Microbe-environment interactions in introduced bee pollinators across diverse landscapes

<p dir="ltr">Introduced species often undergo ecological and physiological changes as they establish in novel environments. Microbial and viral communities associated with their invasive hosts can play a key role in shaping health, survival, and ecological interactions. However, the extent to which environmental conditions and dietary inputs influence these microbial and viral characteristics during biological invasions remains poorly understood. This thesis investigates how environmental and dietary factors shape the gut bacterial and viral communities of two co-occurring introduced pollinators in Tasmania, Australia: the long-established European honeybee (Apis mellifera, introduced in 1831) and the more recent invader, the European buff-tailed bumblebee (Bombus terrestris, introduced in 1992). By integrating landscape-scale sampling with high-throughput sequencing approaches, including 16S rRNA metabarcoding for gut bacteria, ITS2 metabarcoding for corbicular pollen, and metatranscriptomic sequencing for total RNA viruses, this work provides a comprehensive assessment of how gut microbiomes and viromes vary across species and environments. The thesis addresses three main aims: (1) evaluate how environmental factors and corbicular pollen diversity influence the gut microbiome of B. terrestris; (2) compare the gut microbiomes of A. mellifera and B. terrestris and assess how species-specific responses are shaped by foraged pollen and local environment; and (3) characterise and compare the RNA viromes of A. mellifera and B. terrestris and determine how host identity, climate, and geography affect viral diversity and composition in a Varroa-free system. For Aim 1, gut bacterial composition and diversity in B. terrestris were significantly associated with precipitation and pasture percentage, with interaction effects between precipitation and temperature, as well as wind and pollen diversity. Aim 2 revealed distinct species-specific microbiome responses: B. terrestris gut bacterial communities were shaped by precipitation, pasture, wind velocity and pollen diversity, while A. mellifera comparatively showed a lower number of environmental interactions. Under Aim 3, virome composition and diversity in both species were influenced by multiple environmental factors. In A. mellifera, insect and plant virome compositions were only driven by precipitation, whereas in B. terrestris, site longitude, wind velocity and pasture percentage were significant drivers of insect viral composition. Phylogenetic analyses indicated local viral diversification of Black Queen Cell virus in honeybees; presence of two sub-strains of Lake Sinai virus 1 in honeybees and bumblebees; evidence for cross-species transmission of Lake Sinai virus 3 between honeybees and bumblebees; and the first detection of Moku virus in Australia and in bumblebees globally, the latter suggesting novel host associations and potential pathogen spillover among social Hymenoptera. Together, these findings highlight that gut microbial and viral communities of introduced pollinators are shaped by a combination of host identity, environmental conditions, and dietary resources. The greater environmental responses observed on the gut microbiota of B. terrestris, compared to A. mellifera, may have contributed to its recent successful invasion, while in both bees, viral communities appear to be shaped by a combination of host-specific factors and environmental influences. This work provides a valuable baseline for understanding pollinator-microbe-environment interactions in the absence of Varroa destructor and has broader implications for managing pollinator health in the context of invasion, as well as pathogen evolution across diverse landscapes.</p>