HomePublications

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

Research output: Contribution to journalArticle

Open Access permissions

Open

Documents

Links

DOI

Authors

  • Kate Reddington
  • David Eccles
  • Devin M. Drown
  • Lars Hestbjerg Hansen
  • Tue Kjærgaard Nielsen
  • Anne-Lise Ducluzeau
  • Richard M. Leggett
  • Darren Heavens
  • Terrance P. Snutch
  • Anthony Bayega
  • Spyridon Oikonomopoulos
  • Ioannis Ragoussis
  • Thomas Barry
  • Eric van der Helm
  • Dino Jolic
  • Hollian Richardson
  • Hans Jansen
  • John R. Tyson
  • Miten Jain
  • Bonnie L. Brown

Organisational units

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.

Details

Original languageEnglish
Article numbergiaa053
JournalGigaScience
Volume9
Issue number6
Early online date10 Jun 2020
DOIs
Publication statusPublished - 10 Jun 2020
Peer-reviewedYes

Keywords

    Research areas

  • MinION, long-read, nanopore sequencing, temperate river metagenomes

View graph of relations

ID: 182458944