identifier: METPO:1000629
label: halophily preference
definition: A phenotype that is relating to an organism's salt concentration requirements
  or tolerance for growth.
definition_source: DOI:10.1093/femsre/fuy009
trait_category: ENVIRONMENT
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000059
synonyms:
- synonym_text: Physiology and metabolism.halophily.halophily level
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
- synonym_text: range_salinity
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
evidence:
- reference: DOI:10.1093/femsre/fuy009
  snippet: life at high salt concentrations
  notes: Supports salinity and salt concentration as a growth-relevant microbial trait
    axis.
causal_graphs:
- graph_id: halophily_preference_osmoadaptation
  title: Salinity preference and osmoadaptation mechanism
  description: Evidence-backed causal sketch linking environmental salinity, osmotic
    stress, water flux, ion homeostasis, and compatible-solute accumulation to halophily
    preference.
  nodes:
  - node_id: halophily_preference_trait
    label: halophily preference
    node_type: TRAIT
    grounding: METPO:1000629
    description: Growth requirement or tolerance with respect to environmental salt
      concentration.
  - node_id: environmental_salinity
    label: environmental salinity
    node_type: ENVIRONMENTAL_FACTOR
    description: Salt concentration of the growth environment.
  - node_id: osmotic_stress
    label: osmotic stress
    node_type: BIOLOGICAL_PROCESS
    description: Cellular stress caused by a mismatch between external and cytoplasmic
      osmotic potential.
    grounding: GO:0006970
  - node_id: water_flux
    label: water flux across cytoplasmic membrane
    node_type: BIOLOGICAL_PROCESS
    description: Osmotically driven water movement across the membrane.
  - node_id: potassium_ion
    label: potassium ion
    node_type: CHEMICAL
    grounding: CHEBI:29103
    description: Inorganic ion rapidly accumulated during some osmotic upshifts.
  - node_id: compatible_solutes
    label: compatible solutes
    node_type: CHEMICAL
    description: Organic osmolytes accumulated by synthesis or uptake under salt stress.
    grounding: CHEBI:25728
  - node_id: compatible_solute_transport
    label: compatible-solute transport
    node_type: MOLECULAR_FUNCTION
    description: Uptake systems importing osmoprotectants from the environment.
  - node_id: na_h_antiporter
    label: Na+/H+ antiporter
    node_type: GENE_OR_PROTEIN
    description: Secondary transporter that expels cytoplasmic sodium ions using the
      proton electrochemical gradient.
    grounding: UniProtKB:A0A068T423
  - node_id: proton_electrochemical_gradient
    label: proton electrochemical gradient
    node_type: CHEMICAL
    description: Transmembrane proton motive force used as a driving force for ion
      transport.
  - node_id: sodium_ion
    label: sodium ion
    node_type: CHEMICAL
    description: Cytoplasmic sodium ion that must be excluded to relieve toxicity
      under high salinity.
    grounding: CHEBI:29101
  - node_id: acidified_proteome
    label: acidified proteome
    node_type: QUALITY
    description: Proteome enriched in surface acidic residues, characteristic of salt-in
      halophiles.
  - node_id: protein_solubility
    label: protein solubility in hypersaline conditions
    node_type: QUALITY
    description: Maintenance of protein solubility via hydrated cation networks coordinated
      by acidic surface residues.
  - node_id: mechanosensitive_channels
    label: mechanosensitive channels
    node_type: GENE_OR_PROTEIN
    description: Membrane channels acting as safety valves that open during osmotic
      downshock.
  - node_id: solute_efflux
    label: rapid solute efflux
    node_type: BIOLOGICAL_PROCESS
    description: Rapid release of ions and organic solutes during sudden downward
      osmotic shock.
  edges:
  - subject: environmental_salinity
    predicate: regulates
    object: halophily_preference_trait
    description: Salt concentration determines whether growth requires, tolerates,
      or avoids salinity.
    evidence:
    - reference: DOI:10.1093/femsre/fuy009
      snippet: life at high salt concentrations
      notes: Review frames halophily as microbial life under high salt concentration.
    predicate_id: RO:0002211
  - subject: environmental_salinity
    predicate: causes
    object: osmotic_stress
    description: Salinity changes impose osmotic stress on cells.
    evidence:
    - reference: DOI:10.1111/j.1574-6976.2002.tb00598.x
      snippet: overcome salt stress
      notes: Review describes bacterial mechanisms for salt-stress responses.
    predicate_id: biolink:causes
  - subject: osmotic_stress
    predicate: regulates
    object: water_flux
    description: Osmotic imbalance drives water movement across the cytoplasmic membrane.
    evidence:
    - reference: DOI:10.1128/AEM.01934-12
      snippet: balance the osmotic gradient across their cytoplasmic membrane
      notes: Supports osmotic-gradient balancing as central to microbial osmotic stress.
    predicate_id: RO:0002211
  - subject: potassium_ion
    predicate: contributes to
    object: osmotic_stress
    description: Potassium accumulation is an early response to osmotic upshift in
      many bacteria.
    evidence:
    - reference: DOI:10.1128/AEM.01934-12
      snippet: initially importing substantial amounts of potassium ions
      notes: Supports K+ uptake as an emergency osmotic-stress response.
    predicate_id: RO:0002326
  - subject: compatible_solute_transport
    predicate: imports
    object: compatible_solutes
    description: Transport systems import compatible solutes that relieve osmotic
      stress.
    evidence:
    - reference: DOI:10.1016/j.csbj.2021.01.030
      snippet: biosynthesis and/or uptake of compatible solutes
      notes: Review supports uptake and biosynthesis of compatible solutes in bacterial
        high-salinity responses.
    predicate_id: METPO:2000208
  - subject: compatible_solutes
    predicate: mitigates
    object: osmotic_stress
    description: Compatible solutes maintain turgor and protect macromolecular function
      under salt stress.
    evidence:
    - reference: DOI:10.1186/1746-1448-1-5
      snippet: balance external osmotic pressure
      notes: Review supports compatible solutes as osmolytes for osmotic balance.
    predicate_id: METPO:2007407
  - subject: osmotic_stress
    predicate: induces
    object: na_h_antiporter
    description: Osmotic stress drives sodium exclusion via Na+/H+ antiporters.
    evidence:
    - reference: DOI:10.3390/microorganisms12081738
      notes: Sodium ions are expelled from the cytoplasm, usually with the help of
        Na+/H+ antiporters (review, broad across haloarchaea).
  - subject: proton_electrochemical_gradient
    predicate: regulates
    object: na_h_antiporter
    description: The proton electrochemical gradient drives Na+/H+ antiporter activity.
    evidence:
    - reference: DOI:10.3390/microorganisms12081738
      notes: Na+/H+ antiporter uses the electrochemical proton gradient as a driving
        force.
    predicate_id: RO:0002211
  - subject: na_h_antiporter
    predicate: exports
    object: sodium_ion
    description: Na+/H+ antiporter expels cytoplasmic sodium to relieve salt stress.
    evidence:
    - reference: DOI:10.3390/microorganisms12081738
      notes: Sodium is excluded from the cytoplasm with the help of an Na+/H+ antiporter.
    predicate_id: METPO:2000209
  - subject: environmental_salinity
    predicate: regulates
    object: acidified_proteome
    description: High salinity favors a proteome with increased surface acidic residues.
    evidence:
    - reference: DOI:10.3390/microorganisms12081738
      notes: Microorganisms employing the salt-in strategy exhibit an acidified proteome
        essential for protein solubility under hypersaline conditions.
    predicate_id: RO:0002211
  - subject: acidified_proteome
    predicate: promotes
    object: protein_solubility
    description: Surface acidic residues coordinate hydrated cations and keep proteins
      soluble in hypersaline cytoplasm.
    evidence:
    - reference: DOI:10.3390/microorganisms12081738
      notes: The high number of negative surface charges coordinates a network of
        hydrated cations and keeps the protein in solution.
    predicate_id: RO:0002213
  - subject: osmotic_stress
    predicate: regulates
    object: mechanosensitive_channels
    description: Osmotic downshock activates mechanosensitive channels that act as
      safety valves.
    evidence:
    - reference: DOI:10.3390/microorganisms12081738
      notes: Msc channels serve as safety valves, allowing rapid release of ions and
        organic solutes during sudden downward osmotic shocks (broad across halophiles).
    predicate_id: RO:0002211
  - subject: mechanosensitive_channels
    predicate: enables
    object: solute_efflux
    description: Mechanosensitive channels mediate rapid efflux of ions and organic
      solutes during osmotic downshock.
    evidence:
    - reference: DOI:10.3390/microorganisms12081738
      notes: Mechanosensitive channels allow the rapid release of ions and organic
        solutes in case of sudden downward osmotic shocks.
    predicate_id: RO:0002327
curation_history:
- timestamp: '2026-05-05T01:35:46.865794+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 halophily preference trait and added DOI-backed causal graph for
    salinity-driven osmotic stress, ion homeostasis, and compatible-solute osmoadaptation.
  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 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2007407×1).
  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:
    drives → regulates ×1.'
  llm_assisted: true
- timestamp: '2026-05-24T04:13:21Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002211×1).
  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: '2026-05-26T05:00:47Z'
  curator: claude
  action: RENAME_PREDICATE_LABELS
  changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings:
    influences → regulates ×1.'
  llm_assisted: true
- timestamp: '2026-05-26T05:00:49Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002211×1).
  llm_assisted: true
- timestamp: '2026-06-15T07:19:08Z'
  curator: claude
  action: FIX_NODE_GROUNDING_CURIE
  changes: Overwrote 1 causal-node grounding(s) to corrected CURIEs (phase-2 id-label
    fix; 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 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 6 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002211×3, METPO:2000209×1, RO:0002213×1, 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
    (UniProtKB:A0A068T423×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:23:30Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:29101×1).
  llm_assisted: true