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Lotus Lj-SC3 Synthetic Community

Community ID CommunityMech:000040
Ecological State ENGINEERED
Environment rhizosphere
ENVO:00005801 · HabitatMech ↗

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 — ontology label: Mesorhizobium NCBITaxon:68287 · TaxonMech · TraitMech
NITROGEN_FIXING_SYMBIONT
DOMINANT
  • 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"
Mesorhizobium sp. LjNodule215 — ontology label: Mesorhizobium NCBITaxon:68287 · TaxonMech · TraitMech
NITROGEN_FIXING_SYMBIONT
COMMON
  • 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"
Mesorhizobium sp. LjNodule218 — ontology label: Mesorhizobium NCBITaxon:68287 · TaxonMech · TraitMech
NITROGEN_FIXING_SYMBIONT
COMMON
  • 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"
Phyllobacteriaceae bacterium NCBITaxon:1871068 · TaxonMech · TraitMech
SYNTROPHIC_PARTNER
ABUNDANT
  • 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"
Rhizobiaceae bacterium NCBITaxon:1913961 · TaxonMech · TraitMech
SYNTROPHIC_PARTNER
ABUNDANT
  • 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"
Burkholderiaceae bacterium NCBITaxon:2030806 · TaxonMech · TraitMech
SYNTROPHIC_PARTNER
COMMON
  • 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"
Oxalobacteriaceae bacterium — ontology label: Oxalobacteraceae NCBITaxon:75682 · TaxonMech · TraitMech
SYNTROPHIC_PARTNER
COMMON
  • 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"
Pseudomonadaceae bacterium NCBITaxon:1914538 · TaxonMech · TraitMech
SYNTROPHIC_PARTNER
COMMON
  • 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"
Microbacteriaceae bacterium NCBITaxon:1873462 · TaxonMech · TraitMech
SYNTROPHIC_PARTNER
COMMON
  • 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"
Lotus japonicus NCBITaxon:34305 · TaxonMech · TraitMech
PRIMARY_PRODUCER
N/A
  • 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"

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 Lotus Lj-SC3 Synthetic Community 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

Cognate-host preference of commensal SynComs

In living-host FlowPots, mixed LjAt-SC3 commensal communities preferentially colonized roots of their cognate Lotus or Arabidopsis host. The SC3 mono-association experiment did not reproduce this preference. This supports community-context dependence, not facilitation by a particular strain or reciprocal benefit. The sole listed canonical participant is the Lotus host: the current bacterial roster is not a verified SC3 membership list, and Arabidopsis is missing. Broader SC1 exudate and SC2 experiments are not silently relabeled SC3.

Participating Taxa: Lotus japonicus

Biological Processes:

Evidence

  • PMID:34312531 - SUPPORT (IN_VIVO)
    "commensal SynComs preferentially colonized roots of their cognate host"

Resident-community priority effect

SC3 experiment L established communities for four weeks, then challenged them with the complementary host-derived SynCom and harvested two weeks later. Early arrivals retained higher relative proportions in roots and rhizosphere than late arrivals. Arrival order affects assembly, but does not demonstrate absolute exclusion, final equilibrium, selective resource preemption or host-feedback mediation. Secondary inoculation did not significantly increase total bacterial load. The listed Lotus host is only the securely grounded canonical subset, not the microbial roster.

Participating Taxa: Lotus japonicus

Biological Processes:

Evidence

  • PMID:34312531 - SUPPORT (IN_VIVO)
    "early-arriving SynComs invariably reached higher proportions"

Cognate-Root Invasion Advantage Associated With Host Preference

In SC3 experiment L, host-derived SynComs invaded resident communities more successfully in cognate roots than in the other host; that differential invasion advantage was absent in rhizosphere samples. Strain-level host-preference and invasiveness indices were strongly correlated in roots, not the rhizosphere. This is an association, not selective manipulation of host preference establishing it as the causal mediator. Early-arrival advantages persisted, and later equilibrium was not established. The listed Lotus host does not imply complete microbial or comparator-host coverage.

Participating Taxa: Lotus japonicus

Biological Processes:

Evidence

  • PMID:34312531 - SUPPORT (IN_VIVO)
    "correlation between host preference and invasiveness"

Knowledge gaps & discussions (1)

KNOWLEDGE_GAP OPEN Which host and microbial processes mediate SC3 preference and invasion, and which strains belong to SC3?

Retain living-host preference, priority effects and differential root invasion; remove correlation and standing-community-context arrows. Niche preemption, host feedback and unfilled niches are hypotheses. Relative abundance is not absolute exclusion; lack of a significant total-load increase is not proof of invariant abundance. SC1 millifluidic exudates, SC2 experiments, SC3 competition/invasion and mono-associations must remain distinct. Full primary main body and captions read, not original figure pixels, raw data or separate supplements. Public Europe PMC supplemental download timed out after90s with an incomplete archive; no supplement contents certified. Only the canonical Lotus host is confidently grounded for these nodes; the three listed nodule isolates and family-associated bacterium IDs are not validated as the16 SC3 members. Omitted entries expose connectivity warnings rather than being silently certified. #1559 tracks roster/metadata repair, alongside existing #497/#1082.

Attaches to: ecological_interactions#Cognate-host preference of commensal SynComs, ecological_interactions#Resident-community priority effect, ecological_interactions#Cognate-Root Invasion Advantage Associated With Host Preference

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)

View in CultureMech →

pH 7.0
Temperature 28 degrees Celsius
Atmosphere AEROBIC

Composition

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

View in CultureMech →

pH 6.5
Temperature 21 degrees Celsius

Composition

Component Concentration Unit CHEBI
Calcium chloride · MediaIngredientMech 1 mM CHEBI:3312
Magnesium sulfate · MediaIngredientMech 0.5 mM CHEBI:32599
Potassium phosphate · MediaIngredientMech 0.7 mM CHEBI:131527
Iron-EDTA · MediaIngredientMech 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"

Cross-Mech Suite Links

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

HabitatMech: rhizosphere ↗ TaxonMech: Mesorhizobium sp. LjNodule210 ↗ TraitMech: Mesorhizobium sp. LjNodule210 ↗ TaxonMech: Mesorhizobium sp. LjNodule215 ↗ TraitMech: Mesorhizobium sp. LjNodule215 ↗ TaxonMech: Mesorhizobium sp. LjNodule218 ↗ TraitMech: Mesorhizobium sp. LjNodule218 ↗ TaxonMech: Phyllobacteriaceae bacterium ↗ TraitMech: Phyllobacteriaceae bacterium ↗ TaxonMech: Rhizobiaceae bacterium ↗ TraitMech: Rhizobiaceae bacterium ↗ TaxonMech: Burkholderiaceae bacterium ↗ TraitMech: Burkholderiaceae bacterium ↗ CultureMech Growth Media ↗ PathwayMech Pathways ↗