Williams Alexander D, Leung Vivian W, Tang Julian W, Hidekazu Nishimura, Suzuki Nobuhiro, Clarke Andrew C, Pearce David A, Lam Tommy Tsan-Yuk
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.
State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China.
Trends Microbiol. 2025 Feb;33(2):233-249. doi: 10.1016/j.tim.2024.09.010. Epub 2024 Oct 31.
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.
在本综述中，我们描述了与冰冻圈环境（即冰和永久冻土）相关的独特特征集，这些特征为研究古代环境微生物群落（AEMs）带来了挑战和机遇。在一个目前依赖多种假设的领域中，我们讨论了从不同年代的冰和永久冻土中回收微生物核酸（NAs）的理论和实证可行性。我们还总结了污染控制的最佳实践，并强调了对最新方法的考虑，包括鸟枪法宏基因组学和下游生物信息学鉴定方法。我们回顾了现有软件的采用情况，并概述了最近发布的程序，并参考了它们对AEM研究的适用性。最后，我们总结了AEM研究中突出的挑战和可能的未来方向。
