identifier: METPO:1000335
label: NaCl delta
definition: A salinity phenotype with numerical limits expressing the breadth (maximum
  minus minimum) of NaCl concentrations supporting growth of an organism.
definition_source: DOI:10.1093/femsre/fuy009
trait_category: ENVIRONMENT
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000532
- METPO:1000534
evidence:
- reference: DOI:10.1093/femsre/fuy009
  snippet: salinity range
  notes: Osmoadaptation review supports the span of NaCl-tolerance as a halophily
    descriptor; its breadth (delta) reflects euryhaline versus stenohaline physiology.
- reference: DOI:10.1186/1746-1448-4-2
  snippet: cope with the high salt concentrations
  notes: Saline-Systems review supports broad osmoadaptive capacity as the basis of
    a wide NaCl-delta phenotype.
causal_graphs:
- graph_id: nacl_delta_euryhaline_breadth
  title: NaCl-delta euryhaline tolerance breadth
  description: DOI-backed graph linking osmoadaptive flexibility to the breadth of
    the NaCl growth range (delta = max − min).
  nodes:
  - node_id: nacl_delta_trait
    label: NaCl delta
    node_type: TRAIT
    grounding: METPO:1000335
    description: Breadth of the growth-supporting NaCl range.
  - node_id: osmoadaptive_flexibility
    label: osmoadaptive flexibility
    node_type: BIOLOGICAL_PROCESS
    description: Capacity to remodel osmolyte pools and ion transport across a wide
      span of ambient salinities.
  - node_id: euryhaline_physiology
    label: euryhaline physiology
    node_type: BIOLOGICAL_PROCESS
    description: Physiology supporting growth over a broad salinity range.
  - node_id: tolerance_breadth
    label: tolerance breadth
    node_type: BIOLOGICAL_PROCESS
    description: Span between the minimum and maximum growth-supporting NaCl.
  - node_id: hyperosmotic_upshift
    label: hyperosmotic upshift
    node_type: ENVIRONMENTAL_FACTOR
    description: A rise in ambient NaCl/osmolarity imposing osmotic stress.
  - node_id: potassium_uptake
    label: potassium ion uptake
    node_type: BIOLOGICAL_PROCESS
    description: Rapid import of K+ as the principal cytoplasmic cation during osmotic
      upshift.
    grounding: GO:1990573
  - node_id: osmoadaptation
    label: response to osmotic stress
    node_type: BIOLOGICAL_PROCESS
    description: Cellular adjustment of osmolyte and ion pools in response to osmotic
      stress.
    grounding: GO:0006970
  - node_id: compatible_solute_accumulation
    label: compatible solute accumulation
    node_type: BIOLOGICAL_PROCESS
    description: Accumulation or synthesis of neutral compatible solutes (glycine
      betaine, trehalose, ectoine, proline).
  - node_id: salt_out_strategy
    label: salt-out strategy
    node_type: BIOLOGICAL_PROCESS
    description: Osmoadaptation by excluding Na+ while accumulating organic compatible
      solutes.
  - node_id: salt_in_strategy
    label: salt-in strategy
    node_type: BIOLOGICAL_PROCESS
    description: Osmoadaptation by accumulating intracellular KCl matching environmental
      salinity, favored at very high salt.
    grounding: METPO:1007720
  - node_id: high_maximal_nacl_tolerance
    label: high maximal NaCl tolerance
    node_type: QUALITY
    description: Capacity to grow at very high, near-saturating NaCl concentrations.
  - node_id: mechanosensitive_channels
    label: mechanosensitive channels (MscL/MscS)
    node_type: GENE_OR_PROTEIN
    description: Membrane safety-valve channels releasing solutes during sudden hypoosmotic
      shocks.
  - node_id: hypoosmotic_shock
    label: hypoosmotic shock
    node_type: ENVIRONMENTAL_FACTOR
    description: A sudden drop in ambient salinity causing turgor stress.
  edges:
  - subject: osmoadaptive_flexibility
    predicate: enables
    object: euryhaline_physiology
    description: Osmoadaptive flexibility enables euryhaline growth.
    evidence:
    - reference: DOI:10.1186/1746-1448-4-2
      snippet: cope with the high salt concentrations
      notes: Supports osmoadaptive flexibility as the basis of broad-salinity growth.
    predicate_id: RO:0002327
  - subject: euryhaline_physiology
    predicate: produces
    object: tolerance_breadth
    description: Euryhaline physiology produces a wide growth-supporting NaCl range.
    evidence:
    - reference: DOI:10.1093/femsre/fuy009
      snippet: salinity range
      notes: Supports the link between osmoadaptive physiology and tolerance breadth.
    predicate_id: METPO:2000202
  - subject: tolerance_breadth
    predicate: manifests as
    object: nacl_delta_trait
    description: The breadth between minimum and maximum growth-supporting NaCl manifests
      the NaCl-delta phenotype.
    evidence:
    - reference: DOI:10.1093/femsre/fuy009
      snippet: salinity range
      notes: Supports the trait endpoint.
    predicate_id: METPO:2007400
  - subject: compatible_solute_accumulation
    predicate: enables
    object: osmoadaptation
    description: Accumulation of neutral compatible solutes enables osmoadaptation
      and broader salt-supported growth.
    evidence:
    - reference: DOI:10.1128/MMBR.00181-23
      notes: To avoid K+-induced cytotoxicity and high ionic strength, cells accumulate
        or synthesize neutral compatible solutes (glycine betaine, trehalose, ectoine,
        proline).
    predicate_id: RO:0002327
  - subject: hyperosmotic_upshift
    predicate: causes
    object: potassium_uptake
    description: Hyperosmotic upshift triggers rapid K+ import as an early osmoadaptive
      response.
    evidence:
    - reference: DOI:10.1128/MMBR.00181-23
      notes: Cells import large amounts of K+ during osmotic upshift; potassium is
        the principal cytoplasmic cation.
    predicate_id: biolink:causes
  - subject: potassium_uptake
    predicate: contributes to
    object: osmoadaptation
    description: K+ accumulation is a core early osmoadaptive response to increased
      NaCl.
    evidence:
    - reference: DOI:10.1128/MMBR.00181-23
      notes: Cytoplasmic K+ levels ~250 mM (E. coli) to ~500 mM (C. glutamicum, L.
        lactis) accumulate as a core osmoadaptive response.
    predicate_id: RO:0002326
  - subject: salt_out_strategy
    predicate: uses
    object: compatible_solute_accumulation
    description: The salt-out strategy relies on accumulation of organic compatible
      solutes.
    evidence:
    - reference: DOI:10.3390/microorganisms12081738
      notes: Salt-out excludes Na+ while accumulating organic compatible solutes like
        sugars, polyalcohols, ectoine, trehalose, glycine-betaine.
  - subject: salt_in_strategy
    predicate: supports
    object: high_maximal_nacl_tolerance
    description: The salt-in strategy supports very high maximal salinity tolerance,
      extending the upper NaCl limit.
    evidence:
    - reference: DOI:10.3390/microorganisms12081738
      notes: Salt-out is energetically costly and less suited to saturating salinities;
        salt-in is favored at very high salt.
  - subject: mechanosensitive_channels
    predicate: protects against
    object: hypoosmotic_shock
    description: Mechanosensitive channels act as safety valves protecting cells against
      sudden hypoosmotic shocks at the low-salinity end of the range.
    evidence:
    - reference: DOI:10.3390/microorganisms12081738
      notes: Mechanosensitive (Msc) channels and compatible-solute efflux systems
        act as safety valves during sudden hypoosmotic shocks.
curation_history:
- timestamp: '2026-05-05T01:35:46.816534+00:00'
  curator: seed_from_metpo
  action: SEEDED_FROM_METPO
  changes: imported from data/raw/metpo.owl (CLASS)
  llm_assisted: false
- timestamp: '2026-05-12T10:00:00-07:00'
  curator: claude
  action: CURATED_CAUSAL_GRAPH
  changes: Added DOI-backed causal graph linking osmoadaptive flexibility and euryhaline
    physiology to the NaCl-delta breadth phenotype.
  llm_assisted: true
- timestamp: '2026-05-20T03:35:30Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002327×1, METPO:2000202×1).
  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:2007400×1).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 6 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
    (RO:0002327×1, biolink:causes×1, RO:0002326×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:21:17Z'
  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: '2026-06-24T17:23:31Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv
    (GO:1990573×1, GO:0006970×1).
  llm_assisted: true