Despite their widespread distribution and remarkable antiquity no RNA viruses definitively associated with the domain Archaea have been identified. In contrast, 17 families of DNA viruses are known to infect archaea. In an attempt to uncover more of the elusive archaeal virosphere, we investigated the metatranscriptomes of hypersaline lakes that are a rich source of archaea. We sequenced RNA extracted from water filter samples of Lake Tyrrell (Victoria, Australia) and cultures seeded from four lakes in Antarctica. To identify highly divergent viruses in these data, we employed a variety of search tools, including Hidden Markov models (HMMs) and position-specific scoring matrices (PSSMs). From this, we identified 12 highly divergent, RNA virus-like candidate sequences from the virus phyla Artverviricota, Duplornaviricota, Kitrinoviricota, Negarnaviricota, and Pisuviricota, including those with similarity to the RNA-dependent RNA polymerase (RdRp). An additional analysis with an artificial intelligence (AI)-based approach that utilises both sequence and structural information identified seven putative and highly divergent RdRp sequences of uncertain phylogenetic position. A sequence matching the Pisuviricota from Deep Lake in Antarctica had the strongest RNA virus signal. Analyses of the dinucleotide representation of the virus-like candidates in comparison to that of potential host species were in some cases compatible with an association to archaeal or bacterial hosts. Notably, however, the use of archaeal CRISPR spacers as a BLAST database failed to detect any RNA viruses. We also described DNA viruses from the families Pleolipoviridae, Sphaerolipoviridae, Halspiviridae, and the class Caudoviricetes. Although we were unable to provide definitive evidence the existence of an RNA virus of archaea in these hypersaline lakes, this study lays the foundations for further investigations of highly divergent RNA viruses in natural environments.

中文翻译：

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高盐湖病毒群落组成。

尽管RNA病毒分布广泛且历史悠久，但尚未发现与古生菌领域明确相关的RNA病毒。相比之下，已知 17 个 DNA 病毒家族可感染古细菌。为了揭示更多难以捉摸的古细菌病毒圈，我们研究了高盐湖的元转录组，这些湖泊是古细菌的丰富来源。我们对从泰瑞尔湖（澳大利亚维多利亚州）滤水器样本中提取的 RNA 以及从南极洲四个湖泊播种的培养物进行了测序。为了识别这些数据中高度分化的病毒，我们采用了各种搜索工具，包括隐马尔可夫模型（HMM）和特定位置评分矩阵（PSSM）。由此，我们从病毒门 Artverviricota、Duplornaviricota、Kitrinoviricota、Negarnaviricota 和 Pisuviricota 中鉴定出 12 个高度分化的 RNA 病毒样候选序列，包括与 RNA 依赖性 RNA 聚合酶 (RdRp) 相似的序列。采用基于人工智能 (AI) 的方法进行的额外分析，利用序列和结构信息，确定了 7 个推定的、高度分化的、系统发育位置不确定的 RdRp 序列。与来自南极洲深湖的 Pisuviricota 相匹配的序列具有最强的 RNA 病毒信号。与潜在宿主物种相比，对类病毒候选者的二核苷酸表示进行的分析在某些情况下与古细菌或细菌宿主的关联相一致。然而值得注意的是，使用古细菌 CRISPR 间隔区作为 BLAST 数据库未能检测到任何 RNA 病毒。我们还描述了多脂病毒科、球脂病毒科、哈斯皮病毒科和有尾病毒纲的 DNA 病毒。尽管我们无法提供确凿证据证明这些高盐湖中存在古细菌 RNA 病毒，但这项研究为进一步研究自然环境中高度分化的 RNA 病毒奠定了基础。