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green pigmented

METPO:1003025 · CLASS · REVIEWED

A pigmentation phenotype in which microbial colonies or cultures appear green or blue-green due to pigments such as pyocyanin and pyoverdine.

Green pigmentation pyocyanin phenazine mechanism

Evidence-backed causal sketch linking green or blue-green microbial pigmentation to phenazine biosynthesis, phz genes, pyocyanin production, and visible green culture color.

Green pigmentation pyocyanin phenazine mechanism Interactive directed graph showing evidence-backed causal relationships for green pigmented.

Edge evidence

  • phz operons encodes phenazine biosynthesis METPO:2007813

    phz operons encode enzymes required for phenazine biosynthesis.

    • DOI:10.1186/s12934-023-02122-1 phenazine synthesis operons including phzA1, phzA2, phzS, and phzM Supports phz genes as pyocyanin/phenazine biosynthesis machinery.
  • phenazine biosynthesis has output pyocyanin RO:0002234

    Phenazine biosynthesis produces pyocyanin.

    • DOI:10.1128/jb.138.3.846-852.1979 pyocyanine biosynthesis Supports pyocyanin production as a phenazine biosynthetic process.
  • pyocyanin causes visible green color biolink:causes

    Pyocyanin contributes blue-green visible pigmentation.

    • DOI:10.1186/s12934-023-02122-1 Pyocyanin is a blue phenazine pigment Supports pyocyanin as a visible blue/green pigment.
  • visible green color manifests as green pigmented METPO:2007400

    Visible green or blue-green culture color manifests the green-pigmented phenotype.

    • DOI:10.1186/s12934-023-02122-1 lead to the green colorization of the culture plate Supports trait-level green pigmentation from pyocyanin and related pigments in representative cultures.
  • chorismate precursor of phenazine-1-carboxylic acid (PCA)

    Chorismate is the shikimate-pathway precursor of phenazine-1-carboxylic acid.

    • DOI:10.1007/s11274-023-03548-w Biosynthesis of PYO and other phenazines proceeds from chorismate via the shikimate pathway.
  • phenazine-1-carboxylic acid (PCA) precursor of pyocyanin

    Phenazine-1-carboxylic acid is the core intermediate converted toward pyocyanin.

    • DOI:10.1007/s11274-023-03548-w PCA is the central phenazine from which pyocyanin is derived via the shikimate/phenazine pathway.
  • quorum sensing positively regulates pyocyanin RO:0002213

    Quorum sensing positively regulates pyocyanin production.

    • DOI:10.1186/s12934-023-02122-1 Quorum sensing controls pyocyanin synthesis; AHL and PQS autoinducers and LasR-LasI/RhlR-RhlI systems activate pyocyanin expression.
  • pyocyanin redox state and pH modifies visible green color

    Redox state and pH alter the apparent color of pyocyanin pigment.

    • DOI:10.1007/s11274-023-03548-w PYO exhibits blue-green color at neutral/alkaline pH, shifting to pink-red in acidic conditions; oxidized PYO is blue while reduced form is transparent.
  • pyoverdine NRPS enzymes (PvdL/PvdI/PvdJ/PvdD) participates in pyoverdine biosynthesis biolink:participates_in

    PvdL/PvdI/PvdJ/PvdD NRPS enzymes synthesize the pyoverdine peptide backbone.

    • DOI:10.3390/ijms25116013 The pyoverdine peptide backbone is synthesized by four NRPSs (PvdL, PvdI, PvdJ, PvdD).
  • iron-deficient conditions induces pyoverdine biosynthesis

    Iron-deficient conditions induce expression of pyoverdine biosynthetic enzymes.

    • DOI:10.3390/ijms25116013 Expression of the fluorescent (pyoverdine) enzymes was induced by iron-deficient growing conditions.
  • pyoverdine biosynthesis contributes to visible green color RO:0002326

    Pyoverdine, a yellow-green fluorescent pigment, contributes to green coloration alongside pyocyanin.

    • DOI:10.1186/s12934-023-02122-1 Blue (pyocyanin) and yellow (fluorescein/pyoverdine-like) pigments combine to produce green colorization of the culture.

Provenance

Source
METPO (2025-11-25)
Definition source
DOI:10.1186/s12934-023-02122-1

Parent traits (1)

Synonyms (1)

  • Pigment_green RELATED_SYNONYM · metpo.owl

kg-microbe context

Matched 1 kg-microbe node via direct_metpo.

  • METPO:1003025 [-0.292, -0.545, -1.390, +0.056, …]

512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

Nearest neighbors in embedding space

Top-8 cosine-similar METPO traits from the 2026-04-25 deepwalk (512-D).

Deep research

Generated by just research-trait; source: research/traits/morphology/green_pigmented-deep-research-falcon.md

Unreviewed literature output — not curated TraitMech content Ontology identifiers suggested below have not been resolved against their ontologies, and some are known to be wrong. Check any CURIE against the source before using it. 
# Curation report: microbial **green pigmented** trait

## 1. Trait scope

**Trait:** “green pigmented”  
**Identifier:** **METPO:1003025**  
**Category:** MORPHOLOGY; **term kind:** CLASS; **mapping:** REVIEWED  
**Parent:** METPO:1003021  
**Synonym:** Pigment_green

METPO:1003025 should represent an **assay-observed visible phenotype** in which a microbial colony, agar plate, or liquid culture appears green, blue-green, or greenish-blue because extracellular or cell-associated pigments alter the observed color. It is not itself a pathway, pigment identity, fluorescence measurement, or taxonomic diagnosis.

The best-supported mechanistic model has two separable pigment branches:

1. **Pyocyanin branch.** Oxidized pyocyanin is blue to blue-green at neutral or alkaline pH; its appearance is pH- and redox-dependent. In *Pseudomonas aeruginosa*, blue pyocyanin can itself look greenish-blue or combine optically with yellow fluorescent pyoverdine/“fluorescein” to generate the characteristic green culture-plate appearance. Pyocyanin is reported in approximately **90–95%** of *P. aeruginosa* strains, so its absence does not exclude that species. (abdelaziz2023pseudomonasaeruginosa’sgreenishblue pages 2-5, abdelaziz2023pseudomonasaeruginosa’sgreenishblue pages 1-2, jabłonska2023thetwofaces pages 1-2)
2. **Pyoverdine branch.** Pyoverdines are fluorescent siderophores whose chromophore gives fluorescent pseudomonad cultures a characteristic yellow-green or green appearance, especially under iron restriction. This branch can produce a green-associated phenotype without pyocyanin and occurs in multiple fluorescent *Pseudomonas* species, not only *P. aeruginosa*. (schalk2020anoverviewof pages 12-13, ringel2018thebiosynthesisof pages 1-3)

### Boundary cases

- **Fluorescence versus visible pigmentation:** yellow-green fluorescence under UV illumination should be represented as an assay-dependent manifestation of pyoverdine, not automatically equated with green color under white light.
- **Color-state dependence:** pyocyanin is blue-greenish at neutral/alkaline pH, pink-red under acidic conditions, and colorless when reduced. Thus, pigment biosynthetic capacity does not guarantee a green observation in every assay. (jabłonska2023thetwofaces pages 1-2)
- **Other phenazines:** phenazine-1-carboxylic acid, phenazine-1-carboxamide, and related compounds may be yellow, orange, or red and should not independently imply METPO:1003025.
- **Non-pigment color changes:** pH indicators, medium chemistry, mineral precipitation, reflected fluorescence, and mixed-culture coloration are outside scope unless a microbial pigment is demonstrated.
- **Taxonomic inference:** green colonies are suggestive of fluorescent pseudomonads but are not species-specific or sufficient for identification.
- **Downstream activities:** virulence, redox cycling, iron acquisition, antimicrobial activity, and biofilm effects are functions of the pigments, not definitions of the morphology trait.

## 2. Recommended graph architecture

The existing 12-node pyocyanin graph is a useful core but is too narrow for the ontology definition. A robust TraitMech representation should use a **shared terminal phenotype node** with two optional modules:

- **Module A:** chorismate → phenazine-1-carboxylic acid → 5-methyl-PCA → pyocyanin → blue-green/greenish-blue appearance.
- **Module B:** iron restriction → pyoverdine precursor synthesis and maturation → secreted fluorescent pyoverdine → yellow-green/green appearance.

The modules should not be encoded as universally co-required. Their relative contribution depends on taxon, strain, medium, iron, oxygen, pH, redox state, growth mode, and illumination.

## 3. Candidate nodes grouped by type

### Trait and taxon nodes

- **green pigmented** — **METPO:1003025**
- *Pseudomonas aeruginosa* — **NCBITaxon:287**
- fluorescent pseudomonads — label-only group node; avoid treating it as one species
- *Pseudomonas* spp. — use species/strain CURIEs in evidence annotations whenever available

### Pigments, precursors, and nutrients

- pyocyanin — label-only pending identifier verification
- pyoverdine / pyoverdines — label-only because structurally diverse strain-specific congeners exist
- chorismate — label-only pending identifier verification
- phenazine-1-carboxylic acid (PCA) — label-only
- 5-methyl-phenazine-1-carboxylic acid or corresponding methylphenazine intermediate — label-only; nomenclature should be checked against the exact biochemical source
- ferribactin/acylated ferribactin — label-only
- Fe(II), Fe(III), ferripyoverdine — label-only unless identifiers are independently validated
- molecular oxygen — **CHEBI:15379**
- NADH — **CHEBI:57945**; NADPH should be a separate node if used
- reactive oxygen species — **CHEBI:26523**
- zinc oxide nanoparticles — label-only experimental material node

### Genes, proteins, operons, and regulatory systems

Showing the first 60 of 241 lines of findings; the linked file also carries the run's front matter and the prompt it was given — read the full report.

Curation history

  1. · SEEDED_FROM_METPO · seed_from_metpo

    imported from data/raw/metpo.owl (CLASS)

  2. · CURATED_WITH_LITERATURE · codex

    Added DOI-backed definition and causal graph for phz operons, phenazine biosynthesis, pyocyanin, and visible green/blue-green color.

  3. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202×1).

  4. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:causes×1).

  5. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:encodes×1).

  6. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400×1).

  7. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0002047×1).

  8. · ENRICH_CAUSAL_GRAPH · claude

    Added 7 evidence-backed generic edges (7 new nodes) from the deep-research report.

  9. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:participates_in×1, RO:0002326×1).

  10. · GROUND_CAUSAL_NODES · claude

    Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:29748×1, GO:0009372×1).

  11. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213×1).

  12. · MIGRATE_MICROBE_DOMAIN_EDGES · claude

    Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.

  13. · REGROUND_CAUSAL_EDGE · claude

    Re-grounded the `encodes` edge(s) from biolink:encodes to METPO:2007813, issue 342. biolink:encodes is NOT a slot in the pinned biolink 4.4.0 model, so the CURIE resolved to nothing upstream while looking like an upstream term to anyone reading this record -- the disclaimer saying otherwise lived in mappings/predicate_grounding.tsv, which is not read at the point of use. RO:0002205 (has gene product) is the nearest real term but relates a GENE to a gene product, whereas these edges relate a gene cluster or operon to a protein complex or a biosynthetic process, which its range does not admit; that mismatch is why the coinage existed. METPO:2007813 is proposed in proposals/metpo_traitmech_v9 and is a placeholder id until METPO mints it, which puts it in the same state as the rest of that cohort rather than in a category of its own.

  14. · NORMALISE_NODE_TYPE · claude

    Under the PATHWAY-vs-BIOLOGICAL_PROCESS rule, one node_id means one thing corpus-wide (issue 356): phenazine_biosynthesis is typed PATHWAY. PATHWAY is a named, conventionally enumerable multi-step route; BIOLOGICAL_PROCESS is everything else. A named biosynthetic route; both typings say 'Biosynthetic pathway producing phenazine pigments'. The rule breaks the 1-1 tie.