Environmental DNA illuminates the dark diversity of sharks

Applications of environmental DNA monitoring for seaweed reproductive phenology: A case study with giant kelp (Macrocystis pyrifera)

Monitoring the seasonal reproductive cycles of seaweeds is crucial for effective population and ecosystem management, as well as mariculture seedstock collection. Traditional methods, such as visual monitoring by SCUBA diving or snorkeling, are costly, labor-intensive, and limited in temporal and spatial coverage. This study explores substituting these methods with environmental DNA (eDNA) techniques for giant kelp (Macrocystis pyrifera, order Laminariales). This laboratory study aimed to determine the minimum detectable concentration of zoospores and sporophyte tissue needed for detecting the reproductive phenology of M. pyrifera and to assess the ability and sensitivity to discriminate between life stages. The study involved syringe-filtering seawater samples through 0.45-μm pore-size filters before quantitative polymerase chain reaction (qPCR) analysis with species-specific primers. There was a strong positive correlation between zoospore concentration and eDNA copies per μL (ρ = 0.982, p < 0.001), and a weak correlation for sporophyte wet weight (ρ = 0.367, p = 0.134). There was a significant difference between zoospore and zoospore + sporophyte treatments (p = 0.010), indicating the substantial influence of sporophyte tissue on detected eDNA quantity. Sporophyte tissue obscures the zoospore signal, especially at lower zoospore concentrations (<37 zoospores · mL-1), highlighting that eDNA analysis is suitable for monitoring reproductive peaks and broader patterns in seasonal reproduction cycles of giant kelp when zoospore concentrations are high.

Environmental DNA metabarcoding: Current applications and future prospects for freshwater fish monitoring

Fish, as the top predators in freshwater, greatly contribute to maintain ecosystem stability. There has been a sharp decline in freshwater fish stocks due to multiple factors, both natural and anthropogenic. Effective and accurate monitoring of freshwater fish is necessary to inform on ecosystem health and guide environmental management practices. Traditional survey methods are gradually unable to meet the growing monitoring needs. Environmental DNA (eDNA) metabarcoding provides a high sensitivity, fast and affordable approach for surveying and monitoring of aquatic biology. However, due to the limitations of incomplete databases and non-standardized procedures, the use of eDNA techniques for monitoring freshwater fish remains less mature compared to traditional fish monitoring methods. To systematically review the current applications and future prospects of the eDNA metabarcoding for freshwater fish monitoring, this article: (i) summarizes relevant researches on freshwater fish monitoring using eDNA technology (e.g., methodologies, resource surveys, habitat assessments, etc.) over the past decade. (ii) outlines the methodology of eDNA metabarcoding in freshwater fish monitoring, proposes a standardized process for eDNA methods, and suggests ways to eliminate detection errors. (iii) analyzes the current challenges of the eDNA metabarcoding application in resource surveys and ecological quality assessments of freshwater fish. The eDNA technology can be used as a better alternative or supplement to traditional survey methods for monitoring the diversity, biomass, population distribution, and spawning behaviors of freshwater fish, in particular, it has a prominent advantage in monitoring endangered and rare fish species. (iv) investigates the application of eDNA technology in investigating the impact of human activities and invasive species on freshwater fish, and emphasizes the eDNA's potential in assessing the impacts of water projects (e.g., dam construction or removal, water diversion project) on fish habitats, and the effectiveness of fish passage and invasive fish control efforts. (v) discusses the future prospects of eDNA-based freshwater fish monitoring, both in terms of technology and application. This review provides a guidance for the future development and application of eDNA technology in freshwater fish monitoring and ecological quality assessments.

Bridging the gaps through environmental DNA: A review of critical considerations for interpreting the biodiversity data in coral reef ecosystems

Coral reefs, the rainforests of the sea, are vital hotspots for marine biodiversity. However, the persistent challenge of climate change directly threatens the delicate balance of coral reef ecosystems, impacting myriad species and critical ecosystem services. Therefore, this comprehensive review critically discusses the associated challenges in assessing and preserving coral reef diversity, emphasizing the need for novel biomonitoring techniques due to the elusive and cryptic nature of many reef organisms. The review focuses on environmental DNA (eDNA) analysis as a non-invasive tool for coral species monitoring at various ecological levels. The review highlights that using eDNA in coral reef monitoring requires careful consideration of multiple factors, such as strategic assay development, optimization, and marker selection, substrate selection, and sample volume, which are critical for maximizing the probability of species detection. Moreover, integrating environmental RNA (eRNA) provides additional insights into temporal aspects advancing the coral reef biodiversity research and conservation efforts.

Dark diversity of Odonata in Amazonian streams

The biological diversity of a region may not be fully sampled due to the low abundance or rarity of species, or the absence of species determined by their niche specificity. Investigating these species is essential for understanding the unrealized ecological potential in different habitats, identifying gaps in local and regional communities, and gaining a better understanding of the impacts of environmental changes. Therefore, to expand knowledge about the diversity of Odonata in Eastern Amazonia considering the absent species, we tested the hypotheses that: 1) Environmental variables will influence dark diversity, with greater explanation by canopy cover where sites with lower canopy cover will have higher dark diversity values, and; 2) Functional traits associated with better species dispersal will be correlated with low dark diversity of Odonata, such as larger and wider wings for example. For this, adult Odonata specimens were sampled, while structural habitat characteristics and physical and chemical water variables were measured in 128 first- to third-order streams in the Eastern Amazon. Morphological and behavioral data were recorded for each specimen. Generalized linear models were applied to predict the effects of habitat structural characteristics and physical and chemical water variables on the dark diversity of Odonata. Additionally, we assessed which functional traits contribute most to the variation of dark diversity within these communities. Habitat structural features and physical and chemical water variables had no effect on dark diversity. Morphological traits, such as body conformation, with species having narrower wings, longer hind wings, narrower thoraxes, and shorter abdomens, comprised most of the dark diversity. The dispersal limitations of some Odonata species strongly suggest the role of space and time in nature planning and management.

Ecological forensic testing: Using multiple primers for eDNA detection of marine vertebrates in an estuarine lagoon subject to anthropogenic influences

Many critical aquatic habitats are in close proximity to human activity (i.e., adjacent to residences, docks, marinas, etc.), and it is vital to monitor biodiversity in these and similar areas that are subject to ongoing urbanization, pollution, and other environmental disruptions. Environmental DNA (eDNA) metabarcoding is an accessible, non-invasive genetic technique used to detect and monitor species diversity and is a particularly useful approach in areas where traditional biodiversity monitoring methods (e.g., visual surveys or video surveillance) are challenging to conduct. In this study, we implemented an eDNA approach that used a combination of three distinct PCR primer sets to detect marine vertebrates within a canal system of Biscayne Bay, Florida, an ecosystem representative of challenging sampling conditions and a myriad of impacts from urbanization. We detected fish species from aquarium, commercial, and recreational fisheries, as well as invasive, cryptobenthic, and endangered vertebrate species, including charismatic marine mammals such as the protected West Indian manatee, Trichechus manatus. Our results support the potential for eDNA analyses to supplement traditional biodiversity monitoring methods and ultimately serve as an important tool for ecosystem management. This approach minimizes stress or disturbance to organisms and removes the intrinsic risk and logical limitations of SCUBA diving, snorkeling, or deploying sensitive equipment in areas that are subject to high vessel traffic and/or low visibility. Overall, this work sets the framework to understand how biodiversity may change over different spatial and temporal scales in an aquatic ecosystem heavily influenced by urbanization and validates the use of eDNA as a complementary approach to traditional ecological monitoring methods.

Parasite traits, host traits, and environment as determinants of dark diversity affinity in flea and gamasid mite assemblages from the Palearctic

A species set in a site comprises species that are present (realized diversity) and species that could inhabit this site but are absent (dark diversity; DD). DD can be both species-driven (a species' traits preclude its presence, independently of site features) and site-driven (site features preclude the species' presence, independently of its traits). DD affinity (DDA) is a measure of species' tendencies to be absent from sites that they could inhabit or of sites' tendencies to lack species that could be present. Decomposition of DDA into DDA for species (ddasp) and for sites (ddasite) allows (a) disentangling these two mechanisms and (b) detecting species traits and site features contributing to their DDA. The species-site unified model is a Bayesian statistical model aimed at simultaneously estimating ddasp and ddasite. We applied it to flea and mite assemblages (a) within a host species across regions (component metacommunities; CtM; ddasite = ddaregion) and (b) within a region across host species (compound metacommunities; CdM, ddasite = ddahost). In CtMs, ddasp and ddaregion equally contributed to DD, whereas the relative contributions of ddasp and ddahost to DD in CdMs varied from the former being higher than the latter and vice versa. In CtM and CdM, ddasp increased in low-abundance ectoparasites exploiting a restricted number of hosts. In CtMs, ddaregion was associated with the regional environment, but we failed to find host traits affecting ddahost in CdMs. We conclude that ectoparasite species and either regions in CtMs or host species in CdMs independently contribute to DD.

From sight to sequence: Underwater visual census vs environmental DNA metabarcoding for the monitoring of taxonomic and functional fish diversity

Fish monitoring is essential for assessing the effects of natural and anthropic stressors on marine ecosystems. In this context, environmental DNA (eDNA) metabarcoding appears to be a promising tool, due to its efficiency in species detection. However, before this method can be fully implemented in monitoring programs, more studies are needed to evaluate its ability to assess the composition of fish assemblages compared with traditional survey methods that have been used for decades. Here, we used both eDNA metabarcoding and Underwater Visual Census (UVC) to assess the taxonomic and functional diversity (presence-absence data) of Mediterranean fish communities. We collected eDNA samples and performed UVC strip transects inside and outside four Marine Protected Areas in the Mediterranean Sea. Samples for eDNA analysis were collected by filtering seawater simultaneously at the surface and the bottom, and DNA was amplified using a combination of three sets of primers. We found that eDNA alone made an outstanding characterisation of fish composition with the detection of 95 % of the 60 taxa identified in this study, whereas UVC recovered only 58 % of them. Functional diversity was better evaluated with eDNA than with UVC, with the detection of a greater breadth of functional traits. eDNA was even better at characterising functional than taxonomic diversity, providing reliable information on ecosystem functioning with little sampling effort. Together these results suggest that eDNA metabarcoding offers great potential for surveying complex marine ecosystems. Combining eDNA metabarcoding and UVC in integrated monitoring programs would therefore improve monitoring strategies and enhance our understanding of fish communities, a key step promoting their conservation.

Enhanced eDNA monitoring for detection of viable harmful algal bloom species using propidium monoazide

This study investigated the use of propidium monoazide (PMA) to improve the accuracy of environmental DNA (eDNA) monitoring by selectively detecting intracellular DNA (iDNA) from living cells, while excluding extracellular DNA (exDNA) from dead organisms. eDNA samples were collected from various depths off the coast of Tongyeong, South Korea, and analyzed alongside environmental factors, such as temperature, dissolved oxygen, turbidity, and nutrient levels. The results showed that PMA-treated iDNA provided a more accurate estimate of viable harmful algal bloom species (HABs) than total eDNA and DNase-treated iDNA. Strong correlations were found between iDNA (PMA) and environmental factors, particularly nutrient levels and turbidity, suggesting its effectiveness in biological environments. The iDNA (PMA) concentrations were higher in the surface and bottom layers, indicating that these layers were more indicative of living organisms in marine environments. The application of PMA in eDNA monitoring reduces false positives and enhances the detection accuracy of viable HAB species, representing a promising tool for real-time monitoring and management of marine ecosystems.

Enhancing African coelacanth monitoring using environmental DNA

Coelacanths are rare, elusive, ancient lobe-finned fish species, residing in poorly accessible tropical marine caves and requiring close monitoring and protection. Environmental DNA (eDNA) approaches are being increasingly applied in the detection of rare and threatened species. Here we devise an eDNA approach to detect the presence of African coelacanths (Latimeria chalumnae) off the eastern coast of South Africa. Novel coelacanth-specific primers were designed to avoid cross-amplification with other fish lineages and validated for specificity. These primers were tested on field samples in conjunction with remotely operated vehicle (ROV) visual surveys. Samples were collected from a known coelacanth habitat and two adjacent slope habitats a few kilometres apart. Coelacanth DNA was detected from three of 15 samples collected. Two of these positive eDNA detections occurred in the presence of coelacanths, as evidenced by ROV footage, while the third positive detection was at a station where coelacanths had not been previously observed. eDNA detections are discussed in relation to the species' metabolic rate, movement patterns and population size, as well as the local oceanographic features. We demonstrate that eDNA can provide a non-invasive method to extend the knowledge of coelacanth distribution ranges and boost research efforts around these iconic fishes.

Who bit the boat? New DNA collection and genomic methods enable species identification in suspected shark-related incidents

Species identification following shark-related incidents is critical for effective incident management and for collecting data to inform shark-bite mitigation strategies. Witness statements are not always reliable, and species identification is often ambiguous or missing. Alternative methods for species identification include morphological assessments of bite marks, analysis of collected teeth at the scene of the incident, and genetic approaches. However, access to appropriate collection media and robust genetic assays have limited the use of genetic technologies. Here, we present a case study that facilitated a unique opportunity to compare the effectiveness of medical gauze readily available in first-aid kits, and forensic-grade swabs in collecting genetic material for shark-species identification. Sterile medical gauze and forensic-grade swabs were used to collect transfer DNA from the bite margins on a bitten surf ski which were compared to a piece of shark tissue embedded along the bite margin. Witness accounts and the characteristics of the bite mark impressions inferred the involvement of a Carcharodon carcharias (white shark). The morphology of a tooth found on the boat that picked up the surf ski, however, suggested it belonged to an Orectolobus spp. (wobbegong). Genetic analysis of DNA transferred from the shark to the surf ski included the application of a broad-target nested PCR assay followed by Sanger sequencing, with white shark contribution to the 'total sample DNA' determined with a species-specific qPCR assay. The results of the genetic analyses were congruent between sampling methods with respect to species identification and the level of activity inferred by the donor-specific DNA contribution. These data also supported the inferences drawn from the bite mark morphology. DNA from the recovered tooth was PCR amplified with a wobbegong-specific primer pair designed for this study to corroborate the tooth's morphological identification. Following the confirmation of gauze used for sampling in the case study event, two additional isolated incidents occurred and were sampled in situ using gauze, as typically found in a first-aid kit, by external personnel. DNA extracted from these gauze samples resulted in the identification of a white shark as the donor of the DNA collected from the bite marks in both instances. This study, involving three incidents separated by time and location, represents the seminal application of gauze as a sampling media after critical human-shark interactions and strongly supports the practical implementation of these methods in the field.

Is it worthy to use environmental DNA instead of scientific trawling or video survey to monitor taxa in soft-bottom habitats?

Non-extractive techniques such as video analysis are increasingly used by scientists to study marine communities instead of extractive methods such as trawling. Currently, environmental DNA (eDNA) analysis is seen as a revolutionary tool to study taxonomic diversity. We aimed to determine which method is the most appropriate to describe fish and commercial invertebrate diversity comparing bottom trawl hauls, video transects and seawater eDNA. Our results reveal that video detected the lowest number of taxa and trawling the highest. eDNA analysis is powerful to describe marine bony fish communities, but some taxa of importance for the ecosystem such as elasmobranchs, crustaceans or molluscs are poorly detected. This may be due to several factors such as marker specificity, incomplete reference gene databases or low DNA release in the environment. For now, the various methods provide different information and none is exhaustive enough to be used alone for biodiversity characterisation.

Analyzing the Interaction between Tetrahymena pyriformis and Bacteria under Different Physicochemical Conditions When Infecting Guppy Using the eDNA Method

In the aquaculture system of ornamental fish, the interaction between bacterial microbiota and ciliate protozoa can prevent or promote disease outbreaks, and different physicochemical conditions will affect the relationships between them. We investigated the interaction between bacterial microbiota and the parasite Tetrahymena pyriformis when infecting Poecilia reticulata (guppy) under different physicochemical conditions. The abundance of T. pyriformis in water, the relative abundance of bacterial species, and histopathological observation were studied or monitored using environmental DNA (eDNA) extraction technology, the qPCR method, and 16s rRNA sequencing, respectively. The morphological identification and phylogenetic analysis of T. pyriformis were carried out. The infected guppy tissue was also stained by the hematoxylin and eosin methods. The results showed: (1) the bacterial communities of water samples were mainly composed of species assigned to Proteobacteria and Bacteroidetes, and Tabrizicola and Puniceicoccaceae were positively correlated with fish mortality, T. pyriformis abundance, and temperature. (2) Arcicella and Methyloversatilis universalis with different correlations between ciliates appeared in different treatment groups, the result of which proved that environmental factors affected the interaction between bacteria and T. pyriformis. (3) Lower temperatures and a higher pH were more beneficial for preventing disease outbreaks.

First record of a neonate bluntnose sixgill shark (Hexanchus griseus) from Baja California Sur, Mexico

The bluntnose sixgill shark (Hexanchus griseus) is a wide-ranged deep-water shark species found off continental and insular shelves. Despite its global distribution, little is known about the reproductive ecology of the species, particularly with regard to the location and timing of important phenological events such as mating and pupping. In this study, we report the landing of a neonate H. griseus individual from an artisanal fishing camp in Baja California Sur, Mexico. This represents only the ninth confirmed record of the species from the Mexican Pacific and the first to report a neonate specimen in Mexican waters. We discuss this specimen in the context of the environmental conditions in which it was found, ultimately suggesting that these shallow coastal waters may be an important pupping ground for H. griseus in the region. Furthermore, the specimen was found during the winter months (whereas all previous reports have suggested H. griseus pups during the summer), implying regional variation in reproductive periodicity, or the presence of multiple reproductive events per year. This study provides novel insight into the reproductive biology of H. griseus and the ecological characteristics of the species in the Northern Mexican Pacific.

Studying Chondrichthyans Using Baited Remote Underwater Video Systems: A Review

Cartilaginous fish face significant threats due to overfishing and slow reproductive rates, leading to rapid declines in their populations globally. Traditional capture-based surveys, while valuable for gathering ecological information, pose risks to the health and survival of these species. Baited Remote Underwater Video Systems (BRUVS) offer a non-invasive alternative, allowing for standardized surveys across various habitats with minimal disturbance to marine life. This study presents a comprehensive review of BRUVS applications in studying cartilaginous fish, examining 81 peer-reviewed papers spanning from 1990 to 2023. The analysis reveals a significant increase in BRUVS usage over the past three decades, particularly in Australia, South Africa, and Central America. The most common BRUVS configurations include benthic setups, mono-camera systems, and the use of fish from the Clupeidae and Scombridae families as bait. BRUVS have been instrumental in studying 195 chondrichthyan species, providing insights into up to thirteen different aspects of the life histories. Moreover, BRUVS facilitate the monitoring of endangered and data-deficient species, contributing crucial data for conservation efforts. Overall, this study underscores the value of BRUVS as a powerful tool for studying and conserving cartilaginous fish populations worldwide.

Environmental DNA highlights the influence of salinity and agricultural run-off on coastal fish assemblages in the Great Barrier Reef region

Agricultural run-off in Australia's Mackay-Whitsunday region is a major source of nutrient and pesticide pollution to coastal and inshore ecosystems of the Great Barrier Reef. While the effects of run-off are well documented for the region's coral and seagrass habitats, the ecological impacts on estuaries, the direct recipients of run-off, are less known. This is particularly true for fish communities, which are shaped by the physico-chemical properties of coastal waterways that vary greatly in tropical regions. To address this knowledge gap, we used environmental DNA (eDNA) metabarcoding to examine fish assemblages at four locations (three estuaries and a harbour) subjected to varying levels of agricultural run-off during a wet and dry season. Pesticide and nutrient concentrations were markedly elevated during the sampled wet season with the influx of freshwater and agricultural run-off. Fish taxa richness significantly decreased in all three estuaries (F = 164.73, P = <0.001), along with pronounced changes in community composition (F = 46.68, P = 0.001) associated with environmental variables (largely salinity: 27.48% contribution to total variance). In contrast, the nearby Mackay Harbour exhibited a far more stable community structure, with no marked changes in fish assemblages observed between the sampled seasons. Among the four sampled locations, variation in fish community composition was more pronounced within the wet season (F = 2.5, P = 0.001). Notably, variation in the wet season was significantly correlated with agricultural contaminants (phosphorus: 6.25%, pesticides: 5.22%) alongside environmental variables (salinity: 5.61%, DOC: 5.57%). Historically contaminated and relatively unimpacted estuaries each demonstrated distinct fish communities, reflecting their associated catchment use. Our findings emphasise that while seasonal effects play a key role in shaping the community structure of fish in this region, agricultural contaminants are also important contributors in estuarine systems.

eDNA metabarcoding reveals biodiversity and depth stratification patterns of dinoflagellate assemblages within the epipelagic zone of the western Coral Sea

BACKGROUND

Dinoflagellates play critical roles in the functioning of marine ecosystems but also may pose a hazard to human and ecosystem health by causing harmful algal blooms (HABs). The Coral Sea is a biodiversity hotspot, but its dinoflagellate assemblages in pelagic waters have not been studied by modern sequencing methods. We used metabarcoding of the 18 S rRNA V4 amplicon to assess the diversity and structure of dinoflagellate assemblages throughout the water column to a depth of 150 m at three stations in the Western Coral Sea. Additionally, at one station we compared metabarcoding with morphological methods to optimise identification and detection of dinoflagellates.

RESULTS

Stratification of dinoflagellate assemblages was evident in depth-specific relative abundances of taxonomic groups; the greatest difference was between the 5-30 m assemblages and the 130-150 m assemblages. The relative abundance of Dinophyceae (photosynthetic and heterotrophic) decreased with increasing depth, whereas that of Syndiniales (parasitic) increased with increasing depth. The composition of major taxonomic groups was similar among stations. Taxonomic richness and diversity of amplicon sequence variants (ASVs) were similar among depths and stations; however, the abundance of dominant taxa was highest within 0-30 m, and the abundance of rare taxa was highest within 130-150 m, indicating adaptations to specific depth strata. The number of unclassified ASVs at the family and species levels was very high, particularly for Syndinian representatives.

CONCLUSIONS

Dinoflagellate assemblages in open water of the Coral Sea are highly diverse and taxonomically stratified by depth; patterns of relative abundance along the depth gradient reflect environmental factors and ecological processes. Metabarcoding detects more species richness than does traditional microscopical methods of sample analysis, yet the methods are complementary, with morphological analysis revealing additional richness. The large number of unclassified dinoflagellate-ASVs indicates a need for improved taxonomic reference databases and suggests presence of dinoflagellate-crypto and-morphospecies.

Divergent responses of pelagic and benthic fish body-size structure to remoteness and protection from humans

Animal body-size variation influences multiple processes in marine ecosystems, but habitat heterogeneity has prevented a comprehensive assessment of size across pelagic (midwater) and benthic (seabed) systems along anthropic gradients. In this work, we derive fish size indicators from 17,411 stereo baited-video deployments to test for differences between pelagic and benthic responses to remoteness from human pressures and effectiveness of marine protected areas (MPAs). From records of 823,849 individual fish, we report divergent responses between systems, with pelagic size structure more profoundly eroded near human markets than benthic size structure, signifying greater vulnerability of pelagic systems to human pressure. Effective protection of benthic size structure can be achieved through MPAs placed near markets, thereby contributing to benthic habitat restoration and the recovery of associated fishes. By contrast, recovery of the world's largest and most endangered fishes in pelagic systems requires the creation of highly protected areas in remote locations, including on the High Seas, where protection efforts lag.

eDNA based bycatch assessment in pelagic fish catches

Pelagic fish like herring, sardines, and mackerel constitute an essential and nutritious human food source globally. Their sustainable harvest is promoted by the application of precise, accurate, and cost-effective methods for estimating bycatch. Here, we experimentally test the new concept of using eDNA for quantitative bycatch assessment on the illustrative example of the Baltic Sea sprat fisheries with herring bycatch. We investigate the full pipeline from sampling of production water on vessels and in processing factories to the estimation of species weight fractions. Using a series of controlled mixture experiments, we demonstrate that the eDNA signal from production water shows a strong, seasonally consistent linear relationship with herring weight fractions, however, the relationship is influenced by the molecular method used (qPCR or metabarcoding). In four large sprat landings analyzed, despite examples of remarkable consistency between eDNA and visual reporting, estimates of herring bycatch biomass varied between the methods applied, with the eDNA-based estimates having the highest precision for all landings analyzed. The eDNA-based bycatch assessment method has the potential to improve the quality and cost effectiveness of bycatch assessment in large pelagic fisheries catches and in the long run lead to more sustainable management of pelagic fish as a precious marine resource.

Comparing Seamounts and Coral Reefs with eDNA and BRUVS Reveals Oases and Refuges on Shallow Seamounts

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.

First pelagic fish biodiversity assessment of Cosmonaut Sea based on environmental DNA

The Cosmonaut Sea is a typical marginal sea in East Antarctica that has not yet been greatly impacted by climate change. As one of the least explored areas in the Southern Ocean, our knowledge regarding its fish taxonomy and diversity has been sparse. eDNA metabarcoding, as an emerging and promising tool for marine biodiversity research and monitoring, has been widely used across taxa and habitats. During the 38th Chinese Antarctic Research Expedition (CHINARE-38), we collected seawater and surface sediment samples from 38 stations in the Cosmonaut Sea and performed the first, to our knowledge, eDNA analysis of fish biodiversity in the Southern Ocean based on the molecular markers of 12S rRNA and 16S rRNA. There were 48 fish species detected by the two markers in total, with 30 and 34 species detected by the 12S rRNA and 16S rRNA marker, respectively. This was more than the trawling results (19 species) and historical survey records (16 species, "BROKE-West" cruise). With some nonsignificant differences between the Gunnerus Ridge and the Oceanic Area of Enderby Land, the Cosmonaut Sea had a richer fish biodiversity in this research compared with previous studies, and its overall composition and distribution patterns were consistent with what we know in East Antarctica. We also found that the eDNA composition of fish in the Cosmonaut Sea might be related to some environmental factors. Our study demonstrated that the use of the eDNA technique for Antarctic fish biodiversity research is likely to yield more information with less sampling effort than traditional methods. In the context of climate change, the eDNA approach will provide a novel and powerful tool that is complementary to traditional methods for polar ecology research.

Applications of Environmental DNA (eDNA) in Monitoring the Endangered Status and Evaluating the Stock Enhancement Effect of Tropical Sea Cucumber Holothuria Scabra

The tropical sea cucumber Holothuria scabra is naturally found in the Indo-West Pacific. However, due to their commercial value, natural H. scabra populations have declined significantly in recent years, resulting in its status as an endangered species. Surveys of H. scabra resource pose a challenge due to its specific characteristics, such as sand-burrowing behavior. To overcome this problem, our study established a convenient and feasible method for assessing H. scabra resources using environmental DNA (eDNA) monitoring technology. First, H. scabra-specific TaqMan primers and probe were designed based on its cox1 gene, followed by the development of an eDNA monitoring method for H. scabra in two separate sea areas (Xuwen and Daya Bay). The method was subsequently employed to investigate the distribution of H. scabra and assess the effects of aquaculture stock enhancement through juvenile releasing in the Weizhou Island sea area. The H. scabra eDNA monitoring approach was found to be more appropriate and credible than traditional methods, and a positive impact of stocking on H. scabra populations was observed. In summary, this is the first report to quantify eDNA concentration in a Holothuroidea species, and it provides a convenient and accurate method for surveying H. scabra resources. This study introduces novel concepts for eDNA-based detection of endangered marine benthic animals and monitoring their population distribution and abundance.

Gut content metabarcoding of specialized feeders is not a replacement for environmental DNA assays of seawater in reef environments

In tropical marine ecosystems, the coral-based diet of benthic-feeding reef fishes provides a window into the composition and health of coral reefs. In this study, for the first time, we compare multi-assay metabarcoding sequences of environmental DNA (eDNA) isolated from seawater and partially digested gut items from an obligate corallivore butterflyfish (Chaetodon lunulatus) resident to coral reef sites in the South China Sea. We specifically tested the proportional and statistical overlap of the different approaches (seawater vs gut content metabarcoding) in characterizing eukaryotic community composition on coral reefs. Based on 18S and ITS2 sequence data, which differed in their taxonomic sensitivity, we found that gut content detections were only partially representative of the eukaryotic communities detected in the seawater based on low levels of taxonomic overlap (3 to 21%) and significant differences between the sampling approaches. Overall, our results indicate that dietary metabarcoding of specialized feeders can be complimentary to, but is no replacement for, more comprehensive environmental DNA assays of reef environments that might include the processing of different substrates (seawater, sediment, plankton) or traditional observational surveys. These molecular assays, in tandem, might be best suited to highly productive but cryptic oceanic environments (kelp forests, seagrass meadows) that contain an abundance of organisms that are often small, epiphytic, symbiotic, or cryptic.

Biodiversity exploration of Formosa Ridge cold seep in the South China Sea using an eDNA metabarcoding approach

The Formosa Ridge, also named Site F, is an active cold seep marine ecosystem site that has been studied since it was discovered on the continental slope of the northeast South China Sea (SCS). However, few studies have focused on the eukaryotic diversity at Site F. Environmental DNA (eDNA) technology is a non-invasive method applied in biodiversity surveys with a high species detection probability. In the present study, we identified multi-trophic biodiversity using eDNA metabarcoding combined with multiple ribosomal RNA gene (rDNA) markers. We detected 142 phytoplankton, 90 invertebrates, and 64 fish species by amplifying the 18S rRNA gene V4 region, the 18S rRNA gene V9 region, and the 12S rRNA gene. The results elucidated dissimilar trends of different assemblages with depth. The diversity of phytoplankton and invertebrate assemblages markedly decreased with depth, whereas little change was observed within the fish assemblage. We comprehensively assessed the relationship between the three assemblages and environmental factors (temperature, salinity, depth, dissolved oxygen, and chlorophyll a). These factors strongly impacted on phytoplankton and invertebrates, but only slightly on fish. We inferred the finding might be due to fish having a strong migration capacity and wide distribution. This study indicates that eDNA metabarcoding with multiple markers is a powerful tool for marine biodiversity research that is able to provide technical support and knowledge for resource management and biodiversity protection efforts.

A comparison of biomonitoring methodologies for surf zone fish communities

Surf zones are highly dynamic marine ecosystems that are subject to increasing anthropogenic and climatic pressures, posing multiple challenges for biomonitoring. Traditional methods such as seines and hook and line surveys are often labor intensive, taxonomically biased, and can be physically hazardous. Emerging techniques, such as baited remote underwater video (BRUV) and environmental DNA (eDNA) are promising nondestructive tools for assessing marine biodiversity in surf zones of sandy beaches. Here we compare the relative performance of beach seines, BRUV, and eDNA in characterizing community composition of bony (teleost) and cartilaginous (elasmobranch) fishes of surf zones at 18 open coast sandy beaches in southern California. Seine and BRUV surveys captured overlapping, but distinct fish communities with 50% (18/36) of detected species shared. BRUV surveys more frequently detected larger species (e.g. sharks and rays) while seines more frequently detected one of the most abundant species, barred surfperch (Amphistichus argenteus). In contrast, eDNA metabarcoding captured 88.9% (32/36) of all fishes observed in seine and BRUV surveys plus 57 additional species, including 15 that frequent surf zone habitats. On average, eDNA detected over 5 times more species than BRUVs and 8 times more species than seine surveys at a given site. eDNA approaches also showed significantly higher sensitivity than seine and BRUV methods and more consistently detected 31 of the 32 (96.9%) jointly observed species across beaches. The four species detected by BRUV/seines, but not eDNA were only resolved at higher taxonomic ranks (e.g. Embiotocidae surfperches and Sygnathidae pipefishes). In frequent co-detection of species between methods limited comparisons of richness and abundance estimates, highlighting the challenge of comparing biomonitoring approaches. Despite potential for improvement, results overall demonstrate that eDNA can provide a cost-effective tool for long-term surf zone monitoring that complements data from seine and BRUV surveys, allowing more comprehensive surveys of vertebrate diversity in surf zone habitats.

Inadvertent human genomic bycatch and intentional capture raise beneficial applications and ethical concerns with environmental DNA

The field of environmental DNA (eDNA) is advancing rapidly, yet human eDNA applications remain underutilized and underconsidered. Broader adoption of eDNA analysis will produce many well-recognized benefits for pathogen surveillance, biodiversity monitoring, endangered and invasive species detection, and population genetics. Here we show that deep-sequencing-based eDNA approaches capture genomic information from humans (Homo sapiens) just as readily as that from the intended target species. We term this phenomenon human genetic bycatch (HGB). Additionally, high-quality human eDNA could be intentionally recovered from environmental substrates (water, sand and air), holding promise for beneficial medical, forensic and environmental applications. However, this also raises ethical dilemmas, from consent, privacy and surveillance to data ownership, requiring further consideration and potentially novel regulation. We present evidence that human eDNA is readily detectable from 'wildlife' environmental samples as human genetic bycatch, demonstrate that identifiable human DNA can be intentionally recovered from human-focused environmental sampling and discuss the translational and ethical implications of such findings.

Ultrasensitive and on-site eDNA detection for the monitoring of crown-of-thorns starfish densities at the pre-outbreak stage using an electrochemical biosensor

The coral reef crisis has significantly intensified over the last decades, mainly due to severe outbreaks of crown-of-thorns starfish (COTS). Current ecological monitoring has failed to detect COTS densities at the pre-outbreak stage, thus preventing early intervention. In this work, we developed an effective electrochemical biosensor modified by a MoO₂/C nanomaterial, as well as a specific DNA probe that could detect trace COTS environmental DNA (eDNA) at a lower detection limit (LOD = 0.147 ng/μL) with excellent specificity. The reliability and accuracy of the biosensor were validated against the standard methods by an ultramicro spectrophotometer and droplet digital PCR (p > 0.05). The biosensor was then utilized for the on-site analysis of seawater samples from SYM-LD and SY sites in the South China Sea. For the SYM-LD site suffering an outbreak, the COTS eDNA concentrations were 0.33 ng/μL (1 m, depth) and 0.26 ng/μL (10 m, depth), respectively. According to the ecological survey, the COTS density was 500 ind/hm² at the SYM-LD site, verifying the accuracy of our measurements. At the SY site, COTS eDNA was also detected at 0.19 ng/μL, but COTS was not found by the traditional survey. Hence, larvae were possibly present in this region. Therefore, this electrochemical biosensor could be used to monitor COTS populations at the pre-outbreak stages, and potentially serve as a revolutionary early warning method. We will continue to improve this method for picomolar or even femtomolar detection of COTS eDNA.

Assessing without harvesting: Pros and cons of environmental DNA sampling and image analysis for marine biodiversity evaluation

Marine stock assessments or biodiversity monitoring studies, which historically relied on extractive techniques (e.g., trawl or grab surveys), are being progressively replaced by non-extractive approaches. For instance, species abundance indices can be calculated using data obtained from high-definition underwater cameras that enable to identify taxa at low taxonomical level. In biodiversity studies, environmental DNA (eDNA) has proven to be a useful tool for characterising fish species richness. However, several marine phyla remain poorly represented in reference gene databases or release limited amounts of DNA, restricting their detection. The absence of amplification of some invertebrate taxa might also reflect primer bias. We here explore and compare the performance of eDNA and image data in describing the marine communities of several sites in the Bay of Biscay. This was achieved by deploying a remotely operated vehicle to both record images and collect seawater samples. A total of 88 taxa were identified from the eDNA samples and 121 taxa from the images. For both methods, the best characterised phylum was Chordata, with 29 and 27 Actinopterygii species detected using image versus eDNA, respectively. Neither Bryozoa nor Cnidaria was detected in the eDNA samples while the phyla were easily identifiable by imagery. Similarly, Asteroidea (Echinodermata) and Cephalopoda (Mollusca) were scarcely detected in the eDNA samples but present on the images, while Annelida were mostly identified by eDNA (18 taxa vs 7 taxa from imagery). The complementary community descriptions we highlight from these two methods therefore advocate for using both eDNA and imagery in tandem in order to capture the macroscopic biodiversity of bentho-demersal marine communities.

The challenge of implementing environmental DNA metabarcoding to detect elasmobranchs in a resource-limited marine protected area

Elasmobranchs are threatened and eDNA metabarcoding is a powerful tool that can help efforts to better understand and conserve them. Nevertheless, the inter-calibration between optimal methodological practices and its implementation in resource-limited situations is still an issue. Based on promising results from recent studies, the authors applied a cost-effective protocol with parameters that could be easily replicated by any conservationist. Nonetheless, the results with fewer elasmobranchs detected than expected reveal that endorsed primers and sampling strategies still require further optimization, especially for applications in resource-limited conservation programmes.

The alteration of intestinal mucosal α-synuclein expression and mucosal microbiota in Parkinson's disease

Parkinson's disease (PD) is the second most common neurodegenerative disease but still lacks a preclinical strategy to identify it. The diagnostic value of intestinal mucosal α-synuclein (αSyn) in PD has not drawn a uniform conclusion. The relationship between the alteration of intestinal mucosal αSyn expression and mucosal microbiota is unclear. Nineteen PD patients and twenty-two healthy controls were enrolled in our study from whom were collected, using gastrointestinal endoscopes, duodenal and sigmoid mucosal samples for biopsy. Multiplex immunohistochemistry was performed to detect total, phosphorylate, and oligomer α-synuclein. Next-generation 16S rRNA amplicon sequencing was applied for taxonomic analysis. The results implied that oligomer α-synuclein (OSyn) in sigmoid mucosa of PD patients was transferred from the intestinal epithelial cell membrane to the cytoplasm, acinar lumen, and stroma. Its distribution feature was significantly different between the two groups, especially the ratio of OSyn/αSyn. The microbiota composition in mucosa also differed. The relative abundances of Kiloniellales, Flavobacteriaceae, and CAG56 were lower, while those of Proteobacteria, Gammaproteobacteria, Burkholderiales, Burkholdriaceae, Oxalobacteraceae, Ralstonia, Massilla, and Lactoccus were higher in duodenal mucosa of PD patients. The relative abundances of Thermoactinomycetales and Thermoactinomycetaceae were lower, while those of Prevotellaceae and Bifidobacterium longum were higher in patients' sigmoid mucosa. Further, the OSyn/αSyn level was positively correlated with the relative abundances of Proteobacteria, Gammaproteobacteria, Burkholderiales, Pseudomonadales, Burkholderiaceae, and Ralstonia in the duodenal mucosa, while it was negatively correlated with the Chao1 index and observed operational taxonomic units of microbiota in sigmoid mucosa. The intestinal mucosal microbiota composition of PD patients altered with the relative abundances of proinflammatory bacteria in the duodenal mucosa increased. The ratio of the OSyn/αSyn level in the sigmoid mucosa indicated a potential diagnostic value for PD, which also correlated with mucosal microbiota diversity and composition. KEY POINTS: • The distribution of OSyn in sigmoid mucosa differed between PD patients and healthy controls. • Significant alterations in the microbiome were found in PD patients' gut mucosa. • OSyn/αSyn level in sigmoid mucosa indicated a potential diagnostic value for PD.

Capturing marine microbiomes and environmental DNA: A field sampling guide

The expanding interest in marine microbiome and eDNA sequence data has led to a demand for sample collection and preservation standard practices to enable comparative assessments of results across studies and facilitate meta-analyses. We support this effort by providing guidelines based on a review of published methods and field sampling experiences. The major components considered here are environmental and resource considerations, sample processing strategies, sample storage options, and eDNA extraction protocols. It is impossible to provide universal recommendations considering the wide range of eDNA applications; rather, we provide information to design fit-for-purpose protocols. To manage scope, the focus here is on sampling collection and preservation of prokaryotic and microeukaryotic eDNA. Even with a focused view, the practical utility of any approach depends on multiple factors, including habitat type, available resources, and experimental goals. We broadly recommend enacting rigorous decontamination protocols, pilot studies to guide the filtration volume needed to characterize the target(s) of interest and minimize PCR inhibitor collection, and prioritizing sample freezing over (only) the addition of preservation buffer. An annotated list of studies that test these parameters is included for more detailed investigation on specific steps. To illustrate an approach that demonstrates fit-for-purpose methodologies, we provide a protocol for eDNA sampling aboard an oceanographic vessel. These guidelines can aid the decision-making process for scientists interested in sampling and sequencing marine microbiomes and/or eDNA.

Assessing the utility of marine filter feeders for environmental DNA (eDNA) biodiversity monitoring

Aquatic environmental DNA (eDNA) surveys are transforming how marine ecosystems are monitored. The time-consuming preprocessing step of active filtration, however, remains a bottleneck. Hence, new approaches that eliminate the need for active filtration are required. Filter-feeding invertebrates have been proven to collect eDNA, but side-by-side comparative studies to investigate the similarity between aquatic and filter-feeder eDNA signals are essential. Here, we investigated the differences among four eDNA sources (water; bivalve gill-tissue; sponges; and ethanol in which filter-feeding organisms were stored) along a vertically stratified transect in Doubtful Sound, New Zealand using three metabarcoding primer sets targeting fish and vertebrates. Combined, eDNA sources detected 59 vertebrates, while concurrent diver surveys observed eight fish species. There were no significant differences in alpha and beta diversity between water and sponge eDNA and both sources were highly correlated. Vertebrate eDNA was successfully extracted from the ethanol in which sponges were stored, although a reduced number of species were detected. Bivalve gill-tissue dissections, on the other hand, failed to reliably detect eDNA. Overall, our results show that vertebrate eDNA signals obtained from water samples and marine sponges are highly concordant. The strong similarity in eDNA signals demonstrates the potential of marine sponges as an additional tool for eDNA-based marine biodiversity surveys, by enabling the incorporation of larger sample numbers in eDNA surveys, reducing plastic waste, simplifying sample collection, and as a cost-efficient alternative. However, we note the importance to not detrimentally impact marine communities by, for example, nonlethal subsampling, specimen cloning, or using bycatch specimens.

Citizen science provides valuable data to evaluate elasmobranch diversity and trends throughout the French Polynesia's shark sanctuary

Observers of the Polynesian Shark Observatory (ORP), a citizen science network organized mainly through the Polynesian dive centers, collected an unprecedented amount of data from more than 13,916 dives spanning 43% of the islands of French Polynesia between July 8, 2011, and April 11, 2018. The objective for this type of data collection, which is not accessible within the standard research context, was to provide a unique dataset, and the opportunity to explore the specific diversity, distribution, seasonality and abundance of many elasmobranch species spread out throughout the territory of French Polynesia. Since the data are based on random citizen observations, the spatial distribution was biased toward the most frequented sites and islands where scuba diving is most developed. Overall, the increase in observed abundance of rays and sharks observed in French Polynesia, and the three most sampled islands as well as the high specific diversity recorded for the region, provide first evidence on the effectiveness of the French Polynesia's Shark Sanctuary, established in 2006. These data, collected randomly by the volunteers, also provide insights into potential movement patterns and site fidelity of some of the more commonly observed species. While no final conclusions can be drawn, it is clear that the network of volunteers that regularly contributes information to the Polynesian Shark Observatory plays a very important role in the delivery of much needed data for conservation and management action, as well as providing perspectives for new directions in research on sharks and rays in French Polynesia.

Systematic review of marine environmental DNA metabarcoding studies: toward best practices for data usability and accessibility

The emerging field of environmental DNA (eDNA) research lacks universal guidelines for ensuring data produced are FAIR-findable, accessible, interoperable, and reusable-despite growing awareness of the importance of such practices. In order to better understand these data usability challenges, we systematically reviewed 60 peer reviewed articles conducting a specific subset of eDNA research: metabarcoding studies in marine environments. For each article, we characterized approximately 90 features across several categories: general article attributes and topics, methodological choices, types of metadata included, and availability and storage of sequence data. Analyzing these characteristics, we identified several barriers to data accessibility, including a lack of common context and vocabulary across the articles, missing metadata, supplementary information limitations, and a concentration of both sample collection and analysis in the United States. While some of these barriers require significant effort to address, we also found many instances where small choices made by authors and journals could have an outsized influence on the discoverability and reusability of data. Promisingly, articles also showed consistency and creativity in data storage choices as well as a strong trend toward open access publishing. Our analysis underscores the need to think critically about data accessibility and usability as marine eDNA metabarcoding studies, and eDNA projects more broadly, continue to proliferate.

The global depth range of marine fishes and their genetic coverage for environmental DNA metabarcoding

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.

Assessment of Fish Diversity in the Ma'an Archipelago Special Protected Area Using Environmental DNA

This study aimed to investigate the practical validity of the environmental DNA (eDNA) method for evaluating fish composition and diversity in different habitats. We evaluated the fish composition and diversity characteristics of seven different habitats in the Ma'an Archipelago Special Protected Area in April 2020. The results showed that a total of twenty-seven species of fishes belonging to six orders, eighteen families, and twenty-three genera of the Actinopterygii were detected in the marine waters of the Ma'an Archipelago Special Protected Area. The dominant species in each habitat were Larimichthys crocea, Paralichthys olivaceus, and Lateolabrax maculatus. The mussel culture area had the highest number of species, with 19 fish species, while the offshore bulk load shedding platform had the lowest number of species, with 12 fish species. The rest of the habitat was not significantly different. The results showed that the mussel culture area had the highest diversity index (average value of 2.352 ± 0.161), and the offshore bulk load shedding platform had the lowest diversity index (average value of 1.865 ± 0.127); the rest of the habitat diversity indices did not differ significantly. A comparison with historical surveys showed that the eDNA technique can detect species not collected by traditional methods such as gillnets and trawls. Our study demonstrates the role of eDNA technology in obtaining fish diversity in different habitats and provides a theoretical basis for the continuous monitoring and management of fish biodiversity in protected areas.

Towards the fully automated monitoring of ecological communities

High-resolution monitoring is fundamental to understand ecosystems dynamics in an era of global change and biodiversity declines. While real-time and automated monitoring of abiotic components has been possible for some time, monitoring biotic components-for example, individual behaviours and traits, and species abundance and distribution-is far more challenging. Recent technological advancements offer potential solutions to achieve this through: (i) increasingly affordable high-throughput recording hardware, which can collect rich multidimensional data, and (ii) increasingly accessible artificial intelligence approaches, which can extract ecological knowledge from large datasets. However, automating the monitoring of facets of ecological communities via such technologies has primarily been achieved at low spatiotemporal resolutions within limited steps of the monitoring workflow. Here, we review existing technologies for data recording and processing that enable automated monitoring of ecological communities. We then present novel frameworks that combine such technologies, forming fully automated pipelines to detect, track, classify and count multiple species, and record behavioural and morphological traits, at resolutions which have previously been impossible to achieve. Based on these rapidly developing technologies, we illustrate a solution to one of the greatest challenges in ecology: the ability to rapidly generate high-resolution, multidimensional and standardised data across complex ecologies.

Discovering marine biodiversity in the 21st century

We review the current knowledge of the biodiversity of the ocean as well as the levels of decline and threat for species and habitats. The lack of understanding of the distribution of life in the ocean is identified as a significant barrier to restoring its biodiversity and health. We explore why the science of taxonomy has failed to deliver knowledge of what species are present in the ocean, how they are distributed and how they are responding to global and regional to local anthropogenic pressures. This failure prevents nations from meeting their international commitments to conserve marine biodiversity with the results that investment in taxonomy has declined in many countries. We explore a range of new technologies and approaches for discovery of marine species and their detection and monitoring. These include: imaging methods, molecular approaches, active and passive acoustics, the use of interconnected databases and citizen science. Whilst no one method is suitable for discovering or detecting all groups of organisms many are complementary and have been combined to give a more complete picture of biodiversity in marine ecosystems. We conclude that integrated approaches represent the best way forwards for accelerating species discovery, description and biodiversity assessment. Examples of integrated taxonomic approaches are identified from terrestrial ecosystems. Such integrated taxonomic approaches require the adoption of cybertaxonomy approaches and will be boosted by new autonomous sampling platforms and development of machine-speed exchange of digital information between databases.

Environmental DNA persistence and fish detection in captive sponges

Large and hyperdiverse marine ecosystems pose significant challenges to biodiversity monitoring. While environmental DNA (eDNA) promises to meet many of these challenges, recent studies suggested that sponges, as "natural samplers" of eDNA, could further streamline the workflow for detecting marine vertebrates. However, beyond pilot studies demonstrating the ability of sponges to capture eDNA, little is known about the dynamics of eDNA particles in sponge tissue, and the effectiveness of the latter compared to water samples. Here, we present the results of a controlled aquarium experiment to examine the persistence and detectability of eDNA captured by three encrusting sponge species and compare the sponge's eDNA capturing ability with established water filtration techniques. Our results indicate that sponges and water samples have highly similar detectability for fish of different sizes and abundances, but different sponge species exhibit considerable variance in performance. Interestingly, one sponge appeared to mirror the eDNA degradation profile of water samples, while another sponge retained eDNA throughout the experiment. A third sponge yielded virtually no DNA sequences at all. Overall, our study suggests that some sponges will be suitable as natural samplers, while others will introduce significant problems for laboratory processing. We suggest that an initial optimization phase will be required in any future studies aiming to employ sponges for biodiversity assessment. With time, factoring in technical and natural accessibility, it is expected that specific sponge taxa may become the "chosen" natural samplers in certain habitats and regions.

Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward

Vast global declines of freshwater and marine fish diversity and population abundance pose serious threats to both ecosystem sustainability and human livelihoods. Environmental DNA (eDNA)-based biomonitoring provides robust, efficient, and cost-effective assessment of species occurrences and population trends in diverse aquatic environments. Thus, it holds great potential for improving conventional surveillance frameworks to facilitate fish conservation and fisheries management. However, the many technical considerations and rapid developments underway in the eDNA arena can overwhelm researchers and practitioners new to the field. Here, we systematically analysed 416 fish eDNA studies to summarize research trends in terms of investigated targets, research aims, and study systems, and reviewed the applications, rationales, methodological considerations, and limitations of eDNA methods with an emphasis on fish and fisheries research. We highlighted how eDNA technology may advance our knowledge of fish behaviour, species distributions, population genetics, community structures, and ecological interactions. We also synthesized the current knowledge of several important methodological concerns, including the qualitative and quantitative power eDNA has to recover fish biodiversity and abundance, and the spatial and temporal representations of eDNA with respect to its sources. To facilitate ecological applications implementing fish eDNA techniques, recent literature was summarized to generate guidelines for effective sampling in lentic, lotic, and marine habitats. Finally, we identified current gaps and limitations, and pointed out newly emerging research avenues for fish eDNA. As methodological optimization and standardization improve, eDNA technology should revolutionize fish monitoring and promote biodiversity conservation and fisheries management that transcends geographic and temporal boundaries.

Comparing eDNA metabarcoding primers for assessing fish communities in a biodiverse estuary

Metabarcoding of environmental DNA is increasingly used for biodiversity assessments in aquatic communities. The efficiency and outcome of these efforts are dependent upon either de novo primer design or selecting an appropriate primer set from the dozens that have already been published. Unfortunately, there is a lack of studies that have directly compared the efficacy of different metabarcoding primers in marine and estuarine systems. Here we evaluate five commonly used primer sets designed to amplify rRNA barcoding genes in fishes and compare their performance using water samples collected from estuarine sites in the highly biodiverse Indian River Lagoon in Florida. Three of the five primer sets amplify a portion of the mitochondrial 12S gene (MiFish_12S, 171bp; Riaz_12S, 106 bp; Valentini_12S, 63 bp), one amplifies 219 bp of the mitochondrial 16S gene (Berry_16S), and the other amplifies 271 bp of the nuclear 18S gene (MacDonald_18S). The vast majority of the metabarcoding reads (> 99%) generated using the 18S primer set assigned to non-target (non-fish) taxa and therefore this primer set was omitted from most analyses. Using a conservative 99% similarity threshold for species level assignments, we detected a comparable number of species (55 and 49, respectively) and similarly high Shannon’s diversity values for the Riaz_12S and Berry_16S primer sets. Meanwhile, just 34 and 32 species were detected using the MiFish_12S and Valentini_12S primer sets, respectively. We were able to amplify both bony and cartilaginous fishes using the four primer sets with the vast majority of reads (>99%) assigned to the former. We detected the greatest number of elasmobranchs (six species) with the Riaz_12S primer set suggesting that it may be a suitable candidate set for the detection of sharks and rays. Of the total 76 fish species that were identified across all datasets, the combined three 12S primer sets detected 85.5% (65 species) while the combination of the Riaz_12S and Berry_16S primers detected 93.4% (71 species). These results highlight the importance of employing multiple primer sets as well as using primers that target different genomic regions. Moreover, our results suggest that the widely adopted MiFish_12S primers may not be the best choice, rather we found that the Riaz_12S primer set was the most effective for eDNA-based fish surveys in our system.

Applying convolutional neural networks to speed up environmental DNA annotation in a highly diverse ecosystem

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.

A, Pouyaud L, Stuart-Smith RD, Sugeha HY, Valentini A, Vigliola L, Vimono IB, Pellissier L, Manel S. 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.

Environmental DNA provides quantitative estimates of Pacific hake abundance and distribution in the open ocean

All species inevitably leave genetic traces in their environments, and the resulting environmental DNA (eDNA) reflects the species present in a given habitat. It remains unclear whether eDNA signals can provide quantitative metrics of abundance on which human livelihoods or conservation successes depend. Here, we report the results of a large eDNA ocean survey (spanning 86 000 km² to depths of 500 m) to understand the abundance and distribution of Pacific hake (Merluccius productus), the target of the largest finfish fishery along the west coast of the USA. We sampled eDNA in parallel with a traditional acoustic-trawl survey to assess the value of eDNA surveys at a scale relevant to fisheries management. Despite local differences, the two methods yield comparable information about the broad-scale spatial distribution and abundance. Furthermore, we find depth and spatial patterns of eDNA closely correspond to acoustic-trawl estimates for hake. We demonstrate the power and efficacy of eDNA sampling for estimating abundance and distribution and move the analysis eDNA data beyond sample-to-sample comparisons to management relevant scales. We posit that eDNA methods are capable of providing general quantitative applications that will prove especially valuable in data- or resource-limited contexts.

Dark host specificity in two ectoparasite taxa: repeatability, parasite traits, and environmental effects

We applied the concept of dark diversity (species that may potentially inhabit a locality but are absent) to the host spectrum of a parasite and defined it as dark host specificity (DHS). We studied the trait-associated and geographic patterns of dark host specificity in fleas and gamasid mites parasitic on small mammals, asking the following questions: (a) Is dark host specificity repeatable across populations of the same species? (b) Is it associated with morphological and/or ecological species traits? (c) What are the factors associated with geographical variation in the DHS among populations of the same species? The DHS was repeatable within species with a large proportion of variance among samples, accounted for by differences between species. The average DHS of fleas, but not mites, was affected by parasite traits, with the DHS being higher in fleas with larger geographic ranges, higher characteristic abundance levels, and summer reproduction peaks. In the majority of ectoparasites, the regional DHS decreased with an increase in either structural or phylogenetic host specificity. The associations between the DHS and the environmental or host-associated characteristics of a region were revealed in a few species (eight of 22 fleas and three of 12 mites). The DHS decreased with (a) an increase in air temperature in two fleas, (b) a decrease in precipitation in two fleas, and (c) an increase in regional host species richness (in three fleas and three mites). Overall, our results suggest that dark host specificity in arthropod ectoparasites is a species-specific character associated, to a large extent, with the breadth of their host-related niches, while the influences of parasite traits and local environmental conditions are minor.

Unveiling biogeographical patterns of the ichthyofauna in the Tuichi basin, a biodiversity hotspot in the Bolivian Amazon, using environmental DNA

To date, more than 2400 valid fish species have been recorded in the Amazon basin. However, some regions remain poorly documented. This is the case in the Beni basin and in particular in one of its main sub-basins, the Tuichi, an Andean foothills rivers flowing through the Madidi National Park in the Bolivian Amazonia. The knowledge of its ichthyological diversity is, however, essential for the management and protection of aquatic ecosystems, which are threatened by the development of infrastructures (dams, factories and cities), mining and deforestation. Environmental DNA (eDNA) has been relatively little used so far in the Amazon basin. We sampled eDNA from water in 34 sites in lakes and rivers in the Beni basin including 22 sites in the Tuichi sub-basin, during the dry season. To assess the biogeographical patterns of the amazonian ichthyofauna, we implemented a metabarcoding approach using two pairs of specific primers designed and developed in our laboratory to amplify two partially overlapping CO1 fragments, one of 185bp and another of 285bp. We detected 252 fish taxa (207 at species level) among which 57 are newly identified for the Beni watershed. Species compositions are significantly different between lakes and rivers but also between rivers according to their hydrographic rank and altitude. Furthermore, the diversity patterns are related to the different hydro-ecoregions through which the Tuichi flows. The eDNA approach makes it possible to identify and complete the inventory of the ichthyofauna in this still poorly documented Amazon basin. However, taxonomic identification remains constrained by the lack of reference barcodes in public databases and does not allow the assignment of all OTUs. Our results can be taken into account in conservation and management strategies and could serve as a baseline for future studies, including on other Andean tributaries.

Fish Diversity Monitored by Environmental DNA in the Yangtze River Mainstream

Surveys and assessments based on environmental DNA are not only efficient and time-saving, but also cause less harm to monitoring targets. Environmental DNA has become a common tool for the assessment and monitoring of aquatic organisms. In this study, we investigated fish resources in the Yangtze River mainstream using environmental DNA, and the variations in fish during two seasons (spring and autumn) were compared. The results showed that 13 species were identified in spring, and nine species of fish were identified in autumn. The fish with higher eDNA detection were Sinibotia superciliaris, Tachysurus fulvidraco, Cyprinus carpio, Ctenopharyngodon Idella, Monopterus albus, Acanthogobius hasta, Saurogobio dabryi, Oncorhynchus mykiss, Mugil cephalus, Odontamblyopus rubicundus. Seasonal variation between spring and autumn was not significant, and the environmental factors had different effects on fish assemblages during the two seasons. Our study used the eDNA technique to monitor the composition of fish in the spring and autumn in the Yangtze River mainstream, providing a new technology for the long-term management and protection of fishery resources in the region. Of course, problems such as pollution and insufficient databases are the current shortcomings of environmental DNA, which will be the focus of our future research and study.

Using environmental DNA methods to improve detectability in an endangered sturgeon (Acipenser sinensis) monitoring program

Background

To determine the presence and abundance of an aquatic species in large waterbodies, especially when populations are at low densities, is highly challenging for conservation biologists. Environmental DNA (eDNA) has the potential to offer a noninvasive and cost-effective method to complement traditional population monitoring, however, eDNA has not been extensively applied to study large migratory species. Chinese sturgeon (Acipenser sinensis), is the largest anadromous migratory fish in the Yangtze River, China, and in recent years its population has dramatically declined and spawning has failed, bringing this species to the brink of extinction. In this study, we aim to test the detectability of eDNA methods to determine the presence and relative abundance of reproductive stock of the species and whether eDNA can be used as a tool to reflect behavioral patterns. Chinese sturgeon eDNA was collected from four sites along the spawning ground across an eight month period, to investigate the temporal and spatial distribution using droplet digital PCR (ddPCR).

Results

We designed a pair of specific primers for Chinese sturgeon and demonstrated the high sensitivity of ddPCR to detect and quantify the Chinese sturgeon eDNA concentration with the limit of detection 0.17 copies/μl, with Chinese sturgeon eDNA been intermittently detected at all sampling sites. There was a consistent temporal pattern among four of the sampling sites that could reflect the movement characteristics of the Chinese sturgeon in the spawning ground, but without a spatial pattern. The eDNA concentration declined by approximately 2–3 × between December 2018 and December 2019.

Conclusions

The results prove the efficacy of eDNA for monitoring reproductive stock of the Chinese sturgeon and the e decreased eDNA concentration reflect that Chinese sturgeon may survive with an extremely small number of reproductive stock in the Yangtze River. Accordingly, we suggest future conservation measures should focus on both habitat restoration and matured fish restocking to ensure successful spawning. Overall, this study provides encouraging support for the application of eDNA methods to monitor endangered aquatic species.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01948-w.