identifier: METPO:1000731 label: nutrient adaptation definition: A trophic type that involves an organism's physiological and metabolic adaptations to specific nutrient availability. definition_source: DOI:10.1073/pnas.0903507106 trait_category: PHYSIOLOGY term_kind: CLASS mapping_status: REVIEWED parent_traits: - METPO:1000631 created_by: Luke Wang evidence: - reference: DOI:10.1073/pnas.0903507106 snippet: high (copiotrophic) or low (oligotrophic) nutrient concentrations notes: Comparative genomics paper frames nutrient adaptation as a copiotroph/oligotroph life-history axis. - reference: DOI:10.1038/ismej.2014.60 snippet: selection for efficient use of nutrients notes: Streamlining review links chronic nutrient regimes to genomic and cellular adaptation. causal_graphs: - graph_id: nutrient_adaptation_life_history_axis title: Nutrient adaptation life-history axis description: DOI-backed graph linking ambient nutrient availability to sensing, resource-allocation strategy, and the copiotroph/oligotroph life-history phenotypes that fall under nutrient adaptation. nodes: - node_id: nutrient_adaptation_trait label: nutrient adaptation node_type: TRAIT grounding: METPO:1000731 description: Physiological and metabolic adaptation to specific nutrient availability regimes. - node_id: ambient_nutrient_concentration label: ambient nutrient concentration node_type: ENVIRONMENTAL_FACTOR description: Concentration of carbon, nitrogen, and phosphorus available in the habitat. - node_id: nutrient_sensing label: nutrient sensing node_type: BIOLOGICAL_PROCESS description: Cellular detection of nutrient status that adjusts gene expression and growth. grounding: GO:0009594 - node_id: resource_allocation label: resource allocation strategy node_type: BIOLOGICAL_PROCESS description: Allocation of cellular resources between rapid growth machinery and high-affinity uptake or stress tolerance. - node_id: copiotrophic_phenotype label: copiotrophic node_type: TRAIT grounding: METPO:1000642 description: Adaptation favoring fast growth in nutrient-rich conditions. - node_id: oligotrophic_phenotype label: oligotrophic node_type: TRAIT grounding: METPO:1000654 description: Adaptation favoring efficient growth in nutrient-poor conditions. - node_id: nutrient_limitation label: chronic nutrient limitation node_type: ENVIRONMENTAL_FACTOR description: Persistently low nutrient availability imposing selection for efficient resource use. - node_id: genome_streamlining label: genome streamlining node_type: BIOLOGICAL_PROCESS description: Selection-driven reduction of cell and genome size and regulatory complexity under nutrient limitation. - node_id: chemotaxis_motility_genes label: chemotaxis and motility genes node_type: GENE_OR_PROTEIN description: Genes encoding chemotaxis and motility functions. - node_id: motility_signaling_genes label: motility and signal-transduction genes node_type: GENE_OR_PROTEIN description: Genes for motility and signal transduction enabling resource tracking. - node_id: rrn_copy_number label: rrn operon copy number node_type: QUALITY description: Number of ribosomal RNA operons in a genome, a proxy for growth potential. - node_id: maximum_growth_potential label: maximum growth potential node_type: CAPACITY description: Maximum potential growth rate of an organism or community. - node_id: carbohydrate_acquisition_genes label: carbohydrate acquisition gene abundance node_type: GENE_OR_PROTEIN description: Relative abundance of genes for carbohydrate metabolism and resource acquisition. edges: - subject: ambient_nutrient_concentration predicate: causes object: nutrient_sensing description: Ambient nutrient levels are detected by cellular sensing systems. evidence: - reference: DOI:10.1073/pnas.0903507106 snippet: high (copiotrophic) or low (oligotrophic) nutrient concentrations notes: Supports nutrient concentration as the environmental driver of the adaptation axis. predicate_id: biolink:causes - subject: nutrient_sensing predicate: controls object: resource_allocation description: Sensing of nutrient status shifts allocation between growth and maintenance functions. evidence: - reference: DOI:10.1038/ismej.2014.60 snippet: selection for efficient use of nutrients notes: Supports nutrient regime as a driver of resource-allocation strategy. predicate_id: RO:0002211 - subject: resource_allocation predicate: manifests as object: copiotrophic_phenotype description: Allocation favoring rapid growth machinery yields a copiotrophic phenotype under nutrient-rich conditions. evidence: - reference: DOI:10.1073/pnas.0903507106 snippet: high (copiotrophic) nutrient concentrations notes: Supports copiotrophy as one expression of nutrient adaptation. predicate_id: METPO:2007400 - subject: resource_allocation predicate: manifests as object: oligotrophic_phenotype description: Allocation favoring high-affinity uptake and streamlining yields an oligotrophic phenotype under nutrient-poor conditions. evidence: - reference: DOI:10.1038/ismej.2014.60 snippet: small cells and genomes notes: Supports oligotrophy as a streamlining-driven expression of nutrient adaptation. predicate_id: METPO:2007400 - subject: copiotrophic_phenotype predicate: is a object: nutrient_adaptation_trait description: Copiotrophy is a child phenotype of nutrient adaptation. evidence: - reference: DOI:10.1073/pnas.0903507106 snippet: copiotrophic notes: Supports copiotrophy as a recognized nutrient-adaptation phenotype. predicate_id: rdfs:subClassOf - subject: oligotrophic_phenotype predicate: is a object: nutrient_adaptation_trait description: Oligotrophy is a child phenotype of nutrient adaptation. evidence: - reference: DOI:10.1073/pnas.0903507106 snippet: oligotrophic notes: Supports oligotrophy as a recognized nutrient-adaptation phenotype. predicate_id: rdfs:subClassOf - subject: nutrient_limitation predicate: selects for object: genome_streamlining description: Chronic nutrient limitation selects for streamlined small cells and genomes. evidence: - reference: DOI:10.1038/ismej.2014.60 notes: Streamlining theory attributes small cells and genomes to selection for efficient use of nutrients where nutrients limit; broad across oligotrophic microbes. predicate_id: METPO:2007401 - subject: oligotrophic_phenotype predicate: negatively regulates object: chemotaxis_motility_genes description: Oligotrophic adaptation is associated with under-representation of chemotaxis and motility genes. evidence: - reference: DOI:10.1093/ismeco/ycae081 notes: Oligotroph genomes had energy-intensive functions like chemotaxis and motility under-represented. - subject: copiotrophic_phenotype predicate: positively regulates object: motility_signaling_genes description: Copiotrophic strategy is enriched in genes for motility and signal transduction. evidence: - reference: DOI:10.1073/pnas.0903507106 notes: Copiotrophs are enriched in genes for motility and sensing and signal transduction. - subject: rrn_copy_number predicate: positively correlates with object: maximum_growth_potential description: Higher rrn operon copy number associates with higher maximum growth potential. evidence: - reference: DOI:10.1038/s41564-023-01465-0 notes: Secondary life-history dimension correlated with ribosomal gene copy number; positive correlation between potential growth and rrn copy number. - subject: maximum_growth_potential predicate: negatively correlates with object: carbohydrate_acquisition_genes description: Maximum growth potential trades off with abundance of carbohydrate acquisition genes. evidence: - reference: DOI:10.1038/s41467-024-50382-1 notes: Growth potential was negatively correlated with relative abundances of carbohydrate metabolism genes; apparent tradeoff between growth potential and resource acquisition. curation_history: - timestamp: '2026-05-05T01:35:46.909957+00:00' curator: seed_from_metpo action: SEEDED_FROM_METPO changes: imported from data/raw/metpo.owl (CLASS) llm_assisted: false - timestamp: '2026-05-11T22:00:00-07:00' curator: claude action: CURATED_CAUSAL_GRAPH changes: Added DOI-backed causal graph framing nutrient adaptation as a sensing/resource-allocation axis manifesting as copiotrophic and oligotrophic phenotypes. llm_assisted: true - timestamp: '2026-05-20T03:35:31Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf×2). llm_assisted: true - timestamp: '2026-05-23T21:30:07Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400×2, RO:0002211×1). llm_assisted: true - timestamp: '2026-05-26T05:00:48Z' curator: claude action: RENAME_PREDICATE_LABELS changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings: triggers → causes ×1.' llm_assisted: true - timestamp: '2026-05-26T05:00:51Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes×1). llm_assisted: true - timestamp: '2026-06-14T05:51:47Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0009594×1). llm_assisted: true - timestamp: '2026-06-23T00:00:00Z' curator: claude action: ENRICH_CAUSAL_GRAPH changes: Added 5 evidence-backed generic edges (7 new nodes) from the deep-research report. llm_assisted: true - timestamp: '2026-06-24T17:21:14Z' 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