Social organization and physical environment shape the microbiome of harvester ants

All animals harbor microbiomes, which are obtained from the surrounding environment and are impacted by host behavior and life stage. To determine how the physical environment and social organization structure an organism's microbiome, we examined the microbial communities within and around nests of harvester ants (Veromessor andrei). We collected soil and nest content samples from five different nests. We used 16S rRNA sequencing and calculated alpha and beta diversity to compare microbial diversity and community composition across samples. We compared across i) sample types (ants, brood, seeds and reproductives, and soil), ii) soil inside and outside the nest, and iii) soil from different chamber types. Interestingly, we found support that both the environment and social organization structure the microbiome of V. andrei colonies. Soil from the five nests differed from one another in a way that mapped onto their geographical distance. Furthermore, soil from inside the nests resembled the surrounding soil, supporting the physical environment hypothesis. However, the microbiomes of the contents within the nest chambers, i.e. ants, brood, seeds and reproductives, differed from one another in their microbiome and from the surrounding soil, supporting the social organization hypotheses. This study highlights the importance of considering both environmental and social factors in understanding microbiome dynamics.