A combination of host ecology and habitat but not evolutionary history explains differences in the microbiomes associated with rotifers

The holobiont concept places emphasis on the strict relationship between a host and its associated microbiome, with several studies supporting a strong effect of the quality of the microbiome on the host fitness. The generalities of the holobiont have been questioned for several invertebrates, including zooplankton. Here we assess the role of host ecology, habitat, and evolutionary history to explain the differences in the microbiomes associated with rotifers, across a broad taxonomic spectrum and from different habitats. The analyses of 93 rotifer-associated microbiomes from 23 rotifer host species revealed that a combination of effects from the host ecology and its habitat seem to be stronger than host phylogenetic distances in explaining differences in microbial composition of the microbiomes. This pattern is in line with the idea of habitat filtering being a stronger explanation than co-evolution in shaping the relationship between a microbiome and its rotifer host.