EcoFAB 2.0 Root Microbiome Ring Trial

Leveraging microbiomes to promote soil health and plant growth requires understanding underlying molecular mechanisms through reproducible experimental systems. In a global collaborative effort involving five laboratories, we aimed to advance reproducibility in microbiome studies by leveraging recently developed fabricated ecosystems (EcoFAB 2.0). Our inter-laboratory ring trial utilized synthetic bacterial communities (SynComs) to study root microbiome recruitment (analyzed by 16S amplicon sequencing) and exudate composition (analyzed by LC-MS/MS) of the model grass Brachypodium distachyon in EcoFAB 2.0. All participating laboratories replicated permutation-dependent changes in plant phenotype, root exudates, and bacterial community structure. Additionally, we identified factors determining bacterial colonization patterns through comparative genomics of SynCom members, fluorescent microscopy, motility assays, and exudate utilization. The study provides benchmark datasets and detailed protocols to achieve reproducibility and best practices, demonstrating how standardized SynComs and EcoFAB can promote scientific collaboration, improve comparability, and accelerate the application of findings, thus enhancing our understanding of microbiomes in plant and ecosystem science.