Breaking the reproducibility barrier with standardized protocols for plant-microbiome research.
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.
Authors
- Catharine A. Adams (ORCID: https://orcid.org/0000-0002-0914-0806)
- Jacob Calabria (ORCID: https://orcid.org/0009-0003-8735-2470)
- Paul Schulze‐Lefert (ORCID: https://orcid.org/0000-0002-8978-1717)
- Simon Roux (ORCID: https://orcid.org/0000-0002-5831-5895)
- Dor Russ (ORCID: https://orcid.org/0000-0003-4372-7958)
- Vlastimil Novák (ORCID: https://orcid.org/0000-0001-7890-4593)
- Trenton K. Owens (ORCID: https://orcid.org/0000-0002-0574-9614)
- Jana M. Kelm (ORCID: https://orcid.org/0000-0003-4720-1806)
- Adam M. Deutschbauer (ORCID: https://orcid.org/0000-0003-2728-7622)
- Mingfei Chen (ORCID: https://orcid.org/0000-0002-6281-2480)
- Kathrin Wippel (ORCID: https://orcid.org/0000-0001-5901-3381)
- Suzanne M. Kosina (ORCID: https://orcid.org/0000-0003-2885-1248)
- Chris Daum (ORCID: https://orcid.org/0000-0003-3895-5892)
- Borjana Arsova (ORCID: https://orcid.org/0000-0002-0566-2009)
- Benjamin P. Bowen (ORCID: https://orcid.org/0000-0003-1368-3958)
- Daniela Ushizima (ORCID: https://orcid.org/0000-0002-7363-9468)
- Eoghan King (ORCID: https://orcid.org/0000-0001-9495-8858)
- Archana Yadav (ORCID: https://orcid.org/0000-0002-4255-9860)
- Connor R. Fitzpatrick (ORCID: https://orcid.org/0000-0002-7100-9542)
- Karsten Zengler (ORCID: https://orcid.org/0000-0002-8062-3296)
- John P. Vogel (ORCID: https://orcid.org/0000-0003-1786-2689)
- Romy Chakraborty (ORCID: https://orcid.org/0000-0001-9326-554X)
- Jeffery L. Dangl (ORCID: https://orcid.org/0000-0003-3199-8654)
- Michelle Watt (ORCID: https://orcid.org/0000-0001-7843-0957)
- Matthew Zane
- Peter Andeer (ORCID: https://orcid.org/0000-0002-3554-2008)
- Zineb Sordo (ORCID: https://orcid.org/0009-0008-3528-5874)
- Bradie Lee (ORCID: https://orcid.org/0000-0003-2918-2787)
Institutions
- University of North Carolina at Chapel Hill (US)
Publication Details
- Journal
- UNC Libraries
- Published
- 2025-10-09
- DOI
- https://doi.org/10.17615/j1kr-3m82
- Primary Topic
- Research Data Management Practices
- Type
- article
- Field-Weighted Citation Impact
- 0.00