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Jeff Dangl's SynComm 35

Community ID CommunityMech:000022
Ecological State ENGINEERED
Environment rhizosphere
ENVO:00005801 · HabitatMech ↗

A 35-member synthetic community (SynComm 35) composed of genome-sequenced bacterial strains representing typical taxonomic diversity of Arabidopsis root commensals. This community was designed to interrogate plant immune responses, particularly pattern-triggered immunity (PTI/MTI). Of the 35 members, 10 are robust suppressors of MAMP-triggered immunity (flg22 response), 13 are partial suppressors, and 11 are non-suppressors. The community includes 32 strains isolated from Brassicaceae roots (mainly Arabidopsis), 2 strains from unplanted soil, and E. coli DH5α as a control. SynComm 35 collectively suppresses specific transcriptional sectors of plant immunity, particularly WRKY transcription factors, receptor-like kinases, and secondary metabolite biosynthesis genes, while suppressors achieve enhanced colonization capacity.

Taxonomy

Taxon Ontology ID Functional Roles Abundance
Arabidopsis thaliana NCBITaxon:3702 · TaxonMech · TraitMech
PRIMARY_PRODUCER
N/A
  • doi:10.1073/pnas.2100678118 - SUPPORT (IN_VITRO)
    "It is unknown, however, how microbiota composed of commensal bacteria colonize roots in the face of a sophisticated plant immune system that evolved to recognize microbial-associated molecular patterns"
Dyella japonica MF79 — ontology label: Dyella japonica NCBITaxon:231455 · TaxonMech · TraitMech
SYNTROPHIC_PARTNER
COMMON
  • doi:10.1073/pnas.2100678118 - SUPPORT (IN_VITRO)
    "It is unknown, however, how microbiota composed of commensal bacteria colonize roots in the face of a sophisticated plant immune system that evolved to recognize microbial-associated molecular patterns"
Xanthomonadales members — ontology label: Lysobacterales NCBITaxon:135614 · TaxonMech · TraitMech
SYNTROPHIC_PARTNER
COMMON
  • doi:10.1073/pnas.2100678118 - SUPPORT (IN_VITRO)
    "It is unknown, however, how microbiota composed of commensal bacteria colonize roots in the face of a sophisticated plant immune system that evolved to recognize microbial-associated molecular patterns"
Pseudomonas species — ontology label: Pseudomonas NCBITaxon:286 · TaxonMech · TraitMech
SYNTROPHIC_PARTNER
COMMON
  • doi:10.1073/pnas.2100678118 - SUPPORT (IN_VITRO)
    "We report that root-associated commensal bacteria actively suppress the host immune response in the context of a community"
Flavobacterium species — ontology label: Flavobacterium NCBITaxon:237 · TaxonMech · TraitMech
SYNTROPHIC_PARTNER
COMMON
  • doi:10.1073/pnas.2100678118 - SUPPORT (IN_VITRO)
    "It is unknown, however, how microbiota composed of commensal bacteria colonize roots in the face of a sophisticated plant immune system that evolved to recognize microbial-associated molecular patterns"
Stenotrophomonas species — ontology label: Stenotrophomonas NCBITaxon:40323 · TaxonMech · TraitMech
SYNTROPHIC_PARTNER
COMMON
Microbacterium species — ontology label: Microbacterium NCBITaxon:33882 · TaxonMech · TraitMech
SYNTROPHIC_PARTNER
COMMON
Escherichia coli DH5α — ontology label: Escherichia coli DH5[alpha] NCBITaxon:668369 · TaxonMech · TraitMech
CROSS_FEEDER
COMMON
  • doi:10.1073/pnas.2100678118 - SUPPORT (IN_VITRO)
    "We report that root-associated commensal bacteria actively suppress the host immune response in the context of a community"

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 Jeff Dangl's SynComm 35 Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for colonization facilitation. Rare or untyped interactions share the Other symbol; exact curated types remain in the interaction details.
Taxon
Colonization facilitation
Other

Root flg22 Immune Suppression

Live SynCom35 suppresses a sector of the Arabidopsis root flg22 response after establishment. Dyella MF79 is one tested suppressor, not the sole cause of whole-community transcriptional changes. Participants name the host and this canonical member, not the complete 35-strain roster.

Participating Taxa: Arabidopsis thaliana, Dyella japonica MF79

Biological Processes:

Downstream Effects:
→ Suppression-Associated Root Colonization Facilitation

Suppression can facilitate nonsuppressor root colonization under the tested conditions. MF79 wild-type retentate, unlike T2SS-mutant material, countered the flg22-associated reduction in Ochrobactrum MF370 colonization. This does not establish universal facilitation by every suppressor or reciprocal benefit.

Evidence

  • PMID:33879573 - SUPPORT (IN_VITRO)
    "a community of root commensal bacteria modulates a specific and evolutionarily conserved sector of the Arabidopsis immune system"

Community-Associated WRKY Transcript Suppression

SynCom35 suppressed flg22-responsive WRKY transcripts. The host and MF79 participants represent a known subset of the inoculated system, not a demonstrated MF79-specific WRKY mechanism. A regulatory role in colonization homeostasis remains proposed.

Participating Taxa: Arabidopsis thaliana, Dyella japonica MF79

Biological Processes:

Evidence

  • PMID:33879573 - PARTIAL (IN_VITRO)
    "a community of root commensal bacteria modulates a specific and evolutionarily conserved sector of the Arabidopsis immune system"

MF79 Type II Secretion-Dependent Immune Modulation

MF79 secretion-system mutants and cell-free supernatants support T2SS-dependent suppression of the root flg22 response; T3SS was dispensable. The active secreted molecule remains unresolved. This strain-specific requirement is not assigned to every SynCom35 member.

Source Taxon: Dyella japonica MF79

Target Taxon: Arabidopsis thaliana

Biological Processes:

Downstream Effects:
→ Root flg22 Immune Suppression

MF79 T2SS function enables its extracellular suppressive activity in the root reporter assay. This arrow applies to the MF79 component of the suppression node, not necessity of T2SS for the entire SynCom35 phenotype.

Evidence

  • PMID:33879573 - SUPPORT (IN_VITRO)
    "We highlight the importance of extracellular strategies for MTI suppression by showing that the type 2, not the type 3, secretion system is required for the immunomodulatory activity of one robust MTI suppressor"

Suppression-Associated Root Colonization Facilitation

COLONIZATION_FACILITATION

Suppressor-community precolonization enhanced subsequent colonization by tested nonsuppressors; MF79 retentate separately supported Ochrobactrum MF370 under flg22 challenge. Canonical participants are only a subset: Pseudomonas denotes the tested P. viridiflava challenge lineage, not a proven MF79/Pseudomonas mutualism.

Participating Taxa: Arabidopsis thaliana, Dyella japonica MF79, Pseudomonas species

Biological Processes:

Evidence

  • doi:10.1073/pnas.2100678118 - SUPPORT (IN_VITRO)
    "Suppressors and nonsuppressors co-occur in the root microbiome and the presence of the former can enhance the colonization ability of the latter"

Knowledge gaps & discussions (1)

KNOWLEDGE_GAP OPEN Which secreted factors and host regulators mediate strain-specific colonization effects?

Effector identity, causal WRKY mediation and complete canonical strain coverage remain unresolved. The three removed nodes lacked evidence for their asserted relationships; absence of support is not evidence that all such mechanisms are biologically impossible. Supplementary methods/rosters were not retrieved. Neither the removed E. coli control phenotype nor metabolic exchange is certified by this review. Non-graph follow-up: #1378.

Attaches to: ecological_interactions#Root flg22 Immune Suppression, ecological_interactions#Community-Associated WRKY Transcript Suppression, ecological_interactions#MF79 Type II Secretion-Dependent Immune Modulation, ecological_interactions#Suppression-Associated Root Colonization Facilitation

Environmental Factors

Factor Value Unit
MAMP Treatment flg22 (flagellin epitope) nM or µM
  • doi:10.1073/pnas.2100678118 - SUPPORT (IN_VITRO)
    "It is unknown, however, how microbiota composed of commensal bacteria colonize roots in the face of a sophisticated plant immune system that evolved to recognize microbial-associated molecular patterns"
Plant Age 7 days N/A
  • doi:10.1073/pnas.2100678118 - SUPPORT (IN_VITRO)
    "It is unknown, however, how microbiota composed of commensal bacteria colonize roots in the face of a sophisticated plant immune system that evolved to recognize microbial-associated molecular patterns"
Colonization Period 12-14 days N/A
  • doi:10.1073/pnas.2100678118 - SUPPORT (IN_VITRO)
    "Suppressors and nonsuppressors co-occur in the root microbiome and the presence of the former can enhance the colonization ability of the latter"
Growth Conditions axenic N/A
  • doi:10.1073/pnas.2100678118 - SUPPORT (IN_VITRO)
    "It is unknown, however, how microbiota composed of commensal bacteria colonize roots in the face of a sophisticated plant immune system that evolved to recognize microbial-associated molecular patterns"
Immune Response Type Pattern-triggered immunity (PTI/MTI) N/A
  • doi:10.1073/pnas.2100678118 - SUPPORT (IN_VITRO)
    "We report that root-associated commensal bacteria actively suppress the host immune response in the context of a community"
Suppressor Classification 10 robust, 13 partial, 11 non-suppressors N/A
  • doi:10.1073/pnas.2100678118 - SUPPORT (IN_VITRO)
    "Suppressors and nonsuppressors co-occur in the root microbiome and the presence of the former can enhance the colonization ability of the latter"

Growth Media

Tryptic Soy Broth (TSB) for bacterial culture (CultureMech:008226)

View in CultureMech →

pH 7.3
Temperature 28 degrees Celsius
Atmosphere AEROBIC

Composition

Component Concentration Unit CHEBI
Distilled water · MediaIngredientMech 1 G_PER_L N/A
Bacto Tryptic Soy Broth (Difco) · MediaIngredientMech 30 G_PER_L N/A

Preparation notes: General-purpose rich medium used for growing individual bacterial strains from Brassicaceae roots. Cultures grown to stationary phase, washed, and resuspended in sterile water or MgCl2 solution for inoculation into gnotobiotic plant systems.

Evidence

doi:10.1073/pnas.2100678118

"We report that root-associated commensal bacteria actively suppress the host immune response in the context of a community"

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

View in CultureMech →

pH 5.8
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 Arabidopsis growth system with 0.5× MS medium, 1% sucrose, 0.8% agar. Seven-day-old seedlings inoculated with SynComm 35 bacterial suspension (OD600 0.001 per strain). Colonization monitored for 12-14 days post-inoculation.

Evidence

doi:10.1073/pnas.2100678118

"It is unknown, however, how microbiota composed of commensal bacteria colonize roots in the face of a sophisticated plant immune system that evolved to recognize microbial-associated molecular patterns"

Cross-Mech Suite Links

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

HabitatMech: rhizosphere ↗ TaxonMech: Arabidopsis thaliana ↗ TraitMech: Arabidopsis thaliana ↗ TaxonMech: Dyella japonica MF79 ↗ TraitMech: Dyella japonica MF79 ↗ TaxonMech: Xanthomonadales members ↗ TraitMech: Xanthomonadales members ↗ TaxonMech: Pseudomonas species ↗ TraitMech: Pseudomonas species ↗ TaxonMech: Flavobacterium species ↗ TraitMech: Flavobacterium species ↗ TaxonMech: Stenotrophomonas species ↗ TraitMech: Stenotrophomonas species ↗ CultureMech Growth Media ↗ PathwayMech Pathways ↗