A 16-member synthetic soil community from switchgrass-associated soil, optimized for reproducible in vitro and EcoFAB plant-microbe experiments.
Taxonomy
| Taxon | Ontology ID | Functional Roles | Abundance |
|---|---|---|---|
| soil bacterial SynCom members — ontology label: Bacteria | NCBITaxon:2 · TaxonMech · TraitMech | N/A | |
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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.
Low-Nutrient Alpha-Diversity Enrichment
In the initial equally mixed 18-strain community, dilution from 1X to 0.2X or 0.1X R2A lowered total OD600 while increasing Shannon diversity and evenness after three days. Pseudomonas remained relatively dominant. This assay preceded the final 16-member model and does not demonstrate increased absolute viable abundance, partner-specific facilitation or the same response in every community variant.
Participating Taxa: soil bacterial SynCom members
Biological Processes:
- growth (GO:0040007 · PathwayMech)
Evidence
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PMID:36472419 - SUPPORT (IN_VITRO)"the Shannon diversity index and Pielou’s evenness, two α-diversity metrics, were lowest in the 1× medium and increased as the medium dilution increased"
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PMID:36472419 - SUPPORT (IN_VITRO)"an equally mixed community of all 18 strains"
Starting-Ratio Dependent Community Diversity
Adjusting inoculum ratios to favor organisms that became relatively rare in equal mixtures increased Shannon diversity and evenness at two and six days in the tested panels, particularly 2X/3X cutoff communities without Pseudomonas. These are defined starting-composition effects, not a universal optimum or proof of a unique competition mechanism. The 17/18-strain starting-ratio panels and later 16-member dropout experiments are distinct; relative sequencing is not a direct viable-cell count.
Participating Taxa: soil bacterial SynCom members
Biological Processes:
- growth (GO:0040007 · PathwayMech)
Evidence
-
PMID:36472419 - SUPPORT (IN_VITRO)"Starting ratios containing orders of magnitude more of slower-growing organisms (2× cutoff and 3× cutoff) resulted in higher Shannon diversity and evenness values than did the 4 equally mixed conditions"
EcoFAB Brachypodium Rhizosphere Colonization
Equal mixtures of 17 or 18 isolates, without or with Pseudomonas, were inoculated onto 12-day-old Brachypodium in EcoFABs and profiled seven days later. Root-associated community composition differed from the inoculum. These are plant-colonization observations, not demonstrated reciprocal benefit; the single inoculum batch limits taxon-level before/after significance tests. Pseudomonas presence did not significantly change overall EcoFAB composition, unlike the in-vitro diversity response.
Participating Taxa: soil bacterial SynCom members
Biological Processes:
- biological process involved in interspecies interaction between organisms (GO:0044419 · PathwayMech)
Evidence
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PMID:36472419 - SUPPORT (IN_VIVO)"The SynComs grown on plants were significantly different from the original inoculant, as determined by the Bray-Curtis distance"
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PMID:36472419 - SUPPORT (IN_VIVO)"an equally mixed community of 17 or 18 bacterial isolates"
Knowledge gaps & discussions (1)
KNOWLEDGE_GAP OPEN Which interactions explain diversity responses within each defined SynCom variant?
Remove automated assembly and cryopreservation as ecological graph nodes, without rejecting their positive methodological results: automated assembly generally reduced between-assembler variation, and glycerol/R2A regrowth resembled unfrozen controls. Nutrient tests used 18 strains, ratio panels included/excluded Pseudomonas, and EcoFAB Methods specifies 17 or 18 isolates; these are not interchangeable with the final 16-member model excluding Pseudomonas and Sphingomonas. Taxon-dropout experiments support additional diversity effects, while proposed Lysobacter facilitation and three-fast-grower competition remain mechanistic interpretations, not new curated arrows. Relic-DNA controls and DNA spike-ins do not make all abundance values viable-cell counts. Canonical Bacteria remains an aggregate placeholder; #1548 tracks roster and non-graph metadata. Full main text/captions were read, not original images, separate supplements or raw data.
Attaches to: ecological_interactions#Low-Nutrient Alpha-Diversity Enrichment, ecological_interactions#Starting-Ratio Dependent Community Diversity, ecological_interactions#EcoFAB Brachypodium Rhizosphere Colonization
Environmental Factors
| Factor | Value | Unit |
|---|---|---|
| defined synthetic community design | Bottom-up assembly of 16 culturable soil microorganisms commonly found in plant rhizospheres, with tuned inoculum ratios and cryopreservation. | N/A |
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Growth Media
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