The impact of phage treatment on bacterial community structure is negligible compared to antibiotics

Abstract

Abstract Background Phage treatment is suggested as an alternative to antibiotics; however, there is limited knowledge of how phage treatment impacts resident bacterial community characteristics. When phages induce bacterial lysis, resources become available to the resident community. Therefore, the density of the target bacteria is essential to consider when investigating the effect of phage treatment but has never been studied. Thus, we invaded microcosms containing a lake-derived community with Flavobacterium columnare strain Fc7 at no, low or high densities and treated them with either the bacteriophage FCL-2, the antibiotic Penicillin or kept them untreated (3x3 factorial design). The communities were sampled over the course of one week, and bacterial community composition and density were examined by 16S rDNA amplicon sequencing and flow cytometry. Results We show that phage treatment had negligible impacts on the resident community when the phage host F. columnare Fc7 was present, as it caused insignificant differences in bacterial density, α- and β-diversity, successional patterns, and community assembly. However, a significant change was observed in community composition when the phage host was absent, mainly driven by a substantial increase in Aquirufa. In contrast, antibiotics induced significant changes in all community characteristics investigated. The most crucial finding was a bloom of γ-proteobacteria and a shift from selection to ecological drift dominating community assembly. Conclusions This study investigated how phage host density impacts phage treatment effects and provides strong evidence that bacteriophages do not significantly affect the composition of bacterial communities. The findings highlight the importance of considering the density of target bacteria when investigating the effect of phage treatment, as more changes were observed when the phage host was absent. Moreover, higher phage host densities increased the contribution of stochastic community assembly and resulted in a feast-famine like response in bacterial density. This finding emphasises that the invader density used in bacterial invasion studies impacts the experimental reproducibility. Overall, this study supports that phage treatment is substantially less disturbing to bacterial communities than antibiotic treatments.