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A functional microbiome catalogue crowdsourced from North American rivers

  • Vannote, R. L., Minshall, G. W., Cummins, K. W., Sedell, J. R. & Cushing, C. E. The river continuum concept. Can. J. Fish. Aquat. Sci. 37, 130–137 (1980).

    Article 

    Google Scholar
     

  • Wood-Charlson, E. M. et al. The National Microbiome Data Collaborative: enabling microbiome science. Nat. Rev. Microbiol. 18, 313–314 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Arkin, A. P. et al. KBase: the United States Department of Energy Systems Biology Knowledgebase. Nat. Biotechnol. 36, 566–569 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cavicchioli, R. et al. Scientists’ warning to humanity: microorganisms and climate change. Nat. Rev. Microbiol. 17, 569–586 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hutchins, D. A. & Fu, F. Microorganisms and ocean global change. Nat. Microbiol. 2, 17058 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Sunagawa, S. et al. Tara Oceans: towards global ocean ecosystems biology. Nat. Rev. Microbiol. 18, 428–445 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Battin, T. J. et al. River ecosystem metabolism and carbon biogeochemistry in a changing world. Nature 613, 449–459 (2023).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Kroeze, C., Dumont, E. & Seitzinger, S. P. New estimates of global emissions of N2O from rivers and estuaries. Environ. Sci. 2, 159–165 (2005).

    Article 

    Google Scholar
     

  • Butman, D. & Raymond, P. A. Significant efflux of carbon dioxide from streams and rivers in the United States. Nat. Geosci. 4, 839–842 (2011).

    Article 
    ADS 
    CAS 

    Google Scholar
     

  • Anderson, E. P. et al. Understanding rivers and their social relations: a critical step to advance environmental water management. WIREs Water 6, e1381 (2019).

    Article 

    Google Scholar
     

  • Mishra, A., Alnahit, A. & Campbell, B. Impact of land uses, drought, flood, wildfire, and cascading events on water quality and microbial communities: a review and analysis. J. Hydrol. 596, 125707 (2021).

    Article 
    CAS 

    Google Scholar
     

  • Rodríguez-Ramos, J. A. et al. Genome-resolved metaproteomics decodes the microbial and viral contributions to coupled carbon and nitrogen cycling in river sediments. mSystems 7, e00516-22 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ghosh, D., Ghosh, A. & Bhadury, P. Arsenic through aquatic trophic levels: effects, transformations and biomagnification—a concise review. Geosci. Lett. 9, 20 (2022).

    Article 
    ADS 

    Google Scholar
     

  • Boddicker, A. M. & Mosier, A. C. Genomic profiling of four cultivated Candidatus Nitrotoga spp. predicts broad metabolic potential and environmental distribution. ISME J. 12, 2864–2882 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chu, H., Gao, G.-F., Ma, Y., Fan, K. & Delgado-Baquerizo, M. Soil microbial biogeography in a changing world: recent advances and future perspectives. mSystems 5, e00803-19 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Stadler, M. & del Giorgio, P. A. Terrestrial connectivity, upstream aquatic history and seasonality shape bacterial community assembly within a large boreal aquatic network. ISME J. 16, 937–947 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Crump, B. C., Amaral-Zettler, L. A. & Kling, G. W. Microbial diversity in arctic freshwaters is structured by inoculation of microbes from soils. ISME J. 6, 1629–1639 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ruiz-González, C., Niño-García, J. P. & del Giorgio, P. A. Terrestrial origin of bacterial communities in complex boreal freshwater networks. Ecol. Lett. 18, 1198–1206 (2015).

    Article 
    PubMed 

    Google Scholar
     

  • Read, D. S. et al. Catchment-scale biogeography of riverine bacterioplankton. ISME J. 9, 516–526 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Savio, D. et al. Bacterial diversity along a 2600 km river continuum. Environ. Microbiol. 17, 4994–5007 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Payne, J. T., Millar, J. J., Jackson, C. R. & Ochs, C. A. Patterns of variation in diversity of the Mississippi river microbiome over 1,300 kilometers. PLoS ONE 12, e0174890 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Parks, D. H. et al. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat. Microbiol. 2, 1533–1542 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Garner, R. E. et al. A genome catalogue of lake bacterial diversity and its drivers at continental scale. Nat. Microbiol. 8, 1920–1934 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Nayfach, S. et al. A genomic catalog of Earth’s microbiomes. Nat. Biotechnol. 39, 499–509 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Rodríguez-Ramos, J. et al. Spatial and temporal metagenomics of river compartments reveals viral community dynamics in an urban impacted stream. Front. Microbiomes 2, 1199766 (2023).

  • Wilkinson, M. D. et al. The FAIR guiding principles for scientific data management and stewardship. Sci. Data 3, 160018 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Goldman, A. E., Emani, S. R., Pérez-Angel, L. C., Rodríguez-Ramos, J. A. & Stegen, J. C. Integrated, coordinated, open, and networked (ICON) science to advance the geosciences: introduction and synthesis of a special collection of commentary articles. Earth Space Sci. 9, e2021EA002099 (2022).

    Article 
    ADS 

    Google Scholar
     

  • Jezbera, J., Sharma, A. K., Brandt, U., Doolittle, W. F. & Hahn, M. W. ‘Candidatus Planktophila limnetica’, an actinobacterium representing one of the most numerically important taxa in freshwater bacterioplankton. Int. J. Syst. Evol. Microbiol. 59, 2864–2869 (2009).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Stein, L. Y. Insights into the physiology of ammonia-oxidizing microorganisms. Curr. Opin. Chem. Biol. 49, 9–15 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Daims, H. et al. Complete nitrification by Nitrospira bacteria. Nature 528, 504–509 (2015).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Liu, S. et al. Comammox Nitrospira within the Yangtze River continuum: community, biogeography, and ecological drivers. ISME J. 14, 2488–2504 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wrighton, K. C. et al. Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla. Science 337, 1661–1665 (2012).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Lian, Y., Zhen, L., Chen, X., Li, Y. & Li, X. Microbial biomarkers as indication of dynamic and heterogeneous urban water environments. Environ. Sci. Pollut. Res. https://doi.org/10.1007/s11356-022-24539-8 (2022).

  • Regina, A. L. A. et al. A watershed impacted by anthropogenic activities: microbial community alterations and reservoir of antimicrobial resistance genes. Sci. Total Environ. 793, 148552 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ploug, H., Kühl, M. & Buchholzcleven, B. Anoxic aggregates—an ephemeral phenomenon in the pelagic environment? Aquat. Microb. Ecol. 13, 285–294 (1997).

    Article 

    Google Scholar
     

  • Böckelmann, U., Manz, W., Neu, T. R. & Szewzyk, U. Characterization of the microbial community of lotic organic aggregates (‘river snow’) in the Elbe River of Germany by cultivation and molecular methods. FEMS Microbiol. Ecol. 33, 157–170 (2000).

    Article 

    Google Scholar
     

  • Battin, T. J. et al. Biophysical controls on organic carbon fluxes in fluvial networks. Nat. Geosci. 1, 95–100 (2008).

    Article 
    ADS 
    CAS 

    Google Scholar
     

  • Gomes, I. B., Maillard, J.-Y., Simões, L. C. & Simões, M. Emerging contaminants affect the microbiome of water systems—strategies for their mitigation. Npj Clean Water 3, 39 (2020).

    Article 
    CAS 

    Google Scholar
     

  • Li, J., Liu, H. & Paul Chen, J. Microplastics in freshwater systems: a review on occurrence, environmental effects, and methods for microplastics detection. Water Res. 137, 362–374 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Mdee, A. et al. The top 100 global water questions: results of a scoping exercise. One Earth 5, 563–573 (2022).

    Article 
    ADS 

    Google Scholar
     

  • Zrimec, J., Kokina, M., Jonasson, S., Zorrilla, F. & Zelezniak, A. Plastic-degrading potential across the global microbiome correlates with recent pollution trends. mBio 12, e0215521 (2021).

    Article 
    PubMed 

    Google Scholar
     

  • Jia, S. et al. Fate of antibiotic resistance genes and their associations with bacterial community in livestock breeding wastewater and its receiving river water. Water Res. 124, 259–268 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Alcock, B. P. et al. CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database. Nucleic Acids Res. 51, D690–D699 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Yushchuk, O., Binda, E. & Marinelli, F. Glycopeptide antibiotic resistance genes: distribution and function in the producer Actinomycetes. Front. Microbiol. 11, 1173 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Pal, A., He, Y., Jekel, M., Reinhard, M. & Gin, K. Y.-H. Emerging contaminants of public health significance as water quality indicator compounds in the urban water cycle. Environ. Int. 71, 46–62 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Lear, G. et al. The biogeography of stream bacteria. Glob. Ecol. Biogeogr. 22, 544–554 (2013).

    Article 

    Google Scholar
     

  • Dickey, J. R. et al. The utility of macroecological rules for microbial biogeography. Front. Ecol. Evol. 9, 633155 (2021).

  • Smith, L. C. et al. Large-scale drivers of relationships between soil microbial properties and organic carbon across Europe. Glob. Ecol. Biogeogr. 30, 2070–2083 (2021).

    Article 

    Google Scholar
     

  • DeLong, E. F. Microbial community genomics in the ocean. Nat. Rev. Microbiol. 3, 459–469 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Omernik, J. M. Ecoregions of the conterminous United States. Ann. Assoc. Am. Geogr. 77, 118–125 (1987).

    Article 

    Google Scholar
     

  • Fine, A. K., van Es, H. M. & Schindelbeck, R. R. Statistics, scoring functions, and regional analysis of a comprehensive soil health database. Soil Sci. Soc. Am. J. 81, 589–601 (2017).

    Article 
    ADS 
    CAS 

    Google Scholar
     

  • Henson, M. W. et al. Nutrient dynamics and stream order influence microbial community patterns along a 2914 kilometer transect of the Mississippi River. Limnol. Oceanogr. 63, 1837–1855 (2018).

    Article 
    ADS 
    CAS 

    Google Scholar
     

  • Satinsky, B. M. et al. Metagenomic and metatranscriptomic inventories of the lower Amazon River, May 2011. Microbiome 3, 39 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Maiolini, B. & Bruno, M. C. The River Continuum Concept revisited: Lessons from the Alps (Innsbruck Univ. Press, 2023).

  • Mincer, T. J. & Aicher, A. C. Methanol production by a broad phylogenetic array of marine phytoplankton. PLoS ONE 11, e0150820 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • McInerney, M. J. et al. Physiology, ecology, phylogeny, and genomics of microorganisms capable of syntrophic metabolism. Ann. N. Y. Acad. Sci. 1125, 58–72 (2008).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Schink, B. & Zeikus, J. G. Microbial methanol formation: a major end product of pectin metabolism. Curr. Microbiol. 4, 387–389 (1980).

    Article 
    CAS 

    Google Scholar
     

  • Cole, J. J. et al. Plumbing the global carbon cycle: integrating inland waters into the terrestrial carbon budget. Ecosystems 10, 172–185 (2007).

    Article 

    Google Scholar
     

  • Gudmundsson, L. et al. Globally observed trends in mean and extreme river flow attributed to climate change. Science 371, 1159–1162 (2021).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Hundley N. Jr Water and the West: The Colorado River Compact and the Politics of Water in the American West (Univ. California Press, 2009).

  • Arora, B. et al. Building cross-site and cross-network collaborations in critical zone science. J. Hydrol. 618, 129248 (2023).

    Article 

    Google Scholar
     

  • Stegen, J. C. & Goldman, A. E. WHONDRS: a community resource for studying dynamic river corridors. mSystems 3, e00151-18 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Garayburu-Caruso, V. A. et al. Using community science to reveal the global chemogeography of river metabolomes. Metabolites 10, 518 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Toyoda, J. et al. WHONDRS Summer 2019 Sampling Campaign: Global River Corridor Surface Water FTICR-MS, NPOC, and Stable Isotopes https://doi.org/10.15485/1603775 (2020).

  • US Geological Survey. In Book 9: Techniques for Water-Resources Investigations Ch. A4 pubs.er.usgs.gov/publication/twri09A4 (2006).

  • Lee, C. J. & Henderson, R. J. Tracking Water Quality in U. S. Streams and Rivers https://pubs.usgs.gov/publication/fs20213019 (USGS, 2020).

  • Crump, B. C., Kling, G. W., Bahr, M. & Hobbie, J. E. Bacterioplankton community shifts in an Arctic lake correlate with seasonal changes in organic matter source. Appl. Environ. Microbiol. 69, 2253–2268 (2003).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kellogg, C. T. E., McClelland, J. W., Dunton, K. H. & Crump, B. C. Strong seasonality in Arctic estuarine microbial food webs. Front. Microbiol. 10, 2628 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Borton, M. A. Genome Resolved Open Watersheds database (GROWdb). Github https://github.com/jmikayla1991/Genome-Resolved-Open-Watersheds-database-GROWdb (2023).

  • Hill, R. A., Weber, M. H., Leibowitz, S. G., Olsen, A. R. & Thornbrugh, D. J. The Stream-Catchment (StreamCat) Dataset: a database of watershed metrics for the conterminous United States. JAWRA 52, 120–128 (2016).

    ADS 

    Google Scholar
     

  • Blodgett, D., Johnson, J. M. & Bock, A. Generating a reference flow network with improved connectivity to support durable data integration and reproducibility in the coterminous US. Environ. Model. Softw. 165, 105726 (2023).

    Article 

    Google Scholar
     

  • Hijmans, R. J. et al. Package ‘terra’ (2022).

  • Willi, K. R., Matthew R. V. & ROSS. Genome Resolved Open Watersheds Database (GROWdb) Geospatial data puller. Github https://github.com/rossyndicate/GROWdb (2023).

  • Joshi, N. A. & Fass, J. N. Sickle: a windowed adaptive trimming tool for FASTQ files using quality. Github https://github.com/najoshi/sickle (2011).

  • Li, D., Liu, C.-M., Luo, R., Sadakane, K. & Lam, T.-W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31, 1674–1676 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kang, D. D. et al. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ 7, e7359 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Peng, Y., Leung, H. C. M., Yiu, S. M. & Chin, F. Y. L. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28, 1420–1428 (2012).

  • Clum, A. et al. DOE JGI metagenome workflow. mSystems 6, e00804-20 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nurk, S., Meleshko, D., Korobeynikov, A. & Pevzner, P. A. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 27, 824–834 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043–1055 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Olm, M. R., Brown, C. T., Brooks, B. & Banfield, J. F. dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. 11, 2864–2868 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chaumeil, P.-A., Mussig, A. J., Hugenholtz, P. & Parks, D. H. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 36, 1925–1927 (2020).

    Article 
    CAS 

    Google Scholar
     

  • Shaffer, M. et al. DRAM for distilling microbial metabolism to automate the curation of microbiome function. Nucleic Acids Res. 48, 8883–8900 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Woodcroft, B. J. CoverM. Github https://github.com/wwood/CoverM (2023).

  • Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923–930 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139–140 (2010).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Tavormina, P. L., Orphan, V. J., Kalyuzhnaya, M. G., Jetten, M. S. M. & Klotz, M. G. A novel family of functional operons encoding methane/ammonia monooxygenase-related proteins in gammaproteobacterial methanotrophs. Environ. Microbiol. Rep. 3, 91–100 (2011).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Rochman, F. F. et al. Novel copper-containing membrane monooxygenases (CuMMOs) encoded by alkane-utilizing Betaproteobacteria. ISME J. 14, 714–726 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Borton, M. A. et al. Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales. Proc. Natl Acad. Sci. USA 115, E6585–E6594 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Solden, L. M. et al. New roles in hemicellulosic sugar fermentation for the uncultivated Bacteroidetes family BS11. ISME J. 11, 691–703 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Castresana, J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17, 540–552 (2000).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Abascal, F., Zardoya, R. & Posada, D. ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21, 2104–2105 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 49, W293–W296 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Woodcroft, B. J. et al. SingleM and Sandpiper: robust microbial taxonomic profiles from metagenomic data. Preprint at bioRxiv https://doi.org/10.1101/2024.01.30.578060 (2024).

  • Borton, M. A. et al. Data for ‘A functional microbiome catalogue crowdsourced from North American rivers’. Zenodo https://doi.org/10.5281/zenodo.8173286 (2024).

  • Eloe-Fadrosh, E. A. et al. The National Microbiome Data Collaborative Data Portal: an integrated multi-omics microbiome data resource. Nucleic Acids Res. 50, D828–D836 (2022).

    CAS 

    Google Scholar
     

  • Borton, M. A. et al. Data generation scripts for ‘A functional microbiome catalogue crowdsourced from North American rivers’. Zenodo https://doi.org/10.5281/zenodo.11041178 (2024).

  • Borton, M. A. et al. Figure generation code for ‘A functional microbiome catalogue crowdsourced from North American rivers’. Zenodo https://doi.org/10.5281/zenodo.11188634 (2024).

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