A metabolic-model-selected three-strain synthetic community composed of Sphingopyxis sp. DBS4, Sphingopyxis sp. DCP-4, and Achromobacter sp. DCP-11d. Lin et al. built genome-scale metabolic models from five DCPP-enrichment isolates, simulated 15 DBS4-containing two- to five-strain combinations, selected DBS4&DCP-4&DCP-11d as the optimal three-member DCPP degrader, and experimentally verified its DCPP removal and predicted metabolite exchange in mineral medium and DCPP-contaminated soil.
Taxonomy
| Taxon | Ontology ID | Functional Roles | Abundance |
|---|---|---|---|
| Sphingopyxis sp. DBS4 — ontology label: Sphingopyxis | NCBITaxon:165697 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
CROSS_FEEDER
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DOMINANT |
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| Sphingopyxis sp. DCP-4 — ontology label: Sphingopyxis | NCBITaxon:165697 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
CROSS_FEEDER
|
DOMINANT |
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| Achromobacter sp. DCP-11d — ontology label: Achromobacter | NCBITaxon:222 · TaxonMech · TraitMech |
CROSS_FEEDER
PRIMARY_DEGRADER
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DOMINANT |
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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.
Model-selected DCPP degradation
CROSS_FEEDINGCommunity metabolic modelling predicted DBS4&DCP-4&DCP-11d as the best three-strain SynCom, and shake-flask and soil experiments validated that this simplified SynCom degraded DCPP comparably to the larger four- and five-strain designs.
Metabolites: DCPP (CHEBI:75375 · MediaIngredientMech · CMMMech)
Biological Processes:
- xenobiotic metabolic process (GO:0006805 · PathwayMech)
Evidence
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PMID:42613016 - SUPPORT (COMPUTATIONAL)"the combination of DBS4, DCP‐4 and DCP‐11d (DBS4&DCP‐4&DCP‐11d) showed the maximum biomass production"
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PMID:42613016 - SUPPORT (IN_VITRO)"optimal three‐strain SynCom DBS4&DCP‐4&DCP‐11d was comparable to that of the four‐ or five‐strain SynCom"
DBS4 to DCP-11d 2,4-DCP detoxification
CROSS_FEEDINGThe community model predicted 2,4-DCP flow from DBS4 to DCP-11d; experiments then confirmed that the intermediate 2,4-DCP inhibits DBS4 DCPP degradation and that DCP-11d relieves this inhibition by consuming 2,4-DCP.
Source Taxon: Sphingopyxis sp. DBS4
Target Taxon: Achromobacter sp. DCP-11d
Metabolites: 2,4-DCP (CHEBI:16738 · MediaIngredientMech · CMMMech)
Biological Processes:
- xenobiotic metabolic process (GO:0006805 · PathwayMech)
Evidence
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PMID:42613016 - SUPPORT (COMPUTATIONAL)"the model predicted the metabolic flow of the intermediate 2,4‐DCP from the degrader strain DBS4 to the helper strain DCP‐11d"
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PMID:42613016 - SUPPORT (IN_VITRO)"2,4‐DCP inhibits the degradation activity of DBS4, while DCP‐11d alleviates this inhibition"
Predicted exchanged metabolite validation
CROSS_FEEDINGLC-MS analysis of DBS4&DCP-4&DCP-11d co-culture detected six of seven metabolites predicted by the community model, supporting but not fully quantifying the predicted exchange network.
Participating Taxa: Sphingopyxis sp. DBS4, Sphingopyxis sp. DCP-4, Achromobacter sp. DCP-11d
Evidence
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PMID:42613016 - SUPPORT (IN_VITRO)"the optimal consortium (DBS4&DCP‐4&DCP‐11d) was used to detect the secreted metabolites"
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PMID:42613016 - SUPPORT (IN_VITRO)"Except for D‐glucosamine, the other six substances were successfully detected by LC–MS"
Knowledge gaps & discussions (1)
KNOWLEDGE_GAP OPEN What are the relative quantitative contributions of nutrient cross-feeding and 2,4-DCP detoxification to enhanced DBS4&DCP-4&DCP-11d DCPP degradation?
The authors state that both cross-feeding and intermediate detoxification can enhance degradation, but that their wet-lab experiments validated model predictions rather than quantitatively dissecting the mechanisms. Further perturbation or isotope-tracing experiments would be needed to apportion their relative contributions.
Attaches to: ecological_interactions#DBS4 to DCP-11d 2,4-DCP detoxification, ecological_interactions#Predicted exchanged metabolite validation
External Resources
| Name | Repository | Resource ID |
|---|---|---|
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Primary publication - DCPP DBS4-DCP-4-DCP-11d SynCom
PubMed record for the Environ Microbiol metabolic-modelling study that designed and experimentally validated the DBS4&DCP-4&DCP-11d DCPP-degradation SynCom. |
OTHER | PMID:42613016 |
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Publication DOI - DCPP DBS4-DCP-4-DCP-11d SynCom
DOI for the primary Environ Microbiol study of the DBS4&DCP-4&DCP-11d DCPP-degradation SynCom. |
OTHER | doi:10.1111/1462-2920.70404 |
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Environmental Factors
| Factor | Value | Unit |
|---|---|---|
| DCPP herbicide | sole carbon source in mineral medium | N/A |
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| Soil DCPP spike | 5 | mg/kg |
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Growth Media
Cross-Mech Suite Links
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