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

Kate Reddington, David Eccles, Justin O'Grady, Devin M. Drown, Lars Hestbjerg Hansen, Tue Kjærgaard Nielsen, Anne Lise Ducluzeau, Richard M. Leggett, Darren Heavens, Ned Peel, Terrance P. Snutch, Anthony Bayega, Spyridon Oikonomopoulos, Jiannis Ragoussis, Thomas Barry, Eric van der Helm, Dino Jolic, Hollian Richardson, Hans Jansen, John R. TysonMiten Jain, Bonnie L. Brown*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

72 Downloads (Pure)


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.
Original languageEnglish
Article numbergiaa053
Issue number6
Number of pages12
Publication statusPublished - 2020


  • Temperate river metagenomes
  • MinION
  • Long-read
  • Nanopore sequencing


Dive into the research topics of 'Metagenomic analysis of planktonic riverine microbial consortia using nanopore sequencing reveals insight into river microbe taxonomy and function'. Together they form a unique fingerprint.

Cite this