m-CAFEs Brachypodium Reduced Complexity Consortia

A multiplexed enrichment experiment varied root-associated inocula, carbon conditions and 3-day versus 7-day transfer intervals to generate a collection of Brachypodium-derived RCC. It is not one fixed consortium of the ten listed representative taxa. The abiotic selection treatments are experimental inputs, not direct evidence that species partition niches or reduce competition.

Evidence

• PMID:38846575 - SUPPORT (IN_VITRO)
  "We enriched co-localized microbes from Brachypodium roots grown in field soil with carbon substrates mimicking Brachypodium root exudates "
• PMID:38846575 - SUPPORT (IN_VITRO)
  "Thereafter, plates were transferred 10 times at two different intervals, 3 days and 7 days for targeting fast and slow growing microbes. "

Carbon amendments selected different ASVs in inoculum-stratified comparisons. Complex 1/10 R2A supported broad enrichment including Terriglobus and Arthrobacter; asparagine enriched Bradyrhizobium and a related rhizobial clade. The listed participants are representative named taxa, not all enriched ASVs. These relative-abundance changes do not isolate substrate consumption, microbial cooperation or reduced competition as their mechanism.

Participating Taxa: Terriglobus, Arthrobacter, Bradyrhizobium

Biological Processes:

• growth (GO:0040007 · PathwayMech)

Evidence

• PMID:38846575 - SUPPORT (IN_VITRO)
  "1/10 R2A had the highest potential to enrich ASVs compared to other carbon sources "
• PMID:38846575 - SUPPORT (IN_VITRO)
  "significantly enriched ASVs from genera Bradyrhizobium and Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium "

For a fixed carbon source and original inoculum, ASVs more abundant after 7-day transfers than 3-day transfers were called slow growers, and the converse were called fast growers. The comparison used generations 6 and 9. These are operational relative-abundance classes, not measured isolate growth rates; transfer duration also changes other ecological conditions. The reported capacity of 1/10 R2A, asparagine and glucuronic acid to enrich both classes is retained. Network-hub genera are not substituted for the set of ASVs in this differential-abundance analysis.

Biological Processes:

• growth (GO:0040007 · PathwayMech)

Evidence

• PMID:38846575 - SUPPORT (IN_VITRO)
  "microbes significantly more abundant in 7-day interval samples compared to 3-day interval samples were categorized as "
• PMID:38846575 - SUPPORT (IN_VITRO)
  "1/10 R2A medium, along with asparagine and glucuronic acid, demonstrated the greatest capability to enrich both slow and fast-growing microbes "

NetCoMi Pearson-correlation analysis of core ASVs in the 1/10 R2A enrichments identified different high-eigenvector-centrality hubs in 3-day and 7-day networks. The named taxa are representative reported hubs, including the Methylobacterium-Methylorubrum source clade, not an exhaustive community roster. Association centrality does not establish ecological niche partitioning, directly measured growth rate, keystone necessity or plant-growth promotion by those ASVs.

Participating Taxa: Methylobacterium, Stenotrophomonas, Pseudomonas, Terriglobus, Arthrobacter

Evidence

• PMID:38846575 - SUPPORT (COMPUTATIONAL)
  "ASVs belong to genus Methylobacterium-Methylorubrum, Stenotrophomonas, Pseudomonas are hubs for 3-day interval transfers "
• PMID:38846575 - SUPPORT (COMPUTATIONAL)
  "ASVs from family Rhizobiaceae, genus Lactobacillus, Terriglobus, and Arthrobacter are hubs for 7-day interval transfers "
• PMID:38846575 - SUPPORT (COMPUTATIONAL)
  "The hub node (keystone taxa) is identified if the node’s eigenvector centrality value is above the 90% quantile."

Adjacent-generation network comparisons identified recurring hub taxa, including Paenibacillus, Sphingomonas, Mucilaginibacter and Terriglobus. This is persistence of a statistical hub designation across sampled transfers, not a taxon-removal test of community stability or direct measurement of niche partitioning. Inferred importance and PGP traits known for related genera are not validated functions of every enriched ASV.

Participating Taxa: Paenibacillus, Sphingomonas, Mucilaginibacter, Terriglobus

Evidence

• PMID:38846575 - SUPPORT (COMPUTATIONAL)
  "certain keystone species, including members of the Rhizobiaceae family and the genera Paenibacillus, Sphingomonas, Mucilaginibacter, and Terriglobus, were consistent across multiple generations "

Five selected 1/10 R2A RCC stocks were revived and serially propagated, with broadly consistent dominant genera and relative abundances in those tests. This does not establish universal revival of all initial enrichments, exact strain-level identity, or retention of every rare taxon. Burkholderia and Mesorhizobium were shared statistical hubs in the revived-stock networks, not demonstrated causes of revival. The original broad 1/10 R2A enrichments were less stable than most other carbon arms; that result is distinct from stability of these five selected stocks.

Biological Processes:

• growth (GO:0040007 · PathwayMech)

Evidence

• PMID:38846575 - SUPPORT (IN_VITRO)
  "dominant genera from the glycerol stocks (>0.5% in at least one sample) and their relative abundances remained consistent between transfers "
• PMID:38846575 - SUPPORT (COMPUTATIONAL)
  "Genus Burkholderia and Mesorhizobium were shared keystone taxa among 3-day and 7-day intervals "