Integrating 16S and 18S sequencing reveals coupled prokaryotic and eukaryotic relationships in drinking water biofilms

Drinking water biofilms host diverse communities spanning all realms of life. However, despite the known interactions between opportunistic pathogens and microbial eukaryotes such as amoebae, most studies focus only on the prokaryotic populations in these systems. As a result, the degree to which microbial eukaryotes shape biofilm communities and the persistence of opportunistic waterborne pathogens, such as Legionella spp. is still largely unknown. Here we leveraged a set of 128 non-disinfected drinking water shower hose biofilms collected across Switzerland to characterize both communities and quantify eukaryotes' role in shaping prokaryotic communities and Legionella persistence. We found both communities to present a conserved set of core taxa dominated by oligotrophic bacterial families and amoebae. The prevalence of taxa was mainly driven by the phylogenetic diversity among their sequence variants rather than their number alone. We detected prokaryotic and eukaryotic communities to show similar patterns in their richness and composition, influencing each other more than abiotic building-level factors. Legionellaceae bacteria were detected in 82% of samples presenting a diversity extending known reference species and no clear dominant taxa. Legionellaceae richness did not correlate with the richness of known amoebal hosts, but rather other amoebae, indicating that eukaryotic taxa relevant for Legionella persistence extend beyond the classically described hosts. These findings highlight the importance of integrating the eukaryotic communities to understand the microbial ecology in drinking water biofilms and recognize the conditions which allow opportunistic waterborne pathogens such as Legionella to persist.