The gut microbiomes of desert Pachysoma spp. MacLeay (Coleoptera: Scarabaeidae)

Abstract

Microbial communities inhabit many environmental niches including the nutrient-rich gut systems of animals, where they are involved in a number of important processes. Insect gut microbiota may assist the host with several functions including synthesis of nutritional components lacking from the host diet and digestion of lignocellulosic materials. It is generally believed that the diet of the host plays an important role in the structure of the gut microbiome. Numerous studies have focused on insects feeding on lignocellulosic diets such as termites, as well as medically and agriculturally important insect species. Few studies have researched the gut microbiota of adult dung beetles. Most scarab beetle species feed on the liquid component of wet dung, whereas Pachysoma spp. may feed on lignocellulosic materials within their diet of dry dung, plant detritus or both. This feeding behaviour makes Pachysoma an ideal candidate for studying the role that diet has on gut microbiome assembly. Plant detritus feeding P. endroedyi and the dry dung feeding P. striatum were collected from Namaqualand, South Africa. The mid- and hindgut of each individual were dissected and mDNA extracted using a phenol-chloroform method. Amplicon sequencing of the bacterial 16S rRNA gene and the fungal ITS region was used to determine inter- and intra-specific differences in microbial community structures. Shotgun sequencing of the entire gut metagenome was carried out on mDNA extracted from whole gut samples. Shotgun sequencing was used for both taxonomic and functional annotation of the Pachysoma gut microbiomes. Both amplicon and shotgun sequencing detected substantial differences in bacterial and fungal diversity between the two Pachysoma species. Amplicon sequencing showed the number of bacterial phyla ranged from 6-11 and 4-7 (total 14 phyla) for P. endroedyi and P. striatum, respectively. Furthermore, a minimal core microbiome was detected with only 2.57% of the bacterial OTUs shared between the two Pachysoma species studied. Large intraspecific variations were also noted within both Pachysoma species. Fungal communities could not be detected in the gut of P. endroedyi, while only two fungal phyla were detected P. striatum gut samples. Metagenome shotgun sequencing detected a greater bacterial diversity (total of 39 phyla) than the 16S rRNA gene amplicon study, although large differences were noted between the two species. Furthermore, shotgun sequencing demonstrated that fungal communities were present in the guts of both Pachysoma species. Archaea, viruses and other eukaryotic microorganisms were also present in the gut metagenomes of both Pachysoma species. The functional capacity of the Pachysoma spp. gut microbiomes was analysed using shotgun sequencing. Both species had the genetic capacity to degrade cellulose and hemicellulose but not lignin, supporting the suggestion that P. striatum feeds on plant material in the dry dung. Furthermore, the functional capacity of the microbiomes of both Pachysoma species were comparable, suggesting the ability for both species to feed on either dry dung or plant detritus. The similarity of the functional profiles of the two Pachysoma species suggests the existence of a functional rather than phylogenetic core microbiome This primary study has successfully characterised the phylogenetic and functional profiles of the gut microbiomes of two Pachysoma species feeding on different substrates. However, it is still unclear if diet is the primary driver in gut microbiome assembly.