Comparing bacterial microbiome composition of Xylocopa species across populations using PacBio 16S rRNA gene sequencing

The gut microbiota of bees affect nutrition, immunity, and host fitness,
yet the role of diet, sociality, and geographic variation in determining
microbiome structure, including variant-level diversity and relatedness,
remain poorly understood. Here, we use full-length 16S rRNA amplicon
sequencing to compare the crop and gut microbiomes of two incipiently
social carpenter bee species, Xylocopa sonorina and Xylocopa tabaniformis,
from multiple geographic sites within each species’ range. We found that
Xylocopa species share a set of core taxa consisting of
Bombilactobacillus, Bombiscardovia, and Lactobacillus, found in
>95% of all individual bees sampled, and Gilliamella and Apibacter
were also detected in the gut of both species with high frequency. The
crop bacterial community of X. sonorina was comprised nearly entirely of
Apilactobacillus with occasionally abundant nectar bacteria. Despite
sharing core taxa, Xylocopa species’ microbiomes were distinguished by
multiple bacterial lineages, including species-specific variants of core
taxa. The use of long-read amplicons revealed otherwise cryptic species
and population-level differentiation in core microbiome members which was
masked when a shorter fragment of the 16S rRNA (V4) was considered. Of the
core taxa, Bombilactobacillus and Bombiscardovia exhibited differentiation
in ASVs among bee populations, but this was lacking in Lactobacillus,
suggesting that bacterial genera in the gut may be structured by different
processes. We conclude that these Xylocopa species host a distinctive
microbiome, similar to that of previously characterized social corbiculate
apids, which suggests that further investigation to understand the
evolution of bee microbiome and its drivers is warranted.