How Hosts Taxonomy, Trophy, and Endosymbionts Shape Microbiome Diversity in Beetles

Abstract

Bacterial communities play a crucial role in the biology, ecology, and evolution of multicellular organisms. In this research, the microbiome of 24 selected beetle species representing five families (Carabidae, Staphylinidae, Curculionidae, Chrysomelidae, Scarabaeidae) and three trophic guilds (carnivorous, herbivorous, detrivorous) was examined using 16S rDNA sequencing on the Illumina platform. The aim of the study was to compare diversity within and among species on various levels of organization, including evaluation of the impact of endosymbiotic bacteria. Collected data showed that beetles possess various bacterial communities and that microbiota of individuals of particular species hosts are intermixed. The most diverse microbiota were found in Carabidae and Scarabaeidae; the least diverse, in Staphylinidae. On higher organization levels, the diversity of bacteria was more dissimilar between families, while the most distinct with respect to their microbiomes were trophic guilds. Moreover, eight taxa of endosymbiotic bacteria were detected including common genera such as Wolbachia, Rickettsia, and Spiroplasma, as well as the rarely detected Cardinium, Arsenophonus, Buchnera, Sulcia, Regiella, and Serratia. There were no correlations among the abundance of the most common Wolbachia and Rickettsia; a finding that does not support the hypothesis that these bacteria occur interchangeably. The abundance of endosymbionts only weakly and negatively correlates with diversity of the whole microbiome in beetles. Overall, microbiome diversity was found to be more dependent on host phylogeny than on the abundance of endosymbionts. This is the first study in which bacteria diversity is compared between numerous species of beetles in a standardized manner.

Keywords: Bacterial community; Coleoptera; Endosymbionts; Host–microbe interactions; Microbial ecology.

Fig. 1

The plot of the relative share of bacteria in examined specimens of 24 species of beetles showed in relation to a simplified phylogenetic tree of examined beetles. Shown only bacterial operational taxonomic units, which relative frequencies higher than 5% and found in more than half of examined individuals in any of infected host. Photographs of exemplary infected beetle hosts were reprinted from ICONOGRAPHIA COLEOPTERORUM POLONIAE under a CC BY license, with permission (© Copyright. by Prof. Lech Borowiec, Wrocław 2007–2018, Department of Biodiversity and Evolutionary Taxonomy, University of Wroclaw, Poland)

Fig. 2

Box plots of microbiome alpha diversity metrics (observed operational taxonomic units = OTU, Shannon’s diversity index = Shannon, Faith’s Phylogenetic Diversity = Faith, and Pielou’s measure of species evenness = Pielou) presented for beetles from selected families (left panel) and trophic guilds (right panel)

Fig. 3

Principal coordinate analyses of microbiome beta diversity metrics (Bray–Curtis distance = Bray-Curtis and unweighted UniFrac = uwUniFrac) presented for beetles on the level of families and trophic guilds

Fig. 4

Non-metric multidimensional scaling plot of Bray-Curtis dissimilarities between microbiomes found in beetle individuals belonged to particular families (a) and trophic guilds (b). Ellipses = 95% confidence intervals.

Fig. 5

Correlation between a microbiome diversity (presented on example of Faith’s Phylogenetic Diversity) and endosymbiotic bacteria prevalence (numbers of Illumina reads of 16S rDNA sequences) in examined beetles and bWolbachia and Rickettsia prevalence