Rare Taxa and Stochastic Drift Drive the Microbiome Assembly of the Invasive Pest Drosophila suzukii, While Host Filtering Structures the Grape Sour Rot Community

Understanding the processes that shape microbial community structure is a central challenge in ecology. The relative importance of deterministic and stochastic processes in driving the microbiome assembly and composition remains poorly understood across diverse animal and plant hosts. Here, we characterized the bacterial (16 S rRNA) and fungal (ITS rRNA) communities in invasive pest spotted wing Drosophila (SWD, Drosophila suzukii) and sour-rot-affected grapes from seven California vineyards using high-throughput sequencing. We found that while the bacterial microbiome of male and female SWD was compositionally similar, these communities were entirely distinct from those on sour rot-affected grapes, indicating strong host-specific filtering. SWD also harbored substantially higher microbial density and greater diversity compared to grapes. Ecological modeling revealed a fundamental divergence in assembly mechanisms: SWD communities were predominantly shaped by stochastic processes, with a neutral model explaining 40% of the variation. In contrast, sour-rot-affected grape communities were structured by a combination of stochastic and deterministic factors. Importantly, taxa that deviated from neutral predictions, thereby indicating selection, were primarily classified as rare or intermediate in abundance. This suggests that low-abundance taxa may act as keystone drivers of dysbiosis during rot development. These results highlight the differing assembly rules governing a vector-host system: the mobile vector acts as a stochastic reservoir, promoting pathogen dispersal, while the sessile host imposes strict environmental filtering. This underscores the critical role of rare taxa in shaping community structure and ecosystem stability in SWD and its host grapes.