identifier: METPO:1003002
label: alkaphilic
definition: A pH growth preference in which an organism grows optimally at pH values
  above 9.
definition_source: DOI:10.1038/nrmicro2549
trait_category: ENVIRONMENT
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1003000
synonyms:
- synonym_text: alkaliphile
  synonym_type: EXACT_SYNONYM
  source: metpo.owl
- synonym_text: alkaliphilic
  synonym_type: EXACT_SYNONYM
  source: metpo.owl
- synonym_text: alkalophile
  synonym_type: EXACT_SYNONYM
  source: metpo.owl
- synonym_text: alkalophilic
  synonym_type: EXACT_SYNONYM
  source: metpo.owl
evidence:
- reference: DOI:10.1038/nrmicro2549
  snippet: external pH range of 9.5-11.0
  notes: Supports alkaliphilic growth at strongly alkaline external pH.
canonical_examples:
- taxon_id: NCBITaxon:86665
  taxon_label: Halalkalibacterium halodurans
  note: "alkaliphile growing at pH >9.5"
  reference: DOI:10.1093/nar/28.21.4317
- taxon_id: NCBITaxon:2257
  taxon_label: Natronomonas pharaonis
  note: "haloalkaliphilic archaeon"
  reference: PMID:16169924
causal_graphs:
- graph_id: alkaliphilic_na_cycle_homeostasis
  title: Alkaliphilic sodium-cycle pH homeostasis mechanism
  description: Evidence-backed causal sketch linking alkaliphily to high external
    pH, Na+/H+ antiport, and cytoplasmic acidification relative to the medium.
  nodes:
  - node_id: alkaphilic_trait
    label: alkaphilic
    node_type: TRAIT
    grounding: METPO:1003002
    description: Optimal growth occurs at alkaline pH.
  - node_id: alkaline_external_ph
    label: alkaline external pH
    node_type: ENVIRONMENTAL_FACTOR
    description: External pH above neutral, often pH 9 or higher.
    grounding: PATO:0001430
  - node_id: sodium_ion
    label: sodium ion
    node_type: CHEMICAL
    grounding: CHEBI:29101
    description: Sodium ion participating in alkaliphile Na+ cycles.
  - node_id: proton
    label: proton
    node_type: CHEMICAL
    grounding: CHEBI:15378
    description: Hydrogen ion imported or retained to acidify the cytoplasm.
  - node_id: sodium_proton_antiporter
    label: Na+/H+ antiporter
    node_type: GENE_OR_PROTEIN
    description: Secondary transporter exchanging sodium and protons.
    grounding: UniProtKB:A0A068T423
  - node_id: cytoplasmic_ph_homeostasis
    label: cytoplasmic pH homeostasis
    node_type: BIOLOGICAL_PROCESS
    description: Maintenance of internal pH below highly alkaline external pH.
    grounding: GO:0051453
  - node_id: mrp_antiporter_complex
    label: Mrp Na+/H+ antiporter complex
    node_type: GENE_OR_PROTEIN
    description: Multisubunit cation/proton antiporter complex with an indispensable
      role in alkaliphile high-pH homeostasis.
  - node_id: atp_synthase_c_subunit_motifs
    label: ATP synthase c-subunit alkaline-adaptive motifs
    node_type: GENE_OR_PROTEIN
    description: c-subunit motifs that alter rotor shape and promote tight proton
      binding in the ion site at high pH.
  - node_id: atp_synthase_proton_binding
    label: ATP synthase proton binding efficiency at high pH
    node_type: MOLECULAR_FUNCTION
    description: Tight proton binding in the ATP synthase ion site enabling efficient
      operation under alkaline conditions.
  - node_id: acidic_cell_envelope_polymers
    label: acidic secondary cell-wall and S-layer polymers
    node_type: CELLULAR_LOCALIZATION
    description: Acidic secondary cell walls and S-layer proteins on the cell surface
      of alkaliphiles.
  - node_id: surface_proton_retention
    label: proton retention at cell surface
    node_type: BIOLOGICAL_PROCESS
    description: Attraction and retention of protons at the cell surface, buffering
      the cytoplasmic membrane against high external pH.
  edges:
  - subject: alkaline_external_ph
    predicate: selects for
    object: alkaphilic_trait
    description: Alkaline environments select for organisms with alkaline growth optima.
    evidence:
    - reference: DOI:10.1038/nrmicro2549
      snippet: external pH range of 9.5-11.0
      notes: Review supports growth of extreme alkaliphiles at high external pH.
    predicate_id: METPO:2007401
  - subject: alkaline_external_ph
    predicate: challenges
    object: cytoplasmic_ph_homeostasis
    description: High external pH challenges the cell's ability to keep cytoplasm
      near functional pH.
    evidence:
    - reference: DOI:10.1038/nrmicro2549
      snippet: cytoplasmic pH ... below an external pH
      notes: Supports cytoplasmic pH control below alkaline external pH.
    predicate_id: METPO:2007406
  - subject: sodium_proton_antiporter
    predicate: exchanges
    object: sodium_ion
    description: Na+/H+ antiport is central to the sodium cycle in alkaliphiles.
    evidence:
    - reference: DOI:10.1007/BF00762685
      snippet: secondary Na+/H+ antiporter
      notes: Supports Na+/H+ antiport as a key alkaliphile sodium-cycle component.
  - subject: sodium_proton_antiporter
    predicate: imports
    object: proton
    description: Electrogenic Na+/H+ antiport contributes to cytoplasmic acidification
      under alkaline conditions.
    evidence:
    - reference: DOI:10.1016/j.bbamem.2005.09.010
      snippet: promote proton capture and retention
      notes: Review supports proton capture/retention mechanisms in alkaline pH homeostasis.
    predicate_id: METPO:2000208
  - subject: cytoplasmic_ph_homeostasis
    predicate: enables
    object: alkaphilic_trait
    description: Alkaliphilic growth requires maintaining cytoplasmic pH during high-pH
      exposure.
    evidence:
    - reference: DOI:10.1038/nrmicro2549
      snippet: pH sensing and homeostasis
      notes: Supports homeostasis as the enabling process for alkaline growth.
    predicate_id: RO:0002327
  - subject: mrp_antiporter_complex
    predicate: enables
    object: cytoplasmic_ph_homeostasis
    description: Mrp Na+/H+ antiporter complex enables pH homeostasis and is indispensable
      at high pH.
    evidence:
    - reference: DOI:10.1038/nrmicro2549
      notes: Na+/H+ antiporter-dependent pH homeostasis; Mrp plays an indispensible
        role at high pH.
    predicate_id: RO:0002327
  - subject: atp_synthase_c_subunit_motifs
    predicate: increases
    object: atp_synthase_proton_binding
    description: Alkaline-adaptive c-subunit motifs increase tight proton binding
      in the ATP synthase ion site at high pH.
    evidence:
    - reference: DOI:10.1038/nrmicro2549
      notes: Two c-subunit motifs that alter rotor shape and promote tight proton
        binding in the ion site.
    predicate_id: RO:0002213
  - subject: atp_synthase_proton_binding
    predicate: enables
    object: cytoplasmic_ph_homeostasis
    description: Efficient ATP synthase proton binding contributes to bioenergetics
      and pH homeostasis under alkaline conditions.
    evidence:
    - reference: DOI:10.1038/nrmicro2549
      notes: ATP synthase adaptation supports proton-coupled bioenergetics at high
        external pH.
    predicate_id: RO:0002327
  - subject: acidic_cell_envelope_polymers
    predicate: enables
    object: surface_proton_retention
    description: Acidic cell-wall and S-layer polymers attract and retain protons
      at the cell surface.
    evidence:
    - reference: DOI:10.3389/fmicb.2022.842785
      notes: Acidic secondary cell walls and S-layer proteins attract H+.
    predicate_id: RO:0002327
  - subject: surface_proton_retention
    predicate: contributes to
    object: cytoplasmic_ph_homeostasis
    description: Surface proton retention buffers the membrane and supports cytoplasmic
      pH homeostasis at high external pH.
    evidence:
    - reference: DOI:10.3389/fmicb.2022.842785
      notes: Surface proton retention helps maintain a proton-rich microenvironment
        near the membrane.
    predicate_id: RO:0002326
curation_history:
- timestamp: '2026-05-05T01:35:46.937702+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 alkaphilic trait and added DOI-backed evidence and causal graph
    for sodium-cycle alkaline 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 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2007401×1, METPO:2007406×1).
  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: '2026-05-24T05:05:13Z'
  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 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (PATO:0001429×1).
  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: '2026-06-16T06:30:55Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2000208×1).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 5 evidence-backed generic edges (5 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
    (RO:0002327×3, RO:0002213×1, RO:0002326×1).
  llm_assisted: true