Viruses are globally abundant and extremely diverse in their genetic make-up and in the hosts they infect. Although they influence the abundance, diversity and evolution of their hosts, current methods are inadequate for gaining a quantitative understanding of their impact on these processes. Here we report the adaptation of the solid-phase single-molecule PCR polony method for the quantification of taxonomically relevant groups of diverse viruses. Using T7-like cyanophages as our model, we found the polony method to be far superior to regular quantitative PCR methods and droplet digital PCR when degenerate primers were used to encompass the group's diversity. This method revealed that T7-like cyanophages were highly abundant in the Red Sea in spring 2013, reaching 770,000 phages ml^-1, and displaying a similar depth distribution pattern to cyanobacteria. Furthermore, the abundances of two major clades within the T7-like cyanophages differed dramatically throughout the water column: clade B phages that carry the psbA photosynthesis gene and infect either Synechococcus or Prochlorococcus were at least 20-fold more abundant than clade A phages that lack psbA and infect Synechococcus hosts. Such measurements are of paramount importance for understanding virus population dynamics and the impact of viruses on different microbial taxa and for modelling viral influence on ecosystem functioning on a global scale.

中文翻译：

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使用polony方法对环境中各种病毒种群进行定量。

病毒在全球范围内非常丰富，其遗传组成和所感染的宿主也极为多样化。尽管它们影响宿主的数量，多样性和进化，但目前的方法不足以定量地了解其对这些过程的影响。在这里，我们报告了固相单分子PCR polony方法的适应性，用于量化分类学相关组的各种病毒。使用T7样的噬菌体作为我们的模型，当使用简并引物来涵盖群体的多样性时，我们发现polony方法远远优于常规定量PCR方法和液滴数字PCR。该方法表明，2013年春季，红海中T7样的噬菌体非常丰富，达到了770,000噬菌体ml ^-1，并显示出与蓝细菌相似的深度分布模式。此外，在整个水柱中，T7类巨噬细胞内两个主要进化枝的丰度差异显着：携带psbA光合作用基因并感染Synechococcus或Prochlorococcus的进化枝B噬菌体比缺乏的进化枝A噬菌体富集至少20倍。 psbA和感染Synechococcus宿主。这种测量对于了解病毒种群动态以及病毒对不同微生物分类群的影响以及在全球范围内模拟病毒对生态系统功能的影响至关重要。