Eight Metagenome-Assembled Genomes Provide Evidence for Microbial Adaptation in 20,000- to 1,000,000-Year-Old Siberian Permafrost
Abstract
Permafrost microbes may be metabolically active in microscopic layers of liquid brines, even in ancient soil. Metagenomics can help discern whether permafrost microbes show adaptations to this environment. Thirty-three metagenome-assembled genomes (MAGs) were obtained from six depths (3.5 m to 20 m) of freshly cored permafrost from the Siberian Kolyma-Indigirka Lowland region. These soils have been continuously frozen for ~20,000 to 1,000,000 years. Eight of these MAGs were ≥80% complete with <10% contamination and were taxonomically identified as Aminicenantes, Atribacteria, Chloroflexi, and Actinobacteria within bacteria and Thermoprofundales within archaea. MAGs from these taxa have been obtained previously from nonpermafrost environments and have been suggested to show adaptations to long-term energy starvation, but they have never been explored in ancient permafrost. The permafrost MAGs had greater proportions in the Clusters of Orthologous Groups (COGs) categories of energy production and conversion and carbohydrate transport and metabolism than did their nonpermafrost counterparts. They also contained genes for trehalose synthesis, thymine metabolism, mevalonate biosynthesis, and cellulose degradation, which were less prevalent in nonpermafrost genomes. Furthermore, many of these genes are involved in membrane stabilization and osmotic stress responses, consistent with adaptation to the anoxic, high-ionic-strength, cold environments of permafrost brine films. Our results suggestmore »
- Authors:
-
[4];
[1]
- Univ. of Tennessee, Knoxville, TN (United States)
- Institute of Physicochemical and Biological Problems of Soil Science, Pushchino (Russia)
- Princeton Univ., NJ (United States)
- Univ. of Tennessee, Knoxville, TN (United States); Institute of Physicochemical and Biological Problems of Soil Science, Pushchino (Russia)
- Publication Date:
- Research Org.:
- Univ. of Tennessee, Knoxville, TN (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); National Science Foundation (NSF); Russian Foundation for Basic Research
- OSTI Identifier:
- 1991903
- Grant/Contract Number:
- SC0020369; DEB-1442262; DEB-1460058; 9-29-05003-mk
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Applied and Environmental Microbiology
- Additional Journal Information:
- Journal Volume: 87; Journal Issue: 19; Journal ID: ISSN 0099-2240
- Publisher:
- American Society for Microbiology
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; permafrost; MAGs; exobiology; environmental; bioinformatics
Citation Formats
Sipes, Katie, Almatari, Abraham, Eddie, Alexander, Williams, Daniel, Spirina, Elena, Rivkina, Elizaveta, Liang, Renxing, Onstott, Tullis C., Vishnivetskaya, Tatiana A., and Lloyd, Karen G. Eight Metagenome-Assembled Genomes Provide Evidence for Microbial Adaptation in 20,000- to 1,000,000-Year-Old Siberian Permafrost. United States: N. p., 2021.
Web. doi:10.1128/aem.00972-21.
Sipes, Katie, Almatari, Abraham, Eddie, Alexander, Williams, Daniel, Spirina, Elena, Rivkina, Elizaveta, Liang, Renxing, Onstott, Tullis C., Vishnivetskaya, Tatiana A., & Lloyd, Karen G. Eight Metagenome-Assembled Genomes Provide Evidence for Microbial Adaptation in 20,000- to 1,000,000-Year-Old Siberian Permafrost. United States. https://doi.org/10.1128/aem.00972-21
Sipes, Katie, Almatari, Abraham, Eddie, Alexander, Williams, Daniel, Spirina, Elena, Rivkina, Elizaveta, Liang, Renxing, Onstott, Tullis C., Vishnivetskaya, Tatiana A., and Lloyd, Karen G. Fri .
"Eight Metagenome-Assembled Genomes Provide Evidence for Microbial Adaptation in 20,000- to 1,000,000-Year-Old Siberian Permafrost". United States. https://doi.org/10.1128/aem.00972-21. https://www.osti.gov/servlets/purl/1991903.
@article{osti_1991903,
title = {Eight Metagenome-Assembled Genomes Provide Evidence for Microbial Adaptation in 20,000- to 1,000,000-Year-Old Siberian Permafrost},
author = {Sipes, Katie and Almatari, Abraham and Eddie, Alexander and Williams, Daniel and Spirina, Elena and Rivkina, Elizaveta and Liang, Renxing and Onstott, Tullis C. and Vishnivetskaya, Tatiana A. and Lloyd, Karen G.},
abstractNote = {Permafrost microbes may be metabolically active in microscopic layers of liquid brines, even in ancient soil. Metagenomics can help discern whether permafrost microbes show adaptations to this environment. Thirty-three metagenome-assembled genomes (MAGs) were obtained from six depths (3.5 m to 20 m) of freshly cored permafrost from the Siberian Kolyma-Indigirka Lowland region. These soils have been continuously frozen for ~20,000 to 1,000,000 years. Eight of these MAGs were ≥80% complete with <10% contamination and were taxonomically identified as Aminicenantes, Atribacteria, Chloroflexi, and Actinobacteria within bacteria and Thermoprofundales within archaea. MAGs from these taxa have been obtained previously from nonpermafrost environments and have been suggested to show adaptations to long-term energy starvation, but they have never been explored in ancient permafrost. The permafrost MAGs had greater proportions in the Clusters of Orthologous Groups (COGs) categories of energy production and conversion and carbohydrate transport and metabolism than did their nonpermafrost counterparts. They also contained genes for trehalose synthesis, thymine metabolism, mevalonate biosynthesis, and cellulose degradation, which were less prevalent in nonpermafrost genomes. Furthermore, many of these genes are involved in membrane stabilization and osmotic stress responses, consistent with adaptation to the anoxic, high-ionic-strength, cold environments of permafrost brine films. Our results suggest that this ancient permafrost contains DNA of high enough quality to assemble MAGs from microorganisms with adaptations to survive long-term freezing in this extreme environment.},
doi = {10.1128/aem.00972-21},
journal = {Applied and Environmental Microbiology},
number = 19,
volume = 87,
place = {United States},
year = {Fri Sep 10 00:00:00 EDT 2021},
month = {Fri Sep 10 00:00:00 EDT 2021}
}
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