This protocol was developed to support long-term global biodiversity monitoring under the WildinSync initiative, which uses environmental DNA (eDNA) to assess anthropogenic impacts and nature-positive actions on ecosystems. Marine water sampling is performed to capture DNA traces left by animals, enabling detection of species presence and distribution across diverse global marine habitats. The method consists of standardized marine water eDNA sampling to obtain DNA traces from aquatic animals. It provides guidance on required materials, field sampling steps, and preparation of samples for later molecular analyses (e.g., DNA extraction and sequencing). The protocol is applicable across a wide range of habitat types and environmental conditions worldwide. It focuses on surface water sampling either from a boat or from the shore. Applicability may be limited in marine environments where water sampling is not feasible or safe (e.g., high-energy coastlines, rough seas, or inaccessible offshore areas).

Ecosystem state assessments based on indicator taxa are paramount to inform effective conservation measures and address the ongoing biodiversity crisis. Environmental DNA (eDNA) can offer a scalable biomonitoring approach, especially when using analysis methods, such as CRISPR-Dx, which do not rely on sequencing. Here, we investigated to which extent eDNA with metabarcoding or CRISPR-Dx assays can be used to assess ecosystem state similar to traditional kick-sampling for aquatic insects. We compared ecosystem state classifications from eDNA metabarcoding to kick-sampling from 36 catchments. We show that eDNA metabarcoding, based on a 16S insect primer, detects Ephemeroptera sequences effectively and provides ecosystem state classifications corresponding with those measured with traditional surveys. In contrast, some of the designed indicator CRISPR-Dx assays showed non-specific detections which reduced performance when indicating ecosystem state. Low ecosystem state classifications were mainly associated with a high proportion of built environment at the catchment scale. Our results highlight the suitability of eDNA metabarcoding to classify ecosystem state and identify the main associated environmental variables. As more CRISPR-Dx assays are developed and validated, this technology is poised to greatly simplify eDNA analysis, unlocking biomonitoring at unprecedented spatial and temporal scales to support effective conservation efforts.

Abstract Forest ecosystems have been degraded globally and restoration efforts aim to reverse loss of biodiversity and ecosystem function decline including carbon storage from the atmosphere. Assessments of restoration success predominantly emphasize increasing carbon stocks rather than species recovery. To reverse biodiversity loss effectively, we need better methods to monitor it comprehensively across large scales. By applying environmental DNA (eDNA) metabarcoding, which has recently emerged as an efficient tool for monitoring terrestrial communities, to soil and stream water samples, we assessed diversity of mammals, fungi, and soil fauna across neotropical forest recovery gradients (from pasture, through advanced restored forests, to old‐growth forests) in six unique landscapes in Colombia. Richness of mammals, mammal forest specialists, Basidiomycota, soil macrofauna, and mesofauna was lower in pastures compared to restored forests and did not significantly differ between restored and old‐growth forests. Mammal functional evenness was higher in old‐growth forests demonstrating greater clustering of functionally similar species in restored sites. Across taxa, microfauna exhibited the most pronounced differences in compositional dissimilarity between the land uses. We investigated biodiversity responses to canopy height deficit (CHD), calculated as the difference between observed canopy height and its climate‐predicted maximum. CHD in a 50‐m buffer was negatively associated with macrofauna, mesofauna, microfauna, and Basidiomycota richness, and CHD in a 400‐m upstream buffer had a negative effect on mammal phylogenetic diversity and mean nearest taxon distance. Our findings demonstrate the utility of eDNA metabarcoding from soil and streams, coupled with trait and phylogenetic data, in monitoring biodiversity responses to restoration in the tropics. eDNA metabarcoding and CHD can be used to scale up monitoring across many landscapes and ecologically diverse taxa groups, helping to track progress of restoration efforts and study drivers of restoration success.

ABSTRACT Habitat configuration governs the movement of organisms across landscapes, thereby shaping both population structure and community assembly. While theoretical and empirical studies have assessed how habitat connectivity simultaneously influences intra‐ and interspecific diversity, direct comparisons across contrasting biogeographic regions remain limited. Here, we investigate patterns of genetic and species β‐diversity in tropical reef fishes across two ocean basins with distinct spatial configurations: the Caribbean Sea and the Western Indian Ocean. Using a comparative framework based on species occurrence data from five fish families and single nucleotide polymorphism (SNP) data from 19 species, we detected significant isolation by distance at both population and community levels in the Western Indian Ocean, but only at the community level in the Caribbean Sea. Additionally, genetic and species β‐diversity were positively correlated among species in the Western Indian Ocean, but not in the Caribbean Sea. Together, these results suggest that the shorter inter‐reef distances of the Caribbean Sea promote higher connectivity, leading to a decoupling of intra‐ and interspecific β‐diversity patterns.

The ability of environmental DNA (eDNA) to provide rapid assessments of mammal taxa composition at the watershed scale can make it an efficient survey method on large-scale landscapes, complementing camera traps. Due to the rugged and inaccessible terrain of many areas in Bhutan, camera trapping is associated with logistical challenges, increasing the cost of sampling considerably. In this study, conducted in the Upper Punatsangchhu catchment basin of Bhutan, we investigated the ability of eDNA water samples to capture the diversity of terrestrial mammals in comparison with camera trapping, using six watersheds within the basin as a baseline sampling frame. Combined, the two methods detected a total of 72 mammalian species: eDNA metabarcoding identified 60 species, while camera trapping detected 33 species, with an overlap of 21 species between the two methods. In addition, eDNA metabarcoding detected 90% of the IUCN Red List species detected by the camera traps. Small mammals were frequently detected using eDNA metabarcoding, while camera trapping more often detected large mammals. The mean detection probabilities recorded from eDNA were higher for all species grouped by orders and size categories compared with camera trapping. Biodiversity models based on eDNA metabarcoding and camera trapping both retrieved dominant effects of temperature and isolation in structuring the mammal assemblage. We conclude that eDNA sampling based on watersheds accurately represents the spatial distribution of species across each watershed in our study area in Bhutan to provide a rapid assessment of mammals from river water.

ABSTRACT As agricultural intensification expands globally, there is an increasing concern about the impact of food production on global biodiversity. Biodiversity decline is problematic as species provide a wealth of benefits, including pollination, soil fertility, and protection against pests, within agrosystems. Many countries, especially across Europe, have implemented incentives for farmers to introduce biodiversity‐friendly land management practices, from building hedgerows to planting pollinator fields. Quantifying the impacts of these measures on biodiversity at the farm scale is technically challenging. Here, we developed a method involving the collection of environmental DNA (eDNA) samples with drones from crops, demonstrated in a case study on rapeseed fields under three management types: conventional, biological, and IP Suisse. We analyzed swabbed material through metabarcoding of a 16S amplicon to detect the composition of hexapod in the field. After cleaning and taxonomic assignment, we obtained a total of 75 taxa assigned to 19 families, 23 genera, and 33 species. We found that the variance in recovered diversity was significantly higher for replicates between fields than for replicates within a field, suggesting that eDNA swabbing replicates provided consistent local results. We did not detect significant differences between treatments, possibly because of a landscape effect which causes spillover of species from neighboring seminatural habitats. Our results provide a direction for developing a toolbox for biodiversity measurements in agricultural fields, highlighting the potential for expanding these methodologies to suit the needs of scientists, farmers, and other stakeholders in understanding and fostering farm‐scale biodiversity.

ABSTRACT Understanding the intricate dynamics of biodiversity within and across riverine ecosystems, influenced by geological history and environmental factors, is crucial for effective conservation and management strategies. Italy, particularly the Ligurian region, harbors diverse freshwater fish communities and populations shaped by unique geological and hydrological conditions. Here, we investigated the suitability of environmental DNA (eDNA) metabarcoding to identify inter‐ and intraspecific diversity patterns of riverine fish populations in drainage basins on both sides of the main drainage divide (MDD) between the Adriatic and Ligurian river basins in Northern Italy. We collected 96 aquatic eDNA samples across 48 riverine sites, amplified them using a cytochrome b primer pair, and denoised the sequences to retrieve amplicon sequence variants (ASVs). We calculated communities' phylogenetic distance with betaMPD based on genetic distances derived from the ASVs, combined them with conductance‐based landscape metrics, and applied generalized dissimilarity models to assess spatial genetic structure. Our results reveal genetic differentiation among populations of several fish species, with some displaying clustering patterns across the main drainage divide and isolation by distance patterns. Overall, taxon richness was higher on the Adriatic side (12.82 ± 3.57; 26 unique taxa) than on the Ligurian side of the MDD (8.35 ± 3.66 SD, 25 unique taxa), but the other way around for ASV richness across all species (Ligurian side: 51.94 ± 25.79, 308 unique ASV, Adriatic side: 68.00 ± 32.97, 274 unique ASV). Our findings highlight the effectiveness of eDNA metabarcoding in uncovering various facets of diversity, shedding light on hidden genetic diversity among ASVs, and revealing significant spatial genetic structuring in freshwater fish populations across multiple species.

Arctic marine ecosystems are rapidly transforming due to climate change. Warming temperatures and shrinking sea ice are enabling boreal fish to expand northward, possibly disturbing cold-adapted Arctic species assemblages. Species range shifts have been documented in the Bering and Barents Seas, raising concerns about ecosystem restructuring. Range shifts are especially difficult to detect in the Arctic due to sparse and inconsistent data. Here, we studied fish composition from eDNA water samples taken in East Greenland, Svalbard, the Barents Sea, and the Kara Sea during the TOPtoTOP and Arctic Century expeditions. We examined the environmental drivers of fish community structure using global dissimilarity models. We calculated the decadal rate of temperature change to identify the fastest-changing areas. We compared fish detections from eDNA with published historical records for the Kara Sea to assess possible range expansions. We found that temperature was the main factor influencing the taxa turnover of fish communities, with Gadidae and Liparis sp. driving the greatest compositional differences. Over the past 30 years, temperatures increased by 0.2 to 0.6 degrees C per decade at our study sites, with the highest increases in western Svalbard and the lowest in the eastern Kara Sea. Despite the apparent dependence on temperature, we identified only one species detected outside its known latitudinal range, and five species in the Kara Sea with recent occurrences or representing an extended distribution. Our study suggests that temperature, the main driver of fish community assembly, is increasing rapidly in the Arctic, and a few species have likely already shifted recently, or at least their detections are new in some areas. While these detections cannot be definitively linked to range shifts, our results highlight the need to improve monitoring of high-latitude fish communities to detect and predict future ecosystem changes.

Environmental DNA (eDNA) metabarcoding is changing the way biodiversity is surveyed in many types of ecosystems. eDNA surveys are now commonly performed and integrated into biodiversity monitoring programs and public databases. Although it is widely recognized that eDNA records require interpretation in light of taxonomy and biogeography, there remains a range of perceptions about how thoroughly records should be evaluated and which ones should be reported. Here, we present a modular procedure, available as an R script, that uses a set of five steps to assess the confidence of species-level eDNA records by assigning them a score from 0 to 5. This procedure includes evaluations of the known geographic distribution of each taxon, the taxonomic resolution of the marker used, the regional completeness of the reference database, the diversification rate, and the range map of each taxon. We tested the procedure on a large-scale marine fish eDNA dataset (572 samples) covering 15 ecoregions worldwide, from the poles to the tropics, using the teleo marker on the mitochondrial 12S ribosomal gene. Our analysis revealed broad variation in the average confidence score of eDNA records among regions, with the highest scores occurring along the European and Eastern Atlantic coasts. Generalized linear models applied to record covariates highlighted the significant influences of latitude and species richness on low confidence scores (< 2.5). The polar regions notably displayed high proportions of low confidence scores, probably due to the limited completeness of the regional reference databases and the taxonomic resolution of the teleo marker. We conclude that only records with high confidence scores (> 2.5) should be integrated into biodiversity databases. The medium (2.5) to relatively low-confidence (< 2.5) records correspond to species that require further investigation and may be integrated after inspection to ensure high-quality species records.

Assessing species geographic distributions is critical to approximate their ecological niches, understand how global change may reshape their occurrence patterns, and predict their extinction risks. Yet, species records are over-aggregated across taxonomic, geographic, environmental, and anthropogenic dimensions. The under-sampling of remote locations biases the quantification of species geographic distributions and ecological niche for most species. Here, we used nearly one thousand environmental DNA (eDNA) samples across the world's oceans, including polar regions and tropical remote islands, to determine the extent to which the geographic and ecological niche ranges of marine fishes are underestimated through the lens of global occurrence records based on conventional surveys. Our eDNA surveys revealed that the known geographic ranges for 93% of species and the ecological niche ranges for 7% of species were underestimated, and contributed to filling them. We show that the probability to detect a range filling for a given species is primarily shaped by the GBIF/OBIS sampling effort in a cell, but also by the number of occurrences available for the species. Most gap fillings were achieved by addressing a methodological sampling bias, notably when eDNA facilitated the detection of small fishes in previously sampled locations using conventional methods. Using a machine learning model, we found that a local effort of 10 eDNA samples would detect 24 additional fish species on average and a maximum of 98 species in previously unsampled tropical areas. Yet, a null model revealed that only half of ecological niche range fillings would be due to eDNA surveys, beyond a random allocation of classical sampling effort. Altogether, our results suggest that sampling in remote areas and performing eDNA surveys in over-sampled areas may both increase fish ecological niche ranges toward unexpected values with consequences in biodiversity modeling, management, and conservation.

The advent of environmental DNA (eDNA) metabarcoding marks a transformative era in large-scale biodiversity monitoring. However, the analysis of eDNA datasets is limited by incomplete reference databases and the increasing volume of data requiring processing from raw sequences to annotated taxonomic lists. To curate taxonomic lists from eDNA analysis, geographic constraints are used by expert in post-analysis, which may introduce potential biases in assignments. Instead of relying on expert intervention, a combination of taxonomic and geographic co-occurrences could be directly integrated into machine learning to automatize and improve taxonomic annotation. Here, we introduce a deep learning approach applied to the taxonomic assignment of eDNA sequences, which leverages a species reference database, species co-occurrence data, and a phylogeny to enhance annotation directly from raw sequences. The phylogeny provides the structure to the network's embedding space in which DNA sequences are placed utilizing an artificial neural network (ANN). We train an additional ANN from the phylogenetic embedding and co-occurrence species data to learn coherent species combinations from the whole collection of eDNA sequences, as opposed to single sequences only. When applied directly to the raw sequences, this method correctly predicts unseen species (i.e., those not contained in the reference database), out of more than 31,000 possibilities, in about 24% of the tested cases by relying on phylogenetic embeddings and geographic modulation. The trained ANNs discern species relationships accurately from the raw data, which facilitates the process of associating sequences with taxa-even those absent from reference databases. When we use real eDNA samples, our predictions mostly agree with those from a traditional bioinformatic pipeline, highlighting the potential of our method for the annotation of the increasing number of eDNA sequences.

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.

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.

Abstract 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.

AimThe Mediterranean Sea is one of the most anthropized seas in the world but also a marine biodiversity hotspot with many fish species under threat. The main goal of the study is to test whether on the heavily fished and anthropized Mediterranean coast, the less impacted Corsica and Balearic Islands, can be considered as refugia for threatened and elasmobranch fishes independently of protection by marine reserves.LocationThe French Mediterranean coast and three north-western Mediterranean islands: Corsica and also Mallorca and Minorca from the Balearic archipelago.MethodsWe performed 187 fish surveys using environmental DNA metabarcoding on three islands and 109 along the continental coast. Of the 78 surveys on islands 22 correspond to no-take marine reserves and of the 109 continental surveys 26 were carried out within reserves. After eDNA filtration, extraction, amplification, and sequencing we estimated the number of fish species but also the number commercial, threatened and elasmobranch fish species on each sample. We then performed an ANOVA by permutation to test the effect of insularity and protection on these four biodiversity metrics. We also modelled these four biodiversity metrics as a function of protection and human pressure but also environmental, habitat and sampling conditions. We also built species accumulation curves to obtain asymptotes representing the potential regional pools for each species category on both island and continental coasts.ResultsWe obtained a total of 175,982,610 reads over the 187 eDNA samples that were assigned to 153 fish species including 17 elasmobranch species among which 7 were only detected on islands. We observed a higher total fish richness on continental than island surveys regardless of protection but a higher threatened and elasmobranch fish richness on the island than on continental surveys. We obtained a significant, negative and predominant human gravity impact on the diversity of elasmobranch species. The modelled asymptote reached 148 teleostean fish species on islands and 196 on the continental coastline with a very similar rate of diversity increase with sampling effort but the shape of the species accumulation curves differed markedly for elasmobranchs with a stronger increase in diversity with sampling effort on islands.Main ConclusionsOur findings highlight that Mediterranean islands can be refugia for sharks and rays but also threatened fishes in this overexploited region. Our results also suggest that reducing or banning trawling activities may play a key role for conserving vulnerable fishes, beyond the benefits of no-take marine reserves, which appear limited on these large home-range species.

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.

Aim: Coastal fishes have a fundamental role in marine ecosystem functioning and contributions to people, but face increasing threats due to climate change, habitat degradation and overexploitation. The extent to which human pressures are impacting coastal fish biodiversity in comparison with geographic and environmental factors at large spatial scale is still under scrutiny. Here, we took advantage of environmental DNA (eDNA) metabarcoding to investigate the relationship between fish biodiversity, including taxonomic and genetic components, and environmental but also socio-economic factors. Location: Tropical, temperate and polar coastal areas. Time period: Present day. Major taxa studied: Marine fishes. Methods: We analysed fish eDNA in 263 stations (samples) in 68 sites distributed across polar, temperate and tropical regions. We modelled the effect of environmental, geographic and socio-economic factors on alpha-and beta-diversity. We then computed the partial effect of each factor on several fish biodiversity components using taxonomic molecular units (MOTU) and genetic sequences. We also investigated the relationship between fish genetic alpha-and beta-diversity measured from our barcodes, and phylogenetic but also functional diversity. Results: We show that fish eDNA MOTU and sequence alpha-and beta-diversity have the strongest correlation with environmental factors on coastal ecosystems worldwide. However, our models also reveal a negative correlation between biodiversity and human dependence on marine ecosystems. In areas with high dependence, diversity of all fish, cryptobenthic fish and large fish MOTUs declined steeply. Finally, we show that a sequence diversity index, accounting for genetic distance between pairs of MOTUs, within and between communities, is a reliable proxy of phylogenetic and functional diversity. Main conclusions: Together, our results demonstrate that short eDNA sequences can be used to assess climate and direct human impacts on marine biodiversity at large scale in the Anthropocene and can further be extended to investigate biodiversity in its phylogenetic and functional dimensions.

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.

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.