Acetobacteraceae in the honey bee gut comprise two distant clades with diverging metabolism and ecological niches

Abstract

25Various bacteria of the family Acetobacteraceae are associated with the gut 26 environment of insects. Honey bees harbor two distinct Acetobacteraceae in their gut, 27Alpha2.1 and Alpha2.2. While Alpha2.1 seems to be a gut specialist, Alpha2.2 is also 28 found in the diet (e.g. royal jelly), the hypopharyngeal glands, and the larvae of honey 29 bees. Here, we combined amplicon and genome sequencing to better understand 30 functional differences associated with the ecology of Alpha2.1 and Alpha2.2. We find 31 that the two phylotypes are differentially distributed along the worker and queen bee 32 gut. Phylogenetic analysis shows that Alpha2.2 is nested within the acetic acid 33 bacteria and consists of two separate sub-lineages, whereas Alpha2.1 belongs to a 34 basal lineage with an unusual GC content for Acetobacteraceae. Gene content analysis 35 revealed major differences in the central carbon and respiratory metabolism between 36 the two phylotypes. While Alpha2.2 encodes two periplasmic dehydrogenases to 37 carry out oxidative fermentation, Alpha2.1 lacks this capability, but instead harbors 38 a diverse set of cytoplasmic dehydrogenases. These differences are accompanied by 39 the loss of the TCA cycle in Alpha2.2, but not in Alpha2.1. We speculate that Alpha2.2 40 has specialized for fast-resource utilization through incomplete carbohydrate 41 oxidation, giving it an advantage in sugar-rich environments such as royal jelly. On 42 the contrary, the broader metabolic range of Alpha2.1 may provide an advantage in 43 the worker bee hindgut, where competition with other bacteria and flexibility in 44 resource utilization may be relevant for persistence. Our results show that bacteria 45 belonging to the same family may utilize vastly different strategies to colonize niches 46 associated with the animal gut. 47 48According to a recent review on the taxonomy of Alphaproteobacteria (Munoz-49 Gomez, et al. 2019) and the standardized genome phylogeny-based taxonomy of 50 Parks et al. (Parks, et al. 2018), the family Acetobacteraceae (Rhodospirillales) is 51 comprised of an externally branching acidophilic/neutrophilic group and an internal 52 acetous group. The latter group includes acetic acid bacteria (AABs), which constitute 53 the vast majority of the described taxa of the Acetobacteraceae (Komagata, et al. 54 2014). 55 AAB inhabit sugar-rich environments and use a rather exceptional strategy to gain 56 energy. They oxidize sugars or sugar alcohols on the periplasmic side of the cell 57 envelop with the help of membrane-bound dehydrogenases that are linked to the 58 respiratory chain in a process known as oxidative fermentation (Matsushita and 59Matsutani 2016). This particular oxidative metabolism results in the accumulation of 60 fermentation products (such as acetic acid) in the environment. AABs naturally occur 61 in association with plants, flowers, and fruits (Bartowsky and Henschke 2008; 62

Compartmentalization of bacterial and fungal microbiomes in the gut of adult honeybees

“…Bacterial quantification (based on a normalized number of 16S rRNA gene copies) showed a significant compartmentalization of their load along the gut (Fig. 2a, b and Supplementary Table S1 ), with the highest densities observed in the distal compartments (ileum = 1.43 × 10 5 and rectum = 4.23 × 10 5 bacterial cells) than in the proximal compartments (crop = 1.83 × 10 4 and midgut = 1.87 × 10 4 ), thereby confirming the data reported in previous studies 21 , 42 . Furthermore, the gut compartments harbored significantly different bacterial communities ( F 3,16 = 6.6, p = 0.001; Fig.…”

“…In the present study, adult forager honeybees were collected from the front of the hive following exposure to the natural environment (i.e., flowered prairie), thereby enabling the recruitment of main core bacteria from the hive and contact among mates and environmental bacteria during harvest 3 , 29 , 44 . Such recruitment processes are affected by the surrounding environment and pollination landscape (e.g., microbiome variation in nectar, pollen, and hive materials 46 , 58 ), resulting in strong variation among the frequencies and biodiversity of bacteria associated with honeybees 5 , 21 , 29 , 43 . Although we anticipated that the type of environmental bacteria (non-gut bacteria, such as Actinomycetales , Alphaproteobacteria , Enterobacteriaceae , Pseudomonadales , Firmicutes, and Xanthomonadaceae 43 , 58 ) would vary depending on environmental conditions (such as location, season, food source, and climate), their recruitment and distribution was determined by the interaction between the physico-chemical conditions and biological network of the honeybee gut.…”

Genomic Signatures of Honey Bee Association in an Acetic Acid Symbiont

“…Notably, this tree groups B. intestini more closely to the majority of the B. apis strains, whereas Bombella sp. AS1 is more distantly related, and possibly a different species, as suggested by Bonilla-Rosso et al. (2019) .…”

Bombella favorum sp. nov. and Bombella mellum sp. nov., two novel species isolated from the honeycombs of Apis mellifera

“…apis /‘ P. apium ’, it has been hypothesized that several isolates (ESL0385, ESL0378 and AS1) within the ‘alpha 2.2–2 group’ could represent novel taxa within the genus Bombella . Also, they have not yet been formally characterized or published in peer-reviewed studies [16]. Sequence analysis showed that our proposed two novel species do not correspond to those uncharacterized taxa.…”