Faculty of Biology, Technion - Israel Institute of Technology, Haifa, 3200003, Israel.
Nat Microbiol. 2018 Jan;3(1):62-72. doi: 10.1038/s41564-017-0045-y. Epub 2017 Oct 30.
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, 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.
病毒在其遗传构成和感染的宿主方面具有全球性的丰富多样性。尽管它们影响着宿主的丰度、多样性和进化，但目前的方法还不足以定量理解它们对这些过程的影响。在这里，我们报告了固相单分子 PCR 克隆方法的适应性，用于对不同病毒的分类相关群进行定量分析。使用 T7 样蓝藻病毒作为我们的模型，我们发现当使用简并引物来包含该群体的多样性时，克隆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，T7 样蓝藻病毒在红海高度丰富，达到 77 万个噬菌斑/ml，并呈现出与蓝细菌相似的深度分布模式。此外，T7 样蓝藻病毒中两个主要分支的丰度在水柱中差异巨大：携带 psbA 光合作用基因并感染聚球藻或原绿球藻的 B 类噬菌体比缺乏 psbA 并感染聚球藻宿主的 A 类噬菌体至少丰富 20 倍。这些测量对于理解病毒种群动态以及病毒对不同微生物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。
