temperature preference

Deep research

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

# Curation report: microbial temperature preference

## Trait record and recommended interpretation

- **Trait label:** temperature preference
- **Trait identifier:** **`METPO:1000613`**
- **Category / kind / status:** ENVIRONMENT / CLASS / REVIEWED
- **Given definition:** “A phenotype that describes characteristic growth with respect to environmental temperature.”
- **Parent:** `METPO:1000059`
- **Synonyms:** *Physiology and metabolism.culture temp.temperature*; *range_tmp*

### Scope summary

For TraitMech, **temperature preference should be represented as an assay-conditioned microbial growth phenotype**, not as a single intrinsic temperature value. Its core observable is a thermal performance curve relating temperature to a growth endpoint—preferably maximum specific growth rate, μ—and its cardinal parameters:

- **TMIN:** lower boundary permitting detectable growth;
- **TOPT:** temperature giving the maximum specific growth rate, μopt;
- **TMAX:** upper boundary permitting growth.

Thermal growth curves are typically asymmetric or “hump-shaped”; TOPT is therefore not equivalent to the midpoint of TMIN and TMAX. It can also differ from the temperature maximizing biomass yield, product formation, survival, or enzyme activity. Cardinal temperatures are the standard parameters used to delimit the growth niche and its optimum. (noll2020modelingandexploiting pages 6-8, noll2020modelingandexploiting pages 19-20)

The phenotype is **conditional on the assay**. The record should preserve strain, medium and carbon source, pH, oxygen/redox condition, salinity, pressure, inoculum history, acclimation time, temperature-shift versus steady-state design, incubation duration, and measurement endpoint. For example, *Thermoanaerobacter kivui* was assayed in defined or complex medium under strict anoxia, at pH 7.5, with specified carbon sources and growth measured by OD600; its experimentally observed TMIN under those conditions was 39°C. (lehmann2023adaptivelaboratoryevolution pages 2-3, lehmann2023adaptivelaboratoryevolution pages 1-2)

### Boundary cases

1. **Acute thermal survival is not temperature preference.** Heat-shock killing, freeze–thaw survival, or transient stress tolerance measures viability after an insult, whereas temperature preference concerns sustained growth across temperatures. In 2024, *Salmonella* `dnaJ` loss increased acute heat resistance by 10³–10⁵-fold but impaired growth at 37°C and above, directly demonstrating that these phenotypes can oppose one another. (berdejo2024evolutionarytradeoffbetween pages 8-10)
2. **Cold/heat-shock response is not necessarily adaptation of TOPT.** A transient transcriptional or metabolic response may restore homeostasis without shifting the strain’s cardinal temperatures.
3. **Environmental occurrence is not proof of preference.** Detection in ice, hot springs, or hydrothermal sediment does not establish active growth or TOPT.
4. **Enzyme temperature optimum is not organismal TOPT.** Mean enzyme optima correlate with growth temperature, but individual enzymes and genome annotations do not determine organismal preference by themselves. (engqvist2018correlatingenzymeannotations pages 4-6, engqvist2018correlatingenzymeannotations pages 9-10)
5. **Thermotolerance, psychrotolerance, and cardinal-temperature classes should remain separate annotations.** A commonly used scheme defines psychrophiles by TOPT <15°C, mesophiles by approximately 20–45°C, thermophiles by >45°C, extreme thermophiles by >65–70°C, and hyperthermophiles by >80°C. These thresholds are conventions rather than mechanisms. (lehmann2023adaptivelaboratoryevolution pages 1-2)
6. **Growth rate, lag, yield, and product formation are different endpoints.** Evolution at low temperature may shorten lag or improve yield without increasing μ or changing TOPT. (lehmann2023adaptivelaboratoryevolution pages 8-9)

## Current mechanistic model

Temperature simultaneously changes reaction kinetics, protein and nucleic-acid stability, membrane viscosity, diffusion, transport, ribosome function, energy demand, and oxidative damage. Consequently, no universal “temperature-preference gene” is expected. The phenotype emerges from the temperature dependence of multiple cellular subsystems.

The strongest experimentally resolved module is **homeoviscous adaptation**. Cooling packs membrane lipids more tightly and lowers fluidity; cells compensate by increasing unsaturated, branched, or shorter acyl chains. Heating generally favors more saturated or longer chains. In *Escherichia coli*, recent work resolved this response into a temperature-sensitive fatty-acid flux valve plus transcriptional feedback, rather than merely a generic stress response. (hoogerland2024atemperaturesensitivemetabolic pages 1-2)

Other modules include protein folding and degradation, RNA structure and translation, DNA topology and repair, compatible-solute accumulation, ice management, oxidative-stress defense, and central-metabolic buffering. These systems often support growth within a thermal range but do not individually establish TOPT.

## Candidate nodes grouped by type

Identifiers below are supplied only where the grounding is unambiguous. **Label-only nodes are preferable to uncertain or invented CURIEs.** Gene symbols should additionally carry organism-specific locus or UniProt identifiers during implementation.

### Trait and assay nodes

| Candidate node | Suggested grounding or treatment | Curation note |
|---|---|---|
| temperature preference | `METPO:1000613` | Target trait; quote CURIE verbatim |
| minimum growth temperature, TMIN | Label-only or verified METPO term | Assay-derived cardinal parameter |
| optimal growth temperature, TOPT | Label-only or verified METPO term | Temperature maximizing a stated growth endpoint |
| maximum growth temperature, TMAX | Label-only or verified METPO term | Assay-derived upper growth boundary |
| specific growth rate | Label plus verified ontology term if available | Prefer μ from exponential growth |
| growth thermal performance curve | Label-only | Relation among temperature, μ, and cardinal parameters |
| growth medium, pH, oxygen availability, salinity, hydrostatic pressure, substrate, incubation time | ENVO/CHEBI terms after record-level verification | Experimental modifiers, not components of the organism |
| acute heat-shock survival; freeze–thaw survival | Separate phenotype nodes | Must not be merged into `METPO:1000613` |

### Environmental and physical nodes

- Environmental temperature and temperature shift.

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