Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia
Culture-independent methods have contributed substantially to our understanding of global microbial diversity. Recently developed algorithms to construct whole genomes from environmental samples have further refined, corrected and revolutionized understanding of the tree of life. Here, we assembled...
Published in: | Scientific Reports |
---|---|
Main Authors: | , , , |
Format: | Text |
Language: | English |
Published: |
Nature Publishing Group UK
2019
|
Subjects: | |
Online Access: | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6395817/ http://www.ncbi.nlm.nih.gov/pubmed/30816235 https://doi.org/10.1038/s41598-019-39576-6 |
id |
ftpubmed:oai:pubmedcentral.nih.gov:6395817 |
---|---|
record_format |
openpolar |
spelling |
ftpubmed:oai:pubmedcentral.nih.gov:6395817 2023-05-15T16:58:41+02:00 Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia Wilkins, Laetitia G. E. Ettinger, Cassandra L. Jospin, Guillaume Eisen, Jonathan A. 2019-02-28 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6395817/ http://www.ncbi.nlm.nih.gov/pubmed/30816235 https://doi.org/10.1038/s41598-019-39576-6 en eng Nature Publishing Group UK http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6395817/ http://www.ncbi.nlm.nih.gov/pubmed/30816235 http://dx.doi.org/10.1038/s41598-019-39576-6 © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. CC-BY Article Text 2019 ftpubmed https://doi.org/10.1038/s41598-019-39576-6 2019-03-10T01:17:38Z Culture-independent methods have contributed substantially to our understanding of global microbial diversity. Recently developed algorithms to construct whole genomes from environmental samples have further refined, corrected and revolutionized understanding of the tree of life. Here, we assembled draft metagenome-assembled genomes (MAGs) from environmental DNA extracted from two hot springs within an active volcanic ecosystem on the Kamchatka peninsula, Russia. This hydrothermal system has been intensively studied previously with regard to geochemistry, chemoautotrophy, microbial isolation, and microbial diversity. We assembled genomes of bacteria and archaea using DNA that had previously been characterized via 16S rRNA gene clone libraries. We recovered 36 MAGs, 29 of medium to high quality, and inferred their placement in a phylogenetic tree consisting of 3,240 publicly available microbial genomes. We highlight MAGs that were taxonomically assigned to groups previously underrepresented in available genome data. This includes several archaea (Korarchaeota, Bathyarchaeota and Aciduliprofundum) and one potentially new species within the bacterial genus Sulfurihydrogenibium. Putative functions in both pools were compared and are discussed in the context of their diverging geochemistry. This study adds comprehensive information about phylogenetic diversity and functional potential within two hot springs in the caldera of Kamchatka. Text Kamchatka Kamchatka Peninsula PubMed Central (PMC) Kamchatka Peninsula ENVELOPE(160.000,160.000,56.000,56.000) Scientific Reports 9 1 |
institution |
Open Polar |
collection |
PubMed Central (PMC) |
op_collection_id |
ftpubmed |
language |
English |
topic |
Article |
spellingShingle |
Article Wilkins, Laetitia G. E. Ettinger, Cassandra L. Jospin, Guillaume Eisen, Jonathan A. Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia |
topic_facet |
Article |
description |
Culture-independent methods have contributed substantially to our understanding of global microbial diversity. Recently developed algorithms to construct whole genomes from environmental samples have further refined, corrected and revolutionized understanding of the tree of life. Here, we assembled draft metagenome-assembled genomes (MAGs) from environmental DNA extracted from two hot springs within an active volcanic ecosystem on the Kamchatka peninsula, Russia. This hydrothermal system has been intensively studied previously with regard to geochemistry, chemoautotrophy, microbial isolation, and microbial diversity. We assembled genomes of bacteria and archaea using DNA that had previously been characterized via 16S rRNA gene clone libraries. We recovered 36 MAGs, 29 of medium to high quality, and inferred their placement in a phylogenetic tree consisting of 3,240 publicly available microbial genomes. We highlight MAGs that were taxonomically assigned to groups previously underrepresented in available genome data. This includes several archaea (Korarchaeota, Bathyarchaeota and Aciduliprofundum) and one potentially new species within the bacterial genus Sulfurihydrogenibium. Putative functions in both pools were compared and are discussed in the context of their diverging geochemistry. This study adds comprehensive information about phylogenetic diversity and functional potential within two hot springs in the caldera of Kamchatka. |
format |
Text |
author |
Wilkins, Laetitia G. E. Ettinger, Cassandra L. Jospin, Guillaume Eisen, Jonathan A. |
author_facet |
Wilkins, Laetitia G. E. Ettinger, Cassandra L. Jospin, Guillaume Eisen, Jonathan A. |
author_sort |
Wilkins, Laetitia G. E. |
title |
Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia |
title_short |
Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia |
title_full |
Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia |
title_fullStr |
Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia |
title_full_unstemmed |
Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia |
title_sort |
metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in kamchatka, russia |
publisher |
Nature Publishing Group UK |
publishDate |
2019 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6395817/ http://www.ncbi.nlm.nih.gov/pubmed/30816235 https://doi.org/10.1038/s41598-019-39576-6 |
long_lat |
ENVELOPE(160.000,160.000,56.000,56.000) |
geographic |
Kamchatka Peninsula |
geographic_facet |
Kamchatka Peninsula |
genre |
Kamchatka Kamchatka Peninsula |
genre_facet |
Kamchatka Kamchatka Peninsula |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6395817/ http://www.ncbi.nlm.nih.gov/pubmed/30816235 http://dx.doi.org/10.1038/s41598-019-39576-6 |
op_rights |
© The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1038/s41598-019-39576-6 |
container_title |
Scientific Reports |
container_volume |
9 |
container_issue |
1 |
_version_ |
1766050762768515072 |