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temperature delta very low

METPO:1000483 · CLASS · REVIEWED

A temperature delta phenotype with a growth-supporting temperature breadth of approximately 1–5 °C, characteristic of stenothermal physiology.

Trait evidence (1)

  • DOI:10.1146/annurev-micro-091313-103612
    more unsaturated fatty acids

    Membrane-adaptation review supports very narrow thermal-tolerance breadths as the stenothermal phenotype with limited membrane-remodeling flexibility.

Very-low temperature-delta contextual cold-stress branches

DOI-backed contextual graph connecting cold-induced membrane rigidification, unsaturated-fatty-acid membrane remodeling, CspA/CsdA RNA support, and very limited thermal-adaptation flexibility to the 1–5 °C temperature-delta bin.

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.

Very-low temperature-delta contextual cold-stress branches Interactive directed graph showing evidence-backed causal relationships for temperature delta very low.

Edge evidence

  • very limited thermal-adaptation flexibility confers temperature delta very low METPO:2007700

    Very limited thermal-adaptation flexibility yields a 1–5 °C temperature-delta breadth.

  • temperature delta very low is a temperature delta rdfs:subClassOf

    Temperature delta very low is a quantitative bin of the temperature-delta phenotype.

  • unsaturated fatty acid content positively regulates membrane fluidity RO:0002213

    A higher unsaturated-fatty-acid proportion fluidizes bacterial cytoplasmic membranes and counteracts cold rigidification.

    • DOI:10.1146/annurev-micro-091313-103612 incorporation of proportionally more unsaturated fatty acids Verified against the public Annual Review of Microbiology abstract; de Mendoza reviews increased unsaturated fatty acid incorporation as part of homeoviscous adaptation to decreasing growth temperature.
    • DOI:10.1111/mmi.15323 increases with temperature or an increase in the proportion of unsaturated fatty acids and vice versa Verified against the open Molecular Microbiology full text; Singh and Harinarayanan use E. coli unsaturated-fatty-acid perturbations as a route to membrane-fluidity loss.
  • cold shock positively regulates CspA cold-shock protein RO:0002213

    Cold shock strongly increases CspA cold-shock protein synthesis.

    • DOI:10.1046/j.1365-2958.1999.01284.x more than 10% of the total cellular protein synthesis Verified against the open Molecular Microbiology full text; CspA is the major E. coli cold-shock protein and its synthesis rises sharply after temperature downshift.
  • CsdA DEAD-box RNA helicase contributes to 50S ribosomal subunit biogenesis RO:0002326

    CsdA DEAD-box RNA helicase contributes to 50S ribosomal-subunit biogenesis at low temperature.

    • DOI:10.1093/nar/gkh603 CsdA is involved in the biogenesis of the large rather than the small ribosomal subunit Verified against the open Nucleic Acids Research abstract; Charollais et al. place the E. coli CsdA helicase in 50S ribosomal-subunit biogenesis at low temperatures.
  • cold shock negatively regulates membrane fluidity RO:0002212

    Cold exposure drives membrane lipids toward ordered gel states and thereby decreases functional membrane fluidity.

    • DOI:10.1007/s00792-017-0939-x liquid crystalline phase into the rigid gel phase Verified against the Siliakus et al. Springer full text; the review describes low-temperature shifts from liquid-crystalline to rigid gel membrane phases.
  • membrane fluidity contributes to membrane transport at low temperature RO:0002326

    Liquid-crystalline membrane fluidity supports permeability, diffusion, and membrane-protein function at low temperature.

    • DOI:10.1007/s00792-017-0939-x many membrane proteins only function in the liquid crystalline phase Verified against the Siliakus et al. Springer full text; the review links low-temperature membrane phase to membrane-protein function.
  • membrane transport at low temperature contributes to very limited thermal-adaptation flexibility RO:0002326

    Cold preservation of membrane transport is one contextual branch of the thermal-acclimation flexibility represented in this nonmechanistic temperature-breadth graph.

    • DOI:10.1007/s00792-017-0939-x maintain the fluidity of the membrane Verified against the Siliakus et al. Springer full text; this supports the membrane-function branch without asserting a direct universal cause of the 1-5 degree C temperature-delta bin.
  • CspA cold-shock protein contributes to RNA metabolism at low temperature RO:0002326

    CspA RNA chaperone activity supports translation by reducing low-temperature RNA secondary structure.

    • DOI:10.1046/j.1365-2958.1999.01284.x CspA can bind to RNA without apparent sequence specificity Verified against the open Molecular Microbiology full text; the source assigns CspA RNA-chaperone activity a role in low-temperature translation.
  • CsdA DEAD-box RNA helicase contributes to RNA metabolism at low temperature RO:0002326

    CsdA DEAD-box helicase activity supports RNA handling and large ribosomal-subunit maturation in the cold.

    • DOI:10.1093/nar/gkh603 CsdA is involved in ribosome biogenesis Verified against the open Nucleic Acids Research abstract; CsdA supports an RNA helicase-dependent low-temperature ribosome-biogenesis branch.
  • 50S ribosomal subunit biogenesis contributes to RNA metabolism at low temperature RO:0002326

    50S ribosomal-subunit biogenesis is part of the RNA-processing and translation-support module required during cold stress.

    • DOI:10.1093/nar/gkh603 deficit in free 50S subunits at low temperatures Verified against the open Nucleic Acids Research abstract; CsdA defects in the cold appear as impaired 50S subunit accumulation.
  • RNA metabolism at low temperature contributes to very limited thermal-adaptation flexibility RO:0002326

    Cold-supportive RNA chaperone and ribosome-biogenesis functions are a second contextual branch of the thermal-acclimation flexibility represented in this nonmechanistic temperature-breadth graph.

    • DOI:10.1046/j.1365-2958.1999.01541.x RNA chaperone to prevent the formation of secondary structures in RNA molecules Verified against the Europe PMC Phadtare and Inouye abstract; this supports the RNA-function branch without asserting CspA as a universal determinant of the 1-5 degree C temperature-delta bin.

Provenance

Identifier source
METPO (2026-06-12)
Definition source
DOI:10.1146/annurev-micro-091313-103612

Parent traits (1)

Synonyms (1)

  • Td_1_5 RELATED_SYNONYM · metpo.owl

kg-microbe context

Matched 1 kg-microbe node via direct_metpo.

  • METPO:1000483 [-4.820, -3.932, -4.489, +2.974, …]

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/temperature_delta_very_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 report: temperature delta very low

## 1. Scope summary

**Target:** `METPO:1000483` — **temperature delta very low** (`Td_1_5`), an environmental class under `METPO:1000303`.

The trait should represent an **assay-observed growth-temperature breadth of approximately 1–5 °C**: the difference between the lowest and highest temperatures supporting a defined amount of microbial growth under otherwise fixed conditions. It is therefore a phenotype of **very narrow thermal tolerance (stenothermy)**, not a temperature preference or optimum. Thermal tolerance itself is commonly defined as “the temperature range within which a species can grow.” (he2023highspeciationrate pages 1-2)

A defensible measurement should estimate the width of a thermal-performance curve using sufficiently dense temperature intervals. Herren and Baym emphasize that niche breadth can be expressed through the width or area of that curve and that no single metric is appropriate for every population. (herren2022decreasedthermalniche pages 8-9)

### Boundaries and exclusions

Do **not** equate `METPO:1000483` with:

- **Psychrophily or thermophily:** these classify the location of the optimum or limits, not breadth. Psychrophiles can be broad or narrow thermal generalists.
- **Growth at one temperature:** occurrence at a single temperature does not establish a 1–5 °C interval.
- **Cold survival, persistence, or metabolic activity:** viability without population growth is a different endpoint.
- **A narrow realized environmental distribution:** environmental detection can reflect dispersal, nutrients, pH, pressure, competition, or sampling resolution rather than intrinsic growth limits.
- **Acute heat/cold tolerance:** short-term survival thresholds are not equivalent to sustained growth boundaries.

Assay annotations should include strain, medium, atmosphere, pH, salinity, pressure, inoculum, temperature spacing, incubation duration, growth threshold, and biological replication. Incubation time is especially important: *Exiguobacterium chiriqhucha* RW2 required 10 days to score growth at 4 °C, whereas most other temperatures were scored after two days. (white2019thecompletegenome pages 9-10)

No retrieved study directly demonstrated that a particular gene or lipid perturbation creates the exact **1–5 °C** breadth specified by `METPO:1000483`. Consequently, the strongest available graph is a mechanistic scaffold around determinants of thermal breadth, with explicit uncertainty on the final links to the target trait.

## 2. Current understanding and recent developments

The most mature mechanism concerns **membrane homeoviscous adaptation**. Cooling increases lipid ordering, reduces membrane fluidity and permeability, slows diffusion, and impairs embedded proteins. Cells counter this by changing lipid composition—especially increasing cis-unsaturated, short-chain, or selected branched fatty acids—to lower the gel–liquid-crystalline transition temperature and preserve a functional membrane. (collins2019psychrophiliclifestylesmechanisms pages 5-8, siliakus2017adaptationsofarchaeal pages 3-5)

However, these mechanisms normally support thermal accommodation and thus plausibly **broaden**, rather than define, tolerance. The hypothesis relevant to stenothermy is that restricted remodeling capacity causes membrane function to fail after only a small temperature shift. That final inference is biologically coherent but has not been directly tested against a 1–5 °C microbial growth breadth in the retrieved evidence.

Recent work strengthens the ecological and trade-off context rather than identifying a universal stenothermy gene. A 2023 hot-spring survey spanning 54.8–80 °C classified 26,070 OTUs as temperature-sensitive—detected at one sampled temperature—and 524 as temperature-resistant—detected at five or more temperatures. Temperature-sensitive taxa were much less abundant, while community niche breadth narrowed with increasing temperature. These are community-distribution data, not intrinsic 1–5 °C growth assays. (he2023highspeciationrate pages 4-8, he2023highspeciationrate pages 1-2)

A 2024 synthesis emphasizes that microbial growth, adaptability, and survival compete for finite physiological and proteome resources. This supports trade-off models for specialization but does not identify a causal module specific to very-low thermal delta. (zhu2024shapingofmicrobial pages 1-2)

A 2023 genome/proteome/metabolome study of the snow-blight fungus *Phacidium infestans* found antifreeze proteins, trehalose-synthesis enzymes, desaturases, very-long-chain fatty-acid elongation proteins, and stress-response proteins during investigation of freezing-temperature adaptation. The fungus can grow as low as −5 °C, and metabolites differed between −3 and 22 °C. These results identify candidates, but the work did not perturb them or establish narrow thermal breadth. (zerouki2023wholegenomesequenceand pages 1-2)

## 3. Candidate nodes grouped by type

### Trait and assay nodes

- `METPO:1000483` — temperature delta very low.
- Growth-supporting temperature breadth — label-only assay-derived quantity.
- Lower growth-temperature limit — label-only.
- Upper growth-temperature limit — label-only.
- Thermal-performance curve width/area — label-only.
- Stenothermal physiology — label-only; use as a descriptive synonym unless a verified ontology mapping is available.
- Temperature fluctuation periodicity — label-only experimental factor.
- Historical/selective temperature — label-only experimental factor.

### Environmental and experimental factors

- Environmental temperature — candidate `ENVO:01000207` only after ontology verification in the curation environment; otherwise label-only.
- Low-temperature exposure — label-only.
- High-temperature exposure — label-only.
- Constant-temperature habitat — label-only.
- Periodic temperature fluctuation — label-only.
- Random temperature fluctuation — label-only.
- Chloramphenicol exposure — `CHEBI:17698`.
- Freeze–thaw cycling, ice formation, osmotic stress, oxidative stress, hydrostatic pressure, nutrient availability, pH, and salinity — important covariates; add only when measured.

Showing the first 60 of 239 lines of findings; the linked file also carries the run's front matter and the prompt it was given — read the full report.

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 very limited thermal-adaptation flexibility to the stenothermal temperature-delta-very-low 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 4 evidence-backed generic edges (6 new nodes) from the deep-research report.

  5. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213×1).

  6. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007505×1).

  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 temperature_delta_very_low_stenothermal=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (cspa_protein, csda_helicase).

  9. · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex

    Reviewed issue #444 after #591 and left canonical_examples empty: The tracked artifact explicitly found no natural organism with both sustained-growth endpoints establishing a 1-5 degree C breadth. Cold growth, an optimum, or an assay window is not a measured delta under #591. No paid research was used.

  10. · REVIEW_CAUSAL_EVIDENCE · codex

    Reviewed the temperature_delta_very_low_stenothermal graph for issue #183: added exact snippets to 4 membrane and cold-shock evidence items, grounded 3 residual predicates, collapsed 1 backwards membrane-fluidity edge into the supported unsaturated-fatty-acid edge, and retyped unsaturated fatty acid content as a QUALITY node. The record remains an explicitly reviewed nonmechanistic 1-5 degree C temperature-breadth bin. No paid research service was called.

  11. · CONNECT_CAUSAL_GRAPH_COMPONENTS · codex

    Resolved issue #183 graph fragmentation (4 components to 1) by adding 3 contextual cold membrane and RNA nodes plus 8 source- and verbatim-snippet-backed connectors. The connectors join supported cold-stress branches without asserting a direct universal unsaturated-fatty-acid cause of the 1-5 degree C temperature-delta bin. No paid research service was called.

  12. · ADVERSARIAL_REVIEW_REPAIR · codex

    Addressed PR #664 adversarial review: replaced copied nonmechanistic bridge snippets with independent exact source snippets while preserving the existing connector edge scope.

  13. · ADVERSARIAL_REVIEW_REPAIR · codex

    Addressed PR #664 adversarial review issues #678 and #681: removed the unsupported membrane phase-transition temperature branch, requoted the cold RNA connector with exact Phadtare and Inouye wording, and replaced generic Springer endpoint notes with the specific Siliakus et al. full-text endpoint.