identifier: METPO:1000614
label: psychrophilic
definition: A temperature preference in which growth is favored at low temperatures,
  typically near or below ~15 °C.
definition_source: DOI:10.1038/sj.embor.7400662
trait_category: ENVIRONMENT
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000613
evidence:
- reference: DOI:10.1038/sj.embor.7400662
  snippet: growing well at temperatures around the freezing point of water
  notes: Supports psychrophilic growth at low temperatures.
- reference: PMID:28919459
  snippet: psychrophilic Arctic bacterium Psychrobacter sp. DAB_AL43B
  notes: 'Organism example: Psychrobacter sp. DAB_AL43B is described as psychrophilic.'
canonical_examples:
- taxon_id: NCBITaxon:167879
  taxon_label: Colwellia psychrerythraea 34H
  note: "Model marine psychrophile; active growth at and below 0 C."
  reference: PMID:16043709
causal_graphs:
- graph_id: psychrophilic_cold_adaptation
  title: Psychrophilic cold-adaptation mechanism
  description: Evidence-backed causal sketch linking psychrophily to low temperature,
    membrane remodeling, cold-active enzymes, and cryoprotection.
  nodes:
  - node_id: psychrophilic_trait
    label: psychrophilic
    node_type: TRAIT
    grounding: METPO:1000614
    description: Growth is favored at low temperatures.
  - node_id: low_temperature
    label: low temperature
    node_type: ENVIRONMENTAL_FACTOR
    description: Cold environment near the freezing point of water.
    grounding: PATO:0001306
  - node_id: membrane_fluidity
    label: membrane fluidity
    node_type: QUALITY
    description: Physical state of the membrane needed for transport and growth.
    grounding: METPO:1007505
  - node_id: unsaturated_fatty_acids
    label: unsaturated and branched-chain fatty acids
    node_type: CHEMICAL
    description: Membrane lipid features that reduce packing order and maintain fluidity
      at low temperature.
  - node_id: cold_adapted_enzymes
    label: cold-adapted enzymes
    node_type: GENE_OR_PROTEIN
    description: Enzymes with activity at low temperature, often associated with increased
      structural flexibility.
  - node_id: cold_shock_proteins
    label: cold-shock proteins
    node_type: GENE_OR_PROTEIN
    description: Proteins induced during cold shock or cold acclimation.
  - node_id: antifreeze_proteins
    label: antifreeze and ice-binding proteins
    node_type: GENE_OR_PROTEIN
    description: Proteins that mitigate ice formation or recrystallization damage.
  - node_id: transcription_translation
    label: transcription and translation
    node_type: BIOLOGICAL_PROCESS
    description: Macromolecular synthesis processes impaired by cold-induced nucleic-acid
      secondary structure.
  - node_id: compatible_solutes
    label: compatible solutes
    node_type: CHEMICAL
    description: Low-molecular-weight osmolytes (e.g. trehalose, glycine betaine,
      glycerol) accumulated for cryoprotection.
    grounding: CHEBI:25728
  - node_id: trehalose
    label: trehalose
    node_type: CHEMICAL
    description: Disaccharide cryoprotectant with colligative and protein-stabilizing
      effects.
  - node_id: protein_membrane_stability
    label: protein and membrane stability
    node_type: QUALITY
    description: Structural integrity of proteins and membranes maintained against
      cold denaturation.
  - node_id: ice_crystals
    label: ice crystals
    node_type: CHEMICAL
    description: Intracellular/extracellular ice whose growth and recrystallization
      damage cells.
  - node_id: reactive_oxygen_species
    label: reactive oxygen species
    node_type: CHEMICAL
    description: ROS whose concentration rises at low temperature due to increased
      gas solubility.
    grounding: CHEBI:26523
  edges:
  - subject: low_temperature
    predicate: selects for
    object: psychrophilic_trait
    description: Permanently cold environments select for microorganisms able to grow
      near freezing.
    evidence:
    - reference: DOI:10.1038/sj.embor.7400662
      snippet: growing well at temperatures around the freezing point
      notes: Review supports psychrophile growth in near-freezing environments.
    predicate_id: METPO:2007401
  - subject: low_temperature
    predicate: decreases
    object: membrane_fluidity
    description: Cold reduces membrane fluidity, altering transport and waste exchange.
    evidence:
    - reference: DOI:10.1038/sj.embor.7400662
      snippet: decreased membrane fluidity
      notes: Supports membrane rigidification as a low-temperature challenge.
    predicate_id: RO:0002212
  - subject: unsaturated_fatty_acids
    predicate: regulates
    object: membrane_fluidity
    description: Unsaturated and branched-chain fatty acids maintain membrane fluidity
      during cold growth.
    evidence:
    - reference: DOI:10.1146/annurev-micro-091313-103612
      snippet: more unsaturated fatty acids
      notes: Review supports homoviscous membrane adaptation as temperature decreases.
    predicate_id: RO:0002211
  - subject: cold_adapted_enzymes
    predicate: enables
    object: psychrophilic_trait
    description: Cold-active enzymes support catalysis at low temperature.
    evidence:
    - reference: DOI:10.1016/j.tim.2010.05.002
      snippet: genes involved in cold adaptation
      notes: Review connects psychrophile omics signatures with cold-adaptation mechanisms.
    predicate_id: RO:0002327
  - subject: cold_shock_proteins
    predicate: contributes to
    object: psychrophilic_trait
    description: Cold-shock proteins support cellular acclimation to low temperature.
    evidence:
    - reference: DOI:10.1038/sj.embor.7400662
      snippet: Cold-shock proteins have also been described
      notes: Supports cold-shock proteins as psychrophile-associated adaptations.
    predicate_id: RO:0002326
  - subject: antifreeze_proteins
    predicate: protects against
    object: low_temperature
    description: Antifreeze and ice-binding proteins mitigate ice-associated stress
      in cold habitats.
    evidence:
    - reference: DOI:10.1038/sj.embor.7400662
      snippet: intracellular ice formation
      notes: Review identifies ice formation as a cold challenge and cites bacterial
        antifreeze protein activity.
  - subject: cold_shock_proteins
    predicate: regulates
    object: transcription_translation
    description: Cold-shock proteins regulate transcription and translation during
      cold acclimation.
    evidence:
    - reference: DOI:10.1002/embr.201338170
      notes: cold-shock proteins (CSPs) regulate a variety of cellular processes,
        including transcription, translation.
    predicate_id: RO:0002211
  - subject: trehalose
    predicate: prevents
    object: protein_membrane_stability
    description: Trehalose helps prevent protein denaturation and aggregation, acting
      as a cryoprotectant.
    evidence:
    - reference: DOI:10.1038/sj.embor.7400662
      notes: Trehalose is thought to have a colligative effect, but probably also
        helps in preventing protein denaturation and aggregation.
    predicate_id: RO:0002212
  - subject: compatible_solutes
    predicate: maintains
    object: protein_membrane_stability
    description: Compatible solutes depress the freezing point and stabilize proteins
      and membranes.
    evidence:
    - reference: DOI:10.37256/amtt.5220244537
      notes: Compatible solutes depress the freezing point... stabilize proteins and
        membranes.
  - subject: antifreeze_proteins
    predicate: binds to
    object: ice_crystals
    description: Antifreeze/ice-binding proteins bind ice crystals to control ice
      growth and recrystallization.
    evidence:
    - reference: DOI:10.1038/sj.embor.7400662
      notes: Antifreeze proteins (AFPs) have the ability to bind to ice crystals.
  - subject: low_temperature
    predicate: increases
    object: reactive_oxygen_species
    description: Increased gas solubility at low temperature raises reactive oxygen
      species concentrations.
    evidence:
    - reference: DOI:10.1002/embr.201338170
      notes: The solubility of gases increases at lower temperatures, resulting in
        increased concentrations of reactive oxygen species.
    predicate_id: RO:0002213
curation_history:
- timestamp: '2026-05-05T01:35:46.857091+00:00'
  curator: seed_from_metpo
  action: SEEDED_FROM_METPO
  changes: imported from data/raw/metpo.owl (CLASS)
  llm_assisted: false
- timestamp: '2026-05-06T14:58:45-07:00'
  curator: codex
  action: CURATED_WITH_ORGANISM_EXAMPLE
  changes: Added Psychrobacter sp. DAB_AL43B organism example with PMID-backed evidence.
  llm_assisted: true
- timestamp: '2026-05-11T00:00:00-07:00'
  curator: codex
  action: CURATED_WITH_LITERATURE
  changes: Added DOI-backed psychrophily causal graph for cold adaptation, membrane
    fluidity, cold-active enzymes, cold-shock proteins, and cryoprotection.
  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, RO:0002326×1).
  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:2007401×1).
  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:
    maintains → 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 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (PATO:0000383×1).
  llm_assisted: true
- timestamp: '2026-05-24T04:41:03Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (METPO:1007505×1).
  llm_assisted: true
- timestamp: '2026-05-26T02:30:13Z'
  curator: claude
  action: RETYPE_CAUSAL_NODES
  changes: 'Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum
    semantics: membrane fluidity: BIOLOGICAL_PROCESS → QUALITY ×1.'
  llm_assisted: true
- timestamp: '2026-06-13T21:03:25Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002212×1).
  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: '2026-06-17T04:09:43Z'
  curator: claude
  action: REMOVE_REDUNDANT_SYNONYM
  changes: Removed 1 synonym(s) whose text duplicated the label (seeder redundancy;
    no information lost).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 5 evidence-backed generic edges (6 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:11Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002211×1, RO:0002212×1, RO:0002213×1).
  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
    (CHEBI:25728×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:23:31Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:26523×1).
  llm_assisted: true