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Lupinus SC-7 Rhizosphere SynCom

Community ID CommunityMech:000427
Ecological State ENGINEERED
Environment Lupinus rhizosphere — ontology label: rhizosphere
ENVO:00005801 · HabitatMech ↗
Modeled Environment wild Lupinus angustifolius plant-associated environment — ontology label: plant-associated environment
ENVO:01001001 · HabitatMech ↗

A defined twelve-strain bacterial synthetic community, SC-7, assembled from representative Bradyrhizobium, Micromonospora, Caulobacter, Kribbella, Pseudomonas, Pseudoxanthomonas, Rhizobium, Sphingopyxis, Stenotrophomonas, Streptomyces, and Variovorax isolates from the wild Lupinus angustifolius microbiome. The study selected these strains from core-hub-associated, peripheral, and satellite genera in a lupin root co-occurrence network, mixed them at equal optical density for gnotobiotic FlowPot and non-sterile soil inoculation, and found that increasing SynCom complexity reshaped root-associated microbiota while SC-7 gave the strongest lupin growth and transcriptional response among the tested SynComs.

Taxonomy

Taxon Ontology ID Functional Roles Abundance
Bradyrhizobium sp. CAR08 — ontology label: Bradyrhizobium NCBITaxon:374 · TaxonMech · TraitMech DOMINANT
Micromonospora sp. Lupac 08 — ontology label: Micromonospora NCBITaxon:1873 · TaxonMech · TraitMech DOMINANT
  • PMID:42602126 - SUPPORT (IN_VITRO)
    "Lupac 08 Micromonospora sp."
Caulobacter sp. LARHSG274 — ontology label: Caulobacter NCBITaxon:75 · TaxonMech · TraitMech DOMINANT
Kribbella sp. LARHCF250 — ontology label: Kribbella NCBITaxon:182639 · TaxonMech · TraitMech DOMINANT
Pseudomonas sp. LARHCG127 — ontology label: Pseudomonas NCBITaxon:286 · TaxonMech · TraitMech DOMINANT
Pseudoxanthomonas sp. LARHCG66 — ontology label: Pseudoxanthomonas NCBITaxon:83618 · TaxonMech · TraitMech DOMINANT
  • PMID:42602126 - SUPPORT (IN_VITRO)
    "LARHCG66 Pseudoxanthomonas sp."
Rhizobium sp. LARHSG275 — ontology label: Rhizobium NCBITaxon:379 · TaxonMech · TraitMech DOMINANT
Sphingopyxis sp. LARHCG72 — ontology label: Sphingopyxis NCBITaxon:165697 · TaxonMech · TraitMech DOMINANT
Stenotrophomonas sp. LARHCG68 — ontology label: Stenotrophomonas NCBITaxon:40323 · TaxonMech · TraitMech DOMINANT
  • PMID:42602126 - SUPPORT (IN_VITRO)
    "LARHCG68 Stenotrophomonas sp."
Streptomyces sp. LARHCF249 — ontology label: Streptomyces NCBITaxon:1883 · TaxonMech · TraitMech DOMINANT
  • PMID:42602126 - SUPPORT (IN_VITRO)
    "LARHCF249 Streptomyces sp."
Streptomyces sp. LARHCF252 — ontology label: Streptomyces NCBITaxon:1883 · TaxonMech · TraitMech DOMINANT
  • PMID:42602126 - SUPPORT (IN_VITRO)
    "LARHCF252 Streptomyces sp."
Variovorax sp. LARHSF232 — ontology label: Variovorax NCBITaxon:34072 · TaxonMech · TraitMech DOMINANT

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.

Ecological interaction network for Lupinus SC-7 Rhizosphere SynCom Bipartite graph where circles represent taxa and non-circular symbols represent interactions. Rare or untyped interactions share the Other symbol; exact curated types remain in the interaction details.
Taxon
Other

SC-7 high-complexity lupin response

The twelve-strain SC-7 inoculum produced the strongest reported lupin growth response in both gnotobiotic FlowPot and non-sterile CAS-soil experiments. The panel varied richness and strain composition together, so a pure diversity effect is not isolated. The twelve listed canonical participants match the inoculated strain codes in main Table 1, including both Streptomyces strains; they do not represent the missing host or all background soil taxa. Input membership does not establish dominance or equal abundance at harvest.

Participating Taxa: Bradyrhizobium sp. CAR08, Micromonospora sp. Lupac 08, Caulobacter sp. LARHSG274, Kribbella sp. LARHCF250, Pseudomonas sp. LARHCG127, Pseudoxanthomonas sp. LARHCG66, Rhizobium sp. LARHSG275, Sphingopyxis sp. LARHCG72, Stenotrophomonas sp. LARHCG68, Streptomyces sp. LARHCF249, Streptomyces sp. LARHCF252, Variovorax sp. LARHSF232

Evidence

  • PMID:42602126 - SUPPORT (IN_VIVO)
    "Given that SC-7 was the most complex SynCom and led to the highest increase in plant growth "
  • PMID:42602126 - SUPPORT (IN_VIVO)
    "Because community complexity and strain composition varied simultaneously among SynComs, the individual contributions of these factors cannot be disentangled under the conditions tested. "

SC-7-associated host transcriptional reprogramming

RNA-seq of living lupin roots from the FlowPot experiment associated SC-7 with changes in signaling, hormone perception, defense, and primary and secondary metabolic gene sets. Some pathways were upregulated and others downregulated; this is differential expression and enrichment, not direct hormone production, nitrogen-fixation rate or a demonstrated mediator of growth. Leghemoglobin expression and genomic plant-growth annotations do not independently establish functional flux. The inoculated twelve-strain roster does not resolve each strain contribution.

Participating Taxa: Bradyrhizobium sp. CAR08, Micromonospora sp. Lupac 08, Caulobacter sp. LARHSG274, Kribbella sp. LARHCF250, Pseudomonas sp. LARHCG127, Pseudoxanthomonas sp. LARHCG66, Rhizobium sp. LARHSG275, Sphingopyxis sp. LARHCG72, Stenotrophomonas sp. LARHCG68, Streptomyces sp. LARHCF249, Streptomyces sp. LARHCF252, Variovorax sp. LARHSF232

Evidence

  • PMID:42602126 - SUPPORT (IN_VIVO)
    "Upon addition of SC-7, several key pathways related to signalling, hormone perception, and primary and secondary metabolism were significantly upregulated "

Complex SynCom root and rhizosphere reshaping

In non-sterile CAS soil, the SynCom panel including SC-7 was associated with compartment-specific relative microbiome profiles, with the largest reported changes in roots and limited bulk-soil changes. SC-7 had lower root Shannon diversity than uninoculated controls. These results must remain separate from gnotobiotic colonization and FlowPot RNA-seq. Genus-level relative profiles are not absolute exclusion or unambiguous persistence of each inoculated strain; changes after computational removal of inoculant-associated ASVs are not a biological knockout. The Results sentence reporting no significant compartment treatment effects conflicts with its reported PERMANOVA p=0.001, so no blanket significance claim is certified here.

Participating Taxa: Bradyrhizobium sp. CAR08, Micromonospora sp. Lupac 08, Caulobacter sp. LARHSG274, Kribbella sp. LARHCF250, Pseudomonas sp. LARHCG127, Pseudoxanthomonas sp. LARHCG66, Rhizobium sp. LARHSG275, Sphingopyxis sp. LARHCG72, Stenotrophomonas sp. LARHCG68, Streptomyces sp. LARHCF249, Streptomyces sp. LARHCF252, Variovorax sp. LARHSF232

Evidence

  • PMID:42602126 - SUPPORT (IN_VIVO)
    "SynCom inoculation reshaped root-associated microbiota, moderately influenced the rhizosphere, and had limited impact on bulk soil communities. "

Associated Datasets

Dataset Type Repository Accession
Lupinus SynCom sequencing data BioProject PRJNA1178901
One of the NCBI BioProject accessions reported for sequencing data generated in the Lupinus SynCom study. 		MULTI_OMICS NCBI_BIOPROJECT PRJNA1178901
Lupinus SynCom sequencing data BioProject PRJNA1335402
One of the NCBI BioProject accessions reported for sequencing data generated in the Lupinus SynCom study. 		MULTI_OMICS NCBI_BIOPROJECT PRJNA1335402

Knowledge gaps & discussions (2)

KNOWLEDGE_GAP OPEN Which SC-7 phenotypes are caused by increased member richness and which are caused by the presence of Bradyrhizobium, Micromonospora, or other specific strains in the 12-member mixture?

The study's SynCom series changes strain richness and strain composition at the same time, and the authors state that those contributions cannot be disentangled under the tested conditions.

Attaches to: ecological_interactions#SC-7 high-complexity lupin response

KNOWLEDGE_GAP OPEN Which SC-7 functions mediate host growth and compartment-specific community changes?

Preserve all three observations and zero arrows. FlowPot root transcriptomics, gnotobiotic strain profiles and non-sterile CAS-soil relative microbiota are different endpoints. Co-occurrence hubs, no agar inhibition zones and gene annotations do not demonstrate facilitation, coexistence, nitrogen-fixation flux or a growth mediator. Main Table1 verifies twelve input strain codes, not dominance or genome/culture identity; two Streptomyces strains share a genus CURIE and must retain distinct preferred names. The existing richness-versus-membership gap stays open. Main text has conflicting PERMANOVA wording/p-value and six-week incubation/eight-week harvest wording; no reanalysis or supplement/raw-data audit was performed. #1564 tracks these and missing-host/role metadata.

Attaches to: ecological_interactions#SC-7 high-complexity lupin response, ecological_interactions#SC-7-associated host transcriptional reprogramming, ecological_interactions#Complex SynCom root and rhizosphere reshaping

External Resources

Name Repository Resource ID
Primary publication - Lupinus SC-7 Rhizosphere SynCom
Frontiers in Plant Science 2026 primary article describing the wild Lupinus angustifolius isolate collection, seven-strain-complexity SynCom panel, and SC-7 as the full twelve-strain rhizosphere SynCom. 		OTHER PMID:42602126
  • PMID:42602126 - SUPPORT (OTHER)
    "From natural assemblages to synthetic communities in the Lupinus microbiome"

Environmental Factors

Factor Value Unit
SC-7 equal-ratio inoculum OD600 1 individual cultures diluted as a 12-member mixture to OD600 0.02 N/A
  • PMID:42602126 - SUPPORT (IN_VITRO)
    "Bacterial strains were mixed in equal amounts to reach an OD600 of 1."
Gnotobiotic FlowPot plant growth 2:1 sterile peat and vermiculite N/A
  • PMID:42602126 - SUPPORT (IN_VIVO)
    "each FlowPot was then flushed with 50 mL of the inoculum (BD medium/SynCom mix) "
  • PMID:42602126 - SUPPORT (IN_VIVO)
    "containing a matrix of sterile peat and vermiculite (2:1) "
Non-sterile CAS soil assay 3 L pots with Cologne agricultural soil N/A
  • PMID:42602126 - SUPPORT (IN_VIVO)
    "A total of 120 seeds (fifteen seeds per treatment) were transferred to pots (3 L) containing CAS soil (Agricultural Soil from Cologne, Germany). "

Growth Media

TSB or TY broth

Temperature 28 C

Preparation notes: Used to grow SC-7 strains individually before equal-amount mixing.

Evidence

PMID:42602126

"Each strain was grown individually in liquid medium TSB (BD) or TY broth (DSMZ medium 1143) "

Broughton and Dilworth medium without nitrogen

Preparation notes: Final gnotobiotic FlowPot carrier medium for equal-ratio SynCom mixtures.

Evidence

PMID:42602126

"The suspension mixtures were added to Broughton and Dilworth (BD) medium ( Broughton and Dilworth, 1971 ) without nitrogen to a final OD600 of 0.02 "

Cross-Mech Suite Links

Explore related entities across the CultureBotAI X-Mech knowledge bases:

HabitatMech: Lupinus rhizosphere ↗ TaxonMech: Bradyrhizobium sp. CAR08 ↗ TraitMech: Bradyrhizobium sp. CAR08 ↗ TaxonMech: Micromonospora sp. Lupac 08 ↗ TraitMech: Micromonospora sp. Lupac 08 ↗ TaxonMech: Caulobacter sp. LARHSG274 ↗ TraitMech: Caulobacter sp. LARHSG274 ↗ TaxonMech: Kribbella sp. LARHCF250 ↗ TraitMech: Kribbella sp. LARHCF250 ↗ TaxonMech: Pseudomonas sp. LARHCG127 ↗ TraitMech: Pseudomonas sp. LARHCG127 ↗ TaxonMech: Pseudoxanthomonas sp. LARHCG66 ↗ TraitMech: Pseudoxanthomonas sp. LARHCG66 ↗ CultureMech Growth Media ↗ PathwayMech Pathways ↗