New method to recover, detect and characterize bacteriophages and hosts from large drinking water volumes

Diversity and abundance of bacteria in drinking water distribution systems are influenced by abiotic factors such as pH, temperature, presence of growth inhibitors and water sources. But little is known about biotic factors such as the implication of bacteriophages on bacterial communities. Indeed, it is well admitted that bacteriophages can shape those populations.To fill this gap and describe bacteriophage diversity in drinking water, two methods of filtration/concentration were compared with a weekly sample collection, for one month. Non-targeted sequencing was used to characterize bacterial and phage diversities and abundances.Viral fraction represented 1.5 to 2.5 percent of microorganisms detected in samples with most sequences being unassigned. For assigned sequences, majority were associated with Caudovirales order. Moreover, most predicted bacterial hosts belonged to Sphingomonadales, Sphingobacteriales, Rhizobiales, Obscuribacterales, Burkholderiales, Caulobacterales, Clostridiales and Pseudomonadales orders, which were also detected in samples, highlighting the robustness of host prediction tool. Moreover, we were able to identify 277 putative phages present in all samples, called core phageome. We found that 25 195 non-viral contigs aligned to 250 viral contigs of the core phageome. 626 alignments showed a match between the taxonomy of the non-viral contigs and the host prediction of the viral contigs. This method suggests the possibility to get bioinformatics pairs instead of bacteria-phage pairs isolated from the environment, which is quite difficult. These alignments exhibited different alignment configurations. Some were quite small with a high percentage of homology while others were bigger with lower similarities, suggesting genetic exchanges between bacteria and phages.Here, we developed a method to concentrate simultaneously bacteriophages with bacteria from low-biomass environment with a metagenomic approach to describe bacterial and phage diversities. Indeed, majority of studies have separately studied bacteria and bacteriophages from the same sample. This study showed that most detected bacteria were also the most predicted hosts, strengthening the hypothesis saying that when a bacterium is present, an associated phage is also present. Moreover, this method allowed to detect sequence similarities between phages and bacteria, suggesting potential genetic exchanges. Altogether, this study highlights a tight interaction between bacteria and bacteriophages in drinking water and the possibility to study phages and potential hosts at the same time.