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

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Abstract

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.

Data availability

The datasets generated during and/or analyzed during the current study are available in the National Library of Medicine (NCBI) Sequence Read Archive (SRA) repository, [https://www.ncbi.nlm.nih.gov/sra/PRJNA1162420](https:/www.ncbi.nlm.nih.gov/sra/PRJNA1162420).

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Acknowledgements

This work received support and help from FCT/MCTES (LA/P/0008/2020 DOI https://doi.org/10.54499/LA/P/0008/2020, UIDP/50006/2020 DOI https://doi.org/10.54499/UIDP/50006/2020 and UIDB/50006/2020 DOI https://doi.org/10.54499/UIDB50006/2020), through national funds.

Funding

MCS PhD work was supported by Fundação para a Ciência e Tecnologia (FCT), through Grant Number 2021.06319.BD (DOI https://doi.org/10.54499/2021.06319.BD). Research was funded by the FCT DrosuGreen Project (reference PTDC/ASP-PLA/4477/2020).

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Authors and Affiliations

  1. Biology Department, Faculty of Science (FCUP), University of Porto, 4169-007, Porto, Portugal

    Marino Costa-Santos, Sara Sario, Rafael J. Mendes & Conceição Santos

  2. LAQV-REQUIMTE, Biology Department, Faculty of Science (FCUP), University of Porto, 4169-007, Porto, Portugal

    Marino Costa-Santos, Sara Sario, Rafael J. Mendes & Conceição Santos

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  1. Marino Costa-Santos
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  2. Sara Sario
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  3. Rafael J. Mendes
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Contributions

Conceptualization, MCS and CS; Methodology, MCS, SS, RJM, and CS; Validation, MCS; Formal Analysis, MCS, SS, RJM, and CS; Investigation, MCS; Resources, CS; Writing – Original Draft Preparation, MCS; Writing – Review & Editing, MCS, SS, RJM, and CS; Visualization, MCS, SS, RJM, and CS; Supervision, SS, RJM, and CS; Project Administration, SS, and CS; Funding Acquisition, CS.

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Marino Costa-Santos.

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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 (2026). https://doi.org/10.1038/s41598-026-37656-y

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Keywords

  • Spotted-wing drosophila
  • Summer and winter morphotypes
  • Bacteriota
  • Core microbiome
  • Microbiome shifts
  • Host-microbe interaction

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