Microbial life in 25-m-deep boreholes in ancient permafrost illuminated by metagenomics
Abstract This study describes the composition and potential metabolic adaptation of microbial communities in northeastern Siberia, a repository of the oldest permafrost in the Northern Hemisphere. Samples of contrasting depth (1.75 to 25.1 m below surface), age (from ~ 10 kyr to 1.1 Myr) and salinit...
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Online Access: | https://doi.org/10.1186/s40793-023-00487-9 https://doaj.org/article/b4b98b8d6d7148a7af8b9771337728c3 |
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ftdoajarticles:oai:doaj.org/article:b4b98b8d6d7148a7af8b9771337728c3 2023-06-11T04:09:40+02:00 Microbial life in 25-m-deep boreholes in ancient permafrost illuminated by metagenomics Xiaofen Wu Abraham L. Almatari Wyatt A. Cyr Daniel E. Williams Susan M. Pfiffner Elizaveta M. Rivkina Karen G. Lloyd Tatiana A. Vishnivetskaya 2023-04-01T00:00:00Z https://doi.org/10.1186/s40793-023-00487-9 https://doaj.org/article/b4b98b8d6d7148a7af8b9771337728c3 EN eng BMC https://doi.org/10.1186/s40793-023-00487-9 https://doaj.org/toc/2524-6372 doi:10.1186/s40793-023-00487-9 2524-6372 https://doaj.org/article/b4b98b8d6d7148a7af8b9771337728c3 Environmental Microbiome, Vol 18, Iss 1, Pp 1-19 (2023) Arctic Permafrost Metagenomics Metagenome-assembled genomes Metabolic potential Environmental sciences GE1-350 Microbiology QR1-502 article 2023 ftdoajarticles https://doi.org/10.1186/s40793-023-00487-9 2023-04-23T00:36:28Z Abstract This study describes the composition and potential metabolic adaptation of microbial communities in northeastern Siberia, a repository of the oldest permafrost in the Northern Hemisphere. Samples of contrasting depth (1.75 to 25.1 m below surface), age (from ~ 10 kyr to 1.1 Myr) and salinity (from low 0.1–0.2 ppt and brackish 0.3–1.3 ppt to saline 6.1 ppt) were collected from freshwater permafrost (FP) of borehole AL1_15 on the Alazeya River, and coastal brackish permafrost (BP) overlying marine permafrost (MP) of borehole CH1_17 on the East Siberian Sea coast. To avoid the limited view provided with culturing work, we used 16S rRNA gene sequencing to show that the biodiversity decreased dramatically with permafrost age. Nonmetric multidimensional scaling (NMDS) analysis placed the samples into three groups: FP and BP together (10–100 kyr old), MP (105–120 kyr old), and FP (> 900 kyr old). Younger FP/BP deposits were distinguished by the presence of Acidobacteriota, Bacteroidota, Chloroflexota_A, and Gemmatimonadota, older FP deposits had a higher proportion of Gammaproteobacteria, and older MP deposits had much more uncultured groups within Asgardarchaeota, Crenarchaeota, Chloroflexota, Patescibacteria, and unassigned archaea. The 60 recovered metagenome-assembled genomes and un-binned metagenomic assemblies suggested that despite the large taxonomic differences between samples, they all had a wide range of taxa capable of fermentation coupled to nitrate utilization, with the exception of sulfur reduction present only in old MP deposits. Article in Journal/Newspaper Arctic East Siberian Sea permafrost Siberia Directory of Open Access Journals: DOAJ Articles Alazeya ENVELOPE(153.682,153.682,70.859,70.859) Arctic East Siberian Sea ENVELOPE(166.000,166.000,74.000,74.000) Environmental Microbiome 18 1 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Arctic Permafrost Metagenomics Metagenome-assembled genomes Metabolic potential Environmental sciences GE1-350 Microbiology QR1-502 |
spellingShingle |
Arctic Permafrost Metagenomics Metagenome-assembled genomes Metabolic potential Environmental sciences GE1-350 Microbiology QR1-502 Xiaofen Wu Abraham L. Almatari Wyatt A. Cyr Daniel E. Williams Susan M. Pfiffner Elizaveta M. Rivkina Karen G. Lloyd Tatiana A. Vishnivetskaya Microbial life in 25-m-deep boreholes in ancient permafrost illuminated by metagenomics |
topic_facet |
Arctic Permafrost Metagenomics Metagenome-assembled genomes Metabolic potential Environmental sciences GE1-350 Microbiology QR1-502 |
description |
Abstract This study describes the composition and potential metabolic adaptation of microbial communities in northeastern Siberia, a repository of the oldest permafrost in the Northern Hemisphere. Samples of contrasting depth (1.75 to 25.1 m below surface), age (from ~ 10 kyr to 1.1 Myr) and salinity (from low 0.1–0.2 ppt and brackish 0.3–1.3 ppt to saline 6.1 ppt) were collected from freshwater permafrost (FP) of borehole AL1_15 on the Alazeya River, and coastal brackish permafrost (BP) overlying marine permafrost (MP) of borehole CH1_17 on the East Siberian Sea coast. To avoid the limited view provided with culturing work, we used 16S rRNA gene sequencing to show that the biodiversity decreased dramatically with permafrost age. Nonmetric multidimensional scaling (NMDS) analysis placed the samples into three groups: FP and BP together (10–100 kyr old), MP (105–120 kyr old), and FP (> 900 kyr old). Younger FP/BP deposits were distinguished by the presence of Acidobacteriota, Bacteroidota, Chloroflexota_A, and Gemmatimonadota, older FP deposits had a higher proportion of Gammaproteobacteria, and older MP deposits had much more uncultured groups within Asgardarchaeota, Crenarchaeota, Chloroflexota, Patescibacteria, and unassigned archaea. The 60 recovered metagenome-assembled genomes and un-binned metagenomic assemblies suggested that despite the large taxonomic differences between samples, they all had a wide range of taxa capable of fermentation coupled to nitrate utilization, with the exception of sulfur reduction present only in old MP deposits. |
format |
Article in Journal/Newspaper |
author |
Xiaofen Wu Abraham L. Almatari Wyatt A. Cyr Daniel E. Williams Susan M. Pfiffner Elizaveta M. Rivkina Karen G. Lloyd Tatiana A. Vishnivetskaya |
author_facet |
Xiaofen Wu Abraham L. Almatari Wyatt A. Cyr Daniel E. Williams Susan M. Pfiffner Elizaveta M. Rivkina Karen G. Lloyd Tatiana A. Vishnivetskaya |
author_sort |
Xiaofen Wu |
title |
Microbial life in 25-m-deep boreholes in ancient permafrost illuminated by metagenomics |
title_short |
Microbial life in 25-m-deep boreholes in ancient permafrost illuminated by metagenomics |
title_full |
Microbial life in 25-m-deep boreholes in ancient permafrost illuminated by metagenomics |
title_fullStr |
Microbial life in 25-m-deep boreholes in ancient permafrost illuminated by metagenomics |
title_full_unstemmed |
Microbial life in 25-m-deep boreholes in ancient permafrost illuminated by metagenomics |
title_sort |
microbial life in 25-m-deep boreholes in ancient permafrost illuminated by metagenomics |
publisher |
BMC |
publishDate |
2023 |
url |
https://doi.org/10.1186/s40793-023-00487-9 https://doaj.org/article/b4b98b8d6d7148a7af8b9771337728c3 |
long_lat |
ENVELOPE(153.682,153.682,70.859,70.859) ENVELOPE(166.000,166.000,74.000,74.000) |
geographic |
Alazeya Arctic East Siberian Sea |
geographic_facet |
Alazeya Arctic East Siberian Sea |
genre |
Arctic East Siberian Sea permafrost Siberia |
genre_facet |
Arctic East Siberian Sea permafrost Siberia |
op_source |
Environmental Microbiome, Vol 18, Iss 1, Pp 1-19 (2023) |
op_relation |
https://doi.org/10.1186/s40793-023-00487-9 https://doaj.org/toc/2524-6372 doi:10.1186/s40793-023-00487-9 2524-6372 https://doaj.org/article/b4b98b8d6d7148a7af8b9771337728c3 |
op_doi |
https://doi.org/10.1186/s40793-023-00487-9 |
container_title |
Environmental Microbiome |
container_volume |
18 |
container_issue |
1 |
_version_ |
1768383642313162752 |