Dynamics of infection in a novel group of promiscuous phages and hosts of multiple bacterial genera retrieved from river communities

Abstract

Phages are generally described as species- or even strain-specific viruses, implying an inherent limitation for some to be maintained and spread in diverse bacterial communities. Moreover, phage isolation and host range determination rarely consider the phage ecological context, likely biasing our notion on phage specificity. Here we identified and characterized a novel group of promiscuous phages existing in rivers by using diverse bacteria isolated from the same samples, and then used this biological system to investigate infection dynamics in distantly related hosts. We assembled a diverse collection of over 600 native bacterial strains and used them to isolate six podophages, named Atoyac, from different geographic origin and capable of infecting six genera in the Gammaproteobacteria. Atoyac phage genomes are highly similar to each other but not to those currently available in the genome and metagenome public databases. Detailed comparison of the phage's infectivity in diverse hosts and trough hundreds of interactions revealed variation in plating efficiency amongst bacterial genera, implying a cost associated with infection of distant hosts, and between phages, despite their sequence similarity. We show, through experimental evolution in single or alternate hosts of different genera, that plaque production efficiency is highly dynamic and tends towards optimization in hosts rendering low plaque formation. Complex adaptation outcomes observed in the evolution experiments differed between highly similar phages and suggest that propagation in multiple hosts may be key to maintain promiscuity in some viruses. Our study expands our knowledge of the virosphere and uncovers bacteria-phage interactions overlooked in natural systems.

Accurate viral genome reconstruction and host assignment with proximity-ligation sequencing

“…Viral binning has been previously indirectly achieved with custom analysis of select samples by placing multiple viral contigs together with their host genome sequences (29)(30)(31). This approach can fail in events of promiscuous phage infections (32,42,43), which have been observed in all four microbiome samples investigated in this study.…”

“…al remarked on using a custom application of the Louvain algorithm to reconstruct several possible vMAGs (31). However, these approaches rely on the assumption that each prokaryote may only host a single virus and that every virus may infect only one host (32), which is commonly not the case. To our knowledge, there is currently no available software designed for genome-resolved binning of vMAGs from fragmented metagenomic assemblies.…”