A functional microbiome catalogue crowdsourced from North American rivers

Mikayla A. Borton (), Bridget B. McGivern, Kathryn R. Willi, Ben J. Woodcroft, Annika C. Mosier, Derick M. Singleton, Ted Bambakidis, Aaron Pelly, Rebecca A. Daly, Filipe Liu, Andrew Freiburger, Janaka N. Edirisinghe, José P. Faria, Robert Danczak, Ikaia Leleiwi, Amy E. Goldman, Michael J. Wilkins, Ed K. Hall, Christa Pennacchio, Simon Roux, Emiley A. Eloe-Fadrosh, Stephen P. Good, Matthew B. Sullivan, Elisha M. Wood-Charlson, Christopher S. Miller, Matthew R. V. Ross, Christopher S. Henry, Byron C. Crump, James C. Stegen and Kelly C. Wrighton ()
Additional contact information
Mikayla A. Borton: Colorado State University
Bridget B. McGivern: Colorado State University
Kathryn R. Willi: Colorado State University
Ben J. Woodcroft: Translational Research Institute
Annika C. Mosier: University of Colorado Denver
Derick M. Singleton: University of Colorado Denver
Ted Bambakidis: Oregon State University
Aaron Pelly: Pacific Northwest National Laboratory
Rebecca A. Daly: Colorado State University
Filipe Liu: Argonne National Laboratory
Andrew Freiburger: Argonne National Laboratory
Janaka N. Edirisinghe: Argonne National Laboratory
José P. Faria: Argonne National Laboratory
Robert Danczak: Pacific Northwest National Laboratory
Ikaia Leleiwi: Colorado State University
Amy E. Goldman: Pacific Northwest National Laboratory
Michael J. Wilkins: Colorado State University
Ed K. Hall: Colorado State University
Christa Pennacchio: Lawrence Berkeley National Laboratory
Simon Roux: Lawrence Berkeley National Laboratory
Emiley A. Eloe-Fadrosh: Lawrence Berkeley National Laboratory
Stephen P. Good: Oregon State University
Matthew B. Sullivan: The Ohio State University
Elisha M. Wood-Charlson: Lawrence Berkeley National Laboratory
Christopher S. Miller: University of Colorado Denver
Matthew R. V. Ross: Colorado State University
Christopher S. Henry: Argonne National Laboratory
Byron C. Crump: Oregon State University
James C. Stegen: Pacific Northwest National Laboratory
Kelly C. Wrighton: Colorado State University

Nature, 2025, vol. 637, issue 8044, 103-112

Abstract: Abstract Predicting elemental cycles and maintaining water quality under increasing anthropogenic influence requires knowledge of the spatial drivers of river microbiomes. However, understanding of the core microbial processes governing river biogeochemistry is hindered by a lack of genome-resolved functional insights and sampling across multiple rivers. Here we used a community science effort to accelerate the sampling, sequencing and genome-resolved analyses of river microbiomes to create the Genome Resolved Open Watersheds database (GROWdb). GROWdb profiles the identity, distribution, function and expression of microbial genomes across river surface waters covering 90% of United States watersheds. Specifically, GROWdb encompasses microbial lineages from 27 phyla, including novel members from 10 families and 128 genera, and defines the core river microbiome at the genome level. GROWdb analyses coupled to extensive geospatial information reveals local and regional drivers of microbial community structuring, while also presenting foundational hypotheses about ecosystem function. Building on the previously conceived River Continuum Concept1, we layer on microbial functional trait expression, which suggests that the structure and function of river microbiomes is predictable. We make GROWdb available through various collaborative cyberinfrastructures2,3, so that it can be widely accessed across disciplines for watershed predictive modelling and microbiome-based management practices.

Date: 2025
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DOI: 10.1038/s41586-024-08240-z

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