In the face of global changes and the biodiversity crisis, Local Ecological Knowledge of Indigenous communities is increasingly valued for aligning conservation policies with the needs of local communities and enriching conservation strategies through the synergy of diverse knowledge systems. To assess whether conservation policies relying on biodiversity metrics integrate the interconnectedness between nature and Indigenous communities, we evaluated the congruence between standardised biodiversity measurements obtained through environmental DNA (eDNA) and Indigenous Local Ecological Knowledge (LEK). We selected 19 sampling sites along the upper Oyapock River in French Guiana. We collected eDNA from the water to inventory fish and game species, and we conducted biodiversity perception surveys with anglers and hunters from the Wayãpi Indigenous group to collect LEK associated with each site. Across the studied area, Wayãpi LEK presented different pictures of biodiversity compared to standardised biodiversity assessments. This comparative analysis demonstrates that Wayãpi LEK not only reflects species distribution but also encompasses diverse place‐based obligations and relationships. This underscores the need to integrate LEK into conservation policies to promote equitable and sustainable environmental decision‐making. This can be achieved by encouraging participatory processes that incorporate diverse knowledge systems, enabling the identification of local conservation challenges and the determination of the most suitable compromises. Read the free Plain Language Summary for this article on the Journal blog.

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.

Accelerating rate of human impact and environmental change severely affects marine biodiversity and increases the urgency to implement the Convention on Biological Diversity (CBD) 30×30 plan for conserving 30% of sea areas by 2030. However, area-based conservation targets are complex to identify in a 3-dimensional (3D) ocean where deep-sea features such as seamounts have been seldom studied mostly due to challenging methodologies to implement at great depths. Yet, the use of emerging technologies, such as environmental DNA combined with modern modeling frameworks, could help address the problem. We collected environmental DNA, echosounder acoustic, and video data at 15 seamounts and deep island slopes across the Coral Sea. We modeled 7 fish community metrics and the abundances of 45 individual species and molecular operational taxonomic units (MOTUs) in benthic and pelagic waters (down to 600-m deep) with boosted regression trees and generalized joint attribute models to describe biodiversity on seamounts and deep slopes and identify 3D protection solutions for achieving the CBD area target in New Caledonia (1.4 million km 2 ). We prioritized the identified conservation units in a 3D space, based on various biodiversity targets, to meet the goal of protecting at least 30% of the spatial domain, with a focus on areas with high biodiversity. The relationship between biodiversity protection targets and the spatial area protected by the solution was linear. The scenario protecting 30% of each biodiversity metric preserved almost 30% of the considered spatial domain and accounted for the 3D distribution of biodiversity. Our study paves the way for the use of combined data collection methodologies to improve biodiversity estimates in 3D structured marine environments for the selection of conservation areas and for the use of biodiversity targets to achieve area-based international targets.

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.

Understanding how anthropization impacts the assembly of species onto communities is pivotal to go beyond the observation of biodiversity changes and reveal how disturbances affect the environmental and biotic processes shaping biodiversity. Here, we propose a simple framework to measure the assembly processes underpinning functional convergence/divergence patterns. We applied this framework to northern Amazonian fish communities inventoried using environmental DNA in 35 stream sites and 64 river sites. We found that the harsh and unstable environmental conditions characterizing streams conveyed communities towards functional convergence, by filtering traits related to food acquisition and, to a lower extent, dispersal. Such environmental filtering also strengthened competition by excluding species having less competitive food acquisition traits. Instead, random species assembly was more marked in river communities, which may be explained by the downstream position of rivers facilitating the dispersion of species. Although fish assembly rules differed between streams and river fish communities, anthropogenic disturbances reduced functional divergence in both ecosystems, with a reinforcement of both environmental filtering and weaker competitor exclusion. This may explain the substantial biodiversity alterations observed under slight deforestation levels in Neotropical freshwater ecosystems and underlines their vulnerability to anthropic disturbances that not only affect species persistence but also modify community assembly rules.

eDNA metabarcoding is an effective method for studying fish communitiesbut allows only an estimation of relative species abundance (density /biomass). Here, we combine metabarcoding with an estimation of the totalabundance of eDNA amplified by our universal marker (teleo) using a qPCRapproach to infer the absolute abundance of fish species. We carried outa 2850 km eDNA survey within the Danube catchment using a spatialintegrative sampling protocol coupled with traditional electrofishingfor fish biomass and density estimation. Total fish eDNA concentrationsand total fish abundance were highly correlated. The correlation betweeneDNA concentrations per taxon and absolute specific abundance was ofcomparable strength when all sites were pooled and remained significantwhen the sites were considered separately. Furthermore, a non-linearmixed model showed that species richness was underestimated when theamount of teleo-DNA extracted from a sample was below a threshold of0.65.106 copies of eDNA. This result, combined with the decrease inteleo-DNA concentration by several orders of magnitude with river size,highlights the need to increase sampling effort in large rivers. Ourresults show a comprehensive description of longitudinal changes in fishcommunities and underline our combined metabarcoding/qPCR approach forbiomonitoring and bioassessment surveys when a rough estimate ofabsolute species abundance is sufficient.

Various factors can influence the concentration of eDNA found in the environment and blur the link between eDNA results and in situ fish abundances, biomasses or even occurrences. We studied the influence of one abiotic factor, the temperature, and one biotic factor, the fish size class, on the amount of fish eDNA detectable in water. To do so, we conducted two controlled experiments using tench ( Tinca tinca, L ) placed into outdoor mesocosms during 1 week. The quantification of fish eDNA abundances was performed using quantitative PCR after filtrating a large volume of water (30 L). The Bayesian hierarchical ANOVAs performed on qPCR results did not detect the effect of size class on eDNA amount, but fish eDNA concentration was shown to increase significantly when temperature rose by 6°C (no effect detected at 3°C). This suggests that fish assemblage quantification of two thermally contrasting sites through eDNA is not directly comparable.

Background Deforestation is a widespread disturbance for neotropical freshwater ecosystems. While biodiversity declines have been associated with deforestation, its functional consequences for stream and river fish faunas remain poorly understood. In this study, we explored how deforestation affects the different facets of the functional structure of fish communities inventoried using environmental DNA metabarcoding in 64 river and 35 stream sites of French Guiana. Specifically, we investigated how functional richness, divergence, evenness and identity of fish faunas are affected by deforestation. Results We showed that anthropogenic disturbances in French Guiana are modifying the functional diversity of freshwater fish communities. These disturbances not only affected the amount of functional traits held by the communities but also the identity of the traits and the internal structure of the functional space. Consequently, different facets of the functional diversity supported by fish assemblages were altered. In streams, deforestation did not affect the overall diversity of traits but reduced functional redundancy, underlined by a shift in functional identity towards assemblages dominated by pelagic detritivores. In contrast, river fish faunas experienced a decline in functional richness, paired with shifts in functional identity and a loss of fish species with extreme functions. Conclusions The response to deforestation differed between streams and rivers, but it supports the hypothesis that deforestation is linked to functional changes in fish assemblages. By diminishing the range of the functions in rivers or by jeopardizing the redundancy of functions in streams, deforestation could severely hamper the functioning and stability of neotropical freshwater ecosystems.

Seamounts are the least known ocean biome. Considered biodiversity hotspots, biomass oases, and refuges for megafauna, large gaps exist in their real diversity relative to other ecosystems like coral reefs. Using environmental DNA metabarcoding (eDNA) and baited video (BRUVS), we compared fish assemblages across five environments of different depths: coral reefs (15 m), shallow seamounts (50 m), continental slopes (150 m), intermediate seamounts (250 m), and deep seamounts (500 m). We modeled assemblages using 12 environmental variables and found depth to be the main driver of fish diversity and biomass, although other variables like human accessibility were important. Boosted Regression Trees (BRT) revealed a strong negative effect of depth on species richness, segregating coral reefs from deep-sea environments. Surprisingly, BRT showed a hump-shaped effect of depth on fish biomass, with significantly lower biomass on coral reefs than in shallowest deep-sea environments. Biomass of large predators like sharks was three times higher on shallow seamounts (50 m) than on coral reefs. The five studied environments showed quite distinct assemblages. However, species shared between coral reefs and deeper-sea environments were dominated by highly mobile large predators. Our results suggest that seamounts are no diversity hotspots for fish. However, we show that shallower seamounts form biomass oases and refuges for threatened megafauna, suggesting that priority should be given to their protection.

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.

AbstractEnvironmental DNA (eDNA) metabarcoding is a reliable method to assess taxonomic diversity, but the incompleteness of genetic reference databases prevents the assignation of many sequences to a given species. Functional diversity (FD) is a key biodiversity facet to monitor, but it requires the identification of all species within communities to account for their trait values. So, the ability of eDNA‐based inventories to estimate the “true” level of FD is unknown. Here, using fish surveys in two representative temperate and tropical rivers, with a quasi‐exhaustive genetic and trait database, we measured the bias and variability of different FD indices when calculated with uncertainty in taxonomic assignment at the genus and family level. Our results show that when measuring FD indices with species randomly chosen within genera and families, the bias cannot exceed 30% from real observed FD values. The variability is higher for species‐poorer communities and when those communities are composed of genera and families with high functional heterogeneity. Despite taxonomic uncertainty, our results demonstrate the potential of eDNA surveys to estimate reliable FD values.

Environmental DNA (eDNA) analysis allows efficient surveys of freshwater species and is being increasingly used. However, because different authors use different methods, eDNA data cannot easily be summarised for a global overview. One promising approach is to standardise methods for long-term monitoring. Standardised eDNA metabarcoding methods have been implemented in France for an elusive group: freshwater bivalves. All French bivalve species can be detected and identified at each sampling site. Here, we analyse this comprehensive dataset (280 sites across all France; 40 species) to investigate detection probabilities, infer species distributions and reassess conservation status, and finally examine community patterns (richness) and their determinants. Our method gave over 95 % probability of detection for most species. Species distributions inferred from eDNA sampling were compared with currently known distributions. Four invasive species and one species of conservation concern were found outside their known range. Others were found in a surprisingly small number of localities, although they are currently thought to be widespread and not of conservation concern. Indeed, the databases currently used to determine conservation status are biased by the inclusion of old data, mainly based on shell records only, and may include misidentified species. The main drivers of species richness were latitude and distance from the spring. Co-occurrence of species was investigated for the first time. The results highlight the valuable data that eDNA analysis can provide when used on a large scale, for monitoring and ecological studies, as well as providing improved species distributions, which are essential for conservation policymaking.

AbstractMesophotic marine ecosystems are characterized by lower light penetration supporting specialized fish fauna. Due to their depths (−30–−150 m), accessibility is challenging, and the structure of mesophotic fish assemblages is generally less known than either shallow reefs or deep zones with soft bottoms which are generally trawled. Environmental DNA metabarcoding from seawater filtered in situ could improve our ability to monitor the diversity of mesophotic ecosystems. Here, we developed and tested a submersible standalone pumping device allowing targeted marine water filtering to explore the biodiversity of two mesophotic ecosystems, one temperate along the Provence coast in the North‐Western Mediterranean Sea and one tropical at the seamount La Pérouse in the Western Indian Ocean. We filtered water samples from depths ranging between 0 and 200 m in the Mediterranean Sea and between 60 and 140 m in the Indian Ocean and applied a metabarcoding protocol using the teleo primer pair targeting the 12S mitochondrial rDNA (Actinopterygii and Chondrichthyes). For both study regions, our eDNA surveys were able to recover highly diverse fish assemblages, and the compositional analysis of eDNA samples showed both a marked signal of fish compositional turnover and overlapping taxa between depth zones. Further, we observed that a substantial number of species were found in samples collected in depths beyond their reported depth range suggesting an underestimation of species' depth tolerances. eDNA metabarcoding should thus complement existing knowledge of species' geographic distributions across space and depth. Overall, our results demonstrate the potential of eDNA metabarcoding for future mesophotic surveys as it allows fast and broad biodiversity assessment.

AbstractThe global biodiversity crisis from anthropogenic activities significantly weakens the functioning of marine ecosystems and jeopardizes their ecosystem services. Increasing monitoring of marine ecosystems is crucial to understand the breadth of the changes in biodiversity, ecosystem functioning and propose more effective conservation strategies. Such strategies should not only focus on maximizing the number of species (i.e., taxonomic diversity) but also the diversity of phylogenetic histories and ecological functions within communities. To support future conservation decisions, multicomponent biodiversity monitoring can be combined with high‐throughput species assemblage detection methods such as environmental DNA (eDNA) metabarcoding. Here, we used eDNA to assess fish biodiversity along the coast of southern Brittany (France, Iroise Sea). We filtered surface marine water from 17 sampling stations and applied an eDNA metabarcoding approach targeting Actinopterygii and Elasmobranchii taxa. We documented three complementary biodiversity components—taxonomic, phylogenetic, and functional diversity—and three diversity facets—richness, divergence and regularity. We identified a north/south contrast with higher diversity for the three facets of the biodiversity components in the northern part of the study area. The northern communities showed higher species richness, stronger phylogenetic overdispersion and lower functional clustering compared to the ones in the southern part, due to the higher diversity of habitats (reefs, rocky shores) and restricted access for fishing. Moreover, we also detected a higher level of taxonomic, phylogenetic, and functional uniqueness in many offshore stations compared to more coastal ones, with the presence of species typically living at greater depths (> 300 m), which suggests an influence of hydrodynamic structures and currents on eDNA dispersion and hence sample composition. eDNA metabarcoding can, therefore, be used as an efficient sampling method to reveal fine‐scale community compositions and in combination with functional and phylogenetic information to document multicomponent biodiversity gradients in coastal marine systems.

High-throughput DNA sequencing is becoming an increasingly important tool to monitor and better understand biodiversity responses to environmental changes in a standardized and reproducible way. Environmental DNA (eDNA) from organisms can be captured in ecosystem samples and sequenced using metabarcoding, but processing large volumes of eDNA data and annotating sequences to recognized taxa remains computationally expensive. Speed and accuracy are two major bottlenecks in this critical step. Here, we evaluated the ability of convolutional neural networks (CNNs) to process short eDNA sequences and associate them with taxonomic labels. Using a unique eDNA data set collected in highly diverse Tropical South America, we compared the speed and accuracy of CNNs with that of a well-known bioinformatic pipeline (OBITools) in processing a small region (60 bp) of the 12S ribosomal DNA targeting freshwater fishes. We found that the taxonomic labels from the CNNs were comparable to those from OBITools, with high correlation levels for the composition of the regional fish fauna. The CNNs enabled the processing of raw fastq files at a rate of approximately 1 million sequences per minute, which was about 150 times faster than with OBITools. Given the good performance of CNNs in the highly diverse ecosystem considered here, the development of more elaborate CNNs promises fast deployment for future biodiversity inventories using eDNA.

Human activities can degrade the quality of coral reefs, cause a decline in fish species richness and functional diversity and an erosion of the ecosystem services provided. Environmental DNA metabarcoding (eDNA) has been proposed as an alternative to Underwater Visual Census (UVC) to offer more rapid assessment of marine biodiversity to meet management demands for ecosystem health indices. Taxonomic information derived from sequenced eDNA can be combined with functional traits and phylogenetic positions to generate a variety of ecological indices describing ecosystem functioning. Here, we inventoried reef fish assemblages of two contrasted coastal areas of Curaçao, (i) in close proximity to the island’s capital city and (ii) in a more remote area under more limited anthropogenic pressure. We sampled eDNA by filtering large volumes of sea water (2 x 30L) along 2km boat transects, which we coupled with species ecological properties related to habitat use, trophic level and body size to investigate the difference in fish taxonomic composition, functional and phylogenetic indices recovered from eDNA metabarcoding between these two distinct coastal areas. Despite no marked difference in species richness, we found a higher phylogenetic diversity in proximity to the city, but a higher functional diversity on the more isolated reef. Composition differences between coastal areas were associated with different frequencies of reef fish families. Because of a partial reference database, eDNA only partly matched those detected with UVC, but eDNA surveys nevertheless provided rapid and robust species occupancy responses to contrasted environments. eDNA metabarcoding coupled with functional and phylogenetic diversity assessment can serve the management of coastal habitats under increasing threat from global changes.

Environmental DNA data from the spatio-temporal survey of fish in three French lakes.

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.

Assessing 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 <11% in areas up to 30 km upstream from the biodiversity sampling sites were linked to reductions 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.

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.