Persisting roadblocks in arthropod monitoring using non-destructive metabarcoding from collection media of passive traps

Background Broad-scale monitoring of arthropods is often carried out with passive traps (e.g., Malaise traps) that can collect thousands of specimens per sample. The identification of individual specimens requires time and taxonomic expertise, limiting the geographical and temporal scale of research and monitoring studies. DNA metabarcoding of bulk-sample homogenates has been found to be faster, efficient and reliable, but the destruction of samples prevents a posteriori validation of species occurrences and relative abundances. Non-destructive metabarcoding of DNA extracted from collection medium has been applied in a limited number of studies, but further tests of efficiency are required with different trap types and collection media to assess the consistency of the method. Methods We quantified the detection rate of arthropod species when applying non-destructive DNA metabarcoding with a short (127-bp) fragment of mitochondrial COI on two combinations of passive traps and collection media: (1) water with monopropylene glycol (H2O–MPG) used in window-flight traps (WFT, 53 in total); (2) ethanol with monopropylene glycol (EtOH–MPG) used in Malaise traps (MT, 27 in total). We then compared our results with those obtained for the same samples using morphological identification (for WFTs) or destructive metabarcoding of bulk homogenate (for MTs). This comparison was applied as part of a larger study of arthropod species richness in silver fir (Abies alba Mill., 1759) stands across a range of climate-induced tree dieback levels and forest management strategies. Results Of the 53 H2O-MPG samples from WFTs, 16 produced no metabarcoding results, while the remaining 37 samples yielded 77 arthropod MOTUs in total, of which none matched any of the 343 beetle species morphologically identified from the same traps. Metabarcoding of 26 EtOH–MPG samples from MTs detected more arthropod MOTUs (233) than destructive metabarcoding of homogenate (146 MOTUs, 8 orders), of which 71 were shared MOTUs, though MOTU richness per trap was similar between treatments. While we acknowledge the failure of metabarcoding from WFT-derived collection medium (H2O–MPG), the treatment of EtOH-based Malaise trapping medium remains promising. We conclude however that DNA metabarcoding from collection medium still requires further methodological developments and cannot replace homogenate metabarcoding as an approach for arthropod monitoring. It can be used nonetheless as a complementary treatment when enhancing the detection of soft-bodied arthropods like spiders and Diptera

Symbiosis disruption in the olive fruit fly, Bactrocera oleae (Rossi), as a potential tool for sustainable control

International audienceBACKGROUND: The olive fruit fly Bactrocera oleae (Rossi) (OLF) is a major agricultural pest, whose control primarily relies on the use of chemical insecticides. Therefore, development of sustainable control strategies is highly desirable. The primary endo-symbiotic bacterium of OLF, 'Candidatus Erwinia dacicola', is essential for successful larval development in unripe olive fruits. Therefore, targeting this endosymbiont with antimicrobial compounds may result in OLF fitness reduction and may exert control on natural populations of OLF.RESULTS: Here, we evaluate the impact of compounds with antimicrobial activity on the OLF endosymbiont. Copper oxychlor-ide (CO) and the fungal metabolite viridiol (Vi), produced by Trichoderma spp., were used. Laboratory bioassays were carried out to assess the effect of oral administration of these compounds on OLF fitness and molecular analyses (quantitative polymer-ase chain reaction) were conducted to measure the load of OLF-associated microorganisms in treated flies. CO and Vi were both able to disrupt the symbiotic association between OLF and its symbiotic bacteria, determining a significant reduction in the endosymbiont and gut microbiota load as well as a decrease in OLF fitness. CO had a direct negative effect on OLF adults. Conversely, exposure to Vi significantly undermined larval development of the treated female's progeny but did not show any toxicity in OLF adults.CONCLUSIONS: These results provide new insights into the symbiotic control of OLF and pave the way for the development of more sustainable strategies of pest control based on the use of natural compounds with antimicrobial activity

The genome of the nucleopolyhedrosis-causing virus from Tipula oleracea sheds new light on the nudiviridae family

National audienceA large double-stranded DNA (dsDNA) virus that produces occlusion bodies, typical of baculoviruses, has been described to infectcrane fly larvae of the genus Tipula (Diptera, Tipulidae). Because of a lack of genomic data, this virus has remained unclassified.Electron microscopy of an archival virus isolated from Tipula oleracea, T. oleracea nudivirus (ToNV), showed irregularlyshaped occlusion bodies measuring from 2 to 5 min length and 2 min middiameter, filled with rod-shape virions containingsingle nucleocapsids within a bilayer envelope. Whole-genome amplification and Roche 454 sequencing revealed a complete circulargenome sequence of 145.7 kb, containing five direct repeat regions. We predicted 131 open reading frames, including a homologof the polyhedrin gene encoding the major occlusion body protein of T. paludosa nucleopolyhedrovirus (NPV). BLASTsearches demonstrated that ToNV had 21 of the 37 baculovirus core genes but shared 52 genes with nudiviruses (NVs). Phylogenomicanalyses indicated that ToNV clearly belongs to the Nudiviridae family but should probably be assigned to a new genus.Among nudiviruses, ToNV was most closely related to the Penaeus monodon NV and Heliothis zea NV clade but distantly relatedto Drosophila innubia NV, the other nudivirus infecting a Diptera. Lastly, ToNV was found to be most closely related to thenuvidirus ancestor of bracoviruses. This was also reflected in terms of gene content, as ToNV was the only known exogenousvirus harboring homologs of the Cc50C22.6 and 27b (Cc50C22.7) genes found in the nudiviral genomic cluster involved in bracovirusparticle production

Functional annotation of Cotesia congregata bracovirus: identification of the viral genes expressed in parasitized host immune tissues.

International audienceBracoviruses (BV) from Polydnaviridae family are symbiotic viruses used as biological weapons by parasitoid wasps to manipulate lepidopteran host physiology and induce parasitism success. BV particles are produced by wasp ovaries and injected along with the eggs into the caterpillar host body where viral gene expression is necessary for wasp development. Recent sequencing of the proviral genome of Cotesia congregata BV (CcBV) identified 222 predicted virulence genes present on 35 proviral segments integrated in the wasp genome. To date, the expression of only a few selected candidate virulence genes had been studied in the caterpillar host, and we lacked a global vision of viral gene expression. In this study, a large-scale transcriptomic analysis by 454 sequencing of two immune tissues (fat body and hemocytes) of parasitized Manduca sexta caterpillar host allowed detection of expression of 88 CcBV genes expressed 24 h after the onset of parasitism. We could link the expression profile of these genes to several factors, showing that different regulatory mechanisms control viral gene expression in the host. These factors include presence of signal peptides in encoded proteins, diversification of promoter regions, and more surprisingly gene position on the proviral genome. Indeed, most genes for which expression could be detected are localized in particular proviral regions globally producing higher numbers of circles. Moreover this PDV transcriptomic analysis also reveals that a majority of CcBV genes possess at least one intron and an arthropod transcription start site consistent with an insect origin of these virulence genes