Abstract
Microbial communities are shaped by viral predators. Yet, resolving which viruses (phages) and bacteria are interacting is a major challenge in the context of natural levels of microbial diversity. Thus, fundamental features of how phage-bacteria interactions are structured and evolve in the wild remain poorly resolved. Here we use large-scale isolation of environmental marine Vibrio bacteria and their phages to obtain estimates of strain-level phage predator loads, and use all-by-all host range assays to discover how phage and host genomic diversity shape interactions. We show that lytic interactions in environmental interaction networks (as observed in agar overlay) are sparse—with phage predator loads being low for most bacterial strains, and phages being host-strain-specific. Paradoxically, we also find that although overlap in killing is generally rare between tailed phages, recombination is common. Together, these results suggest that recombination during cryptic co-infections is an important mode of phage evolution in microbial communities. In the development of phages for bioengineering and therapeutics it is important to consider that nucleic acids of introduced phages may spread into local phage populations through recombination, and that the likelihood of transfer is not predictable based on lytic host range.
Highlights
We found that whereas overlap in killing is high between phages within VIC-species, it is low between phages in different species
At the VICspecies level we found that concordance values were generally high (Fig. 4d), with phages in 10 VIC-species showing perfect overlap in their host range, including 3 VIC-species with member phages isolated on different days
At the VICspecies level we found that homologous recombination was the greater contributor (r/m > 1; one-sample Wilcoxon test, null hypothesis mean = 1, p-value 0.0002) to diversification for the majority of VIC-species with sufficient members to test (Fig. 4e, Source Data Fig. 4 sheet D)
Summary
Seawater was passed first through a 63um plankton net and sequentially through 5um (Whatman 111113 or Sterlitech PCT5047100), 1um (Whatman 111110 or Sterlitech PCT1047100), and 0.2um (Whatman 111106) hydrophilic polycarbonate filters; material recovered on the filters was resuspended by shaking for 20 min; dilution series of resuspended cells were filtered onto 0.2um polyethersulfone filters (Pall 66234) in a carrier solution of artificial seawater (40 g Sigma Sea Salts, S9883; 0.2um filtered), and filters placed directly onto Vibrio-selective MTCBS plates (BD Difco TCBS Agar 265020, supplemented with with 10 g NaCl per liter to 2% final w/v). Colonies (96) from each of three replicates of each size fraction were selected from the dilution plates with the fewest numbers of colonies (1,152 isolates per isolation day). Glycerol stocks were prepared by combining 100 ul of culture with 100 ul of 50% glycerol (BDH 1172-4LP) in 96-well microtiter plates and sealed with adhesive aluminum foil for preservation at −80 °C
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