What lurks beneath the humped back? - The patterns of bacterial abundance, diversity and distribution across communities of a dipteran family

Symbiotic microorganisms have diverse effects on insect life history traits and fitness and can be transmitted within populations and across species. At the level of populations and communities, symbionts can shape insect responses and adaptation to environmental challenges. Despite their importance, our understanding of microbiota in natural insect communities remains limited, particularly for dark taxa - hyperdiverse, abundant, broadly distributed, yet severely understudied groups.

Here, we asked about the abundance, diversity, and distribution of microbiota in natural communities of insects in one such dark taxon, scuttle flies (Diptera: Phoridae), with particular emphasis on their dominant facultative endosymbiont, Wolbachia . We did this using high-throughput host and bacterial marker gene amplicons sequencing, including microbiota quantification, for a set of 1,842 humped-back flies representing ca. 186 species from six sites in Northern Sweden.

The resulting dataset, likely the largest microbiota survey for a non-model insect clade to date, provided novel and biologically realistic insights into host-microbe symbioses. We observed significant differences in bacterial abundance among individual insects, with variations up to four orders of magnitude even among flies of the same sex, species, and population. Females consistently harboured more bacteria than males, at least partly due to the consistently higher prevalence and abundance of facultative endosymbionts, especially Wolbachia and Rickettsia . Within this group, we noted consistent patterns in the prevalence of symbiont genera between host species. Other less abundant bacteria included Serratia, Providencia, Carnobacterium, Pseudomonas, Erwinia, Amycolatopsis and Spiroplasma .

Our study highlights the critical role of high-throughput sequencing and integrative methods in revealing the complexity and ecological significance of symbiotic microorganisms in dark taxa, advancing our understanding of their influence on natural communities.