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. 2020 Jun 1;9(6):giaa053.
doi: 10.1093/gigascience/giaa053.

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

Kate Reddington  1 , David Eccles  2 , Justin O'Grady  3   4 , Devin M Drown  5 , Lars Hestbjerg Hansen  6   7 , Tue Kjærgaard Nielsen  6   7 , Anne-Lise Ducluzeau  8 , Richard M Leggett  9 , Darren Heavens  9 , Ned Peel  9 , Terrance P Snutch  10 , Anthony Bayega  11 , Spyridon Oikonomopoulos  11 , Ioannis Ragoussis  11 , Thomas Barry  12 , Eric van der Helm  13 , Dino Jolic  14 , Hollian Richardson  4 , Hans Jansen  15 , John R Tyson  10 , Miten Jain  16 , Bonnie L Brown  17
Affiliations

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

Kate Reddington et al. Gigascience. .

Erratum in

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.

Keywords: MinION; long-read; nanopore sequencing; temperate river metagenomes.

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Figures

Figure 1:
Figure 1:
Rarefaction curves of the numbers of annotated species for 13 samples from 11 rivers and waterways based on MinION metagenomic data.
Figure 2:
Figure 2:
Concurrence of PCAs based on normalized data among 13 metagenomes from 11 rivers and waterways. A: Families annotated in Kraken2, B: Families annotated in MG-RAST, C: Subsystem Functions identified by MG-RAST.
Figure 3:
Figure 3:
Detected Subsystems, KO, and COG functions versus read count for 13 river and waterway metagenomes.
See this image and copyright information in PMC

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