A defined two-member marine phytoplankton-bacterium model community composed of the diatom Thalassiosira pseudonana CCMP1335 and the heterotrophic roseobacter Ruegeria pomeroyi DSS-3. The coculture is used to study bacterial recognition by a diatom, phytoplankton-derived metabolite transfer, and bacterial use of recent photosynthate in a controlled marine algal medium.
Taxonomy
| Taxon | Ontology ID | Functional Roles | Abundance |
|---|---|---|---|
| Thalassiosira pseudonana CCMP1335 | NCBITaxon:296543 · TaxonMech · TraitMech |
PRIMARY_PRODUCER
CROSS_FEEDER
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N/A |
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| Ruegeria pomeroyi DSS-3 | NCBITaxon:246200 · TaxonMech · TraitMech |
CROSS_FEEDER
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N/A |
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Ecological Interactions
The graph shows only explicitly linked interaction participants. Community members without an asserted participant link are omitted; membership alone does not imply an interaction.
Putative Diatom Recognition Response to Ruegeria
In the 2017 B12-limited coculture experiment, T. pseudonana CCMP1335 differentially expressed genes with annotations consistent with recognition and signaling in response to R. pomeroyi DSS-3. The proposed plant-like cascade is inferred from homology and transcript patterns, not selectively demonstrated. Little attachment was observed during exponential growth. This is a directed diatom response to bacterial presence, not a measured colonization benefit or proof that recognition causes the separate chitin/lipid transcriptional response.
Source Taxon: Ruegeria pomeroyi DSS-3
Target Taxon: Thalassiosira pseudonana CCMP1335
Biological Processes:
- cell communication (GO:0007154 · PathwayMech)
- biological process involved in interspecies interaction between organisms (GO:0044419 · PathwayMech)
Evidence
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PMID:28631440 - SUPPORT (IN_VITRO)"Bacterium Ruegeria pomeroyi DSS-3 triggered differential expression of >80 genes in diatom Thalassiosira pseudonana CCMP1335"
Phytoplankton Metabolite Transfer to Ruegeria
CROSS_FEEDINGDiatom-derived organic compounds support R. pomeroyi growth when the diatom is the only organic-carbon source. Individual substrate assignments have different evidence strengths: in the 2020 R. pomeroyi column of Table 1, DMSP and N-acetyl-D-glucosamine are supported by gene expression, whereas proline and guanosine have net exometabolite-drawdown evidence. These are three separate bacterial pair cultures, not a mixed three-bacterium competition experiment. Neither transcript induction nor net concentration changes alone trace a compound-specific transfer flux or demonstrate that bacterial consumption causes the diatom chitin response.
Source Taxon: Thalassiosira pseudonana CCMP1335
Target Taxon: Ruegeria pomeroyi DSS-3
Metabolites: dimethylsulfoniopropionate (CHEBI:16457 · MediaIngredientMech · CMMMech), N-acetyl-D-glucosamine (CHEBI:506227 · MediaIngredientMech · CMMMech), proline (CHEBI:26271 · MediaIngredientMech · CMMMech), guanosine (CHEBI:16750 · MediaIngredientMech · CMMMech)
Biological Processes:
- photosynthesis (GO:0015979 · PathwayMech)
- carbohydrate metabolic process (GO:0005975 · PathwayMech)
- sulfur compound metabolic process (GO:0006790 · PathwayMech)
- biological process involved in interspecies interaction between organisms (GO:0044419 · PathwayMech)
Evidence
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PMID:28631440 - PARTIAL (IN_VITRO)"we hypothesize that nine diatom metabolites supported the majority of bacterial growth, among them sulfonates, sugar derivatives and organic nitrogen compounds"
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PMID:33097854 - SUPPORT (IN_VITRO)"marine phytoplankter T. pseudonana CCMP1335 served as the sole carbon source for three bacterial strains"
Diatom Chitin and Lipid Response During Coculture
In the 2017 study, cocultured diatoms downregulated lipid biosynthesis and upregulated chitin metabolism genes relative to B12-replete axenic controls. These are measured transcriptional changes, not demonstrated Ruegeria-to-diatom substrate feeding, polymer production fluxes or selectively established outputs of a recognition cascade. The bacterium also supported B12-limited diatom growth, a distinct relationship missing from the present topology and tracked in #1883; it must not be inferred from this chitin/lipid node. The later L1 substrate-partitioning assay does not negate the earlier B12-limited benefit.
Source Taxon: Ruegeria pomeroyi DSS-3
Target Taxon: Thalassiosira pseudonana CCMP1335
Biological Processes:
- carbohydrate metabolic process (GO:0005975 · PathwayMech)
- biological process involved in interspecies interaction between organisms (GO:0044419 · PathwayMech)
Evidence
-
PMID:28631440 - SUPPORT (IN_VITRO)"Co-cultured diatoms also downregulated lipid biosynthesis genes and upregulated chitin metabolism genes."
Associated Datasets
| Dataset | Type | Repository | Accession |
|---|---|---|---|
|
Exact-composition publication - Thalassiosira-Ruegeria recognition cascade
Primary two-member model-system publication reporting T. pseudonana CCMP1335 responses to R. pomeroyi DSS-3 and inferred metabolite transfer. |
PHENOTYPE | OTHER | PMID:28631440 |
|
Exact-composition publication - pairwise diatom exometabolite use by Ruegeria
Follow-up pairwise coculture publication that includes T. pseudonana as the substrate source for R. pomeroyi DSS-3 and compares exometabolite use across bacterial partners. |
METABOLOMICS | OTHER | PMID:33097854 |
|
Diatom-bacterium coculture RNA-seq BioProject
Public RNA-seq data associated with pairwise T. pseudonana coculture experiments. |
METATRANSCRIPTOMICS | NCBI_BIOPROJECT | PRJNA448168 |
|
Diatom-bacterium coculture metabolomics data
MetaboLights datasets for intracellular and exometabolite measurements used in the pairwise diatom-bacterium coculture study. |
METABOLOMICS | OTHER | MTBLS1751; MTBLS1544 |
Knowledge gaps & discussions (1)
KNOWLEDGE_GAP OPEN Which signaling steps mediate the transcript response, and how should B12-dependent growth support be represented separately?
The 2017 PDF Figure 1 and Results support rescue of B12-limited diatom growth; that reciprocal interaction is missing from the current graph. Edison dry run completed, but the authorized real invocation stopped before submission because the configured key loader returned no key. New topology remains #1883, not silently replaced by the chitin response. Two existing arrows were removed because co-occurring transcript changes and shared substrate names do not establish those directions. Receptor/cue identity and causal mediation require further evidence; assay-metadata reconciliation is #1885.
Attaches to: ecological_interactions#Putative Diatom Recognition Response to Ruegeria, ecological_interactions#Phytoplankton Metabolite Transfer to Ruegeria, ecological_interactions#Diatom Chitin and Lipid Response During Coculture
1 evidence item(s)
induced a potential recognition cascade
The abstract explicitly qualifies the recognition cascade; the full paper separately reports B12-limited growth support.
Environmental Factors
| Factor | Value | Unit |
|---|---|---|
| organic carbon-free L1 +Si medium | L1 +Si medium without added organic carbon | N/A |
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| diatom culture age at inoculation | bacteria inoculated after 7 days of diatom growth | N/A |
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| marine photosynthate availability | dissolved metabolites released by T. pseudonana | N/A |
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Growth Media
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