Development and validation of a real-time PCR assay protocol for the specific detection and quantification of pelagiphages in seawater samples

Earth is inhabited by numerous adaptations of cellular forms shaped by the persistent scrutiny of natural selection. Thus, as natural selection has fixed beneficial adaptations of functional traits, cellular life has conquered almost all environmental niches on our planet. However, cellular life succumbs in number and genetic diversity to viruses. Among all viruses, phages are highly prevalent in diverse environments, and due to their vast genetic diversity and abundance, their relevant role as significant players in several ecological processes is now fully recognized. Pelagiphages, bacteriophages infecting bacteria of the SAR11 clade, are the most abundant viruses in the oceans. However, the ecological contribution of pelagiphages on populations of Pelagibacterales remains largely underestimated. An essential aspect of estimating the impact of bacteriophages is their absolute and precise quantification, which provides relevant information about the host-virus interactions and the structure of viral assemblages. Consequently, due to its abundance and claimed influence in the biogeochemical cycling of elements, the accurate quantification of pelagiphages results in an essential task. This study describes the development and validation of a sensitive, specific, accurate and reproducible qPCR platform targeting pelagiphages. Moreover, this method allowed the detection and quantification of pelagiphages in the Gulf of California for the first time.

Automated summary

Earth is home to various cellular forms that have adapted through natural selection. However, viruses outnumber and outdiversify cellular life. Among them, phages are prevalent and play significant roles in ecological processes. Pelagiphages, the most abundant viruses in the oceans, are understudied in their ecological contribution to Pelagibacterales populations. Accurate quantification of pelagiphages is crucial due to their abundance and claimed influence in element cycling. This study developed and validated a sensitive and specific qPCR platform for pelagiphages, allowing their detection and quantification in the Gulf of California for the first time.