Transpacific coalescent pathways of coconut rhinoceros beetle biotypes: Resistance to biological control catalyses resurgence of an old pest

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.

Genomic identification of Oryctes rhinoceros nudivirus isolates, a biocontrol agent for coconut rhinoceros beetle

The coconut rhinoceros beetle (Oryctes rhinoceros, CRB) is a serious pest of coconut and oil palms. It is native to South and Southeast Asia and was inadvertently introduced to Samoa in 1909. It has invaded many other Pacific countries throughout the last century. Oryctes rhinoceros nudivirus (OrNV), a natural pathogen of CRB in its native range, was successfully introduced as a classical biocontrol agent and has effectively suppressed invasive CRB populations for decades. However, resurgence of CRB has been recorded, with new invasions detected in several Pacific Island Countries and Territories. Additionally, new populations of CRB are emerging in some invaded areas that have a degree of resistance to the virus isolates commonly released for CRB biocontrol. Here, we designed a fast and reliable tool for distinguishing between different OrNV isolates that can help with the selection process to identify effective isolates for management of new CRB invasions. A comparison of 13 gene/gene region sequences within the OrNV genome of 16 OrNV isolates from native and invaded ranges allowed us to identify unique Single Nucleotide Polymorphisms (SNPs). With these SNPs, we developed an assay using multiplex PCR-amplicon-based nanopore sequencing to distinguish between OrNV isolates. We found that as few as four gene fragments were sufficient to identify 15 out of 20 OrNV isolates. This method can be used as a tool to monitor the establishment and distribution of OrNV isolates selected for release as biocontrol agents in CRB-infected areas.

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.

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.

Coconut Rhinoceros Beetle in Samoa: Review of a Century-Old Invasion and Prospects for Control in a Changing Future

Simple Summary

Coconut rhinoceros beetle (CRB) is one of the major pests of coconut and oil palms in the Asia-Pacific region. Since its accidental introduction in Samoa in 1909, the invasive CRB has spread to several countries and territories within the Pacific and Indian Oceans, severely damaging coconut palms and affecting peoples’ livelihoods. In the 100 years since CRB established on Samoa, it remains the primary pest on the island with periods of heavy damage when integrated pest management (IPM) breaks down. The Samoan case is an excellent example of implementing biocontrol and IPM in a dynamic Pacific environment. As society and the economics of production in Samoa have changed, the level of control has varied, with recent concern about surges of the pest. The review synthesizes historical lessons and provide recommendations on how to protect coconut palms in the changing environment of Samoa which are also applicable for protection of palms in the wider Asia/Pacific region.

Abstract

It is now more than 100 years since the coconut rhinoceros beetle (CRB: Oryctes rhinoceros L.) was first detected in the Pacific Island state of Samoa. The exotic pest from Asia became the principal pest of coconut palms in Samoa and, from this first point of invasion, spread to several surrounding countries in the South-West Pacific Ocean. An intensive control operation was initiated, but the beetle could not be eliminated. Various pest management strategies were attempted but had limited success until the introduction of a biological control agent (BCA), Oryctes rhinoceros nudivirus (OrNV), during the late 1960s and early 1970s. The biocontrol release was very successful and became the prime example of “classical biological control” of an insect pest by a virus. Changing economic and social conditions in Samoa and other islands of the Pacific require a re-evaluation of the threat of CRB to coconut production to suggest how the IPM system may be modified to meet future needs. Therefore, it is timely to review the history of CRB in Samoa and summarize experiences in development of an integrated pest management (IPM) system limiting the impact of the pest. We also present results from a recent study conducted in 2020 on the island of Upolu to define the current status of the CRB population and its BCA, OrNV. The lessons from Samoa, with its long history of containment and management of CRB, are applicable to more recent invasion sites. Recommendations are provided to modify the IPM programme to enhance the sustainable control of CRB and support the ongoing coconut replantation program promoted by the Samoan government.

Identification of Components of the Aggregation Pheromone of the Guam Strain of Coconut Rhinoceros Beetle, Oryctes rhinoceros, and Determination of Stereochemistry

The coconut rhinoceros beetle, Oryctes rhinoceros (Linnaeus 1758) (Coleoptera: Scarabaeidae: Dynastinae) (CRB), is endemic to tropical Asia where it damages both coconut and oil palm. A new invasion by CRB occurred on Guam in 2007 and eradication attempts failed using commonly applied Oryctes rhinoceros nudivirus (OrNV) isolates. This and subsequent invasive outbreaks were found to have been caused by a previously unrecognized haplotype, CRB-G, which appeared to be tolerant to OrNV. The male-produced aggregation pheromone of the endemic, susceptible strain of O. rhinoceros (CRB-S) was previously identified as ethyl 4-methyloctanoate. Following reports from growers that commercial lures containing this compound were not attractive to CRB-G, the aim of this work was to identify the pheromone of CRB-G. Initial collections of volatiles from virgin male and female CRB-G adults from the Solomon Islands failed to show any male- or female-specific compounds as candidate pheromone components. Only after five months were significant quantities of ethyl 4-methyloctanoate and 4-methyloctanoic acid produced by males but not by females. No other male-specific compounds could be detected, in particular methyl 4-methyloctanoate, 4-methyl-1-octanol, or 4-methyl-1-octyl acetate, compounds identified in volatiles from some other species of Oryctes. Ethyl 4-methyloctanoate elicited a strong electroantennogram response from both male and female CRB-G, but these other compounds, including 4-methyloctanoic acid, did not. The enantiomers of ethyl 4-methyloctanoate and 4-methyloctanoic acid were conveniently prepared by enzymatic resolution of the commercially-available acid, and the enantiomers of the acid, but not the ester, could be separated by gas chromatography on an enantioselective cyclodextrin phase. Using this approach, both ethyl 4-methyloctanoate and 4-methyloctanoic acid produced by male CRB-G were shown to be exclusively the (R)-enantiomers whereas previous reports had suggested male O. rhinoceros produced the (S)-enantiomers. However, re-examination of the ester and acid produced by male CRB-S from Papua New Guinea showed that these were also the (R)-enantiomers. In field trapping experiments carried out in the Solomon Islands, both racemic and ethyl (R)-4-methyloctanoate were highly attractive to both male and female CRB-G beetles. The (S)-enantiomer and the corresponding acids were only weakly attractive. The addition of racemic 4-methyloctanoic acid to ethyl 4-methyloctanoate did significantly increase attractiveness, but the addition of (R)- or (S)-4-methyloctanoic acid to the corresponding ethyl esters did not. Possible reasons for the difference in assignment of configuration of the components of the CRB pheromone are discussed along with the practical implications of these results.

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.

Omics technologies used in pesticide residue detection and mitigation in crop

In agriculture, the convenience and efficacy of chemical pesticides have become inevitable to manage cultivated crop production. Here, we review the worldwide use of pesticides based on their categories, mode of actions and toxicity. Excessive use of pesticides may lead to hazardous pesticide residues in crops, causing adverse effects on human health and the environment. A wide range of high-tech-analytical methods are available to analyse pesticide residues. However, they are mostly time-consuming and inconvenient for on-site detection, calling for the development of biosensors that detect cellular changes in crops. Such new detection methods that combine biological and physicochemical knowledge may overcome the shortage in current farming to develop sustainable systems that support environmental and human health. This review also comprehensively compiles domestic pesticide residues removal tips from vegetables and fruits. Synthetic pesticide alternatives such as biopesticide and nanopesticide are greener to the environment. However, its safety assessment for large-scale application needs careful evaluation. Lastly, we strongly call for reversions of pesticide application trends based on the changing climate, which is lacking in the current scenario.

Confirmation of Oryctes rhinoceros nudivirus infections in G-haplotype coconut rhinoceros beetles (Oryctes rhinoceros) from Palauan PCR-positive populations

Coconut rhinoceros beetle (CRB), Oryctes rhinoceros, is a pest of palm trees in the Pacific. Recently, a remarkable degree of palm damage reported in Guam, Hawaii, Papua New Guinea and Solomon Islands has been associated with a particular haplotype (clade I), known as "CRB-G". In the Palau Archipelago, both CRB-G and another haplotype (clade IV) belonging to the CRB-S cluster coexist in the field. In this study, more than 75% of pheromone trap-captured adults of both haplotypes were Oryctes rhinoceros nudivirus (OrNV)-positive by PCR. No significant difference in OrNV prevalence between the haplotypes was detected. In PCR-positive CRB-G tissue specimens from Palau, viral particles were observed by electron microscopy. Hemocoel injection of CRB larvae with crude virus homogenates from these tissues resulted in viral infection and mortality. OrNV isolated from Palauan-sourced CRB was designated as OrNV-Palau1. Both OrNV-Palau1 and OrNV-X2B, a CRB biological control isolate released in the Pacific, were propagated using the FRI-AnCu-35 cell line for production of inoculum. However, the OrNV-Palau1 isolate exhibited lower viral production levels and longer larval survival times compared to OrNV-X2B in O. rhinoceros larvae. Full genome sequences of the OrNV-Palau1 and -X2B isolates were determined and found to be closely related to each other. Altogether these results suggest CRB adults in Palau are infected with a less virulent virus, which may affect the nature and extent of OrNV-induced pathology in Palauan populations of CRB.

Can Biological Control Overcome the Threat From Newly Invasive Coconut Rhinoceros Beetle Populations (Coleoptera: Scarabaeidae)? A Review

The coconut rhinoceros beetle (CRB: Oryctes rhinoceros Linnaeus) is one of the most damaging pests to coconut and oil palms in Asia and the Pacific Islands. Adults bore into the crown and damage developing fronds, which affects tree development and yield. The insect is native to South and Southeast Asia and was inadvertently introduced into the Pacific in 1909. It has since spread to several Pacific island nations and territories, causing significant economic impact on these important coconut and palm-growing regions. In the 1950s and 1960s, an international biological control effort was initiated to search for and release natural enemy species. Release of the Oryctes rhinoceros nudivirus Huger (OrNV) and the species complex of Metarhizium Sorokin (Hypocreales: Clavicipitaceae) was successful in controlling CRB in its invaded range. Recently a new biotype of the beetle, known as CRB-G, has spread into the Pacific Islands causing unprecedented levels of damage due to the failure of previously successful biological control agents (BCAs) to suppress this biotype. The re-emergence of CRB as a serious pest warrants a rigorous re-evaluation of potential BCAs and a new search for effective natural enemies if necessary. In this article, we review literature on CRB to 1) analyze past introductions of BCAs and their effectiveness; 2) identify potentially important natural enemies and their geographical origins; and 3) assess possible approaches for utilization of BCAs against the new wave of CRB invasion. Research gaps and directions deserving future attention are highlighted and a strategy for renovation of biological controls for CRB suggested.

Examination of population genetics of the Coconut Rhinoceros Beetle (Oryctes rhinoceros) and the incidence of its biocontrol agent (Oryctes rhinoceros nudivirus) in the South Pacific Islands

Recently, incursions of the Coconut rhinoceros beetle (CRB), Oryctes rhinoceros, have been detected in south Pacific countries that were previously free of the pest. It has been suggested that this range expansion is related to an O. rhinoceros haplotype that is reported to show reduced susceptibility to the well-established classical biocontrol agent, Oryctes rhinoceros nudivirus (OrNV). We investigated O. rhinoceros population genetics and the OrNV status of specimens collected in Fiji, New Caledonia, Papua New Guinea (PNG), Samoa, Solomon Islands, Tonga, Vanuatu and the Philippines. Based on the sequence of the mitochondrial CoxI gene, we found three major mitochondrial haplotype groups (CRB-G, CRB-PNG and CRB-S) across the region. Haplotype diversity varied between and within countries and a high incidence of OrNV infection was detected in all haplotypes wherever they occurred. The O. rhinoceros population in some countries was monotypic and all individuals tested belonged to a single haplotype group. However, in Samoa we detected CRB-S and CRB-PNG and in Solomon Islands we detected all three haplotype groups. Genotyping-by-Sequencing (GBS) showed genetic differentiation in the O. rhinoceros nuclear genome across populations on different islands and provided evidence for gene flow, resulting in a well-mixed population, despite the presence of different CoxI haplotypes in Solomon Islands. Evidence of admixture was also detected on both islands of Samoa. The current CoxI based method is not a reliable diagnostic marker for phenotypic traits, especially in countries such as Solomon Islands where the mitochondrial haplotypes have come back into sympatry and are mixed. To identify possible mechanisms of resistance to OrNV, further molecular analyses O. rhinoceros in response to virus infection is required. To improve biological control of O. rhinoceros, such analyses will need to be combined with an improved understanding of the population genetics of the pest and the evolutionary history of OrNV in the region.

Multiple invasions of a generalist herbivore-Secondary contact between two divergent lineages of Nezara viridula Linnaeus in Australia

The presence of distinct evolutionary lineages within herbivorous pest insect taxa requires close attention. Scientific understanding, biosecurity planning and practice, and pest management decision-making each suffer when such situations remain poorly understood. The pest bug Nezara viridula Linnaeus has been recorded from numerous host plants and has two globally distributed mitochondrial (mtDNA) lineages. These mtDNA lineages co-occur in few locations globally, and the consequences of their divergence and recent secondary contact have not been assessed. We present evidence that both mtDNA lineages of N. viridula are present in Australia and their haplotype groups have a mostly separate distribution from one another. The north-western population has only Asian mtDNA haplotypes, and the population with an eastern distribution is characterized mostly by European mtDNA haplotypes. Haplotypes of both lineages were detected together at only one site in the north of eastern Australia, and microsatellite data indicate that this secondary contact has resulted in mating across the lineages. Admixture and the movement of mtDNA haplotypes outside of this limited area of overlap has not, however, been extensive. Some degree of mating incompatibility or differences in the climatic requirements and tolerances of the two lineages, and perhaps a combination of these influences, might limit introgression and the movement of individuals, but this needs to be tested. This work provides the foundation for further ecological investigation of the lineages of N. viridula, particularly the consequences of admixture on the ecology of this widespread pest. We propose that for now, the Asian and European lineages of N. viridula would best be investigated as subspecies, so that "pure" and admixed populations of this bug can each be considered directly with respect to management and research priorities.

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.

Highly variable COI haplotype diversity between three species of invasive pest fruit fly reflects remarkably incongruent demographic histories

Distance decay principles predict that species with larger geographic ranges would have greater intraspecific genetic diversity than more restricted species. However, invasive pest species may not follow this prediction, with confounding implications for tracking phenomena including original ranges, invasion pathways and source populations. We sequenced an 815 base-pair section of the COI gene for 441 specimens of Bactrocera correcta, 214 B. zonata and 372 Zeugodacus cucurbitae; three invasive pest fruit fly species with overlapping hostplants. For each species, we explored how many individuals would need to be included in a study to sample the majority of their haplotype diversity. We also tested for phylogeographic signal and used demographic estimators as a proxy for invasion potency. We find contrasting patterns of haplotype diversity amongst the species, where B. zonata has the highest diversity but most haplotypes were represented by singletons; B. correcta has ~7 dominant haplotypes more evenly distributed; Z. cucurbitae has a single dominant haplotype with closely related singletons in a 'star-shape' surrounding it. We discuss how these differing patterns relate to their invasion histories. None of the species showed meaningful phylogeographic patterns, possibly due to gene-flow between areas across their distributions, obscuring or eliminating substructure.

Complete genome sequence of Oryctes rhinoceros nudivirus isolated from the coconut rhinoceros beetle in Solomon Islands

Oryctes rhinoceros nudivirus (OrNV) has been an effective biocontrol agent against the insect pest Oryctes rhinoceros (Coleoptera: Scarabaeidae) for decades, but there is evidence that resistance could be evolving in some host populations. We detected OrNV infection in O. rhinoceros from Solomon Islands and used Oxford Nanopore Technologies (ONT) long-read sequencing to determine the full length of the virus genomic sequence isolated from an individual belonging to a mitochondrial lineage (CRB-G) that was previously reported as resistant to OrNV. The complete circular genome of the virus consisted of 125,917 nucleotides, 1.698 bp shorter than the originally-described full genome sequence of Ma07 strain from Malaysia. We found 130 out of 139 previously annotated ORFs (seven contained interrupted/non-coding sequences, two were identified as duplicated versions of the existing genes), as well as a putatively inverted regions containing four genes. These results demonstrate the usefulness of a long-read sequencing technology for resolving potential structural variations when describing new virus isolates. While the Solomon Islands isolate exhibited 99.41 % nucleotide sequence identity with the originally described strain, we found several genes, including a core gene (vlf-1), that contained multiple amino acid insertions and/or deletions as putative polymorphisms of large effect. Our complete annotated genome sequence of a newly found isolate in Solomon Islands provides a valuable resource to help elucidate the mechanisms that compromise the efficacy of OrNV as a biocontrol agent against the coconut rhinoceros beetle.