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 | NCBITaxon:53335 |
PRIMARY_DEGRADER
CROSS_FEEDER
|
DOMINANT |
| Pseudomonas sp. GM17 | NCBITaxon:306 |
PRIMARY_DEGRADER
CROSS_FEEDER
|
DOMINANT |
| Sphingobium sp. AP49 | NCBITaxon:165695 |
CROSS_FEEDER
|
N/A |
| Rhizobium sp. CF142 | NCBITaxon:379 |
CROSS_FEEDER
|
N/A |
| Variovorax sp. CF313 | NCBITaxon:34072 |
CROSS_FEEDER
|
N/A |
| Bacillus sp. BC15 | NCBITaxon:1386 |
CROSS_FEEDER
|
N/A |
| Caulobacter sp. AP07 | NCBITaxon:75 |
CROSS_FEEDER
|
N/A |
| Duganella sp. CF402 | NCBITaxon:75654 |
CROSS_FEEDER
|
N/A |
| Streptomyces mirabilis YR139 | NCBITaxon:68239 |
CROSS_FEEDER
|
N/A |
| Paraburkholderia sp. BT03 | NCBITaxon:1822464 |
CROSS_FEEDER
|
N/A |
Ecological Interactions
Medium-Dependent Cross-Feeding
CROSS_FEEDINGSource Taxon: Pseudomonas sp. GM17
Target Taxon: Variovorax sp. CF313
Biological Processes:
- interspecies interaction between organisms (GO:0044419)
- metabolic process (GO:0008152)
Evidence
-
PMID:33995895 - SUPPORT (IN_VITRO)"To unravel the underlying metabolic interactions, flux balance analysis was used to model microbial growth and identify potential metabolic exchanges involved in shaping the microbial communities"
Selective Antagonism During Assembly
COMPETITIONSource Taxon: Pseudomonas sp. GM17
Target Taxon: Pantoea sp. YR343
Biological Processes:
- interspecies interaction between organisms (GO:0044419)
Evidence
-
PMID:33995895 - SUPPORT (IN_VITRO)"Final community selection can also depend on selective antagonistic relationships and metabolic exchanges"
Metabolite Exchange with Pantoea
CROSS_FEEDINGSource Taxon: Pantoea sp. YR343
Target Taxon: Sphingobium sp. AP49
Biological Processes:
- interspecies interaction between organisms (GO:0044419)
- metabolic process (GO:0008152)
Evidence
-
PMID:33995895 - SUPPORT (IN_VITRO)"To unravel the underlying metabolic interactions, flux balance analysis was used to model microbial growth and identify potential metabolic exchanges involved in shaping the microbial communities"
Cross-Feeding with Rhizobium
CROSS_FEEDINGSource Taxon: Pantoea sp. YR343
Target Taxon: Rhizobium sp. CF142
Biological Processes:
- interspecies interaction between organisms (GO:0044419)
- metabolic process (GO:0008152)
Evidence
-
PMID:33995895 - SUPPORT (IN_VITRO)"To unravel the underlying metabolic interactions, flux balance analysis was used to model microbial growth and identify potential metabolic exchanges involved in shaping the microbial communities"
Cross-Feeding with Bacillus
CROSS_FEEDINGSource Taxon: Pseudomonas sp. GM17
Target Taxon: Bacillus sp. BC15
Biological Processes:
- interspecies interaction between organisms (GO:0044419)
- metabolic process (GO:0008152)
Evidence
-
PMID:33995895 - SUPPORT (IN_VITRO)"To unravel the underlying metabolic interactions, flux balance analysis was used to model microbial growth and identify potential metabolic exchanges involved in shaping the microbial communities"
Cross-Feeding with Caulobacter
CROSS_FEEDINGSource Taxon: Pseudomonas sp. GM17
Target Taxon: Caulobacter sp. AP07
Biological Processes:
- interspecies interaction between organisms (GO:0044419)
- metabolic process (GO:0008152)
Evidence
-
PMID:33995895 - SUPPORT (IN_VITRO)"To unravel the underlying metabolic interactions, flux balance analysis was used to model microbial growth and identify potential metabolic exchanges involved in shaping the microbial communities"
Cross-Feeding with Duganella
CROSS_FEEDINGSource Taxon: Pantoea sp. YR343
Target Taxon: Duganella sp. CF402
Biological Processes:
- interspecies interaction between organisms (GO:0044419)
- metabolic process (GO:0008152)
Evidence
-
PMID:33995895 - SUPPORT (IN_VITRO)"To unravel the underlying metabolic interactions, flux balance analysis was used to model microbial growth and identify potential metabolic exchanges involved in shaping the microbial communities"
Cross-Feeding with Streptomyces
CROSS_FEEDINGSource Taxon: Pseudomonas sp. GM17
Target Taxon: Streptomyces mirabilis YR139
Biological Processes:
- interspecies interaction between organisms (GO:0044419)
- metabolic process (GO:0008152)
Evidence
-
PMID:33995895 - SUPPORT (IN_VITRO)"To unravel the underlying metabolic interactions, flux balance analysis was used to model microbial growth and identify potential metabolic exchanges involved in shaping the microbial communities"
Cross-Feeding with Paraburkholderia
CROSS_FEEDINGSource Taxon: Pantoea sp. YR343
Target Taxon: Paraburkholderia sp. BT03
Biological Processes:
- interspecies interaction between organisms (GO:0044419)
- metabolic process (GO:0008152)
Evidence
-
PMID:33995895 - SUPPORT (IN_VITRO)"To unravel the underlying metabolic interactions, flux balance analysis was used to model microbial growth and identify potential metabolic exchanges involved in shaping the microbial communities"
Associated Datasets
| Dataset | Type | Repository | Accession |
|---|---|---|---|
|
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 |
Environmental Factors
| Factor | Value | Unit |
|---|---|---|
| Growth medium context | two media environments | N/A |
| Stabilization timeframe | around 5 growth cycles | N/A |