TraitMech

TraitMech › ENVIRONMENT

NaCl range low

METPO:1000469 · CLASS · REVIEWED

A NaCl range phenotype in which the upper bound of growth-supporting NaCl concentration is at or below approximately 1% (w/v), characteristic of non-halophilic or halotolerant organisms.

Trait evidence (1)

  • DOI:10.1093/femsre/fuy009
    salinity range

    Osmoadaptation review supports growth limited to ≤ ~1% NaCl as the non-halophilic / halotolerant range.

NaCl-range-low non-halophile range

DOI-backed graph linking limited high-salt tolerance to a growth-supporting NaCl range capped at ~1% (w/v).

NONMECHANISTIC · This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.

NaCl-range-low non-halophile range Interactive directed graph showing evidence-backed causal relationships for NaCl range low.

Edge evidence

  • limited high-salt tolerance confers NaCl range low METPO:2007700

    Limited tolerance to elevated NaCl caps growth at low salt.

  • NaCl range low is a NaCl range rdfs:subClassOf

    NaCl range low is a quantitative bin of the NaCl-range phenotype.

  • NaCl concentration causes hyperosmotic stress biolink:causes

    Increased external NaCl concentration causes hyperosmotic stress.

    • DOI:10.1093/femsml/uqad020 hyperosmotic stress by addition of either non-ionic osmolyte sucrose or ionic solute NaCl Verified against the open Bhowmick et al. review; the edge is retained as a broad NaCl-to-hyperosmotic-stress step, not as a direct determinant of the <=1% range bin.
  • hyperosmotic stress increases compatible solute accumulation RO:0002213

    Hyperosmotic stress increases compatible-solute accumulation as a later osmoadaptive response.

    • DOI:10.1093/femsml/uqad020 external osmotic upshifts by increasing the cellular concentration of cations (e.g. K+) and compatible solutes Verified against the open Bhowmick et al. review; this keeps compatible-solute accumulation as a broad osmotic-upshift response.
  • mechanosensitive channels MscL/MscS mitigates hypoosmotic shock METPO:2007407

    Mechanosensitive channels mitigate turgor stress during sudden hypoosmotic shocks at the low-salinity end of the range.

    • DOI:10.1093/femsml/uqad020 emergency reaction essential for preventing turgor increase Verified against the open Bhowmick et al. review; the edge is reversed from ungrounded shock-opens-channel wording to a grounded mitigation predicate.
  • cyclic di-AMP inhibits OpuA/OpuC compatible-solute importers RO:0002212

    c-di-AMP binds and inhibits OpuA/OpuC compatible-solute importers.

    • DOI:10.1128/mmbr.00181-23 Cyclic di-AMP binds to the CBS domains of compatible solute importers Verified against public Foster et al. text; OpuA/OpuC are retained as representative CBS-domain osmolyte importers.
  • choline uptake enables glycine betaine biosynthesis RO:0002327

    Choline uptake enables synthesis of glycine betaine, a key compatible solute.

    • DOI:10.1126/sciadv.ado6229 uptake of external choline for synthesizing the osmoprotective glycine betaine Verified against public Yang et al. abstract text; choline uptake is retained as the substrate-supply step for glycine-betaine biosynthesis.

Provenance

Identifier source
METPO (2026-06-12)
Definition source
DOI:10.1093/femsre/fuy009

Parent traits (1)

Synonyms (3)

  • Halotolerant EXACT_SYNONYM · metpo.owl
  • Non-halophile EXACT_SYNONYM · metpo.owl
  • NaR_<=1 RELATED_SYNONYM · metpo.owl

kg-microbe context

Matched 1 kg-microbe node via direct_metpo.

  • METPO:1000469 [-3.957, -1.727, +0.312, +1.025, …]

512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

Nearest neighbors in embedding space

Top-8 cosine-similar METPO traits from the 2026-04-25 deepwalk (512-D).

Deep research

Generated by just research-trait; source: research/traits/environment/nacl_range_low-deep-research-falcon.md

Unreviewed literature output — not curated TraitMech content Ontology identifiers suggested below have not been resolved against their ontologies, and some are known to be wrong. Check any CURIE against the source before using it. 
# Curation-focused research report: NaCl range low

## Executive assessment

**Trait:** NaCl range low
**Identifier:** `METPO:1000469`
**Parent:** `METPO:1000334`

This trait should be treated as an **assay-observed upper growth boundary**, not as a single conserved molecular mechanism. Operationally, an organism belongs in this class when growth is supported up to approximately **1% (w/v) NaCl** but not above that range under a stated medium, temperature, pH, inoculum, aeration, incubation time, and growth endpoint. One percent NaCl is approximately **10 g/L or 171 mM NaCl**. The supplied threshold is approximate, so measurements near it should retain the original concentration series and uncertainty.

The strongest mechanistic interpretation is that low-range organisms have insufficient capacity to offset the combined effects of elevated extracellular osmolarity and, potentially, Na⁺-specific ionic stress. High external osmolality drives water efflux, lowers hydration and turgor, and increases cytoplasmic crowding; microorganisms normally counter these effects through K⁺ homeostasis and accumulation of compatible solutes by synthesis or import. These are authoritative general mechanisms, but the available literature does **not** establish that every organism with a ≤1% maximum lacks any particular transporter or pathway (bremer2019responsesofmicroorganisms pages 3-5).

## 1. Scope and boundary cases

### Included phenotype

`METPO:1000469` represents the **upper bound of growth-supporting NaCl concentration**. Evidence should ideally report growth across a NaCl series containing concentrations below, at, and above 1% (w/v), with an explicit no-growth or strongly inhibited-growth endpoint above the boundary.

### Important distinctions

1. **Tolerance is not requirement.** A non-halophile can grow without added NaCl; a halophile may require salt. The trait records the upper growth boundary, not the minimum or optimum.
2. **Maximum is not optimum.** An organism may grow best near 0% NaCl yet retain weak growth at 1%, or grow best at 1% and fail above it. These should not be conflated.
3. **“Halotolerant” is broader than ≤1%.** Published usage often describes non-halophiles capable of tolerating concentrations far above 1%. Consequently, the supplied synonym “Halotolerant” is ambiguous and should not be used alone to infer `METPO:1000469`.
4. **NaCl stress is not identical to osmotic stress.** An isosmotic sucrose or sorbitol control separates general water-activity effects from Na⁺/Cl⁻ toxicity and ion-homeostasis effects.
5. **Growth is not survival.** Persistence or colony recovery after salt exposure does not prove active growth at that concentration.
6. **Chronic hyperosmotic growth is not hypoosmotic-shock survival.** Mechanosensitive channels chiefly protect cells when osmolarity suddenly falls; they are mechanistically adjacent but do not directly explain a low upper NaCl growth limit (bremer2019responsesofmicroorganisms pages 3-5, goszcz2025bacterialosmoprotectants—away pages 4-5).
7. **Medium composition matters.** Peptides, yeast extract, choline, glycine betaine, proline, ectoine, K⁺, Mg²⁺, pH buffers, and carbon source can shift the observed maximum by supplying osmoprotectants or changing ionic activity.

## 2. Candidate causal-graph nodes

### Trait and assay nodes

- NaCl range low — `METPO:1000469`
- Parent NaCl-range phenotype — `METPO:1000334`
- Growth at or below approximately 1% NaCl — label-only assay state
- Growth inhibition above approximately 1% NaCl — label-only assay outcome
- NaCl concentration series — label-only experimental factor
- Medium composition, temperature, pH, aeration, inoculum, incubation time, growth endpoint — label-only covariates

### Environmental and chemical nodes

- Sodium chloride — `CHEBI:26710`
- Sodium ion — `CHEBI:29101`
- Potassium ion — `CHEBI:29103`
- Glycine betaine — `CHEBI:17750`
- L-proline — `CHEBI:17203`
- L-glutamate — `CHEBI:30796`
- 4-aminobutanoate/GABA — `CHEBI:16865`
- Ectoine — `CHEBI:142654`
- Trehalose, choline, water, and chloride — use validated CHEBI mappings during implementation rather than assigning unverified identifiers here
- High external osmolality, reduced water activity, ionic stress — label-only candidate states

### Processes and physiological states

- Response to osmotic stress — `GO:0006970`
- Response to salt stress — `GO:0009651`
- Water efflux
- Loss of cellular hydration
- Reduced turgor
- Increased cytoplasmic molecular crowding

Showing the first 60 of 223 lines of findings; the linked file also carries the run's front matter and the prompt it was given — read the full report.

Canonical examples (1)

Organisms cited as exemplars of this trait. Taxon ids are NCBITaxon and link out to the NCBI record.

  • Sphingomonas oligoaromativorans NCBITaxon:575322 DOI:10.1099/ijs.0.052894-0 Type strain SY-6T grew from 0 to 0.5% (w/v) NaCl, with a 0.01% optimum; the complete reported range lies below the approximately 1% upper bound.

Curation history

  1. · SEEDED_FROM_METPO · seed_from_metpo

    imported from data/raw/metpo.owl (CLASS)

  2. · CURATED_CAUSAL_GRAPH · claude

    Added DOI-backed definition and causal graph linking limited high-salt tolerance to the non-halophile NaCl-range bin.

  3. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202×1, rdfs:subClassOf×1).

  4. · ENRICH_CAUSAL_GRAPH · claude

    Added 5 evidence-backed generic edges (9 new nodes) from the deep-research report.

  5. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes×1, RO:0002212×1, RO:0002327×1).

  6. · GROUND_CAUSAL_NODES · claude

    Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:71578×1, GO:0031456×1).

  7. · MIGRATE_MICROBE_DOMAIN_EDGES · claude

    Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.

  8. · REVIEW_GRAPH_PROTEIN_TAXON · claude

    Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope nacl_range_low_non_halophile=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (mechanosensitive_channels, opu_solute_importers).

  9. · ADD_CANONICAL_EXAMPLES · codex

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Sphingomonas oligoaromativorans (NCBITaxon:575322; DOI:10.1099/ijs.0.052894-0). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

  10. · REVIEW_CAUSAL_EVIDENCE · codex

    Reviewed the nacl_range_low_non_halophile graph for issue #183: added exact snippets to 5 causal-edge evidence items, grounded 2 residual predicates, and repaired 1 local node-type conflict. No paid research service was called.

  11. · ADVERSARIAL_REVIEW_REPAIR · codex

    Addressed PR #664 adversarial review: replaced the unsupported compatible-solute bridge snippet with exact Bhowmick et al. wording that normalizes the K+ superscript and names both cation and compatible-solute accumulation after an external osmotic upshift.