Metagenomics of wild bees across urban landscapes reveal core bacteria and plants and detection of potential pathogens

Background/Question/Methods

As urbanization continues to increase globally, altered landscapes and introductions of non-native species create unnatural diversity shifts within ecosystems, promote species invasions, and threaten the longevity of native species. To ensure conservation efforts are efficient and effective for at-risk wildlife, employing a metagenomic approach can be valuable as it allows one to explore the relationship of other organisms interacting directly or indirectly with wildlife of concern. Genomic tools can provide monitoring of invasive species, diseases and compare microbiomes - which are indicative of healthy or compromised populations - among species of concern. Globally, bee populations are in serious decline due to anthropogenically driven climate change, urbanization, and habitat fragmentation which are negatively altering their microbiomes and introducing pathogens. While most conservation efforts are focused on social bees such as honey bees and bumble bees, most bees are solitary and obtain their microbiome via interactions with their environment. In this study, we employ a metagenomic approach to characterize the metagenome (including arachnids, bacteria, fungi, nematodes, plants, protists, and viruses) of the native small carpenter bee, Ceratina calcarata. We further characterize the population genomics of this bee and the influences of isolation by distance, resistance, and environment across urban landscapes.

Results/Conclusions

Bees sampled from sites with low precipitation had significant overrepresentation of Enterobacteriaceae. Bees sampled from high temperature urban sites were overrepresented by various plants and protists, suggesting that urban centres may promote plant diversity and potential pathogens. In outer suburban areas, we found significant underrepresentation and homogenization of plant diversity, suggesting poorer resources available for wild bees and other native pollinators. The microbiome conformed to the core bacteria known in other managed and wild bee studies, but also detected Serratia, known honey bee pathogens. The metagenome consisted of several plant families, but was dominated by asters. At the genus level, Solanum (Solanaceae) and Gossypium (Malvaceae) were detected in C. calcarata in over 50% of the sites. Observed plant diversity revealed key genera associated with C. calcarata, consistent with former studies on their dietary breadth, and perhaps critical for their habitat. This study detected several known pollinator pathogens and parasites in various urban sites, emphasizing the need for monitoring of solitary bees across landscapes as populations may act as hubs or vectors for transmission. Overall, our metagenomic study found significant environmental variation in bee microbiomes and nutritional resources, as well as the potential early detection of stressors to bee health.