A 10-member synthetic bacterial community (PD10) assembled by the Oak Ridge National Laboratory Plant-Microbe Interfaces (PMI) team from Populus deltoides rhizosphere isolates. The community was used as a bottom-up model system to study assembly dynamics, medium-dependent community structure, metabolic exchange, and antagonistic interactions during stable community formation.
Taxonomy
| Taxon | Ontology ID | Functional Roles | Abundance |
|---|---|---|---|
| Pantoea sp. YR343 — ontology label: Pantoea | NCBITaxon:53335 · TaxonMech · TraitMech | DOMINANT | |
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| Pseudomonas sp. GM17 — ontology label: Pseudomonas sp. | NCBITaxon:306 · TaxonMech · TraitMech | DOMINANT | |
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| Sphingobium sp. AP49 — ontology label: Sphingobium | NCBITaxon:165695 · TaxonMech · TraitMech | N/A | |
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| Rhizobium sp. CF142 — ontology label: Rhizobium | NCBITaxon:379 · TaxonMech · TraitMech | N/A | |
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| Variovorax sp. CF313 — ontology label: Variovorax | NCBITaxon:34072 · TaxonMech · TraitMech | N/A | |
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| Bacillus sp. BC15 — ontology label: Bacillus <firmicutes> | NCBITaxon:1386 · TaxonMech · TraitMech | N/A | |
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| Caulobacter sp. AP07 — ontology label: Caulobacter | NCBITaxon:75 · TaxonMech · TraitMech | N/A | |
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| Duganella sp. CF402 — ontology label: Duganella | NCBITaxon:75654 · TaxonMech · TraitMech | N/A | |
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| Streptomyces mirabilis YR139 — ontology label: Streptomyces mirabilis | NCBITaxon:68239 · TaxonMech · TraitMech | N/A | |
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| Paraburkholderia sp. BT03 — ontology label: Paraburkholderia | NCBITaxon:1822464 · TaxonMech · TraitMech | 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.
Medium-Dependent Serial-Passage Selection
Serial passage of the same ten-strain inoculum in MOPS-glucose versus R2A selected distinct persistent communities. The controlled medium comparison supports medium-dependent assembly, not uniquely demonstrated niche partitioning. Main-text trajectories distinguish the MOPS four-strain pattern from passage 4 and R2A stable coexistence from passage 10; the abstract summary of about five cycles is not a universal threshold.
Biological Processes:
- interspecies interaction between organisms (GO:0044419 · PathwayMech)
Serial passage in the MOPS-glucose condition selected the persistent Pseudomonas, Variovorax, Rhizobium and Sphingobium assemblage, in contrast to the R2A outcome from the same inoculum. The condition-to-composition effect is supported without isolating nutrient competition from proposed exchange mechanisms.
Serial passage in the R2A condition selected the Pantoea-dominated 16S assemblage with Pseudomonas and Sphingobium, while metaproteomics also recovered notable Bacillus proteins. The medium effect on community composition is retained without equating protein-relative abundance with directly counted viable biomass.
Evidence
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PMID:33995895 - SUPPORT (IN_VITRO)"In this study, 10 bacterial strains isolated from the Populus deltoides rhizosphere were combined and passaged in two different media environments to form stable microbial communities"
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PMID:33995895 - SUPPORT (IN_VITRO)"The membership and relative abundances of the strains stabilized after around 5 growth cycles and resulted in just a few dominant strains that depended on the medium"
Pairwise Growth Phenotypes on R2A Agar
R2A agar pairwise screens found GM17-associated inhibition of multiple lawns and YR343-associated growth promotion of CF142 and CF313. These are measured colony phenotypes, not a direct test of their contribution to liquid-community selection or a uniquely established nutrient-competition or antimicrobial mechanism. AP49, CF142 and CF313 still coexisted with GM17 in liquid culture; positive exchanges and the agar-versus-liquid conditions are alternative explanations.
Participating Taxa: Pseudomonas sp. GM17, Pantoea sp. YR343
Biological Processes:
- interspecies interaction between organisms (GO:0044419 · PathwayMech)
Evidence
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PMID:33995895 - SUPPORT (IN_VITRO)"Pseudomonas sp. GM17 cells were antagonistic to the growth of the majority of the other community members, while Pantoea sp. YR343 demonstrated positive interactions with several strains"
Pantoea-Centered R2A Metabolite Export
CROSS_FEEDINGHYPOTHESIZED - In the three-member R2A community FBA model, Pantoea sp. YR343 exports predicted organic acids, purine derivatives and biogenic amines that could support other modeled members, Pseudomonas sp. GM17 and Sphingobium sp. AP49. This is a constrained, gapfilled model conditioned on endpoint 16S proportions; pathway proteins support metabolic capacity, not measured exchange flux or proof that export caused long-term persistence.
Source Taxon: Pantoea sp. YR343
Participating Taxa: Pantoea sp. YR343, Pseudomonas sp. GM17, Sphingobium sp. AP49
Metabolites: organic acid (CHEBI:64709 · MediaIngredientMech · CMMMech)
HYPOTHESIZED - Predicted YR343 secretion could provide growth substrates that help sustain the R2A partners. The source proposes this mechanism, but FBA uses final community proportions as inputs and does not independently establish temporal assembly or measured cross-feeding; enzyme detection is not exchange-flux validation.
Evidence
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PMID:33995895 - SUPPORT (COMPUTATIONAL)"In the community model using R2A medium, metabolite exchange can also be predicted. Here, the dominant strain Pantoea sp. YR343, based on the 16S rRNA marker data, is expected to export a greater range of metabolites than it receives from the other two members of the community"
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PMID:33995895 - SUPPORT (COMPUTATIONAL)"Organic acids, purine derivatives and biogenic amines are predicted to be excreted and support the growth of the other community members"
MOPS Minimal-Medium Four-Strain Coexistence
In MOPS-glucose, GM17 dominated while CF313, CF142 and AP49 persisted in consistent relative proportions from approximately passage 4. This positive coexistence result does not establish obligate mutualism or niche partitioning. The paper also predicts MOPS-specific exchanges, but their missing graph structure requires separate causal research and must not be borrowed from the distinct R2A model.
Participating Taxa: Pseudomonas sp. GM17, Variovorax sp. CF313, Rhizobium sp. CF142, Sphingobium sp. AP49
Biological Processes:
- interspecies interaction between organisms (GO:0044419 · PathwayMech)
Evidence
-
PMID:33995895 - SUPPORT (IN_VITRO)"In MOPS medium, Pseudomonas sp. GM17 is the most abundant member along with three other strains, Variovorax sp. CF313, Rhizobium sp. CF142 and Sphingobium sp. AP49, that persist in consistent proportions"
R2A Pantoea-Dominated Stable Community
In R2A, YR343, GM17 and AP49 dominated the 16S profile, with stable coexistence reported from passage 10 and YR343 most abundant after 15 passages. Metaproteomics recovered notable BC15 proteins and different YR343 proportions. Sporulation-related detection bias and relic DNA were proposed explanations; protein-relative abundance is not a direct viable-cell count or proof of a uniform four-strain abundance ranking.
Participating Taxa: Pantoea sp. YR343, Pseudomonas sp. GM17, Sphingobium sp. AP49, Bacillus sp. BC15
Biological Processes:
- interspecies interaction between organisms (GO:0044419 · PathwayMech)
Evidence
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PMID:33995895 - SUPPORT (IN_VITRO)"For 16S rRNA gene amplicon sequencing, three members dominate in abundance when grown in R2A complex medium, and Pantoea sp. YR343 is the member with highest content after 15 passages"
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PMID:33995895 - SUPPORT (IN_VITRO)"Additionally, there is a notable abundance of Bacillus sp. BC15 not seen in 16S rRNA gene amplicon sequencing data."
Associated Datasets
| Dataset | Type | Repository | Accession |
|---|---|---|---|
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Populus PD10 16S rRNA gene amplicon data
Time-series 16S rRNA community profiling across serial passages in MOPS and R2A media. |
AMPLICON_16S | NCBI_BIOPROJECT | PRJNA658537 |
Knowledge gaps & discussions (1)
KNOWLEDGE_GAP OPEN Which exact-system measurements distinguish the observed outcome from the proposed mechanism?
Keep the controlled medium-dependent assembly and persistent survivor patterns, including slow-growing CF142 in MOPS. Separate the ten-strain experimental inoculum from the four-member MOPS and three-member R2A models. Endpoint proportions constrain the FBA model, so model agreement is not an independent demonstration of assembly causation. Metaproteomics supports pathways but does not measure exchange flux. Agar inhibition and liquid coexistence can differ because of positive interactions or culture conditions; neither explanation was selectively isolated. Purine alkaloid and aromatase inhibitor are not valid equivalents for the two predicted generic metabolite classes, so those groundings are removed without inventing specific compounds. The omitted MOPS exchange structure remains needs_research pending scoped causal research; prior removal of analysis-workflow arrows remains intact.
Attaches to: ecological_interactions#Medium-Dependent Serial-Passage Selection, ecological_interactions#Pairwise Growth Phenotypes on R2A Agar, ecological_interactions#Pantoea-Centered R2A Metabolite Export, ecological_interactions#MOPS Minimal-Medium Four-Strain Coexistence, ecological_interactions#R2A Pantoea-Dominated Stable Community
External Resources
| Name | Repository | Resource ID |
|---|---|---|
|
KBase narrative (MOPS medium workflow)
Community Modeling and Flux Balance Analysis of Synthetic Bacterial Community in MOPS Medium. |
KBASE | ws.73218.obj.75 |
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Environmental Factors
| Factor | Value | Unit |
|---|---|---|
| Growth medium context | two media environments | N/A |
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| Stabilization timeframe | around 5 growth cycles | N/A |
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Growth Media
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