Microbiome structure of a wild Drosophila community along tropical elevational gradients and comparison to laboratory lines

While the biogeography of free-living microbial communities is well-studied, community turnover along environmental gradients in host-associated communities is not well understood. In particular, patterns of host-microbiome diversity along elevational gradients remain largely uncharacterized. Because elevational gradients may serve as natural proxies for climate change, understanding these temperature-influenced patterns can inform our understanding of the threats facing hosts and their microbes in a warming world. In this study, we analysed microbiomes from pupae & adults of four Drosophila species native to Australian tropical rainforests. We sampled wild individuals at high and low elevation along two mountain gradients, to determine natural diversity patterns, and sampled laboratory-reared individuals from isofemale lines established from the same localities, to see if any natural patterns would be retained in the lab. In both environments, we controlled for diet to help elucidate other deterministic patterns of microbiome composition. Microbiome community composition differed radically between laboratory-reared and field-caught flies but did not significantly differ across elevation. We found some notable taxonomic differences in Drosophila microbiomes between different species and elevations. We also found similar microbiome composition from both types of provided food, and we therefore suggest the significant differences in richness are the products of environments with different bacterial species pools. We conclude that elevational differences in temperature are not a major factor in determining Drosophila microbiome composition and we caution against determining microbiome composition from lab-only specimens, particularly long-term cultures. ImportanceBacteria form microbiome communities inside many different hosts. These communities vary widely in diversity, and form differently, depending on a wide variety of factors. Diet is often an important factor for microbiome composition. We controlled diet in our study by providing the same food sources. We looked at how host-microbiome communities differed in four Drosophila species over two mountain gradients in tropical Australia, to see if temperature-driven differences in elevation affected host-microbiomes. We also compared these results to individuals kept in the laboratory to understand how different settings changed microbiome communities. We found that field samples had substantially greater microbiome diversity than those from the lab and found minimal differences in microbiome communities over elevation. Our study shows that environmental sources of bacteria matter for Drosophila microbiome composition, and caution should be exercised when interpreting microbiome results from lab-only studies.