EcoFAB 2.0 Root Microbiome Ring Trial SynCom17

Community ID CommunityMech:000025

Ecological State ENGINEERED

Environment EcoFAB 2.0 hydroponic device
ENVO:01001405

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	NCBITaxon:1822464	PRIMARY_DEGRADER	DOMINANT
PMID:40920748 - SUPPORT (IN_VITRO) "Paraburkholderia sp. OAS925 could dramatically shift microbiome composition"
Rhodococcus sp. OAS809	NCBITaxon:1827	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	NCBITaxon:1763	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	NCBITaxon:407	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	NCBITaxon:34072		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	NCBITaxon:379		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	NCBITaxon:85413		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	NCBITaxon:374		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	NCBITaxon:68		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	NCBITaxon:1667		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	NCBITaxon:86795		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	NCBITaxon:79328		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	NCBITaxon:423349		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	NCBITaxon:354354		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	NCBITaxon:2837503		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	NCBITaxon:55080		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	NCBITaxon:44249		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

Taxon

Cross-feeding

Mutualism

Syntrophy

Competition

Commensalism

Niche partitioning

Colonization facilitation

Strain competition

Predation

Paraburkholderia Competitive Exclusion

COMPETITION

Source Taxon: Paraburkholderia sp. OAS925

Target Taxon: Rhodococcus sp. OAS809

Evidence

PMID:40920748 - SUPPORT (IN_VITRO)

"Paraburkholderia sp. OAS925 could dramatically shift microbiome composition"

Root Exudate Modulation

CROSS_FEEDING

Source Taxon: Paraburkholderia sp. OAS925

Target Taxon: Methylobacterium sp. OAE515

Metabolites: shikimic acid (CHEBI:36215), p-coumaric acid (CHEBI:32374)

Evidence

doi:10.1126/sciadv.adg7888 - SUPPORT (IN_VITRO)

"nitrogen deficiency decreased nitrogen-containing compounds but increased shikimates-phenylpropanoids"

SynCom16 Community Assembly with Rhodococcus

CROSS_FEEDING

Source Taxon: Rhodococcus sp. OAS809

Target Taxon: Variovorax sp. OAS795

Biological Processes:

interspecies interaction between organisms (GO:0044419)

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"

Cross-Feeding with Rhizobium

CROSS_FEEDING

Source Taxon: Mycobacterium sp. OAE908

Target Taxon: Rhizobium sp. OAE497

Biological Processes:

interspecies interaction between organisms (GO:0044419)

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"

Cross-Feeding with Bosea

CROSS_FEEDING

Source Taxon: Methylobacterium sp. OAE515

Target Taxon: Bosea sp. OAE506

Biological Processes:

interspecies interaction between organisms (GO:0044419)

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"

Cross-Feeding with Bradyrhizobium

CROSS_FEEDING

Source Taxon: Rhodococcus sp. OAS809

Target Taxon: Bradyrhizobium sp. OAE829

Biological Processes:

interspecies interaction between organisms (GO:0044419)

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"

Cross-Feeding with Lysobacter

CROSS_FEEDING

Source Taxon: Mycobacterium sp. OAE908

Target Taxon: Lysobacter sp. OAE881

Biological Processes:

interspecies interaction between organisms (GO:0044419)

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"

Cross-Feeding with Arthrobacter

CROSS_FEEDING

Source Taxon: Rhodococcus sp. OAS809

Target Taxon: Arthrobacter sp. OAP107

Biological Processes:

interspecies interaction between organisms (GO:0044419)

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"

Cross-Feeding with Marmoricola

CROSS_FEEDING

Source Taxon: Methylobacterium sp. OAE515

Target Taxon: Marmoricola sp. OAE513

Biological Processes:

interspecies interaction between organisms (GO:0044419)

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"

Cross-Feeding with Chitinophaga

CROSS_FEEDING

Source Taxon: Mycobacterium sp. OAE908

Target Taxon: Chitinophaga sp. OAE865

Biological Processes:

interspecies interaction between organisms (GO:0044419)

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"

Cross-Feeding with Mucilaginibacter

CROSS_FEEDING

Source Taxon: Rhodococcus sp. OAS809

Target Taxon: Mucilaginibacter sp. OAE612

Biological Processes:

interspecies interaction between organisms (GO:0044419)

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"

Cross-Feeding with Niastella

CROSS_FEEDING

Source Taxon: Methylobacterium sp. OAE515

Target Taxon: Niastella sp. OAS944

Biological Processes:

interspecies interaction between organisms (GO:0044419)

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"

Cross-Feeding with Gottfriedia

CROSS_FEEDING

Source Taxon: Mycobacterium sp. OAE908

Target Taxon: Gottfriedia sp. OAE603

Biological Processes:

interspecies interaction between organisms (GO:0044419)

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"

Cross-Feeding with Brevibacillus

CROSS_FEEDING

Source Taxon: Rhodococcus sp. OAS809

Target Taxon: Brevibacillus sp. OAP136

Biological Processes:

interspecies interaction between organisms (GO:0044419)

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"

Cross-Feeding with Paenibacillus

CROSS_FEEDING

Source Taxon: Methylobacterium sp. OAE515

Target Taxon: Paenibacillus sp. OAE614

Biological Processes:

interspecies interaction between organisms (GO:0044419)

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"

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.	GENOME	JGI_IMG	Gp0588949-Gp0589682

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