Genomic reconstruction of fossil and living microorganisms in ancient Siberian permafrost

• Published in: Microbiome
• Main Authors: Renxing Liang, Zhou Li, Maggie C. Y. Lau Vetter, Tatiana A. Vishnivetskaya, Oksana G. Zanina, Karen G. Lloyd, Susan M. Pfiffner, Elizaveta M. Rivkina, Wei Wang, Jessica Wiggins, Jennifer Miller, Robert L. Hettich, Tullis C. Onstott
• Format: Article in Journal/Newspaper
• Language: English
• Published: BMC 2021
• Subjects: Ancient permafrost; Metagenome-assembled genome; Fossil and living microorganisms; Long-term survivability; Adaptive strategy; Asgard archaea; Microbial ecology; QR100-130; permafrost
• Online Access: https://doi.org/10.1186/s40168-021-01057-2; https://doaj.org/article/13daa8b3aa1c498da53104717998e3c9

Abstract 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 ...