identifier: METPO:1000467 label: NaCl optimum mid2 definition: A NaCl optimum phenotype with the best-growth NaCl concentration approximately between 3 and 8% (w/v), corresponding to moderate-halophile or halotolerant physiology. definition_source: DOI:10.1093/femsre/fuy009 trait_category: ENVIRONMENT term_kind: CLASS mapping_status: REVIEWED parent_traits: - METPO:1000333 synonyms: - synonym_text: Halotolerant synonym_type: EXACT_SYNONYM source: metpo.owl - synonym_text: Moderate halophile synonym_type: EXACT_SYNONYM source: metpo.owl - synonym_text: NaO_3_to_8 synonym_type: RELATED_SYNONYM source: metpo.owl evidence: - reference: DOI:10.1093/femsre/fuy009 snippet: moderate halophile notes: Osmoadaptation review supports the 3–8% NaCl optimum range as the moderate-halophile category. causal_graphs: - graph_id: nacl_optimum_mid2_moderate_halophile title: NaCl-optimum-mid2 moderate-halophile setpoint description: DOI-backed graph linking pronounced compatible-solute accumulation at elevated NaCl to a 3–8% (w/v) NaCl-optimum (moderate halophile). nodes: - node_id: nacl_optimum_mid2_trait label: NaCl optimum mid2 node_type: TRAIT grounding: METPO:1000467 description: NaCl optimum approximately 3–8% w/v. - node_id: nacl_optimum label: NaCl optimum node_type: TRAIT grounding: METPO:1000333 description: NaCl concentration supporting maximal growth. - node_id: elevated_nacl label: elevated NaCl node_type: ENVIRONMENTAL_FACTOR description: External NaCl ~3–8% w/v, typical of saline lakes and salt marshes. - node_id: pronounced_compatible_solutes label: pronounced compatible-solute accumulation node_type: BIOLOGICAL_PROCESS description: Substantial accumulation of organic osmolytes (ectoine, glycine betaine) under moderately hypersaline conditions. - node_id: ectoine_biosynthesis_module label: ectoine biosynthesis module (ectABC) node_type: PATHWAY description: Canonical ectABC (ectA/ectB/ectC) pathway producing the compatible solute ectoine. - node_id: ectoine label: ectoine node_type: CHEMICAL description: Major organic compatible solute (CHEBI:22563) accumulated during osmoadaptation. grounding: CHEBI:27592 - node_id: compatible_solute_strategy label: compatible-solute strategy node_type: BIOLOGICAL_PROCESS description: Osmoadaptation strategy buffering osmotic stress via accumulation of small organic osmolytes. - node_id: glycine_betaine label: glycine betaine node_type: CHEMICAL description: Organic compatible solute (CHEBI:17750) used in compatible-solute osmoadaptation. grounding: CHEBI:17750 - node_id: l_proline label: L-proline node_type: CHEMICAL description: Organic compatible solute (CHEBI:26271) used in compatible-solute osmoadaptation. edges: - subject: elevated_nacl predicate: regulates object: pronounced_compatible_solutes description: Elevated NaCl drives substantial compatible-solute accumulation. evidence: - reference: DOI:10.1093/femsre/fuy009 snippet: synthesize organic osmotic solutes notes: Supports compatible-solute accumulation as the osmoadaptive response at elevated NaCl. predicate_id: RO:0002211 - subject: pronounced_compatible_solutes predicate: produces object: nacl_optimum_mid2_trait description: Pronounced compatible-solute accumulation yields a 3–8% NaCl-optimum setpoint. evidence: - reference: DOI:10.1093/femsre/fuy009 snippet: moderate halophile notes: Supports the 3–8% optimum as the moderate-halophile outcome. predicate_id: METPO:2000202 - subject: nacl_optimum_mid2_trait predicate: is a object: nacl_optimum description: NaCl optimum mid2 is a quantitative bin of the NaCl-optimum phenotype. evidence: - reference: DOI:10.1093/femsre/fuy009 snippet: optimal NaCl notes: Supports the 3–8% optimum as a value within the NaCl-optimum distribution. predicate_id: rdfs:subClassOf - subject: elevated_nacl predicate: induces object: ectoine_biosynthesis_module description: Elevated salinity (>3% NaCl) triggers the canonical ectoine biosynthesis pathway. evidence: - reference: DOI:10.1128/aem.01905-23 notes: Exposure to salt concentrations higher than 3% NaCl triggers biosynthesis and intracellular accumulation of ectoine as a major compatible solute (Zou et al. 2024). - subject: elevated_nacl predicate: upregulates object: ectoine_biosynthesis_module description: Salt stress at ~6% w/v NaCl (within the 3-8% window) upregulates the ectoine biosynthesis module. evidence: - reference: DOI:10.1186/s12934-024-02515-w notes: Transcriptomics showed the ectoine biosynthesis module is upregulated under salt stress, with 60 g/L NaCl (~6% w/v, inside 3-8% window) optimal for growth (Chen et al. 2024). - subject: ectoine_biosynthesis_module predicate: produces object: ectoine description: The ectABC pathway synthesizes the compatible solute ectoine. evidence: - reference: DOI:10.1128/aem.01905-23 notes: Biosynthesis and intracellular accumulation of ectoine as a major compatible solute via the ectoine pathway (Zou et al. 2024). predicate_id: METPO:2000202 - subject: pronounced_compatible_solutes predicate: is a object: compatible_solute_strategy description: Pronounced organic-osmolyte accumulation is an instance of the compatible-solute osmoadaptation strategy. evidence: - reference: DOI:10.3390/biotech14020049 notes: The compatible-solute strategy accumulates small organic osmolytes including glycine, betaine, and ectoine (Neagu & Stancu 2025). predicate_id: rdfs:subClassOf - subject: compatible_solute_strategy predicate: uses object: ectoine description: Compatible-solute osmoadaptation employs ectoine as an organic osmolyte. evidence: - reference: DOI:10.1186/s12934-025-02757-2 notes: Many species naturally produce the osmolyte ectoine (plus hydroxyectoine, betaine, glycine, proline) (Coimbra et al. 2025). - subject: compatible_solute_strategy predicate: uses object: glycine_betaine description: Compatible-solute osmoadaptation employs glycine betaine as an organic osmolyte. evidence: - reference: DOI:10.3390/biotech14020049 notes: Identified compatible solutes include glycine, betaine, and ectoine (Neagu & Stancu 2025). - subject: compatible_solute_strategy predicate: uses object: l_proline description: Compatible-solute osmoadaptation employs L-proline as an organic osmolyte. evidence: - reference: DOI:10.1186/s12934-025-02757-2 notes: Many species naturally produce the osmolyte ectoine plus hydroxyectoine, betaine, glycine, proline (Coimbra et al. 2025). curation_history: - timestamp: '2026-05-05T01:35:46.834715+00:00' curator: seed_from_metpo action: SEEDED_FROM_METPO changes: imported from data/raw/metpo.owl (CLASS) llm_assisted: false - timestamp: '2026-05-12T10:00:00-07:00' curator: claude action: CURATED_CAUSAL_GRAPH changes: Added DOI-backed definition and causal graph linking pronounced compatible-solute accumulation at elevated NaCl to the moderate-halophile NaCl-optimum bin. 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 (METPO:2000202×1, rdfs:subClassOf×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: drives → 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: '2026-06-23T00:00:00Z' curator: claude action: ENRICH_CAUSAL_GRAPH changes: Added 7 evidence-backed generic edges (5 new nodes) from the deep-research report. llm_assisted: true - timestamp: '2026-06-24T17:21:10Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202×1, rdfs:subClassOf×1). llm_assisted: true - timestamp: '2026-06-24T17:23:31Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:27592×1, CHEBI:17750×1). llm_assisted: true