Little is known about viruses in oxygen-deficient water columns (ODWCs). In surface ocean waters, viruses are known to act as gene vectors among susceptible hosts. Some of these genes may have metabolic functions and are thus termed auxiliary metabolic genes (AMGs). AMGs introduced to new hosts by viruses can enhance viral replication and/or potentially affect biogeochemical cycles by modulating key microbial pathways. Here we identify 748 viral populations that cluster into 94 genera along a vertical geochemical gradient in the Cariaco Basin, a permanently stratified and euxinic ocean basin. The viral communities in this ODWC appear to be relatively novel as 80 of these viral genera contained no reference viral sequences, likely due to the isolation and unique features of this system. We identify viral elements that encode AMGs implicated in distinctive processes, such as sulfur cycling, acetate fermentation, signal transduction, [Fe–S] formation, and N-glycosylation. These AMG-encoding viruses include two putative Mu-like viruses, and viral-like regions that may constitute degraded prophages that have been modified by transposable elements. Our results provide an insight into the ecological and biogeochemical impact of viruses oxygen-depleted and euxinic habitats.

对缺氧水柱（ODWC）中的病毒知之甚少。在海洋表层水域中，已知病毒在易感宿主之间充当基因载体。这些基因中的某些可能具有代谢功能，因此被称为辅助代谢基因（AMG）。通过病毒引入新宿主的AMG可以通过调节关键微生物途径来增强病毒复制和/或潜在地影响生物地球化学循环。在这里，我们确定了在Cari​​aco盆地（一个永久分层且富营养的海洋盆地）中沿垂直地球化学梯度聚集到94属的748个病毒种群。ODWC中的病毒群落似乎相对较新，因为其中80个病毒属不包含参考病毒序列，这可能是由于该系统的分离和独特特征所致。我们确定了编码AMG的病毒元素，这些AMG参与了独特的过程，例如硫循环，乙酸盐发酵，信号转导，[Fe–S]形成和N-糖基化。这些编码AMG的病毒包括两种假定的Mu样病毒和可能构成降解的原噬菌体的病毒样区域，这些原噬菌体已被转座因子修饰。我们的结果提供了对缺氧和富氧生境病毒的生态和生物地球化学影响的见解。