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

Reddington, Kate, Eccles, David, O'Grady, Justin, Drown, Devin M., Hansen, Lars Hestbjerg, Nielsen, Tue Kjærgaard, Ducluzeau, Anne-Lise, Leggett, Richard M., Heavens, Darren, Peel, Ned, Snutch, Terrance P., Bayega, Anthony, Oikonomopoulos, Spyridon, Ragoussis, Ioannis, Barry, Thomas, van der Helm, Eric, Jolic, Dino, Richardson, Hollian, Jansen, Hans, Tyson, John R., Jain, Miten and Brown, Bonnie L. (2020) Metagenomic analysis of planktonic riverine microbial consortia using nanopore sequencing reveals insight into river microbe taxonomy and function. GigaScience, 9 (6). ISSN 2047-217X

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Abstract

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.

Item Type: Article
Uncontrolled Keywords: minion,long-read,nanopore sequencing,temperate river metagenomes,computer science applications,health informatics ,/dk/atira/pure/subjectarea/asjc/1700/1706
Faculty \ School: Faculty of Medicine and Health Sciences > Norwich Medical School
Faculty of Science > School of Biological Sciences
Related URLs:
Depositing User: LivePure Connector
Date Deposited: 17 Jun 2020 00:14
Last Modified: 01 Nov 2020 00:55
URI: https://ueaeprints.uea.ac.uk/id/eprint/75625
DOI: 10.1093/gigascience/giaa053

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