Abstract
Symbiosis with bacteria is common across insects, resulting in adaptive host phenotypes. The recently described bacterial symbionts Lactobacillus micheneri, Lactobacillus timberlakei, and Lactobacillus quenuiae are found in wild bee pollen provisions, bee guts, and flowers but have small genomes in comparison to other lactobacilli. We sequenced, assembled, and analyzed 27 new L. micheneri clade genomes to identify their possible ecological functions in flower and bee hosts. We determined possible key functions for the L. micheneri clade by identifying genes under positive selection, balancing selection, genes gained or lost, and population structure. A host adherence factor shows signatures of positive selection, whereas other orthologous copies are variable within the L. micheneri clade. The host adherence factors serve as strong evidence that these lactobacilli are adapted to animal hosts as their targets are found in the digestive tract of insects. Next, the L. micheneri clade is adapted toward a nutrient-rich environment, corroborating observations of where L. micheneri is most abundant. Additionally, genes involved in osmotolerance, pH tolerance, temperature resistance, detoxification, and oxidative stress response show signatures of selection that allow these bacteria to thrive in pollen and nectar masses in bee nests and in the bee gut. Altogether, these findings not only suggest that the L. micheneri clade is primarily adapted to the wild bee gut but also exhibit genomic features that would be beneficial to survival in flowers.
Highlights
Bees are important for wild and agricultural ecosystems but are in decline (Potts et al 2010; Burkle et al 2013)
These findings suggest that the L. micheneri clade is primarily adapted to the wild bee gut and exhibit genomic features that would be beneficial to survival in flowers
Given the largely absent metabolic and biosynthetic capability of the L. micheneri clade, it is unlikely that L. micheneri clade wild bee associates are biosynthetic mutualists
Summary
Bees are important for wild and agricultural ecosystems but are in decline (Potts et al 2010; Burkle et al 2013). Research on the bee microbiome has increased in the past decade, due to the new interest in bee health (Engel et al 2016). A monophyletic clade of bees in family Apidae which notably includes bumble bees and honey bees, have a specific core microbiome that is important for bee health (Martinson et al 2011; Li et al 2015; Kwong et al 2017). Strains of Gilliamella apicola have the capability to metabolize carbohydrates toxic to the host (Zheng et al 2016). Honey bee and bumble bee core gut lactobacilli ferment a wide variety of simple carbohydrates in the gut, whereas Snodgrassella can convert fermented products to pyruvate for metabolism (Kwong, Engel, et al 2014; Kwong, Mancenido, et al 2014)
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