Dynamics of the Queensland fruit fly microbiome under changes in host environment

Tephritid fruit flies are the most economically damaging insect pests of fruits and vegetables globally. Their biology is intimately linked to their microbiome. However, the complexities of the tephritid microbiomes remain poorly understood, largely because of the technical limitations of culture-dependent methods. To address this knowledge gap, the present study comprehensively characterized the bacterial and fungal microbiome of the Queensland fruit fly, Bactrocera tryoni (Froggatt) (aka: 'Qfly'), using Next-Generation Sequencing (NGS) to analyse both 16s rRNA and ITS amplicons on the Illumina MiSeq platform. Qfly is a highly polyphagous species that is Australia's most widespread and economically important fruit fly pest of horticulture. This thesis explores the microbial communities in wild Qfly larvae and their relationship to their host fruits. Qfly larvae from fruit infested in nature are found to harbour a diverse array of bacteria and fungi. The fungal microbiome, most of which comprises previously undescribed yeasts and yeast like fungi, closely reflects that of the host fruit indicating horizontal transfer as a dominant influence, although there are also some differences that suggest a closer association between larvae and some components of the fungal microbiome, likely reflecting vertical transfer during egg laying. The culture-independent approach enabled assessment of gut microbiome communities across all developmental stages in the wild-type flies prior to the domestication process. This comparative analysis between larvae, pupae and the adult gut microbiome revealed diverse microbial communities of bacteria and fungi in the larvae and adults. However, different bacteria and fungal taxa are abundant in the larvae and adult gut, which is likely related to differences in their nutritional biology. This thesis also includes the first comparative study of how artificial larval diets affect microbial communities across all developmental stages in the Qfly during the domestication process. The taxonomic profile of microbiome was different between carrot and the gel diet reared Qfly across all developmental stages whereby species richness was significantly higher in Qfly reared on the gel-based diet. Qfly reared on the gel diet reared scored higher in quality metrics than did those reared on the carrot diet at generation 5. Overall, my thesis provides valuable insights for understanding tephritid microbiomes and related ecology, in particular the Qfly's ability to infest a vast diversity of fruit types, and as well as for laboratory and factory-scale rearing. This knowledge may enable manipulation of the gut bacteria and fungi to improve the quality of artificially reared Qfly, and may also provide useful starting points for the development of pest management solutions -- summary.