Metagenomic analysis of planktonic riverine microbial consortia using nanopore sequencing reveals insight into river microbe taxonomy and function: [incl. Erratum]
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Metagenomic analysis of planktonic riverine microbial consortia using nanopore sequencing reveals insight into river microbe taxonomy and function : [incl. Erratum]. / 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, Jiannis; Barry, Thomas; van der Helm, Eric; Jolic, Dino; Richardson, Hollian; Jansen, Hans; Tyson, John R.; Jain, Miten; Brown, Bonnie L.
In: GigaScience, Vol. 9, No. 6, 053, 2020.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Metagenomic analysis of planktonic riverine microbial consortia using nanopore sequencing reveals insight into river microbe taxonomy and function
T2 - [incl. Erratum]
AU - Reddington, Kate
AU - Eccles, David
AU - O'Grady, Justin
AU - Drown, Devin M.
AU - Hansen, Lars Hestbjerg
AU - Nielsen, Tue Kjærgaard
AU - Ducluzeau, Anne-Lise
AU - Leggett, Richard M.
AU - Heavens, Darren
AU - Peel, Ned
AU - Snutch, Terrance P.
AU - Bayega, Anthony
AU - Oikonomopoulos, Spyridon
AU - Ragoussis, Jiannis
AU - Barry, Thomas
AU - van der Helm, Eric
AU - Jolic, Dino
AU - Richardson, Hollian
AU - Jansen, Hans
AU - Tyson, John R.
AU - Jain, Miten
AU - Brown, Bonnie L.
N1 - Corrigendum to: Metagenomic analysis of planktonic riverine microbial consortia using nanopore sequencing reveals insight into river microbe taxonomy and function https://doi.org/10.1093/gigascience/giaa074
PY - 2020
Y1 - 2020
N2 - 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 . 10(6) 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.
AB - 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 . 10(6) 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.
KW - temperate river metagenomes
KW - MinION
KW - long-read
KW - nanopore sequencing
KW - BACTERIAL COMMUNITY
KW - BIOTIC INTEGRITY
UR - https://academic.oup.com/gigascience/article/9/6/giaa074/5861904?login=false
U2 - 10.1093/gigascience/giaa053
DO - 10.1093/gigascience/giaa053
M3 - Journal article
C2 - 32520351
VL - 9
JO - GigaScience
JF - GigaScience
SN - 2047-217X
IS - 6
M1 - 053
ER -
ID: 249480756