Lotus Lj-SC3 Synthetic Community

Community ID CommunityMech:000040

Ecological State ENGINEERED

Environment rhizosphere
ENVO:00005801

A 16-member synthetic community (Lj-SC3) derived from Lotus japonicus roots and nodules, designed to study host preference and community assembly dynamics in legume-microbe interactions. The community represents bacterial families from the Lj-SPHERE culture collection, including nitrogen-fixing symbionts from Rhizobiaceae and Phyllobacteriaceae families, as well as commensal bacteria from Burkholderiaceae, Oxalobacteriaceae, Pseudomonadaceae, and Microbacteriaceae. This community exhibits host preference when co-inoculated with Arabidopsis-derived strains, preferentially colonizing Lotus roots in a community context. The SC3 community enables investigation of nitrogen fixation, nodulation, priority effects during microbiota assembly, and bacterial invasiveness in the rhizosphere.

Taxonomy

Taxon	Ontology ID	Functional Roles	Abundance
Mesorhizobium sp. LjNodule210	NCBITaxon:68287	PRIMARY_PRODUCER	DOMINANT
Mesorhizobium sp. LjNodule215	NCBITaxon:68287	PRIMARY_PRODUCER	COMMON
Mesorhizobium sp. LjNodule218	NCBITaxon:68287	PRIMARY_PRODUCER	COMMON
Phyllobacteriaceae bacterium	NCBITaxon:1871068	SYNTROPHIC_PARTNER	ABUNDANT
Rhizobiaceae bacterium	NCBITaxon:1913961	SYNTROPHIC_PARTNER	ABUNDANT
Burkholderiaceae bacterium	NCBITaxon:2030806	SYNTROPHIC_PARTNER	COMMON
Oxalobacteriaceae bacterium	NCBITaxon:75682	SYNTROPHIC_PARTNER	COMMON
Pseudomonadaceae bacterium	NCBITaxon:1914538	SYNTROPHIC_PARTNER	COMMON
Microbacteriaceae bacterium	NCBITaxon:1873462	SYNTROPHIC_PARTNER	COMMON
Lotus japonicus	NCBITaxon:34305	PRIMARY_PRODUCER	N/A

Ecological Interactions

Taxon

Cross-feeding

Mutualism

Syntrophy

Competition

Commensalism

Symbiotic Nitrogen Fixation

MUTUALISM

Source Taxon: Mesorhizobium sp. LjNodule210

Target Taxon: Lotus japonicus

Metabolites: dinitrogen (CHEBI:17997), ammonia (CHEBI:16134)

Biological Processes:

nitrogen fixation (GO:0009399)
nodulation (GO:0009877)
symbiotic process (GO:0044403)

Evidence

PMID:34312531 - SUPPORT (IN_VITRO)

"Sequential inoculation experiments revealed priority effects during root microbiota assembly, where established communities are resilient to invasion by latecomers, and that host preference of commensal bacteria confers a competitive advantage in their cognate host"

Host Preference and Selective Colonization

MUTUALISM

Source Taxon: Phyllobacteriaceae bacterium

Target Taxon: Lotus japonicus

Biological Processes:

symbiotic process (GO:0044403)
root colonization (GO:0044409)

Evidence

PMID:34312531 - SUPPORT (IN_VITRO)

"Sequential inoculation experiments revealed priority effects during root microbiota assembly, where established communities are resilient to invasion by latecomers, and that host preference of commensal bacteria confers a competitive advantage in their cognate host"

Priority Effects and Community Assembly

COMPETITION

Source Taxon: Phyllobacteriaceae bacterium

Target Taxon: Burkholderiaceae bacterium

Biological Processes:

interspecies interaction between organisms (GO:0044419)

Evidence

PMID:34312531 - SUPPORT (IN_VITRO)

"Sequential inoculation experiments revealed priority effects during root microbiota assembly, where established communities are resilient to invasion by latecomers, and that host preference of commensal bacteria confers a competitive advantage in their cognate host"

Plant Growth Promotion

MUTUALISM

Source Taxon: Rhizobiaceae bacterium

Target Taxon: Lotus japonicus

Biological Processes:

regulation of plant growth (GO:0080001)
response to nitrogen compound (GO:1901698)

Evidence

PMID:34312531 - SUPPORT (IN_VITRO)

"It remains unclear to what extent the host actively selects these communities and whether commensals are adapted to a specific plant species"

Nitrogen Fixation by Mesorhizobium LjNodule215

MUTUALISM

Source Taxon: Mesorhizobium sp. LjNodule215

Target Taxon: Lotus japonicus

Metabolites: dinitrogen (CHEBI:17997), ammonia (CHEBI:16134)

Biological Processes:

nitrogen fixation (GO:0009399)
symbiotic process (GO:0044403)

Evidence

PMID:34312531 - SUPPORT (IN_VITRO)

"To address this question, we assembled a sequence-indexed bacterial culture collection from roots and nodules of Lotus japonicus that contains representatives of most species previously identified using metagenomics"

Nitrogen Fixation by Mesorhizobium LjNodule218

MUTUALISM

Source Taxon: Mesorhizobium sp. LjNodule218

Target Taxon: Lotus japonicus

Metabolites: dinitrogen (CHEBI:17997), ammonia (CHEBI:16134)

Biological Processes:

nitrogen fixation (GO:0009399)
symbiotic process (GO:0044403)

Evidence

PMID:34312531 - SUPPORT (IN_VITRO)

"Sequential inoculation experiments revealed priority effects during root microbiota assembly, where established communities are resilient to invasion by latecomers, and that host preference of commensal bacteria confers a competitive advantage in their cognate host"

Rhizosphere Colonization by Oxalobacteriaceae

MUTUALISM

Source Taxon: Oxalobacteriaceae bacterium

Target Taxon: Lotus japonicus

Biological Processes:

plant-bacterium mutualism (GO:0044403)

Evidence

PMID:34312531 - SUPPORT (IN_VITRO)

"japonicus and Arabidopsis thaliana in a multi-species gnotobiotic system and detected signatures of host preference among commensal bacteria in a community context, but not in mono-associations"

Root Association by Pseudomonadaceae

MUTUALISM

Source Taxon: Pseudomonadaceae bacterium

Target Taxon: Lotus japonicus

Biological Processes:

plant-bacterium mutualism (GO:0044403)

Evidence

PMID:34312531 - SUPPORT (IN_VITRO)

"Sequential inoculation experiments revealed priority effects during root microbiota assembly, where established communities are resilient to invasion by latecomers, and that host preference of commensal bacteria confers a competitive advantage in their cognate host"

Commensal Colonization by Microbacteriaceae

MUTUALISM

Source Taxon: Microbacteriaceae bacterium

Target Taxon: Lotus japonicus

Biological Processes:

plant-bacterium mutualism (GO:0044403)

Evidence

PMID:34312531 - SUPPORT (IN_VITRO)

"japonicus and Arabidopsis thaliana in a multi-species gnotobiotic system and detected signatures of host preference among commensal bacteria in a community context, but not in mono-associations"

Environmental Factors

Factor	Value	Unit
Host plant species	Lotus japonicus	N/A
Nodulation status	nitrogen-fixing nodules present	N/A
Community context dependence	host preference requires multi-species community	N/A
Priority effects	invasion resistance	N/A
Taxonomic diversity	16 bacterial families	N/A
Agricultural relevance	legume-microbe symbiosis model	N/A

Growth Media

Tryptic Soy Agar (TSA) for bacterial isolation (CultureMech:008227)

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pH 7.0

Temperature 28 degrees Celsius

Atmosphere AEROBIC

Composition

Component	Concentration	Unit	CHEBI
Distilled water	1	G_PER_L	N/A
Bacto Tryptic Soy Agar (Difco)	40	G_PER_L	N/A

Preparation notes: General-purpose medium used for isolation and maintenance of bacteria from Lotus japonicus roots and nodules. Mesorhizobium and other rhizosphere bacteria cultured individually before community assembly.

Evidence

PMID:34312531

"To address this question, we assembled a sequence-indexed bacterial culture collection from roots and nodules of Lotus japonicus that contains representatives of most species previously identified using metagenomics"

Nitrogen-free B&D medium for Lotus japonicus growth (CultureMech:015437)

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pH 6.5

Temperature 21 degrees Celsius

Composition

Component	Concentration	Unit	CHEBI
Calcium chloride	1	mM	CHEBI:3312
Magnesium sulfate	0.5	mM	CHEBI:32599
Potassium phosphate	0.7	mM	CHEBI:131527
Iron-EDTA	50	μM	N/A

Preparation notes: Modified Broughton and Dilworth nitrogen-free plant nutrient medium for studying symbiotic nitrogen fixation and nodulation. Gnotobiotic system allowing visualization of root colonization and nodule formation by Mesorhizobium strains. Medium supports both nitrogen-fixing symbionts and non-nodulating commensal bacteria.

Evidence

PMID:34312531

"Sequential inoculation experiments revealed priority effects during root microbiota assembly, where established communities are resilient to invasion by latecomers, and that host preference of commensal bacteria confers a competitive advantage in their cognate host"