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

Why tiny gut communities matter for a big farm problem

The spotted-wing drosophila, Drosophila suzukii, is a tiny fruit fly that causes big headaches for growers of berries and soft fruits around the world. Unlike most fruit flies, it can pierce ripening fruit, making it hard to control with insecticides and costly for farmers. This study asks a deceptively simple question with far-reaching implications: how do the communities of bacteria living in and on these flies change with the seasons, and could those microbes be helping the insect survive winter and invade new regions?

The troublemaker behind damaged berries

Drosophila suzukii is an invasive species from Southeast Asia that has spread through Europe and North America, partly because it tolerates cold winters and can feed on a wide variety of fruits. Females have a saw-like egg-laying organ that lets them cut into fresh berries, where their larvae develop protected inside the fruit. Climate change and limited control options have helped this pest flourish. Scientists already knew that the fly shows different body forms in summer and winter, with darker, larger winter flies better suited to survive the cold. What was not clear is whether the fly’s resident bacteria also shift with the seasons and whether some bacterial partners stay with the insect all year long.

Tracking the flies and their bacterial passengers

To explore this, researchers followed a wild population of D. suzukii on an organic farm in northern Portugal over roughly a year. They trapped flies in spring, summer, and autumn of 2022 and in winter of 2023, separating males and females and pooling a few individuals per sample. Using DNA-based methods that read a standard bacterial marker gene (16S rRNA), they catalogued which bacteria were present and in what proportions. They then used statistical tools to compare bacterial diversity by season and sex, and computational methods to predict what kinds of metabolic jobs those microbes might be doing inside the fly.

A stable bacterial core with seasonal accents

Across all samples, a consistent set of bacterial groups kept showing up. The microbiome was dominated by Proteobacteria, with genera such as Gluconobacter, Pseudomonas, Commensalibacter, Pantoea, Acetobacter and the intracellular partner Wolbachia appearing frequently and often at substantial levels. By looking at how often these genera appeared above a small abundance threshold, the authors defined a “core microbiome” that seemed to persist regardless of season or sex. When they added flies collected from several other farms in northern Portugal, the same key genera reappeared, suggesting that this core microbiome is not unique to one orchard but may be characteristic of regional D. suzukii populations.

Winter-specialist microbes without a winter-specialist toolbox

Season, but not sex, clearly influenced which non-core bacteria were present. Females tended to have slightly more even and diverse bacterial communities than males, likely reflecting their higher activity and broader contact with food sources, yet overall community structure was similar between sexes. In contrast, samples from different seasons separated statistically: spring and summer clustered together, while autumn and winter formed another group. Several bacterial genera were enriched in winter flies, including Morganella, Methanosaeta, Serratia, Duganella, Frateuria, Suttonella and Janthinobacterium. Many of these microbes are known from cold environments, decomposing organic matter, or roles in breaking down plant chemicals and recycling nutrients—features that could help flies survive when ripe fruit is scarce and temperatures drop. However, when the team used prediction tools to infer microbial functions, they found that the overall metabolic potential of the microbiome changed little across seasons. Despite shuffling which species were present, the community seemed to maintain a similar set of capabilities, a pattern known as functional redundancy.

What this means for pest control and future research

The study shows that D. suzukii carries a stable core set of bacteria year-round, overlaid with a flexible, season-dependent layer of additional microbes, especially in winter. These winter-associated bacteria may help the fly cope with cold, poor diets, and plant or pesticide toxins, even though the basic functions performed by the community remain broadly similar. For growers and pest managers, this work suggests that targeting the fly’s microbial partners—either by disrupting helpful winter bacteria or exploiting vulnerable points in the core microbiome—could one day complement existing control strategies. For now, the research provides a crucial baseline map of the fly’s bacterial world and points the way toward experiments that test how specific microbes influence survival, reproduction, and the success of biological control methods.

Citation: Costa-Santos, M., Sario, S., Mendes, R.J. et al. Seasonal dynamics and core stability of the bacterial microbiome of a Drosophila suzukii wild population. Sci Rep 16, 6569 (2026). https://doi.org/10.1038/s41598-026-37656-y

Keywords: Drosophila suzukii, microbiome, seasonal adaptation, invasive pest, gut bacteria