Impact of Rearing Conditions on the Ambrosia Beetle’s Microbiome

Abstract

Ambrosia beetles, along with termites and leafcutter ants, are the only fungus-farming lineages within the tree of life. Bacteria harbored by ambrosia beetles may play an essential role in the nutritional symbiotic interactions with their associated fungi; however, little is known about the impact of rearing conditions on the microbiota of ambrosia beetles. We have used culture-independent methods to explore the effect of rearing conditions on the microbiome associated with Xyleborus affinis, Xyleborus bispinatus, and Xyleborus volvulus, evaluating different media in laboratory-controlled conditions and comparing wild and laboratory conditions. Our results revealed that rearing conditions affected the fungal and bacterial microbiome structure and had a strong influence on bacterial metabolic capacities. We propose that the rearing conditions influence the ambrosia-associated fungal and bacterial communities. Furthermore, bacterial microbiome flexibility may help beetles adapt to different substrates.

Evidence for Succession and Putative Metabolic Roles of Fungi and Bacteria in the Farming Mutualism of the Ambrosia Beetle Xyleborus affinis

“…Second, their metabarcoding methods were inadequate for the ambrosia beetles that we focus on, because their models are associated with Ophiostomatales fungi for which internal transcribed spacer (ITS) metabarcoding does not work ( 63 – 65 ). In contrast, our 18S metabarcoding approach delivered results that are consistent with a previous isolation study, which has shown a lower abundance of OTUs in lab-reared ambrosia beetles than in wild-reared ambrosia beetles ( 46 ).…”

“…Among these OTUs, the five most abundant OTUs belonged to the genera Saccharomycopsis, Candida, and Raffaelea. These results correspond with the culturing results from other bark and ambrosia beetles (25,38,46,71). Both our metabarcoding and SEM visualizations showed that the yeasts are dominant in young galleries, after which filamentous Raffaelea species follow.…”

“…The most abundant and widely distributed bacterial genera were Enterobacter and Stenotrophomonas. Both genera have been isolated from other bark and ambrosia beetles ( 4 , 27 , 46 , 66 – 70 ). Their relative abundance negatively correlated with the diversity of bacteria, suggesting that they might be able to structure (i.e., dominate) the bacterial communities, possibly by secondary metabolites (see Fig.…”

“…To gain insights into the metabolic potential of the fungi associated with the ambrosia beetles, available genomes of the phylogenetically most closely related fungi (n ϭ 33 genomes; see Table S5 at https://doi.org/10.6084/m9.figshare.12477593) were selected, and the core genome and their metabolic profile were determined following the methodology reported by Ibarra-Juarez et al (46). Additionally, the presence of genes and specific metabolic pathways (degradation of plant and fungal cell wall components; biosynthesis of essential amino acids, cofactors and vitamins; nitrogen fixation; quorum sensing and biofilm production) were analyzed and plotted in a heatmap using "ggplot2" and "vegan" for R (v. To infer the metabolic capability of the bacterial microbiome in specific pathways, the relative frequencies of all genes involved in these pathways were calculated per sample.…”

“…There is a long history of studying fungal and bacterial associates in ambrosia beetles, e.g., by using traditional culturing techniques ( 32 , 34 , 36 – 38 , 45 ) or culture-independent approaches ( 4 , 27 , 46 , 47 ). Some of these studies have monitored fungal symbionts over time ( 37 , 38 , 48 – 50 ).…”