A functional microbiome catalogue crowdsourced from North American rivers

Borton, Mikayla A.; McGivern, Bridget B.; Willi, Kathryn R.; Woodcroft, Ben J.; Mosier, Annika C.; Singleton, Derick M.; Bambakidis, Ted; Pelly, Aaron; Daly, Rebecca A.; Liu, Filipe; Freiburger, Andrew; Edirisinghe, Janaka N.; Faria, José P.; Danczak, Robert; Leleiwi, Ikaia; Goldman, Amy E.; Wilkins, Michael J.; Hall, Ed K.; Pennacchio, Christa; Roux, Simon; Eloe-Fadrosh, Emiley A.; Good, Stephen P.; Sullivan, Matthew B.; Wood-Charlson, Elisha M.; Miller, Christopher S.; Ross, Matthew R. V.; Henry, Christopher S.; Crump, Byron C.; Stegen, James C.; Wrighton, Kelly C.

doi:10.1038/s41586-024-08240-z

A functional microbiome catalogue crowdsourced from North American rivers

Journal Article · Wed Nov 20 00:00:00 EST 2024 · Nature (London)

DOI:https://doi.org/10.1038/s41586-024-08240-z· OSTI ID:3012451

^[1]; ^[1]; Willi, Kathryn R. ^[1]; ^[2]; ^[3]; Singleton, Derick M. ^[3]; ^[4]; Pelly, Aaron ^[5]; Daly, Rebecca A. ^[1]; Liu, Filipe ^[6]; Freiburger, Andrew ^[6]; Edirisinghe, Janaka N. ^[6]; ^[6]; Danczak, Robert ^[5]; Leleiwi, Ikaia ^[1]; ^[5]; ^[1]; Hall, Ed K. ^[1]; ^[7]; Roux, Simon ^[8] more »

Colorado State Univ., Fort Collins, CO (United States)
Queensland University of Technology (Australia)
Univ. of Colorado, Denver, CO (United States)
Oregon State Univ., Corvallis, OR (United States)
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
Argonne National Laboratory (ANL), Argonne, IL (United States)
USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
The Ohio State Univ., Columbus, OH (United States)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); Washington State Univ., Pullman, WA (United States)

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 Concept, 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 cyberinfrastructures, so that it can be widely accessed across disciplines for watershed predictive modelling and microbiome-based management practices.

View Accepted Manuscript (DOE)

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States); Colorado State Univ., Fort Collins, CO (United States); Colorado State University, Fort Collins, CO (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); University of Colorado, Denver, CO (United States)

Sponsoring Organization:: National Science Foundation (NSF); US National Science Foundation (NSF); USDOE Joint Genome Institute (JGI); USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF); USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE Office of Science (SC), Biological and Environmental Research (BER). Earth & Environmental Systems Science (EESS)

Grant/Contract Number:: 89233218CNA000001; AC02-05CH11231; AC02-06CH11357; AC02-98CH10886; AC05-00OR22725; AC05-76RL01830; SC0021350; SC0023084

OSTI ID:: 3012451

Alternate ID(s):: OSTI ID: 2481480
OSTI ID: 2549355
OSTI ID: 2570298
OSTI ID: 2480661

Report Number(s):: PNNL-SA--188353

Journal Information:: Nature (London), Journal Name: Nature (London) Journal Issue: 8044 Vol. 637; ISSN 1476-4687; ISSN 0028-0836

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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carbon cycle
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water microbiology

A functional microbiome catalogue crowdsourced from North American rivers

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