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#Metabarcoding

2 posts1 participant0 posts today
Public
Frédéric Rimet

Happy to announce a new paper of my 0hd 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.
Public
Frédéric Rimet

Une offre de post-doc de 1 an renouvelable 1 an :
> Finaliser le développement d’une méthode d’identification moléculaire du phytoplancton utilisant le séquençage ADN haut-débit #metabarcoding

> CDD post-doc de 1 an, reconductible 1 an : démarrage à partir de mai 2025, Lieu : UMR Carrtel, Thonon fr-carrtel.lyon-grenoble.hub.i

> Projet pluriannuel #OFB et le projet européen #eDNAquaPlan

> candidature : frederic.rimet@inrae.fr

> plus de détails : filesender.renater.fr/?s=downl

fr-carrtel.lyon-grenoble.hub.inrae.frAccueilAccueil
Public
Frédéric Rimet

and this paper also in MBMG erally nice : good work Tiina 😀
mbmg.pensoft.net/article/13083
Technology Readiness Level of biodiversity monitoring with molecular methods – where are we on the road to routine implementation?
by Laamanen et al.
#edna #methods #TRL #metabarcoding #standardisation

Metabarcoding and MetagenomicsTechnology Readiness Level of biodiversity monitoring with molecular methods – where are we on the road to routine implementation?Human activities are causing rapid biodiversity loss across ecosystems, affecting human well-being and crucial ecosystem services. Traditional biodiversity monitoring tools cannot keep up with the increasing demands of monitoring due to their limited spatial or temporal coverage, high costs, and lack of taxonomic expertise. Thus, implementation of novel molecular monitoring methods such as environmental DNA (eDNA) and DNA metabarcoding, are necessary. Molecular monitoring methods offer significant benefits for biodiversity monitoring and environmental assessment: high sensitivity and accuracy, non-invasive sampling, broad taxonomic range and cost and time efficiency. However, the diverse methodological approaches lead to poor comparability between studies and surveys, highlighting the need for standardised assessments. We used the Technology Readiness Level (TRL) framework to evaluate the maturity of molecular monitoring methods, providing a structured assessment of their readiness for routine use. In a systematic literature review, 420 articles fulfilling the study criteria were assessed and both individual studies and method categories ranked according to the TRL scale. The findings revealed a growing number of studies, particularly in aquatic environments, with most studies validating molecular technologies on a small scale but lacking large-scale system demonstrations. Aquatic eDNA-based methods targeting fish showed overall higher technology readiness compared to other sample types and taxa and applications of molecular monitoring methods ranked into the highest TRL were predominantly freshwater studies. Key barriers to the broader implementation of molecular methods to monitoring include the need for international standards, better quantitative estimates and comprehensive reference libraries. National and international cooperation is crucial for establishing common standards, ensuring reliable and comparable results and expediting the routine use of molecular methods in biodiversity monitoring. Recent efforts towards international standardisation are encouraging, but further coordinated actions are necessary for the global implementation and acceptance of these methods.
Public
Lukas VFN 🇪🇺

Researchers partner with #IndigenousKnowledge holders to protect threatened great desert skink Tjakuṟa phys.org/news/2025-01-partner-

#Metabarcoding clarifies the diet of the elusive and vulnerable Australian #tjakura (Great Desert #Skink, Liopholis kintorei) frontiersin.org/journals/ecolo

"Tjakuṟa is a large #lizard that lives in multi-tunneled communal burrows in #Australia... scientists rely on #Aṉangu Traditional Knowledge to locate Tjakuṟa burrows, estimate burrow occupancy, identify predator tracks"

photo of a lizard next to a burrow in dry red soil
Public
Ingeborg Klarenberg

Quick #introduction.

I am a #terrestrial #ecologist 👩‍🔬 interested in #polar ❄️ #ecosystems. Currently #postdoc at #VUAmsterdam working on #Antarctic 🇦🇶 #microbes 🦠 and #invertebrates 🐜 living in #mosses and #lichens.

When not doing #science, I take photos 🎞️ (ingeborgklarenberg.nl), and spend as much time as possible outside #running 🏃‍♀️, #climbing 🧗‍♀️, hiking and bird watching.

#eDNA #metabarcoding #nitrogenfixation #molecularecology
#symbiosis

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