identifier: METPO:1003005
label: facultatively alkaphilic
definition: A pH growth preference in which an organism can grow at alkaline pH but
  does not require it.
definition_source: DOI:10.3389/fbioe.2015.00075
trait_category: ENVIRONMENT
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1003000
synonyms:
- synonym_text: facultative alkaliphile
  synonym_type: EXACT_SYNONYM
  source: metpo.owl
- synonym_text: facultative alkaphilic
  synonym_type: EXACT_SYNONYM
  source: metpo.owl
- synonym_text: facultatively alkaliphilic
  synonym_type: EXACT_SYNONYM
  source: metpo.owl
evidence:
- reference: DOI:10.3389/fbioe.2015.00075
  snippet: capable of growing near neutral pH
  notes: Supports facultative alkaliphiles as alkaline-growing organisms that also
    grow near neutral pH.
canonical_examples:
- taxon_id: NCBITaxon:79885
  taxon_label: Alkalihalophilus pseudofirmus
  note: "facultative alkaliphile (pH 7.5 to >11)"
  reference: PMID:21951522
causal_graphs:
- graph_id: facultatively_alkaphilic_sodium_cycle_homeostasis
  title: Facultative alkaliphily sodium-cycle pH homeostasis mechanism
  description: Evidence-backed causal sketch linking facultative alkaliphily to alkaline
    growth capacity, near-neutral growth, and sodium-dependent pH homeostasis.
  nodes:
  - node_id: facultatively_alkaphilic_trait
    label: facultatively alkaphilic
    node_type: TRAIT
    grounding: METPO:1003005
    description: Growth can occur at alkaline pH but does not require alkaline pH.
  - node_id: alkaline_external_ph
    label: alkaline external pH
    node_type: ENVIRONMENTAL_FACTOR
    description: External pH above neutral, often near or above pH 9 for alkaliphiles.
    grounding: PATO:0001430
  - node_id: near_neutral_external_ph
    label: near-neutral external pH
    node_type: ENVIRONMENTAL_FACTOR
    description: External pH near neutrality compatible with facultative alkaliphile
      growth.
    grounding: PATO:0001428
  - node_id: sodium_ion
    label: sodium ion
    node_type: CHEMICAL
    grounding: CHEBI:29101
    description: Sodium ion participating in alkaliphile sodium cycles.
  - node_id: proton
    label: proton
    node_type: CHEMICAL
    grounding: CHEBI:15378
    description: Hydrogen ion imported or retained to acidify the cytoplasm under
      alkaline conditions.
  - node_id: sodium_proton_antiporter
    label: Na+/H+ antiporter
    node_type: GENE_OR_PROTEIN
    description: Antiporter exchanging sodium ions and protons during alkaline pH
      homeostasis.
    grounding: UniProtKB:A0A068T423
  - node_id: cytoplasmic_ph_homeostasis
    label: cytoplasmic pH homeostasis
    node_type: BIOLOGICAL_PROCESS
    description: Maintenance of intracellular pH across alkaline and near-neutral
      environments.
    grounding: GO:0051453
  - node_id: na_h_antiport_activity
    label: Na+/H+ antiport activity
    node_type: MOLECULAR_FUNCTION
    description: Electrogenic exchange of cytoplasmic Na+ for a larger number of entering
      protons.
  - node_id: acidic_cell_wall_components
    label: acidic secondary cell-wall components
    node_type: CELLULAR_LOCALIZATION
    description: Negatively charged secondary cell-wall polymers and S-layer components
      at the cell surface.
  - node_id: f1fo_atp_synthase
    label: F1Fo-ATP synthase
    node_type: GENE_OR_PROTEIN
    description: Proton-coupled ATP synthase complex operating at alkaline pH.
  - node_id: atp_production_alkaline
    label: ATP production at alkaline pH
    node_type: BIOLOGICAL_PROCESS
    description: ATP synthesis sustained despite low bulk proton-motive force at alkaline
      pH.
  edges:
  - subject: alkaline_external_ph
    predicate: enables
    object: facultatively_alkaphilic_trait
    description: Facultative alkaliphiles grow well under alkaline pH conditions.
    evidence:
    - reference: DOI:10.3389/fbioe.2015.00075
      snippet: grow well at pH values exceeding pH 9
      notes: Supports alkaline growth capacity of alkaliphilic microorganisms.
    predicate_id: RO:0002327
  - subject: near_neutral_external_ph
    predicate: is compatible with
    object: facultatively_alkaphilic_trait
    description: Facultative alkaliphiles retain growth capacity near neutral pH.
    evidence:
    - reference: DOI:10.3389/fbioe.2015.00075
      snippet: capable of growing near neutral pH
      notes: Review explicitly distinguishes facultative alkaliphiles from obligate
        alkaliphiles.
  - subject: alkaline_external_ph
    predicate: challenges
    object: cytoplasmic_ph_homeostasis
    description: Alkaline external pH requires cytoplasmic proton accumulation or
      retention.
    evidence:
    - reference: DOI:10.1038/nrmicro2549
      snippet: active proton accumulation or generation in the cytoplasm
      notes: Supports alkaline-pH homeostasis mechanisms.
    predicate_id: METPO:2007406
  - subject: sodium_proton_antiporter
    predicate: exports
    object: sodium_ion
    description: Sodium efflux is one limb of the alkaliphile Na+ cycle.
    evidence:
    - reference: DOI:10.1016/S0005-2728(00)00285-1
      snippet: Na+ efflux
      notes: Supports sodium efflux through Na+/H+ antiporters.
    predicate_id: METPO:2000209
  - subject: sodium_proton_antiporter
    predicate: accumulates
    object: proton
    description: Na+/H+ antiport contributes to net proton accumulation during alkaline
      pH homeostasis.
    evidence:
    - reference: DOI:10.1016/S0005-2728(00)00285-1
      snippet: net H+ accumulation
      notes: Supports proton accumulation by antiporters in alkaliphiles.
    predicate_id: METPO:2000210
  - subject: cytoplasmic_ph_homeostasis
    predicate: enables
    object: facultatively_alkaphilic_trait
    description: Growth across alkaline and near-neutral pH requires pH homeostasis.
    evidence:
    - reference: DOI:10.1016/S0005-2728(00)00285-1
      snippet: pH homeostasis ... appears to set the upper pH limit for growth
      notes: Supports pH homeostasis as a determinant of alkaliphilic growth range.
    predicate_id: RO:0002327
  - subject: alkaline_external_ph
    predicate: selects for
    object: na_h_antiport_activity
    description: Alkaline external pH selects for electrogenic Na+/H+ antiport that
      acidifies the cytoplasm.
    evidence:
    - reference: DOI:10.3389/fbioe.2015.00075
      notes: electrogenic exchange of outwardly moving sodium ions for a greater number
        of entering protons; broadly supported core adaptation.
    predicate_id: METPO:2007401
  - subject: na_h_antiport_activity
    predicate: maintains
    object: cytoplasmic_ph_homeostasis
    description: Na+/H+ antiport keeps the cytoplasm 2-2.3 units below external pH
      under alkaline conditions.
    evidence:
    - reference: DOI:10.1007/978-981-19-1573-4_3
      notes: maintain cytoplasmic pH 2-2.3 units below the external pH; generic alkaliphile
        homeostasis edge.
  - subject: acidic_cell_wall_components
    predicate: attracts
    object: proton
    description: Surface acidity enriches protons and repels hydroxide, supporting
      alkaline adaptation.
    evidence:
    - reference: DOI:10.3389/fmicb.2018.02331
      notes: acidic secondary cell wall components attract H+ and repel OH-; process-level
        cell-envelope buffering.
  - subject: f1fo_atp_synthase
    predicate: supports
    object: atp_production_alkaline
    description: Proton-coupled ATP synthase sustains ATP production despite low bulk
      PMF at alkaline pH.
    evidence:
    - reference: DOI:10.3389/fbioe.2015.00075
      notes: alkaliphilic aerobes often use proton-coupled ATP synthases despite an
        apparently low bulk proton-motive force; general bioenergetics edge.
curation_history:
- timestamp: '2026-05-05T01:35:46.939582+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 alkaphilic trait and added DOI-backed evidence and
    causal graph for alkaline and near-neutral pH growth capacity.
  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:2007406×1).
  llm_assisted: true
- timestamp: '2026-05-24T04:13:18Z'
  curator: claude
  action: RENAME_PREDICATE_LABELS
  changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings:
    supports → enables ×1.'
  llm_assisted: true
- timestamp: '2026-05-24T04:13:20Z'
  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: '2026-05-24T04:37:59Z'
  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: '2026-05-24T05:05:14Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (UniProtKB:A0A068T423×1).
  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:0001429×1, PATO:0001432×1).
  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: '2026-06-16T06:30:55Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2000209×1, METPO:2000210×1).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 4 evidence-backed generic edges (4 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:09Z'
  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