOGICAL_PROCESS
    description: Maintenance of intracellular pH across acidic and near-neutral environments.
    grounding: GO:0051453
  - node_id: proton_export_pumps
    label: proton export pumps and antiporters
    node_type: GENE_OR_PROTEIN
    description: Transport systems proposed to remove protons or exchange ions during
      acid stress.
  - node_id: cytoplasmic_buffering
    label: cytoplasmic buffering
    node_type: BIOLOGICAL_PROCESS
    description: Cellular buffering and proton-consuming reactions that mitigate acidification.
  - node_id: near_neutral_cytoplasm
    label: near-neutral cytoplasm
    node_type: STATE
    description: Cytoplasmic pH maintained near neutrality despite low external pH.
  - node_id: potassium_ion
    label: potassium ion
    node_type: CHEMICAL
    description: Intracellular cation accumulated to oppose proton influx.
    grounding: CHEBI:29103
  - node_id: inside_positive_membrane_potential
    label: inside-positive membrane potential
    node_type: QUALITY
    description: Reversed (inside-positive) transmembrane potential opposing proton
      entry.
  - node_id: hopanoid_biosynthesis
    label: hopanoid biosynthetic process
    node_type: BIOLOGICAL_PROCESS
    description: Synthesis of hopanoids that rigidify the membrane against proton
      influx.
    grounding: GO:0019746
  - node_id: membrane_proton_permeability
    label: membrane proton permeability
    node_type: QUALITY
    description: Permeability of the cell membrane to protons.
  - node_id: impermeable_membrane
    label: rigid impermeable membrane
    node_type: CELLULAR_LOCALIZATION
    description: A rigid, low-permeability membrane that acts as a barrier to proton
      entry.
  - node_id: glutamate_decarboxylase_system
    label: glutamate decarboxylase system
    node_type: GENE_OR_PROTEIN
    description: Decarboxylase (Gad) system consuming intracellular protons during
      acid stress.
  - node_id: intracellular_ph
    label: intracellular pH
    node_type: QUALITY
    description: Cytoplasmic pH value stabilized by buffering and homeostatic systems.
  edges:
  - subject: acidic_external_ph
    predicate: selects for
    object: facultatively_acidophilic_trait
    description: Acidic pH selects for acidophilic growth capacity.
    evidence:
    - reference: DOI:10.3389/fmicb.2021.822229
      snippet: acidic optimal growth pH
      notes: Supports acidophilic classification by acidic growth optimum.
    predicate_id: METPO:2007401
  - subject: near_neutral_external_ph
    predicate: is compatible with
    object: facultatively_acidophilic_trait
    description: Facultatively acidophilic growth can extend into near-neutral pH.
    evidence:
    - reference: DOI:10.1099/ijs.0.066175-0
      snippet: capable of growth at pH 4.0-7.2
      notes: Species-level evidence supports acidic-to-near-neutral growth range;
        this edge is qualified rather than generalized to all taxa.
  - subject: acidic_external_ph
    predicate: increases gradient of
    object: proton
    description: Acidic pH imposes an external-to-internal proton gradient.
    evidence:
    - reference: DOI:10.3389/fmicb.2021.822229
      snippet: external to internal proton gradient
      notes: Supports proton-gradient stress during low-pH growth.
    predicate_id: METPO:2007601
  - subject: proton_export_pumps
    predicate: contributes to
    object: cytoplasmic_ph_homeostasis
    description: Proton export and antiport systems contribute to acid-stress homeostasis.
    evidence:
    - reference: DOI:10.3389/fmicb.2021.822229
      snippet: proton export pumps and antiporters
      notes: Supports transporter-mediated pH homeostasis mechanisms.
    predicate_id: RO:0002326
  - subject: cytoplasmic_buffering
    predicate: contributes to
    object: cytoplasmic_ph_homeostasis
    description: Buffering and proton-consuming reactions reduce cytoplasmic acidification.
    evidence:
    - reference: DOI:10.3389/fmicb.2021.822229
      snippet: cytoplasmic buffering
      notes: Supports buffering as a proposed acid resistance mechanism.
    predicate_id: RO:0002326
  - subject: cytoplasmic_ph_homeostasis
    predicate: enables
    object: facultatively_acidophilic_trait
    description: Growth across acidic and near-neutral pH requires intracellular pH
      control.
    evidence:
    - reference: DOI:10.1038/nrmicro2549
      snippet: robust mechanisms for cytoplasmic pH homeostasis
      notes: Supports cytoplasmic pH homeostasis for growth outside the preferred
        cytoplasmic pH range.
    predicate_id: RO:0002327
  - subject: acidic_external_ph
    predicate: necessitates maintenance of
    object: near_neutral_cytoplasm
    description: Acidophilic growth requires preserving near-neutral cytoplasm against
      a steep proton gradient.
    evidence:
    - reference: DOI:10.3389/fmicb.2021.822229
      notes: maintain a near-neutral cytoplasm despite an external-to-internal proton
        gradient up to 10^5-fold.
  - subject: potassium_ion
    predicate: generates
    object: inside_positive_membrane_potential
    description: Intracellular K+ accumulation generates an inside-positive potential
      that opposes proton influx.
    evidence:
    - reference: DOI:10.3389/fmicb.2021.822229
      notes: internal positive membrane potential thought to be generated by potassium
        ions.
    predicate_id: biolink:produces
  - subject: inside_positive_membrane_potential
    predicate: contributes to
    object: cytoplasmic_ph_homeostasis
    description: An inside-positive membrane potential is a first-line defense reducing
      proton entry, supporting pH homeostasis.
    evidence:
    - reference: DOI:10.3389/fmicb.2021.822229
      notes: Inside-positive potential generated by K+ opposes proton influx as a
        first-line defense.
    predicate_id: RO:0002326
  - subject: hopanoid_biosynthesis
    predicate: reduces
    object: membrane_proton_permeability
    description: Hopanoids stiffen the membrane and reduce proton permeability under
      low pH.
    evidence:
    - reference: DOI:10.3389/fmicb.2021.822229
      notes: membrane alterations via inclusion of hopanoids linked to acidophilic
        lifestyle.
    predicate_id: METPO:2000017
  - subject: impermeable_membrane
    predicate: limits
    object: proton
    description: A rigid, impermeable membrane acts as a barrier limiting proton entry
      into the cell.
    evidence:
    - reference: DOI:10.3389/fmicb.2023.1149903
      notes: acidophiles use a rigid and impermeable membrane that resists proton
        entry.
    predicate_id: RO:0002212
  - subject: proton_export_pumps
    predicate: expels
    object: proton
    description: Proton export pumps and antiporters directly remove protons that
      enter the cytoplasm.
    evidence:
    - reference: DOI:10.3389/fmicb.2021.822229
      notes: proton export pumps and antiporters listed among mechanisms maintaining
        pH homeostasis.
  - subject: glutamate_decarboxylase_system
    predicate: consumes
    object: proton
    description: Glutamate decarboxylation consumes intracellular protons as a second-line
      acid resistance route.
    evidence:
    - reference: DOI:10.3389/fmicb.2021.822229
      notes: proton consuming reactions such as glutamate decarboxylase; gadABC among
        acid-adaptation genes.
    predicate_id: biolink:consumes
  - subject: cytoplasmic_buffering
    predicate: stabilizes
    object: intracellular_ph
    description: Cytoplasmic buffering dampens pH fluctuations to stabilize intracellular
      pH.
    evidence:
    - reference: DOI:10.3389/fmicb.2023.1149903
      notes: shared mechanisms include cytoplasmic buffering that stabilizes intracellular
        pH.
curation_history:
- timestamp: '2026-05-05T01:35:46.940835+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 facultatively acidophilic trait and added DOI-backed evidence
    and causal graph for acidic and near-neutral pH growth capacity. Near-neutral
    growth evidence is species-level and should be treated as qualified.
  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 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2007401×1).
  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: '2026-05-24T08:14:32Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv
    (PATO:0001428×1, PATO:0001432×1).
  llm_assisted: true
- timestamp: '2026-06-14T07:26:19Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2007601×1).
  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: '2026-06-15T07:21:43Z'
  curator: claude
  action: FIX_NODE_GROUNDING_CURIE
  changes: Overwrote 2 pH causal-node grounding(s) to corrected PATO CURIEs (phase-2;
    verified vs OAK).
  llm_assisted: true
- timestamp: '2026-06-17T04:09:43Z'
  curator: claude
  action: REMOVE_REDUNDANT_SYNONYM
  changes: Removed 1 synonym(s) whose text duplicated the label (seeder redundancy;
    no information lost).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 8 evidence-backed generic edges (8 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:09Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (biolink:produces×1, RO:0002326×1, METPO:2000017×1, RO:0002212×1, biolink:consumes×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:23:30Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:29103×1, GO:0019746×1).
  llm_assisted: true