Wild bees and their nests host Paenibacillus bacteria with functional potential of avail

Abstract

BackgroundIn previous studies, the gram-positive firmicute genus Paenibacillus was found with significant abundances in nests of wild solitary bees. Paenibacillus larvae is well-known for beekeepers as a severe pathogen causing the fatal honey bee disease American foulbrood, and other members of the genus are either secondary invaders of European foulbrood or considered a threat to honey bees. We thus investigated whether Paenibacillus is a common bacterium associated with various wild bees and hence poses a latent threat to honey bees visiting the same flowers.ResultsWe collected 202 samples from 82 individuals or nests of 13 bee species at the same location and screened each for Paenibacillus using high-throughput sequencing-based 16S metabarcoding. We then isolated the identified strain Paenibacillus MBD-MB06 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. Phylogenomic analysis revealed a closer relationship to strains of root-associated Paenibacillus rather than strains causing foulbrood or other accompanying diseases. We found anti-microbial evidence within the genome, confirmed by experimental bioassays with strong growth inhibition of selected fungi as well as gram-positive and gram-negative bacteria.ConclusionsThe isolated wild bee associate Paenibacillus MBD-MB06 is a common, but irregularly occurring part of wild bee microbiomes, present on adult body surfaces and guts and within nests especially in megachilids. It was phylogenetically and functionally distinct from harmful members causing honey bee colony diseases, although it shared few conserved proteins putatively toxic to insects that might indicate ancestral predisposition for the evolution of insect pathogens within the group. By contrast, our strain showed anti-microbial capabilities and the genome further indicates abilities for chitin-binding and biofilm-forming, suggesting it is likely a useful associate to avoid fungal penetration of the bee cuticula and a beneficial inhabitant of nests to repress fungal threats in humid and nutrient-rich environments of wild bee nests.Electronic supplementary materialThe online version of this article (10.1186/s40168-018-0614-1) contains supplementary material, which is available to authorized users.

Susceptibility of Red Mason Bee Larvae to Bacterial Threats Due to Microbiome Exchange with Imported Pollen Provisions

“…These three genera also co-occurred significantly together (all cor >0.35, bootstrapped pseudo- p < 0.001 ***). The dominant Paenibacillus was further taxonomically classifiable into to the Paenibacillus pabuli / amylolyticus / xylanexedens phylogenetic cluster [ 52 ] with 100% sequence identity given the short investigated marker V4 16S rRNA gene. The bacterial communities in the respective pollen provisions were slightly more homogeneous between samples for healthy larvae (beta dispersity: 0.48) than for deceased larvae (beta dispersity: 0.57).…”

“…P. alvei is a saprophytic, aerobic bacterium which does not grow in healthy bee larvae, but can establish in diseased honey bee colonies in larval remains [ 58 ]. On the other hand, other members of the genus are associated with beneficial functions in solitary and stingless bee nests [ 52 , 59 ], protecting them from molding and other fungal threats. The here identified Paenibacillus was further taxonomically closely related to P. pabuli, P. amylolyticus , and P. xylanexedens , which are usually considered to be environmental, but are associated with co-infections with other bacteria in vertebrates [ 57 , 60 ].…”

Linking pollen foraging of megachilid bees to their nest bacterial microbiota

“…On the bee side, if plants act as reservoirs or transfer hubs for bacteria (Keller et al, ; McFrederick et al, ), then specialized bee–plant interactions in a landscape could secure specialized bee–bacteria relationships. Thus, plant availability and specialized interactions with plants would be significant not only for the nutrition of the bees, but also for the maintenance of their nest microbiota.…”

“…On the other hand, solitary bee nests harbor highly diverse bacterial communities (Keller, Grimmer, & Steffan‐Dewenter, ; Lozo et al, ; McFrederick & Rehan, ; Mohr & Tebbe, ; Voulgari‐Kokota, Grimmer, Steffan‐Dewenter, & Keller, ). However, only few studies have dealt with their role in larval health (Keller et al, ; McFrederick, Vuong, & Rothman, ) or their acquisition routes (McFrederick et al, ; Voulgari‐Kokota, McFrederick, Steffan‐Dewenter, & Keller, ). Bees leading a solitary lifestyle with no direct contact between multiple generations are excluded from the benefits of a social structure, where individuals are in constant interaction with their nestmates, and their nest microbiota is more susceptible to environmentally introduced bacteria (Keller et al, ; McFrederick et al, ; Rothman, Andrikopoulos, Cox‐Foster, & McFrederick, ; Voulgari‐Kokota, Grimmer, et al, ; Voulgari‐Kokota, McFrederick, et al, ).…”

Quantitative and Qualitative Characterization of Plant Endo-bacteriome by Plant Dna-free Sequencing Method

“…Highthroughput sequencing and bioinformatics tools have the potential to reveal the full structure of plant endo-bacteriomes. Next-generation sequencing (NGS) of the 16S rRNA gene (16S) has been widely used to decipher microbiomes associated with humans and other animals, soil, plants, and various environmental niches [5][6][7][8][9][10][11]. By amplifying all 16S sequences from a sample and sequencing the acquired 16S amplicon library, the complete bacterial composition and the relative aundance of each bacterium can be determined [12][13][14][15].…”