Biology subjects

Rimet, F.

Publications and source records attributed to Rimet, F..

4 recordsLinked to original sources

bioRxiv2024

An annotated reference library for supporting DNA metabarcoding analysis of aquatic macroinvertebrates in French freshwater environments

Freshwater ecosystems are increasingly threatened by human activities, leading to biodiversity loss and ecosystem degradation. Effective biodiversity monitoring, particularly through the use of aquatic macroinvertebrates as bioindicators, is crucial for assessing ecological health. While traditional morphological methods face limitations, DNA metabarcoding offers higher accuracy and efficiency in species identification using environmental DNA. However, the success of metabarcoding is contingent on the quality of reference libraries, which are often incomplete or biased. This study aimed to construct a comprehensive COI-based DNA barcode library for freshwater macroinvertebrates in France, specifically targeting short gene regions amplified with fwhF2/fwhR2N primers, suitable for degraded DNA. A list of species occurring in French freshwater ecosystems was established from official national checklists and Alpine lake surveys. The resulting library was analyzed for taxonomic completeness, barcode coverage and genetic diversity. The checklist consisted of 2,841 species across 10 phyla, for which 56% had at least one COI-5P sequences available in the Barcode of Life Data System (BOLD). Alignment challenges with the primers were identified for certain taxa, particularly among Coleoptera, Diptera, and Malacostraca. The genetic diversity approached by the number of haplotypes per species highlighted that most of the species have limited diversity, with only 3 species having more than 100 haplotypes. Finally, this study showed that a total of 57 haplotypes were shared among 116 distinct species. This work emphasized the need for expanded sequencing efforts to improve barcode coverage and highlighted the pitfalls associated with the use of these primers for further biodiversity assessment of macroinvertebrates with degraded DNA.

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

Die hard in Lake Bourget! The case of Planktothrix rubescens

Blooms of Planktothrix rubescens have been recorded for 15 years in Lake Bourget (France), from 1995 to 2009. Then, the presence of this filamentous and toxic cyanobacterium became anecdotic between 2010 and 2015 and it was clearly thought that such a proliferation was over. However, against all odds, blooms occurred again in 2016 and 2017 despite apparent very low phosphorus concentrations in surface waters of the lake. Aims of this study were thus to explain the reasons of this come back in order to propose scenarios likely to be helpful to stakeholders who need to know if such proliferations may occur again in the future. We show that phosphorus input, both from the main tributaries to the lake and possibly from the sediments, were likely the triggers of the new development of the cyanobacterium since a minimum autumn/winter inoculum of P. rubescens was detected the year before. Then, the bloom, that was observed deeper than previous years, was associated to a conjunction of factors already well-known to favour the development of this very competitive species (i.e. mild winter temperature, water column stability, available light at depth, surface water transparency, low predation, etc...). Although many factors and processes could account for the occurrence and bloom of the cyanobacterium, not observed, measured or taken into account here, a plausible scenario could be proposed and may be useful to deciders. One thing remains unclear: where do the cyanobacterium hides when it is not observed during the routine monitoring survey and thus from which place it could initiate its development (nearshore, in the pelagic zone, from the sediment?), unless it is simply not sampled and observed due to methodological bias.

ecology↗

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↗