Estimating the extended and hidden species diversity from environmental DNA in hyper-diverse regions

Species inventories are the building blocks of our assessment of biodiversity patterns and human impact. Yet, historical inventories based on visual observations are often incomplete, impairing subsequent analyses of ecological mechanisms, extinction risk and management success. Environmental DNA (eDNA) metabarcoding is an emerging tool that can provide wider biodiversity assessments than classical visual-based surveys. However, eDNA-based inventories remain limited by sampling effort and reference database incompleteness. In this study, we propose a new framework coupling eDNA surveys and sampling-theory methods to estimate species richness in under-sampled and hyper-diverse regions where some species remain absent from the checklist or undetected by visual surveys. We applied this framework to the coastal fish diversity in the heart of the coral triangle, the richest marine biodiversity hotspot worldwide. Combining data from 279 underwater visual censuses, 92 eDNA samples and an extensive custom genetic reference database, we show that eDNA metabarcoding recorded 196 putative species not detected by underwater visual census including 37 species absent from the regional checklist. We provide an updated checklist of marine fishes in the ‘Raja Ampat Bird's Head Peninsula' ecoregion with 2534 species including 1761 confirmed and 773 highly probable presences. The Chao lower-bound diversity estimator, based on the incidence of rare species, shows that the region potentially hosts an additional 123 fish species, including pelagic, cryptobenthic and vulnerable species. The extended and hidden biodiversity along with their asymptotic estimates highlight the ability of eDNA to expand regional inventories and species distributions to better guide conservation strategies

Journée de formation Polar

En lien avec le rectorat de Lyon, le réseau des bibliothèques municipales de Lyon et la DRAC Auvergne-Rhône-Alpes, cette journée a pour but de sensibiliser les enseignants et bibliothécaires au polar et de leur donner des pistes pour amorcer un travail sur le genre avec les adultes et les enfants. Le programme de cette journée s’articule autour d’interventions d’éditeurs, auteurs, libraires et autres professionnels du livre qui viendront notamment présenter des nouveautés polar 2018-2019, apporter des éclairages sur les raisons du succès du polar nordique et aborderont les spécificités du roman policier jeunesse

Cross-ocean patterns and processes in fish biodiversity on coral reefs through the lens of eDNA metabarcoding

Increasing speed and magnitude of global change threaten the world's biodiversity and particularly coral reef fishes. A better understanding of large-scale patterns and processes on coral reefs is essential to prevent fish biodiversity decline but it requires new monitoring approaches. Here, we use environmental DNA metabarcoding to reconstruct well-known patterns of fish biodiversity on coral reefs and uncover hidden patterns on these highly diverse and threatened ecosystems. We analysed 226 environmental DNA (eDNA) seawater samples from 100 stations in five tropical regions (Caribbean, Central and Southwest Pacific, Coral Triangle and Western Indian Ocean) and compared those to 2047 underwater visual censuses from the Reef Life Survey in 1224 stations. Environmental DNA reveals a higher (16%) fish biodiversity, with 2650 taxa, and 25% more families than underwater visual surveys. By identifying more pelagic, reef-associated and crypto-benthic species, eDNA offers a fresh view on assembly rules across spatial scales. Nevertheless, the reef life survey identified more species than eDNA in 47 shared families, which can be due to incomplete sequence assignment, possibly combined with incomplete detection in the environment, for some species. Combining eDNA metabarcoding and extensive visual census offers novel insights on the spatial organization of the richest marine ecosystems

An optical in-situ tool for visualizing and understanding wetting dynamics in membrane distillation

This paper describes the development of a new optical tool to detect in-situ wetting in membrane distillation. The principle of the detection tool is based on the phenomenon of light transmission. A dedicated experimental setup was developed. The proof of concept of this optical tool is validated using in parallel the Detection of Dissolved Tracer Intrusion (DDTI) method that was previously developed, and which is based on the detection of remaining salt traces in wetted pores by scanning electron microscopy and x-ray dispersion spectroscopy. The in-situ tool was used in standard operating conditions (feed temperature 40 degrees C, laminar flow and vacuum pressure 6 kPa) for vacuum membrane distillation with deionized water, a synthetic saline solution, and seawaters. Controlled wetting was then induced by adding a surfactant in the feed after 30 min of operation and wetting dynamics could be effectively visualized. Additionally, the scalability (macro and mesoscales) of this tool was verified and wetting was visualized at different locations on the membrane surface and compared with the wetting observations made at a global scale. A definition of pore wetting is also proposed

Caractérisation expérimentale des transferts de chaleur dans un canal d'eau avec changement de phase

International audienceUne expérience de canal chauffé avec picots et alimenté en eau liquide a été conçue et fabriquée. Il s’agit d’étudier les phénomènes liés à l’ébullition de l’eau chauffée par la paroi inférieure du canal. Lors de la campagne d’essais les visualisations de l’écoulement montrent la génération de la vapeur dans l’écoulement fluide autour des picots. Des mesures de température dans la paroi et les valeurs de la puissance fournie ont conduit à identifier le flux de chaleur et la température à l’interface fluide/paroi. A partir du bilan thermique dans le fluide, sa température est calculée ce qui permet d’identifier le coefficient d’échange pariétal en présence de l’ébullition

GAPeDNA: Assessing and mapping global species gaps in genetic databases for metabarcoding studies

Environmental DNA metabarcoding has recently emerged as a non-invasive tool for aquatic biodiversity inventories, frequently surpassing traditional methods for detecting a wide range of taxa in most habitats. One of the major limitations currently impairing the large-scale application of DNA-based inventories, such as eDNA or bulk-sample analysis is the lack of species sequences available in public genetic databases. These gaps are still largely unknown spatially and taxonomically for most regions of the world, which can hinder targeted future sequencing efforts. We propose GAPeDNA, a user-friendly web-interface (Fig. 1) that provides a global overview of genetic database completeness for a given taxon across space and conservation status. As an initial application, we synthetized data from regional checklists for marine and freshwater fishes along with their IUCN conservation status to provide global maps of species coverage using the European Nucleotide Archive public reference database for 19 metabarcoding primers. This tool automatizes the scanning of gaps in these databases to guide future sequencing efforts and support the deployment of DNA-based inventories at larger scale. It is flexible and can be expanded to other taxa and primers upon data availability. Using our global fish case study, we show that gaps increase toward the tropics where species diversity and the number of threatened species were the highest. It highlights priority areas for fish sequencing like the Congo, the Mekong and the Mississippi freshwater basins which host more than 60 non-sequenced threatened fish species. For marine fishes, the Caribbean and East Africa host up to 42 non-sequenced threatened species. As an open-acces, updatable and flexible tool, GAPeDNA can be used to evaluate the completeness of sequence reference libraries of various markers and for any taxonomic group

GAPeDNA: Assessing and mapping global species gaps in genetic databases for eDNA metabarcoding

Aim Environmental DNA metabarcoding has recently emerged as a non‐invasive tool for aquatic biodiversity inventories, frequently surpassing traditional methods for detecting a wide range of taxa in most habitats. The major limitation currently impairing the large‐scale application of eDNA‐based inventories is the lack of species sequences available in public genetic databases. Unfortunately, these gaps are still unknown spatially and taxonomically, hindering targeted future sequencing efforts. Innovation We propose GAPeDNA, a user‐friendly web interface that provides a global overview of genetic database completeness for a given taxon across space and conservation status. As an application, we synthetized data from regional checklists for marine and freshwater fishes along with their IUCN conservation status to provide global maps of species coverage using the European Nucleotide Archive public reference database for 19 metabarcoding primers. This tool automatizes the scanning of gaps in these databases to guide future sequencing efforts and support the deployment of eDNA inventories at larger scale. This tool is flexible and can be expanded to other taxa and primers upon data availability. Main conclusions Using our global fish case study, we show that gaps increase towards the tropics where species diversity and the number of threatened species are the highest. It highlights priority areas for fish sequencing like the Congo, the Mekong and the Mississippi freshwater basins which host more than 60 non‐sequenced threatened fish species. For marine fishes, the Caribbean and East Africa host up to 42 non‐sequenced threatened species. By presenting the global genetic database completeness for several primers on any taxa and building an open‐access, updatable and flexible tool, GAPeDNA appears as a valuable contribution to support any kind of eDNA metabarcoding study

Aquatic eDNA for monitoring French Guiana biodiversity

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Amazonian mammal monitoring using aquatic environmental DNA

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Low level of anthropization linked to harsh vertebrate biodiversity declines in Amazonia

International audienceAssessing the impact of human activity on ecosystems often links local biodiversity to disturbances measured within the same locality. However, remote disturbances may also affect local biodiversity. Here, we used environmental DNA metabarcoding to evaluate the relationships between vertebrate biodiversity (fish and mammals) and disturbance intensity in two Amazonian rivers. Measurements of anthropic disturbance -here forest cover losses- were made from the immediate vicinity of the biodiversity sampling sites to up to 90 km upstream. The findings suggest that anthropization had a spatially extended impact on biodiversity. Forest cover losses of 22% in taxonomic and functional richness of both terrestrial and aquatic fauna. This underscores the vulnerability of Amazonian biodiversity even to low anthropization levels. The similar responses of aquatic and terrestrial fauna to remote disturbances indicate the need for cross-ecosystem conservation plans that consider the spatially extended effects of anthropization