A 15-member reduced-complexity Sorghum bicolor synthetic root community rationally derived from the 57-member Sorghum Root Consortium 1 (SRC1). SRC2v4 was designed by ranking SRC1 strains by cumulative root abundance in a prior permutational membership experiment, prioritizing known sorghum root-exudate users when abundance rankings were highly similar, and selecting 15 high-colonization isolates with unique 16S rRNA gene sequences in the V3-V4 region. In gnotobiotic 5-l sterile microboxes, SRC2v4 showed exceptional compositional fidelity relative to its inoculum, stably colonized roots and rhizospheres, promoted plant growth as a live community but not as a heat-killed inoculum, and induced coordinated S. bicolor transcriptional and metabolomic responses centered on flavonoid biosynthesis.
Taxonomy
| Taxon | Ontology ID | Functional Roles | Abundance |
|---|---|---|---|
| Burkholderia anthina SO8-2 — ontology label: Burkholderia anthina | NCBITaxon:179879 · TaxonMech · TraitMech | COMMON | |
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| Chryseobacterium proteolyticum TBS_027 — ontology label: Chryseobacterium proteolyticum | NCBITaxon:118127 · TaxonMech · TraitMech | COMMON | |
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| Pseudomonas sp. TBS_028 — ontology label: Pseudomonas | NCBITaxon:286 · TaxonMech · TraitMech | COMMON | |
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| Enterobacter ludwigii PH2 — ontology label: Enterobacter ludwigii | NCBITaxon:299767 · TaxonMech · TraitMech | COMMON | |
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| Sphingobium sp. Sin1 — ontology label: Sphingobium | NCBITaxon:165695 · TaxonMech · TraitMech | COMMON | |
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| Flavobacterium sp. SO6b — ontology label: Flavobacterium | NCBITaxon:237 · TaxonMech · TraitMech | COMMON | |
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| Kribbella shirazensis SAI_226 — ontology label: Kribbella shirazensis | NCBITaxon:1105143 · TaxonMech · TraitMech | COMMON | |
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| Streptomyces ambofaciens SAI_104 — ontology label: Streptomyces ambofaciens | NCBITaxon:1889 · TaxonMech · TraitMech | COMMON | |
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| Rhizobium pusense TBS_045 — ontology label: Agrobacterium pusense | NCBITaxon:648995 · TaxonMech · TraitMech | COMMON | |
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| Paraburkholderia sp. CO4 — ontology label: Paraburkholderia | NCBITaxon:1822464 · TaxonMech · TraitMech | COMMON | |
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| Pseudomonas sp. NA2a — ontology label: Pseudomonas | NCBITaxon:286 · TaxonMech · TraitMech | COMMON | |
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| Acinetobacter sp. SO6a — ontology label: Acinetobacter | NCBITaxon:469 · TaxonMech · TraitMech | COMMON | |
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| Pseudomonas sp. SO8-1 — ontology label: Pseudomonas | NCBITaxon:286 · TaxonMech · TraitMech | COMMON | |
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| Pseudomonas entomophila NA8 — ontology label: Pseudomonas entomophila | NCBITaxon:312306 · TaxonMech · TraitMech | COMMON | |
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| Chryseobacterium gleum TBS_030 — ontology label: Chryseobacterium gleum | NCBITaxon:250 · TaxonMech · TraitMech | COMMON | |
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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.
SRC2v4 Composition Relative to Its Inoculum
In the controlled gnotobiotic comparison, SRC2v4 was the most compositionally representative of its inoculum among the four tested variants, with no member shift detected by the reported differential-abundance test. Nonsignificance does not establish invariant abundance, equivalence or universal stability. The result does not identify one organism facilitating another, and the paper's prose and figure caption differ on root diversity loss.
Evidence
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PMID:42454401 - SUPPORT (IN_VIVO)"Across all variants, SRC2v4 was the most compositionally representative of its inoculum, suggesting greater compositional stability within the controlled gnotobiotic environment used here."
Live SRC2v4 Plant Growth Promotion
In the reported gnotobiotic comparison, live SRC2v4 increased shoot fresh weight, shoot dry weight and root fresh weight; the heat-killed treatment did not significantly induce plant growth promotion. This is a host phenotype under the tested conditions, not demonstrated reciprocal microbial fitness benefit, field efficacy or identification of a specific living-cell mechanism.
Biological Processes:
- plant growth (GO:0040007 · PathwayMech)
Evidence
-
PMID:42454401 - SUPPORT (IN_VIVO)"Live SRC2v4 treatment increased shoot fresh weight, shoot dry weight, and root fresh weight."
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PMID:42454401 - PARTIAL (IN_VIVO)"host interaction with live SRC2v4 was required for PGP"
SRC2v4 Host Flavonoid Response
SRC2v4 treatment was associated with dynamic host flavonoid-pathway transcription and enriched flavone-related metabolites in root and rhizosphere samples. These observations do not establish that flavonoids facilitate colonization or mediate the host growth response. The paper leaves recruitment versus prevention of colonization unresolved; correlations restricted to SRC2v4-treated samples were not significant.
Biological Processes:
- biological process involved in interspecies interaction between organisms (GO:0044419 · PathwayMech)
Evidence
-
PMID:42454401 - SUPPORT (IN_VIVO)"functional enrichment analysis confirmed that the flavonoid biosynthetic pathway was strongly regulated"
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PMID:42454401 - SUPPORT (IN_VIVO)"Notably, five enriched flavones in the root in addition to Flavone +1O; OMe in the rhizosphere"
Associated Datasets
| Dataset | Type | Repository | Accession |
|---|---|---|---|
|
SRC2 raw sequencing datasets
NCBI BioProject containing the SRC2 isolate genomes, 16S rRNA amplicon sequencing, host plant RNA-seq, and rhizosphere metatranscriptomics raw files. |
MULTI_OMICS | NCBI_BIOPROJECT | PRJNA1404338 |
|
SRC2 LC-MS raw data
LC-MS raw data files for SRC2 root and rhizosphere metabolomics. |
METABOLOMICS | MASSIVE | MSV000100573 |
Knowledge gaps & discussions (1)
KNOWLEDGE_GAP OPEN Do the reported composition and flavonoid responses establish a specific ecological mechanism in SRC2v4?
They support observations, not a demonstrated interspecies fitness sign or flavonoid-mediated colonization. Differential-abundance nonsignificance is not invariance; the main text and Fig.2 caption also differ on root diversity loss. No raw-data reanalysis was performed. The source leaves flavonoid function unresolved. Preserve the absence of assay-order edges fixed in #782. No new growth, colonization, infection or genetic-design procedures are added; existing non-graph protocols are outside this review.
Attaches to: ecological_interactions#SRC2v4 Composition Relative to Its Inoculum, ecological_interactions#Live SRC2v4 Plant Growth Promotion, ecological_interactions#SRC2v4 Host Flavonoid Response
1 evidence item(s)
Roles for both recruitment and prevention of colonization by plant-produced flavonoids remain open.
The authors explicitly leave the direction and mechanism unresolved.
External Resources
| Name | Repository | Resource ID |
|---|---|---|
|
SRC2 paper analysis repository
Paper-linked repository containing analysis scripts and formulation tables for the SRC2 rational-reduction study. |
GITHUB | deanpettinga/src2_paper |
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Growth Media
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