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#Metabarcoding

1 post1 participant0 posts today
Frédéric Rimet

We have a post-doc position for 15 months in the framework of the dnaquaimg.eu/ project (11 countries) at UMR Carrtel carrtel.lyon-grenoble.hub.inra (Lake Geneva, France).
If you have good skills in molecular biology, aquatic ecology, biomonitoring, and if you want to join a good team working in a great place surrounded by mountains and lakes have a look to our job offer:
jobs.inrae.fr/en/ot-27021
#metabarcoding #thonon #lake #geneva #postdoc #job

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Frédéric Rimet

Coming soon in @Mol_Ecol
Omics to study and manage aquatic environments: a snapshot from the AquaEcOmics meeting (Evian-les-Bains, 2025)
F Rimet, C Lemonnier, B Alric, P Beja, L Bittner, J Bylemans, F Leese, R Logares, K Meissner, F Not, L Orsini, B Paix, N Rodríguez-Ezpeleta, R Siano, B Thalinger, N Tromas, V Vasselon, I Domaizon

Thanks to all co-authors! Great to work with you and to summarize this great #aquaecomics meeting #omics #metabarcoding #eDNA #metabolomics #dpcr #metagenomics

Teresita Porter 🙋🏻‍♀️

Applying environmental DNA metabarcoding to calculate an index of biotic
integrity for freshwater fish

biorxiv.org/content/10.1101/20

bioRxiv · Applying environmental DNA metabarcoding to calculate an index of biotic integrity for freshwater fishMulti-metric indices like the Index of Biotic Integrity (IBI) are important biomonitoring tools for Clean Water Act compliance in the United States (US) but have also been implemented worldwide across many taxonomic groups. Environmental DNA (eDNA) metabarcoding could complement IBIs by increasing detection sensitivity for rare taxa while also reducing monitoring costs. To date, no studies have examined the efficacy of using eDNA metabarcoding to calculate IBIs in the US. Here, we used eDNA metabarcoding to calculate a fish-based IBI for streams and rivers of the Tennessee River Basin in northern Alabama, US. We collected water samples from 50 stream and river sites across a gradient of land use intensity, extracted eDNA from these samples, and sequenced the eDNA using vertebrate-specific primers. We compared our eDNA-IBI to a previous fish-IBI implemented by the state of Alabama using conventional sampling, as well as predicted biological condition of these streams from the US Environmental Protection Agency (EPA) based on a benthic macroinvertebrate multi-metric index (BMMI). We found a highly significant, positive relationship between the eDNA-IBI and fish-IBI for the same streams but a weaker, non-significant positive relationship between the eDNA-IBI and BMMI. Notably, the former was recovered despite eDNA-IBI sampling being conducted nine years after the conventional fish sampling at slightly different locations, the fish-IBI having used greater sampling effort throughout the year (including spring and autumn rather than only summer sampling), and a lack of reference DNA sequences that prevented eDNA detection for some species detected by conventional fish sampling. Accordingly, our study provides a baseline for how an eDNA-IBI may work relative to multi-metric indices calculated from conventional sampling, which can be improved through future directions identified and discussed in our paper. ### Competing Interest Statement The authors have declared no competing interest. US Department of Agriculture (USDA) National Institute of Food and Agriculture (NIFA) Hatch Project, ILLU-875-976 University of Illinois Urbana-Champaign Graduate College Dissertation Travel Grant Harley J. van Cleave Research Award University of Illinois Urbana-Champaign Graduate College Dissertation Completion Fellowship Program in Ecology, Evolution, and Conservation Biology summer research stipend supported by USDA NIFA Hatch Project, ILLU-875-984
#environmentalDNA#eDNA#metabarcoding
Frédéric Rimet

We are excited to share our new promo video for the #BIOLAWEB project!
With narration by Srđan Miletić, this video showcases all the activities realised during the BIOLAWEB project thanks to the incredible team, colleagues, and students.

#edna #metabarcoding #metagenomics #omics

youtu.be/vodGY2SRVls?si=28ENW6

youtu.be- YouTubeEnjoy the videos and music you love, upload original content, and share it all with friends, family, and the world on YouTube.
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Frédéric Rimet

Happy to announce a new paper of my Phd student Paula Gauvin:
An annotated reference library for supporting DNA metabarcoding analysis of aquatic macroinvertebrates in French freshwater environments
mbmg.pensoft.net/article/13777
#metabarcoding #eDNA #reference #library @pensoft @mbmg

Metabarcoding and MetagenomicsAn annotated reference library for supporting DNA metabarcoding analysis of aquatic macroinvertebrates in French freshwater environmentsFreshwater 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 and share 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 analysed for taxonomic completeness, barcode coverage and cryptic diversity. The checklist consisted of 2,841 species across 10 phyla, for which 56% had at least one COI-5P sequence available in the Barcode of Life Data System (BOLD). The analysis of cryptic diversity, based on Barcode Index Numbers (BINs) highlighted a potential high rate of cryptic diversity, although it might have been overestimated due to the wide geographic origin of the sequences. Alignment challenges with the primers were identified for certain taxa, particularly amongst 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 three species having more than 100 haplotypes. Finally, this study showed that a total of 57 haplotypes were shared amongst 116 distinct species. This work emphasises 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 DNA.
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