在过去的十年里,环境研究表明,古细菌在自然界中丰富而广泛,在全球范围内发挥着重要的生态作用。目前,然而,大多数古细菌谱系不能在实验室条件下培养,并且完全或几乎完全通过宏基因组学已知。类似的趋势延伸到古细菌病毒层,其中分离的代表可用于少数模型古细菌病毒宿主系统。病毒宏基因组学提供了一种替代方法来规避基于培养的病毒发现的局限性,并提供了对多样性的见解,分布,以及未培养的古细菌病毒对环境的影响。目前,宏基因组学方法已成功应用于探索与极端和中温古细菌的各种谱系相关的病毒,包括阿斯加德古细菌(Asgardarcheota),ANME-1古细菌(Methanophagales),Thaumarchaera(Nitrosossphaeria),阿尔蒂亚(Altiarchaota),和海洋第二类古细菌(海神)。这里,我们概述了古细菌病毒宏基因组学中广泛使用的方法,覆盖metavirome制备,基因组注释,系统发育和系统发育分析,和考古宿主分配。我们希望这一总结将有助于进一步探索和表征潜伏在不同环境中的神秘古菌病毒。
During the past decade, environmental research has demonstrated that archaea are abundant and widespread in nature and play important ecological roles at a global scale. Currently, however, the majority of archaeal lineages cannot be cultivated under laboratory conditions and are known exclusively or nearly exclusively through metagenomics. A similar trend extends to the archaeal virosphere, where isolated representatives are available for a handful of model archaeal virus-host systems. Viral metagenomics provides an alternative way to circumvent the limitations of culture-based virus discovery and offers insight into the diversity, distribution, and environmental impact of uncultured archaeal viruses. Presently, metagenomics approaches have been successfully applied to explore the viromes associated with various lineages of extremophilic and mesophilic archaea, including Asgard archaea (Asgardarchaeota), ANME-1 archaea (Methanophagales), thaumarchaea (Nitrososphaeria), altiarchaea (Altiarchaeota), and marine group II archaea (Poseidoniales). Here, we provide an overview of methods widely used in archaeal virus metagenomics, covering metavirome preparation, genome annotation, phylogenetic and phylogenomic analyses, and archaeal host assignment. We hope that this summary will contribute to further exploration and characterization of the enigmatic archaeal virome lurking in diverse environments.