Divergence and convergence of gut microbiomes of wild insect pollinators

Abstract

Pollination services provided by wild insect pollinators are critical to natural ecosystems and crops around the world. There is an increasing appreciation that the gut microbiota of these insects influences their health and consequently their services. However, pollinator gut microbiota studies have focused on well-described social bees, but rarely include other, more phylogenetically divergent insect pollinators. To expand our understanding, we explored the insect pollinator microbiomes across three insect orders through two DNA sequencing approaches. First, in an exploratory 16S amplicon sequencing analysis of taxonomic community assemblages, we found lineage-specific divergences of dominant microbial genera and microbiota community composition across divergent insect pollinator genera. However, we found no evidence for a strong broad-scale phylogenetic signal, which we see for community relatedness at finer scales. Subsequently, we utilized metagenomic shotgun sequencing to obtain metagenome-assembled genomes and assess the functionality of the microbiota from pollinating flies and social wasps. We uncover a novel gut microbe from pollinating flies in the family Orbaceae that is closely related to Gilliamella spp. from social bees but with divergent functions. We propose this novel species be named Candidatus Gilliamella eristali. Further metagenomes of dominant fly and wasp microbiome members suggest that they are largely not host-insect adapted and instead may be environmentally derived. Overall, this study suggests selective processes involving ecology or physiology, or neutral processes determining microbe colonization may predominate in the turnover of lineages in insect pollinators broadly, while evolution with hosts may occur only under certain circumstances and on smaller phylogenetic scales. IMPORTANCE Wild insect pollinators provide many key ecosystem services, and the microbes associated with these insect pollinators may influence their health. Therefore, understanding the diversity in microbiota structure and function, along with the potential mechanisms shaping the microbiota across diverse insect pollinators, is critical. Our study expands beyond existing knowledge of well-studied social bees, like honey bees, including members from other bee, wasp, butterfly, and fly pollinators. We infer ecological and evolutionary factors that may influence microbiome structure across diverse insect pollinator hosts and the functions that microbiota members may play. We highlight significant differentiation of microbiomes among diverse pollinators. Closer analysis suggests that dominant members may show varying levels of host association and functions, even in a comparison of closely related microbes found in bees and flies. This work suggests varied importance of ecological, physiological, and non-evolutionary filters in determining structure and function across largely divergent wild insect pollinator microbiomes.

Keywords: Gilliamella; Orbaceae; insect pollinator; microbiomes; microbiota; symbionts.

Fig 1

Per host genera relative abundance of microbial families with at least 1% abundance in the data set (>296,547 reads).

Fig 2

Observed species richness and Shannon alpha diversity index of gut communities for each host genus. Bars represent the medians, and the boxes show the interquartile ranges. Whiskers are the upper and lower values, with outliers shown as individual data points beyond these.

Fig 3

Ordination plot of the Bray-Curtis beta diversity distance among individual host microbiomes. Host genera are represented by shape and color combinations. The inset represents the same but with the genera Apis and Bombus removed.

Fig 4

Orbaceae family phylogeny from selected core genes from the fly-associated metagenome-assembled genome assigned as Gilliamella sp. and existing genomes. Coloring shows different species while the branch length shows amino acid substitution rates. Pseudomonas aeruginosa is used as an outgroup.

Fig 5

Fly-associated Candidatus Gilliamella eristali reconstructed metabolic pathways in comparison with other Gilliamella species. Solid black lines are genes/pathways shared by Candidatus G. eristali and other Gilliamella species. Dotted black lines are genes/pathways lacking across Gilliamella species. Dotted red lines are genes/pathways found in bee-associated Gilliamella but not in Candidatus G. eristali. Blue solid lines are genes/pathways found in Candidatus G. eristali but not in bee-associated Gilliamella species.