Viruses are key members of microbial communities that exert control over host abundance and metabolism, thereby influencing ecosystem processes and biogeochemical cycles. Aquifers are known to host taxonomically diverse microbial life, yet little is known about viruses infecting groundwater microbial communities. Here, we analyzed 16 metagenomes from a broad range of groundwater physicochemistries. We recovered 1571 viral genomes that clustered into 468 high-quality viral operational taxonomic units (vOTUs). At least 15% were observed to be transcriptionally active, although lysis was likely constrained by the resource-limited groundwater environment. Most were unclassified (95%), and the remaining 5% were Caudoviricetes. Comparisons with viruses inhabiting other aquifers revealed no shared species, indicating substantial unexplored viral diversity. In silico predictions linked 22.4% of the viruses to microbial host populations, including to ultra-small prokaryotes, such as Patescibacteria and Nanoarchaeota. Many predicted hosts were associated with the biogeochemical cycling of carbon, nitrogen, and sulfur. Metabolic predictions revealed the presence of 205 putative auxiliary metabolic genes, involved in diverse processes associated with the utilization of the host’s intracellular resources for biosynthesis and transformation reactions, including those involved in nucleotide sugar, glycan, cofactor, and vitamin metabolism. Viruses, prokaryotes overall, and predicted prokaryotic hosts exhibited narrow spatial distributions, and relative abundance correlations with the same groundwater parameters (e.g., dissolved oxygen, nitrate, and iron), consistent with host control over viral distributions. Results provide insights into underexplored groundwater viruses, and indicate the large extent to which viruses may manipulate microbial communities and biogeochemistry in the terrestrial subsurface.

中文翻译：

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地下水病毒的高生态位特异性和宿主遗传多样性

病毒是微生物群落的关键成员，它们控制宿主的丰度和新陈代谢，从而影响生态系统过程和生物地球化学循环。众所周知，含水层蕴藏着分类学上多样化的微生物，但人们对感染地下水微生物群落的病毒却知之甚少。在这里，我们分析了来自广泛地下水物理化学的 16 个宏基因组。我们恢复了 1571 个病毒基因组，这些基因组聚集成 468 个高质量病毒操作分类单元 (vOTU)。至少 15% 被观察到具有转录活性，尽管裂解可能受到资源有限的地下水环境的限制。大多数是未分类的 (95%)，其余 5% 是有尾病毒纲。与居住在其他含水层的病毒进行比较，发现没有共享物种，这表明存在大量未经探索的病毒多样性。计算机预测将 22.4% 的病毒与微生物宿主群体联系起来，包括超小型原核生物，如 Patescibacteria 和 Nanoarchaeota。许多预测的宿主与碳、氮和硫的生物地球化学循环有关。代谢预测揭示了 205 个假定的辅助代谢基因的存在，这些基因参与与利用宿主细胞内资源进行生物合成和转化反应相关的多种过程，包括那些涉及核苷酸糖、聚糖、辅因子和维生素代谢的基因。病毒、原核生物和预测的原核宿主表现出狭窄的空间分布，以及与相同地下水参数（例如溶解氧、硝酸盐和铁）的相对丰度相关性，这与宿主对病毒分布的控制一致。结果提供了对尚未开发的地下水病毒的深入了解，并表明病毒可以在很大程度上操纵陆地地下的微生物群落和生物地球化学。