Journal article
Metagenomic analysis of planktonic riverine microbial consortia using nanopore sequencing reveals insight into river microbe taxonomy and function
National University of Ireland1
University of East Anglia2
Future Genomics Technologies B.V.3
University of California at Santa Cruz4
University of New Hampshire5
Malaghan Institute of Medical Research6
Norwich Research Park7
University of Alaska Fairbanks8
Aarhus University9
University of British Columbia10
McGill University11
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark12
Max Planck Institute for Developmental Biology13
...and 3 moreBackground: 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.
Language: | English |
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Publisher: | Oxford University Press |
Year: | 2020 |
ISSN: | 2047217x |
Types: | Journal article |
DOI: | 10.1093/gigascience/giaa053 |
ORCIDs: | 0000-0003-0027-1524 , 0000-0001-6610-8450 , 0000-0002-7451-8246 and van der Helm, Eric |