Potential effect of Wolbachia on virus restriction in the spider mite T. truncatus

The mite <i>T. truncatus</i> is a significant agricultural pest and may serve as a potential vector for viral transmission. However, the virome of <i>T. truncatus</i> remains understudied. Through metatranscriptomic analyses of publicly available data, we uncovered a diverse range of viruses associated with the spider mite, including crop-infecting pathogenic species such as <i>Potato virus Y</i> and <i>Cherry virus A</i>, and fourteen previously unknown viruses across several families (e.g., <i>Virgaviridae</i>, <i>Dicistroviridae</i>, <i>Kitaviridae</i>, <i>Betaflexiviridae</i>, and <i>Nudiviridae</i>). Taking advantage of mite samples under different conditions, we also assessed the impact of biotic (<i>Wolbachia</i> and <i>Spiroplasma</i> infection) and abiotic stresses (pesticide exposure and temperature stress) on the <i>T. truncatus</i> virome. Interestingly, <i>Wolbachia</i> appeared to restrict viral infections in <i>T. truncatus</i> by reducing viral diversity and abundance, with a pronounced effect on dicistroviruses. Surprisingly, a similar effect also observed with <i>Spiroplasma</i>. However, the viral restriction phenotype vanishes in co-infected mites. Transcriptomics analysis of singly-infected mites revealed upregulation of piRNA and autophagy-related genes, while lipid metabolism processes-related genes were downregulated, indicating an endosymbiont-sharing mechanisms of viral interference. Although the impact of abiotic stressors on the virome was not statistically significant, <i>Potato virus Y</i> and TtDV-2 viruses were absent in abamectin-exposed mites, suggesting a potential reduction in the viral diversity, while heat-stressed mites exhibited slightly higher viral diversity compared to those raised at regular temperatures. Overall, our work provides a detailed analysis of the <i>T. truncatus</i> virome, shedding light on how endosymbionts and environmental factors shape viral dynamics and offering potential insights for pest management strategies.