Host-associated bacterial communities vary between genotypes but not by genetic distance in Daphnia galeata. D. galeata host genotype and bacterial communities

Host genotype and environment may interact to shape host-associated bacterial communities (commonly referred to as microbiomes). We sought to determine the extent of influence of the host genotype and exposure to lake sediment from different time periods, on bacterial communities of the water flea Daphnia galeata. We used 16S amplicon sequencing to profile the gut and body bacterial communities of eight D. galeata clonal lines hatched from resting eggs; these were isolated from two distinct sediment layers (dating to 1989 and 2009) of a single sediment core of the lake Greifensee, and maintained in a common garden in laboratory cultures for five years. Both the gut and body bacterial communities of D. galeata varied significantly in beta diversity, compositionally and phylogenetically among genotypes, but not between sediment layers, while medium bacterial community compositions did not. However, the beta diversity in bacterial community composition in Daphnia guts and bodies did not correlate with genetic distances between the genotypes. Our results indicate that Daphnia bacterial community structure is determined by both a host genetic component and possible interspecies interactions within the host-associated bacterial community.