identifier: METPO:1003003
label: acidophilic
definition: A pH growth preference in which an organism grows optimally at pH values
  below 5.
definition_source: DOI:10.1038/nrmicro2549
trait_category: ENVIRONMENT
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1003000
synonyms:
- synonym_text: acidophil
  synonym_type: EXACT_SYNONYM
  source: metpo.owl
- synonym_text: acidophile
  synonym_type: EXACT_SYNONYM
  source: metpo.owl
evidence:
- reference: DOI:10.1038/nrmicro2549
  snippet: growing at pH 1.0-3.0
  notes: Supports acidophilic growth at strongly acidic external pH.
canonical_examples:
- taxon_id: NCBITaxon:46632
  taxon_label: Picrophilus oshimae
  note: "Among the most extreme acidophiles known - growth optimum ~pH 0.7, grows near pH 0; co-canonical with P. torridus."
  reference: DOI:10.1073/pnas.0401356101
causal_graphs:
- graph_id: acidophilic_ph_homeostasis
  title: Acidophilic pH homeostasis mechanism
  description: Evidence-backed causal sketch linking acidophily to acidic environments,
    proton exclusion, and cytoplasmic pH homeostasis.
  nodes:
  - node_id: acidophilic_trait
    label: acidophilic
    node_type: TRAIT
    grounding: METPO:1003003
    description: Optimal growth occurs at acidic pH.
  - node_id: acidic_external_ph
    label: acidic external pH
    node_type: ENVIRONMENTAL_FACTOR
    description: External pH below neutral, often below pH 5 for acidophiles.
    grounding: PATO:0001429
  - node_id: proton
    label: proton
    node_type: CHEMICAL
    grounding: CHEBI:15378
    description: Hydrogen ion whose gradient threatens cytoplasmic pH.
  - node_id: cytoplasmic_ph_homeostasis
    label: cytoplasmic pH homeostasis
    node_type: BIOLOGICAL_PROCESS
    description: Maintenance of a less acidic cytoplasm during growth at low pH.
    grounding: GO:0051453
  - node_id: low_proton_permeability_membrane
    label: low proton permeability membrane
    node_type: CELLULAR_LOCALIZATION
    description: Membrane properties that reduce inward proton leak.
  - node_id: reversed_membrane_potential
    label: reversed membrane potential
    node_type: BIOLOGICAL_PROCESS
    description: Positive-inside membrane potential reducing proton influx.
  - node_id: primary_proton_pumps
    label: primary proton pumps
    node_type: GENE_OR_PROTEIN
    description: Proton-pumping respiratory chain complexes that actively translocate
      protons.
  - node_id: proton_coupled_atpases
    label: proton-coupled ATPases
    node_type: GENE_OR_PROTEIN
    description: ATP-driven primary pumps that actively transport protons across the
      membrane.
  - node_id: cation_pumping
    label: pumping K+ and Na+ into cytoplasm
    node_type: BIOLOGICAL_PROCESS
    description: Active uptake of K+ and Na+ that reduces proton influx by electrostatic
      repulsion.
  - node_id: hopanoid_and_membrane_proteins
    label: hopanoid lipids and membrane proteins (Omp40, PspA)
    node_type: CELLULAR_LOCALIZATION
    description: Structural membrane adaptations (hopanoid lipids, Omp40, PspA) used
      for proton exclusion.
  - node_id: proton_exclusion
    label: proton exclusion
    node_type: BIOLOGICAL_PROCESS
    description: Exclusion of protons from the cytoplasm via membrane adaptations.
  - node_id: bipolar_tetraether_lipids
    label: bipolar tetraether lipids (GDNT/GDGT)
    node_type: CHEMICAL
    description: Archaeal monolayer-forming tetraether membrane lipids reducing passive
      proton permeability.
  - node_id: low_passive_proton_permeability
    label: low passive proton permeability
    node_type: QUALITY
    description: A low passive proton permeability allowing maintenance of near-neutral
      intracellular pH.
  edges:
  - subject: acidic_external_ph
    predicate: selects for
    object: acidophilic_trait
    description: Acidic environments select for organisms whose optimal growth is
      below neutral pH.
    evidence:
    - reference: DOI:10.1038/nrmicro2549
      snippet: growing at pH 1.0-3.0
      notes: Review supports growth of extreme acidophiles at strongly acidic pH.
    predicate_id: METPO:2007401
  - subject: acidic_external_ph
    predicate: increases gradient of
    object: proton
    description: Acidic external pH imposes a proton gradient across the membrane.
    evidence:
    - reference: DOI:10.1016/j.tim.2007.02.005
      snippet: major contributor to the proton motive force
      notes: Review links low-pH growth to the transmembrane proton gradient.
    predicate_id: METPO:2007601
  - subject: low_proton_permeability_membrane
    predicate: limits influx of
    object: proton
    description: Low proton permeability helps acidophiles avoid cytoplasmic acidification.
    evidence:
    - reference: DOI:10.1016/j.tim.2007.02.005
      snippet: highly impermeable cell membranes
      notes: Supports membrane impermeability as an acidophile mechanism.
  - subject: reversed_membrane_potential
    predicate: mitigates influx of
    object: proton
    description: A reversed membrane potential can reduce inward proton movement.
    evidence:
    - reference: DOI:10.1016/j.tim.2007.02.005
      snippet: reversed membrane potential
      notes: Supports reversed membrane potential as a shared acidophile feature.
  - subject: cytoplasmic_ph_homeostasis
    predicate: enables
    object: acidophilic_trait
    description: Acidophilic growth requires maintaining cytoplasmic pH compatible
      with biomolecular function.
    evidence:
    - reference: DOI:10.1038/nrmicro2549
      snippet: maintain a cytoplasmic pH of approximately 6.0
      notes: Supports cytoplasmic pH homeostasis during growth at low external pH.
    predicate_id: RO:0002327
  - subject: primary_proton_pumps
    predicate: catalyzes active transport of
    object: proton
    description: Primary proton pumps such as respiratory-chain complexes actively
      export protons, contributing to pH homeostasis.
    evidence:
    - reference: DOI:10.1038/nrmicro2549
      notes: primary proton pumps such as the proton-pumping respiratory chain complexes
  - subject: proton_coupled_atpases
    predicate: catalyzes active transport of
    object: proton
    description: Proton-coupled ATPases actively transport protons across the membrane.
    evidence:
    - reference: DOI:10.1038/nrmicro2549
      notes: Such transporters include primary proton pumps such as proton-coupled
        ATPases
  - subject: acidic_external_ph
    predicate: selects for
    object: cytoplasmic_ph_homeostasis
    description: Low external pH / acid challenge imposes the demands of cytoplasmic
      pH homeostasis, a unifying principle of bacterial pH homeostasis.
    evidence:
    - reference: DOI:10.1038/nrmicro2549
      notes: A major unifying principle of bacterial pH homeostasis... the demands
        of pH homeostasis
    predicate_id: METPO:2007401
  - subject: cation_pumping
    predicate: reduces influx of
    object: proton
    description: Pumping K+ and Na+ into the cytoplasm reduces proton influx by electrostatic
      repulsion.
    evidence:
    - reference: DOI:10.1111/1758-2229.70019
      notes: can pump cations such as K+ and Na+ into the cytoplasm to reduce the
        influx of protons by electrostatic repulsion
  - subject: hopanoid_and_membrane_proteins
    predicate: enables
    object: proton_exclusion
    description: Hopanoid lipids and membrane proteins (Omp40, PspA) are structural
      adaptations used for proton exclusion.
    evidence:
    - reference: DOI:10.1111/1758-2229.70019
      notes: hopanoid lipids... or membrane proteins such as Omp40 and PspA, are structural
        adaptations used for proton exclusion
    predicate_id: RO:0002327
  - subject: bipolar_tetraether_lipids
    predicate: maintains
    object: low_passive_proton_permeability
    description: Bipolar tetraether lipids maintain a low passive proton permeability,
      enabling a near-neutral intracellular pH.
    evidence:
    - reference: DOI:10.3389/frbis.2023.1338019
      notes: As such, a low passive proton permeability and a near neutral intracellular
        pH can be maintained
curation_history:
- timestamp: '2026-05-05T01:35:46.938355+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 acidophilic trait and added DOI-backed evidence and causal graph
    for acidic pH homeostasis.
  llm_assisted: true
- timestamp: '2026-05-20T03:35:29Z'
  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: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 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (PATO:0001428×1).
  llm_assisted: true
- timestamp: '2026-06-14T07:26:18Z'
  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 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 6 evidence-backed generic edges (7 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:09Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2007401×1, RO:0002327×1).
  llm_assisted: true