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EcoFAB 2.0 Root Microbiome Ring Trial SynCom17

Community ID CommunityMech:000025
Ecological State ENGINEERED
Environment EcoFAB 2.0 hydroponic device — ontology label: laboratory environment
ENVO:01001405 · HabitatMech ↗

A 17-member synthetic bacterial community (SynCom17) used in a standardized inter-laboratory ring trial across five international laboratories (LBNL, UNC Chapel Hill, Max Planck Cologne, Forschungszentrum Julich, U Melbourne) to study root microbiome recruitment and exudate composition of the model grass Brachypodium distachyon in EcoFAB 2.0 fabricated ecosystem devices. All 17 members were originally isolated from switchgrass rhizosphere soil and span four bacterial phyla (Actinomycetota, Bacillota, Bacteroidota, Pseudomonadota). In the full SynCom17, Paraburkholderia sp. OAS925 reproducibly dominates root colonization (~98% relative abundance) across all five labs, uniquely possessing a Type 3 Secretion System (T3SS), high motility, and acid resistance. Removing Paraburkholderia (SynCom16) yields a more variable community dominated by Rhodococcus sp. OAS809 (~68%), Mycobacterium sp. OAE908 (~14%), and Methylobacterium sp. OAE515 (~15%). The study demonstrated that EcoFAB 2.0 with standardized protocols achieves reproducible plant phenotype, exudate, and community structure data across continents, providing benchmark datasets for plant-microbiome research.

Taxonomy

Taxon Ontology ID Functional Roles Abundance
Paraburkholderia sp. OAS925 — ontology label: Paraburkholderia NCBITaxon:1822464 · TaxonMech · TraitMech
PRIMARY_DEGRADER
DOMINANT
  • PMID:40920748 - SUPPORT (IN_VITRO)
    "Paraburkholderia sp. OAS925 could dramatically shift microbiome composition"
Rhodococcus sp. OAS809 — ontology label: Rhodococcus <high G+C Gram-positive bacteria> NCBITaxon:1827 · TaxonMech · TraitMech
PRIMARY_DEGRADER
RARE
  • PMID:40920748 - SUPPORT (IN_VITRO)
    "All participating laboratories observed consistent inoculum-dependent changes in plant phenotype, root exudate composition, and final bacterial community structure"
Mycobacterium sp. OAE908 — ontology label: Mycobacterium NCBITaxon:1763 · TaxonMech · TraitMech
PRIMARY_DEGRADER
N/A
  • PMID:40920748 - SUPPORT (IN_VITRO)
    "All participating laboratories observed consistent inoculum-dependent changes in plant phenotype, root exudate composition, and final bacterial community structure"
Methylobacterium sp. OAE515 — ontology label: Methylobacterium NCBITaxon:407 · TaxonMech · TraitMech
CROSS_FEEDER
N/A
  • PMID:40920748 - SUPPORT (IN_VITRO)
    "All participating laboratories observed consistent inoculum-dependent changes in plant phenotype, root exudate composition, and final bacterial community structure"
Variovorax sp. OAS795 — ontology label: Variovorax NCBITaxon:34072 · TaxonMech · TraitMech N/A
  • PMID:40920748 - SUPPORT (IN_VITRO)
    "All participating laboratories observed consistent inoculum-dependent changes in plant phenotype, root exudate composition, and final bacterial community structure"
Rhizobium sp. OAE497 — ontology label: Rhizobium NCBITaxon:379 · TaxonMech · TraitMech N/A
  • PMID:40920748 - SUPPORT (IN_VITRO)
    "All participating laboratories observed consistent inoculum-dependent changes in plant phenotype, root exudate composition, and final bacterial community structure"
Bosea sp. OAE506 — ontology label: Allobosea NCBITaxon:85413 · TaxonMech · TraitMech N/A
  • PMID:40920748 - SUPPORT (IN_VITRO)
    "All participating laboratories observed consistent inoculum-dependent changes in plant phenotype, root exudate composition, and final bacterial community structure"
Bradyrhizobium sp. OAE829 — ontology label: Bradyrhizobium NCBITaxon:374 · TaxonMech · TraitMech N/A
  • PMID:40920748 - SUPPORT (IN_VITRO)
    "All participating laboratories observed consistent inoculum-dependent changes in plant phenotype, root exudate composition, and final bacterial community structure"
Lysobacter sp. OAE881 — ontology label: Lysobacter NCBITaxon:68 · TaxonMech · TraitMech N/A
  • PMID:40920748 - SUPPORT (IN_VITRO)
    "All participating laboratories observed consistent inoculum-dependent changes in plant phenotype, root exudate composition, and final bacterial community structure"
Arthrobacter sp. OAP107 — ontology label: Arthrobacter sp. NCBITaxon:1667 · TaxonMech · TraitMech RARE
  • PMID:40920748 - SUPPORT (IN_VITRO)
    "All participating laboratories observed consistent inoculum-dependent changes in plant phenotype, root exudate composition, and final bacterial community structure"
Marmoricola sp. OAE513 — ontology label: Marmoricola NCBITaxon:86795 · TaxonMech · TraitMech N/A
  • PMID:40920748 - SUPPORT (IN_VITRO)
    "All participating laboratories observed consistent inoculum-dependent changes in plant phenotype, root exudate composition, and final bacterial community structure"
Chitinophaga sp. OAE865 — ontology label: Chitinophaga NCBITaxon:79328 · TaxonMech · TraitMech N/A
  • PMID:40920748 - SUPPORT (IN_VITRO)
    "All participating laboratories observed consistent inoculum-dependent changes in plant phenotype, root exudate composition, and final bacterial community structure"
Mucilaginibacter sp. OAE612 — ontology label: Mucilaginibacter NCBITaxon:423349 · TaxonMech · TraitMech N/A
  • PMID:40920748 - SUPPORT (IN_VITRO)
    "All participating laboratories observed consistent inoculum-dependent changes in plant phenotype, root exudate composition, and final bacterial community structure"
Niastella sp. OAS944 — ontology label: Niastella NCBITaxon:354354 · TaxonMech · TraitMech N/A
  • PMID:40920748 - SUPPORT (IN_VITRO)
    "All participating laboratories observed consistent inoculum-dependent changes in plant phenotype, root exudate composition, and final bacterial community structure"
Gottfriedia sp. OAE603 — ontology label: Gottfriedia NCBITaxon:2837503 · TaxonMech · TraitMech N/A
  • PMID:40920748 - SUPPORT (IN_VITRO)
    "All participating laboratories observed consistent inoculum-dependent changes in plant phenotype, root exudate composition, and final bacterial community structure"
Brevibacillus sp. OAP136 — ontology label: Brevibacillus NCBITaxon:55080 · TaxonMech · TraitMech N/A
  • PMID:40920748 - SUPPORT (IN_VITRO)
    "All participating laboratories observed consistent inoculum-dependent changes in plant phenotype, root exudate composition, and final bacterial community structure"
Paenibacillus sp. OAE614 — ontology label: Paenibacillus NCBITaxon:44249 · TaxonMech · TraitMech N/A
  • PMID:40920748 - SUPPORT (IN_VITRO)
    "All participating laboratories observed consistent inoculum-dependent changes in plant phenotype, root exudate composition, and final bacterial community structure"

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 EcoFAB 2.0 Root Microbiome Ring Trial SynCom17 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

SynCom17 EcoFAB Ring-Trial Perturbation

The full 17-member inoculum was applied to 10-day-old Brachypodium distachyon plants in EcoFAB 2.0 devices and compared with axenic plants, SynCom16 lacking OAS925, and plant-free medium controls in five laboratories. Its three downstream arrows represent whole-treatment effects on root composition, bulk spent-medium profiles and plant development, not a claim that protocol standardization itself is a biological mechanism or that every member facilitates colonization.

Participating Taxa: Paraburkholderia sp. OAS925, Rhodococcus sp. OAS809, Mycobacterium sp. OAE908, Methylobacterium sp. OAE515, Variovorax sp. OAS795, Rhizobium sp. OAE497, Bosea sp. OAE506, Bradyrhizobium sp. OAE829, Lysobacter sp. OAE881, Arthrobacter sp. OAP107, Marmoricola sp. OAE513, Chitinophaga sp. OAE865, Mucilaginibacter sp. OAE612, Niastella sp. OAS944, Gottfriedia sp. OAE603, Brevibacillus sp. OAP136, Paenibacillus sp. OAE614

Downstream Effects:
→ Paraburkholderia-Dominated SynCom17 Root Assembly

SynCom17 inoculation supplied the 17-member community from which the OAS925-dominated root profile developed by 22 DAI. The SynCom16 omission comparison supports an inoculum-composition effect, not identification of the molecular mechanism or absolute loss of the other members.

→ Treatment-Structured Rhizosphere Exometabolites

SynCom17 inoculation altered the plant-microbe system and thereby changed the measured bulk spent-medium metabolite profile relative to the control treatments. This is a treatment-level effect; microbial versus plant production, uptake and extracellular enzyme activity were not separated.

→ SynCom17 Plant Biomass and Root Development Decrease

The SynCom17 inoculation treatment reduced shoot biomass in the combined-laboratory comparison with axenic plants and reduced root development from 14 DAI onward. The experiment establishes a whole-treatment response, not OAS925-only toxicity, competition for a specific nutrient or one necessary member.

Evidence

  • PMID:40920748 - SUPPORT (IN_VITRO)
    "All participating laboratories observed consistent inoculum-dependent changes in plant phenotype, root exudate composition, and final bacterial community structure"

Paraburkholderia Acid-Tolerant Root Colonization Traits

OAS925 carried uniquely detected surveyed acid-resistance and type III secretion modules among the 17 genomes. Separate RFP-isolate plant assays showed root colonization at 1 DAI and biofilm at 3 DAI; separate culture assays showed high liquid growth and acid-tolerant motility. OAS925 was sixth, not first, in the biofilm assay. These are one-strain observations, not facilitation of another taxon. No selective gene or trait perturbation established which mechanism causes dominance in SynCom17.

Source Taxon: Paraburkholderia sp. OAS925

Downstream Effects:
→ Paraburkholderia-Dominated SynCom17 Root Assembly

HYPOTHESIZED - acid-tolerant motility, colonization traits and associated genomic modules may help OAS925 establish and expand on roots, contributing to its relative dominance. Separate isolate assays and gene annotation support candidate mechanisms, but none was selectively disrupted or rescued in the 17-member community.

Evidence

  • PMID:40920748 - SUPPORT (COMPUTATIONAL)
    "Comparative genomic analysis showed that the Paraburkholderia sp. OAS925 genome"
  • PMID:40920748 - SUPPORT (IN_VITRO)
    "Clear RFP signals were detected at the root tip and in the maturation zone at 1 DAI"

Paraburkholderia-Dominated SynCom17 Root Assembly

At 22 DAI, OAS925 accounted for about 98% of root bacterial 16S reads in SynCom17 across the five laboratories. SynCom16 lacking OAS925 had more variable relative profiles dominated by Rhodococcus, Mycobacterium and Methylobacterium. The listed participants identify the inoculum roster, not equal final abundance or proven competition. Relative read dominance does not establish extinction, absolute suppression of the other members, or mediation of the spent-medium response.

Participating Taxa: Paraburkholderia sp. OAS925, Rhodococcus sp. OAS809, Mycobacterium sp. OAE908, Methylobacterium sp. OAE515, Variovorax sp. OAS795, Rhizobium sp. OAE497, Bosea sp. OAE506, Bradyrhizobium sp. OAE829, Lysobacter sp. OAE881, Arthrobacter sp. OAP107, Marmoricola sp. OAE513, Chitinophaga sp. OAE865, Mucilaginibacter sp. OAE612, Niastella sp. OAS944, Gottfriedia sp. OAE603, Brevibacillus sp. OAP136, Paenibacillus sp. OAE614

Evidence

  • PMID:40920748 - SUPPORT (IN_VITRO)
    "the root microbiome inoculated with SynCom17 was dominated by Paraburkholderia sp. OAS925 across all laboratories"

Treatment-Structured Rhizosphere Exometabolites

Bulk spent EcoFAB medium showed treatment-dependent targeted and untargeted LC-MS profiles, including an amino-acid-rich cluster depleted under SynCom17 and other clusters elevated under SynCom17 or SynCom16. This is net extracellular abundance in a plant-microbe system, not identified donor-to-recipient cross-feeding. Plant or microbial production and uptake, and extracellular enzyme activity, remain alternative contributors; OAS925-specific amino-acid flux was not isolated.

Participating Taxa: Paraburkholderia sp. OAS925, Rhodococcus sp. OAS809, Mycobacterium sp. OAE908, Methylobacterium sp. OAE515, Variovorax sp. OAS795, Rhizobium sp. OAE497, Bosea sp. OAE506, Bradyrhizobium sp. OAE829, Lysobacter sp. OAE881, Arthrobacter sp. OAP107, Marmoricola sp. OAE513, Chitinophaga sp. OAE865, Mucilaginibacter sp. OAE612, Niastella sp. OAS944, Gottfriedia sp. OAE603, Brevibacillus sp. OAP136, Paenibacillus sp. OAE614

Metabolites: amino acid (CHEBI:33709 · MediaIngredientMech · CMMMech)

Evidence

  • PMID:40920748 - SUPPORT (IN_VITRO)
    "A second large cluster consisted of metabolites with lower relative concentrations in the SynCom17 treatment, represented mainly by amino acids"

SynCom17 Plant Biomass and Root Development Decrease

Compared with axenic plants, SynCom17 reduced shoot fresh and dry biomass in the combined-laboratory analysis and reduced root development from 14 DAI onward. SynCom16 had a smaller shoot effect. These are whole-treatment plant outcomes with laboratory variation, not a demonstrated microbial competition mechanism, direct OAS925-only effect or reciprocal symbiosis.

Participating Taxa: Paraburkholderia sp. OAS925, Rhodococcus sp. OAS809, Mycobacterium sp. OAE908, Methylobacterium sp. OAE515, Variovorax sp. OAS795, Rhizobium sp. OAE497, Bosea sp. OAE506, Bradyrhizobium sp. OAE829, Lysobacter sp. OAE881, Arthrobacter sp. OAP107, Marmoricola sp. OAE513, Chitinophaga sp. OAE865, Mucilaginibacter sp. OAE612, Niastella sp. OAS944, Gottfriedia sp. OAE603, Brevibacillus sp. OAP136, Paenibacillus sp. OAE614

Biological Processes:

Evidence

  • PMID:40920748 - SUPPORT (IN_VITRO)
    "SynCom17 caused a consistent decrease in root development observed after 14 DAI onwards"

Associated Datasets

Dataset Type Repository Accession
16S rRNA Amplicon Sequencing
16S rRNA amplicon sequencing data from all five ring trial laboratories for root and medium samples. 		AMPLICON_16S NCBI_BIOPROJECT PRJNA1151037
Untargeted Metabolomics (LC-MS/MS)
HILIC-pos untargeted metabolomics with feature annotations and .mzml files for root exudate analysis. 		METABOLOMICS GNPS gnps.task:2ccbf82840724c99a2acc2c9e512a302
Raw LC-MS/MS Files
Raw LC-MS/MS files (.raw format) for root exudate metabolomics. 		METABOLOMICS MASSIVE MSV000095476
NMDC Integrated Study
Integrated study record in the National Microbiome Data Collaborative, linking amplicon, metabolomics, and phenotype data. 		OTHER NMDC nmdc:sty-11-ev70y104
Phenotype and Raw Data Collection
Plant phenotypes, sterility tests, metabolite identifications, and in vitro assay data from all five laboratories. 		PHENOTYPE FIGSHARE doi:10.6084/m9.figshare.c.7373842
Bacterial Genome Annotations
Annotated whole genome sequences for all 17 SynCom bacterial isolates, searchable by isolate name or GOLD Project ID. 		GENOMICS JGI_IMG Gp0588949-Gp0589682

Knowledge gaps & discussions (1)

KNOWLEDGE_GAP OPEN Which OAS925 traits and plant-microbe fluxes mediate the SynCom17 outcomes?

The three treatment arrows are retained, the trait-to-assembly arrow remains HYPOTHESIZED, and the assembly-to-metabolome arrow is removed because a common treatment does not isolate mediation. Single-isolate assays, relative reads and net spent-medium profiles do not resolve trait necessity or cross-feeding. The removed nitrogen-status node belongs to doi:10.1126/sciadv.adg7888, whose EcoFAB plants were sterile and whose 14 bacterial bioassays were individual cultures, not the SynCom17 trial. Protocol and non-graph role/uptake claims remain under #1427; canonical Allobosea grounding is preserved.

Attaches to: ecological_interactions#SynCom17 EcoFAB Ring-Trial Perturbation, ecological_interactions#Paraburkholderia Acid-Tolerant Root Colonization Traits, ecological_interactions#Paraburkholderia-Dominated SynCom17 Root Assembly, ecological_interactions#Treatment-Structured Rhizosphere Exometabolites, ecological_interactions#SynCom17 Plant Biomass and Root Development Decrease

Environmental Factors

Factor Value Unit
Nitrogen Source NH4NO3 mM
  • doi:10.1126/sciadv.adg7888 - SUPPORT (IN_VITRO)
    "the three inorganic nitrogen forms caused differential exudation, generalized by abundant amino acids-peptides and alkaloids"
Light Regime 16h/8h light/dark N/A
Growth Medium 0.5x Murashige-Skoog N/A

Growth Media

R2A (bacterial preculture); half-strength Murashige-Skoog (MS) basal salts for the EcoFAB 2.0 plant system

Temperature 27 °C

Preparation notes: SynCom strains were grown from single colonies in R2A liquid at 27 °C (the Paraburkholderia RFP strain grown overnight in R2A shaken at 200 rpm at 27 °C), washed in ½ MS basal salts, and used to inoculate 3-day-old B. distachyon seedlings in EcoFAB 2.0 devices; plants were grown in a chamber at 26 °C (light) / 20 °C (dark) with 110-140 µmol/m²/s PPFD and 70% humidity.

Evidence

PMID:40920748

"The Paraburkholderia sp. OAS925 expressing RFP was grown overnight in 7 mL of R2A medium with Kan 20 mg/L, shaken at 200 rpm at 27 °C."

PMID:40920748

"The plates were then moved to the growth chamber with a 14 h photoperiod (16 h for lab C) at 26 °C and 10 h dark at 20 °C with photosynthetic photon flux density (PPFD) at 110–140 µmol/m2/s and 70% humidity if tunable."

Cross-Mech Suite Links

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

HabitatMech: EcoFAB 2.0 hydroponic device ↗ TaxonMech: Paraburkholderia sp. OAS925 ↗ TraitMech: Paraburkholderia sp. OAS925 ↗ TaxonMech: Rhodococcus sp. OAS809 ↗ TraitMech: Rhodococcus sp. OAS809 ↗ TaxonMech: Mycobacterium sp. OAE908 ↗ TraitMech: Mycobacterium sp. OAE908 ↗ TaxonMech: Methylobacterium sp. OAE515 ↗ TraitMech: Methylobacterium sp. OAE515 ↗ TaxonMech: Variovorax sp. OAS795 ↗ TraitMech: Variovorax sp. OAS795 ↗ TaxonMech: Rhizobium sp. OAE497 ↗ TraitMech: Rhizobium sp. OAE497 ↗ CultureMech Growth Media ↗ PathwayMech Pathways ↗