Daphnia microbiome Lake Maggiore

Natural water bodies contain interconnected biotic and abiotic habitats for microbes; yet, little is known on the extent to which microbial communities are shared between such habitats. We here analysed the microbial communities (through 16S rDNA) of water at 10m and 40m depth, daphnids, copepods, sediments, and epilithic biofilms of a large subalpine lake. The communities of each habitat were clearly distinguishable and significantly different in α-diversity, with the sediment having the highest richness and the animal samples the lowest. Nonetheless, all samples shared similar numbers of taxa in pair-wise comparison. A large fraction of the diversity found in other samples was also harboured in the sediment. Most of the taxa found were habitat specialists and only few taxa were generalists. Within each specific habitat, the most abundant taxa were rarely more specialist for the habitat then the other taxa. The highest number of specialists was found in the sediment, followed by epilithic biofilms. Most generalist were affiliated with Flavobacteria, Beta- and Alpha-proteobacteria, whereas the specialist were from several classes. Our results suggest that bacterial taxa are indeed shared between habitats in a lake, but that the specific conditions therein select for a rather specialised subset of a lake’s microbiome