Eight Metagenome-Assembled Genomes Provide Evidence for Microbial Adaptation in 20,000- to 1,000,000-Year-Old Siberian Permafrost

Sipes, Katie; Almatari, Abraham; Eddie, Alexander; Williams, Daniel; Spirina, Elena; Rivkina, Elizaveta; Liang, Renxing; Onstott, Tullis C.; Vishnivetskaya, Tatiana A.; Lloyd, Karen G.

doi:10.1128/aem.00972-21

Title: Eight Metagenome-Assembled Genomes Provide Evidence for Microbial Adaptation in 20,000- to 1,000,000-Year-Old Siberian Permafrost

Journal Article · 10 September 2021 · Applied and Environmental Microbiology

DOI: https://doi.org/10.1128/aem.00972-21 · OSTI ID:1991903

Sipes, Katie ^[1]; Almatari, Abraham ^[2]; Eddie, Alexander ^[2]; Williams, Daniel ^[2]; Spirina, Elena ^[3]; Rivkina, Elizaveta ^[3]; Liang, Renxing ^[4]; Onstott, Tullis C. ^[4];

^[5];

^[2]

Univ. of Tennessee, Knoxville, TN (United States); University of Tennessee
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)

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.

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Research Organization:: Univ. of Tennessee, Knoxville, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); National Science Foundation (NSF); Russian Foundation for Basic Research

Grant/Contract Number:: SC0020369

OSTI ID:: 1991903

Journal Information:: Applied and Environmental Microbiology, Journal Name: Applied and Environmental Microbiology Journal Issue: 19 Vol. 87; ISSN 0099-2240

Publisher:: American Society for MicrobiologyCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
MAGs
bioinformatics
environmental
exobiology
permafrost

Title: Eight Metagenome-Assembled Genomes Provide Evidence for Microbial Adaptation in 20,000- to 1,000,000-Year-Old Siberian Permafrost

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