identifier: traitmech:000048
label: free-living
definition: A habitat association in which an organism lives independently in the
  environment, not obligately associated with a host.
definition_source: DOI:10.1038/nrmicro1341
trait_category: ECOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- traitmech:000047
evidence:
- reference: DOI:10.1038/nrmicro1341
  notes: Martiny et al. support biogeographic patterning of free-living microbial
    taxa across environments.
- reference: DOI:10.1038/nrmicro.2017.171
  notes: Poole et al. describe rhizobia in their free-living soil phase, contrasting
    it with the host-associated endosymbiotic phase.
canonical_examples:
- taxon_id: NCBITaxon:155892
  taxon_label: Caulobacter vibrioides
  note: "free-living oligotroph"
  reference: PMID:11259647
- taxon_id: NCBITaxon:303
  taxon_label: Pseudomonas putida
  note: "free-living soil bacterium"
  reference: PMID:15560824
causal_graphs:
- graph_id: free_living_environmental_habitat
  title: Free-living lifestyle is independent of host association
  description: Evidence-backed causal sketch linking environmental habitat occupancy
    to a host-independent free-living lifestyle.
  nodes:
  - node_id: free_living_trait
    label: free-living
    node_type: TRAIT
    grounding: traitmech:000048
    description: Persistent life in the environment, not obligately host-bound.
  - node_id: environmental_habitat
    label: environmental habitat
    node_type: ENVIRONMENTAL_FACTOR
    description: Soil, water, air, or other non-host habitat.
  - node_id: biogeographic_structure
    label: biogeographic community structure
    node_type: QUALITY
    description: Patterned distribution of free-living taxa across environments.
  - node_id: complete_metabolic_capacity
    label: complete metabolic capacity for carbon/nitrogen/sulfur/cofactors
    node_type: CAPACITY
    description: Self-sufficient biosynthetic pathways for core nutrients and cofactors,
      not dependent on a host.
  - node_id: osmotic_stress_tolerance
    label: osmotic stress tolerance
    node_type: BIOLOGICAL_PROCESS
    description: Cellular response maintaining viability under osmotic/salinity stress
      in fluctuating environments.
  - node_id: ectoine_biosynthesis
    label: ectoine biosynthetic pathway
    node_type: PATHWAY
    description: Biosynthesis of the compatible solute ectoine for osmoadaptation.
  - node_id: glycine_betaine_system
    label: glycine betaine transport/biosynthesis
    node_type: PATHWAY
    description: betA/betB/betI and Opu/ProV/ProX systems producing/importing the
      osmoprotectant glycine betaine.
  - node_id: trehalose_biosynthesis
    label: trehalose biosynthesis/transport
    node_type: PATHWAY
    description: Synthesis and transport of the compatible solute trehalose for stress
      protection.
  - node_id: environmental_stress_tolerance
    label: stress tolerance in fluctuating environments
    node_type: BIOLOGICAL_PROCESS
    description: Cellular persistence under variable environmental stress conditions.
  edges:
  - subject: environmental_habitat
    predicate: enables
    object: free_living_trait
    description: Persistent occupancy of environmental habitats realizes the free-living
      lifestyle.
    evidence:
    - reference: DOI:10.1038/nrmicro1341
      notes: Martiny et al. document biogeographic patterning of free-living microbial
        taxa.
    predicate_id: RO:0002327
  - subject: free_living_trait
    predicate: associated with
    object: biogeographic_structure
    description: Free-living taxa show environment-structured global distributions.
    evidence:
    - reference: DOI:10.1038/nrmicro.2017.171
      notes: Poole et al. describe the free-living soil phase of rhizobia distinct
        from their host-associated phase.
    predicate_id: biolink:associated_with
  - subject: complete_metabolic_capacity
    predicate: required for
    object: free_living_trait
    description: Self-sufficient metabolic pathways for carbon, nitrogen, sulfur and
      cofactors are required for a host-independent free-living life strategy.
    evidence:
    - reference: DOI:10.1186/s12915-024-02013-w
      notes: Reversion to free-living is rare because parasites often lose metabolic
        pathways essential to a free-living life strategy.
    - reference: DOI:10.1128/aem.01900-23
      notes: Symbiotic Fluviibacter showed reduced metabolic capacities and host dependence
        for carbon, organic nitrogen, sulfur, and cofactors.
  - subject: ectoine_biosynthesis
    predicate: enables
    object: osmotic_stress_tolerance
    description: Ectoine synthesis provides compatible solutes that confer osmotic
      stress tolerance during environmental persistence.
    evidence:
    - reference: DOI:10.48550/arxiv.2302.00582
      notes: Crossing salinity barriers requires osmotic-stress mechanisms; marine
        adaptation includes components involved in ectoine synthesis.
    - reference: DOI:10.1371/journal.pone.0287947
      notes: Paracoccus carried the ectoine cluster in all strains.
    predicate_id: RO:0002327
  - subject: glycine_betaine_system
    predicate: enables
    object: osmotic_stress_tolerance
    description: Glycine betaine transport/biosynthesis confers osmoprotection under
      environmental stress.
    evidence:
    - reference: DOI:10.1371/journal.pone.0287947
      notes: betA-betB, betI operon and multiple glycine-betaine transporters link
        these systems to persistence under environmental stress.
    predicate_id: RO:0002327
  - subject: trehalose_biosynthesis
    predicate: enables
    object: environmental_stress_tolerance
    description: Trehalose synthesis/transport provides compatible-solute protection
      under fluctuating environmental conditions.
    evidence:
    - reference: DOI:10.1371/journal.pone.0287947
      notes: Trehalose synthesis/transport widely encoded; compatible-solute systems
        discussed as persistence traits, lost in some host-associated lineages.
    predicate_id: RO:0002327
  - subject: osmotic_stress_tolerance
    predicate: promotes
    object: free_living_trait
    description: Osmoadaptation supports persistence in unstable/saline environments
      characteristic of the free-living lifestyle.
    evidence:
    - reference: DOI:10.48550/arxiv.2302.00582
      notes: Ectoine-related osmoadaptation is highlighted as part of adaptation to
        unstable or saline environmental conditions in free-living lineages.
    predicate_id: RO:0002213
curation_history:
- timestamp: '2026-06-02T00:00:00Z'
  curator: claude
  action: PROPOSED_FROM_RESEARCH
  changes: Proposed candidate ECOLOGY trait (free-living); sub-variant of habitat
    association.
  llm_assisted: true
- timestamp: '2026-06-09T14:00:00Z'
  curator: claude
  action: CURATED_CAUSAL_GRAPH
  changes: Added evidence-backed causal graph (free-living / environmental habitat)
    with RO/biolink predicate groundings; promoted PROPOSED to REVIEWED.
  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: '2026-06-24T17:21:09Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002327×3, RO:0002213×1).
  llm_assisted: true
discussions:
- discussion_id: kgscan-d5aefedf82bb
  prompt: 'Knowledge gap for free-living: Interactions between parasites and the gut
    microbiota play a key role in immune responses and susceptibility to zoonotic
    diseases; however, many aspects of how protozoan infections alter microbial diversity
    and how these changes influence parasite pathogenicity and host defense remain
    poorly understood.'
  kind: KNOWLEDGE_GAP
  status: OPEN
  rationale: 'Surfaced by the Europe PMC literature gap-signal scan (categories: explicit_gap,
    future_work, limitations_barriers, unclear_unknown). Curator review required:
    set attaches_to, refine the prompt, and weigh the cited evidence.'
  attaches_to: []
  evidence:
  - reference: PMID:41989588
    supports: NO_EVIDENCE
    evidence_source: abstract
    snippet: Interactions between parasites and the gut microbiota play a key role
      in immune responses and susceptibility to zoonotic diseases; however, many aspects
      of how protozoan infections alter microbial diversity and how these changes
      influence parasite pathogenicity and host defense remain poorly understood.
    explanation: Gap-signal sentence (unclear_unknown) from the cited abstract.
  - reference: PMID:42039802
    supports: NO_EVIDENCE
    evidence_source: abstract
    snippet: Engineered microbial assemblies tailored to specific host plants and
      environmental conditions have shown potential in stabilizing crop performance
      during drought, salinity, and nutrient limitations.
    explanation: Gap-signal sentence (limitations_barriers) from the cited abstract.
  - reference: PMID:41943163
    supports: NO_EVIDENCE
    evidence_source: abstract
    snippet: 'OBJECTIVES: Oxo-polyethylene (oxo-PE) is marketed as a biodegradable
      plastic, yet its environmental degradation remains poorly understood, particularly
      in marine contexts.'
    explanation: Gap-signal sentence (unclear_unknown) from the cited abstract.
  - reference: PMID:42125129
    supports: NO_EVIDENCE
    evidence_source: abstract
    snippet: However, contradictions persist regarding pH's effect on microbial diversity,
      with unresolved questions about how specific environmental conditions regulate
      microbial taxa.
    explanation: Gap-signal sentence (explicit_gap) from the cited abstract.
  posed_by: kg-microbe-kgscan