Seasonal dynamics and core stability of the bacterial microbiome of a Drosophila suzukii wild population

Drosophila suzukii (spotted-wing drosophila, SWD) is an invasive pest with pronounced sexual dimorphism and seasonal polyphenism. While seasonal morphotypes are well documented, how these phenotypic traits shape the SWD microbiome remains poorly understood. Here, we investigate how sex and seasonal phenotypes shape microbiome composition in SWD. We hypothesize that these factors drive microbial shifts, with some taxa varying between phenotypes and others forming a stable core. Understanding these patterns may reveal microbiome-associated adaptations relevant to SWD ecology and management. To investigate this, we monitored SWD microbiome dynamics over one year by collecting individuals during spring, summer, and autumn of 2022 and winter of 2023 from an organic farm in northern Portugal. Bacterial communities were compared using 16 S rRNA amplicon sequencing. This SWD population retained a core bacterial community, highly represented by Gluconobacter, Pseudomonas, Commensalibacter and Pantoea, consistent with other SWD Portuguese populations. Moreover, microbiome composition varied significantly across seasons but not between sexes, although females exhibited higher microbial alpha diversity. Linear discriminant analysis of relative abundance (LEfSe) revealed enrichment of Morganella, Methanosaeta, Serratia, Duganella, Frateuria, Suttonella, and Janthinobacterium in winter groups. However, functional prediction analyses revealed no significant differences in microbiome functional potential across seasons, suggesting functional redundancy despite taxonomic variation. This study offers baseline insights into the seasonal stability and plasticity of the D. suzukii microbiome, contributing to a deeper ecological understanding of this invasive pest.