Contrasting Life Strategies of Viruses that Infect Photo- and Heterotrophic Bacteria, as Revealed by Viral Tagging

Abstract

Ocean viruses are ubiquitous and abundant and play important roles in global biogeochemical cycles by means of their mortality, horizontal gene transfer, and manipulation of host metabolism. However, the obstacles involved in linking viruses to their hosts in a high-throughput manner bottlenecks our ability to understand virus-host interactions in complex communities. We have developed a method called viral tagging (VT), which combines mixtures of host cells and fluorescent viruses with flow cytometry. We investigated multiple viruses which infect each of two model marine bacteria that represent the slow-growing, photoautotrophic genus Synechococcus (Cyanobacteria) and the fast-growing, heterotrophic genus Pseudoalteromonas (Gammaproteobacteria). Overall, viral tagging results for viral infection were consistent with plaque and liquid infection assays for cyanobacterial myo-, podo- and siphoviruses and some (myo- and podoviruses) but not all (four siphoviruses) heterotrophic bacterial viruses. Virus-tagged Pseudoalteromonas organisms were proportional to the added viruses under varied infection conditions (virus-bacterium ratios), while no more than 50% of the Synechococcus organisms were virus tagged even at viral abundances that exceeded (5 to 10×) that of their hosts. Further, we found that host growth phase minimally impacts the fraction of virus-tagged Synechococcus organisms while greatly affecting phage adsorption to Pseudoalteromonas. Together these findings suggest that at least two contrasting viral life strategies exist in the oceans and that they likely reflect adaptation to their host microbes. Looking forward to the point at which the virus-tagging signature is well understood (e.g., for Synechococcus), application to natural communities should begin to provide population genomic data at the proper scale for predictively modeling two of the most abundant biological entities on Earth.

Water column stratification structures viral community composition in the Sargasso Sea

“…The present study demonstrated that ssDN A phage at the BATS site are quite diverse and display temporal patterns in community composition similar to those of dsDN A viruses. As a first step towards deciphering the ecological impact of ssDNA phage, future studies should attempt to link the ssDNA phage with their potential host communities, a task that will be greatly aided by emerging singlecell methods such as phageFISH and viral tagging (Deng et al 2012, Allers et al 2013, Dang & Sullivan 2014, Brum & Sullivan 2015. This study's goal was to obtain an overview of the viral communities over 2 depths, 2 seasons, and several years, by using 4 different methods.…”

Rising to the challenge: accelerated pace of discovery transforms marine virology

“…This has been applied to model systems (for example, marine Pseudoalteromonas and its phages) 102 , but is readily transferable to the field if knowledge of host and viral gene markers is available. Finally, viral tagging identifies phages that can infect a cultivated microbial host, and does not require the use of marker genes 103,104 (FIG. 3d).…”

“…The example shown here demonstrates the ability of phageFISH to detect different stages of infection. d | In viral tagging 103,104 , fluorescently stained wild viruses are mixed with cultivated microorganisms, allowing adsorption of viruses to their host. Cells are then sorted by flow cytometry to separate cells with and without attached viruses, and then metagenomic sequencing is used to assemble the genomes of viruses that infect the cultivated host microorganism.…”

40 Years of archaeal virology: Expanding viral diversity

“…In a similar approach, we have utilized the analysis of the CRISPR/ Cas loci derived from single cell genomics from archaeal dominated hot springs to link viral genomes detected by viral metagenomics to their hosts. Other approaches developed in marine systems such as viral tagging (Deng et al, 2012(Deng et al, , 2014b and FISH tools (Allers et al, 2013;Sheik et al, 2014) provide a direct and rapid means to link virus types to their hosts in natural systems. Further advances will likely result in the development of novel techniques to temporally monitor total virus infection in natural environments.…”