Preprint

FZJ-2025-00643

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Multi-laboratory Study Establishes Reproducible Methods for Plant-MicrobiomeResearch in Fabricated Ecosystems

Novak, V. ; Andeer, P. F. ; King, E. ; Calabria, J. ; Fitzpatrick, C. ; Kelm, J.FZJ* ; Wippel, K. ; Kosina, S. M. ; Daum, C. ; Zane, M. ; Yadav, A. ; Chen, M. ; Russ, D. ; Adams, C. A. ; Owens, T. K. ; Lee, B. ; Ding, Y. ; Sordo, Z. ; Chakraborty, R. ; Roux, S. ; Deutschbauer, A. M. ; Ushizima, D. ; Zengler, K. ; Arsova, B.FZJ* ; Dangl, J. L. ; Schulze-Lefert, P. ; Watt, M. ; Vogel, J. P. (Corresponding author) ; Northen, T. R. (Corresponding author)

2024

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Please use a persistent id in citations: doi:10.1101/2024.10.02.615924  doi:10.34734/FZJ-2025-00643

Abstract: Inter-laboratory replicability is crucial yet challenging in microbiome research. Leveraging microbiomes to promote soil health and plant growth requires understanding underlying molecular mechanisms using reproducible experimental systems. In a global collaborative effort involving five laboratories, we aimed to help advance reproducibility in microbiome studies by testing our ability to replicate synthetic community assemblyexperiments. Our study compared fabricated ecosystems constructed using two different synthetic bacterial communities, the model grass Brachypodium distachyon, and sterile EcoFAB 2.0 devices. All participating laboratories observed consistent inoculum-dependent changes inplant phenotype, root exudate composition, and final bacterial community structure where Paraburkholderia sp. OAS925 could dramatically shift microbiome composition. Comparative genomics and exudate utilization linked the pH-dependent colonization ability ofParaburkholderia, which was further confirmed with motility assays. The study provides detailed protocols, benchmarking datasets, and best practices to help advance replicable science and inform future multi-laboratory reproducibility studies.

Keyword(s): Biology (2nd) ; Instrument and Method Development (2nd)

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Contributing Institute(s):

1. Pflanzenwissenschaften (IBG-2)

Research Program(s):

1. 2171 - Biological and environmental resources for sustainable use (POF4-217) (POF4-217)

Appears in the scientific report 2024

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