Different substrates within a lake harbour connected but specialised microbial communities

Natural water bodies contain physically interconnected habitats suitable for microbes, such as different water layers and substrates for biofilms. Yet, little is known on the extent to which microbial communities are shared between such habitats and whether differences and similarities are consistent between sites. Here we explicitly tested hypotheses on similarities between aquatic bacterial communities found floating in water, in association with daphnids and with copepods, within bottom sediments, and on littoral stones of a lake. Through high-throughput 16S rDNA amplicon sequencing, distinguishable patterns were retrieved between habitats. In particular, community composition was more similar between the two zooplankton taxa, between the two water depths, and was rather different in sediments, where a large fraction of the total diversity was present. Most bacterial taxa were restricted to one or few habitats, whereas only few were found as generalists on different habitats. Our results indicate a limited role of source–sink dynamics between habitats for aquatic bacteria. Similarly to patterns of diversity in larger organisms, community composition was different between habitats, potentially because of specific mechanisms creating and maintaining habitat filtering.