identifier: METPO:1003006
label: obligately acidophilic
definition: A pH growth preference characterized by the requirement for acidic environments
  (pH below 5.5) for growth, with inability to grow at neutral or alkaline pH values.
definition_source: DOI:10.3389/fmicb.2021.822229
trait_category: ENVIRONMENT
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1003000
synonyms:
- synonym_text: obligate acidophile
  synonym_type: EXACT_SYNONYM
  source: metpo.owl
created_by: Jed Dongjin Kim-Ozaeta
evidence:
- reference: DOI:10.3389/fmicb.2021.822229
  snippet: acidic optimal growth pH
  notes: Supports acidophilic growth as a phenotype defined by acidic optimal pH.
canonical_examples:
- taxon_id: NCBITaxon:46632
  taxon_label: Picrophilus oshimae
  note: "obligate extreme acidophile (pH ~0.7)"
  reference: PMID:8522509
- taxon_id: NCBITaxon:920
  taxon_label: Acidithiobacillus ferrooxidans
  note: "obligate acidophile (pH ~2)"
  reference: PMID:31861345
causal_graphs:
- graph_id: obligately_acidophilic_ph_homeostasis
  title: Obligate acidophily pH homeostasis mechanism
  description: Evidence-backed causal sketch linking obligate acidophily to acidic
    external pH, proton stress, and constitutive pH homeostasis mechanisms.
  nodes:
  - node_id: obligately_acidophilic_trait
    label: obligately acidophilic
    node_type: TRAIT
    grounding: METPO:1003006
    description: Growth requires acidic pH and does not extend to neutral or alkaline
      pH values.
  - node_id: acidic_external_ph
    label: acidic external pH
    node_type: ENVIRONMENTAL_FACTOR
    description: External pH in the acidic range supporting acidophile growth.
    grounding: PATO:0001429
  - node_id: proton
    label: proton
    node_type: CHEMICAL
    grounding: CHEBI:15378
    description: Hydrogen ion whose high external activity drives proton stress.
  - node_id: cytoplasmic_ph_homeostasis
    label: cytoplasmic pH homeostasis
    node_type: BIOLOGICAL_PROCESS
    description: Maintenance of near-neutral intracellular pH during acidic growth.
    grounding: GO:0051453
  - node_id: low_proton_permeability_membrane
    label: low proton permeability membrane
    node_type: CELLULAR_LOCALIZATION
    description: Cell envelope properties that reduce inward proton leak.
  - node_id: reversed_membrane_potential
    label: reversed membrane potential
    node_type: BIOLOGICAL_PROCESS
    description: Positive-inside membrane potential that suppresses proton influx.
  - 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: k_uptake_system_kdp_kef
    label: K+ uptake system (Kdp/Kef)
    node_type: GENE_OR_PROTEIN
    description: Potassium-transporting ATPases and K+ uptake systems (kdp, kef) that
      establish an inside-positive membrane potential.
  - node_id: p_type_proton_atpase
    label: P-type proton-translocating ATPase
    node_type: GENE_OR_PROTEIN
    description: Active proton-efflux ATPase that pumps protons out of the cytoplasm
      during acid stress.
  - node_id: proton_efflux
    label: proton efflux from cytoplasm
    node_type: BIOLOGICAL_PROCESS
    description: Active export of protons from the cytoplasm to maintain near-neutral
      intracellular pH.
  - node_id: na_h_antiporter
    label: Na+/H+ antiporter (Nha)
    node_type: GENE_OR_PROTEIN
    description: Sodium/proton antiporters (nhaA, nhaB) that exchange cytoplasmic
      protons for sodium ions.
  - node_id: hopanoid_membrane
    label: hopanoid-containing membrane
    node_type: CELLULAR_LOCALIZATION
    description: Membrane enriched in hopanoid lipids that reduces proton permeability.
  - node_id: cyclopropane_fatty_acids
    label: cyclopropane fatty acids
    node_type: CHEMICAL
    description: Cyclopropane-fatty-acyl phospholipids that rigidify the membrane
      and lower proton permeability.
  - node_id: glutamate_decarboxylase
    label: glutamate decarboxylase system (Gad)
    node_type: GENE_OR_PROTEIN
    description: Glutamate decarboxylase (gadA/gadB/gadC) that consumes cytoplasmic
      protons during decarboxylation.
  edges:
  - subject: acidic_external_ph
    predicate: selects for
    object: obligately_acidophilic_trait
    description: Acidic environments select for organisms with acidic pH growth optima.
    evidence:
    - reference: DOI:10.3389/fmicb.2021.822229
      snippet: acidic optimal growth pH
      notes: Review supports acidophile classification by acidic optimum pH; the obligate
        neutral-pH exclusion remains from the METPO definition.
    predicate_id: METPO:2007401
  - subject: acidic_external_ph
    predicate: increases gradient of
    object: proton
    description: Low external pH creates a steep proton gradient across the membrane.
    evidence:
    - reference: DOI:10.3389/fmicb.2021.822229
      snippet: proton gradient across the cytoplasmic membrane
      notes: Supports external-to-internal proton gradient under low-pH growth.
    predicate_id: METPO:2007601
  - subject: low_proton_permeability_membrane
    predicate: limits influx of
    object: proton
    description: Reduced membrane permeability helps obligate acidophiles maintain
      intracellular pH.
    evidence:
    - reference: DOI:10.1016/j.tim.2007.02.005
      snippet: highly impermeable cell membranes
      notes: Supports proton exclusion by membrane properties in acidophiles.
  - subject: reversed_membrane_potential
    predicate: suppresses influx of
    object: proton
    description: Reversed membrane potential reduces passive proton entry.
    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: proton_export_pumps
    predicate: contributes to
    object: cytoplasmic_ph_homeostasis
    description: Proton export and antiport systems contribute to intracellular pH
      control during acid stress.
    evidence:
    - reference: DOI:10.3389/fmicb.2021.822229
      snippet: proton export pumps and antiporters
      notes: Supports transporter-mediated acid resistance mechanisms.
    predicate_id: RO:0002326
  - subject: cytoplasmic_ph_homeostasis
    predicate: enables
    object: obligately_acidophilic_trait
    description: Obligate acidophilic growth requires maintaining cytoplasmic pH despite
      acidic external pH.
    evidence:
    - reference: DOI:10.1038/nrmicro2549
      snippet: maintain a cytoplasmic pH of approximately 6.0
      notes: Supports intracellular pH control during extreme acidophilic growth.
    predicate_id: RO:0002327
  - subject: k_uptake_system_kdp_kef
    predicate: increases
    object: reversed_membrane_potential
    description: K+ uptake systems generate the inside-positive (reversed) membrane
      potential that forms an electrochemical barrier to protons.
    evidence:
    - reference: DOI:10.3389/fmicb.2023.1149903
      notes: Review describes inside-positive membrane potential via potassium-transporting
        ATPases and K+ uptake systems (kdp, Kef) forming an electrochemical barrier
        to proton influx.
    predicate_id: RO:0002213
  - subject: p_type_proton_atpase
    predicate: increases
    object: proton_efflux
    description: P-type ATPases actively export protons from the cytoplasm.
    evidence:
    - reference: DOI:10.3389/fmicb.2023.1149903
      notes: Dopson review lists active proton efflux via P-type ATPases as a pH homeostasis
        strategy in acidophiles.
    predicate_id: RO:0002213
  - subject: proton_efflux
    predicate: contributes to
    object: cytoplasmic_ph_homeostasis
    description: Active proton efflux helps maintain near-neutral cytoplasmic pH under
      acidic conditions.
    evidence:
    - reference: DOI:10.3389/fmicb.2023.1149903
      notes: Proton pumps/ATPases maintain a near-neutral cytoplasm during acidophilic
        growth.
    predicate_id: RO:0002326
  - subject: na_h_antiporter
    predicate: exports
    object: proton
    description: Na+/H+ antiporters exchange cytoplasmic protons for extracellular
      sodium, contributing to proton export.
    evidence:
    - reference: DOI:10.3389/fmicb.2023.1149903
      notes: Dopson lists Na+/H+ exchange (nhaA sodium/proton antiporter) among acidophile
        pH-homeostasis systems.
    predicate_id: METPO:2000209
  - subject: hopanoid_membrane
    predicate: decreases
    object: low_proton_permeability_membrane
    description: Hopanoid membrane lipids reduce membrane proton permeability, reinforcing
      proton exclusion.
    evidence:
    - reference: DOI:10.1111/1758-2229.70019
      notes: Acid resistance is linked to hopanoid membrane lipids and reduced proton
        permeability as a core proton-exclusion strategy.
    predicate_id: RO:0002212
  - subject: cyclopropane_fatty_acids
    predicate: decreases
    object: low_proton_permeability_membrane
    description: Cyclopropane fatty acid formation reduces membrane proton permeability.
    evidence:
    - reference: DOI:10.3389/fmicb.2023.1149903
      notes: Review includes cyclopropane-fatty-acyl-phospholipid synthase among membrane
        adaptations that reduce proton permeability.
    predicate_id: RO:0002212
  - subject: glutamate_decarboxylase
    predicate: consumes
    object: proton
    description: Glutamate decarboxylase consumes cytoplasmic protons during decarboxylation,
      buffering intracellular pH.
    evidence:
    - reference: DOI:10.3389/fmicb.2023.1149903
      notes: Review lists decarboxylases (Adi, Gad) as cytoplasmic proton-consuming
        systems used in acidophile pH homeostasis.
    predicate_id: biolink:consumes
curation_history:
- timestamp: '2026-05-05T01:35:46.940216+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 obligately acidophilic trait and added DOI-backed evidence and
    causal graph for acidic pH homeostasis. The graph does not assert a specific molecular
    cause of the obligate neutral-pH growth exclusion because that varies by lineage.
  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:0002326×1, 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: '2026-05-24T04:38:00Z'
  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: '2026-06-14T07:26:19Z'
  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 1 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 7 evidence-backed generic edges (7 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:10Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 7 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002213×2, RO:0002212×2, RO:0002326×1, METPO:2000209×1, biolink:consumes×1).
  llm_assisted: true