Biology subjects

Trouche, B.

Publications and source records attributed to Trouche, B..

4 recordsLinked to original sources

bioRxiv2025

Wolbachia and its pWCP plasmid show differential dynamics during the development of Culex mosquitoes

Mosquitoes are major vectors of pathogens such as arboviruses and parasites, causing significant health impacts each year. Wolbachia, an intracellular bacterium widely distributed among arthropods, represents a promising vector control solution. This bacterium can reduce the transmission of dengue, Zika and chikungunya arboviruses and manipulate the reproduction of its host through its prophage WO. Although research on the Wolbachia mobilome primarily focuses on WO and the phenotypes it induces, the function of Wolbachia plasmid pWCP, recently discovered and reported to be strikingly conserved worldwide, remains unknown. In this study, we analyzed the presence and abundance of pWCP as well as Wolbachia in two different species of Culex mosquitoes, one of the most widespread genera in the world and a vector of numerous diseases. We compared relative densities of the bacterium and its mobile genetic element in Culex pipiens molestus and Culex quinquefasciatus, a facultatively autogenous and a anautogenous species, respectively, throughout their development from larval stage L1 to adult individual specimen using quantitative PCR. Our results suggest that 2-5 copies of pWCP occur in Wolbachia cells on average, and the plasmid co-replicates with Wolbachia cells. Moreover, Wolbachia and pWCP exhibit differential levels of abundance at specific development stages throughout the mosquitos life cycle in each species. These findings indicate important, and likely beneficial, roles for the plasmid in the bacteriums biology in different mosquito species as well as complex interaction dynamics between Wolbachia and its host during its life cycle. ImportanceMosquitoes of the Culex genus are critical vectors for numerous diseases, causing significant public health concerns. The intracellular bacterium Wolbachia has emerged as a promising vector control solution due to its ability to interfere with pathogen transmission and manipulate mosquito reproduction. However, unlike the extensively studied WO phage, the biological significance and function of Wolbachias pWCP plasmid, a recently discovered and strikingly conserved mobile genetic element in Culex species, remains unknown. This study investigates the developmental dynamics of pWCP and Wolbachia in two Culex mosquito species, Culex pipiens molestus and Culex quinquefasciatus across their life cycle. In general, the abundance levels of Wolbachia and the plasmid were found to vary across life stages and differ between the two species. However, a relatively small number of pWCP copies were observed per Wolbachia cell, together with a co-replication of the plasmid with the bacterium for most developmental stages. Altogether, these findings suggest a likely beneficial and non-parasitic role for pWCP in Wolbachias biology, that may contribute to the intricate interactions between the bacterium and its mosquito hosts.

microbiology↗

bioRxiv2019

An assessment of environmental metabarcoding protocols aiming at favouring contemporary biodiversity in inventories of deep-sea communities

O_LIThe abyssal seafloor covers more than 50% of planet Earth and is a large reservoir of still mostly undescribed biodiversity. It is increasingly under target of resource-extraction industries although being drastically understudied. In such remote and hard-to-access ecosystems, environmental DNA (eDNA) metabarcoding is a useful and efficient tool for studying biodiversity and implementing environmental impact assessments. Yet, eDNA analysis outcomes may be biased towards describing past rather than present communities as sediments contain both contemporary and ancient DNA. C_LIO_LIUsing commercially available kits, we investigated the impacts of five molecular processing methods on DNA metabarcoding biodiversity inventories targeting prokaryotes (16S-V4V5), unicellular eukaryotes (18S-V4), and metazoans (18S-V1, COI). As the size distribution of ancient DNA is skewed towards small fragments, we evaluated the effect of removing short DNA fragments via size-selection and ethanol reconcentration using DNA extracted from 10 g of sediment at five deep-sea sites. We also compare communities revealed by DNA and RNA co-extracted from 2 g of sediment at the same sites. C_LIO_LIResults show that removing short DNA fragments does not affect alpha and beta diversity estimates in any of the biological compartments investigated. Results also confirm doubts regarding the possibility to better describe live communities using environmental RNA (eRNA). With ribosomal loci, RNA, while resolving similar spatial patterns than co-extracted DNA, resulted in significantly higher richness estimates, supporting hypotheses of increased persistence of ribosomal RNA (rRNA) in the environment and unmeasured bias due to over-abundance of rRNA and RNA release. With the mitochondrial locus, RNA detected lower metazoan richness and resolved less spatial patterns than co-extracted DNA, reflecting high messenger RNA lability. Results also highlight the importance of using large amounts of sediment ([≥]10 g) for accurately surveying eukaryotic diversity. C_LIO_LIWe conclude that DNA should be favoured over RNA for logistically realistic, repeatable, and reliable surveys, and confirm that large sediment samples ([≥]10 g) deliver more complete and accurate assessments of benthic eukaryotic biodiversity and that increasing the number of biological rather than technical replicates is important to infer robust ecological patterns. C_LI

genomics↗

bioRxiv2019

A flexible pipeline combining bioinformatic correction tools for prokaryotic and eukaryotic metabarcoding

Environmental metabarcoding is an increasingly popular tool for studying biodiversity in marine and terrestrial biomes. With sequencing costs decreasing, multiple-marker metabarcoding, spanning several branches of the tree of life, is becoming more accessible. However, bioinformatic approaches need to adjust to the diversity of taxonomic compartments targeted as well as to each barcode gene specificities. We built and tested a pipeline based on Illumina read correction with DADA2 allowing analyzing metabarcoding data from prokaryotic (16S) and eukaryotic (18S, COI) life compartments. We implemented the option to cluster Amplicon Sequence Variants (ASVs) into Operational Taxonomic Units (OTUs) with swarm v2, a network-based clustering algorithm, and to further curate the ASVs/OTUs based on sequence similarity and co-occurrence rates using a recently developed algorithm, LULU. Finally, flexible taxonomic assignment was implemented via Ribosomal Database Project (RDP) Bayesian classifier and BLAST. We validate this pipeline with ribosomal and mitochondrial markers using eukaryotic mock communities and 42 deep-sea sediment samples. The results show that ASVs, reflecting genetic diversity, may not be appropriate for alpha diversity estimation of organisms fitting the biological species concept. The results underline the advantages of clustering and LULU-curation for producing more reliable metazoan biodiversity inventories, and show that LULU is an effective tool for filtering metazoan molecular clusters, although the minimum identity threshold applied to co-occurring OTUs has to be increased for 18S. The comparison of BLAST and the RDP Classifier underlined the potential of the latter to deliver very good assignments, but highlighted the need for a concerted effort to build comprehensive, ecosystem-specific, databases adapted to the studied communities.

bioinformatics↗

bioRxiv2017

Soil classification predicts differences in prokaryotic communities across a range of geographically distant soils once pH is accounted for

Agricultural land is typically managed based on visible plant life at the expense of the belowground majority. However, microorganisms mediate processes sustaining plant life and the soil environment. To understand the role of microbes we first must understand what controls soil microbial community assembly. We assessed the distribution and composition of prokaryotic communities from soils representing four geographic regions on the South Island of New Zealand. These soils are under three different uses (dairy, sheep and beef, and high country farming) and are representative of major soil classification groups (brown, pallic, gley and recent). We hypothesized that pH would account for major community patterns based on 16S profiles, but that land use and location would be secondary modifiers. Community diversity and structure was linked to pH, coinciding with land use. Soil classification correlated with microbial community structure and evenness, but not richness in high country and sheep and beef communities. The impact of land use and pH remained significant at the regional scale, but soil classification provided support for community variability not explained by either of those factors. These results suggest that several edaphic properties must be examined at multiple spatial scales to robustly examine soil prokaryotic communities.

microbiology↗