identifier: METPO:1000620
label: halophilic
definition: A halophily preference in which an organism requires high concentrations
  of salt for growth and survival.
definition_source: PMID:19329623
trait_category: ENVIRONMENT
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000629
evidence:
- reference: PMID:19329623
  snippet: Salinicoccus albus sp. nov., a halophilic bacterium from a salt mine
  notes: 'Organism example: Salinicoccus albus is described as halophilic.'
canonical_examples:
- taxon_id: NCBITaxon:2242
  taxon_label: Halobacterium salinarum
  note: "extreme halophile"
  reference: PMID:31797576
- taxon_id: NCBITaxon:2746
  taxon_label: Halomonas elongata
  note: "moderate halophile"
  reference: PMID:20849449
causal_graphs:
- graph_id: halophilic_osmoadaptation
  title: Halophilic osmoadaptation mechanism
  description: Evidence-backed causal sketch linking halophilic growth to high-salt
    environments and osmotic adaptation strategies.
  nodes:
  - node_id: halophilic_trait
    label: halophilic
    node_type: TRAIT
    grounding: METPO:1000620
    description: Requires high salt concentrations for growth and survival.
  - node_id: high_salt_environment
    label: high-salt environment
    node_type: ENVIRONMENTAL_FACTOR
    description: Hypersaline or elevated NaCl condition.
    grounding: ENVO:01001040
  - node_id: sodium_chloride
    label: sodium chloride
    node_type: CHEMICAL
    grounding: CHEBI:26710
    description: NaCl as the dominant salt exposure in many halophilic habitats.
  - node_id: osmotic_stress
    label: osmotic stress
    node_type: BIOLOGICAL_PROCESS
    description: Cellular water and turgor stress caused by external salinity.
    grounding: GO:0006970
  - node_id: compatible_solutes
    label: compatible solutes
    node_type: CHEMICAL
    description: Organic osmolytes such as ectoine and glycine betaine.
    grounding: CHEBI:25728
  - node_id: salt_in_strategy
    label: salt-in strategy
    node_type: BIOLOGICAL_PROCESS
    description: Intracellular inorganic ion accumulation for osmotic balance.
    grounding: METPO:1007720
  - node_id: na_h_antiporter
    label: Na+/H+ antiporter
    node_type: GENE_OR_PROTEIN
    description: Membrane antiporter that exports sodium from the cytoplasm in exchange
      for protons.
    grounding: UniProtKB:A0A068T423
  - node_id: sodium_ion
    label: sodium ion
    node_type: CHEMICAL
    description: Na+ cation that must be excluded from the cytoplasm.
    grounding: CHEBI:29101
  - node_id: k_uniport
    label: K+ uniport system
    node_type: GENE_OR_PROTEIN
    description: Uniport transport system that imports potassium into the cell.
  - node_id: potassium_ion
    label: potassium ion
    node_type: CHEMICAL
    description: K+ cation accumulated intracellularly during salt-in osmoadaptation.
    grounding: CHEBI:29103
  - node_id: acidified_proteome
    label: acidified proteome
    node_type: STATE
    description: Proteome enriched in acidic residues, characteristic of salt-in adapted
      organisms.
  - node_id: oxidative_stress
    label: oxidative stress
    node_type: BIOLOGICAL_PROCESS
    description: Reactive-oxygen-mediated cellular stress induced by NaCl shock.
  - node_id: ectABC_operon
    label: ectABC operon
    node_type: GENE_OR_PROTEIN
    description: Evolutionarily conserved operon encoding the ectoine biosynthesis
      pathway.
  - node_id: ectoine
    label: ectoine
    node_type: CHEMICAL
    description: Compatible solute synthesized de novo from L-aspartic acid.
    grounding: CHEBI:27592
  - node_id: l_aspartic_acid
    label: L-aspartic acid
    node_type: CHEMICAL
    description: Precursor metabolite for de novo ectoine biosynthesis.
  edges:
  - subject: high_salt_environment
    predicate: selects for
    object: halophilic_trait
    description: Halophilic microorganisms are adapted to growth in high-salt environments.
    evidence:
    - reference: DOI:10.1093/femsre/fuy009
      snippet: Hypersaline environments ... inhabited by halophilic
      notes: Review supports hypersaline habitats as the environmental context for
        halophily.
    predicate_id: METPO:2007401
  - subject: sodium_chloride
    predicate: causes
    object: osmotic_stress
    description: Elevated NaCl creates osmotic pressure that requires cellular adaptation.
    evidence:
    - reference: DOI:10.1186/1746-1448-4-2
      snippet: ways they cope with the high salt concentrations
      notes: Review frames halophily around coping with high environmental salt.
    predicate_id: biolink:causes
  - subject: compatible_solutes
    predicate: mitigates
    object: osmotic_stress
    description: Compatible solutes are one major osmoadaptation mechanism in halophilic
      microorganisms.
    evidence:
    - reference: DOI:10.1093/femsre/fuy009
      snippet: synthesize organic osmotic solutes
      notes: Supports organic compatible-solute accumulation as an osmotic adaptation
        mechanism.
    predicate_id: METPO:2007407
  - subject: salt_in_strategy
    predicate: mitigates
    object: osmotic_stress
    description: Salt-in ion accumulation is an alternative osmoadaptation strategy.
    evidence:
    - reference: DOI:10.1093/femsre/fuy009
      snippet: KCl accumulating Halobacterium salinarum
      notes: Supports intracellular KCl accumulation as a high-salt adaptation.
    predicate_id: METPO:2007407
  - subject: compatible_solutes
    predicate: contributes to
    object: halophilic_trait
    description: Compatible-solute accumulation supports growth under high salinity.
    evidence:
    - reference: DOI:10.1371/journal.pone.0168818
      snippet: allows microorganisms to cope with high salinities
      notes: Halomonas elongata study supports compatible solutes as a mechanism enabling
        halophilic growth.
    predicate_id: RO:0002326
  - subject: na_h_antiporter
    predicate: expels
    object: sodium_ion
    description: Sodium is excluded from the cytoplasm with the help of an Na+/H+
      antiporter.
    evidence:
    - reference: DOI:10.3390/microorganisms12081738
      notes: sodium is excluded from the cytoplasm with the help of an Na+/H+ antiporter
  - subject: k_uniport
    predicate: imports
    object: potassium_ion
    description: Potassium enters the cell through a uniport system during salt-in
      osmoadaptation.
    evidence:
    - reference: DOI:10.3390/microorganisms12081738
      notes: Potassium enters the cell through a uniport system
    predicate_id: METPO:2000208
  - subject: salt_in_strategy
    predicate: associated with
    object: acidified_proteome
    description: Organisms employing the salt-in strategy exhibit an acidified proteome.
    evidence:
    - reference: DOI:10.3390/microorganisms12081738
      notes: microorganisms employing this strategy exhibit an acidified proteome
    predicate_id: biolink:associated_with
  - subject: sodium_chloride
    predicate: induces
    object: oxidative_stress
    description: NaCl shock induces oxidative stress in addition to osmotic stress.
    evidence:
    - reference: DOI:10.1186/s12934-024-02358-5
      notes: NaCl shock induced two major stresses, namely osmotic stress and oxidative
        stress
  - subject: ectABC_operon
    predicate: biosynthesizes
    object: ectoine
    description: The conserved ectABC operon performs de novo biosynthesis of ectoine.
    evidence:
    - reference: DOI:10.1128/aem.00479-23
      notes: Biosynthesis of ectoine is de novo from L-aspartic acid, performed by
        the conserved operon ectABC
  - subject: l_aspartic_acid
    predicate: is precursor of
    object: ectoine
    description: Ectoine is biosynthesized de novo from L-aspartic acid.
    evidence:
    - reference: DOI:10.1128/aem.00479-23
      notes: Biosynthesis of ectoine is de novo from L-aspartic acid
  - subject: ectoine
    predicate: is a
    object: compatible_solutes
    description: Ectoine is a major organic compatible solute used in osmoadaptation.
    evidence:
    - reference: DOI:10.1128/aem.00479-23
      notes: Ectoine is a canonical compatible solute synthesized via the ectABC operon.
    predicate_id: rdfs:subClassOf
curation_history:
- timestamp: '2026-05-05T01:35:46.860938+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 Salinicoccus albus 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 halophilic osmoadaptation mechanisms.
  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:0002326×1).
  llm_assisted: true
- timestamp: '2026-05-20T05:49:24Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (biolink:causes×1).
  llm_assisted: true
- timestamp: '2026-05-23T21:30:06Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2007407×2, METPO:2007401×1).
  llm_assisted: true
- timestamp: '2026-05-24T04:38:00Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv
    (GO:0006970×1, 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: '2026-06-16T06:54:39Z'
  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: '2026-06-17T04:09:43Z'
  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 (9 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:10Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2000208×1, biolink:associated_with×1, rdfs:subClassOf×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
    (UniProtKB:A0A068T423×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:23:30Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:29101×1, CHEBI:29103×1, CHEBI:27592×1).
  llm_assisted: true