Metagenomic analysis of planktonic riverine microbial consortia using nanopore sequencing reveals insight into river microbe taxonomy and function.

Autor: Reddington K; Microbial Diagnostics Research Laboratory, Microbiology, School of Natural Sciences, National University of Ireland, University Road, Galway, Ireland H91 TK33, Ireland., Eccles D; Malaghan Institute of Medical Research, Gate 7, Victoria University Kelburn Parade, Wellington 6140, Wellington 6242, New Zealand., O'Grady J; Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK.; Norwich Medical School, University of East Anglia, James Watson Rd, Norwich NR4 7TJ, UK., Drown DM; Department of Biology and Wildlife, Institute of Arctic Biology, University of Alaska Fairbanks, 2140 Koyukuk Drive, Fairbanks, AK 9975-7000, USA., Hansen LH; Department of Environmental Science, Aarhus University, PO Box 358, Frederiksborgvej 399, DK-4000 Roskilde, Denmark.; Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark., Nielsen TK; Department of Environmental Science, Aarhus University, PO Box 358, Frederiksborgvej 399, DK-4000 Roskilde, Denmark.; Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark., Ducluzeau AL; Institute of Arctic Biology, University of Alaska Fairbanks, 311 Irving 1 Building P.O. Box 757000 2140 Koyukuk Drive Fairbanks, AK 99775-7000, USA., Leggett RM; Earlham Institute, Norwich Research Park, Norwich NR4 7UQ, UK., Heavens D; Earlham Institute, Norwich Research Park, Norwich NR4 7UQ, UK., Peel N; Earlham Institute, Norwich Research Park, Norwich NR4 7UQ, UK., Snutch TP; Michael Smith Laboratories and Department of Zoology, University of British Columbia, #301-2185 East Mall Vancouver, BC V6T 1Z4, Canada., Bayega A; McGill University and Genome Quebec Innovation Centre, Department of Human Genetics, McGill University, 3640 rue University, Montreal, Quebec H3A 0C7, Canada., Oikonomopoulos S; McGill University and Genome Quebec Innovation Centre, Department of Human Genetics, McGill University, 3640 rue University, Montreal, Quebec H3A 0C7, Canada., Ragoussis I; McGill University and Genome Quebec Innovation Centre, Department of Human Genetics, McGill University, 3640 rue University, Montreal, Quebec H3A 0C7, Canada., Barry T; Nucleic Acid Diagnostics Research Laboratory, Microbiology, School of Natural Sciences, National University of Ireland, University Road, Galway, Ireland H91 TK33, Ireland., van der Helm E; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark., Jolic D; Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5 72076 Tübingen, Germany., Richardson H; Norwich Medical School, University of East Anglia, James Watson Rd, Norwich NR4 7TJ, UK., Jansen H; Future Genomics Technologies B.V., Nucleus building, Sylviusweg 74, 2333 BE Leiden, The Netherlands., Tyson JR; Michael Smith Laboratories and Department of Zoology, University of British Columbia, #301-2185 East Mall Vancouver, BC V6T 1Z4, Canada., Jain M; UC Santa Cruz Genomics Institute, 1156 High Street, Santa Cruz, CA 95064, USA., Brown BL; Department of Biological Sciences, University of New Hampshire, 38 Academic Way, Durham, NH 03824, USA.
Jazyk: angličtina
Zdroj: GigaScience [Gigascience] 2020 Jun 01; Vol. 9 (6).
DOI: 10.1093/gigascience/giaa053
Abstrakt: Background: Riverine ecosystems are biogeochemical powerhouses driven largely by microbial communities that inhabit water columns and sediments. Because rivers are used extensively for anthropogenic purposes (drinking water, recreation, agriculture, and industry), it is essential to understand how these activities affect the composition of river microbial consortia. Recent studies have shown that river metagenomes vary considerably, suggesting that microbial community data should be included in broad-scale river ecosystem models. But such ecogenomic studies have not been applied on a broad "aquascape" scale, and few if any have applied the newest nanopore technology.
Results: We investigated the metagenomes of 11 rivers across 3 continents using MinION nanopore sequencing, a portable platform that could be useful for future global river monitoring. Up to 10 Gb of data per run were generated with average read lengths of 3.4 kb. Diversity and diagnosis of river function potential was accomplished with 0.5-1.0 ⋅ 106 long reads. Our observations for 7 of the 11 rivers conformed to other river-omic findings, and we exposed previously unrecognized microbial biodiversity in the other 4 rivers.
Conclusions: Deeper understanding that emerged is that river microbial consortia and the ecological functions they fulfil did not align with geographic location but instead implicated ecological responses of microbes to urban and other anthropogenic effects, and that changes in taxa manifested over a very short geographic space.
(© The Author(s) 2020. Published by Oxford University Press.)
Databáze: MEDLINE
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