scholarly journals Culturing-Enriched Metabarcoding Analysis of the Oryctes rhinoceros Gut Microbiome

Insects ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 782
Author(s):  
Matan Shelomi ◽  
Ming-Ju Chen
Keyword(s):  
Bacillus Cereus ◽  
Fat Body ◽  
Cellulase Activity ◽  
Gut Contents ◽  
Cellulolytic Activity ◽  
Gut Microbes ◽  
Oryctes Rhinoceros ◽  
Rhinoceros Beetle ◽  
Unculturable Bacteria ◽  
Insect Gut

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.

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

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Matan Shelomi ◽  
Shih-Shun Lin ◽  
Li-Yu Liu
Keyword(s):  
Pacific Islands ◽  
Plant Cell Wall ◽  
Fat Body ◽  
Molecular Data ◽  
Cell Wall Degrading Enzymes ◽  
Tropical Asia ◽  
Oryctes Rhinoceros ◽  
Rhinoceros Beetle ◽  
Microbial Symbionts ◽  
Decaying Wood

Abstract Background The coconut rhinoceros beetle, Oryctes rhinoceros, is a major pest of palm crops in tropical Asia and the Pacific Islands. Little molecular data exists for this pest, impeding our ability to develop effective countermeasures and deal with the species’ growing resistance to viral biocontrols. We present the first molecular biology analyses of this species, including a metagenomic assay to understand the microbiome of different sections of its digestive tract, and a transcriptomics assay to complement the microbiome data and to shed light on genes of interest like plant cell wall degrading enzymes and immunity and xenobiotic resistance genes. Results The gut microbiota of Oryctes rhinoceros larvae is quite similar to that of the termite gut, as both species feed on decaying wood. We found the first evidence for endogenous beta-1,4-endoglucanase in the beetle, plus evidence for microbial cellobiase, suggesting the beetle can degrade cellulose together with its gut microfauna. A number of antimicrobial peptides are expressed, particularly by the fat body but also by the midgut and hindgut. Conclusions This transcriptome provides a wealth of data about the species’ defense against chemical and biological threats, has uncovered several potentially new species of microbial symbionts, and significantly expands our knowledge about this pest.

scholarly journals Genomic structural and transcriptional variation of Oryctes rhinoceros nudivirus (OrNV) in Coconut Rhinoceros Beetle

2020 ◽  
Author(s):  
Kayvan Etebari ◽  
Rhys Parry ◽  
Marie Joy B. Beltran ◽  
Michael J. Furlong
Keyword(s):  
Gene Expression ◽  
Solomon Islands ◽  
Dna Helicase ◽  
The Philippines ◽  
Comparative Genomic ◽  
Viral Gene ◽  
Geographic Population ◽  
Oryctes Rhinoceros ◽  
Synonymous Mutations ◽  
Rhinoceros Beetle

AbstractOryctes rhinoceros nudivirus (OrNV) is a large circular double-stranded DNA virus which has been used as a biological control agent to suppress Coconut Rhinoceros Beetle (Oryctes rhinoceros) in Southeast Asia and the Pacific Islands. Recently a new wave of O. rhinoceros incursions in Oceania in previously non-infested areas is thought to be related to the presence of low virulence isolates of OrNV or virus tolerant haplotypes of beetles. In this study, chronically infected O. rhinoceros adults were field collected from the Philippines, Fiji, Papua New Guinea and the Solomon Islands. We extracted total RNA from these samples to investigate the global viral gene expression profiles and comparative genomic analysis of structural variations between the four different populations. Maximum likelihood phylogenic analysis indicated that OrNV strains from the Solomon Islands and the Philippines are closely related to while OrNV strains from PNG and Fiji formed a distinct adjacent clade. We detected several polymorphic sites with a frequency higher than 35% in 892 positions of the viral genome. The highest number of structural variants, including single nucleotide variants (SNV), insertion, deletion and non-synonymous mutations, were found in strains from Fiji and PNG when compared to complete recently sequenced Solomon Islands OrNV reference genome. Non-synonymous mutations were detected in several hypothetical proteins, and 15 nudivirus core genes such as OrNV_gp034 (DNA Helicase), lef-8, lef-4 and vp91. For examination of the global gene expression profile of OrNV in chronically infected populations, we found limited evidence of variation between geographic populations. Only a few genes such as OrNV_gp01 (DNA polymerase B), OrNV_gp022 and OrNV_gp107 (Pif-3) were differentially expressed among different strains. Additionally, small RNA sequencing from the Solomon Islands population suggests that OrNV is targeted by the host RNA interference (RNAi) response with abundant 21nt small RNAs. Additionally, we identified a highly abundant putative 22 nt miRNA from the 3’ of a pre-miRNA-like hairpin originating from OrNV-gp-098. These findings provide valuable resources for future studies to improve our understanding of the OrNV genetic variation. Some of these structural changes are specific to the geographic population and could be related to particular phenotypic characteristics of the strain, such as viral pathogenicity or transmissibility, and this requires further investigation.

scholarly journals Genetic structure of the Coconut Rhinoceros Beetle (Oryctes rhinoceros) population and the incidence of its biocontrol agent (Oryctes rhinoceros nudivirus) in the South Pacific Islands

2020 ◽  
Author(s):  
Kayvan Etebari ◽  
James Hereward ◽  
Apenisa Sailo ◽  
Emeline M Ahoafi ◽  
Robert Tautua ◽  
...  
Keyword(s):  
Biocontrol Agent ◽  
New Caledonia ◽  
Solomon Islands ◽  
South Pacific ◽  
The Philippines ◽  
Mitochondrial Lineage ◽  
The South ◽  
Oryctes Rhinoceros ◽  
Rhinoceros Beetle ◽  
The Pacific

Incursions of the Coconut rhinoceros beetle (CRB), Oryctes rhinoceros, have been detected in several countries of the south-west Pacific in recent years, resulting in an expansion of the pest's geographic range. It has been suggested that this resurgence is related to an O. rhinoceros mitochondrial lineage (previously referred to as the CRB-G biotype) 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 adult specimens collected in the Philippines and seven different South Pacific island countries (Fiji, New Caledonia, Papua New Guinea (PNG), Samoa, Solomon Islands, Tonga, and Vanuatu). Based on the presence of single nucleotide polymorphisms (snps) in the mitochondrial Cytochrome C Oxidase subunit I (CoxI) gene, we found three major mitochondrial lineages (CRB-G, a PNG lineage (CRB-PNG) and the South Pacific lineage (CRB-S)) across the region. Haplotype diversity varied considerably between and within countries. The O. rhinoceros population in most countries was monotypic and all individuals tested belonged to a single mitochondrial lineage (Fiji, CRB-S; Tonga, CRB-S; Vanuatu, CRB-PNG; PNG (Kimbe), CRB-PNG; New Caledonia CRB-G; Philippines, CRB-G). However, in Samoa we detected CRB-S and CRB-PNG and in Solomon Islands we detected all three haplotype groups. Genotyping-by-Sequencing (GBS) methods were used to genotype 10,000 snps from 230 insects across the Pacific and showed genetic differentiation in the O. rhinoceros nuclear genome among different geographical populations. The GBS data also provided evidence for gene flow and admixture between different haplotypes in Solomon Islands. Therefore, contrary to earlier reports, CRB-G is not solely responsible for damage to the coconut palms reported since the pest was first recorded in Solomon Islands in 2015. We also PCR-screened a fragment of OrNV from 260 insects and detected an extremely high prevalence of viral infection in all three haplotypes in the region. We conclude that the haplotype groups CRB-G, CRB-S, and PNG, do not represent biotypes, subspecies, or cryptic species, but simply represent different invasions of O. rhinoceros across the Pacific. This has important implications for management, especially biological control, of Coconut rhinoceros beetle in the region.

scholarly journals First Report of Black Soft Rot of Indian Gooseberry Caused by Syncephalastrum racemosum

Plant Disease ◽  
2004 ◽  
Vol 88 (5) ◽  
pp. 575-575 ◽  
Author(s):  
Neelima Garg ◽  
Om Prakash ◽  
B. K. Pandey ◽  
B. P. Singh ◽  
G. Pandey
Keyword(s):  
Cellulase Activity ◽  
Basal Medium ◽  
Petri Dish ◽  
Soft Rot ◽  
Cellulolytic Activity ◽  
Academic Press ◽  
First Report ◽  
Syncephalastrum Racemosum ◽  
Indian Gooseberry ◽  
Pathogenicity Tests

Indian gooseberry (Emblica officinalis Gaertn.) is a medicinal plant with high nutraceutical value. During November and December 2003, soft rot was noticed on harvested and stored (20 ± 5°C and 65 ± 5% relative humidity) fruits at the experimental farm in Rehmanhera, Lucknow, India (26°50′N, 80°54′E). These fruits had numerous, minute brown necrotic lesions showing white mycelial growth. A pronounced halo of water-soaked, faded tissue surrounded the lesion between the fringe of mycelium and healthy tissues. The rotted surface was covered with a black, powdery layer of spores. On Czapek yeast extract agar, fungal colonies were blackish grey, moderately dense, and covered the entire petri dish. The fungus produced aseptate mycelium. The sporangial heads were 30 to 50 μm in diameter with sporangiospores found linearly within cylindrical sacs (merosporangia) borne on spicules around the columella. Sporangiospores, spherical to cylindrical in shape and borne in chains, measured 3.0 to 5.0 μm long. The fungus was morphologically and physiologically identified as Syncephalastrum racemosum Schr. (2). For pathogenicity tests, healthy fruits (10 replicates) were surface sterilized and punctured inoculated aseptically with 1.0 × 106 conidia and incubated at 20 ± 5°C Typical symptoms of the disease appeared after 4 days. The fungus exhibited a strong level of cellulolytic activity as indicated by prolific growth on Indian gooseberry fiber waste under solid-state fermentation conditions. The level of cellulase activity (1) was 21 filter paper activity unit per ml at 72 hr in culture supernatant of basal medium having carboxymethyl cellulose as the carbon source. The fungus showed resistance to tannins (as much as 2%), since it could grow well in liquid growth medium (Czapek Dox broth) with 2% tannins and aonla juice with 1.8% tannins. Since Indian gooseberry is rich in fiber (2.5 to 3.4%) and tannins (1.5 to 2.0%), this may be an important pathogen. To our knowledge, this is the first report of the occurrence of Syncephalastrum racemosum on Indian gooseberry fruits. References: (1) T. K. Ghose. Pure Appl. Chem. 59(2):257, 1987. (2) J. I. Pitt and A. D. Hocking. Fungi and Food Spoilage. Academic Press. North Ryde, Australia, 1985.

scholarly journals Transcription Profile and Genomic Variations of Oryctes Rhinoceros Nudivirus in Coconut Rhinoceros Beetles

2020 ◽  
Vol 94 (22) ◽  
Author(s):  
Kayvan Etebari ◽  
Rhys Parry ◽  
Marie Joy B. Beltran ◽  
Michael J. Furlong
Keyword(s):  
Gene Expression ◽  
Southeast Asia ◽  
Pacific Islands ◽  
Biocontrol Agent ◽  
Viral Gene Expression ◽  
Viral Gene ◽  
Content Type ◽  
Oryctes Rhinoceros ◽  
Rhinoceros Beetle ◽  
The Pacific

ABSTRACT Oryctes rhinoceros nudivirus (OrNV) is a double-stranded DNA (dsDNA) virus which has been used as a biocontrol agent to suppress the coconut rhinoceros beetle (Oryctes rhinoceros) in Southeast Asia and the Pacific Islands. A new wave of O. rhinoceros incursions in Oceania is thought to be related to the presence of low-virulence isolates of OrNV or virus-tolerant haplotypes of beetles. In this study, chronically infected beetles were collected from Philippines, Fiji, Papua New Guinea (PNG), and the Solomon Islands (SI). RNA sequencing (RNA-seq) was performed to investigate the global viral gene expression profiles and for comparative genomic analysis of structural variations. Maximum likelihood phylogenic analysis indicated that OrNV strains from the SI and Philippines are closely related, while OrNV strains from PNG and Fiji formed a distinct adjacent clade. We detected several polymorphic sites with a frequency higher than 35% in 892 positions of the viral genome. Nonsynonymous mutations were detected in several hypothetical proteins and 15 nudivirus core genes, such as gp034, lef-8, lef-4, and vp91. We found limited evidence of variation in viral gene expression among geographic populations. Only a few genes, such as gp01, gp022, and gp107, were differentially expressed among different strains. Additionally, small RNA sequencing from the SI population suggested that OrNV is targeted by the host RNA interference (RNAi) response with abundant 21-nucleotide small RNAs. Some of these genomic changes are specific to the geographic population and could be related to particular phenotypic characteristics of the strain, such as viral pathogenicity or transmissibility, and this requires further investigation. IMPORTANCE Oryctes rhinoceros nudivirus has been an effective biocontrol agent against the coconut rhinoceros beetle in Southeast Asia and the Pacific Islands for decades. The recent outbreak of these beetles in many South Pacific islands has had a significant impact on livelihoods in the region. It has been suggested that the resurgence and spread of the pest are related to the presence of low-virulence isolates of OrNV or virus-tolerant haplotypes of beetles. We examined viral genomic and transcriptional variations in chronically infected beetles from different geographical populations. A high number of polymorphic sites among several geographical strains of OrNV were identified, but potentially only a few of these variations in the genome are involved in functional changes and can potentially alter the typical function. These findings provide valuable resources for future studies to improve our understanding of the OrNV genetic variations in different geographic regions and their potential link to virus pathogenicity.

scholarly journals Oviposition Preferences and Behavior of Wild-Caught and Laboratory-Reared Coconut Rhinoceros Beetle, Oryctes rhinoceros (Coleoptera: Scarabaeidae), in Relation to Substrate Particle Size

Insects ◽  
2018 ◽  
Vol 9 (4) ◽  
pp. 141 ◽  
Author(s):  
Megan Manley ◽  
Michael Melzer ◽  
Helen Spafford
Keyword(s):  
Particle Size ◽  
Oviposition Behavior ◽  
Particle Sizes ◽  
Breeding Sites ◽  
Oryctes Rhinoceros ◽  
Rhinoceros Beetle ◽  
Oviposition Preferences ◽  
Choice Tests ◽  
And Behavior ◽  
Substrate Particle

The coconut rhinoceros beetle (CRB), Oryctes rhinoceros (L.) (Coleoptera: Scarabaeidae), has become one of the most important coconut and oil palm pests. This species was detected attacking coconut palms on Oʻahu, Hawaiʻi in December 2013, and an eradication program was initiated. One of the major challenges for eradication has been the identification of new breeding sites. Information on the factors influencing oviposition is needed to aid in finding sites likely to host the immature stages of this insect. In this study, a series of choice tests were conducted to assess the oviposition preferences of both laboratory-reared and wild-caught CRB. Mated females, of both lab-reared and wild-caught beetles, were offered for oviposition a choice between sand and two mulch substrates, one with small and one with large particle sizes. Both types of CRB laid eggs preferentially in substrate of small particle size rather than large and none laid eggs in sand. Lab-reared and wild-caught CRB differed in their oviposition behavior and size. These results can be used to aid in the identification of breeding sites for management programs and eradication efforts.

A multicomponent sugar phosphate sensor system specifically induced in Bacillus cereus during infection of the insect gut

2012 ◽  
Vol 26 (8) ◽  
pp. 3336-3350 ◽  
Author(s):  
Fuping Song ◽  
Qi Peng ◽  
Julien Brillard ◽  
Christophe Buisson ◽  
Mark Been ◽  
...  
Keyword(s):  
Bacillus Cereus ◽  
Sensor System ◽  
Sugar Phosphate ◽  
Insect Gut ◽  
Phosphate Sensor
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