Incipiently social carpenter bees (Xylocopa) host distinctive gut bacterial communities and display geographic structure as revealed by full-length 16S sequencing

Abstract

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 strain-level diversity and relatedness, remain poorly understood. Here, we use full-length 16S 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 apis, 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 both species 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 strains of core taxa. In both bee species, bacterial species exhibited geographic patterns in the presence of specific sequence variants. 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 (V4) was considered. We conclude that these Xylocopa species host a distinctive microbiome, similar to that of previously characterized social apids, which suggests that further investigation to understand the evolution of bee microbiome and its drivers is warranted.

Bee breweries: The unusually fermentative, lactobacilli-dominated brood cell microbiomes of cellophane bees

“…Lactobacillus is present in adult guts as well as Agave nectar, but at much lower and more variable relative abundances than in larval provisions ( Figure 2 ). In addition to Lactobacillus , adult gut microbiomes contain a variety of bacterial genera common among bees and other pollinating insects, such as Entomomonas and Fructobacillus ( McFrederick et al, 2017 ; Hammer et al, 2020 ; Wang et al, 2020 ; Handy et al, 2023 ). In a smaller set of samples, collected in 2018 from the same site in Arizona, adult guts of Ptiloglossa , Caupolicana , and Protoxaea gloriosa (Andrenidae) were all dominated by Lactobacillus ( Figure 2 ).…”

“…Larval provisions of Ptiloglossa and Caupolicana specifically harbor Apilactobacillus while those of Crawfordapis harbor unique and potentially novel Lactobacillus -related taxa. Thus, diphaglossine bees fit an emerging pattern of symbiotic interactions between bees and lactobacilli, spanning solitary species, social species, the adult stage, and brood cells ( Kwong and Moran, 2016 ; McFrederick et al, 2017 ; Voulgari-Kokota et al, 2019 ; Tang et al, 2021 ; Handy et al, 2023 ).…”

“…Where and when filtering takes place are also unknown, but given that Apilactobacillus dominates even freshly provisioned brood cells, one possibility is that it begins in the female bee’s crop. Microbes have been observed at higher densities in the bee crop as compared with nectar ( Batra et al, 1973 ), and the crop of Xylocopa sonorina bees is strongly enriched in Apilactobacillus ( Handy et al, 2023 ). We cannot directly address this hypothesis because our adult bee samples include the midgut and hindgut in addition to the crop, and these regions may have highly distinct microbiomes ( Kwong and Moran, 2016 ).…”

“…Saccharibacter is sporadically abundant in Ptiloglossa brood cells and adults, and in Agave nectar. Saccharibacter and other aerobic, acid-tolerant, and osmophilic Acetobacteraceae are commonly found in insects with sugar-rich diets ( Crotti et al, 2010 ), on pollen ( Jojima et al, 2004 ), and in the crop ( Handy et al, 2023 ) and pollen provisions of bees ( McFrederick et al, 2012 ). Fungal sequences are also present, but at very low relative abundances, in shotgun metagenomes from Ptiloglossa larval provisions.…”

Bumble bee microbiota shows temporal succession and increase of lactic acid bacteria when exposed to outdoor environments

“…They were proposed as a new genus of Xylocopilactobacillus gen. nov (Kawasaki et al, 2023). Although carpenter bees (Xylocopa) are not eusocial (but rather facultatively, incipiently or sub-social), their microbiota shows surprising parallels to that of Bombus species, with similar conserved core-taxa including Schmidhempelia, Bombilactobacillus and Bombiscardovia (Gu et al, 2023;Handy et al, 2023). Here it can be speculated that the long life expectancy of the females in Xylocopa species which share the nests with the offspring adult generation (Velthuis and Gerling, 1983), allows for a similar microbial transfer as otherwise only known from eusocial corbiculate bees.…”