A twelve-strain bacterial synthetic community assembled from isolates recovered from Sclerotinia sclerotiorum sclerotia after 5 days in flooded non-autoclaved soil. The SynCom spans Caballeronia, Cupriavidus, Massilia, Paraburkholderia, Ralstonia and Trinickia isolates, was co-cultured with mature fungal sclerotia in 10 mL tubes, and was resolved spatiotemporally by a 10x Genomics Xenium panel targeting all twelve members. Sclerotia inoculated with the full SynCom reached 100% mortality by day 14, and the dropout design identified Trinickia sp. MC, proposed in the paper as Trinickia sclerotiorum sp. nov. type strain MC, as the apparent key bacterial contributor.
Taxonomy
| Taxon | Ontology ID | Functional Roles | Abundance |
|---|---|---|---|
| Caballeronia zhejiangensis N8 — ontology label: Caballeronia zhejiangensis | NCBITaxon:871203 · TaxonMech · TraitMech |
PATHOGEN_ANTAGONIST
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COMMON |
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| Cupriavidus sp. N4 — ontology label: Cupriavidus | NCBITaxon:106589 · TaxonMech · TraitMech |
PATHOGEN_ANTAGONIST
|
COMMON |
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| Massilia sp. R20 — ontology label: Massilia | NCBITaxon:149698 · TaxonMech · TraitMech |
PATHOGEN_ANTAGONIST
|
ABUNDANT |
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| Massilia sp. TB221 — ontology label: Massilia | NCBITaxon:149698 · TaxonMech · TraitMech |
PATHOGEN_ANTAGONIST
|
ABUNDANT |
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| Massilia sp. RB201 — ontology label: Massilia | NCBITaxon:149698 · TaxonMech · TraitMech |
PATHOGEN_ANTAGONIST
|
COMMON |
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| Massilia sp. RB202 — ontology label: Massilia | NCBITaxon:149698 · TaxonMech · TraitMech |
PATHOGEN_ANTAGONIST
|
COMMON |
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| Paraburkholderia sp. I59 — ontology label: Paraburkholderia | NCBITaxon:1822464 · TaxonMech · TraitMech |
PATHOGEN_ANTAGONIST
|
COMMON |
|
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| Paraburkholderia phenoliruptrix TB211 — ontology label: Paraburkholderia phenoliruptrix | NCBITaxon:252970 · TaxonMech · TraitMech |
PATHOGEN_ANTAGONIST
|
COMMON |
|
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| Paraburkholderia phymatum R7 — ontology label: Paraburkholderia phymatum | NCBITaxon:148447 · TaxonMech · TraitMech |
PATHOGEN_ANTAGONIST
|
COMMON |
|
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| Paraburkholderia sp. T17 — ontology label: Paraburkholderia | NCBITaxon:1822464 · TaxonMech · TraitMech |
PATHOGEN_ANTAGONIST
|
COMMON |
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| Ralstonia sp. R4 — ontology label: Ralstonia | NCBITaxon:48736 · TaxonMech · TraitMech |
PATHOGEN_ANTAGONIST
|
COMMON |
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| Trinickia sclerotiorum sp. nov. MC — ontology label: Trinickia | NCBITaxon:2571160 · TaxonMech · TraitMech |
PATHOGEN_ANTAGONIST
|
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.
Twelve-Strain SynCom Suppression of Sclerotinia Sclerotia
The full twelve-member inoculum increased sclerotium mortality relative to the control in the reported laboratory comparison. This establishes a community treatment effect, not equal antagonistic contributions by every member, resource competition with the fungus or a demonstrated cellular defense-response pathway.
Target Taxon: Sclerotinia sclerotiorum
Participating Taxa: Caballeronia zhejiangensis N8, Cupriavidus sp. N4, Massilia sp. R20, Massilia sp. TB221, Massilia sp. RB201, Massilia sp. RB202, Paraburkholderia sp. I59, Paraburkholderia phenoliruptrix TB211, Paraburkholderia phymatum R7, Paraburkholderia sp. T17, Ralstonia sp. R4, Trinickia sclerotiorum sp. nov. MC
Evidence
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PMID:42523014 - SUPPORT (IN_VITRO)"When sclerotia were inoculated with the SynCom, sclerotia mortality was significantly increased after 1-day co-culture with the SynCom, gradually reaching 100.0% mortality by 14-day co-culture"
Trinickia MC Key Contribution to Sclerotia Mortality
The dropout series and single-member comparison identify Trinickia MC as the strongest resolved contributor to accelerated sclerotium mortality. Its contribution is context- and time-dependent, not proof that MC is uniquely necessary for all eventual mortality or that every other member reinforces it. The primary discussion reports attenuation by the remaining nine-member group and eventual mortality from assemblies lacking MC. This node records the named member's contribution to the community intervention; Sclerotinia is the external challenge context, not a thirteenth consortium member.
Target Taxon: Sclerotinia sclerotiorum
Participating Taxa: Trinickia sclerotiorum sp. nov. MC
The decrease in mortality following MC removal supports a causal contribution to the full-community outcome over the measured time course. This is not an additive decomposition of member effects or proof of universal necessity; other-member effects can attenuate MC and later reach the same endpoint.
Evidence
-
PMID:42523014 - SUPPORT (IN_VITRO)"dropping TsMC significantly decreased mortality and its mono-inoculation alone could accelerate sclerotia mortality"
Spatial Invasion of Sclerotia by SynCom Members
Spatial profiling detected early interior colonization by Massilia TB221 and R20, later interior enrichment of Ralstonia R4 and Trinickia MC, and MC dominance across the sampled layers at the final observation. These distribution and timing observations are not demonstrated competition-reducing niche partitioning or evidence that early colonization itself causes mortality. The MC contribution is supported independently by the dropout comparison, not inferred solely from its location.
Participating Taxa: Massilia sp. TB221, Massilia sp. R20, Ralstonia sp. R4, Trinickia sclerotiorum sp. nov. MC
Evidence
-
PMID:42523014 - SUPPORT (IN_VITRO)"By 3-day co-culture, Massilia sp. TB221 and Massilia sp. R20 had reached the interior sclerotia (layer 1 to 4)"
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PMID:42523014 - SUPPORT (IN_VITRO)"At 5- to 7-day co-culture, the relative abundance of Ralstonia sp. R4 and Trinickia sp. MC increased progressively in the interior layers"
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PMID:42523014 - SUPPORT (IN_VITRO)"By 14-day co-culture, when sclerotia viability was completely suppressed, the relative abundance of Trinickia sp. MC exceeded all other SynCom members simultaneously across layer 1 to 5"
Associated Datasets
| Dataset | Type | Repository | Accession |
|---|---|---|---|
|
Sclerotinia sclerotia microbiome and Trinickia MC genome
NCBI BioProject carrying the PacBio sclerotia microbiome reads and the whole-genome sequence data for Trinickia sclerotiorum sp. nov. MC. |
MULTI_OMICS | NCBI_BIOPROJECT | PRJNA1475221 |
|
Sclerotinia sclerotia SynCom spatial microbiome Dataverse
Harvard Dataverse deposit associated with the spatial microbiome and SynCom analysis. |
OTHER | OTHER | doi:10.7910/DVN/DEERTV |
Knowledge gaps & discussions (3)
KNOWLEDGE_GAP OPEN Has Trinickia sclerotiorum sp. nov. MC been assigned an NCBITaxon species identifier or stable strain genome assembly accession that should replace the current genus-level grounding?
The 2026 paper describes MC as a novel Trinickia species using core-gene phylogeny, ANI and dDDH, but the local NCBITaxon snapshot resolves Trinickia and not the proposed species name.
Attaches to: taxonomy#Trinickia sclerotiorum sp. nov. MC
1 evidence item(s)
These results indicate TsMC does not belong to any known Trinickia species and thus we describe this strain as a new species, Trinickia sclerotiorum sp. nov. type strain MC
Supports the novel-species status that is not yet available as a species-level local NCBITaxon term.
KNOWLEDGE_GAP OPEN Which additional bacteria in the 5-day flooded-soil sclerotium microbiome account for the abundance not captured by the twelve-strain SynCom?
The SynCom covered most of the 5-day SF microbiome at genus level but only 56.3% at species level, so the full flooded-soil sclerotium microbiome may include interaction complexity absent from the defined assembly.
Attaches to: engineering_design, ecological_interactions#Twelve-Strain SynCom Suppression of Sclerotinia Sclerotia
1 evidence item(s)
As our SynCom represents only 56.3% bacterial abundance of 5-day SF microbiome, higher level of the complexity in the bacteria-bacteria interaction may not be captured in this study
Records the authors' caveat about the partial species-level coverage of the defined SynCom.
KNOWLEDGE_GAP OPEN Which mechanisms explain the context-dependent antagonism and spatial associations?
Mortality contrasts support the community and MC treatment effects, while the spatial profile alone does not establish facilitation, resource competition or reduced competition among bacteria. Nonadditive effects and eventual mortality in assemblies lacking MC limit an essential-member interpretation. Molecular mechanisms remain unresolved; no new pathway, culturing procedure or genetic design is introduced. Existing taxonomic and partial-coverage discussions remain unchanged.
Attaches to: ecological_interactions#Twelve-Strain SynCom Suppression of Sclerotinia Sclerotia, ecological_interactions#Trinickia MC Key Contribution to Sclerotia Mortality, ecological_interactions#Spatial Invasion of Sclerotia by SynCom Members
1 evidence item(s)
dropping TsMC significantly decreased mortality and its mono-inoculation alone could accelerate sclerotia mortality
Supports a dropout-resolved MC contribution in the tested comparisons, not universal necessity or an additive contribution model.
External Resources
| Name | Repository | Resource ID |
|---|---|---|
|
PubMed - Sclerotinia sclerotia 12-strain biocontrol SynCom
PubMed record for the ISME Journal article describing the Sclerotinia sclerotia spatial microbiome and SynCom. |
OTHER | PMID:42523014 |
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DOI - Sclerotinia sclerotia 12-strain biocontrol SynCom
DOI for the ISME Journal article describing the Sclerotinia sclerotia spatial microbiome and SynCom. |
OTHER | doi:10.1093/ismejo/wrag201 |
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Environmental Factors
| Factor | Value | Unit |
|---|---|---|
| flooded non-autoclaved soil source condition | 5-day burial under flooding | N/A |
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| SynCom co-culture incubation temperature | 25 | °C |
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Growth Media
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