Genome: Non-virulent Paenibacillus are beneficial parts of wild bee microbiomes

In previous studies, the gram-positive firmicute genus Paenibacillus was found with significant abundances in nests of wild solitary bees. Paenibacillus larvae are well-known for beekeepers as severe pathogens causing the fatal honey bee disease American Foulbrood and other members of the genus are either secondary invaders of other diseases or considered as a threat. We thus investigated whether Paenibacillus is a common bacterium associated with various wild bees, and hence might pose a latent threat to honey bees visiting the same floral resources. We collected 204 samples from 16 bee species at the same location and screened each for Paenibacillus using high-throughput-sequencing based 16S metabarcoding. We then isolated the identified strain from a solitary bee nest and sequenced its genome. We did find conserved toxin genes and such encoding for chitin-binding proteins, yet none specifically related to foulbrood virulence or chitinases. Thus the bacterium is unlikely a latent foulbrood threat to honey bees with wild bees as intermediate hosts. Phylogenomic analysis revealed a closer relationship to strains of root-associated Paenibacillus than such causing foulbrood or accompanying other diseases. We found anti-microbial evidence within the genome, confirmed with bioassays as strong growth inhibition of fungi, gram-positive and gram-negative bacteria. These properties might be beneficial for adult bees to reduce fungal infection risks and the development of larvae, considering the mold-friendly humid and nutrient-rich environment of brood cells of wild bee nest.