Biology subjects

Bouchez, A.

Publications and source records attributed to Bouchez, A..

4 recordsLinked to original sources

bioRxiv2024

Environmental biofilms versus POCIS: efficiency to highlight environmental presence of pharmaceuticals and their effect on biofilm microbiome

Pharmaceutical compounds (PhC) are an important environmental issue, because of their high variety, potentially toxic byproducts and bioactivity at low concentrations. PhC concentrations in WWTP effluents often exhibit large and rapid variations that are difficult to record. Passive samplers are helpful to incorporate spot pollution events and register PhC occurrence at low concentrations. In this work, we aim at (i) studying PhC accumulation in polar organic chemical integrative samplers (POCIS) and environmental biofilms exposed to urban (U) and hospital (H) treated effluents and (ii) evaluating the capacity of POCIS to predict changes in biofilm microbiome over a defined time period. Moreover, we (iii) determine the enrichment of PhC in the recipient river to evaluate levels of environmental contamination and potential effects on microbial biofilms. Biofilms and POCIS were installed in treated effluents and in the recipient river to measure the accumulation of PhC. In parallel, microbial biofilm communities were studied using DNA metabarcoding. The duration of each deployment was one month and the experiment was repeated six times. The performance of POCIS and biofilms to quantify PhC was depending on the compound. POCIS appeared well adapted to reveal contamination trends similar to these in the water column and to identify key PhC drivers of microbial changes. POCIS have the potential to predict pharmaceutical effects on biofilm community structure.

ecology↗

bioRxiv2022

Best practice recommendations for sample preservation in metabarcoding studies: a case study on diatom environmental samples

The development of DNA metabarcoding and High-Throughput Sequencing for diatoms is nowadays offering an interesting approach to assess their communities in freshwater and marine ecosystems. In the context of the implementation of these genomic methods to environmental monitoring, protocol constraints are moving from scientific to operational applications, requiring operational guidelines and standards. In particular, the first steps of the diatom metabarcoding process, which consist of sampling and storage, have been addressed in various ways in scientific and pilot studies. The objective of this study was to compare three currently applied preservation protocols through different storage durations (ranging from one day to one year) for phytobenthos and phytoplankton samples intended for diatom DNA metabarcoding analysis. The experimental design included four freshwater and two marine samples from sites of diverse ecological characteristics. The impact of the preservation and storage was assessed through diatom metabarcoding endpoints: DNA quality and quantity, diversity and richness, community composition and ecological index values (for freshwater samples). The yield and quality of extracted DNA only decreased for freshwater phytobenthos samples preserved with ethanol. Diatom diversity was not affected and their taxonomic composition predominantly reflects the site origin. Only rare taxa (below 100 reads) differed among methods and durations. Thus, importance of preservation method choice is important for low-density species (rare, invasive, threatened or toxic species). However, for biomonitoring purposes, freshwater ecological index values were not affected whatever the preservation method and duration considered (including ethanol preservation), reflecting the site ecological status. This study proved that diatom metabarcoding is robust enough to replace or complement the current approach based on morphotaxonomy, paving the way to new possibilities for biomonitoring. Thus, accompanied by operational standards, the method will be ready to be confidently deployed and prescribed in future regulatory monitoring.

molecular biology↗

bioRxiv2021

Passive sampling of environmental DNA in aquatic environments using 3D-printed hydroxyapatite samplers

O_LIThe study of environmental DNA released by aquatic organisms in their habitat offers a fast, non-invasive and sensitive approach to monitor their presence. Common eDNA sampling methods such as filtration and precipitation are time consuming, require human intervention and are not applicable to a wide range of habitats such as turbid waters and poorly-accessible environments. To circumvent these limitations, we propose to use the binding properties of minerals to create a passive eDNA sampler. C_LIO_LIWe have designed 3D-printed samplers made of hydroxyapatite (HAp samplers), a mineral known for its high binding affinity with DNA. The shape and the geometry of the samplers have been designed to facilitate their handling in laboratory and field. Here we describe and test the ability of HAp samplers to recover artificial DNA and eDNA. C_LIO_LIWe show that HAp samplers efficiently recover DNA and are effective even on small amounts of eDNA (<1 ng). However, we also observed large variations in the amount of DNA recovered even under controlled conditions. C_LIO_LIBy better understanding the physico-chemical interactions between DNA and the HAp sampler surface, one could improve the repeatability of the sampling process and provide an easy-to-use eDNA sampling tool for aquatic environments. C_LI

molecular biology↗

bioRxiv2019

DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work

Effective identification of species using short DNA fragments (DNA barcoding and DNA metabarcoding) requires reliable sequence reference libraries of known taxa. Both taxonomically comprehensive coverage and content quality are important for sufficient accuracy. For aquatic ecosystems in Europe, reliable barcode reference libraries are particularly important if molecular identification tools are to be implemented in biomonitoring and reports in the context of the EU Water Framework Directive (WFD) and the Marine Strategy Framework Directive (MSFD). We analysed gaps in the two most important reference databases, Barcode of Life Data Systems (BOLD) and NCBI GenBank, with a focus on the taxa most frequently used in WFD and MSFD. Our analyses show that coverage varies strongly among taxonomic groups, and among geographic regions. In general, groups that were actively targeted in barcode projects (e.g. fish, true bugs, caddisflies and vascular plants) are well represented in the barcode libraries, while others have fewer records (e.g. marine molluscs, ascidians, and freshwater diatoms). We also found that species monitored in several countries often are represented by barcodes in reference libraries, while species monitored in a single country frequently lack sequence records. A large proportion of species (up to 50%) in several taxonomic groups are only represented by private data in BOLD. Our results have implications for the future strategy to fill existing gaps in barcode libraries, especially if DNA metabarcoding is to be used in the monitoring of European aquatic biota under the WFD and MSFD. For example, missing species relevant to monitoring in multiple countries should be prioritized. We also discuss why a strategy for quality control and quality assurance of barcode reference libraries is needed and recommend future steps to ensure full utilization of metabarcoding in aquatic biomonitoring.

ecology↗