Methodological optimization and standardization of the metabarcoding of insects gut microbiome

Metabarcoding analysis of microbiota could help understand how Orthopteran species cope with challenges associated with environmental changes. Since microbial symbionts have a mutually beneficial relationship with its host and play important roles in the immune and physiological systems, they likely impact its ecology and evolution (i.e. plant range, life history, behaviour). In addition, the analysis of the complex pathogenic communities associated with locusts could be useful to discover unexplored pathogens and develop future research on biological control innovation. Yet, current knowledge of Orthopteran-associated microbial communities is limited. This is partly because recognizing cryptic, diverse, and numerous microorganisms hosted by insects is a difficult task. Despite the design of standard genes for their identification and the latest advances in high throughput sequencing, difficulties persist when we look at the microbiota of insects, including Orthopterans. (1) DNA purification is an essential step in all cultivationindependent approaches to characterize microbial diversity. Indeed, the microbial composition is mainly biased by the efficiency of cell lysis. (2) Another critical step for unbiased representation analysis and high taxonomic resolution is the choice of amplicon and primers. In particular, we showed that Enterobacteriacea, common in insects, were poorly resolved with some of currently used amplicons. (3) Moreover, in the case of phytophagous insects, it is necessary to avoid the amplification of plant remains contained in the digestive tract. In this study, we use (1) three mock community standards that contained equal and logarithmic numbers of eight species (ZymoBIOMICS), and equal numbers of twenty other species (ATCC), and (2) six samplesrepresenting the six main orders of insects (Orthoptera, Diptera, Hemiptera, Coleoptera, Hymenoptera and Lepidoptera). On these dedicated samples, we first statistically evaluate the most commonly used DNA purification kit (Qiagen DNeasy Blood and Tissue), two microorganisms-specific DNA purification kits (ZymoBIOMICS-96 bashing beads and DNeasy UltraClean 96 Microbial Kit) and two homemade procedures (bashing beads and enzymatic cocktails added to Qiagen DNeasy Blood and Tissue). These methods are compared on the basis of DNA yield, DNA shearing, reproducibility, and most importantly representation of microbial diversityin 16S rRNA gene sequences. . Secondly, we are currently evaluating the taxonomic representativity and resolution of different 16S gene primers to avoid plant chloroplast genes amplifications. Second, we evaluate, using in silico analyses, (1) the PCR efficiency (representativity), (2) the taxonomic resolution and (3) the risk to amplify plant chloroplasts of already published primers on various variable regions of the 16S gene (V3, V4, V6, V9) and of the rpoB gene. We then test and validate in vitro the best primer candidates on the dedicated samples

SESAME (SEquence Sorter & AMplicon Explorer): genotyping based on high-throughput multiplex amplicon sequencing

Summary: Characterizing genetic diversity through genotyping short amplicons is central to evolutionary biology. Next-generation sequencing (NGS) technologies changed the scale at which these type of data are acquired. SESAME is a web application package that assists genotyping of multiplexed individuals for several markers based on NGS amplicon sequencing. It automatically assigns reads to loci and individuals, corrects reads if standard samples are available and provides an intuitive graphical user interface (GUI) for allele validation based on the sequences and associated decision-making tools. The aim of SESAME is to help allele identification among a large number of sequences

Modeling spatiotemporal dynamics of outbreaking species: influence of environment and migration in a locust

Many pest species exhibit huge fluctuations in population abundance. Understanding their large-scale and long-term dynamics is necessary to develop effective control and management strategies. Occupancy models represent a promising approach to unravel interactions between environmental factors and spatiotemporal dynamics of outbreaking populations. Here, we investigated population dynamics of the Australian plague locust, Chortoicetes terminifera, using density data collected between 1988 and 2010 by the Australian Plague Locust Commission over more than 3 million km2 in eastern Australia. We applied multistate and autologistic multi-season occupancy models to test competing hypotheses about environmental and demographic processes affecting the large-scale dynamics of the Australian plague locust. We found that rainfall and land cover predictors best explained the spatial variability in outbreak probability across eastern Australia. Outbreaks are more likely to occur in temperate than tropical regions, with a faster and more continuous response to rainfall in desert than in agricultural areas. Our results also support the hypothesis that migration tends to propagate outbreaks only locally (over distances lower than 400 km) rather than across climatic regions. Our study suggests that locust outbreak forecasting and management systems could be improved by implementing key environmental factors and migration in hierarchical spatial models. Finally, our modeling framework can be seen as a step towards bridging the gap between mechanistic and more phenomenological models in the spatial analysis of fluctuating populations

Parasites and invasions: changes in gastrointestinal helminth assemblages in invasive and native rodents in Senegal

Understanding why some exotic species become widespread and abundant in their colonised range is a fundamental issue that still needs to be addressed. Among many hypotheses, newly established host populations may benefit from a parasite loss ("enemy release" hypothesis) through impoverishment of their original parasite communities or reduced infection levels. Moreover, the fitness of competing native hosts may be negatively affected by the acquisition of exotic taxa from invaders ("parasite spillover") and/or by an increased transmission risk of native parasites due to their amplification by invaders ("parasite spillback"). We focused on gastrointestinal helminth communities to determine whether these predictions could explain the ongoing invasion success of the commensal house mouse (Mus musculus domesticus) and black rat (Rattus rattus), as well as the associated decrease in native Mastomys spp., in Senegal. For both invasive species, our results were consistent with the predictions of the enemy release hypothesis. A decrease in overall gastrointestinal helminth prevalence and infracommunity species richness was observed along the invasion gradients as well as lower specific prevalence/abundance (Aspiculuris tetraptera in Mus musculus domesticus, Hymenolepis diminuta in Rattus rattus) on the invasion fronts. Conversely, we did not find strong evidence of GIH spillover or spillback in invasion fronts, where native and invasive rodents co-occurred. Further experimental research is needed to determine whether and how the loss of gastrointestinal helminths and reduced infection levels along invasion routes may result in any advantageous effects on invader fitness and competitive advantage

Rise of oceanographic barriers in continuous populations of a cetacean: the genetic structure of harbour porpoises in Old World waters

<p>Abstract</p> <p>Background</p> <p>Understanding the role of seascape in shaping genetic and demographic population structure is highly challenging for marine pelagic species such as cetaceans for which there is generally little evidence of what could effectively restrict their dispersal. In the present work, we applied a combination of recent individual-based landscape genetic approaches to investigate the population genetic structure of a highly mobile extensive range cetacean, the harbour porpoise in the eastern North Atlantic, with regards to oceanographic characteristics that could constrain its dispersal.</p> <p>Results</p> <p>Analyses of 10 microsatellite loci for 752 individuals revealed that most of the sampled range in the eastern North Atlantic behaves as a 'continuous' population that widely extends over thousands of kilometres with significant isolation by distance (IBD). However, strong barriers to gene flow were detected in the south-eastern part of the range. These barriers coincided with profound changes in environmental characteristics and isolated, on a relatively small scale, porpoises from Iberian waters and on a larger scale porpoises from the Black Sea.</p> <p>Conclusion</p> <p>The presence of these barriers to gene flow that coincide with profound changes in oceanographic features, together with the spatial variation in IBD strength, provide for the first time strong evidence that physical processes have a major impact on the demographic and genetic structure of a cetacean. This genetic pattern further suggests habitat-related fragmentation of the porpoise range that is likely to intensify with predicted surface ocean warming.</p

GroundBeetles.zip

Sample coordinates and genetic distances computed between samples<br

Présence en France de Neoderelomus piriformis (Hoffmann, 1938) sur le palmier Phoenix canariensis Hort. (Coleoptera, Curculionidae, Derelomini)

First record of Neoderelomus piriformis (Hoffmann, 1938) from France on Phoenix canariensis Hort., Arecaceae (Coleoptera, Curculionidae, Derelomini) . The weevil Neoderelomus piriformis (Hoffmann, 1938) is first recorded from France. We describe its biology, so far unknown. Its host-plant is Phoenix canariensis Hort. and the preimaginal stages develop in male flowers. We describe these preimaginal stages and provide hints on the life cycle of this species. The genera Derelomus and Neoderelomus are keyed.Nous signalons pour la première fois la présence en France du charançon Neoderelomus piriformis (Hoffmann, 1938). Nous présentons sa biologie, jusqu'alors inconnue, sur les fleurs mâles de Phoenix canariensis Hort. (Arecaceae) où se développent les stades préimaginaux. Nous proposons une clé pour séparer les genres Derelomus et Neoderelomus.Piry Sylvain, Gompel Nicolas. Présence en France de Neoderelomus piriformis (Hoffmann, 1938) sur le palmier Phoenix canariensis Hort. (Coleoptera, Curculionidae, Derelomini). In: Bulletin de la Société entomologique de France, volume 107 (5), décembre 2002. pp. 529-534

Présence en France de Neoderelomus piriformis (Hoffmann, 1938) sur le palmier Phoenix canariensis Hort. (Coleoptera, Curculionidae, Derelomini)

First record of Neoderelomus piriformis (Hoffmann, 1938) from France on Phoenix canariensis Hort., Arecaceae (Coleoptera, Curculionidae, Derelomini) . The weevil Neoderelomus piriformis (Hoffmann, 1938) is first recorded from France. We describe its biology, so far unknown. Its host-plant is Phoenix canariensis Hort. and the preimaginal stages develop in male flowers. We describe these preimaginal stages and provide hints on the life cycle of this species. The genera Derelomus and Neoderelomus are keyed.Nous signalons pour la première fois la présence en France du charançon Neoderelomus piriformis (Hoffmann, 1938). Nous présentons sa biologie, jusqu'alors inconnue, sur les fleurs mâles de Phoenix canariensis Hort. (Arecaceae) où se développent les stades préimaginaux. Nous proposons une clé pour séparer les genres Derelomus et Neoderelomus.Piry Sylvain, Gompel Nicolas. Présence en France de Neoderelomus piriformis (Hoffmann, 1938) sur le palmier Phoenix canariensis Hort. (Coleoptera, Curculionidae, Derelomini). In: Bulletin de la Société entomologique de France, volume 107 (5), décembre 2002. pp. 529-534