At-RSPHERE SynCom - CommunityMech

Community ID CommunityMech:000003

Ecological State ENGINEERED

Environment rhizosphere
ENVO:00005801

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	PRIMARY_PRODUCER	N/A
Pseudomonas sp.	NCBITaxon:306	SYNTROPHIC_PARTNER	DOMINANT
Variovorax sp.	NCBITaxon:1871043	SYNTROPHIC_PARTNER	DOMINANT
Rhodococcus sp.	NCBITaxon:1827	SYNTROPHIC_PARTNER	COMMON
Streptomyces sp.	NCBITaxon:1931	SYNTROPHIC_PARTNER	COMMON
Flavobacterium sp.	NCBITaxon:239	SYNTROPHIC_PARTNER	COMMON

Ecological Interactions

Taxon

Cross-feeding

Mutualism

Syntrophy

Competition

Commensalism

Plant-Microbe Mutualism

MUTUALISM

Source Taxon: Pseudomonas sp.

Target Taxon: Arabidopsis thaliana

Biological Processes:

symbiotic process (GO:0044403)
root system development (GO:0022622)
plant-bacterium mutualism (GO:0044403)

Evidence

doi:10.1038/nature16192 - SUPPORT (IN_VITRO)

"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"

Carbon Cycling and Nutrient Exchange

MUTUALISM

Source Taxon: Variovorax sp.

Target Taxon: Arabidopsis thaliana

Biological Processes:

carbon utilization (GO:0015976)
nutrient acquisition (GO:0006810)
plant-bacterium mutualism (GO:0044403)

Evidence

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"

Root Colonization and Microbiota Assembly

MUTUALISM

Source Taxon: Rhodococcus sp.

Target Taxon: Arabidopsis thaliana

Biological Processes:

interspecies interaction between organisms (GO:0044419)
biofilm formation (GO:0042710)

Evidence

doi:10.1038/nature16192 - SUPPORT (IN_VITRO)

"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"

Bioactive Metabolite Production and Plant Growth Promotion

MUTUALISM

Source Taxon: Streptomyces sp.

Target Taxon: Arabidopsis thaliana

Biological Processes:

secondary metabolite biosynthetic process (GO:0044550)
plant-bacterium mutualism (GO:0044403)

Evidence

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"

Organic Matter Degradation and Nutrient Cycling

MUTUALISM

Source Taxon: Flavobacterium sp.

Target Taxon: Arabidopsis thaliana

Biological Processes:

organic substance metabolic process (GO:0071704)
plant-bacterium mutualism (GO:0044403)

Evidence

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"

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)

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pH 7.2

Temperature 28 degrees Celsius

Atmosphere AEROBIC

Composition

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

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pH 5.7

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 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"