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At-RSPHERE SynCom

Community ID CommunityMech:000003
Ecological State ENGINEERED
Environment rhizosphere
ENVO:00005801 · HabitatMech ↗

A synthetic bacterial community derived from the Arabidopsis root microbiota culture collection (At-RSPHERE), representing 16 bacterial families isolated from Arabidopsis thaliana roots grown in natural soil. This community was established to study plant-microbe interactions and their effects on plant productivity and carbon cycling in the rhizosphere. The consortium members were selected to represent a broad taxonomic range covering the major bacterial phyla (Proteobacteria, Actinobacteria, and Bacteroidetes) found in the Arabidopsis root microbiome. Assembly sizes vary from 5-20 members depending on experimental design, enabling reductionist studies of root microbiota assembly and function.

Taxonomy

Taxon Ontology ID Functional Roles Abundance
Arabidopsis thaliana NCBITaxon:3702 · TaxonMech · TraitMech
PRIMARY_PRODUCER
N/A
  • doi:10.1038/nature16192 - SUPPORT (IN_VITRO)
    "We established Arabidopsis leaf- and root-derived microbiota culture collections representing the majority of bacterial species that are reproducibly detectable by culture-independent community sequencing"
Pseudomonas sp. NCBITaxon:306 · TaxonMech · TraitMech DOMINANT
  • doi:10.1038/nature16192 - SUPPORT (IN_VITRO)
    "We established Arabidopsis leaf- and root-derived microbiota culture collections representing the majority of bacterial species that are reproducibly detectable by culture-independent community sequencing"
Pseudomonas brassicacearum Root401 — ontology label: Pseudomonas brassicacearum NCBITaxon:930166 · TaxonMech · TraitMech N/A
  • PMID:40663585 - SUPPORT (IN_VITRO)
    "P. brassicacearum R401 was originally isolated from At Col-0 plants growing in agricultural soil and is part of the At-RSPHERE culture collection"
Variovorax sp. NCBITaxon:1871043 · TaxonMech · TraitMech DOMINANT
  • doi:10.1038/nature16192 - SUPPORT (IN_VITRO)
    "We established Arabidopsis leaf- and root-derived microbiota culture collections representing the majority of bacterial species that are reproducibly detectable by culture-independent community sequencing"
Rhodococcus sp. — ontology label: Rhodococcus <high G+C Gram-positive bacteria> NCBITaxon:1827 · TaxonMech · TraitMech COMMON
  • doi:10.1038/nature16192 - SUPPORT (IN_VITRO)
    "We established Arabidopsis leaf- and root-derived microbiota culture collections representing the majority of bacterial species that are reproducibly detectable by culture-independent community sequencing"
Streptomyces sp. NCBITaxon:1931 · TaxonMech · TraitMech COMMON
  • doi:10.1038/nature16192 - SUPPORT (IN_VITRO)
    "We established Arabidopsis leaf- and root-derived microbiota culture collections representing the majority of bacterial species that are reproducibly detectable by culture-independent community sequencing"
Flavobacterium sp. NCBITaxon:239 · TaxonMech · TraitMech COMMON
  • doi:10.1038/nature16192 - SUPPORT (IN_VITRO)
    "We established Arabidopsis leaf- and root-derived microbiota culture collections representing the majority of bacterial species that are reproducibly detectable by culture-independent community sequencing"

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 At-RSPHERE 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

At-RSPHERE Root SynCom Recolonization

Defined root-derived bacterial mixtures recolonized living Arabidopsis plants and resembled natural root microbiota at coarse taxonomic levels. The Bai study's main root/soil mixture contained 188 isolates; this is distinct from the later 17-member AtSC5/AtSC6 assays. The graph participant list is deliberately non-exhaustive, not a verified strain roster or evidence of partner facilitation.

Target Taxon: Arabidopsis thaliana

Participating Taxa: Arabidopsis thaliana

Biological Processes:

Evidence

  • doi:10.1038/nature16192 - SUPPORT (IN_VIVO)
    "Using defined bacterial communities and a gnotobiotic Arabidopsis plant system we show that the isolates form assemblies resembling natural microbiota on their cognate host organs, but are also capable of ectopic leaf or root colonization"

R401 Exometabolite Antagonism of At-SynCom Members

Root401 DAPG/pyoverdine biosynthetic disruption decreased in-vitro antagonism against At- and Lj-derived commensals. This supports exometabolite-dependent inhibition, not a uniform reciprocal fitness cost or a verified identity for every inherited representative taxon. Only the source-established canonical Root401 entry is listed here.

Participating Taxa: Pseudomonas brassicacearum Root401

Metabolites: 2,4-diacetylphloroglucinol (CHEBI:78688 · MediaIngredientMech · CMMMech), pyoverdine (CHEBI:84046 · MediaIngredientMech · CMMMech)

Biological Processes:

Downstream Effects:
→ DAPG/Pyoverdine-Dependent AtSC6 Remodeling

PARTIAL - Root401 exometabolites support commensal inhibition and are required for the characteristic AtSC6 root-composition shift. The in-vitro inhibition magnitude did not predict individual in-planta abundance changes, so this arrow links experimentally supported processes without claiming quantitative mediation across assays.

Evidence

  • PMID:40663585 - SUPPORT (IN_VITRO)
    "we confirmed the significant decrease of antagonism toward At-derived and Lj-derived commensal bacteria used in our study"

DAPG/Pyoverdine-Dependent AtSC6 Remodeling

Wild-type Root401 changed AtSC6 composition on Col-0 roots, while the pvdY/phlD mutant lost the characteristic shift. This is a host-associated community-composition result, not reciprocal competitive harm to all members. Listed participants identify the host and invader, not all 17 community strains.

Participating Taxa: Arabidopsis thaliana, Pseudomonas brassicacearum Root401

Metabolites: 2,4-diacetylphloroglucinol (CHEBI:78688 · MediaIngredientMech · CMMMech), pyoverdine (CHEBI:84046 · MediaIngredientMech · CMMMech)

Biological Processes:

Downstream Effects:
→ R401 Root Invasion of AtSC6-Precolonized Arabidopsis

PARTIAL - the authors infer that exometabolite-dependent AtSC6 remodeling permits Root401 invasion. Mutation changes inhibition, remodeling and invasion together; it does not independently establish that the composition shift is the necessary mediator.

Evidence

  • PMID:40663585 - SUPPORT (IN_VIVO)
    "R401wt-induced remodeling of AtSC6 composition was directly linked to both invasion and disease and requires production of pyoverdine and DAPG"

R401 Root Invasion of AtSC6-Precolonized Arabidopsis

Wild-type Root401 invaded AtSC6-precolonized Arabidopsis roots by the reported relative-abundance readout; invasion was partly impaired by loss of DAPG/pyoverdine production, and At-derived communities then protected the plant. Root invasion contrasts with failed invasion of established liquid AtSC6. Competitive exclusion is an experimentally supported community phenotype in this study, but these endpoints do not establish reciprocal harm to every listed participant or identify a unique limiting resource.

Participating Taxa: Arabidopsis thaliana, Pseudomonas brassicacearum Root401

Evidence

  • PMID:40663585 - SUPPORT (IN_VIVO)
    "Inspection of R401 levels based on RA in root samples revealed that R401wt efficiently invaded roots pre-colonized by AtSC6, and this colonization phenotype was partially impaired for R401mut"
  • PMID:40663585 - SUPPORT (IN_VIVO)
    "At SynCom inability to protect against wild-type R401 (R401wt) reported above (Fig 1A) was causally linked to R401 exometabolite-mediated inhibition of AtSC5 and AtSC6 members"

Knowledge gaps & discussions (1)

KNOWLEDGE_GAP OPEN Which root-context interactions mediate exometabolite-dependent invasion, and which strains belong to each tested mixture?

Bai's large recolonization mixture and the 17-member 2025 assays are distinct systems. S1 Table gives strain/family identities but does not validate the inherited six representative taxa as their membership. The graph list is non-exhaustive. Mutant, strain-swap and dropout results support protective community effects; composition mediation and resource identity remain unresolved. Non-graph umbrella membership and medium claims are not certified by this review.

Attaches to: ecological_interactions#At-RSPHERE Root SynCom Recolonization, ecological_interactions#R401 Exometabolite Antagonism of At-SynCom Members, ecological_interactions#DAPG/Pyoverdine-Dependent AtSC6 Remodeling, ecological_interactions#R401 Root Invasion of AtSC6-Precolonized Arabidopsis

Environmental Factors

Factor Value Unit
Bacterial diversity 16 families N/A
Assembly size 5-20 members N/A
Taxonomic coverage multi-phylum N/A
Functional capacity carbon cycling and plant productivity N/A
Application plant microbiome research N/A

Growth Media

R2A Agar for bacterial isolation and maintenance (CultureMech:002706)

View in CultureMech →

pH 7.2
Temperature 28 degrees Celsius
Atmosphere AEROBIC

Composition

Component Concentration Unit CHEBI
Yeast extract · MediaIngredientMech 0.5 G_PER_L N/A
Proteose peptone no. 3 · MediaIngredientMech 0.5 G_PER_L N/A
Casamino acids · MediaIngredientMech 0.5 G_PER_L N/A
Glucose · MediaIngredientMech 0.5 G_PER_L N/A
Starch · MediaIngredientMech 0.5 G_PER_L N/A
Sodium pyruvate · MediaIngredientMech 0.3 G_PER_L N/A
K2HPO4 · MediaIngredientMech 0.3 G_PER_L N/A
MgSO4 x 7 H2O · MediaIngredientMech 0.05 G_PER_L N/A
Agar · MediaIngredientMech 15 G_PER_L N/A

Preparation notes: Low-nutrient medium used for isolation and maintenance of soil and rhizosphere bacteria from Arabidopsis roots. R2A supports slow-growing oligotrophic bacteria common in soil environments.

Evidence

doi:10.1038/nature16192

"We established Arabidopsis leaf- and root-derived microbiota culture collections representing the majority of bacterial species that are reproducibly detectable by culture-independent community sequencing"

Half-strength Murashige-Skoog medium for Arabidopsis growth (CultureMech:015433)

View in CultureMech →

pH 5.7
Temperature 22 degrees Celsius

Composition

Component Concentration Unit CHEBI
Murashige-Skoog basal salts · MediaIngredientMech 0.5 x (half-strength) N/A
Sucrose · MediaIngredientMech 1 % CHEBI:17992
Agar · MediaIngredientMech 0.8 % N/A

Preparation notes: Gnotobiotic plant growth system with 0.5× MS medium supplemented with 1% sucrose and 0.8% agar. Seeds surface-sterilized prior to inoculation. Plates oriented vertically to allow root observation and bacterial colonization tracking.

Evidence

doi:10.1038/nature16192

"Using defined bacterial communities and a gnotobiotic Arabidopsis plant system we show that the isolates form assemblies resembling natural microbiota on their cognate host organs, but are also capable of ectopic leaf or root colonization"

Cross-Mech Suite Links

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

HabitatMech: rhizosphere ↗ TaxonMech: Arabidopsis thaliana ↗ TraitMech: Arabidopsis thaliana ↗ TaxonMech: Pseudomonas sp. ↗ TraitMech: Pseudomonas sp. ↗ TaxonMech: Pseudomonas brassicacearum Root401 ↗ TraitMech: Pseudomonas brassicacearum Root401 ↗ TaxonMech: Variovorax sp. ↗ TraitMech: Variovorax sp. ↗ TaxonMech: Rhodococcus sp. ↗ TraitMech: Rhodococcus sp. ↗ TaxonMech: Streptomyces sp. ↗ TraitMech: Streptomyces sp. ↗ CultureMech Growth Media ↗ PathwayMech Pathways ↗