MinION sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes
Abstract Genome reconstruction from metagenomes enables detailed study of individual community members, their metabolisms, and their survival strategies. Obtaining high quality metagenome-assembled genomes (MAGs) is particularly valuable in extreme environments like sea ice cryoconites, where the na...
Published in: | Scientific Reports |
---|---|
Main Authors: | , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
Springer Science and Business Media LLC
2021
|
Subjects: | |
Online Access: | http://dx.doi.org/10.1038/s41598-021-00026-x https://www.nature.com/articles/s41598-021-00026-x.pdf https://www.nature.com/articles/s41598-021-00026-x |
id |
crspringernat:10.1038/s41598-021-00026-x |
---|---|
record_format |
openpolar |
spelling |
crspringernat:10.1038/s41598-021-00026-x 2023-05-15T17:48:03+02:00 MinION sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes Maggiori, Catherine Raymond-Bouchard, Isabelle Brennan, Laura Touchette, David Whyte, Lyle 2021 http://dx.doi.org/10.1038/s41598-021-00026-x https://www.nature.com/articles/s41598-021-00026-x.pdf https://www.nature.com/articles/s41598-021-00026-x en eng Springer Science and Business Media LLC https://creativecommons.org/licenses/by/4.0 https://creativecommons.org/licenses/by/4.0 CC-BY Scientific Reports volume 11, issue 1 ISSN 2045-2322 Multidisciplinary journal-article 2021 crspringernat https://doi.org/10.1038/s41598-021-00026-x 2022-01-04T12:52:02Z Abstract Genome reconstruction from metagenomes enables detailed study of individual community members, their metabolisms, and their survival strategies. Obtaining high quality metagenome-assembled genomes (MAGs) is particularly valuable in extreme environments like sea ice cryoconites, where the native consortia are recalcitrant to culture and strong astrobiology analogues. We evaluated three separate approaches for MAG generation from Allen Bay, Nunavut sea ice cryoconites—HiSeq-only, MinION-only, and hybrid (HiSeq + MinION)—where field MinION sequencing yielded a reliable metagenome. The hybrid assembly produced longer contigs, more coding sequences, and more total MAGs, revealing a microbial community dominated by Bacteroidetes. The hybrid MAGs also had the highest completeness, lowest contamination, and highest N50. A putatively novel species of Octadecabacter is among the hybrid MAGs produced, containing the genus’s only known instances of genomic potential for nitrate reduction, denitrification, sulfate reduction, and fermentation. This study shows that the inclusion of MinION reads in traditional short read datasets leads to higher quality metagenomes and MAGs for more accurate descriptions of novel microorganisms in this extreme, transient habitat and has produced the first hybrid MAGs from an extreme environment. Article in Journal/Newspaper Nunavut Sea ice Springer Nature (via Crossref) Allen Bay ENVELOPE(-36.533,-36.533,-54.183,-54.183) Nunavut Scientific Reports 11 1 |
institution |
Open Polar |
collection |
Springer Nature (via Crossref) |
op_collection_id |
crspringernat |
language |
English |
topic |
Multidisciplinary |
spellingShingle |
Multidisciplinary Maggiori, Catherine Raymond-Bouchard, Isabelle Brennan, Laura Touchette, David Whyte, Lyle MinION sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes |
topic_facet |
Multidisciplinary |
description |
Abstract Genome reconstruction from metagenomes enables detailed study of individual community members, their metabolisms, and their survival strategies. Obtaining high quality metagenome-assembled genomes (MAGs) is particularly valuable in extreme environments like sea ice cryoconites, where the native consortia are recalcitrant to culture and strong astrobiology analogues. We evaluated three separate approaches for MAG generation from Allen Bay, Nunavut sea ice cryoconites—HiSeq-only, MinION-only, and hybrid (HiSeq + MinION)—where field MinION sequencing yielded a reliable metagenome. The hybrid assembly produced longer contigs, more coding sequences, and more total MAGs, revealing a microbial community dominated by Bacteroidetes. The hybrid MAGs also had the highest completeness, lowest contamination, and highest N50. A putatively novel species of Octadecabacter is among the hybrid MAGs produced, containing the genus’s only known instances of genomic potential for nitrate reduction, denitrification, sulfate reduction, and fermentation. This study shows that the inclusion of MinION reads in traditional short read datasets leads to higher quality metagenomes and MAGs for more accurate descriptions of novel microorganisms in this extreme, transient habitat and has produced the first hybrid MAGs from an extreme environment. |
format |
Article in Journal/Newspaper |
author |
Maggiori, Catherine Raymond-Bouchard, Isabelle Brennan, Laura Touchette, David Whyte, Lyle |
author_facet |
Maggiori, Catherine Raymond-Bouchard, Isabelle Brennan, Laura Touchette, David Whyte, Lyle |
author_sort |
Maggiori, Catherine |
title |
MinION sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes |
title_short |
MinION sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes |
title_full |
MinION sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes |
title_fullStr |
MinION sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes |
title_full_unstemmed |
MinION sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes |
title_sort |
minion sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes |
publisher |
Springer Science and Business Media LLC |
publishDate |
2021 |
url |
http://dx.doi.org/10.1038/s41598-021-00026-x https://www.nature.com/articles/s41598-021-00026-x.pdf https://www.nature.com/articles/s41598-021-00026-x |
long_lat |
ENVELOPE(-36.533,-36.533,-54.183,-54.183) |
geographic |
Allen Bay Nunavut |
geographic_facet |
Allen Bay Nunavut |
genre |
Nunavut Sea ice |
genre_facet |
Nunavut Sea ice |
op_source |
Scientific Reports volume 11, issue 1 ISSN 2045-2322 |
op_rights |
https://creativecommons.org/licenses/by/4.0 https://creativecommons.org/licenses/by/4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1038/s41598-021-00026-x |
container_title |
Scientific Reports |
container_volume |
11 |
container_issue |
1 |
_version_ |
1766153234986041344 |