identifier: METPO:1000621
label: haloalkaliphilic
definition: A halophily preference in which an organism requires both high salt concentrations
  and alkaline pH for optimal growth.
definition_source: PMID:17203963
trait_category: ENVIRONMENT
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000629
evidence:
- reference: PMID:17203963
  snippet: aerobic, haloalkaliphilic archaeon Natronomonas pharaonis
  notes: 'Organism example: Natronomonas pharaonis is described as haloalkaliphilic.'
canonical_examples:
- taxon_id: NCBITaxon:2257
  taxon_label: Natronomonas pharaonis
  note: "soda-lake haloalkaliphile"
  reference: PMID:16169924
- taxon_id: NCBITaxon:1053
  taxon_label: Halorhodospira halophila
  note: "haloalkaliphilic purple sulfur bacterium"
  reference: PMID:39915441
causal_graphs:
- graph_id: haloalkaliphilic_salt_alkaline_adaptation
  title: Haloalkaliphilic salt and alkaline-pH adaptation mechanism
  description: Evidence-backed causal sketch linking haloalkaliphily to combined hypersaline
    and alkaline conditions.
  nodes:
  - node_id: haloalkaliphilic_trait
    label: haloalkaliphilic
    node_type: TRAIT
    grounding: METPO:1000621
    description: Requires both high salt and alkaline pH for optimal growth.
  - node_id: soda_lake_environment
    label: saline soda lake environment
    node_type: ENVIRONMENTAL_FACTOR
    description: Sodium carbonate-rich, alkaline, saline habitat.
  - node_id: high_salt_environment
    label: high-salt environment
    node_type: ENVIRONMENTAL_FACTOR
    description: Saline or salt-saturated environmental condition.
    grounding: ENVO:01001040
  - node_id: alkaline_ph
    label: alkaline pH
    node_type: ENVIRONMENTAL_FACTOR
    description: High pH growth condition.
  - node_id: compatible_solutes
    label: compatible solutes
    node_type: CHEMICAL
    description: Ectoine, glycine betaine, or related osmoprotectants.
    grounding: CHEBI:25728
  - node_id: alkaline_ph_homeostasis
    label: alkaline pH homeostasis
    node_type: BIOLOGICAL_PROCESS
    description: Cellular maintenance of internal pH under alkaline conditions.
  - node_id: compatible_solute_strategy
    label: compatible-solute (salt-out) strategy
    node_type: BIOLOGICAL_PROCESS
    description: Osmoadaptation by biosynthesis/accumulation of organic compatible
      solutes.
  - node_id: salt_in_strategy
    label: salt-in strategy
    node_type: BIOLOGICAL_PROCESS
    description: Osmoadaptation by intracellular accumulation of inorganic ions (e.g.
      K+).
    grounding: METPO:1007720
  - node_id: na_h_antiport
    label: Na+/H+ antiporter activity
    node_type: MOLECULAR_FUNCTION
    description: Sodium:proton antiport that expels Na+ and assists cytoplasmic pH
      regulation.
  - node_id: na_efflux_ph_regulation
    label: Na+ efflux and pH regulation
    node_type: BIOLOGICAL_PROCESS
    description: Coupled extrusion of sodium and maintenance of intracellular pH.
  - node_id: ectoine
    label: ectoine
    node_type: CHEMICAL
    description: Cyclic amino-acid-derived compatible solute.
    grounding: CHEBI:27592
  - node_id: choline_oxidation_pathway
    label: choline oxidation pathway
    node_type: PATHWAY
    description: De novo biosynthesis of glycine betaine via oxidation of choline.
  - node_id: glycine_betaine
    label: glycine betaine
    node_type: CHEMICAL
    description: Quaternary ammonium compatible solute.
    grounding: CHEBI:17750
  edges:
  - subject: soda_lake_environment
    predicate: provides
    object: high_salt_environment
    description: Soda lakes combine salinity with alkaline chemistry.
    evidence:
    - reference: DOI:10.1016/j.femsre.2004.10.005
      snippet: alkaline sodium carbonate/bicarbonate fraction
      notes: Review supports soda lakes as alkaline saline environments.
  - subject: soda_lake_environment
    predicate: provides
    object: alkaline_ph
    description: Soda lake buffering maintains high pH.
    evidence:
    - reference: DOI:10.1016/j.femsre.2004.10.005
      snippet: stable, high-to-extremely high pH
      notes: Supports persistent alkaline pH in haloalkaliphilic habitats.
  - subject: high_salt_environment
    predicate: contributes to
    object: haloalkaliphilic_trait
    description: Haloalkaliphiles require high-salt adaptation.
    evidence:
    - reference: DOI:10.1021/pr060352q
      snippet: survive in salt-saturated lakes of pH 11
      notes: Natronomonas pharaonis proteomics paper supports combined salt and alkaline
        survival.
    predicate_id: RO:0002326
  - subject: alkaline_ph
    predicate: contributes to
    object: haloalkaliphilic_trait
    description: Haloalkaliphiles also require adaptation to high pH.
    evidence:
    - reference: DOI:10.1021/pr060352q
      snippet: salt-saturated lakes of pH 11
      notes: Supports high-pH component of the haloalkaliphilic trait.
    predicate_id: RO:0002326
  - subject: compatible_solutes
    predicate: contributes to
    object: haloalkaliphilic_trait
    description: Compatible solutes support osmoadaptation in haloalkaliphiles.
    evidence:
    - reference: DOI:10.1139/cjm-2014-0233
      snippet: ectoine and glycine betaine
      notes: Review supports compatible solutes as osmoadaptation mechanisms in haloalkaliphiles.
    predicate_id: RO:0002326
  - subject: alkaline_ph_homeostasis
    predicate: enables
    object: haloalkaliphilic_trait
    description: pH homeostasis is required for growth under alkaline conditions.
    evidence:
    - reference: DOI:10.1038/nrmicro2549
      snippet: bacterial pH homeostasis is a cell-wide physiological process
      notes: Review supports pH homeostasis as a physiological mechanism integrated
        with salinity and other factors.
    predicate_id: RO:0002327
  - subject: haloalkaliphilic_trait
    predicate: can use
    object: compatible_solute_strategy
    description: Haloalkaliphiles can osmoadapt via compatible-solute accumulation.
    evidence:
    - reference: DOI:10.1038/s44185-024-00050-w
      notes: 'Review: halophiles use two broad osmoadaptation strategies, including
        biosynthesis/accumulation of compatible solutes.'
  - subject: haloalkaliphilic_trait
    predicate: can use
    object: salt_in_strategy
    description: Haloalkaliphiles can osmoadapt via the intracellular salt-in strategy.
    evidence:
    - reference: DOI:10.1038/s44185-024-00050-w
      notes: 'Review: halophiles use two broad osmoadaptation strategies, including
        the intracellular ''salt-in'' strategy.'
  - subject: na_h_antiport
    predicate: contributes to
    object: na_efflux_ph_regulation
    description: Na+/H+ antiporters expel Na+ and help regulate intracellular pH.
    evidence:
    - reference: DOI:10.3389/fmicb.2025.1550346
      notes: Na+/H+ antiporters (nhaA/B/C and the mnh complex) expel Na+ and help
        pH regulation; generalized mechanistic edge relevant to haloalkaliphiles.
    predicate_id: RO:0002326
  - subject: na_efflux_ph_regulation
    predicate: enables
    object: alkaline_ph_homeostasis
    description: Sodium efflux coupled to proton import supports pH homeostasis under
      alkaline conditions.
    evidence:
    - reference: DOI:10.3389/fmicb.2025.1550346
      notes: Na+/H+ antiport expels Na+ while helping pH regulation, supporting cytoplasmic
        pH homeostasis.
    predicate_id: RO:0002327
  - subject: compatible_solute_strategy
    predicate: involves biosynthesis of
    object: ectoine
    description: Compatible-solute strategy includes ectoine biosynthesis/uptake.
    evidence:
    - reference: DOI:10.3389/fmicb.2025.1550346
      notes: Salt-out strategy involved biosynthesis and uptake of compatible solutes
        including ectoine; strong for hypersaline adaptation broadly.
  - subject: choline_oxidation_pathway
    predicate: biosynthesizes
    object: glycine_betaine
    description: Glycine betaine is produced de novo via the choline oxidation pathway.
    evidence:
    - reference: DOI:10.1038/s44185-024-00050-w
      notes: 'Review: de novo biosynthesis of glycine betaine via the choline oxidation
        pathway.'
curation_history:
- timestamp: '2026-05-05T01:35:46.861455+00:00'
  curator: seed_from_metpo
  action: SEEDED_FROM_METPO
  changes: imported from data/raw/metpo.owl (CLASS)
  llm_assisted: false
- timestamp: '2026-05-06T14:15:44-07:00'
  curator: codex
  action: CURATED_WITH_ORGANISM_EXAMPLE
  changes: Added Natronomonas pharaonis organism example with PMID-backed evidence.
  llm_assisted: true
- timestamp: '2026-05-10T00:00:00-07:00'
  curator: codex
  action: ADDED_CAUSAL_GRAPH
  changes: Added DOI-backed causal graph for combined high-salt and alkaline-pH adaptation
    in haloalkaliphily.
  llm_assisted: true
- timestamp: '2026-05-20T03:35:29Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002326×3, 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
    (CHEBI:65015×1).
  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
    (ENVO:01000687×1).
  llm_assisted: true
- timestamp: '2026-06-15T07:19:08Z'
  curator: claude
  action: FIX_NODE_GROUNDING_CURIE
  changes: Overwrote 2 causal-node grounding(s) to corrected CURIEs (phase-2 id-label
    fix; 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 6 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 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002326×1, RO:0002327×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:21:16Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (METPO:1007720×1).
  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:27592×1, CHEBI:17750×1).
  llm_assisted: true