The Plasticene era: Current uncertainties in estimates of the hazards posed by tiny plastic particles on soils and terrestrial invertebrates.

Plastics are ubiquitous in our daily life. Large quantities of plastics leak in the environment where they weather and fragment into micro- and nanoparticles. This potentially releases additives, but rarely leads to a complete mineralization, thus constitutes an environmental hazard. Plastic pollution in agricultural soils currently represents a major challenge: quantitative data of nanoplastics in soils as well as their effects on biodiversity and ecosystem functions need more attention. Plastic accumulation interferes with soil functions, including water dynamics, aeration, microbial activities, and nutrient cycling processes, thus impairing agricultural crop yield. Plastic debris directly affects living organisms but also acts as contaminant vectors in the soils, increasing the effects and the threats on biodiversity. Finally, the effects of plastics on terrestrial invertebrates, representing major taxa in abundance and diversity in the soil compartment, need urgently more investigation from the infra-individual to the ecosystem scales.

Strong resistance to ß-cyfluthrin in a strain of the beetle Alphitobius diaperinus: a de novo transcriptome analysis.

The lesser mealworm, Alphitobius diaperinus, is an invasive tenebrionid beetle and a vector of pathogens. Due to the emergence of insecticide resistance and consequent outbreaks that generate significant phytosanitary and energy costs for poultry farmers, it has become a major insect pest worldwide. To better understand the molecular mechanisms behind this resistance, we studied a strain of A. diaperinus from a poultry house in Brittany that was found to be highly resistant to the ß-cyfluthrin. The strain survived ß-cyfluthrin exposures corresponding to more than 100 times the recommended dose. We used a comparative de novo RNA-Seq approach to explore genes expression in resistant versus sensitive strains. Our de novo transcriptomic analyses showed that responses to ß-cyfluthrin likely involved a whole set of resistance mechanisms. Genes related to detoxification, metabolic resistance, cuticular hydrocarbon biosynthesis and proteolysis were found to be constitutively overexpressed in the resistant compared to the sensitive strain. Follow-up enzymatic assays confirmed that the resistant strain exhibited high basal activities for detoxification enzymes such as cytochrome P450 monooxygenase and glutathione-S-transferase. The in-depth analysis of differentially expressed genes suggests the involvement of complex regulation of signaling pathways. Detailed knowledge of these resistance mechanisms is essential for the establishment of effective pest control.

Influential Insider: Wolbachia, an Intracellular Symbiont, Manipulates Bacterial Diversity in Its Insect Host.

Facultative intracellular symbionts like the α-proteobacteria Wolbachia influence their insect host phenotype but little is known about how much they affect their host microbiota. Here, we quantified the impact of Wolbachia infection on the bacterial community of the cabbage root fly Delia radicum by comparing the microbiota of Wolbachia-free and infected adult flies of both sexes. We used high-throughput DNA sequencing (Illumina MiSeq, 16S rRNA, V5-V7 region) and performed a community and a network analysis. In both sexes, Wolbachia infection significantly decreased the diversity of D. radicum bacterial communities and modified their structure and composition by reducing abundance in some taxa but increasing it in others. Infection by Wolbachia was negatively correlated to 8 bacteria genera (Erwinia was the most impacted), and positively correlated to Providencia and Serratia. We suggest that Wolbachia might antagonize Erwinia for being entomopathogenic (and potentially intracellular), but would favor Providencia and Serratia because they might protect the host against chemical plant defenses. Although they might seem prisoners in a cell, endocellular symbionts can impact the whole microbiota of their host, hence its extended phenotype, which provides them with a way to interact with the outside world.

"Generalist" Aphid Parasitoids Behave as Specialists at the Agroecosystem Scale.

The degree of trophic specialization of interacting organisms impacts on the structure of ecological networks and has consequences for the regulation of crop pests. However, it remains difficult to assess in the case of parasitoids. Host ranges are often established by listing host records from various years and geographic areas in the literature. Here, we compared the actual hosts exploited at a local farm-scale by aphid parasitoids (Hymenoptera: Aphidiinae), to the available species listed as hosts for each parasitoid species. We sampled aphids and their parasitoids in cultivated and uncultivated areas in an experimental farm from April to November 2014 and thereafter used DNA-based data to determine whether a differentiation in sequences existed. Twenty-nine parasitoid species were found on 47 potential aphid hosts. Our results showed that the great majority of the parasitoid tested used fewer host species than expected according to data published in the literature and parasitized a limited number of hosts even when other potential hosts were available in the environment. Moreover, individuals of the most generalist species differed in their DNA sequences, according to the aphid species and/or the host plant species. At a local scale, only obligate or facultative specialist aphid parasitoids were detected. Local specialization has to be considered when implementing the use of such parasitoids in pest regulation within agroecosystems.

Climate warming alters the structure of farmland tritrophic ecological networks and reduces crop yield.

It is unclear how sustained increases in temperature and changes in precipitation, as a result of climate change, will affect crops and their interactions with agricultural weeds, insect pests and predators, due to the difficulties in quantifying changes in such complex relationships. We simulated the combined effects of increasing temperature (by an average of 1.4°C over a growing season) and applying additional rainwater (10% of the monthly mean added weekly, 40% total) using a replicated, randomized block experiment within a wheat crop. We examined how this affected the structure of 24 quantitative replicate plant-aphid-parasitoid networks constructed using DNA-based methods. Simulated climate warming affected species richness, significantly altered consumer-resource asymmetries and reduced network complexity. Increased temperature induced an aphid outbreak, but the parasitism rates of aphids by parasitoid wasps remained unchanged. It also drove changes in the crop, altering in particular the phenology of the wheat as well as its quality (i.e., fewer, lighter seeds). We discuss the importance of considering the wider impacts of climate change on interacting species across trophic levels in agroecosystems.

Determining plant-leaf miner-parasitoid interactions: a DNA barcoding approach.

A major challenge in network ecology is to describe the full-range of species interactions in a community to create highly-resolved food-webs. We developed a molecular approach based on DNA full barcoding and mini-barcoding to describe difficult to observe plant-leaf miner-parasitoid interactions, consisting of animals commonly regarded as agricultural pests and their natural enemies. We tested the ability of universal primers to amplify the remaining DNA inside leaf miner mines after the emergence of the insect. We compared the results of a) morphological identification of adult specimens; b) identification based on the shape of the mines; c) the COI Mini-barcode (130 bp) and d) the COI full barcode (658 bp) fragments to accurately identify the leaf-miner species. We used the molecular approach to build and analyse a tri-partite ecological network of plant-leaf miner-parasitoid interactions. We were able to detect the DNA of leaf-mining insects within their feeding mines on a range of host plants using mini-barcoding primers: 6% for the leaves collected empty and 33% success after we observed the emergence of the leaf miner. We suggest that the low amplification success of leaf mines collected empty was mainly due to the time since the adult emerged and discuss methodological improvements. Nevertheless our approach provided new species-interaction data for the ecological network. We found that the 130 bp fragment is variable enough to identify all the species included in this study. Both COI fragments reveal that some leaf miner species could be composed of cryptic species. The network built using the molecular approach was more accurate in describing tri-partite interactions compared with traditional approaches based on morphological criteria.

Larval hitch-hiking and adult flight are two ways of aphidiinae parasitoids long-range dispersal.

Dispersal strategies and success of pests' natural enemies widely influence the efficiency of biological control. In this study, we compare two dispersal strategies among Aphidiinae parasitoids: eggs and larvae dispersal through winged aphid flight and active dispersal by adult parasitoids. Using a molecular method applied to a sample of >2,000 winged migratory aphids captured in a suction trap situated in Western France, we assessed the proportion of winged aphids carrying an aphidiine larva. In the six most abundant aphid species, we found an average parasitism rate of migrating aphids close to 1% and identified seven different, mainly generalist, parasitoid species. We also identified the species and the sex of adult Aphidiinae captured by the suction trap based on morphological criteria. We found that dispersing adult parasitoids were almost exclusively female. Parasitoid dispersal strategy seems to be species-dependant but this result needs to be confirmed by an exhaustive analysis of winged aphids captured. We discuss the possible impact of the low parasitism rate of winged aphids on parasitoid population dynamics and the importance of these results in the context of biological control and of the study of food webs between aphids and their natural enemies.

Genetic alterations and cancer formation in a European flatfish at sites of different contaminant burdens.

Fish diseases are an indicator for marine ecosystem health since they provide a biological end-point of historical exposure to stressors. Liver cancer has been used to monitor the effects of exposure to anthropogenic pollution in flatfish for many years. The prevalence of liver cancer can exceed 20%. Despite the high prevalence and the opportunity of using flatfish to study environmentally induced cancer, the genetic and environmental factors driving tumor prevalence across sites are poorly understood. This study aims to define the link between genetic deterioration, liver disease progression, and anthropogenic contaminant exposures in the flatfish dab (Limanda limanda). We assessed genetic changes in a conserved cancer gene, Retinoblastoma (Rb), in association with histological diagnosis of normal, pretumor, and tumor pathologies in the livers of 165 fish from six sites in the North Sea and English Channel. The highest concentrations of metals (especially cadmium) and organic chemicals correlated with the presence of tumor pathology and with defined genetic profiles of the Rb gene, from these sites. Different Rb genetic profiles were found in liver tissue near each tumor phenotype, giving insight into the mechanistic molecular-level cause of the liver pathologies. Different Rb profiles were also found at sampling sites of differing contaminant burdens. Additionally, profiles indicated that histological "normal" fish from Dogger sampling locations possessed Rb profiles associated with pretumor disease. This study highlights an association between Rb and specific contaminants (especially cadmium) in the molecular etiology of dab liver tumorigenesis.

Molecular analysis reveals high compartmentalization in aphid-primary parasitoid networks and low parasitoid sharing between crop and noncrop habitats.

The ecosystem service of insect pest regulation by natural enemies, such as primary parasitoids, may be enhanced by the presence of uncultivated, semi-natural habitats within agro-ecosystems, although quantifying such host-parasitoid interactions is difficult. Here, we use rRNA 16S gene sequencing to assess both the level of parasitism by Aphidiinae primary parasitoids and parasitoid identity on a large sample of aphids collected in cultivated and uncultivated agricultural habitats in Western France. We used these data to construct ecological networks to assess the level of compartmentalization between aphid and parasitoid food webs of cultivated and uncultivated habitats. We evaluated the extent to which uncultivated margins provided a resource for parasitoids shared between pest and nonpest aphids. We compared the observed quantitative ecological network described by our molecular approach to an empirical qualitative network based on aphid-parasitoid interactions from traditional rearing data found in the literature. We found that the molecular network was highly compartmentalized and that parasitoid sharing is relatively rare between aphids, especially between crop and noncrop compartments. Moreover, the few cases of putative shared generalist parasitoids were questionable and could be due to the lack of discrimination of cryptic species or from intraspecific host specialization. Our results suggest that apparent competition mediated by Aphidiinae parasitoids is probably rare in agricultural areas and that the contribution of field margins as a source of these biocontrol agents is much more limited than expected. Further large-scale (spatial and temporal) studies on other crops and noncrop habitats are needed to confirm this.

A universal method for the detection and identification of Aphidiinae parasitoids within their aphid hosts.

Molecular methods are increasingly used to detect and identify parasites in their hosts. However, existing methods are generally not appropriate for studying complex host-parasite interactions because they require prior knowledge of species composition. DNA barcoding is a molecular method that allows identifying species using DNA sequences as an identification key. We used DNA amplification with primers common to aphid parasitoids and sequencing of the amplified fragment to detect and identify parasitoids in their hosts, without prior knowledge on the species potentially present. To implement this approach, we developed a method based on 16S rRNA mitochondrial gene and LWRh nuclear gene. First, we designed two primer pairs specific to Aphidiinae (Hymenoptera), the main group of aphid parasitoids. Second, we tested whether the amplified regions could correctly identify Aphidiinae species and found that 61 species were accurately identified of 75 tested. We then determined the ability of each primer pair to detect immature parasitoids inside their aphid host. Detection was earlier for 16S than for LWRh, with parasitoids detected, respectively, 24 and 48 h after egg injection. Finally, we applied this method to assess parasitism rate in field populations of several aphid species. The interest of this tool for analysing aphid-parasitoid food webs is discussed.

Identification of molecular markers for DNA barcoding in the Aphidiinae (Hym. Braconidae).

Reliable identification of Aphidiinae species (Braconidae) is a prerequisite for conducting studies on aphid-parasitoid interactions at the community level. However, morphological identification of Aphidiinae species remains problematic even for specialists and is almost impossible with larval stages. Here, we compared the efficiency of two molecular markers [mitochondrial cytochrome c oxydase I (COI) and nuclear long wavelength rhodopsin (LWRh)] that could be used to accurately identify about 50 species of Aphidiinae that commonly occur in aphid-parasitoid networks in northwestern Europe. We first identified species on a morphological basis and then assessed the consistency of genetic and morphological data. Probably because of mitochondrial introgression, Aphidius ervi and A. microlophii were indistinguishable on the basis of their COI sequences, whereas LWRh sequences discriminated these species. Conversely, because of its lower variability, LWRh failed to discriminate two pairs of species (Aphidius aquilus, Aphidius salicis, Lysiphlebus confusus and Lysiphlebus fabarum). Our study showed that no unique locus but a combination of two genes should be used to accurately identify members of Aphidiinae.