Ancient environmental microbiomes and the cryosphere.

David A Pearce, Tommy Tsan-Yuk Lam, Julian W Tang, Nobuhiro Suzuki, Alexander D Williams, Vivian W Leung, Nishimura Hidekazu, Andrew C Clarke

Journal: Trends in microbiology 2025;33(2):233-249

PMID: 39487079

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Abstract

In this review, we delineate the unique set of characteristics associated with cryosphere environments (namely, ice and permafrost) which present both challenges and opportunities for studying ancient environmental microbiomes (AEMs). In a field currently reliant on several assumptions, we discuss the theoretical and empirical feasibility of recovering microbial nucleic acids (NAs) from ice and permafrost with varying degrees of antiquity. We also summarize contamination control best practices and highlight considerations for the latest approaches, including shotgun metagenomics, and downstream bioinformatic authentication approaches. We review the adoption of existing software and provide an overview of more recently published programs, with reference to their suitability for AEM studies. Finally, we summarize outstanding challenges and likely future directions for AEM research.

Address: Laboratory of Data Discovery for Health Limited (D(2)4H), 12/F, Building 19W, 19 Science Park West Avenue, Hong Kong Science Park, Hong Kong Special Administrative Region of China; State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China. Electronic address: [email protected].; State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China.; Respiratory Sciences, University of Leicester, Leicester, UK; Clinical Microbiology, University Hospitals of Leicester, Leicester, UK.; Virus Research Center, Clinical Research Division, Sendai Medical Center, Sendai 983-8520, Japan.; Institute of Plant Science and Resources, Okayama University, Chuou 2-20-1, Kurashiki, Okayama 710-0046, Japan.; School of Biosciences, University of Nottingham, College Road, Sutton Bonington, LE12 5RD, UK.; Department of Applied Science, Faculty of Health and Life Sciences, Northumbria University at Newcastle, Newcastle, NE1 8ST, UK; British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, UK. Electronic address: [email protected].; Laboratory of Data Discovery for Health Limited (D(2)4H), 12/F, Building 19W, 19 Science Park West Avenue, Hong Kong Science Park, Hong Kong Special Administrative Region of China; State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China. Electronic address: [email protected].

DOI: 10.1016/j.tim.2024.09.010

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MeSH Terms: Microbiota, Permafrost, Metagenomics, Ice, Environmental Microbiology, Bacteria, Computational Biology