Diversity of the Microbiomes in the Larval and Adult Stages of the European Cherry Fruit Fly (Rhagoletis cerasi) and Identification of Potential Biocontrol Candidate Taxa

Abstract

The cherry fruit fly (Rhagoletis cerasi) is a significant pest of cherries (Prunus avium) worldwide, causing fruit discoloration, rotting, and premature drop, with damage exceeding 80% in heavily infested areas. Traditional control methods, such as the use of chemical pesticides and cultural management, face limitations, including environmental risks, high costs, and the development of resistance. The insect microbiome plays an important role in enabling insects to survive under both normal and stressful environmental conditions. Beneficial microbes support nutrition, vitamin synthesis, and defense against pathogens, whereas pathogenic or imbalanced microbes can impair development, reproduction, and disease resistance. However, much remains unknown about the microbiome of R. cerasi. To address this knowledge gap, this study employed metatranscriptomics to profile and compare the microbiome of R. cerasi in both larval and adult stages. DNA- and RNA-based microorganisms were identified, including candidate microbial taxa previously reported as insect-associated or insecticidal in other insect systems. Analysis of 317 individuals, including larvae and adults, revealed striking differences in microbial composition across developmental stages. Among the assembled non-host transcripts, 57.8% were classified as microbial in adults, compared to only 6.39% in larvae. The most abundant candidate bacterial taxa with reported insecticidal/entomopathogenic associations in other insect systems included Pseudomonas fluorescens, Serratia entomophila, Serratia proteamaculans, Lysinibacillus sphaericus, Bacillus thuringiensis, and Paenibacillus spp., along with additional insect-associated taxa such as Enterococcus gallinarum and Pseudomonas aeruginosa. In addition, the intracellular endosymbiont Wolbachia was abundant across life stages, consistent with its well-known association with R. cerasi and its potential relevance to reproduction-based control strategies. This study provides the first detailed characterization of the R. cerasi microbiome, highlighting stage-specific differences in microbial composition and identifying potential candidates for biocontrol strategies.