Jeff Dangl's SynComm 35 - CommunityMech

Community ID CommunityMech:000022

Ecological State ENGINEERED

Environment rhizosphere
ENVO:00005801

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	PRIMARY_PRODUCER	N/A
Dyella japonica MF79	NCBITaxon:231455	SYNTROPHIC_PARTNER	COMMON
Xanthomonadales members	NCBITaxon:135614	SYNTROPHIC_PARTNER	COMMON
Pseudomonas species	NCBITaxon:286	SYNTROPHIC_PARTNER	COMMON
Flavobacterium species	NCBITaxon:237	SYNTROPHIC_PARTNER	COMMON
Stenotrophomonas species	NCBITaxon:40323	SYNTROPHIC_PARTNER	COMMON
Microbacterium species	NCBITaxon:33882	SYNTROPHIC_PARTNER	COMMON
Escherichia coli DH5α	NCBITaxon:668369	CROSS_FEEDER	COMMON

Ecological Interactions

Taxon

Cross-feeding

Mutualism

Syntrophy

Competition

Commensalism

MAMP-Triggered Immunity Suppression

COMMENSALISM

Source Taxon: Dyella japonica MF79

Target Taxon: Arabidopsis thaliana

Biological Processes:

pattern recognition receptor signaling pathway (GO:0002221)
defense response to bacterium (GO:0042742)
regulation of innate immune response (GO:0045088)

Evidence

doi:10.1073/pnas.2100678118 - SUPPORT (IN_VITRO)

"Significance In natural environments, plants establish intimate interactions with a wide diversity of microbes"

WRKY Transcription Factor Suppression

COMMENSALISM

Source Taxon: Dyella japonica MF79

Target Taxon: Arabidopsis thaliana

Biological Processes:

regulation of defense response (GO:0031347)
regulation of transcription, DNA-templated (GO:0006355)

Evidence

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"

Type II Secretion-Mediated Immune Modulation

COMMENSALISM

Source Taxon: Dyella japonica MF79

Biological Processes:

protein secretion (GO:0009306)
modulation by symbiont of host defense response (GO:0052031)

Evidence

doi:10.1073/pnas.2100678118 - SUPPORT (IN_VITRO)

"We highlight the role of a specific sector of the plant immune system and its suppression in gating microbial access to the roots."

Enhanced Colonization Through Community Cooperation

MUTUALISM

Source Taxon: Dyella japonica MF79

Target Taxon: Pseudomonas species

Biological Processes:

interspecies interaction between organisms (GO:0044419)

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"

Taxonomic Diversity Enabling Functional Complementarity

MUTUALISM

Source Taxon: Xanthomonadales members

Target Taxon: Flavobacterium species

Biological Processes:

interspecies interaction between organisms (GO:0044419)

Evidence

doi:10.1073/pnas.2100678118 - SUPPORT (IN_VITRO)

"Significance In natural environments, plants establish intimate interactions with a wide diversity of microbes"

Community Member Metabolic Cooperation

CROSS_FEEDING

Source Taxon: Microbacterium species

Target Taxon: Stenotrophomonas species

Metabolites: amino-acid (CHEBI:33709)

Biological Processes:

interspecies interaction between organisms (GO:0044419)

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"

Negative Control Strain Baseline Response

COMPETITION

Source Taxon: Escherichia coli DH5α

Target Taxon: Dyella japonica MF79

Biological Processes:

defense response to bacterium (GO:0042742)

Evidence

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"

Environmental Factors

Factor	Value	Unit
MAMP Treatment	flg22 (flagellin epitope)	nM or µM
Plant Age	7 days	N/A
Colonization Period	12-14 days	N/A
Growth Conditions	axenic	N/A
Immune Response Type	Pattern-triggered immunity (PTI/MTI)	N/A
Suppressor Classification	10 robust, 13 partial, 11 non-suppressors	N/A

Growth Media

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

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pH 7.3

Temperature 28 degrees Celsius

Atmosphere AEROBIC

Composition

Component	Concentration	Unit	CHEBI
Distilled water	1	G_PER_L	N/A
Bacto Tryptic Soy Broth (Difco)	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 synthetic bacterial community."

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

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pH 5.8

Temperature 22 degrees Celsius

Composition

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