Dr. Virginie Marques

The biodiversity crisis driven by anthropogenic pressures significantly threatens marine ecosystems. The rate of climate change and anthropogenic impacts outpace our traditional observation tools' capabilities, underscoring the urgency for new assessment methods. Environmental DNA (eDNA; DNA traces released by organisms) metabarcoding, a non-invasive method widely developed over the last decade, represents a promising biomonitoring tool thanks to a large spatio-temporal coverage, high detection of rare species and its time and cost-effectiveness. However, capturing fish diversity using eDNA requires genetic reference databases, currently lacking. Improving reference databases relies on opportunistic sampling enabling the reporting of sequences for new species. The data provided here consists of barcoding 86 species of fishes over the 12S mitochondrial DNA gene. We generated 156 sequences of the mitochondrial 12S gene adapted to the “Teleo” barcodes from fishes sampled in the Bay of Biscay (BoB; Northeast Atlantic, France) between 2017 and 2019. In addition, we provided each individual the barcode details (Genbank accession number, chromatograms), a photograph, 5 ecomorphological measures and 11 life-history traits documenting ecological functions (e.g., dispersion, habitat use, diet). Furthermore, we provided the sampling metadata (e.g., date, time, gear, coordinates, depth) and environmental variables measured in situ (e.g., conductivity, water/air temperature). This data set is valuable to improve the Northeast Atlantic eDNA genetic database, thus helping to better understand the effects of environmental forcing in the BoB, a transition zone housing mixed assemblages of boreal, temperate, and subtropical fish species susceptible to display variability in functional traits to adapt to changing conditions. The detailed Metadata for this abstract published in the Data Article section of the journal is available in MetaCat in JaLTER at https://jalter.diasjp.net/data/ERDP-2024-09.

Islands have been used as model systems to study ecological and evolutionary processes, and they provide an ideal set-up for validating new biodiversity monitoring methods. The application of environmental DNA metabarcoding for monitoring marine biodiversity requires an understanding of the spatial scale of the eDNA signal, which is best tested in island systems. Here, we investigated the variation in Actinopterygii and Elasmobranchii species composition recovered from eDNA metabarcoding along a gradient of distance-to-reef in four of the five French Scattered Islands in the Western Indian Ocean. We collected surface water samples at an increasing distance from reefs (0 m, 250 m, 500 m, 750 m). We used a metabarcoding protocol based on the 'teleo' primers to target marine reef fishes and classified taxa according to their habitat types (benthic or pelagic). We investigated the effect of distance-to-reef on β diversity variation using generalised linear mixed models and estimated species-specific distance-to-reef effects using a model-based approach for community data. Environmental DNA metabarcoding analyses recovered distinct fish species compositions across the four inventoried islands and variations along the distance-to-reef gradient. The analysis of β-diversity variation showed significant taxa turnover between the eDNA samples on and away from the reefs. In agreement with a spatially localised signal from eDNA, benthic species were distributed closer to the reef than pelagic ones. Our findings demonstrate that the combination of eDNA inventories and spatial modelling can provide insights into species habitat preferences related to distance-to-reef gradients at a small scale. As such, eDNA can not only recover large compositional differences among islands but also help understand habitat selection and distribution of marine species at a finer spatial scale.

Spatial and temporal monitoring of species threatened with extinction is of critical importance for conservation and ecosystem management. In the Mediterranean coast, the fan mussel (Pinna nobilis) is listed as critically endangered after suffering from a mass mortality event since 2016, leading to 100% mortality in most marine populations. Conventional monitoring for this macroinvertebrate is done using scuba, which is challenging in dense meadows or with low visibility. Here we developed an environmental DNA assay targeting the fan mussel and assessed the influence of several environmental parameters on the species detectability in situ. We developed and tested an eDNA molecular marker and collected 48 water samples in two sites at the Thau lagoon (France) with distinct fan mussel density, depths and during two seasons (summer and autumn). Our marker can amplify fan mussel DNA but lacks specificity since it also amplifies a conspecific species (Pinna rudis). We successfully amplified fan mussel DNA from in situ samples with 46 positive samples (out of 48) using ddPCR, although the DNA concentrations measured were low over almost all samples. Deeper sampling depth slightly increased DNA concentrations, but no seasonal effect was found. We highlight a putative spawning event on a single summer day with much higher DNA concentration compared to all other samples. We present an eDNA molecular assay able to detect the endangered fan mussel and provide guidelines to optimize the sampling protocol to maximize detectability. Effective and non-invasive monitoring tools for endangered species are promising to monitor remaining populations and have the potential of ecological restoration or habitat recolonization following a mass mortality event.

The bathymetric and geographical distribution of marine species represent a key information in biodiversity conservation. Yet, deep-sea ecosystems are among the least explored on Earth and are increasingly impacted by human activities. Environmental DNA (eDNA) metabarcoding has emerged as a promising method to study fish biodiversity but applications to the deep-sea are still scarce. A major limitation in the application of eDNA metabarcoding is the incompleteness of species sequences available in public genetic databases which reduces the extent of detected species. This incompleteness by depth is still unknown. Here, we built the global bathymetric and geographical distribution of 10,826 actinopterygian and 960 chondrichthyan fish species. We assessed their genetic coverage by depth and by ocean for three main metabarcoding markers used in the literature: teleo and MiFish-U/E. We also estimated the number of primer mismatches per species amplified by in silico polymerase chain reaction which influence the probability of species detection. Actinopterygians show a stronger decrease in species richness with depth than Chondrichthyans. These richness gradients are accompanied by a continuous species turnover between depths. Fish species coverage with the MiFish-U/E markers is higher than with teleo while threatened species are more sequenced than the others. "Deep-endemic" species, those not ascending to the shallow depth layer, are less sequenced than not threatened species. The number of primer mismatches is not higher for deep-sea species than for shallower ones. eDNA metabarcoding is promising for species detection in the deep-sea to better account for the 3-dimensional structure of the ocean in marine biodiversity monitoring and conservation. However, we argue that sequencing efforts on "deep-endemic" species are needed.

Arctic fjords are experiencing rapid environmental shifts due to climate change, which may have significant impacts on marine biodiversity and ecosystem functioning. However, the impact of climate change on fjord biodiversity is difficult to quantify given the low accessibility and high cost to sample these areas. In this study, we sampled locations from inside to outside an Arctic fjord and used environmental DNA metabarcoding to assess how the biodiversity of fish and eukaryotic plankton communities relate with environmental conditions. We detected a total of 12 fish taxa and 872 MOTUs for eukaryotes and found marked gradients of temperature and salinity driven by the distance to the glacier at the terminal part of the fjord and depth. Eukaryotic richness was mainly associated with lower temperature and chlorophyll a. Moreover, co-inertia analyses showed a shared structure between eukaryotes assemblages and the environmental gradients. A partial association between eukaryote and fishes suggest a potential shared effect of environmental gradients among these taxa. Our findings provide a baseline for future studies to assess how these assemblages may be impacted by ongoing environmental changes and highlight how fjord ice loss and warming might shift environmental gradients and species distribution under climate change.

Environmental DNA (eDNA) metabarcoding is a method to detect taxa from environmental samples. It is increasingly used for marine biodiversity surveys. As it only requires water collection, eDNA metabarcoding is less invasive than scientific trawling and might be more cost effective. Here, we analysed data from both sampling methods applied in the same scientific survey targeting Northeast Atlantic fish in the Bay of Biscay. We compared the methods regarding the distribution of taxonomic, phylogenetic, and functional diversity. We found that eDNA captured more taxonomic and phylogenetic richness than bottom trawling and more functional richness at the local scale. eDNA was less selective than trawling and detected species in local communities spanning larger phylogenetic and functional breadths, especially as it detected large pelagic species that escaped the trawl, even though trawling detected more flat fish. eDNA indicated differences in fish community composition that were comparable to those based on trawling. However, consistency between abundance estimates provided by eDNA metabarcoding and trawl catches was low, even after accounting for allometric scaling in eDNA production. We conclude that eDNA metabarcoding is a promising method that can complement scientific trawling for multi-component biodiversity monitoring based on presence/absence, but not yet for abundance.