Journal Article

FZJ-2026-00384

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Breaking the reproducibility barrier with standardized protocols for plant–microbiome research

Novak, V. ; Andeer, P. F. ; King, E. ; Calabria, J. ; Fitzpatrick, C. ; Kelm, J. M.FZJ* ; Wippel, K. ; Kosina, S. M. ; Bowen, B. P. ; 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)

2025
PLoS Lawrence, KS

This record in other databases:  

Please use a persistent id in citations: doi:10.1371/journal.pbio.3003358  doi:10.34734/FZJ-2026-00384

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 assembly experiments. 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 in plant 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 of Paraburkholderia, 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.

---

Contributing Institute(s):

1. Pflanzenwissenschaften (IBG-2)

Research Program(s):

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

---

Database coverage:
; ; ; ; Article Processing Charges ; BIOSIS Previews ; Biological Abstracts ; Clarivate Analytics Master Journal List ; Current Contents - Agriculture, Biology and Environmental Sciences ; Current Contents - Life Sciences ; DOAJ Seal ; Ebsco Academic Search ; Essential Science Indicators ; Fees ; SCOPUS ; Science Citation Index Expanded ; Web of Science Core Collection ; Zoological Record

---