Differences in microbiota between two multilocus lineages of the sugarcane Aphid (Melanaphis sacchari) in the continental United States

The sugarcane aphid (SCA), Melanaphis Sacchari (Zehntner) (Hemiptera: Aphididae), has been considered an invasive pest of sugarcane in the continental United States since 1977. Then, in 2013, SCA abruptly became a serious pest of U.S. sorghum and is now a sorghum pest in 22 states across the continental United States. Changes in insect-associated microbial community composition are known to influence host-plant range in aphids. In this study, we assessed whether changes in microbiota composition may explain the SCA outbreak in U.S. sorghum. We characterized the SCA bacterial microbiota on sugarcane and grain sorghum in four U.S. states, using a metabarcoding approach. In addition, we used taxon-specific polymerase chain reaction (PCR) primers to screen for bacteria commonly reported in aphid species. As anticipated, all SCA harbored the primary aphid endosymbiont Buchnera aphidicola, an obligate mutualistic bacterial symbiont. Interestingly, none of the secondary symbionts, facultative bacteria typically associated with aphids (e.g., Arsenophonus, Hamiltonella, Regiella) were present in either the metabarcoding data or PCR screens (with the exception of Rickettsiella and Serratia, which were detected by metabarcoding at low abundances <1%). However, our metabarcoding detected bacteria not previously identified in aphids (Arcobacter, Bifidobacterium, Citrobacter). Lastly, we found microbial host-associated differentiation in aphids that seems to correspond to genetically distinct aphid lineages that prefer to feed on grain sorghum (MLL-F) versus sugarcane (MLL-D)

ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations.

Environmental DNA (eDNA) metabarcoding is becoming a core tool in ecology and conservation biology, and is being used in a growing number of education, biodiversity monitoring, and public outreach programs in which professional research scientists engage community partners in primary research. Results from eDNA analyses can engage and educate natural resource managers, students, community scientists, and naturalists, but without significant training in bioinformatics, it can be difficult for this diverse audience to interact with eDNA results. Here we present the R package ranacapa, at the core of which is a Shiny web app that helps perform exploratory biodiversity analyses and visualizations of eDNA results. The app requires a taxonomy-by-sample matrix and a simple metadata file with descriptive information about each sample. The app enables users to explore the data with interactive figures and presents results from simple community ecology analyses. We demonstrate the value of ranacapa to two groups of community partners engaging with eDNA metabarcoding results

What goes in, must come out:combining scat-based molecular diet analysis and quantification of ingested microplastics in a marine top predator

Context: Microplastics (plastic particles &lt;5 mm in size) are highly available for ingestion by a wide range of organisms, either through direct consumption or indirectly, via trophic transfer, from prey to predator. The latter is a poorly understood, but potentially major, route of microplastic ingestion for marine top predators.Approach: We developed a novel and effective methodology pipeline to investigate dietary exposure of wild top predators (grey seals; Halichoerus grypus) to microplastics, by combining scat-based molecular techniques with a microplastic isolation method. We employed DNA metabarcoding, a rapid method of biodiversity assessment, to garner detailed information on prey composition from scats, and investigated the potential relationship between diet and microplastic burden.Results: Outcomes of the method development process and results of both diet composition from metabarcoding analysis and detection of microplastics are presented. Importantly, the pipeline performed well and initial results suggest the frequency of microplastics detected in seal scats may be related to the type of prey consumed. Conclusions: Our non-invasive, data rich approach maximises time and resource-efficiency, while minimising costs and sample volumes required for analysis. This pipeline could be used to underpin a much-needed increase in understanding of the relationship between diet composition and rates of microplastic ingestion in high trophic-level species.<br/

Development of a multigenic metabarcoding of prokaryotic microbiota: application to Bacteria and Archaea of agronomical interest encountered in the rice rhizosphere of Camargue

It is our hypothesis that soil and plant microbiota are playing an eminent role in shaping both natural ecosystems and agricultural production systems. It is now widely admitted that bacterial communities show a great diversity in the rhizosphere and in the endosphere as endophytes. These microbial communities affect the fitness of both the hosts and the microbes and further play important roles in C and N cycles. Much less is known about the role played (if any) by archaea within both the plant rhizosphere and endosphere. Interestingly, a recent study has revealed a relatively high archaeal concentration in internal plant tissues (Müller et al., 2015). The objective of our study is to develop a multigenic metabarcoding approach to accurately describe the biodiversity of relevant microbial communities interacting with rice paddies in the Rhône delta region. This pilot agro-ecosystem was selected because it is annually subjected to several abiotic stresses (water stress associated to rice paddies flooding, soil salinity, etc.) that are likely to enhance archaeal growth. We will retain universal prokaryotic primers and archaeal specific primers within the 16S rRNA gene, two housekeeping genes, gyrB(encoding the ß subunit of the DNA gyrase) and rpoB (encoding the ß subunit of the RNA polymerase) for bacteria, and the thermosome TF55 gene (encoding a type II chaperonin) for archaea. Primers evaluation will be conducted on mock cultures and by sampling rice plants during both rice paddies flooding and drying periods. This study is likely to be a first step towards better understanding the dynamics of Camargue rice paddies microbial communities in relation with abiotic constraints

Applications of next-generation sequencing technologies and computational tools in molecular evolution and aquatic animals conservation studies : a short review

Aquatic ecosystems that form major biodiversity hotspots are critically threatened due to environmental and anthropogenic stressors. We believe that, in this genomic era, computational methods can be applied to promote aquatic biodiversity conservation by addressing questions related to the evolutionary history of aquatic organisms at the molecular level. However, huge amounts of genomics data generated can only be discerned through the use of bioinformatics. Here, we examine the applications of next-generation sequencing technologies and bioinformatics tools to study the molecular evolution of aquatic animals and discuss the current challenges and future perspectives of using bioinformatics toward aquatic animal conservation efforts

Exploring within-host diversity of plant viruses in rice agrosystems using two high-throughput sequencing strategies

The virome is an essential component of the phytobiome as viruses correspond to the most abundant and diverse biological entity in Nature and interact with all living organisms. The recent advances in high-throughput sequencing (HTS) has proven efficient for characterizing within-host diversity of several viruses, which has shed light on the influence of this diversity on the global fitness and virulence of viruses. We here aimed at evaluating the impact of rice management on the within-host diversity of Rice yellow mottle virus (RYMV) in order to optimize the cultural practices and to limit the burden of Rice yellow mottle disease in Africa. We worked on rice plants collected from traditional and intensive rice fields in East Africa, which is the center of origin of Rice yellow mottle virus. Interestingly, several strains with contrasted pathogenic and epidemiological parameters co -exist in this region and recombination between strains were identified recently. We selected twelve RYMV sympto-matic samples from fields managed under different types of practices that were analyzed using two HTS strategies: a metagenomics-based approach and a RYMV specific sequencing approach. Combining both strategies, we tested if the RYMV was associated with other viral species in rice, and if some cases of co-infections between RYMV strains occurred. Both approaches indicate a significant within-host RYMV diversity, which allows us to perceive the diversification processes of RYMV strains at the field scale. The detection of recombinants and the comparison of the within-host genetic diversity depending on the cultivation practices are underway