Aquatic environmental DNA: A review of the macro-organismal biomonitoring revolution

Machine learning classification of quorum sensing-induced bacterial aggregation using flow rate assays on paper chips toward bacterial species identification in potable water sources

Preventing waterborne disease caused by bacteria is especially important in low-resource settings, where skilled personnel and laboratory equipment are scarce. This work reports a straightforward method for classifying bacterial species by monitoring the capillary flow rates on a multi-channel paper microfluidic chip, where quorum sensing (QS)-induced bacterial aggregation leads to measurable changes in flow rates, enabling species differentiation. It required no fluorescent molecules, microscope, particles, covalent conjugation, or surface immobilization. Five representative QS molecules and control were added to each bacterial sample, and their different extents of bacterial aggregation resulted in varied flow rates. Flow rates were collected for the duration of the flow to build the learning database, and the XGBoost machine learning algorithm predicted the accuracy for classifying ten bacterial species, including 7 gram-negative and 3 gram-positive species. Three different algorithms were developed for high, medium, and low bacterial concentration ranges, and the classification accuracies of all the algorithms exceeded 75.0 %. Using XGBoost and the previously established database, we tested bacteria in the field water samples and successfully predicted the dominant species. The technology developed in this study, using only QS molecules and a paper microfluidic chip, offers a simple system for detecting microorganisms in drinking water to help prevent waterborne diseases.

Monitoring marine pollution effects through targeted environmental DNA (eDNA) testing in the Pacific northwest

Globally, coastal waters experience degradation from pollution associated with multiple discharges, including industrial and agricultural runoff, and municipal wastewater. Certain benthic infaunal taxa are tolerant of high nutrient input and anoxic conditions, while others are sensitive to these conditions. Using these indicator taxa as proxies for assessing organic enrichment is well established to characterize subsequent pollution impacts. Conventional assessment of macroinfauna involves the detailed analysis of each individual specimen within a sample by taxonomic experts, a resource intensive process. As an alternative, we developed sensitive quantitative polymerase chain reaction (qPCR) assays to detect these indicator taxa in a scalable and reliable way. Using whole genome shotgun sequencing, we generated full mitogenome sequences of selected indicator macroinfaunal polychaetes routinely used for monitoring programs in Pacific Northwest marine environments. These sequences were used to design five new, rigorously validated environmental DNA (eDNA) assays capable of detecting low levels of DNA that can be isolated from environmental samples. For nine sites at a wastewater treatment plant outfall in Vancouver, British Columbia, we tested three eDNA sample collection types: active filtration, a passive dip filter from water containing collected macroinfauna, and active filtration from water collected near the sea floor. Generalized linear models indicated that eDNA signal strength correlated with organism count particularly with passive dip sample collection type. eDNA occupancy modelling techniques estimated detection probabilities corresponding with organism count. The present study emphasizes the value of integrating eDNA into marine outfall monitoring efforts to enhance the assessment of environmental effects.

Hydrological Connectivity Enhances Fish Biodiversity in Amazonian Mining Ponds: Insights From eDNA and Traditional Sampling

Artisanal and small-scale gold mining (ASGM) expansion in the Madre de Dios region of the Peruvian Amazon has transformed primary forests into a novel wetland complex of thousands of abandoned mining ponds. Despite their ecological relevance, post-mining recovery of these systems remains understudied, particularly regarding fish biodiversity and recolonisation. In this study, we evaluate fish community richness and composition in mining ponds of different dimensions, years post abandonment, physicochemical properties and degree of pulse flood connectivity using traditional collection-based methods and environmental DNA (eDNA) with the 12S and COI markers. We compared these two methods of biodiversity inventory and contrasted results from ASGM waterbodies with those obtained from nearby pristine oxbow lakes. Overall, we registered more fish richness at all sites using eDNA versus traditional methods, especially with the 12S marker. We identified 14 and 13 unique genera using traditional methods and eDNA, respectively, with 40 genera detected by both approaches, evidencing their complementarity. Notably, we found that the degree of pulse flooding connectivity was the main predictor of species richness among the abandoned mining ponds (p-value < 0.05). We registered 11-22, 23-71 and 56 morphospecies in non-flooded mining ponds, pulse flooded mining ponds and nearby oxbow lakes, respectively. Furthermore, the fish community composition of mining ponds most influenced by pulse flooding was similar to that of pristine lakes. Our findings highlight the role of hydrological connectivity in ecological recovery within mining-impacted wetlands. Future restoration efforts should enhance aquatic connectivity to accelerate recovery in post-mining environments.

Molecular detection and identification of Trichobilharzia: development of a LAMP, qPCR, and multiplex PCR toolkit

BACKGROUND

Cercarial dermatitis (CD), or swimmer's itch, is a water-borne allergic skin reaction caused by the penetration of the larval stages of bird schistosomes (cercariae) into the skin. Members of the genus Trichobilharzia are the primary causative agents of CD worldwide. Due to the increasing number of cases, CD is regarded as a (re)emerging disease. Outbreaks in recreational waters can significantly impact public health and local economies. Environmental monitoring of Trichobilharzia is crucial for outbreak prediction and public health management. However, conventional methods, such as cercarial shedding and snail dissections, are labour-intensive and lack sensitivity. To overcome these limitations, we present a molecular toolkit that combines loop-mediated isothermal amplification (LAMP), quantitative polymerase chain reaction (qPCR), and multiplex PCR for rapid, sensitive, and accurate detection and identification of Trichobilharzia spp. from various biological samples.

METHODS

Tricho-LAMP and Tricho-qPCR were designed and optimised for Trichobilharzia DNA detection. A multiplex PCR assay was also developed and optimised to identify the three main species causing CD in Europe (Trichobilharzia franki, T. szidati, and T. regenti).

RESULTS

Tricho-LAMP specifically detected T. regenti and T. franki at 10-3 ng, and T. szidati at 10-2 ng per reaction with genomic DNA. Using gBlocks synthetic DNA, Tricho-LAMP achieved 100% amplification at 10,000 copies and 85% amplification at 1000 copies, with decreasing success at lower concentrations. Tricho-qPCR showed the highest sensitivity, detecting all species down to 10-4 ng per reaction and showing a limit of detection at 10 copies of synthetic DNA in the reaction. Multiplex PCR allowed reliable species differentiation via gel electrophoresis of the PCR products, but the assay had the lowest sensitivity.

CONCLUSIONS

We provide a molecular toolkit consisting of LAMP, qPCR, and multiplex PCR. By exhibiting high sensitivity, Tricho-LAMP and Tricho-qPCR assays are potentially suitable for environmental DNA (eDNA)-based environmental monitoring of bird schistosomes, by both researchers and public health authorities. Multiplex PCR can be used for species determination without the need for further sequencing.

Exploiting taxonomic information from metagenomes to infer bacterial bioindicators and environmental quality at salmon aquaculture installations

Environmental DNA (eDNA) metabarcoding has emerged as a powerful method for assessing the environmental impacts of marine Atlantic salmon aquaculture by identifying bacterial bioindicators and inferring biotic indices. However, because this approach relies on the PCR amplification of 16S rRNA gene fragments, it may introduce errors that compromise bioindicator reliability. In contrast, metagenomic analysis which captures the complete set of genetic material directly extracted from environmental samples circumvents biases inherent to PCR amplification. We hypothesized that metagenomic data could offer superior assessments of benthic environmental impacts associated with salmon aquaculture compared to metabarcoding. To test this, we compared bacterial community structures derived from both metabarcoding and metagenomic analyses of 68 sediment samples obtained from aquaculture installation sites characterized by varying degrees of benthic impact as determined by macroinvertebrate inventories. Bacterial bioindicators were identified from each dataset, and Random Forest models were used to predict the degrees of benthic impacts. Metagenomics identified a greater number of bioindicators at both the family and individual sequence variant levels, resulting in higher predictive accuracy for impact assessments. Notably, only a few bioindicators were common to both methods, suggesting that methodological limitations and distorted abundance patterns in metabarcoding data may lead to spurious indicators. These findings highlight both the challenges and potential advantages of employing metagenomics for reliable environmental impact assessments.

Advancing schistosomiasis surveillance: standardization and application of an environmental DNA (eDNA)-based approach for detecting Schistosoma mansoni in Brazil

BACKGROUND

Schistosoma sp. transmission is linked to water bodies, poor sanitation, and the presence of intermediate hosts. Nevertheless, parasite detection in snails is hampered by challenges in snail sampling and low infection rates, mainly in moderate and low-endemic areas, as well as requiring specialized personnel and being time-consuming. Thus, there is a need to improve tools to assist schistosomiasis surveillance and an environmental DNA (eDNA) approach may help to overcome these limitations. Here, we standardized and used an eDNA-based approach to monitor Schistosoma mansoni occurrence in two schistosomiasis endemic areas from Minas Gerais, Brazil.

METHODS

The eDNA approach was standardized for local conditions by evaluating the specificity of the qPCR assay in detecting the parasite DNA. Water from snail breeding tanks containing Biomphalaria glabrata, either infected or not with S. mansoni, was used to standardize the eDNA filtration and extraction protocols. Three molecular techniques- Low-Stringency PCR (LS-PCR), Loop-mediated isothermal amplification (LAMP), and quantitative PCR (qPCR)- were applied to investigate samples from snail tanks and two field surveys. Additionally, malacological surveys and measurements of water physicochemical and microbiological parameters were conducted at the same locations to know the species of mollusks present and the ideal environmental conditions to identify hotspots.

RESULTS

The qPCR assay was specifically amplified Schistosoma sp. DNA without amplifying other trematodes presents in Brazil, ensuring accurate detection without cross-amplification. All three molecular assays efficiently detected S. mansoni DNA only from eDNA samples from tanks with infected snails. The eDNA approach, associated with LAMP and qPCR assays, successfully identified S. mansoni DNA at the same collection points where snails releasing cercariae were found and at one additional site, that was missed by traditional methods, underscoring its sensitivity.

CONCLUSIONS

This study illustrates the potential of employing eDNA sampling combined with molecular techniques as an effective strategy for monitoring and identifying potential schistosomiasis transmission foci in endemic areas. This approach aligns with the WHO's roadmap for schistosomiasis elimination by 2030 and has implications for public health interventions and control measures.

Spatio-temporal distribution of environmental DNA from amphibian and turtle species in a pond ecosystem

Environmental DNA (eDNA) analysis has emerged as a transformative tool for biodiversity monitoring and conservation. However, uncertainties in the ecological processes of eDNA in aquatic environments decrease the reliability of eDNA-based surveys. Understanding the distribution and persistence patterns of eDNA is essential to effectively correlate eDNA data with species occurrence across spatial and temporal scales. Here, we investigated the spatio-temporal distribution of eDNA from amphibian and turtle species in a pond ecosystem, by establishing controlled eDNA sources from American bullfrogs (Lithobates catesbeianus) and red-eared sliders (Trachemys scripta elegans), and quantifying eDNA concentrations from different water layers and sediment samples using droplet digital PCR. Our results showed that eDNA from both species was highly concentrated within 2-5 m of the biological sources, with dispersal distance independent of the duration of organism' presence in the pond and exhibiting a vertically increasing trend over time. eDNA concentration and persistence varied significantly depending on species and substrate type, with bullfrogs showing notably higher eDNA detectability. The average eDNA concentration in sediment was 1.4 × 104 times higher than in water, and eDNA persisted approximately one week longer. Our findings demonstrate that the strong aggregation patterns of eDNA can provide valuable insights into the spatial distribution of amphibians and turtles in pond systems. eDNA from surface water showed greater timeliness for biodiversity monitoring and aquatic invasive species management. The specificity of target taxa and the temporal complementarity of sedimentary eDNA should be carefully considered in future eDNA sampling designs.

A comprehensive assessment of non-indigenous species requires the combination of multi-marker eDNA metabarcoding with classical taxonomic identification

In marine environment, non-indigenous species (NIS) can alter natural habitats and cause biodiversity loss with important consequences for ecosystems and socio-economic activities. With more than 1000 NIS introduced over the last century, the Mediterranean Sea is one of the most threatened regions worldwide, requiring an early identification of newly entered alien species for a proper environmental management. Here, we carried out environmental-DNA (eDNA) metabarcoding analyses, using multiple molecular markers (i.e., 18S rRNA, COI, and rbcL) and different genetic databases (i.e., NCBI, PR2, SILVA, MIDORI2, MGZDB, and BOLD), on seawater and sediment samples collected on a seasonal basis in three Mediterranean ports located in the North Adriatic, Ionian and Tyrrhenian Sea to identify marine species, and particularly NIS. The use of the multi-marker eDNA metabarcoding allowed the identification of a higher number of species compared to the morphological analyses (1484 vs. 752 species), with a minor portion of species shared by both approaches. Overall, only 4 NIS were consistently identified by both morphological and molecular approaches, whereas 27 and 17 NIS were exclusively detected by using eDNA metabarcoding and classical taxonomic analyses, respectively. The eDNA metabarcoding allowed also identifying the genetic signatures of 5 NIS never reported in the Italian waters. We conclude that eDNA metabarcoding can represent a highly sensitive tool for the early identification of NIS, but a comprehensive census of the NIS requires the combination of molecular and morphological approaches.

Sampling eDNA at outflows from artificial drainage systems: what is the potential to monitor landscape degradation?

Wetlands have been drained extensively for productive land use, transforming the biodiversity of whole landscapes. Such transformation primarily affects the huge biodiversity across the terrestrial and aquatic environments that is difficult to observe directly, especially in the case of microorganisms. We explored whether environmental DNA (eDNA) from the flowing water could serve as a data source for characterizing the level of biological degradation of drained and managed forest-wetland landscapes. We took spatially and seasonally replicated samples from nine hydrologically monitored outflows at small drained catchments in Estonia in order to understand the variation in their eDNA-based diversity. Using PacBio long-read sequencing, we detected a large taxonomic diversity of eukaryotes (approx. 6000 operational taxonomic units (OTUs)), which was spatially and seasonally structured, but also highly variable within individual ditches. Even in fungi (the best-represented taxon group), the OTU accumulation curves did not level off despite high volumes of filtered water; however, many interesting species records were obtained (particularly on pathogenic microorganisms). We conclude that eDNA can provide valuable insights into the biodiversity of hydrologically drained areas, but our results indicate high heterogeneity among samples (apparently due to both actual assemblage differences and sampling errors) as a major problem for standard environmental assessment. Combining eDNA methods with other ecological assessment techniques is a priority for further research in these systems.

Active or passive? A multi-marker approach to compare active and passive eDNA sampling in riverine environments

Environmental DNA (eDNA) is increasingly used in biodiversity monitoring with several collection techniques proposed. Those applied to aquatic eDNA can now be divided into two categories: active and passive sampling. Active sampling involves the deliberate and controlled collection of environmental samples, and the most common method is water filtration. Passive sampling is a more recent technique that involves capturing eDNA by relying on its adsorption to samplers, which can be fabricated from various materials, and submerged for minutes, hours or weeks. In this study, we compared the performance of water filtration and Passive eDNA Sampling (PEDS) with granular active carbon in terms of detected taxa collected from four different sites of the same river system. eDNA samples were amplified for three molecular markers for 18S rRNA, 12S rRNA and COI genes, with primers according to the literature that target invertebrates and vertebrates. The study revealed that PEDS detected on average more species in 18S rRNA and 12S rRNA assays, with 18S rRNA results presenting a significantly higher homogeneity of read variances between samples. Biological communities captured differed between PEDS and filters. The former method retrieved a significant number of microinvertebrates and chironomids (Chironomidae, Diptera), detecting a similar number of vertebrates to filters, but with lower performance in the detection of fish. Notably, both methods performed well with amphibians, successfully identifying all species linked to lotic environments in the studied area. Compared to PEDS, the eDNA capture protocol using filters yielded more sequences identified as ephemeropterans, trichopterans, and acarines. In addition, PEDS was more cost-effective and environmentally sustainable. These findings imply that there is no definitive superior eDNA sampling method. Consequently, in conjunction with studies proposing new methods of eDNA sampling, studies comparing their performance with a broad taxonomic representation will be pivotal.

Contrasting the contributions of 12S eDNA metabarcoding, visual surveys and anaesthetic collections to the historical regional diversity of cryptobenthic and conspicuous fish

Taxonomic gaps in community biodiversity assessments are now commonly addressed by combining traditional monitoring methods and environmental DNA (eDNA) metabarcoding, widely recognized for having the ability to uncover rare and cryptic diversity. However, only a few studies have assessed the efficacy of this novel technique for detecting cryptobenthic fishes and tested the limitations of incomplete genetic reference availability for a historically neglected component of fish communities. Our goals were (i) to compare cryptobenthic and conspicuous fish detections by 12S eDNA metabarcoding, visual surveys and anaesthetic fish collections, and (ii) to compare emerging regional diversity patterns against a long-term historical record for the Gulf of California. Despite adding new local references for 36 cryptobenthic fishes, 12S eDNA metabarcoding detected only seven taxa. Visual surveys provided similar results, highlighting fish collections as the primary source, with 57 cryptobenthic fishes recovered. Conspicuous fishes had an equal and highly complementary contribution by 12S eDNA and visual surveys. When combining contemporary detections from all methods, we recovered 43% of cryptobenthic and 16% of conspicuous fishes, relative to the historical records. The spatial community structure for detected cryptobenthic fishes differed from historical expectations and conspicuous fishes, showing no differences in community richness nor composition between Northern and Central Gulf communities. Our study highlights the limitations of eDNA for monitoring cryptobenthic fishes, and that their patterns of community structuring are driven by distinct factors compared to conspicuous fishes.

A Comprehensive Evaluation of Taxonomic Classifiers in Marine Vertebrate eDNA Studies

Environmental DNA (eDNA) metabarcoding is a widely used tool for surveying marine vertebrate biodiversity. To this end, many computational tools have been released and a plethora of bioinformatic approaches are used for eDNA-based community composition analysis. Simulation studies and careful evaluation of taxonomic classifiers are essential to establish reliable benchmarks to improve the accuracy and reproducibility of eDNA-based findings. Here we present a comprehensive evaluation of nine taxonomic classifiers exploring three widely used mitochondrial markers (12S rDNA, 16S rDNA and COI) in Australian marine vertebrates. Curated reference databases and exclusion database tests were used to simulate diverse species compositions, including three positive control and two negative control datasets. Using these simulated datasets ranging from 36 to 302 marker genes, we were able to identify between 19% and 89% of marine vertebrate species using mitochondrial markers. We show that MMSeqs2 and Metabuli generally outperform BLAST with 10% and 11% higher F1 scores for 12S and 16S rDNA markers, respectively, and that Naive Bayes Classifiers such as Mothur outperform sequence-based classifiers except MMSeqs2 for COI markers by 11%. Database exclusion tests reveal that MMSeqs2 and BLAST are less susceptible to false positives compared to Kraken2 with default parameters. Based on these findings, we recommend that MMSeqs2 is used for taxonomic classification of marine vertebrates given its ability to improve species-level assignments while reducing the number of false positives. Our work contributes to the establishment of best practices in eDNA-based biodiversity analysis to ultimately increase the reliability of this monitoring tool in the context of marine vertebrate conservation.

Parameterizing the particle size distribution of environmental DNA provides insights into its improved availability from the water

Previous studies estimated the particle size distribution (PSD) of environmental DNA (eDNA) to infer its persistence state in the water and to determine the size fraction in which eDNA particles are concentrated. These results, however, depend on the combination of filter pore sizes and may not necessarily provide the proper implications for the eDNA state and availability in the water. To address this issue, the present study proposes parameterizing the PSD using the Weibull distribution model, which has been widely used for various materials. Re-analyses of previous datasets show the Weibull parameters (representing the PSD profiles) significantly depend on species traits, marker types, temperature, and time passages after the removal of the individuals. The results allowed for calculating the proportion of eDNA captured using a given filter pore size and the filter pore size required to collect a given percentage of eDNA particles under various study designs and environmental conditions. The results also posed caveats indicating that the strategy for a sufficient eDNA collection method is not always uniform across experimental and environmental conditions. The findings contribute to a better understanding of the eDNA state and improved eDNA availability, refining eDNA-based biodiversity and ecosystem monitoring.

Biodiversity monitoring in remote marine environments: Advancing environmental DNA/RNA sampling workflows

Understanding biodiversity is crucial for protecting unique environments, but acquiring this knowledge is challenging in isolated areas due to limited availability of easy-to-implement biomonitoring tools. To determine optimal sampling strategies in remote regions, environmental DNA and RNA (eDNA and eRNA) sampling workflows were evaluated at 12 sites in three fiords within Fiordland National Park, Aotearoa-New Zealand. For filtration comparison, a modified cruising speed net was used to concentrate eDNA/eRNA onto 20 μm nylon filters, while water from the net's cod-end was filtered through a 5 μm Smith-Root self-preserving filter using the eDNA Citizen Scientist Sampler. To compare preservation methods, Smith-Root filters were cut in half, with one half preserved in the self-preserving unit and the other in DNA/RNA Shield™ buffer. Biodiversity screening was performed by sequencing the 18S rRNA gene for eukaryotes and two mitochondrial 16S rRNA genes for fish and marine vertebrates. Comparable amplicon sequence variant (ASVs) richness was observed between methods, yet samples preserved with buffer showed higher richness of fish and marine vertebrate taxa and higher PCR amplification success. There was little variation in community composition, except for 16S rRNA targeting fish, where distinct patterns emerged based on preservation methods. Overall, sampling workflows showed similar community composition and alpha diversity across both nucleic acids. These results confirm that enhancing eDNA/eRNA yields for sparse taxa requires consideration of collection and preservation methods. However, abundant taxa biodiversity is captured consistently, allowing for adjustments without compromising robustness. These insights support streamlined eDNA/eRNA sampling, emphasizing adaptive strategies based on targeted taxa.

Investigating passive eDNA samplers and submergence times for marine surveillance

Passive environmental DNA (eDNA) samplers offer a cost-effective and scalable approach to marine biodiversity monitoring, potentially aiding detections of non-indigenous species. This study explored the efficiency of passive eDNA samplers to detect a variety of globally problematic marine invasive species in field conditions: Sabella spallanzanii, Styela clava, Bugula neritina and Undaria pinnatifida. Four passive sampler substrates, nylon filters, positively charged nylon discs, nylon mesh, and artificial sponges, were tested across six submergence times, ranging from 10 to 720 min, against standard filtration-based approaches. Our results demonstrated that passive samplers could achieve comparable or even higher eDNA yields than traditional active filtration methods, indicating their potential for biosecurity surveillance. Species-specific droplet-digital PCR (ddPCR) assays provided sensitive and quantifiable eDNA signals, though assay validation remains crucial to avoid false negatives. Significant variation in eDNA signal detection highlighted the importance of considering both material selection and submersion time, depending on the targeted organisms. Furthermore, 18S rRNA metabarcoding was undertaken to assess how the overall detected biodiversity might interfere with species-specific detections. Certain sessile organisms, such as ascidians and polychaetes, dominated early representation on the passive filters but did not interfere with species-specific detection. By optimizing material selection, submersion time, and assay validation, passive eDNA sampling can enhance the sensitivity and reliability of eDNA-based monitoring, contributing to improved marine biosecurity and conservation efforts.

Design and Validation of an Open-Close Device for Integrated Environmental DNA Sampling Detects A Depth Gradient in Indian Ocean Deep-Sea Fish Assemblages

Advances in methods for collecting environmental DNA (eDNA) are revolutionizing biomonitoring capabilities. The goal of this study was to leverage existing survey technology to design and test an eDNA sampler that captures an integrated eDNA sample over the length of a deep-water transect. We manufactured a 300 × 100 × 100 mm mountable, open-ended box made of high-density polyethylene that could be attached to the frame of a preexisting deep tow camera system. The box (OCD; open-close device) was equipped with an actuator that attached to hinged doors at both ends, enabling it to be opened and closed remotely at depths up to 6000 m through preexisting communications, thereby exposing the internal chamber to the surrounding water upon activation. A sterile active carbon sponge was inserted into the internal chamber for eDNA capture during each deployment. The OCD sampler was field tested during a voyage to the Gascoyne Marine Park region off northwest Australia. We compared three different methods for processing the captured eDNA from the sampler: filtering OCD water, extracting eDNA from sponge pieces, and filtering sponge rinse water. Using fish as our example organism, we also compared the identities of fishes from eDNA detections with bottom trawl survey data collected during the same survey, and the known regional species pool, to confirm the eDNA identifications were plausible. A large number of fishes (193 taxa, from 87 families) were detected, and the majority were found within their expected depth ranges (> 75%), and in the trawl catches (60%). We discuss design and manufacturing lessons, ideas for increased eDNA capture efficiency for improved methodologies in sample processing, and how to establish appropriate field controls. We also discuss how this technology could advance our scientific understanding in ocean studies in terms of ecological metrics provided and the trade-offs compared to other sampling tools.

Monitoring the Land and Sea: Enhancing Efficiency Through CRISPR-Cas Driven Depletion and Enrichment of Environmental DNA

Characterizing biodiversity using environmental DNA (eDNA) represents a paradigm shift in our capacity for biomonitoring complex environments, both aquatic and terrestrial. However, eDNA biomonitoring is limited by biases toward certain species and the low taxonomic resolution of current metabarcoding approaches. Shotgun metagenomics of eDNA enables the collection of whole ecosystem data by sequencing all molecules present, allowing characterization and identification. Clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-associated proteins (Cas)-based methods have the potential to improve the efficiency of eDNA metagenomic sequencing of low-abundant target organisms and simplify data analysis by enrichment of target species or nontarget DNA depletion before sequencing. Implementation of CRISPR-Cas in eDNA has been limited due to a lack of interest and support in the past. This perspective synthesizes current approaches of CRISPR-Cas to study underrepresented taxa and advocate for further application and optimization of depletion and enrichment methods of eDNA using CRISPR-Cas, holding promise for eDNA biomonitoring.

Microbial, holobiont, and Tree of Life eDNA/eRNA for enhanced ecological assessment

Microbial environmental DNA and RNA (collectively 'eNA') originate from a diverse and abundant array of microbes present in environmental samples. These eNA signals, largely representing whole organisms, serve as a powerful complement to signals derived from fragments or remnants of larger organisms. Integrating microbial data into the toolbox of ecosystem assessments and biotic indices therefore has the potential to transform how we use eNA data to understand biodiversity dynamics and ecosystem functions, and to inform the next generation of environmental monitoring. Incorporating holobiont and Tree of Life approaches into eNA analyses offers further holistic insight into the range of ecological interactions between microbes and other organisms, paving the way for advancing our understanding of, and ultimately manipulating ecosystem properties pertinent to environmental management, conservation, wildlife health, and food production.

Impact of Surface Adsorption on DNA Structure and Stability: Implications for Environmental DNA Interactions with Iron Oxide Surfaces

Environmental DNA (eDNA), i.e., DNA found in the environment, can interact with various geochemical surfaces, yet little is known about these interactions. Mineral surfaces may alter the structure, stability, and reactivity of eDNA, impacting the cycling of genetic information and the reliability of eDNA-based detection tools. Understanding how eDNA interacts with surfaces is crucial for predicting its fate in the environment. In this study, we examined the surface interaction and stability of herring testes DNA, a model system for eDNA, on two common iron oxide phases present in the environment: α-FeOOH (goethite) and α-Fe2O3 (hematite). Utilizing spectroscopic probes, including attenuated total reflection Fourier-transform infrared (ATR-FTIR) and UV-vis spectroscopy, we quantified the DNA adsorption capacity at pH 5 and determined its secondary structure. DNA adsorbed irreversibly at pH 5 and 25 °C, primarily through its phosphate groups, and retained the solution-phase B-form structure. However, the infrared data also indicated some distortion of the B-form likely due to additional interactions between nitrogenous bases when adsorbed on the α-Fe2O3 particle surfaces. The distortion in the double helical structure of adsorbed DNA on α-Fe2O3 led to a lower melting temperature (Tm) of 60 °C compared to 70 °C for DNA in solution. In contrast, DNA adsorbed on α-FeOOH melted at higher temperatures relative to solution-phase DNA and in two distinct phases. Upon testing adsorbed DNA stability at higher pH values, there were distinct differences between the two iron oxide phases. For α-FeOOH, nearly 50% of the DNA desorbed from the surface when the solution pH changed from 5 to 8, while less than 5% desorbed from α-Fe2O3 under the same conditions. Overall, these findings underscore the importance of mineral-specific eDNA-surface interactions and their role in adsorbed eDNA stability, in terms of DNA melting and the impact of solution-phase pH changes.

Environmental DNA barcoding reveals general biodiversity patterns in the large tropical rift Lake Albert

Lake Albert, Africa's seventh-largest lake and a biodiversity hotspot, faces significant environmental challenges, including unregulated anthropogenic pressure and a lack of comprehensive biological studies. To address the scarcity of biodiversity data, we utilized environmental DNA (eDNA) metabarcoding to assess the lake's eukaryotic and metazoan communities. Surface water samples were collected at three distinct locations: close to the southern inflow of the Semliki River, the central part of the lake, and close to the northern inflow of the Victoria Nile and outflow of the Albert Nile. We aimed to study ecological patterns across the lake, focusing on sequence variant richness and community composition, testing for differences among locations and between shoreline and pelagic zones. Consistent with previous morphology-based observations, our results revealed differences in community composition among the three sites, with cyclopoid copepods dominating the communities. Distance from shore was a significant factor influencing community composition, confirming expectations about the effects of nutrient and oxygen availability gradients. However, the lack of comprehensive reference sequence data limited accurate taxonomic assignments. Despite these limitations, our study demonstrates that eDNA metabarcoding is highly useful for assessing biodiversity in underexplored tropical freshwater ecosystems. We advocate for urgent efforts to generate reference sequences from tropical regions to enhance the utility of eDNA for biodiversity monitoring and conservation. Our findings underscore the potential of eDNA in providing insights into ecological patterns of entire communities and emphasize the need for comprehensive studies addressing the full taxonomic spectrum in tropical freshwater ecosystems.

Methodological assessment for efficient collection of Schistosoma mansoni environmental DNA and improved schistosomiasis surveillance in tropical wetlands

Schistosomiasis, caused by trematodes of genus Schistosoma, is among the most seriously neglected tropical diseases. Although rapid surveillance of risk areas for Schistosoma transmission is vital to control schistosomiasis, the habitat and infection status of this parasite are difficult to assess. Environmental DNA (eDNA) analysis, involving the detection of extra-organismal DNA in water samples, facilitates cost-efficient and sensitive biomonitoring of aquatic environments and is a promising tool to identify Schistosoma habitat and infection risk areas. However, in tropical wetlands, highly turbid water causes filter clogging, thereby decreasing the filtration volume and increasing the risk of false negatives. Therefore, in this study, we aimed to conduct laboratory experiments and field surveys in Lake Victoria, Mbita, to determine the appropriate filter pore size for S. mansoni eDNA collection in terms of particle size and filtration volume. In the laboratory experiment, aquarium water was sequentially filtered using different pore size filters. Targeting >3 µm size fraction was found to be sufficient to capture S. mansoni eDNA particles, regardless of their life cycle stage (egg, miracidia, and cercaria). In the field surveys, GF/D (2.7 µm nominal pore size) filter yielded 2.5-times the filtration volume obtained with a smaller pore size filter and pre-filtration methods under the same time constraints. Moreover, a site-occupancy model was applied to the field detection results to estimate S. mansoni eDNA occurrence and detection probabilities and assess the number of water samples and PCR replicates necessary for efficient eDNA detection. Overall, this study reveals an effective method for S. mansoni eDNA detection in turbid water, facilitating the rapid and sensitive monitoring of its distribution and cost-effective identification of schistosomiasis transmission risk areas.

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.

Novel Drop-Sampler for Simultaneous Collection of Stereo-Video, Environmental DNA and Oceanographic Data

There is an increasing interest in environmental DNA (eDNA) as a method to survey marine biota, enhancing traditional survey methods, and a need to ground truth eDNA-based interpretations with visual surveys to understand biases in both the eDNA and visual datasets. We designed and tested a rapidly deployable, robust method pairing water sampling for eDNA collection and stereo-video imagery, comparing inferred fish assemblages with interspersed baited remote underwater video (stereo-BRUV) samples. The system is capable of rapidly collecting simultaneous wide-field stereo-video imagery, oceanographic measurements and multiple water samples across a range of habitats and depths (up to 600 m). A platform demonstration was conducted in a no-take National Park Zone of the Ningaloo Marine Park, Western Australia, with samples being collected whilst the system is resting on the seafloor. Combining simultaneous visual survey data with eDNA species estimates increased the total diversity of the fish assemblage by ca. 6.5% over eDNA estimates alone, whilst the analysis of the assemblage composition sampled by each method revealed significant differences. The platform demonstration highlights the biases of each sampling method and their complementarity to one another. We suggest that these biases will be better understood by advancements that allow eDNA metabarcoding to discriminate the abundance and life stage of marine biota. Furthermore, investigation of the relationship between eDNA metabarcoding data and concomitant imagery-derived length, age and habitat data is needed.

Long-distance Southern Ocean environmental DNA (eDNA) transect provides insights into spatial marine biota and invasion pathways for non-native species

The Southern Ocean surrounding Antarctica harbours some of the most pristine marine environments remaining, but is increasingly vulnerable to anthropogenic pressures, climate change, and invasion by non-native species. Monitoring biotic responses to cumulative impacts requires temporal and spatial baselines and ongoing monitoring - traditionally, this has been obtained by continuous plankton recorder (CPR) surveys. Here, we conduct one of the longest environmental DNA (eDNA) transects yet, spanning over 3000 nautical miles from Hobart (Australia) to Davis Station (Antarctica). We evaluate eDNA sampling strategies for long-term open ocean biomonitoring by comparing two water volume and filter pore size combinations: large (12 l with 20 μm) and small (2 l with 0.45 μm). Employing a broad COI metabarcoding assay, we found the large sample/pore combination was better suited to open ocean monitoring, detecting more target DNA and rare or low abundance species. Comparisons with four simultaneously conducted CPR transects revealed that eDNA detections were more diverse than CPR, with 7 (4 unique) and 4 (1 unique) phyla detections respectively. While both methods effectively delineated biodiversity patterns across the Southern Ocean, eDNA enables surveys in the presence of sea-ice where CPR cannot be conducted. Accordingly, 16 species of concern were detected along the transect using eDNA, notably in the Antarctic region (south of 60°S). These were largely attributed to hull biofouling, a recognized pathway for marine introductions into Antarctica. Given the vulnerability of Antarctic environments to potential introductions in a warming Southern Ocean, this work underscores the importance of continued biosecurity vigilance. We advocate integrating eDNA metabarcoding with long-term CPR surveys in the Southern Ocean, emphasising the urgency of its implementation. We anticipate temporal and spatial interweaving of CPR, eDNA, and biophysical data will generate a more nuanced picture of Southern Ocean ecosystems, with significant implications for the conservation and preservation of Antarctic ecosystems.

Scanning amplicons with CRISPR-Dx detects endangered amphibians in environmental DNA

More efficient methods for extensive biodiversity monitoring are required to support rapid measures to address the biodiversity crisis. While environmental DNA (eDNA) metabarcoding and quantitative PCR (qPCR) methods offer advantages over traditional monitoring approaches, their large-scale application is limited by the time and labour required for developing assays and/or for analysis. CRISPR (clustered regularly interspaced short palindromic repeats) diagnostic technologies (Dx) may overcome some of these limitations, but they have been used solely with species-specific primers, restricting their versatility for biodiversity monitoring. Here, we demonstrate the feasibility of designing species-specific CRISPR-Dx assays in silico within a short metabarcoding fragment using a general primer set, a methodology we term 'ampliscanning', for 18 of the 22 amphibian species in Switzerland. We sub-selected nine species, including three classified as regionally endangered, to test the methodology using eDNA sampled from ponds at nine sites. We compared the ampliscanning detections to data from traditional monitoring at these sites. Ampliscanning was successful at detecting target species with different prevalences across the landscape. With only one visit, we detected more species per site than three traditional monitoring visits (visual and acoustic detections by trained experts), in particular more elusive species and previously undocumented but expected populations. Ampliscanning detected 25 species/site combinations compared to 12 with traditional monitoring. Sensitivity analyses showed that larger numbers of field visits and PCR replicates are more important for reliable detection than many technical replicates at the CRISPR-Dx assay level. Given the reduced sampling and analysis effort, our results highlight the benefits of eDNA and CRISPR-Dx combined with universal primers for large-scale monitoring of multiple endangered species across landscapes to inform conservation measures.

Environmental DNA as a complementary tool for biodiversity monitoring: A multi-technique and multi-trophic approach to investigate cetacean distribution and feeding ecology

The use of environmental DNA (eDNA) to assess the presence of biological communities has emerged as a promising monitoring tool in the marine conservation landscape. Moreover, advances in Next-Generation Sequencing techniques, such as DNA metabarcoding, enable multi-species detection in mixed samples, allowing the study of complex ecosystems such as oceanic ones. We aimed at using these molecular-based techniques to characterize cetacean communities, as well as potential prey on the northern coast of Mainland Portugal. During four seasonal campaigns (summer 2021 to winter 2022/2023), seawater samples were collected along with visual records of cetacean occurrence. The eDNA isolated from 64 environmental samples was sequenced in an Illumina platform, with universal primers targeting marine vertebrates. Five cetacean species were identified by molecular detection: common dolphin (Delphinus delphis), bottlenose dolphin (Tursiops truncatus), Risso's dolphin (Grampus griseus), harbor porpoise (Phocoena phocoena) and fin whale (Balaenoptera physalus). Overall, except for the latter (not sighted during the campaigns), this cetacean community composition was similar to that obtained through visual monitoring, and the complementary results suggest their presence in the region all year round. In addition, the positive molecular detections of Balaenoptera physalus are of special relevance since there are no records of this species reported on scientific bibliography in the area. The detection of multiple known prey of the identified dolphins indicates an overlap between predator and prey in the study area, which suggests that these animals may use this coastal area for feeding purposes. While this methodological approach remains in a development stage, the present work highlights the benefits of using eDNA to study marine communities, with specific applications for research on cetacean distribution and feeding ecology.

Biofouling sponges as natural eDNA samplers for marine vertebrate biodiversity monitoring

Environmental DNA (eDNA) analysis has now become a core approach in marine biodiversity research, which typically involves the collection of water or sediment samples. Yet, recently, filter-feeding organisms have received much attention for their potential role as natural eDNA samplers. While the indiscriminate use of living organisms as 'sampling tools' might in some cases raise conservation concerns, there are instances in which highly abundant sessile organisms may become a nuisance as biofouling on artificial marine structures. Here we demonstrate how a sea sponge species that colonizes the moorings of the world's largest curtain of hydroacoustic receivers can become a powerful natural collector of fish biodiversity information. By sequencing eDNA extracted from Vazella pourtalesii retrieved from moorings during routine biofouling maintenance, we detected 23 species of marine fish and mammals, compared to 19 and 15 species revealed by surface and bottom water eDNA respectively, and 28 species captured by groundfish survey in the surrounding area, which are more ecologically impactful and involve higher additional costs. Sponge-based species inventories proved at least as informative as those obtained by traditional survey methods, and are also able to detect seasonal differences in fish assemblages. We conclude that opportunistic sampling of marine sponge biofouling may become an efficient way to document and monitor biodiversity in our rapidly changing oceans.

Streamlining large-scale oceanic biomonitoring using passive eDNA samplers integrated into vessel's continuous pump underway seawater systems

Passive samplers are enabling the scaling of environmental DNA (eDNA) biomonitoring in our oceans, by circumventing the time-consuming process of water filtration. Designing a novel passive sampler that does not require extensive sample handling time and can be connected to ocean-going vessels without impeding normal underway activities has potential to rapidly upscale global biomonitoring efforts onboard the world's oceanic fleet. Here, we demonstrate the utility of an artificial sponge sampler connected to the continuous pump underway seawater system as a means to enable oceanic biomonitoring. We compared the performance of this passive sampling protocol with standard water filtration at six locations during a research voyage from New Zealand to Antarctica in early 2023. Eukaryote metabarcoding of the mitochondrial COI gene revealed no significant difference in phylogenetic α-diversity between sampling methods and both methods delineated a progressive reduction in number of Zero-Radius Operational Taxonomic Units (ZOTUs) with increased latitudes. While both sampling methods revealed comparable trends in geographical community compositions, distinct clusters were identified for passive samplers and water filtration at each location. Additionally, greater variability between replicates was observed for passive samplers, resulting in an increased estimated level of replication needed to recover 90 % of the biodiversity. Furthermore, traditional water filtration failed to detect three phyla observed by passive samplers and extrapolation analysis estimated passive samplers recover a larger number of ZOTUs compared to water filtration for all six locations. Our results demonstrate the potential of this passive eDNA sampler protocol and highlight areas where this emerging technology could be improved, thereby enabling large-scale offshore marine eDNA biomonitoring by leveraging the world's oceanic fleet without interfering with onboard activities.

Unlocking Antarctic molecular time-capsules - Recovering historical environmental DNA from museum-preserved sponges

Marine sponges have recently emerged as efficient natural environmental DNA (eDNA) samplers. The ability of sponges to accumulate eDNA provides an exciting opportunity to reconstruct contemporary communities and ecosystems with high temporal and spatial precision. However, the use of historical eDNA, trapped within the vast number of specimens stored in scientific collections, opens up the opportunity to begin to reconstruct the communities and ecosystems of the past. Here, we define the term 'heDNA' to denote the historical environmental DNA that can be obtained from the recent past with high spatial and temporal accuracy. Using a variety of Antarctic sponge specimens stored in an extensive marine invertebrate collection, we were able to recover information on Antarctic fish biodiversity from specimens up to 20 years old. We successfully recovered 64 fish heDNA signals from 27 sponge specimens. Alpha diversity measures did not differ among preservation methods, but sponges stored frozen had a significantly different fish community composition compared to those stored dry or in ethanol. Our results show that we were consistently and reliably able to extract the heDNA trapped within marine sponge specimens, thereby enabling the reconstruction and investigation of communities and ecosystems of the recent past with a spatial and temporal resolution previously unattainable. Future research into heDNA extraction from other preservation methods, as well as the impact of specimen age and collection method, will strengthen and expand the opportunities for this novel resource to access new knowledge on ecological change during the last century.

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.

Multi-method survey rediscovers critically endangered species and strengthens Madagascar's freshwater fish conservation

Freshwater ecosystems are crucial for global biodiversity through supporting plant and animal species and providing essential resources. These ecosystems are under significant threat, particularly in island environments such as Madagascar. Our study focuses on the Amboaboa River basin, home to the rare and endemic fish species Rheocles derhami, last recorded in 2013. To assess the status of this and other threatened fish species including Ptychochromis insolitus and Paretroplus gymnopreopercularis, and to understand freshwater fish population dynamics in this biodiversity hotspot, we conducted a comprehensive survey using both environmental DNA (eDNA) and traditional fishing methods. While traditional methods effectively captured a diverse range of species, including several invasive aliens and the critically endangered endemic species that were the focus of this study, the eDNA approach detected only a fraction of these introduced species and struggled to identify some critically endangered endemics at the species level. This highlights the value of combining methods to enhance species detection. We also investigated the trade-offs associated with multi-primer assessments in eDNA analysis, focusing on three different primer combinations targeting the 12S mitochondrial gene: MiFish, Tele02, and Riaz. Additionally, we provided 12S reference barcodes for 10 species across 9 genera of fishes from the region to increase the coverage of the public reference databases. Overall, our study elucidates the current state of freshwater biodiversity in the Amboaboa River basin and underscores the value of employing multiple methods for effective conservation strategies.

Integrative approach to monitoring metazoan diversity and distribution in two Mediterranean coastal sites through morphology and organismal eDNA

Marine and coastal ecosystems respond to climate change in various ways, such as the type of ecosystem, the species composition, interactions, and distribution, and the effect of local stressors. Metazoan organisms, particularly zooplankton, are important indicators for monitoring the effects climate-driven warming in marine coastal ecosystems over the long term. In this study, the diversity and distribution of zooplankton communities in the Mediterranean Sea (Canyon Dohrn and LTER-MareChiara, Gulf of Naples), a known biodiversity and climate changes hotspot, have been assessed using the integration of morphological-based identification and organismal eDNA. Our findings showed that the multi-locus strategy including the mitochondrial cytochrome c oxidase I (COI) gene and the hypervariable region V9 of the 18S rDNA (18S V9) as targets, improved the taxonomic overview, with the COI gene being more effective than the 18S V9 region for metazoans at the species level. However, appendicularians were detected only with the 18S V9 region. Overall, organismal eDNA is a powerful approach for revealing hidden biodiversity, especially for gelatinous and meroplankton components, and provided new insights into biodiversity patterns. The ecological importance of calanoid copepods in coastal ecosystems has been confirmed. In contrast, the discovery of 13 new metazoan records in the Mediterranean Sea, including two non-indigenous copepod species, suggested that local stressors affect zooplankton community structure and resilience, highlighting the importance of biomonitoring and protecting marine coastal ecosystems.

DNA at the whim of the water: environmental DNA as a course-based undergraduate research experience

Course-based undergraduate research experiences (CUREs) increase student access to high impact research experiences. CUREs engage students in the scientific process by learning how to pose scientific questions, develop hypotheses, and generate data to test them. Environmental DNA (eDNA) is a growing field of research that is gaining accessibility through decreasing laboratory costs, which can make a foundation for multiple, engaging CUREs. This manuscript describes three case studies that used eDNA in an upper year undergraduate course. The first focusses on a systematic literature review of eDNA metadata reporting. The second describes the biomonitoring of brook trout in southern Ontario using eDNA. The third involves eDNA metabarcoding for freshwater fish detection in southern Ontario. Undergraduates were involved in the development and execution of experiments, scientific communication, the peer review process, and fundraising. Through this manuscript, we show the novel application of eDNA CUREs and provide a roadmap for other instructors interested in implementing similar projects. Interviews with seven students from these courses indicate the benefits experienced from taking these courses. We argue that the use of eDNA in CUREs should be expanded in undergraduate biology programs due to the benefit to students and the increasing accessibility of this technology.

Marine eDNA sampling from submerged surfaces with paint rollers

Environmental DNA (eDNA) analyses of species present in marine environments is the most effective biological diversity measurement tool currently available. eDNA sampling methods are an intrinsically important part of the eDNA biodiversity analysis process. Identification and development of eDNA sampling methods that are as rapid, affordable, versatile and practical as possible will improve rates of detection of marine species. Optimal outcomes of eDNA biodiversity surveys come from studies employing high levels of sampling replication, so any methods that make sampling faster and cheaper will improve scientific outcomes. eDNA sampling methods that can be applied more widely will also enable sampling from a greater range of marine surface micro-habitats, resulting in detection of a wider range of organisms. In this study, we compared diversity detection by several methods for sampling eDNA from submerged marine surfaces: polyurethane foam, nylon swabs, microfibre paint rollers, and sediment scoops. All of the methods produced a diverse range of species identifications, with >250 multicellular species represented by eDNA at the study site. We found that widely-available small paint rollers were an effective, readily available and affordable method for sampling eDNA from underwater marine surfaces. This approach enables the sampling of marine eDNA using extended poles, or potentially by remotely operated vehicles, where surface sampling by hand is impractical.

Measuring the state of aquatic environments using eDNA-upscaling spatial resolution of biotic indices

Aquatic macroinvertebrates, including many aquatic insect orders, are a diverse and ecologically relevant organismal group yet they are strongly affected by anthropogenic activities. As many of these taxa are highly sensitive to environmental change, they offer a particularly good early warning system for human-induced change, thus leading to their intense monitoring. In aquatic ecosystems there is a plethora of biotic monitoring or biomonitoring approaches, with more than 300 assessment methods reported for freshwater taxa alone. Ultimately, monitoring of aquatic macroinvertebrates is used to calculate ecological indices describing the state of aquatic systems. Many of the methods and indices used are not only hard to compare, but especially difficult to scale in time and space. Novel DNA-based approaches to measure the state and change of aquatic environments now offer unprecedented opportunities, also for possible integration towards commonly applicable indices. Here, we first give a perspective on DNA-based approaches in the monitoring of aquatic organisms, with a focus on aquatic insects, and how to move beyond traditional point-based biotic indices. Second, we demonstrate a proof-of-concept for spatially upscaling ecological indices based on environmental DNA, demonstrating how integration of these novel molecular approaches with hydrological models allows an accurate evaluation at the catchment scale. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.

Tree of life metabarcoding can serve as a biotic benchmark for shifting baselines in urbanized estuaries

Urbanization of estuaries drastically changed existing shorelines and bathymetric contours, in turn modifying habitat for marine foundational species that host critical biodiversity. And yet we lack approaches to characterize a significant fraction of the biota that inhabit these ecosystems on time scales that align with rates of urbanization. Environmental DNA (or eDNA) metabarcoding that combines multiple assays targeting a broad range of taxonomic groups can provide a solution, but we need to determine whether the biological communities it detects ally with different habitats in these changing aquatic environments. In this study, we tested whether tree of life metabarcoding (ToL-metabarcoding) data extracted from filtered seawater samples correlated with four known geomorphic habitat zones across a heavily urbanized estuary (Sydney Harbour, Australia). Using this method, we substantially expanded our knowledge on the composition and spatial distribution of marine biodiversity across the tree of life in Sydney Harbour, particularly for organisms where existing records are sparse. Excluding terrestrial DNA inputs, we identified significant effects of both distance from the mouth of Sydney Harbour and geomorphic zone on biological community structure in the ToL-metabarcoding dataset (entire community), as well as in each of the taxonomic subgroups that we considered (fish, macroinvertebrates, algae and aquatic plants, bacteria). This effect appeared to be driven by taxa as a collective versus a few individual taxa, with each taxon explaining no more than 0.62% of the variation between geomorphic zones. Similarly, taxonomic richness was significantly higher within geomorphic zones with large sample sizes, but also decreased by 1% with each additional kilometer from the estuary mouth, a result consistent with a reduction in tidal inputs and available habitat in upper catchments. Based on these results, we suggest that ToL-metabarcoding can be used to benchmark biological monitoring in other urbanized estuaries globally, and in Sydney Harbour at future time points based on detection of bioindicators across the tree of life. We also suggest that robust biotic snapshots can be archived following extensive curation of taxonomic assignments that incorporates ecological affinities, supported by records from relevant and regional biodiversity repositories.

An Observatory to monitor range extension of the Mediterranean monk seal based on its eDNA traces: collecting data and delivering results in the "Open Science" era

The monk seal is the most endangered pinniped in the world and the only one found in the Mediterranean, where its distribution and abundance have suffered a drastic decline in the last few decades. Data on its status are scattered due to both its rarity and evasiveness and records are biased towards occasional, mostly coastal encounters. Nowadays, molecular techniques allow us to detect and quantify minute amounts of DNA traces released into the environment (eDNA) by any organism. A species-specific molecular assay is now available for detecting the recent presence of the monk seal in the water column through the analysis of sea-water samples collected from the sea surface. The project "Spot the Monk" uses this non-invasive detection tool to monitor monk seal occurrence in Mediterranean waters by means of eDNA analysis. The simplicity in the acquisition of samples together with the need to collect samples in multiple points simultaneously made the project well suited to the involvement of the general public. Up to today, about 350 samples have been collected and analysed in the central-western Mediterranean by researchers and a multifarious range of citizen scientists - from recreational sailing organisations, both amateur and competitive sportsmen, to fishermen. This work announces the launch of an open-source Observatory (https://www.spot-the-monk-observatory.com/) where the project outcomes are publicly accessible as soon as they are produced. Embracing the principles of Open Science, we believe that such an approach can contribute to filling the knowledge gap about the distribution of this charismatic species in our seas, providing, at the same time, a proof of concept on how data collected by a variety of actors can be returned to the scientific and non-scientific communities in an innovative format for immediate consultation.

Environmental DNA: The next chapter

Molecular tools are an indispensable part of ecology and biodiversity sciences and implemented across all biomes. About a decade ago, the use and implementation of environmental DNA (eDNA) to detect biodiversity signals extracted from environmental samples opened new avenues of research. Initial eDNA research focused on understanding population dynamics of target species. Its scope thereafter broadened, uncovering previously unrecorded biodiversity via metabarcoding in both well-studied and understudied ecosystems across all taxonomic groups. The application of eDNA rapidly became an established part of biodiversity research, and a research field by its own. Here, we revisit key expectations made in a land-mark special issue on eDNA in Molecular Ecology in 2012 to frame the development in six key areas: (1) sample collection, (2) primer development, (3) biomonitoring, (4) quantification, (5) behaviour of DNA in the environment and (6) reference database development. We pinpoint the success of eDNA, yet also discuss shortfalls and expectations not met, highlighting areas of research priority and identify the unexpected developments. In parallel, our retrospective couples a screening of the peer-reviewed literature with a survey of eDNA users including academics, end-users and commercial providers, in which we address the priority areas to focus research efforts to advance the field of eDNA. With the rapid and ever-increasing pace of new technical advances, the future of eDNA looks bright, yet successful applications and best practices must become more interdisciplinary to reach its full potential. Our retrospect gives the tools and expectations towards concretely moving the field forward.

Wastewater sequencing as a powerful tool to reveal SARS-CoV-2 variant introduction and spread in French Guiana, South America

The origin of introduction of a new pathogen in a country, the evolutionary dynamics of an epidemic within a country, and the role of cross-border areas on pathogen dynamics remain complex to disentangle and are often poorly understood. For instance, cross-border areas represent the ideal location for the sharing of viral variants between countries, with international air travel, land travel and waterways playing an important role in the cross-border spread of infectious diseases. Unfortunately, monitoring the point of entry and the evolutionary dynamics of viruses in space and time within local populations remain challenging. Here we tested the efficiency of wastewater-based epidemiology and genotyping in monitoring Covid-19 epidemiology and SARS-CoV-2 variant dynamics in French Guiana, a tropical country located in South America. Our results suggest that wastewater-based epidemiology and genotyping are powerful tools to monitor variant introduction and disease evolution within a tropical country but the inclusion of both clinical and wastewater samples could still improve our understanding of genetic diversity co-circulating. Wastewater sequencing also revealed the cryptic transmission of SARS-CoV-2 variants within the country. Interestingly, we found some amino acid changes specific to the variants co-circulating in French Guiana, suggesting a local evolution of the SARS-CoV-2 variants after their introduction. More importantly, our results showed that the proximity to bordering countries was not the origin of the emergence of the French Guianese B.1.160.25 variant, but rather that this variant emerged from an ancestor B.1.160 variant introduced by European air plane travelers, suggesting thus that air travel remains a significant risk for cross-border spread of infectious diseases. Overall, we suggest that wastewater-based epidemiology and genotyping provides a cost effective and non-invasive approach for pathogen monitoring and an early-warning tool for disease emergence and spread within a tropical country.

Harnessing eDNA metabarcoding to investigate fish community composition and its seasonal changes in the Oslo fjord

In the face of global ecosystem changes driven by anthropogenic activities, effective biomonitoring strategies are crucial for mitigating impacts on vulnerable aquatic habitats. Time series analysis underscores a great significance in understanding the dynamic nature of marine ecosystems, especially amidst climate change disrupting established seasonal patterns. Focusing on Norway's Oslo fjord, our research utilises eDNA-based monitoring for temporal analysis of aquatic biodiversity during a one year period, with bi-monthly sampling along a transect. To increase the robustness of the study, a taxonomic assignment comparing BLAST+ and SINTAX approaches was done. Utilising MiFish and Elas02 primer sets, our study detected 63 unique fish species, including several commercially important species. Our findings reveal a substantial increase in read abundance during specific migratory cycles, highlighting the efficacy of eDNA metabarcoding for fish composition characterization. Seasonal dynamics for certain species exhibit clear patterns, emphasising the method's utility in unravelling ecological complexities. eDNA metabarcoding emerges as a cost-effective tool with considerable potential for fish community monitoring for conservation purposes in dynamic marine environments like the Oslo fjord, contributing valuable insights for informed management strategies.

Optimizing waterborne eDNA capture from waterholes in savanna systems under remote field conditions

Environmental DNA (eDNA) is used for biodiversity assessments in a variety of ecosystems across the globe, whereby different eDNA concentration, preservation and extraction methods can outperform others depending on the sampling conditions and environment. Tropical and subtropical ecosystems in Africa are among the less studied systems concerning eDNA-based monitoring. Waterholes in arid parts of southern Africa represent important agglomeration points for terrestrial mammals, and the eDNA shed into such waterbodies provides a powerful source of information for monitoring mammalian biodiversity in the surrounding area. However, the applied methods for eDNA sampling, preservation and filtering in different freshwater systems vary greatly, and rigorous protocol testing in African freshwater systems is still lacking. This study represents the first attempt to examine variations in eDNA concentration, preservation and extraction methods under remote field conditions using waterborne eDNA in a savanna system. Collected samples were heavily affected by microalgal and bacterial growth, impeding eDNA capture and PCR success. We demonstrate clear effects of the methodological choices, which also depend on the state of eDNA. A preliminary metabarcoding run showed little taxonomic overlap in mammal species detection between two metabarcoding primers tested. We recommend water filtering (using filters with pore sizes >1 μm) over centrifugation for eDNA concentration, Longmire's solution for ambient temperature sample preservation and Qiagen's DNeasy PowerSoil Pro Kit for DNA extraction of these inhibitor-prone samples. Furthermore, at least two independent metabarcoding markers should be utilized in order to maximize species detections in metabarcoding studies.

Predicting downstream transport distance of fish eDNA in lotic environments

Environmental DNA (eDNA) is an effective tool for describing fish biodiversity in lotic environments, but the downstream transport of eDNA released by organisms makes it difficult to interpret species detection at the local scale. In addition to biophysical degradation and exchanges at the water-sediment interface, hydrological conditions control the transport distance. A new eDNA transport model described in this paper considers downstream retention and degradation processes in combination with hydraulic conditions and assumes that the sedimentation rate of very fine particles is a correct estimate of the eDNA deposition rate. Based on meta-analyses of available studies, the particle size distribution of fish eDNA (PSD), the relationship between the sedimentation rate and the size of very fine particles in suspension, and the influence of temperature on the degradation rate of fish eDNA were successively modelled. After combining the results in a mechanistic-based model, the eDNA uptake distances (distance required to retain 63.21% of the eDNA particles in the riverbed) observed in a compilation of previous experimental studies were correctly simulated. eDNA degradation is negligible at low flow and temperature but has a comparable influence to background transfer when hydraulic conditions allow a long uptake distance. The wide prediction intervals associated with the simulations reflect the complexity of the processes acting on eDNA after shedding. This model can be useful for estimating eDNA detection distance downstream from a source point and discussing the possibility of false positive detection in eDNA samples, as shown in an example.

TICI: a taxon-independent community index for eDNA-based ecological health assessment

Global biodiversity is declining at an ever-increasing rate. Yet effective policies to mitigate or reverse these declines require ecosystem condition data that are rarely available. Morphology-based bioassessment methods are difficult to scale, limited in scope, suffer prohibitive costs, require skilled taxonomists, and can be applied inconsistently between practitioners. Environmental DNA (eDNA) metabarcoding offers a powerful, reproducible and scalable solution that can survey across the tree-of-life with relatively low cost and minimal expertise for sample collection. However, there remains a need to condense the complex, multidimensional community information into simple, interpretable metrics of ecological health for environmental management purposes. We developed a riverine taxon-independent community index (TICI) that objectively assigns indicator values to amplicon sequence variants (ASVs), and significantly improves the statistical power and utility of eDNA-based bioassessments. The TICI model training step uses the Chessman iterative learning algorithm to assign health indicator scores to a large number of ASVs that are commonly encountered across a wide geographic range. New sites can then be evaluated for ecological health by averaging the indicator value of the ASVs present at the site. We trained a TICI model on an eDNA dataset from 53 well-studied riverine monitoring sites across New Zealand, each sampled with a high level of biological replication (n = 16). Eight short-amplicon metabarcoding assays were used to generate data from a broad taxonomic range, including bacteria, microeukaryotes, fungi, plants, and animals. Site-specific TICI scores were strongly correlated with historical stream condition scores from macroinvertebrate assessments (macroinvertebrate community index or MCI; R2 = 0.82), and TICI variation between sample replicates was minimal (CV = 0.013). Taken together, this demonstrates the potential for taxon-independent eDNA analysis to provide a reliable, robust and low-cost assessment of ecological health that is accessible to environmental managers, decision makers, and the wider community.

Detecting kelp-forest associated metazoan biodiversity with eDNA metabarcoding

Environmental DNA (eDNA) metabarcoding is a promising tool for monitoring marine biodiversity, but remains underutilised in Africa. In this study, we evaluated the ability of aquatic eDNA metabarcoding as a tool for detecting biodiversity associated with a South African kelp forest, an ecosystem that harbours high diversity of species, many of which are endemic, but are also sensitive to changing environmental conditions and anthropogenic pressures. Using fine-scale spatial (1 m and 8 m) and temporal (every four hours for 24 h) sampling of aquatic environmental DNA and targeting two gene regions (mtDNA COI and 12S rRNA), metabarcoding detected 880 OTUs representing 75 families in the broader metazoan community with 44 OTUs representing 24 fish families. We show extensive variability in the eDNA signal across space and time and did not recover significant spatio-temporal structure in OTU richness and community assemblages. Metabarcoding detected a broad range of taxonomic groups, including arthropods, ascidians, cnidarians, echinoderms, ctenophores, molluscs, polychaetes, ichthyofauna and sponges, as well as Placozoa, previously not reported from South Africa. Fewer than 3% of OTUs could be identified to species level using available databases (COI = 19 OTUs, 12S = 11 OTUs). Our study emphasizes that kelp-forest associated biodiversity in South Africa is understudied, but that with careful consideration for sampling design in combination with increased barcoding efforts and the construction of regional databases, eDNA metabarcoding will become a powerful biomonitoring tool of kelp-forest associated biodiversity.

Critical considerations for communicating environmental DNA science

The economic and methodological efficiencies of environmental DNA (eDNA) based survey approaches provide an unprecedented opportunity to assess and monitor aquatic environments. However, instances of inadequate communication from the scientific community about confidence levels, knowledge gaps, reliability, and appropriate parameters of eDNA-based methods have hindered their uptake in environmental monitoring programs and, in some cases, has created misperceptions or doubts in the management community. To help remedy this situation, scientists convened a session at the Second National Marine eDNA Workshop to discuss strategies for improving communications with managers. These include articulating the readiness of different eDNA applications, highlighting the strengths and limitations of eDNA tools for various applications or use cases, communicating uncertainties associated with specified uses transparently, and avoiding the exaggeration of exploratory and preliminary findings. Several key messages regarding implementation, limitations, and relationship to existing methods were prioritized. To be inclusive of the diverse managers, practitioners, and researchers, we and the other workshop participants propose the development of communication workflow plans, using RACI (Responsible, Accountable, Consulted, Informed) charts to clarify the roles of all pertinent individuals and parties and to minimize the chance for miscommunications. We also propose developing decision support tools such as Structured Decision-Making (SDM) to help balance the benefits of eDNA sampling with the inherent uncertainty, and developing an eDNA readiness scale to articulate the technological readiness of eDNA approaches for specific applications. These strategies will increase clarity and consistency regarding our understanding of the utility of eDNA-based methods, improve transparency, foster a common vision for confidently applying eDNA approaches, and enhance their benefit to the monitoring and assessment community.

Using eDNA to survey amphibians: Methods, applications, and challenges

In recent years, environmental DNA (eDNA) has received attention from biologists due to its sensitivity, convenience, labor and material efficiency, and lack of damage to organisms. The extensive application of eDNA has opened avenues for the monitoring and biodiversity assessment of amphibians, which are frequently small and difficult to observe in the field, in areas such as biodiversity survey assessment and detection of specific, rare and threatened, or alien invasive species. However, the accuracy of eDNA can be influenced by factors such as ambient temperature, pH, and false positives or false negatives, which makes eDNA an adjunctive tool rather than a replacement for traditional surveys. This review provides a concise overview of the eDNA method and its workflow, summarizes the differences between applying eDNA for detecting amphibians and other organisms, reviews the research progress in eDNA technology for amphibian monitoring, identifies factors influencing detection efficiency, and discusses the challenges and prospects of eDNA. It aims to serve as a reference for future research on the application of eDNA in amphibian detection.

rCRUX: A Rapid and Versatile Tool for Generating Metabarcoding Reference libraries in R

The sequencing revolution requires accurate taxonomic classification of DNA sequences. Key to making accurate taxonomic assignments are curated, comprehensive reference barcode databases. However, the generation and curation of such databases has remained challenging given the large and continuously growing volumes of both DNA sequence data and novel reference barcode targets. Monitoring and research applications require a greater diversity of specialized gene regions and targeted taxa then are currently curated by professional staff. Thus there is a growing need for an easy to implement computational tool that can generate comprehensive metabarcoding reference libraries for any bespoke locus. We address this need by reimagining CRUX from the Anacapa Toolkit and present the rCRUX package in R which, like it's predecessor, relies on sequence homology and PCR primer compatibility instead of keyword-searches to avoid limitations of user-defined metadata. The typical workflow involves searching for plausible seed amplicons (get_seeds_local() or get_seeds_remote()) by simulating in silico PCR to acquire a set of sequences analogous to PCR products containing a user-defined set of primer sequences. Next, these seeds are used to iteratively blast search seed sequences against a local copy of the National Center for Biotechnology Information (NCBI) formatted nt database using a taxonomic-rank based stratified random sampling approach ( blast_seeds() ). This results in a comprehensive set of sequence matches. This database is dereplicated and cleaned (derep_and_clean_db()) by identifying identical reference sequences and collapsing the taxonomic path to the lowest taxonomic agreement across all matching reads. This results in a curated, comprehensive database of primer-specific reference barcode sequences from NCBI. Databases can then be compared (compare_db()) to determine read and taxonomic overlap. We demonstrate that rCRUX provides more comprehensive reference databases for the MiFish Universal Teleost 12S, Taberlet trnl, fungal ITS, and Leray CO1 loci than CRABS, MetaCurator, RESCRIPt, and ecoPCR reference databases. We then further demonstrate the utility of rCRUX by generating 24 reference databases for 20 metabarcoding loci, many of which lack dedicated reference database curation efforts. The rCRUX package provides a simple to use tool for the generation of curated, comprehensive reference databases for user-defined loci, facilitating accurate and effective taxonomic classification of metabarcoding and DNA sequence efforts broadly.

Groundwater is a hidden global keystone ecosystem

Groundwater is a vital ecosystem of the global water cycle, hosting unique biodiversity and providing essential services to societies. Despite being the largest unfrozen freshwater resource, in a period of depletion by extraction and pollution, groundwater environments have been repeatedly overlooked in global biodiversity conservation agendas. Disregarding the importance of groundwater as an ecosystem ignores its critical role in preserving surface biomes. To foster timely global conservation of groundwater, we propose elevating the concept of keystone species into the realm of ecosystems, claiming groundwater as a keystone ecosystem that influences the integrity of many dependent ecosystems. Our global analysis shows that over half of land surface areas (52.6%) has a medium-to-high interaction with groundwater, reaching up to 74.9% when deserts and high mountains are excluded. We postulate that the intrinsic transboundary features of groundwater are critical for shifting perspectives towards more holistic approaches in aquatic ecology and beyond. Furthermore, we propose eight key themes to develop a science-policy integrated groundwater conservation agenda. Given ecosystems above and below the ground intersect at many levels, considering groundwater as an essential component of planetary health is pivotal to reduce biodiversity loss and buffer against climate change.

New insights into the on-site monitoring of probiotics eDNA using biosensing technology for heat-stress relieving in coral reefs

Coral probiotics can improve the tolerance of corals to heat stress, thus mitigating the process of coral thermal bleaching. Sensitive and specific detection of coral probiotics at low abundances is highly desirable but remains challenging, especially for rapid and on-site detection of coral probiotics. Since the electrochemical biosensor has been recently used in the field of environmental DNA (eDNA) detection, herein, an efficient electrochemical biosensor was developed based on CoS2/CoSe2-NC HNCs electrode material with a specific DNA probe for the C. marina detection. After optimization, the lower limit of detection (LOD) values of such biosensors for the target DNA and genomic DNA were 1.58 fM and 6.5 pM, respectively. On this basis, a portable device was constructed for the practical detection of C. marina eDNA, and its reliability and accuracy were verified by comparison with the ddPCR method (P > 0.05). For each analysis, the average cost was only ∼ $1.08 and could be completed within 100 min with reliable sensitivity and specificity. Overall, the biosensor could reflect the protective effect of probiotics on coral heat stress, and the proposed technique will put new insights into the rapid and on-site detection of coral probiotics to assist corals against global warming.

Validating post-enrichment steps in environmental RNA analysis for improving its availability from water samples

Environmental RNA (eRNA) analysis is expected to inclusively provide the physiological information of a population and community without individual sampling, having the potential for the improved monitoring of biodiversity and ecosystem function. Protocol development for maximizing eRNA availability is crucial to interpret its detection and quantification results with high accuracy and reliability, but the methodological validation and improvement of eRNA collection and processing methods are scarce. In this study, the technical steps after eRNA extraction, including genomic DNA (gDNA) removal and reverse transcription, were focused on and their performances were compared by zebrafish (Danio rerio) aquarium experiments. Additionally, this study also focused on the eRNA quantification variabilities between replicates and compared them between the PCR and sample levels. Results showed that (i) there was a trade-off between gDNA removal approaches and eRNA yields and an excess gDNA removal could lead to the false-negative eRNA detection, (ii) the use of the gene-specific primers for reverse transcription could increase the eRNA yields for multiple mitochondrial and nuclear genes compared with the random hexamer primers, and (iii) the coefficient of variation (CV) values of eRNA quantifications between PCR replicates were substantially lower for those between samples. Including the study, further knowledge for the sensitive and precise detection of macro-organismal eRNA should be needed for increasing the reliability and robustness of eRNA-based biomonitoring.