Transcriptome and microbiome of coconut rhinoceros beetle (Oryctes rhinoceros) larvae

Evidence for the independent evolution of a rectal complex within the beetle superfamily Scarabaeoidea

Rectal or cryptonephridial complexes have evolved repeatedly in arthropods, including in beetles where they occur in ∼190,000 species of Cucujiformia + Bostrichoidea, and Lepidoptera where they occur in ∼160,000 species. Sections of the Malpighian/renal tubules coat the outer surface of the rectum, acting as powerful recycling systems of the gut contents, recovering water and specific solutes. There are hints that a rectal complex evolved independently within another beetle group, Scarabaeoidea. Here we report our observations of rectal complexes in Scarabaeoidea, which support this view. We did not find a rectal complex in the related group, Staphylinoidea, or in Lucanidae, a basal group of Scarabaeoidea. We did observe rectal complexes in Melolontha melolontha (Melolonthini), Pachnoda marginata and Cetonia aurata (Cetoniinae), consistent with previous reports from these groups. Intriguingly we found that rectal complexes occur in adult, but not M. melolontha larvae, and larvae but not adults within Cetoniinae, indicating dramatic pupal remodelling of these organ systems. Insights into the structure of the rectal complexes of Scarabaeoidea are compared with the well-studied rectal complexes of Cucujiformia. Finally, we discuss possible functions of the rectal complexes of beetles within Scarabaeoidea, and future approaches to address this question.

The hindgut microbiota of coconut rhinoceros beetles (Oryctes rhinoceros) in relation to their geographical populations

The coconut rhinoceros beetle (CRB, Oryctes rhinoceros) is a palm tree pest capable of rapidly expanding its population in new territories. Previous studies identified a digestive symbiosis between CRB and its gut microbes. However, no research compared the genetic variation of CRBs with their hindgut microbiota on a global scale. This study aims to investigate the genetic divergence of CRB and the compositional variation of CRB's microbiota across different geographical locations, and explore the association between them and their predicted functional profiles and environmental data. The research reveals a distinct and consistent microbial community within local populations, but it varies across different geographical populations. The microbial functional profiles linked to the production of digestive enzymes, including cellulases and ligninases, are nonetheless globally conserved. This suggests that CRBs employ specific mechanisms to select and maintain microbes with functional benefits, contributing to host adaptability, stress tolerance, and fitness. The CRB microbial communities did not appear to recapitulate the genetic variation of their hosts. Rather than depend on obligate symbionts, CRBs seem to establish similar digestive associations with whatever environmentally acquired microbes are available wherever they are, aiding them in successfully establishing after invading a new location.IMPORTANCECoconut rhinoceros beetles (CRBs) are notorious pests on Arecaceae plants, posing destructive threats to countries highly reliant on coconut, oil palm, and date palm as economic crops. In the last century, CRBs have rapidly expanded their presence to territories that were once free of these beetles. The United States, for instance, has officially designated CRBs as invasive and alien pests. Given their remarkable ability to swiftly adapt to new environments, their gut microbes may play a crucial role in this process. While the microbiota of CRBs vary depending on geographical location, these beetles consistently exhibit a functionally identical digestive association with locally acquired microbes. This underscores the significance of CRB-microbe association in shaping the adaptive strategies of this agricultural pest.

Genome reduction and horizontal gene transfer in the evolution of Endomicrobia-rise and fall of an intracellular symbiosis with termite gut flagellates

Bacterial endosymbionts of eukaryotic hosts typically experience massive genome reduction, but the underlying evolutionary processes are often obscured by the lack of free-living relatives. Endomicrobia, a family-level lineage of host-associated bacteria in the phylum Elusimicrobiota that comprises both free-living representatives and endosymbionts of termite gut flagellates, are an excellent model to study evolution of intracellular symbionts. We reconstructed 67 metagenome-assembled genomes (MAGs) of Endomicrobiaceae among more than 1,700 MAGs from the gut microbiota of a wide range of termites. Phylogenomic analysis confirmed a sister position of representatives from termites and ruminants, and allowed to propose eight new genera in the radiation of Endomicrobiaceae. Comparative genome analysis documented progressive genome erosion in the new genus Endomicrobiellum, which comprises all flagellate endosymbionts characterized to date. Massive gene losses were accompanied by the acquisition of new functions by horizontal gene transfer, which led to a shift from a glucose-based energy metabolism to one based on sugar phosphates. The breakdown of glycolysis and many anabolic pathways for amino acids and cofactors in several subgroups was compensated by the independent acquisition of new uptake systems, including an ATP/ADP antiporter, from other gut microbiota. The putative donors are mostly flagellate endosymbionts from other bacterial phyla, including several, hitherto unknown lineages of uncultured Alphaproteobacteria, documenting the importance of horizontal gene transfer in the convergent evolution of these intracellular symbioses. The loss of almost all biosynthetic capacities in some lineages of Endomicrobiellum suggests that their originally mutualistic relationship with flagellates is on its decline.IMPORTANCEUnicellular eukaryotes are frequently colonized by bacterial and archaeal symbionts. A prominent example are the cellulolytic gut flagellates of termites, which harbor diverse but host-specific bacterial symbionts that occur exclusively in termite guts. One of these lineages, the so-called Endomicrobia, comprises both free-living and endosymbiotic representatives, which offers the unique opportunity to study the evolutionary processes underpinning the transition from a free-living to an intracellular lifestyle. Our results revealed a progressive gene loss in energy metabolism and biosynthetic pathways, compensated by the acquisition of new functions via horizontal gene transfer from other gut bacteria, and suggest the eventual breakdown of an initially mutualistic symbiosis. Evidence for convergent evolution of unrelated endosymbionts reflects adaptations to the intracellular environment of termite gut flagellates.

Coconut rhinoceros beetle digestive symbiosis with potential plant cell wall degrading microbes

Coconut rhinoceros beetle (CRB, Oryctes rhinoceros) is an invasive palm pest whose larvae eat wood, yet lack the necessary digestive enzymes. This study confirmed endogenous CRB cellulase is inactive, suggesting microbial fermentation. The inner lining of the CRB hindgut has tree-like structures covered with a conspicuous biofilm. To identify possible symbionts, 16 S rRNA amplicon sequencing was used on individuals from across Taiwan. Several taxa of Clostridia, an anaerobic class including many cellulolytic bacteria, were highly abundant in most individuals from all locations. Whole metagenome sequencing further confirmed many lignocellulose degrading enzymes are derived from these taxa. Analyses of eggs, larvae, adults, and soil found these cellulolytic microbes are not transmitted vertically or transstadially. The core microbiomes of the larval CRB are likely acquired and enriched from the environment with each molt, and enable efficient digestion of wood.

Core microbiota for nutrient digestion remained and ammonia utilization increased after continuous batch culture of rumen microbiota in vitro

Introduction

This study aimed to investigate the digestive function, urea utilization ability, and bacterial composition changes in rumen microbiota under high urea (5% urea in diet) over 23 days of continuous batch culture in vitro.

Methods

The gas production, dry matter digestibility, and bacterial counts were determined for the continuously batch-cultured rumen fluid (CRF). The changes in fermentation parameters, NH3-N utilization efficiency, and microbial taxa were analyzed in CRF and were compared with that of fresh rumen fluid (RF), frozen rumen fluid (FRF, frozen rumen fluid at -80°C for 1 month), and the mixed rumen fluid (MRF, 3/4 RF mixed with 1/4 CRF) with in vitro rumen fermentation.

Results

The results showed that the dry matter digestibility remained stable while both the microbial counts and diversity significantly decreased over the 23 days of continuous batch culture. However, the NH3-N utilization efficiency of the CRF group was significantly higher than that of RF, FRF, and MRF groups (p < 0.05), while five core genera including Succinivibrio, Prevotella, Streptococcus, F082, and Megasphaera were retained after 23 days of continuous batch culture. The NH3-N utilization efficiency was effectively improved after continuous batch culture in vitro, and Streptococcus, Succinivibrio, Clostridium_sensu_stricto_1, p.251.o5, Oxalobacter, Bacteroidales_UCG.001, and p.1088.a5_gut_group were identified to explain 75.72% of the variation in NH3-N utilization efficiency with the RandomForest model.

Conclusion

Thus, core bacterial composition and function retained under high urea (5% urea in diet) over 23 days of continuous batch culture in vitro, and bacterial biomarkers for ammonia utilization were illustrated in this study. These findings might provide potential applications in improving the efficiency and safety of non-protein nitrogen utilization in ruminants.

Marked variations in diversity and functions of gut microbiota between wild and domestic stag beetle Dorcus Hopei Hopei

BACKGROUND

Although stag beetles are a popular saprophytic insect, their gut microbiome has been poorly studied. Here, 16 S rRNA gene sequencing was employed to reveal the gut microbiota composition and functional variations between wild and domestic Dorcus hopei hopei (Dhh) larval individuals.

RESULTS

The results indicated a significant difference between the wild and domestic Dhh gut microbiota., the domestic Dhh individuals contained more gut microbial taxa (e.g. genera Ralstonia and Methyloversatilis) with xenobiotic degrading functions. The wild Dhh possesses gut microbiota compositions (e.g. Turicibacter and Tyzzerella ) more appropriate for energy metabolism and potential growth. This study furthermore assigned all Dhh individuals by size into groups for data analysis; which indicated limited disparities between the gut microbiota of different-sized D. hopei hopei larvae.

CONCLUSION

The outcome of this study illustrated that there exists a significant discrepancy in gut microbiota composition between wild and domestic Dhh larvae. In addition, the assemblage of gut microbiome in Dhh was primarily attributed to environmental influences instead of individual differences such as developmental potential or size. These findings will provide a valuable theoretical foundation for the protection of wild saprophytic insects and the potential utilization of the insect-associated intestinal microbiome in the future.

Detection and substrate portrayal on the serum phenoloxidase activity from the grub of rhinoceros beetle, Oryctes rhinoceros

Phenoloxidase (PO) is a significant biomolecule involved in humoral defence mechanism of invertebrates. Spontaneous melanization of insect haemolymph is the major hinderance for studying PO activity, as haemolymph was collected devoid of phenylthiourea. In the study, no visible melanization was observed in crude serum from the grub of Oryctes rhinoceros up to 30 min of incubation amongst crude haemolymph, diluted haemolymph, crude serum and diluted serum that were subjected to visual observation for spontaneous melanization reaction. Accordingly, crude serum was taken for evaluating PO activity. At the same time, as PO substrates tend to auto-oxidize and provide false optical density value, tris-buffered saline devoid of any substrates were used as blank for PO assays. The ideal wavelength at which maximum PO activity occurred for each substrate, namely, tyrosine, tyramine, dopamine, L-dopa, DL-dopa, catechol, protocatechuic acid and pyrogallol was determined as 407, 410, 429, 465, 403, 466, 428 and 400 nm, respectively. Additionally, time course of oxidation for each phenolic substrate by the serum PO were examined and DL-dopa was identified as the specific substrate for serum PO in the grub of O. rhinoceros. Furthermore, maximum PO activity was observed at 5 min of incubation for 10 mM of DL-dopa that was considered as optimum concentration. The ideal pH and temperature for serum PO activity was observed as 7.5 and 20°C, respectively. These results suggested that standardizing a suitable substrate is an essential prerequisite to evaluate the real PO activity of serum which might significantly fluctuate in each insect model.

Predominant contribution of an endogenous cellulase (OlCel) to the cellulolysis in the digestive system of larvae of banana pseudostem weevil, Odoiporus longicollis (Coleoptera: Curculionidae)

Insects have evolved with effective strategies to utilize cellulose as an energy source by possessing cellulolytic enzymes which can be used as an optimal resource in the bioenergy sector. The study was aimed at evaluating the cellulolytic enzyme in the larval gut of the banana pseudostem weevil, Odoiporus longicollis Olivier (Coleoptera: Curculionidae). Primarily, cellulase activity was localized along the gut, in which the midgut showed the highest activity (2858 U/mg). The thermo-tolerance of cellulase activity was found to be up to 80°C (highest at 60°C), and the enzyme was stable at a pH between 5 and 6. Various concentrations of divalent cations (CaCl2 , MgCl2 , and CuCl2 ) have differential enhancing and inhibitory effects on cellulase activity. The cellulase (OlCel) was purified using anion exchange chromatography. The molecular weight of the cellulase was determined to be 47 kDa. The physicochemical parameters of the purified enzyme were similar to that of enzyme activity of whole gut extract. Mass spectrometry results identified sequence similarities of purified cellulase to the glycosyl hydrolase family 5 (GHF5) family. The gut microbial cellulase activity as exogenous source showed no competence compared with the endogenous activity.

Genomic resources for population analyses of an invasive insect pest Oryctes rhinoceros

Over the last few years, various types of NGS data have been accumulating for the coconut rhinoceros beetle (CRB, Oryctes rhinoceros), reflecting the growing interest in curtailing this invasive pest of palm trees. Whilst reference-free analyses of RNA-seq and RAD-seq datasets have been done for different CRB collections, recent availability of the CRB's genome assembly provides an opportunity to collate diverse data and create a reference-based population dataset. Here, I release such a dataset containing 6,725,935 SNPs and genotypes called across 393 individual samples from 16 populations, using the previously published raw sequences generated in 9 different experiments (RAD-Seq, RNA-Seq, WGS). I also provide reference-based datasets for the CRB's mitochondrial variants and for variants of its viral biocontrol agent Oryctes rhinoceros nudivirus. SNP data provide high resolution for determining the geographic origin of invasive CRB. With these genomic resources, new data can be analysed without re-processing the published samples and then integrated to expand the reference datasets.

Diversity of cellulolytic and xylanolytic fungi associated with the digestive tract of aquatic insect larvae in streams of the Amazon Forest and Cerrado in Brazil

The study of the relationship between fungi and insects brings important contributions to the knowledge of fungal biodiversity and to the understanding of mutualistic ecological interactions. This study reports the occurrence of a community of filamentous fungi in the digestive tract (DT) of mining insect larvae belonging to genus Stenochironomus in streams of two Brazilian biomes. Fungi were obtained from the digestive tract of larvae found on trunks and leaves of low-order streams in the Amazon Forest and Cerrado in the north of Brazil. The fungal community was screened for xylanolytic and cellulolytic activities. The diversity of fungal species in the DT of larvae is possibly related to the diversity of diets of species of that genus and the diversity of substrates in the ecosystems. The diversity and richness of fungal species were influenced by ecological differences between locations more than by the types of substrates in which they were collected (trunk and leaf). Most fungi in the DT of Stenochironomus larvae sampled in leaves exhibited cellulolytic enzyme activity. Such results stress that the mycobiomes of the DT of Stenochiromonus larvae produce enzymes that contribute to the process of breaking down plant remains in their hosts.

Larval gut microbiome of Pelidnota luridipes (Coleoptera: Scarabaeidae): high bacterial diversity, different metabolic profiles on gut chambers and species with probiotic potential

Pelidnota luridipes Blanchard (1850) is a tropical beetle of the family Scarabaeidae, whose larvae live on wood without parental care. Microbiota of mid- and hindgut of larvae was evaluated by culture-dependent and independent methods, and the results show a diverse microbiota, with most species of bacteria and fungi shared between midgut and hindgut. We isolated 272 bacterial and 29 yeast isolates, identified in 57 and 7 species, respectively, while using metabarcoding, we accessed 1,481 and 267 OTUs of bacteria and fungi, respectively. The composition and abundance of bacteria and fungi differed between mid- and hindgut, with a tendency for higher richness and diversity of yeasts in the midgut, and bacteria on the hindgut. Some taxa are abundant in the intestine of P. luridipes larvae, such as Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria; as well as Saccharomycetales and Trichosporonales yeasts. Mid- and hindgut metabolic profiles differ (e.g. biosynthesis of amino acids, cofactors, and lipopolysaccharides) with higher functional diversity in the hindgut. Isolates have different functional traits such as secretion of hydrolytic enzymes and antibiosis against pathogens. Apiotrichum siamense L29A and Bacillus sp. BL17B protected larvae of the moth Galleria mellonella, against infection by the pathogens Listeria monocytogenes ATCC19111 and Pseudomonas aeruginosa ATCC 9027. This is the first work with the larval microbiome of a Rutelini beetle, demonstrating its diversity and potential in prospecting microbial products as probiotics. The functional role of microbiota for the nutrition and adaptability of P. luridipes larvae needs to be evaluated in the future.

The Role of Feeding Characteristics in Shaping Gut Microbiota Composition and Function of Ensifera (Orthoptera)

Feeding habits were the primary factor affecting the gut bacterial communities in Ensifera. However, the interaction mechanism between the gut microbiota and feeding characteristics is not precisely understood. Here, the gut microbiota of Ensifera with diverse feeding habits was analyzed by shotgun metagenomic sequencing to further clarify the composition and function of the gut microbiota and its relationship with feeding characteristics. Our results indicate that under the influence of feeding habits, the gut microbial communities of Ensifera showed specific characteristics. Firstly, the gut microbial communities of the Ensifera with different feeding habits differed significantly, among which the gut microbial diversity of the herbivorous Mecopoda niponensis was the highest. Secondly, the functional genes related to feeding habits were in high abundance. Thirdly, the specific function of the gut microbial species in the omnivorous Gryllotalpa orientalis showed that the more diverse the feeding behavior of Ensifera, the worse the functional specificity related to the feeding characteristics of its gut microbiota. However, feeding habits were not the only factors affecting the gut microbiota of Ensifera. Some microorganisms' genes, whose functions were unrelated to feeding characteristics but were relevant to energy acquisition and nutrient absorption, were detected in high abundance. Our results were the first to report on the composition and function of the gut microbiota of Ensifera based on shotgun metagenomic sequencing and to explore the potential mechanism of the gut microbiota's association with diverse feeding habits.

Soil Environments Influence Gut Prokaryotic Communities in the Larvae of the Invasive Japanese Beetle Popillia japonica Newman

Invasive scarab beetles, like the Japanese beetle Popillia japonica Newman (JB), spend most of their lives as larvae feeding in the soil matrix. Despite the potential importance of the larval gut microbial community in driving the behavior, physiology, and nutritional ecology of this invasive insect, the role of soil biological and physicochemical characteristics in shaping this community are relatively unknown. Our objectives were to (1) characterize the degree to which larval gut microbial communities are environmentally acquired, (2) examine the combined effects of the gut region (i.e., midgut, hindgut) and local soil environments on gut microbial communities, and (3) search for soil physicochemical correlates that could be useful in future studies aimed at characterizing gut microbial community variation in soil-dwelling scarabs. Gut communities from neonates that were never in contact with the soil were different from gut communities of third instar larvae collected from the field, with neonate gut communities being significantly less rich and diverse. The influence of compartment (soil, midgut, or hindgut) on prokaryotic α- and β-diversity varied with location, suggesting that JB larval gut communities are at least partially shaped by the local environment even though the influence of compartment was more pronounced. Midgut microbiota contained transient communities that varied with the surrounding soil environment whereas hindgut microbiota was more conserved. Prokaryotic communities in the hindgut clustered separately from those of soil and midgut, which displayed greater interspersion in ordination space. Soil cation exchange capacity, organic matter, water holding capacity, and texture were moderately correlated (≥29%) with gut prokaryotic microbial composition, especially within the midgut. Findings suggest that microbial communities associated with the JB gut are partially a function of adaptation to local soil environments. However, conditions within each gut compartment appear to shape those communities in transit through the alimentary canal.

A diverse and partially cellulolytic fungal community contributes to the diet of three species of the aquatic insect Phylloicus (Trichoptera: Calamoceratidae) in Amazonian streams

Investigations on the fungal community associated with the digestive tract (DT) of insects have provided insights into the diversity of associated microorganisms and their potential roles in the interaction with their hosts. However, most studies have focused on terrestrial insects, with few studies focusing on aquatic insects in Neotropical regions. We studied fungal taxa associated with the DT of larval stages of the aquatic shredders Phylloicus amazonas, P. elektoros and P. fenestratus in the Brazilian Amazon Forest. Filamentous fungi were isolated, purified and screened for cellulolytic activity. A total of 33 fungal taxa was identified through the combination of classical and molecular taxonomy. The genus Penicillium was the most frequent in DT of Phylloicus spp. (18.75%). The occurrence of fungal taxa among hosts was quite variable, with more than half of the associated fungi being exclusive of each host species. A significant portion of the fungal community associated with each host presented cellulolytic activity (± 50%). It was concluded that the fungal community associated with Phylloicus spp. larvae consist mainly of fungal taxa from food items, which come from riparian vegetation (whose plant species are variable) or are indigenous of the aquatic ecosystems, which is the habitat of these larvae.

Diverse Host Immune Responses of Different Geographical Populations of the Coconut Rhinoceros Beetle to Oryctes Rhinoceros Nudivirus (OrNV) Infection

Incursions of the coconut rhinoceros beetle (CRB), Oryctes rhinoceros, into different islands in the South Pacific have been detected in recent years. It has been suggested that this range expansion is related to an O. rhinoceros haplotype reported to show reduced susceptibility to the well-established classical biocontrol agent, Oryctes rhinoceros nudivirus (OrNV). Our understanding of the genetic characteristics which distinguish the population of O. rhinoceros that has recently established in Solomon Islands from other well-established populations across the region is very limited. Here, we hypothesized that the recently established O. rhinoceros population should have greater innate immune responses when challenged by OrNV than those of well-established and native O. rhinoceros populations. We used the RNA sequencing (RNA-Seq) approach to generate gene expression profiles of midgut tissue from OrNV-infected and noninfected individuals collected in the Solomon Islands (recent incursion), Papua New Guinea and Fiji (previously established), and the Philippines (within the native range). The collections included individuals from each of the three major mitochondrial lineages (CRB-G, CRB-PNG, and CRB-S) known to the region, allowing us to explore the specific responses of each haplotype to infection. Although insects from the Philippines and Solomon Islands that were tested belong to the same mitochondrial lineage (CRB-G), their overall responses to infection were different. The number of differentially expressed genes between OrNV-infected and noninfected wild-caught individuals from the four different locations varied from 148 to 252. Persistent OrNV infection caused a high level of induced antimicrobial activity and immune responses in O. rhinoceros, but the direction and magnitude of the responses were population specific. The insects tested from the Solomon Islands displayed extremely high expression of genes which are known to be involved in immune responses (e.g. coleoptericin, cecropin, and serpin). These variations in the host immune system among insects from different geographical regions might be driven by variations in the virulence of OrNV isolates, and this requires further investigation. Overall, our current findings support the importance of immunity in insect pest incursion and an expansion of the pest's geographic range. IMPORTANCE Oryctes rhinoceros nudivirus (OrNV) is a double-stranded DNA (dsDNA) virus which has been used as a biocontrol agent to suppress coconut rhinoceros beetle (CRB) in the Pacific Islands. Recently a new wave of CRB incursions in Oceania is thought to be related to the presence of low-virulence isolates of OrNV or virus-tolerant haplotypes of beetles (CRB-G). Our comparative analysis of OrNV-infected and noninfected CRBs revealed that specific sets of genes were induced by viral infection in the beetles. This induction was much stronger in beetles collected from the Solomon Islands, a newly invaded country, than in individuals collected from within the beetle's native range (the Philippines) or from longer-established populations in its exotic range (Fiji and Papua New Guinea [PNG]). Beetles from the Philippines and the Solomon Islands that were tested in this study all belonged to the CRB-G haplotype, but the country-specific responses of the beetles to OrNV infection were different.

Gut bacterial communities across 12 Ensifera (Orthoptera) at different feeding habits and its prediction for the insect with contrasting feeding habits

Insect microbial symbioses play a critical role in insect lifecycle, and insect gut microbiome could be influenced by many factors. Studies have shown that host diet and taxonomy have a strong influence on insect gut microbial community. In this study, we performed sequencing of V3-V4 region of 16S rRNA gene to compare the composition and diversity of 12 Ensifera from 6 provinces of China. Moreover, the influences of feeding habits and taxonomic status of insects on their gut bacterial community were evaluated, which might provide reference for further application research. The results showed that Proteobacteria (45.66%), Firmicutes (34.25%) and Cyanobacteria (7.7%) were the predominant bacterial phyla in Ensifera. Moreover, the gut bacterial community composition of samples with different feeding habits was significantly different, which was irrespective of their taxa. The highest diversity of gut bacteria was found in the omnivorous Ensifera. Furthermore, common and unique bacteria with biomarkers were found based on the dietary characteristics of the samples. However, the bacterial community structure of the Ensifera samples was significantly different from that of Caelifera. Therefore, we concluded that feeding habits and taxonomic status jointly affect the gut bacterial community composition of the samples from Orthoptera. However, the influence of feeding habit dominates when taxonomy category below the suborder level. In addition, the dominant, common and unique bacterial community structure could be used to predict the contrastic feeding habits of insects belonging to Ensifera.

The complete mitochondrial genome sequence of Oryctes rhinoceros (Coleoptera: Scarabaeidae) based on long-read nanopore sequencing

BACKGROUND

The coconut rhinoceros beetle (CRB, Oryctes rhinoceros) is a severe and invasive pest of coconut and other palms throughout Asia and the Pacific. The biocontrol agent, Oryctes rhinoceros nudivirus (OrNV), has successfully suppressed O. rhinoceros populations for decades but new CRB invasions started appearing after 2007. A single-SNP variant within the mitochondrial cox1 gene is used to distinguish the recently-invading CRB-G lineage from other haplotypes, but the lack of mitogenome sequence for this species hinders further development of a molecular toolset for biosecurity and management programmes against CRB. Here we report the complete circular sequence and annotation for CRB mitogenome, generated to support such efforts.

METHODS

Sequencing data were generated using long-read Nanopore technology from genomic DNA isolated from a CRB-G female. The mitogenome was assembled with Flye v.2.5, using the short-read Illumina sequences to remove homopolymers with Pilon, and annotated with MITOS. Independently-generated transcriptome data were used to assess the O. rhinoceros mitogenome annotation and transcription. The aligned sequences of 13 protein-coding genes (PCGs) (with degenerate third codon position) from O. rhinoceros, 13 other Scarabaeidae taxa and two outgroup taxa were used for the phylogenetic reconstruction with the Maximum likelihood (ML) approach in IQ-TREE and Bayesian (BI) approach in MrBayes.

RESULTS

The complete circular mitogenome of O. rhinoceros is 20,898 bp in length, with a gene content canonical for insects (13 PCGs, two rRNA genes, and 22 tRNA genes), as well as one structural variation (rearrangement of trnQ and trnI) and a long control region (6,204 bp). Transcription was detected across all 37 genes, and interestingly, within three domains in the control region. ML and BI phylogenies had the same topology, correctly grouping O. rhinoceros with one other Dynastinae taxon, and recovering the previously reported relationship among lineages in the Scarabaeidae. In silico PCR-RFLP analysis recovered the correct fragment set that is diagnostic for the CRB-G haplogroup. These results validate the high-quality of the O. rhinoceros mitogenome sequence and annotation.

Blattella germanica displays a large arsenal of antimicrobial peptide genes

Defence systems against microbial pathogens are present in most living beings. The German cockroach Blattella germanica requires these systems to adapt to unhealthy environments with abundance of pathogenic microbes, in addition to potentially control its symbiotic systems. To handle this situation, four antimicrobial gene families (defensins, termicins, drosomycins and attacins) were expanded in its genome. Remarkably, a new gene family (blattellicins) emerged recently after duplication and fast evolution of an attacin gene, which is now encoding larger proteins with the presence of a long stretch of glutamines and glutamic acids. Phylogenetic reconstruction, within Blattellinae, suggests that this duplication took place before the divergence of Blattella and Episymploce genera. The latter harbours a long attacin gene (pre-blattellicin), but the absence of the encoded Glx-region suggests that this element evolved recently in the Blattella lineage. A screening of AMP gene expression in available transcriptomic SR projects of B. germanica showed that, while some AMPs are expressed during almost the whole development, others are restricted to shorter periods. Blattellicins are highly expressed only in adult females. None of the available SR tissue projects could be associated with blattellicins’ expression, suggesting that it takes place in other tissues, maybe the gut.

Culturing-Enriched Metabarcoding Analysis of the Oryctes rhinoceros Gut Microbiome

Simple Summary

The coconut rhinoceros beetle is a pest of palm trees, which may have symbiotic gut microbes that help it digest its food. These microbes may produce enzymes like cellulase, which have uses in human industry. If the microbes are essential for the beetle’s survival, then finding ways to attack the microbes could help fight the pest. We sampled microbes from the guts of larval beetles collected in coconut trees in southern Taiwan, and identified the microbes both by culturing and with molecular biology methods. We found several species of bacteria and a yeast, Candida xylanolytica, with potential digestive functions for the beetle. Some of these microbes had been reported in these beetles before while others are new. Broader surveys of the beetle microbiome are needed to determine whether or not they have a conserved microbiome.

Abstract

Wood-feeding insects should have a source of enzymes like cellulases to digest their food. These enzymes can be produced by the insect, or by microbes living in the wood and/or inside the insect gut. The coconut rhinoceros beetle, Oryctes rhinoceros, is a pest whose digestive microbes are of considerable interest. This study describes the compartments of the O. rhinoceros gut and compares their microbiomes using culturing-enriched metabarcoding. Beetle larvae were collected from a coconut grove in southern Taiwan. Gut contents from the midgut and hindgut were plated on nutrient agar and selective carboxymethylcellulose agar plates. DNA was extracted from gut and fat body samples and 16S rDNA metabarcoding performed to identify unculturable bacteria. Cellulase activity tests were performed on gut fluids and microbe isolates. The midgut and hindgut both showed cellulolytic activity. Bacillus cereus, Citrobacter koseri, and the cellulolytic fungus Candida xylanilytica were cultured from both gut sections in most larvae. Metabarcoding did not find Bacillus cereus, and found that either Citrobacter koseri or Paracoccus sp. were the dominant gut microbes in any given larva. No significant differences were found between midgut and hindgut microbiomes. Bacillus cereus and Citrobacter koseri are common animal gut microbes frequently found in Oryctes rhinoceros studies while Candida xylanilytica and the uncultured Paracoccus sp. had not been identified in this insect before. Some or all of these may well have digestive functions for the beetle, and are most likely acquired from the diet, meaning they may be transient commensalists rather than obligate mutualists. Broader collection efforts and tests with antibiotics will resolve ambiguities in the beetle–microbe interactions.

Predicting antimicrobial susceptibility from the bacterial genome: A new paradigm for one health resistance monitoring

The laboratory identification of antibacterial resistance is a cornerstone of infectious disease medicine. In vitro antimicrobial susceptibility testing has long been based on the growth response of organisms in pure culture to a defined concentration of antimicrobial agents. By comparing individual isolates to wild-type susceptibility patterns, strains with acquired resistance can be identified. Acquired resistance can also be detected genetically. After many decades of research, the inventory of genes underlying antimicrobial resistance is well known for several pathogenic genera including zoonotic enteric organisms such as Salmonella and Campylobacter and continues to grow substantially for others. With the decline in costs for large scale DNA sequencing, it is now practicable to characterize bacteria using whole genome sequencing, including the carriage of resistance genes in individual microorganisms and those present in complex biological samples. With genomics, we can generate comprehensive, detailed information on the bacterium, the mechanisms of antibiotic resistance, clues to its source, and the nature of mobile DNA elements by which resistance spreads. These developments point to a new paradigm for antimicrobial resistance detection and tracking for both clinical and public health purposes.

Identification of a Novel Picorna-like Virus in Coconut Rhinoceros Beetles (Oryctes rhinoceros)

A novel Picorna-like virus, tentatively named Oryctes rhinoceros Picorna-like virus 1 (OrPV1), was identified in coconut rhinoceros beetle (Oryctes rhinoceros) larvae in Taiwan. The complete genome sequence consisted of 9,665 nucleotides with a polyA tail and included one open reading frame. Conserved structural domains such as Picornavirus capsid protein, RNA helicase, Peptidase and RNA-dependent RNA polymerase (RdRp) were identified through Pfam domain searches. The genome shares approximately 27-28% identity with other unclassified Picornavirales that infect honey bees (Darwin bee virus 2, Bundaberg bee virus 5, and Sacbrood virus) and a recently reported virus from Asian lady beetle (Harmonia axyridis virus 1). We did not detect this virus in any other geographical populations of O. rhinoceros collected from the South Pacific Islands and the Philippines. Analysis of the deduced RdRp amino acid sequences showed that the virus clustered with other Picorna-like viruses and separated from other members of family Dicistroviridae and Iflaviridae.