identifier: METPO:1000473
label: pH delta very low
definition: A pH delta phenotype with a very narrow growth-supporting pH breadth of
  at most approximately 1 pH unit, characteristic of stenotopic pH-sensitive physiology.
definition_source: DOI:10.1038/nrmicro2549
trait_category: ENVIRONMENT
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000232
synonyms:
- synonym_text: pHd_<=1
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
evidence:
- reference: DOI:10.1038/nrmicro2549
  snippet: pH homeostasis
  notes: pH-homeostasis review supports very narrow pH-tolerance breadths as the stenotopic
    / pH-sensitive phenotype.
causal_graphs:
- graph_id: ph_delta_very_low_stenotopic
  title: pH-delta-very-low stenotopic breadth
  description: DOI-backed graph linking very limited pH-homeostasis flexibility to
    a pH growth breadth of at most ~1 pH unit.
  nodes:
  - node_id: ph_delta_very_low_trait
    label: pH delta very low
    node_type: TRAIT
    grounding: METPO:1000473
    description: pH growth-supporting breadth ≤ ~1 pH unit.
  - node_id: ph_delta
    label: pH delta
    node_type: TRAIT
    grounding: METPO:1000232
    description: Breadth of the growth-supporting external pH range.
  - node_id: very_limited_ph_homeostasis
    label: very limited pH-homeostasis flexibility
    node_type: BIOLOGICAL_PROCESS
    description: Narrow capacity to remodel proton extrusion and envelope buffering
      across changes in external pH.
  - node_id: external_ph_stress
    label: external pH stress
    node_type: ENVIRONMENTAL_FACTOR
    description: Deviation of external pH from the cytoplasmic optimum imposing stress
      on the cell.
  - node_id: pmf_partitioning
    label: PMF partitioning (delta-pH / delta-psi)
    node_type: BIOLOGICAL_PROCESS
    description: Adjustable partitioning of the proton motive force between the transmembrane
      pH gradient and membrane potential.
  - node_id: constitutive_ph_homeostasis_expression
    label: constitutive pH-homeostasis machinery expression
    node_type: BIOLOGICAL_PROCESS
    description: Constitutive expression of pH-homeostatic machinery typical of pH
      extremophiles.
  - node_id: energetic_cost
    label: energetic cost on growth near neutral pH
    node_type: STATE
    description: Energetic/proteomic cost that impairs growth at near-neutral pH.
  - node_id: na_h_antiporter_activity
    label: Na+/H+ antiporter activity
    node_type: MOLECULAR_FUNCTION
    description: Sodium:proton antiporter activity contributing to pH homeostasis.
  - node_id: alkaline_ph_homeostasis
    label: alkaline pH homeostasis
    node_type: BIOLOGICAL_PROCESS
    description: Maintenance of cytoplasmic pH under alkaline external conditions.
  - node_id: f1fo_atpase_proton_pumping
    label: F1Fo-ATPase hydrolytic proton pumping
    node_type: MOLECULAR_FUNCTION
    description: ATP-dependent hydrolytic proton extrusion by the F1Fo-ATPase under
      acid stress.
  - node_id: acid_stress_survival
    label: acid stress survival
    node_type: BIOLOGICAL_PROCESS
    description: Survival of the cell under low external pH (acid) stress.
  - node_id: glutamate_decarboxylase_system
    label: glutamate decarboxylase GadB + GABA/glutamate antiporter
    node_type: PATHWAY
    description: Decarboxylase/antiporter acid-resistance module that consumes cytoplasmic
      protons.
  - node_id: cytoplasmic_proton_consumption
    label: cytoplasmic proton consumption
    node_type: BIOLOGICAL_PROCESS
    description: Consumption of cytoplasmic protons buffering internal acidification.
  edges:
  - subject: very_limited_ph_homeostasis
    predicate: produces
    object: ph_delta_very_low_trait
    description: Very limited pH-homeostasis flexibility yields a narrow pH-delta
      breadth.
    evidence:
    - reference: DOI:10.1038/nrmicro2549
      snippet: pH homeostasis
      notes: Supports very limited pH-homeostasis flexibility as the basis of stenotopic
        breadth.
    predicate_id: METPO:2000202
  - subject: ph_delta_very_low_trait
    predicate: is a
    object: ph_delta
    description: pH delta very low is a quantitative bin of the pH-delta phenotype.
    evidence:
    - reference: DOI:10.1016/j.tim.2007.02.005
      snippet: proton motive force
      notes: Supports a very narrow breadth as a value within the pH-delta distribution.
    predicate_id: rdfs:subClassOf
  - subject: external_ph_stress
    predicate: alters
    object: pmf_partitioning
    description: External pH stress alters partitioning of the proton motive force
      between delta-pH and delta-psi.
    evidence:
    - reference: DOI:10.1038/nrmicro2549
      notes: The two PMF components, delta-psi and delta-pH, are adjustable according
        to pH demand and can even reverse orientation under strong pH stress; broad
        foundational pH-homeostasis edge.
  - subject: constitutive_ph_homeostasis_expression
    predicate: imposes energetic cost on
    object: energetic_cost
    description: Constitutive expression of pH-homeostatic machinery imposes an energetic
      cost impairing growth near neutral pH.
    evidence:
    - reference: DOI:10.1038/nrmicro2549
      notes: Extremophiles often express major pH homeostatic mechanisms constitutively;
        this preparedness imposes an energetic cost and can impair growth at near-neutral
        pH (inferred breadth-constraint mechanism).
  - subject: na_h_antiporter_activity
    predicate: enables
    object: alkaline_ph_homeostasis
    description: Na+/H+ antiporter activity enables alkaline pH homeostasis.
    evidence:
    - reference: DOI:10.1038/nrmicro2549
      notes: Na+/H+ antiport (notably the hetero-oligomeric Mrp system) is a major,
        causally important strategy for alkaline pH homeostasis.
    predicate_id: RO:0002327
  - subject: f1fo_atpase_proton_pumping
    predicate: promotes
    object: acid_stress_survival
    description: Hydrolytic F1Fo-ATPase proton pumping promotes acid stress survival.
    evidence:
    - reference: DOI:10.1038/nrmicro2549
      notes: Hydrolytic F1Fo-ATPase activity can be increased for ATP-dependent H+
        extrusion under acid stress; strong acid-side homeostasis mechanism.
    predicate_id: RO:0002213
  - subject: glutamate_decarboxylase_system
    predicate: consumes
    object: cytoplasmic_proton_consumption
    description: Glutamate decarboxylase GadB coupled with a GABA/glutamate antiporter
      consumes cytoplasmic protons.
    evidence:
    - reference: DOI:10.1038/nrmicro2549
      notes: Amino acid decarboxylases like GadB with its antiporter coupling; canonical
        acid-resistance mechanism consuming cytoplasmic protons.
    predicate_id: biolink:consumes
curation_history:
- timestamp: '2026-05-05T01:35:46.838042+00:00'
  curator: seed_from_metpo
  action: SEEDED_FROM_METPO
  changes: imported from data/raw/metpo.owl (CLASS)
  llm_assisted: false
- timestamp: '2026-05-13T10:00:00-07:00'
  curator: claude
  action: CURATED_CAUSAL_GRAPH
  changes: Added DOI-backed definition and causal graph linking very limited pH-homeostasis
    flexibility to the stenotopic pH-delta-very-low 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: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 5 evidence-backed generic edges (10 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:10Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002327×1, RO:0002213×1, biolink:consumes×1).
  llm_assisted: true