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Genomic reconstruction of fossil and living microorganisms in ancient Siberian permafrost

文献类型：期刊论文

作者Liang, Renxing1; Li, Zhou2; Lau Vetter, Maggie C. Y.1,3; Vishnivetskaya, Tatiana A.4,5; Zanina, Oksana G.5; Lloyd, Karen G.4; Pfiffner, Susan M.4; Rivkina, Elizaveta M.5; Wang, Wei6; Wiggins, Jessica6
刊名MICROBIOME
出版日期2021-05-17
卷号9期号:1页码:20
关键词Ancient permafrost Metagenome-assembled genome Fossil and living microorganisms Long-term survivability Adaptive strategy Asgard archaea
ISSN号2049-2618
DOI10.1186/s40168-021-01057-2
英文摘要Background: Total DNA (intracellular, iDNA and extracellular, eDNA) from ancient permafrost records the mixed genetic repository of the past and present microbial populations through geological time. Given the exceptional preservation of eDNA under perennial frozen conditions, typical metagenomic sequencing of total DNA precludes the discrimination between fossil and living microorganisms in ancient cryogenic environments. DNA repair protocols were combined with high throughput sequencing (HTS) of separate iDNA and eDNA fraction to reconstruct metagenome-assembled genomes (MAGs) from ancient microbial DNA entrapped in Siberian coastal permafrost. Results: Despite the severe DNA damage in ancient permafrost, the coupling of DNA repair and HTS resulted in a total of 52 MAGs from sediments across a chronosequence (26-120 kyr). These MAGs were compared with those derived from the same samples but without utilizing DNA repair protocols. The MAGs from the youngest stratum showed minimal DNA damage and thus likely originated from viable, active microbial species. Many MAGs from the older and deeper sediment appear related to past aerobic microbial populations that had died upon freezing. MAGs from anaerobic lineages, including Asgard archaea, however exhibited minimal DNA damage and likely represent extant living microorganisms that have become adapted to the cryogenic and anoxic environments. The integration of aspartic acid racemization modeling and metaproteomics further constrained the metabolic status of the living microbial populations. Collectively, combining DNA repair protocols with HTS unveiled the adaptive strategies of microbes to long-term survivability in ancient permafrost. Conclusions: Our results indicated that coupling of DNA repair protocols with simultaneous sequencing of iDNA and eDNA fractions enabled the assembly of MAGs from past and living microorganisms in ancient permafrost. The genomic reconstruction from the past and extant microbial populations expanded our understanding about the microbial successions and biogeochemical alterations from the past paleoenvironment to the present-day frozen state. Furthermore, we provided genomic insights into long-term survival mechanisms of microorganisms under cryogenic conditions through geological time. The combined strategies in this study can be extrapolated to examine other ancient non-permafrost environments and constrain the search for past and extant extraterrestrial life in permafrost and ice deposits on Mars.
WOS关键词ASPARTIC-ACID RACEMIZATION ; BACTERIAL COMMUNITY ; EXTRACELLULAR DNA ; SP NOV. ; SEDIMENTS ; BIODIVERSITY ; PROTEOME ; CULTURES ; REVEALS ; ARCHAEA
资助项目NSF[DEB-1442262] ; NSF[DEB-1442059] ; NSF[EAR-1528492] ; NSF International Research Experience for Students grant[IIA-1460058] ; U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, Genomic Science Program[DE-SC0020369] ; Russian Government Assignment[AAAA-A18-118013190181-6] ; Russian Government Assignment[RFBR 19-29-05003]
WOS研究方向Microbiology
语种英语
WOS记录号WOS:000657671300002
出版者BMC
资助机构NSF ; NSF International Research Experience for Students grant ; U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, Genomic Science Program ; Russian Government Assignment
源URL[http://ir.idsse.ac.cn/handle/183446/8710]  
专题深海科学研究部_地外海洋系统研究室
通讯作者Liang, Renxing
作者单位1.Princeton Univ, B88,Guyot Hall, Princeton, NJ 08544 USA
2.Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN USA
3.Chinese Acad Sci, Inst Deep Sea Sci & Engn, Sanya, Peoples R China
4.Univ Tennessee, Knoxville, TN USA
5.Russian Acad Sci, Inst Physicochem & Biol Problems Soil Sci, Pushchino, Moscow Region, Russia
6.Princeton Univ, Genom Core Facil, Princeton, NJ 08544 USA
推荐引用方式
GB/T 7714		 Liang, Renxing,Li, Zhou,Lau Vetter, Maggie C. Y.,et al. Genomic reconstruction of fossil and living microorganisms in ancient Siberian permafrost[J]. MICROBIOME,2021,9(1):20.
APA Liang, Renxing.,Li, Zhou.,Lau Vetter, Maggie C. Y..,Vishnivetskaya, Tatiana A..,Zanina, Oksana G..,...&Onstott, Tullis C..(2021).Genomic reconstruction of fossil and living microorganisms in ancient Siberian permafrost.MICROBIOME,9(1),20.
MLA Liang, Renxing,et al."Genomic reconstruction of fossil and living microorganisms in ancient Siberian permafrost".MICROBIOME 9.1(2021):20.

入库方式： OAI收割

来源：深海科学与工程研究所

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