The ecology of environmental DNA and implications for conservation genetics

Environmental DNA is more effective than hand sorting in evaluating earthworm biodiversity recovery under regenerative agriculture

Regenerating soil biodiversity can help to reverse declines in soil health caused by cultivation and continuous arable cropping, and support sustainable food production and agro-ecosystem services. Earthworms are key functional components of soil biodiversity, with different ecological categories and species delivering specific beneficial soil functions. Conventional monitoring by hand-sorting from soil pits is highly labour intensive, can reliably identify only adults to species, and may under-record anecics (deep-burrowers). Here, we compare soil environmental DNA (eDNA) metabarcoding using two different primer sets and next-generation sequencing, with earthworm hand-sorting from standard soil-pits, in four conventionally managed arable fields into which strips of grass-clover ley had been introduced three years earlier. Earthworm populations had been recorded by hand-sorting in the previous three years and our goal was to assess the effects of the three-year leys compared to arable cropping using both hand-sorting and eDNA. The eDNA method found the same eight earthworm species as hand-sorting, but had greater power for detecting anecic earthworms and quantifying local species richness. Earthworm abundance increased by over 55% into the third year of the leys, surpassing abundances in adjacent permanent grasslands, helping to explain the observed soil health regeneration. Both overall relative read abundances and site occupancy proportions of earthworm eDNA were found to have potential as proxies for abundance, and the performance of each of these measures and the implications for further work are discussed. We show that eDNA can improve earthworm diversity monitoring and recommend its wider use both to better understand soil management effects on earthworm populations, and to guide agricultural policy and practice decisions affecting soil health.

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

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

Navigating Past Oceans: Comparing Metabarcoding and Metagenomics of Marine Ancient Sediment Environmental DNA

The condition of ancient marine ecosystems provides context for contemporary biodiversity changes in human-impacted oceans. Sequencing sedimentary ancient DNA (sedaDNA) is an emerging method for generating high-resolution biodiversity time-series data, offering insights into past ecosystems. However, few studies directly compare the two predominant sedaDNA sequencing approaches: metabarcoding and shotgun-metagenomics, and it remains unclear if these methodological differences affect diversity metrics. We compared these methods using sedaDNA from an archived marine sediment record sampled in the Skagerrak, North Sea, spanning almost 8000 years. We performed metabarcoding of a eukaryotic 18S rRNA region (V9) and sequenced 153-229 million metagenomic reads per sample. Our results show limited overlap between metabarcoding and metagenomics, with only three metazoan genera detected by both methods. For overlapping taxa, metabarcoding detections became inconsistent for samples older than 2000 years, while metagenomics detected taxa throughout the time series. We observed divergent patterns of alpha diversity, with metagenomics indicating decreased richness towards the present and metabarcoding showing an increase. However, beta diversity patterns were similar between methods, with discrepancies only in metazoan data comparisons. Our findings demonstrate that the choice of sequencing method significantly impacts detected biodiversity in an ancient marine sediment record. While we stress that studies with limited variation in DNA degradation among samples may not be strongly affected, researchers should exonerate methodological explanations for observed biodiversity changes in marine sediment cores, particularly when considering alpha diversity, before making ecological interpretations.

Assessing the impact of three fish drugs on tetrahymenosis in Fish using environmental DNA techniques

Tetrahymenosis has resulted in significant economic losses for the ornamental fish farming industry in Harbin. While previous studies have investigated the outbreaks and histopathology of Tetrahymena pyriformis in fish, there is still a lack of study on the use of the application of fish drugs for prevention and treatment. This experiment aims to evaluate the efficacy of three fish drugs (copper, Nitrofural, Methylene Blue) in combating tetrahymenosis in goldfish. We utilized eDNA-based 16 s rDNA gene amplifiers sequencing and qPCR technologies to extract environmental samples and conducted high-throughput sequencing to assess the interaction between the diversity of T. pyriformis and other microorganisms in aquaculture water following the introduction of various fish medications. Our findings revealed that among the three fish drugs test, Nitrofural displayed the most promising effects, followed by Methylene Blue, while copper sulfate proved to be the least effective. Consequently, our study provides a treatment plan for addressing tetrahymenosis in goldfish and offers insights into the pathological changes in goldfish tissues following the onset of the disease.

The Use of Environmental DNA as Preliminary Description of Invertebrate Diversity in Three Sicilian Lakes

Freshwater ecosystems are among the most severely affected environments by species loss caused by climate change and intense anthropogenic pressure. To preserve biodiversity, biomonitoring plays a key role by providing reliable data on biological diversity and ecological status. Environmental DNA (eDNA) metabarcoding has emerged as a powerful and non-invasive alternative to traditional morphology-based sampling and identification methods. This study represents the first application of eDNA analysis to assess the invertebrate communities in three Sicilian Lakes: Poma, Piana degli Albanesi and Scanzano. Water samples were collected at two points in each lake and after filtration with nitrocellulose membranes, eDNA was extracted and metabarcoding analysis was performed. A total of 27 species were identified, belonging to Phyla of Annelida, Arthropoda and Rotifera. Notably, the analysis revealed the presence of alien species (Daphnia parvula and Acanthocyclops americanus), a dangerous species associated with the transmission of viral diseases (Culex pipiens), and potential new records for Sicily (Stylaria lacustris, Platypalpus exilis, Pammene aurana, Limnephilus rhombicus). These results provide a preliminary snapshot of invertebrate biodiversity at these sites, demonstrating how eDNA has the potential to complement, but not replace, traditional methods, contributing to the assessment of ecosystem status.

Insights into the representativeness of biodiversity assessment in large reservoir through eDNA metabarcoding

Monitoring biodiversity on a large scale, such as in hydropower reservoirs, poses scientific challenges. Conventional methods such as passive fishing gear are prone to various biases, while the utilization of environmental DNA (eDNA) metabarcoding has been restricted. Most eDNA studies have primarily focused on replicating results from traditional methods, which themselves have limitations regarding representativeness and bias. In our study, we employed eDNA metabarcoding with three markers (12SrRNA, COI, and 16SrRNA) to evaluate the biodiversity of an 800 km2 reservoir. We utilized hydrodynamic modeling to determine water flow velocity and the water renewal ratio throughout the study area. Additionally, we conducted statistical comparisons-rarefaction curves and multivariate methods-among samples as an alternative approach to assess biodiversity representation. The eDNA identified taxa previously documented in the reservoir by traditional monitoring methods, as well as revealed 29 -nine fishes and 20 non-fish-previously unreported species. These results highlight the robustness of eDNA as a biodiversity monitoring technique. Our findings also indicated that by randomly sampling 30% of the original number of samples, we could effectively capture the same biodiversity. This approach enabled us to comprehend the reservoir's biodiversity profile and propose a straightforward, cost-effective monitoring protocol for the future based on eDNA.

Environmental DNA and Hydroacoustic Surveys for Monitoring the Spread of the Invasive European Catfish (Silurus glanis Linnaeus, 1758) in the Guadalquivir River Basin, Spain

The European catfish (Silurus glanis Linnaeus, 1758) was introduced into the Ebro Basin in Spain in 1974 for recreational fishing. Since then, the species has spread throughout the country's river basins, reaching the Iznájar Reservoir (Guadalquivir River Basin) in 2011. This area is of great ecological and economic relevance, especially as it includes the Doñana National Park, one of the most important nature reserves in Europe. Recently, the presence of catfish has been reported in the lower reaches of the river. In this work, we used non-invasive vertical and horizontal hydroacoustic surveys and environmental DNA river sampling to unravel the actual distribution and dispersal pattern of the species in the lower Guadalquivir River. The hydroacoustic profiles and the species-specific detections by real-time PCR (qPCR) and droplet digital PCR (ddPCR) showed that these non-invasive methods allow the detection and quantification of catfish and provide valuable information on the species' presence. We have confirmed the presence of catfish in most of the study area, including downstream areas of the Guadalquivir Basin. The results suggest the possibility of other isolated introductions and/or human-mediated movements of specimens, and imply that a coordinated catfish prevention and mitigation strategy is therefore urgently needed.

Experimental assessment of Acanthopagrus schlegelii biomass based on environmental DNA technology

The Environmental DNA (eDNA) technology has attracted significant attention due to its convenience and high sensitivity. However, the variations of eDNA across diverse environments and biological species remain complex. Therefore, a detailed exploration of the release patterns of eDNA for specific species under different environments is crucial for the scientific utilization of eDNA detection techniques. This study conducted an experiment involving the aquaculture of Acanthopagrus schlegelii to explore the release and degradation mechanisms of eDNA. It also analyzed the influence of salinity and biomass on the concentration of eDNA in water. Through model simulations, the variation patterns of A. schlegelii eDNA were revealed. The study achieved three key findings: (1) The research on the release and degradation mechanisms of A. schlegelii eDNA indicated that the Generalized Additive Model (GAM) effectively fits the variation patterns of eDNA concentration. The peak concentration of eDNA released by A. schlegelii was observed at 42 h, and the degradation process exhibited two stages: rapid and slow degradation, with a negative correlation between eDNA concentration and time. (2) By investigating the relationship between the concentration of A. schlegelii eDNA and biomass, it was demonstrated that Linear Models (LM) effectively captured this relationship, indicating a correlation between eDNA concentration and biomass. (3) The detection of A. schlegelii eDNA concentration under different salinity conditions revealed that the GAM model better reflected the relationship between eDNA and salinity, exhibiting a negative correlation. As salinity increased, the concentration of eDNA decreased. This study lays a foundation for future assessments of the A. schlegelii biomass in natural waters using eDNA quantitative detection techniques, and provides relevant references for quantitative eDNA detection techniques in other marine fish species.

Environmental RNA metabarcoding for ballast water microbial diversity: Minimizing false positives

While maritime transport boosts global trade by shipping bulk goods, it raises concerns about the spread of harmful bacteria via ballast water. Moreover, the dark and cold environments of ballast tanks often harbor extracellular DNA from dead organisms, leading to false positives in traditional environmental DNA (eDNA) metabarcoding analyses. Here, we alternatively employed environmental RNA (eRNA) metabarcoding to assess its potential for reducing false positive in ballast water monitoring. We collected eDNA and eRNA in parallel from ballast water before and after disinfection in three vessels. High-throughput sequencing of the 16S rRNA V4-V5 regions and cDNA counterparts was conducted to compare bacterial community composition. Our findings showed that over 80 % of the top 150 abundant amplicon sequence variants (ASVs) were detected by both eRNA and eDNA metabarcoding. Samples sequenced separately using DNA and RNA consistently clustered together, indicating similar community recovery efficacy. However, 42 % of ASVs were detected exclusively in DNA, resulting in significantly higher bacterial diversity compared to RNA, which suggests false positives in the DNA method. In treated samples with higher dead cell counts, the RNA method showed significantly lower bacterial diversity, indicating its effectiveness in detecting live bacteria. In summary, eRNA metabarcoding offers comparable recovery efficiency while maintaining a lower false-positive rate than eDNA metabarcoding.

Angling and trolling for eDNA: A novel and effective approach for passive eDNA capture in natural waters

The conventional water filtration approach for collecting environmental DNA (eDNA) has critical limitations. The collection of eDNA via passive eDNA samplers (PEDS) has been proposed as an alternative to the water filtration method. Here, we developed a novel and rapid eDNA sampling approach and evaluated the extent to which this method enhances eDNA sampling efficiency. We drove boats along transects across nine large natural lakes and deployed PEDS either by briefly submerging them at each sampling location ("angling") or towing them in the water ("trolling"). One liter of water was also collected at each location and processed via the filtration method. Fish biodiversity was determined by metabarcoding analysis of eDNA extracts. Despite a short total submersion time (42-66 min of "angling") and substantially fewer samples (PEDS: 3-6 samples; filtration: 21-33 samples per lake), PEDS generally detected more fish species in each lake as well as per sample compared with filtration. Detection probabilities for fish species were significantly higher for PEDS compared with the filtration method. PEDS are also superior to the filtration method since sampling requires less equipment, labor, time, and costs. Our innovative sampling strategy is thus effective and could be used for the eDNA biomonitoring of large water systems.

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.

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

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

Taxonomic and abundance biases affect the record of marine eukaryotic plankton communities in sediment DNA archives

Environmental DNA (eDNA) preserved in marine sediments is increasingly being used to study past ecosystems. However, little is known about how accurately marine biodiversity is recorded in sediment eDNA archives, especially planktonic taxa. Here, we address this question by comparing eukaryotic diversity in 273 eDNA samples from three water depths and the surface sediments of 24 stations in the Nordic Seas. Analysis of 18S-V9 metabarcoding data reveals distinct eukaryotic assemblages between water and sediment eDNA. Only 40% of Amplicon Sequence Variants (ASVs) detected in water were also found in sediment eDNA. Remarkably, the ASVs shared between water and sediment accounted for 80% of total sequence reads suggesting that a large amount of plankton DNA is transported to the seafloor, predominantly from abundant phytoplankton taxa. However, not all plankton taxa were equally archived on the seafloor. The plankton DNA deposited in the sediments was dominated by diatoms and showed an underrepresentation of certain nano- and picoplankton taxa (Picozoa or Prymnesiophyceae). Our study offers the first insights into the patterns of plankton diversity recorded in sediment in relation to seasonality and spatial variability of environmental conditions in the Nordic Seas. Our results suggest that the genetic composition and structure of the plankton community vary considerably throughout the water column and differ from what accumulates in the sediment. Hence, the interpretation of sedimentary eDNA archives should take into account potential taxonomic and abundance biases when reconstructing past changes in marine biodiversity.

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

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

eDNA-Based Survey of Fish Species in Water Bodies Using Loop-Mediated Isothermal Amplification (LAMP) for Application of Developing Automatic Sampler

The monitoring of species in a habitat is important to ensure biological diversity. Environmental DNA (eDNA) can infer the presence-absence of species and enable rapid action to avoid threatening factors in ecosystems in the case of non-indigenous species. Loop-mediated isothermal amplification (LAMP) assays for molecular amplification are rapidly gaining popularity in species detection, but LAMP remains an underutilized method for eDNA-based monitoring practices. The most effective combination for successful species monitoring may be the collection of eDNA or biological traces collected by nanofiltration followed by LAMP-based species detection initiatives. Here, we used LAMP analysis to detect the eDNA of Esox lucius (Northern Pike), Anguilla anguilla (European Eel), and Salmo salar (Atlantic Salmon) in Borre Lake and in the Drammen River. The selection of species is based on the categories of regionally invasive species, endangered species, and species of least concern. Two target genes were considered for each species and LAMP primers were designed. Our study showed that LAMP is an effective tool for discovering specific fish eDNA (analysis) to maintain aquatic ecosystems.

Effect of environmental DNA sampling resolution in detecting nearshore fish biodiversity compared to capture surveys

Sampling and sequencing marine environmental DNA (eDNA) provides a tool that can increase our ability to monitor biodiversity, but movement and mixing of eDNA after release from organisms before collection could affect our inference of species distributions. To assess how conditions at differing spatial scales influence the inferred species richness and compositional turnover, we conducted a paired eDNA metabarcoding and capture (beach seining) survey of fishes on the coast of British Columbia. We found more taxa were typically detected using eDNA compared to beach seining. eDNA identified more taxa with alternative habitat preferences, and this richness difference was greater in areas of high seawater movement, suggesting eDNA has a larger spatial grain influenced by water motion. By contrast, we found that eDNA consistently missed low biomass species present in seining surveys. Spatial turnover of communities surveyed using beach seining differed from that of the eDNA and was better explained by factors that vary at small (10-1000s meters) spatial scales. Specifically, vegetation cover and shoreline exposure explained most species turnover from seining, while eDNA turnover was not explained by those factors and showed a distance decay pattern (a change from 10% to 25% similarity from 2 km to 10 km of distance), suggesting unmeasured environmental variation at larger scales drives its turnover. Our findings indicate that the eDNA sample grain is larger than that of capture surveys. Whereas seining can detect differences in fish distributions at scales of 10s-100s of meters, eDNA can best summarize fish biodiversity at larger scales possibly more relevant to regional biodiversity assessments.

Macrobial airborne environmental DNA analysis: A review of progress, challenges, and recommendations for an emerging application

In the context of looming global biodiversity loss, effective species detection represents a critical concern for ecological research and management. Environmental DNA (eDNA) analysis, which refers to the collection and taxonomic identification of genetic fragments that are shed from an organism into its surroundings, emerged approximately 15 years ago as a sensitive tool for species detection. Today, one of the frontiers of eDNA research concerns the collection and analysis of genetic material in dust and other airborne materials, termed airborne eDNA analysis. As the study of airborne eDNA matures, it is an appropriate time to review the foundational and emerging studies that make up the current literature, and use the reviewed literature to summarize, synthesize, and forecast the major challenges and opportunities for this advancing research front. Specifically, we use the "ecology of eDNA" framework to organize our findings across the origin, state, transport, and fate of airborne genetic materials in the environment, and summarize what is so far known of their interactions with surrounding abiotic and biotic factors, including population and community ecologies and ecosystem processes. Within this work we identify key challenges, opportunities, and future directions associated with the application of airborne eDNA development. Lastly, we discuss the development of applications, partnerships, and messaging that promote development and growth of the field. Together, the broad potential of eDNA analysis and the rate at which research is accelerating in this field suggest that the sky's the limit for airborne eDNA science.

Mosquitoes on a chip-environmental DNA-based detection of invasive mosquito species using high-throughput real-time PCR

The monitoring of mosquitoes is of great importance due to their vector competence for a variety of pathogens, which have the potential to imperil human and animal health. Until now mosquito occurrence data is mainly obtained with conventional monitoring methods including active and passive approaches, which can be time- and cost-consuming. New monitoring methods based on environmental DNA (eDNA) could serve as a fast and robust complementary detection system for mosquitoes. In this pilot study already existing marker systems targeting the three invasive mosquito species Aedes (Ae.) albopictus, Ae. japonicus and Ae. koreicus were used to detect these species from water samples via microfluidic array technology. We compared the performance of the high-throughput real-time PCR (HT-qPCR) system Biomark HD with real-time PCR (qPCR) and also tested the effect of different filter media (Sterivex® 0.45 µm, Nylon 0.22 µm, PES 1.2 µm) on eDNA detectability. By using a universal qPCR protocol and only 6-FAM-MGB probes we successfully transferred these marker systems on the HT-qPCR platform. All tested marker systems detected the target species at most sites, where their presence was previously confirmed. Filter media properties, the final filtration volume and observed qPCR inhibition did not affect measured Ct values via qPCR or HT-qPCR. The Ct values obtained from HT-qPCR were significantly lower as Ct values measured by qPCR due to the previous preamplification step, still these values were highly correlated. Observed incongruities in eDNA detection probability, as manifested by non-reproducible results and false positive detections, could be the result of methodological aspects, such as sensitivity and specificity issues of the used assays, or ecological factors such as varying eDNA release patterns. In this study, we show the suitability of eDNA-based detection of mosquito species from water samples using a microfluidic HT-qPCR platform. HT-qPCR platforms such as Biomark HD allow for massive upscaling of tested species-specific assays and sampling sites with low time- and cost-effort, thus this methodology could serve as basis for large-scale mosquito monitoring attempts. The main goal in the future is to develop a robust (semi)-quantitative microfluidic-based eDNA mosquito chip targeting all haematophagous culicid species occurring in Western Europe. This chip would enable large-scale eDNA-based screenings to assess mosquito diversity, to monitor species with confirmed or suspected vector competence, to assess the invasion progress of invasive mosquito species and could be used in pathogen surveillance, when disease agents are incorporated.

Molecular Detection and Phylogenetic Relationships of Honey Bee-Associated Viruses in Bee Products

In the last few years, the isolation and amplification of DNA or RNA from the environment (eDNA/eRNA) has proven to be an alternative and non-invasive approach for molecular identification of pathogens and pests in beekeeping. We have recently demonstrated that bee pollen and bee bread represent suitable biological material for the molecular identification of viral RNA. In the present study, we extracted total RNA from different bee products (pollen, n = 25; bee bread, n = 17; and royal jelly, n = 15). All the samples were tested for the presence of six of the most common honey bee-associated viruses-Deformed wing virus (DWV), Acute bee paralysis virus (ABPV), Chronic bee paralysis virus (CBPV), Sacbrood virus (SBV), Kashmir bee virus (KBV), and Black queen cell virus (BQCV)-using a reverse transcription polymerase chain reaction (RT-PCR). We successfully detected six records of DWV (10.5%, 6/57), four of ABPV (7.0%, 4/57), three of Israeli acute paralysis virus (IAPV) (5.3%, 3/57), and two of BQCV (3.5%, 2/57). Using ABPV primers, we also successfully detected the presence of IAPV. The obtained viral sequences were analyzed for phylogenetic relationships with the highly similar sequences (megablast) available in the GenBank database. The Bulgarian DWV isolates revealed a high homology level with strains from Syria and Turkey. Moreover, we successfully detected a DWV strain B for the first time in Bulgaria. In contrast to DWV, the ABPV isolates formed a separate clade in the phylogenetic tree. BQCV was closely grouped with Russian isolates, while Bulgarian IAPV formed its own clade and included a strain from China. In conclusion, the present study demonstrated that eRNA can be successfully used for molecular detection of honey bee-associated viruses in bee products. The method can assist the monitoring of the health status of honey bee colonies at the local, regional, and even national levels.

Taxonomic accuracy and complementarity between bulk and eDNA metabarcoding provides an alternative to morphology for biological assessment of freshwater macroinvertebrates

Determining biological status of freshwater ecosystems is critical for ensuring ecosystem health and maintaining associated services to such ecosystems. Freshwater macroinvertebrates respond predictably to environmental disturbances and are widely used in biomonitoring programs. However, many freshwater species are difficult to capture and sort from debris or substrate and morphological identification is challenging, especially larval stages, damaged specimens, or hyperdiverse groups such as Diptera. The advent of high throughput sequencing technologies has enhanced DNA barcoding tools to automatise species identification for whole communities, as metabarcoding is increasingly used to monitor biodiversity. However, recent comparisons have revealed little congruence between morphological and molecular-based identifications. Using broad range universal primers for DNA barcode marker cox1, we compare community composition captured between morphological and molecular-based approaches from different sources - tissue-based (bulk benthic and bulk drift samples) and environmental DNA (eDNA, filtered water) metabarcoding - for samples collected along a gradient of anthropogenic disturbances. For comparability, metabarcoding taxonomic assignments were filtered by taxa included in the standardised national biological metric IBMWP. At the family level, bulk benthic metabarcoding showed the highest congruence with morphology, and the most abundant taxa were captured by all techniques. Richness captured by morphology and bulk benthic metabarcoding decreased along the gradient, whereas richness recorded by eDNA remained constant and increased downstream when sequencing bulk drift. Estimates of biological metrics were higher using molecular than morphological identification. At species level, diversity captured by bulk benthic samples were higher than the other techniques. Importantly, bulk benthic and eDNA metabarcoding captured different and complementary portions of the community - benthic versus water column, respectively - and their combined use is recommended. While bulk benthic metabarcoding can likely replace morphology using similar benthic biological indices, water eDNA will require new metrics because this technique sequences a different portion of the community.

Vertical and horizontal environmental DNA (eDNA) patterns of fish in a shallow and well-mixed North Sea area

The integration of eDNA metabarcoding into monitoring programs provides valuable information about fish community structures. Despite the growing body of evidence supporting the method's effectiveness in distinguishing fine-scale eDNA signals, there is a limited understanding of eDNA distribution in shallow, well-mixed environments, especially related to sampling depth. We analyzed 167 samples collected from the surface and bottom water at 17 locations of the Belgian Part of the North Sea (BPNS), where the deepest sampling point was 31 m, and compared this to beam trawl catch data collected simultaneously at the same locations. eDNA metabarcoding identified an additional 22 species compared to beam trawl catch data. Diversity measures and patterns were very similar between surface and bottom samples and revealed community patterns that were previously described by long-term beam trawl catch data. Surface and bottom samples had 39 fish species in common, while six and eight rare species were uniquely detected, respectively. Our results demonstrate that eDNA metabarcoding effectively identifies spatial community patterns of fishes in the highly dynamic environment of the BPNS regardless of sampling depth. Out of the six most common species tested, eDNA metabarcoding read abundances correlated strongly with catch-based abundance data for one species, but moderately for two others, indicating that inferring fish abundance and biomass via eDNA metabarcoding remains challenging.

Innovative and practical tools for monitoring and assessing biodiversity status and impacts of multiple human pressures in marine systems

Human activities at sea can produce pressures and cumulative effects on ecosystem components that need to be monitored and assessed in a cost-effective manner. Five Horizon European projects have joined forces to collaboratively increase our knowledge and skills to monitor and assess the ocean in an innovative way, assisting managers and policy-makers in taking decisions to maintain sustainable activities at sea. Here, we present and discuss the status of some methods revised during a summer school, aiming at better management of coasts and seas. We include novel methods to monitor the coastal and ocean waters (e.g. environmental DNA, drones, imaging and artificial intelligence, climate modelling and spatial planning) and innovative tools to assess the status (e.g. cumulative impacts assessment, multiple pressures, Nested Environmental status Assessment Tool (NEAT), ecosystem services assessment or a new unifying approach). As a concluding remark, some of the most important challenges ahead are assessing the pros and cons of novel methods, comparing them with benchmark technologies and integrating these into long-standing time series for data continuity. This requires transition periods and careful planning, which can be covered through an intense collaboration of current and future European projects on marine biodiversity and ecosystem health.

The forensic potential of environmental DNA (eDNA) in freshwater wildlife crime investigations: From research to application

Environmental DNA (eDNA) is widely used in biodiversity, conservation, and ecological studies but despite its successes, similar approaches have not yet been regularly applied to assist in wildlife crime investigations. The purpose of this paper is to review current eDNA methods and assess their potential forensic application in freshwater environments considering collection, transport and persistence, analysis, and interpretation, while identifying additional research required to present eDNA evidence in court. An extensive review of the literature suggests that commonly used collection methods can be easily adapted for forensic frameworks providing they address the appropriate investigative questions and take into consideration the uniqueness of the target species, its habitat, and the requirements of the end user. The use of eDNA methods to inform conservationists, monitor biodiversity and impacts of climate change, and detect invasive species and pathogens shows confidence within the scientific community, making the acceptance of these methods by the criminal justice system highly possible. To contextualise the potential application of eDNA on forensic investigations, two test cases are explored involving i) species detection and ii) species localisation. Recommendations for future work within the forensic eDNA discipline include development of suitable standardised collection methods, considered collection strategies, forensically validated assays and publication of procedures and empirical research studies to support implementation within the legal system.

Advances in environmental DNA monitoring: standardization, automation, and emerging technologies in aquatic ecosystems

Environmental DNA (eDNA) monitoring, a rapidly advancing technique for assessing biodiversity and ecosystem health, offers a noninvasive approach for detecting and quantifying species from various environmental samples. In this review, a comprehensive overview of current eDNA collection and detection technologies is provided, emphasizing the necessity for standardization and automation in aquatic ecological monitoring. Furthermore, the intricacies of water bodies, from streams to the deep sea, and the associated challenges they pose for eDNA capture and analysis are explored. The paper delineates three primary eDNA survey methods, namely, bringing back water, bringing back filters, and bringing back data, each with specific advantages and constraints in terms of labor, transport, and data acquisition. Additionally, innovations in eDNA sampling equipment, including autonomous drones, subsurface samplers, and in-situ filtration devices, and their applications in monitoring diverse taxa are discussed. Moreover, recent advancements in species-specific detection and eDNA metabarcoding are addressed, highlighting the integration of novel techniques such as CRISPR-Cas and nanopore sequencing that enable precise and rapid detection of biodiversity. The implications of environmental RNA and epigenetic modifications are considered for future applications in providing nuanced ecological data. Lastly, the review stresses the critical role of standardization and automation in enhancing data consistency and comparability for robust long-term biomonitoring. We propose that the amalgamation of these technologies represents a paradigm shift in ecological monitoring, aligning with the urgent call for biodiversity conservation and sustainable management of aquatic ecosystems.

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'.

Exploring uncharted territory: new frontiers in environmental DNA for tropical fisheries management

Tropical ecosystems host a significant share of global fish diversity contributing substantially to the global fisheries sector. Yet their sustainable management is challenging due to their complexity, diverse life history traits of tropical fishes, and varied fishing techniques involved. Traditional monitoring techniques are often costly, labour-intensive, and/or difficult to apply in inaccessible sites. These limitations call for the adoption of innovative, sensitive, and cost-effective monitoring solutions, especially in a scenario of climate change. Environmental DNA (eDNA) emerges as a potential game changer for biodiversity monitoring and conservation, especially in aquatic ecosystems. However, its utility in tropical settings remains underexplored, primarily due to a series of challenges, including the need for a comprehensive barcode reference library, an understanding of eDNA behaviour in tropical aquatic environments, standardized procedures, and supportive biomonitoring policies. Despite these challenges, the potential of eDNA for sensitive species detection across varied habitats is evident, and its global use is accelerating in biodiversity conservation efforts. This review takes an in-depth look at the current state and prospects of eDNA-based monitoring in tropical fisheries management research. Additionally, a SWOT analysis is used to underscore the opportunities and threats, with the aim of bridging the knowledge gaps and guiding the more extensive and effective use of eDNA-based monitoring in tropical fisheries management. Although the discussion applies worldwide, some specific experiences and insights from Indian tropical fisheries are shared to illustrate the practical application and challenges of employing eDNA in a tropical context.

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.

An integrated spatio-temporal view of riverine biodiversity using environmental DNA metabarcoding

Anthropogenically forced changes in global freshwater biodiversity demand more efficient monitoring approaches. Consequently, environmental DNA (eDNA) analysis is enabling ecosystem-scale biodiversity assessment, yet the appropriate spatio-temporal resolution of robust biodiversity assessment remains ambiguous. Here, using intensive, spatio-temporal eDNA sampling across space (five rivers in Europe and North America, with an upper range of 20-35 km between samples), time (19 timepoints between 2017 and 2018) and environmental conditions (river flow, pH, conductivity, temperature and rainfall), we characterise the resolution at which information on diversity across the animal kingdom can be gathered from rivers using eDNA. In space, beta diversity was mainly dictated by turnover, on a scale of tens of kilometres, highlighting that diversity measures are not confounded by eDNA from upstream. Fish communities showed nested assemblages along some rivers, coinciding with habitat use. Across time, seasonal life history events, including salmon and eel migration, were detected. Finally, effects of environmental conditions were taxon-specific, reflecting habitat filtering of communities rather than effects on DNA molecules. We conclude that riverine eDNA metabarcoding can measure biodiversity at spatio-temporal scales relevant to species and community ecology, demonstrating its utility in delivering insights into river community ecology during a time of environmental change.

Validation and development of eDNA metabarcoding primers for comprehensive assessment of Chinese amphibians

Environmental DNA (eDNA) metabarcoding has emerged as a powerful, non-invasive tool for biodiversity assessments. However, the accuracy and limitations of these assessment techniques are highly dependent on the choice of primer pairs being used. Although several primer sets have been used in eDNA metabarcoding studies of amphibians, there are few comparisons of their reliability and efficiency. Here, we employed lab- and field-tested sets of publicly available and de novo-designed primers in amplifying 83 species of amphibian from all three orders (Anura, Caudata, and Gymnophiona) and 13 families present in China to evaluate the versatility and specificity of these primers sets in amphibian eDNA metabarcoding studies. Three pairs of primers were highly effective, as they could successfully amplify all the major clades of Chinese amphibians in our study. A few non-amphibian taxa were also amplified by these primers, which implies that further optimization of amphibian-specific primers is still needed. The simultaneous use of three primer sets can completely cover all the species obtained by conventional survey methods and has even effectively distinguished quite a number of species (n = 20) in the Wenshan National Nature Reserve. No single primer set could individually detect all of the species from the studied region, indicating that multiple primers might be necessary for a comprehensive survey of Chinese amphibians. Besides, seasonal variations in amphibian species composition were also revealed by eDNA metabarcoding, which was consistent with traditional survey methods. These results indicate that eDNA metabarcoding has the potential to be a powerful tool for studying spatial and temporal community changes in amphibian species richness.

Bioaerosol Sampling Devices and Pretreatment for Bacterial Characterization: Theoretical Differences and a Field Experience in a Wastewater Treatment Plant

Studies on bioaerosol bacterial biodiversity have relevance in both ecological and health contexts, and molecular methods, such as 16S rRNA gene-based barcoded sequencing, provide efficient tools for the analysis of airborne bacterial communities. Standardized methods for sampling and analysis of bioaerosol DNA are lacking, thus hampering the comparison of results from studies implementing different devices and procedures. Three samplers that use gelatin filtration, swirling aerosol collection, and condensation growth tubes for collecting bioaerosol at an aeration tank of a wastewater treatment plant in Trieste (Italy) were used to determine the bacterial biodiversity. Wastewater samples were collected directly from the untreated sewage to obtain a true representation of the microbiological community present in the plant. Different samplers and collection media provide an indication of the different grades of biodiversity, with condensation growth tubes and DNA/RNA shieldTM capturing the richer bacterial genera. Overall, in terms of relative abundance, the air samples have a lower number of bacterial genera (64 OTUs) than the wastewater ones (75 OTUs). Using the metabarcoding approach to aerosol samples, we provide the first preliminary step toward the understanding of a significant diversity between different air sampling systems, enabling the scientific community to orient research towards the most informative sampling strategy.

From DNA to diagnostics: A case study using macroinvertebrate metabarcoding to assess the effectiveness of restoration measures in a Dutch stream

Stream ecosystems are under pressure due to multiple stressors. Restoration measures can halt further degradation and improve their ecological status. However, assessment of the effectiveness of the implemented measures is often insufficient because of logistic and financial constraints. DNA-metabarcoding has been proposed to scale up sample processing, although its application as a diagnostic tool has received less attention. The aim of our study was to evaluate if DNA-metabarcoding of stream macroinvertebrates can be used to compute a stressor-specific index to assess the effectiveness of a stream restoration project. For this purpose, we sampled the upstream, restored, and downstream section of a recently restored lowland stream in the Netherlands. At each site, we applied three different methods of macroinvertebrate identification: morphological identification of bulk samples (morphology), DNA-metabarcoding of the same bulk samples (DNA) and metabarcoding of eDNA extracted from the water (eDNA). First, we compared the community composition identified by each method. The communities identified by morphology and DNA were highly similar, whereas the communities generated by the eDNA differed. Second, we analysed whether the identification methods could be used to assess the effectiveness of the restoration project, focussing on a stressor-specific index for flow as the restoration measures aimed at improving flow conditions. Both the morphology and bulk DNA samples indicated improved flow conditions in the restored section of the stream (i.e., less stress from the reduction or absence of flow than in the unrestored sections). Contrary, the eDNA-water samples did not differentiate the amount of stress throughout the catchment, although applying recent developments in eDNA sampling could lead to more robust results. In conclusion, this study forms proof of concept that DNA from bulk samples can be utilized to assess the effectiveness of restoration measures, showing the added value of this approach for water managers.

Emerging use of air eDNA and its application to forensic investigations - A review

Biological material is routinely collected at crime scenes and from exhibits and is a key type of evidence during criminal investigations. Improvements in DNA technologies allow collection and profiling of trace samples, comprised of few cells, significantly expanding the types of exhibits targeted for DNA analysis to include touched surfaces. However, success rates from trace and touch DNA samples tend to be poorer compared to other biological materials such as blood. Simultaneously, there have been recent advances in the utility of environmental DNA collection (eDNA) in identification and tracking of different biological organisms and species from bacteria to naked mole rats in different environments, including, soil, ice, snow, air and aquatic. This paper examines the emerging methods and research into eDNA collection, with a special emphasis on the potential forensic applications of human DNA collection from air including challenges and further studies required to progress implementation.

Benthic foraminiferal community structure and its response to environmental factors revealed using high-throughput sequencing in the Zhoushan Fishing Ground, East China Sea

Benthic foraminifera are excellent tools for monitoring marine environments and reconstructing paleoenvironments. This study investigated the structure and diversity of benthic foraminiferal communities in 20 superficial sediment samples obtained from the Zhoushan Fishing Ground (ZFG) using high-throughput sequencing based on small subunit ribosomal DNA and RNA amplification. The results revealed Rotaliida as the most dominant group, with spatial heterogeneity in foraminiferal distribution. Total benthic foraminiferal communities exhibited higher species richness and diversity compared to active communities. While heavy metal pollution in the ZFG was moderate, areas with elevated concentrations of heavy metals exhibited low diversity and richness in foraminiferal communities. Total foraminiferal community structure was primarily influenced by factors such as water depth and Hg, Pb, Cd, and Zn levels. Notably, Hg levels emerged as a critical factor impacting the structure and diversity of the active foraminiferal community. The dominant species, Operculina, exhibited tolerance toward heavy metal pollution.

Linkage between spatiotemporal distribution of environmental DNA and phenological activity in an amphidromous fish, ayu Plecoglossus altivelis altivelis, in a river located in its northernmost distributional area

Environmental DNA (eDNA) is a promising tool for the continuous monitoring of fish ecology and diversity. However, its potential for describing the phenological activity of fish has rarely been examined. This study aimed to elucidate a linkage between the spatiotemporal distribution of eDNA and the phenology of an amphidromous fish, ayu Plecoglossus altivelis altivelis, in a river in Hokkaido, Japan, which is its northernmost distributional area. A significant positive correlation between eDNA concentration and catch per unit effort of P. a. altivelis in the river confirmed the use of eDNA as a surrogate for the abundance of P. a. altivelis. eDNA of P. a. altivelis was first detected in late April on a sandy beach adjacent to the river mouth. Subsequent to its first detection at the lowest site in the river in early May, eDNA spread throughout the river, indicating the upstream migration of P. a. altivelis. Spawning activity was also represented by a rapid increase in eDNA concentration and its surge at night in the lowest reaches of the river during September and October. These results suggest that upstream migration and spawning primarily commenced when the water temperature reached 10°C and decreased below 20°C, respectively. This observation is consistent with the behavioral responses observed in P. a. altivelis populations from other regions of Japan. Consequently, this study demonstrated that eDNA distribution was closely linked to the phenological activity of P. a. altivelis and that eDNA is a powerful tool for studying the phenology of migratory fishes.

eDNA Adsorption onto Microplastics: Impacts of Water Chemistry and Polymer Physiochemical Properties

Adsorption of biomacromolecules onto polymer surfaces, including microplastics (MPs), occurs in multiple environmental compartments, forming an ecocorona. Environmental DNA (eDNA), genetic material shed from organisms, can adsorb onto MPs which can potentially either (1) promote long-range transport of antibiotic resistant genes or (2) serve to gain insights into the transport pathways and origins of MPs by analyzing DNA sequences on MPs. However, little is known about the capacity of MPs to adsorb eDNA or the factors that influence sorption, such as polymer and water chemistries. Here we investigated the adsorption of extracellular linear DNA onto a variety of model MP fragments composed of three of the most environmentally prevalent polymers (polyethylene, polyethylene terephthalate, and polystyrene) in their pristine and photochemically weathered states. Batch adsorption experiments in a variety of water chemistries were complemented with nonlinear modeling to quantify the rate and extent of eDNA sorption. Ionic strength was shown to strongly impact DNA adsorption by reducing or inhibiting electrostatic repulsion. Polyethylene terephthalate exhibited the highest adsorption capacity when normalizing for MP specific surface area, likely due to the presence of ester groups. Kinetics experiments showed fast adsorption (majority adsorbed under 30 min) before eventually reaching equilibrium after 1-2 h. Overall, we demonstrated that DNA quickly binds to MPs, with pseudo-first- and -second-order models describing adsorption kinetics and the Freundlich model describing adsorption isotherms most accurately. These insights into DNA sorption onto MPs show that there is potential for MPs to act as vectors for genetic material of interest, especially considering that particle-bound DNA typically persists longer in the environment than dissolved DNA.

DNA Methylation Machinery in Gastropod Mollusks

The role of DNA methylation in mollusks is just beginning to be understood. This review synthesizes current knowledge on this potent molecular hallmark of epigenetic control in gastropods-the largest class of mollusks and ubiquitous inhabitants of diverse habitats. Their DNA methylation machinery shows a high degree of conservation in CG maintenance methylation mechanisms, driven mainly by DNMT1 homologues, and the presence of MBD2 and MBD2/3 proteins as DNA methylation readers. The mosaic-like DNA methylation landscape occurs mainly in a CG context and is primarily confined to gene bodies and housekeeping genes. DNA methylation emerges as a critical regulator of reproduction, development, and adaptation, with tissue-specific patterns being observed in gonadal structures. Its dynamics also serve as an important regulatory mechanism underlying learning and memory processes. DNA methylation can be affected by various environmental stimuli, including as pathogens and abiotic stresses, potentially impacting phenotypic variation and population diversity. Overall, the features of DNA methylation in gastropods are complex, being an essential part of their epigenome. However, comprehensive studies integrating developmental stages, tissues, and environmental conditions, functional annotation of methylated regions, and integrated genomic-epigenomic analyses are lacking. Addressing these knowledge gaps will advance our understanding of gastropod biology, ecology, and evolution.

Larger particle size distribution of environmental RNA compared to environmental DNA: a case study targeting the mitochondrial cytochrome b gene in zebrafish (Danio rerio) using experimental aquariums

Environmental RNA (eRNA) analysis is conventionally expected to infer physiological information about organisms within their ecosystems, whereas environmental DNA (eDNA) analysis only infers their presence and abundance. Despite the promise of eRNA application, basic research on eRNA characteristics and dynamics is limited. The present study conducted aquarium experiments using zebrafish (Danio rerio) to estimate the particle size distribution (PSD) of eRNA in order to better understand the persistence state of eRNA particles. Rearing water samples were sequentially filtered using different pore-size filters, and the resulting size-fractioned mitochondrial cytochrome b (CytB) eDNA and eRNA data were modeled with the Weibull complementary cumulative distribution function (CCDF) to estimate the parameters characterizing the PSDs. It was revealed that the scale parameter (α) was significantly higher (i.e., the mean particle size was larger) for eRNA than eDNA, while the shape parameter (β) was not significantly different between them. This result supports the hypothesis that most eRNA particles are likely in a protected, intra-cellular state, which mitigates eRNA degradation in water. Moreover, these findings also imply the heterogeneous dispersion of eRNA relative to eDNA and suggest an efficient method of eRNA collection using a larger pore-size filter. Further studies on the characteristics and dynamics of eRNA particles should be pursued in the future.

Biodiversity and distribution patterns of blooming jellyfish in the Bohai Sea revealed by eDNA metabarcoding

BACKGROUND

The mass occurrence of scyphozoan jellyfish severely affects marine ecosystems and coastal economies, and the study of blooming jellyfish population dynamics has emerged in response. However, traditional ecological survey methods required for such research have difficulties in detecting cryptic life stages and surveying population dynamics owing to high spatiotemporal variations in their occurrence. The environmental DNA (eDNA) technique is an effective tool for overcoming these limitations.

RESULTS

In this study, we investigated the biodiversity and spatial distribution characteristics of blooming jellyfish in the Bohai Sea of China using an eDNA metabarcoding approach, which covered the surface, middle, and bottom seawater layers, and sediments. Six jellyfish taxa were identified, of which Aurelia coerulea, Nemopilema nomurai, and Cyanea nozakii were the most dominant. These three blooming jellyfish presented a marked vertical distribution pattern in the offshore regions. A. coerulea was mainly distributed in the surface layer, whereas C. nozakii and N. nomurai showed a upper-middle and middle-bottom aggregation, respectively. Horizontally, A. coerulea and C. nozakii were more abundant in the inshore regions, whereas N. nomurai was mainly distributed offshore. Spearman's correlation analysis revealed a strong correlation between the eDNA of the three dominant blooming jellyfish species and temperature, salinity, and nutrients.

CONCLUSIONS

Our study confirms the applicability of the eDNA approach to both biodiverstiy evaluation of blooming jellyfish and investigating their spatial distribution, and it can be used as a supplementary tool to traditional survey methods.

Simplified capture, extraction, and amplification of cellular DNA from water samples

DNA analysis in water samples is attracting attention in various fields. However, conventional methods for DNA analysis require a work-intensive and time-consuming sample pre-treatment. In this study, a simplified pre-treatment method for analyzing DNA in water samples was evaluated. The process consists of filtration, DNA extraction, and amplification, which can be achieved within a short time. In the filtration process, two types of filters, firstly a tissue paper (Kimwipe) and then a glass filter (GF/F), were used in sequence. The first large pore size filter enabled a reduction in filtration time by removing large particulate matter impurities present in river water matrix. Cells spiked into 1 L of river water were recovered at more than 90% within approximately 5 min filtration time. Also, DNA was extracted from the captured cells directly on the surface of the filter in only 5 min. Thus, DNA collection and extraction from a water sample can be completed within about 10 min. Furthermore, PCR amplification was performed directly from DNA-attached filter sections, which greatly reduced the number of required pre-treatment steps. Finally, we succeeded in establishing a simple and fast on-site pre-treatment system by using a hand-driven syringe filtration method. This pre-treatment system is expected to offer the possibility for the future establishment of a rapid and easy DNA analysis method applicable to various types of water samples.

Vertical eDNA distribution of cold-water fishes in response to environmental variables in stratified lake

In summer, the survival zones of cold-water species are predicted to narrow by both increasing water temperatures from the surface and by expanding hypoxic zones from the lake bottom. To examine how the abundance of cold-water fishes changes along environmental gradients, we assessed the vertical environmental DNA (eDNA) distributions of three salmonid species which may have different water temperature tolerances during both stratification and turnover periods using quantitative PCR (qPCR). In addition, we examined on the vertical distribution of diverse fish fauna using an eDNA metabarcoding assay. The results suggested that the kokanee salmon (Oncorhynchus nerka) eDNA were abundant in deep, cold waters. On the other hand, rainbow trout (O. mykiss) eDNA were distributed uniformly throughout the water column, suggesting that they may have high water-temperature tolerance compared with kokanee salmon. The eDNA concentrations of masu salmon (O. masou) were below the detection limit (i.e., <10 copies μL-1) at all stations and depths and hence could not be quantified during stratification. Together with the finding that the eDNA distributions of other prey fish species were also constrained vertically in species-specific ways, our results suggest that climate change will result in substantial changes in the vertical distributions of lake fish species and thus affect their populations and interactions.

How good are global DNA-based environmental surveys for detecting all protist diversity? Arcellinida as an example of biased representation

Metabarcoding approaches targeting microeukaryotes have deeply changed our vision of protist environmental diversity. The public repository EukBank consists of 18S v4 metabarcodes from 12,672 samples worldwide. To estimate how far this database provides a reasonable overview of all eukaryotic diversity, we used Arcellinida (lobose testate amoebae) as a case study. We hypothesised that (1) this approach would allow the discovery of unexpected diversity, but also that (2) some groups would be underrepresented because of primer/sequencing biases. Most of the Arcellinida sequences appeared in freshwater and soil, but their abundance and diversity appeared underrepresented. Moreover, 84% of ASVs belonged to the suborder Phryganellina, a supposedly species-poor clade, whereas the best-documented suborder (Glutinoconcha, 600 described species) was only marginally represented. We explored some possible causes of these biases. Mismatches in the primer-binding site seem to play a minor role. Excessive length of the target region could explain some of these biases, but not all. There must be some other unknown factors involved. Altogether, while metabarcoding based on ribosomal genes remains a good first approach to document microbial eukaryotic clades, alternative approaches based on other genes or sequencing techniques must be considered for an unbiased picture of the diversity of some groups.

Drop it all: extraction-free detection of targeted marine species through optimized direct droplet digital PCR

Molecular biomonitoring programs increasingly use environmental DNA (eDNA) for detecting targeted species such as marine non-indigenous species (NIS) or endangered species. However, the current molecular detection workflow is cumbersome and time-demanding, and thereby can hinder management efforts and restrict the "opportunity window" for rapid management responses. Here, we describe a direct droplet digital PCR (direct-ddPCR) approach to detect species-specific free-floating extra-cellular eDNA (free-eDNA) signals, i.e., detection of species-specific eDNA without the need for filtration or DNA extraction, with seawater samples. This first proof-of-concept aquarium study was conducted with three distinct marine species: the Mediterranean fanworm Sabella spallanzanii, the ascidian clubbed tunicate Styela clava, and the brown bryozoan Bugula neritina to evaluate the detectability of free-eDNA in seawater. The detectability of targeted free-eDNA was assessed by directly analysing aquarium marine water samples using an optimized species-specific ddPCR assay. The results demonstrated the consistent detection of S. spallanzanii and B. neritina free-eDNA when these organisms were present in high abundance. Once organisms were removed, the free-eDNA signal exponentially declined, noting that free-eDNA persisted between 24-72 h. Results indicate that organism biomass, specimen characteristics (e.g., stress and viability), and species-specific biological differences may influence free-eDNA detectability. This study represents the first step in assessing the feasibility of direct-ddPCR technology for the detection of marine species. Our results provide information that could aid in the development of new technology, such as a field development of ddPCR systems, which could allow for automated continuous monitoring of targeted marine species, enabling point-of-need detection and rapid management responses.

Revolutionizing early-stage green tide monitoring: eDNA metabarcoding insights into Ulva prolifera and microecology in the South Yellow Sea

Green tides, characterized by excessive Ulva prolifera blooms, pose significant ecological and economic challenges, especially in the South Yellow Sea. We successfully employed 18S environmental DNA (eDNA) metabarcoding to detect Ulva prolifera micropropagules, confirming the technique's reliability and introducing a rapid green tide monitoring method. Our investigation revealed notable disparities in the eukaryotic microbial community composition within Ulva prolifera habitats across different regions. Particularly, during the early stages of the South Yellow Sea green tide outbreak, potential interactions emerged between Ulva prolifera micropropagules and certain previously undocumented microorganisms from neighboring waters. These findings enhance our comprehension of early-stage green tide ecosystem dynamics, underscoring the value of merging advanced molecular techniques with conventional ecological methods to gain a comprehensive understanding of the impact of green tide on the local ecosystem. Overall, our study advances our understanding of green tide dynamics, offering novel avenues for control, ecological restoration, and essential scientific support for sustainable marine conservation and management.

Spider webs capture environmental DNA from terrestrial vertebrates

Environmental DNA holds significant promise as a non-invasive tool for tracking terrestrial biodiversity. However, in non-homogenous terrestrial environments, the continual exploration of new substrates is crucial. Here we test the hypothesis that spider webs can act as passive biofilters, capturing eDNA from vertebrates present in the local environment. Using a metabarcoding approach, we detected vertebrate eDNA from all analyzed spider webs (N = 49). Spider webs obtained from an Australian woodland locality yielded vertebrate eDNA from 32 different species, including native mammals and birds. In contrast, webs from Perth Zoo, less than 50 km away, yielded eDNA from 61 different vertebrates and produced a highly distinct species composition, largely reflecting exotic species hosted in the zoo. We show that higher animal biomass and proximity to animal enclosures increased eDNA detection probability in the zoo. Our results indicate a tremendous potential for using spider webs as a cost-effective means to monitor terrestrial vertebrates.

Environmental DNA reveals temporal variation in mesophotic reefs of the Humboldt upwelling ecosystems of central Chile: Toward a baseline for biodiversity monitoring of unexplored marine habitats

Temperate mesophotic reef ecosystems (TMREs) are among the least known marine habitats. Information on their diversity and ecology is geographically and temporally scarce, especially in highly productive large upwelling ecosystems. Lack of information remains an obstacle to understanding the importance of TMREs as habitats, biodiversity reservoirs and their connections with better-studied shallow reefs. Here, we use environmental DNA (eDNA) from water samples to characterize the community composition of TMREs on the central Chilean coast, generating the first baseline for monitoring the biodiversity of these habitats. We analyzed samples from two depths (30 and 60 m) over four seasons (spring, summer, autumn, and winter) and at two locations approximately 16 km apart. We used a panel of three metabarcodes, two that target all eukaryotes (18S rRNA and mitochondrial COI) and one specifically targeting fishes (16S rRNA). All panels combined encompassed eDNA assigned to 42 phyla, 90 classes, 237 orders, and 402 families. The highest family richness was found for the phyla Arthropoda, Bacillariophyta, and Chordata. Overall, family richness was similar between depths but decreased during summer, a pattern consistent at both locations. Our results indicate that the structure (composition) of the mesophotic communities varied predominantly with seasons. We analyzed further the better-resolved fish assemblage and compared eDNA with other visual methods at the same locations and depths. We recovered eDNA from 19 genera of fish, six of these have also been observed on towed underwater videos, while 13 were unique to eDNA. We discuss the potential drivers of seasonal differences in community composition and richness. Our results suggest that eDNA can provide valuable insights for monitoring TMRE communities but highlight the necessity of completing reference DNA databases available for this region.

Distribution of Culex pipiens life stages across urban green and grey spaces in Leiden, The Netherlands

BACKGROUND

There is an urgent need for cities to become more climate resilient; one of the key strategies is to include more green spaces in the urban environment. Currently, there is a worry that increasing green spaces might increase mosquito nuisance. As such, this study explores a comprehensive understanding of how mosquitoes utilise contrasting grey and green habitats at different life stages and which environmental factors could drive these distributions.

METHODS

We used a setup of six paired locations, park (green) vs. residential (grey) areas in a single model city (Leiden, The Netherlands), where we sampled the abundances of different mosquito life stages (eggs, larvae, adults) and the local microclimatic conditions. In this study, we focused on Culex pipiens s.l., which is the most common and abundant mosquito species in The Netherlands.

RESULTS

Our results show that while Cx. pipiens ovipositioning rates (number of egg rafts) and larval life stages were far more abundant in residential areas, adults were more abundant in parks. These results coincide with differences in the number of suitable larval habitats (higher in residential areas) and differences in microclimatic conditions (more amenable in parks).

CONCLUSIONS

These findings suggest that Cx. pipiens dispersal may be considerably more important than previously thought, where adult Cx. pipiens seek out the most suitable habitat for survival and breeding success. Our findings can inform more targeted and efficient strategies to mitigate and reduce mosquito nuisance while urban green spaces are increased, which make cities more climate resilient.

eDNA-based monitoring of Batrachochytrium dendrobatidis and Batrachochytrium salamandrivorans with ddPCR in Luxembourg ponds: taking signals below the Limit of Detection (LOD) into account

BACKGROUND

Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans (Bsal) are two pathogenic fungi that are a significant threat to amphibian communities worldwide. European populations are strongly impacted and the monitoring of the presence and spread of these pathogens is crucial for efficient decision-making in conservation management.

RESULTS

Here we proposed an environmental DNA (eDNA) monitoring of these two pathogenic agents through droplet digital PCR (ddPCR) based on water samples from 24 ponds in Luxembourg. In addition, amphibians were swabbed in eight of the targeted ponds in order to compare the two approaches at site-level detection. This study allowed the development of a new method taking below-Limit of Detection (LOD) results into account thanks to the statistical comparison of the frequencies of false positives in no template controls (NTC) and below-LOD results in technical replicates. In the eDNA-based approach, the use of this method led to an increase in Bd and Bsal detection of 28 and 50% respectively. In swabbing, this resulted in 8% more positive results for Bd. In some samples, the use of technical replicates allowed to recover above-LOD signals and increase Bd detection by 35 and 33% respectively for eDNA and swabbing, and Bsal detection by 25% for eDNA.

CONCLUSIONS

These results confirmed the usefulness of technical replicates to overcome high levels of stochasticity in very low concentration samples even for a highly sensitive technique such as ddPCR. In addition, it showed that below-LOD signals could be consistently recovered and the corresponding amplification events assigned either to positive or negative detection via the method developed here. This methodology might be particularly worth pursuing in pathogenic agents' detection as false negatives could have important adverse consequences. In total, 15 ponds were found positive for Bd and four for Bsal. This study reports the first record of Bsal in Luxembourg.

Evaluating environmental DNA detection of a rare fish in turbid water using field and experimental approaches

Detection sensitivity of aquatic species using environmental DNA (eDNA) generally decreases in turbid water but is poorly characterized. In this study, eDNA detection targeted delta smelt (Hypomesus transpacificus), a critically endangered estuarine fish associated with turbid water. eDNA sampling in the field was first paired with a trawl survey. Species-specific detection using a Taqman qPCR assay showed concordance between the methods, but a weak eDNA signal. Informed by the results of field sampling, an experiment was designed to assess how turbidity and filtration methods influence detection of a rare target. Water from non-turbid (5 NTU) and turbid (50 NTU) estuarine sites was spiked with small volumes (0.5 and 1 mL) of water from a delta smelt tank to generate low eDNA concentrations. Samples were filtered using four filter types: cartridge filters (pore size 0.45 μm) and 47 mm filters (glass fiber, pore size 1.6 μm and polycarbonate, pore sizes 5 and 10 μm). Prefiltration was also tested as an addition to the filtration protocol for turbid water samples. eDNA copy numbers were analyzed using a censored data method for qPCR data. The assay limits and lack of PCR inhibition indicated an optimized assay. Glass fiber filters yielded the highest detection rates and eDNA copies in non-turbid and turbid water. Prefiltration improved detection in turbid water only when used with cartridge and polycarbonate filters. Statistical analysis identified turbidity as a significant effect on detection probability and eDNA copies detected; filter type and an interaction between filter type and prefilter were significant effects on eDNA copies detected, suggesting that particulate-filter interactions can affect detection sensitivity. Pilot experiments and transparent criteria for positive detection could improve eDNA surveys of rare species in turbid environments.

Monitoring of multiple fish species by quantitative environmental DNA metabarcoding surveys over two summer seasons

Periodic monitoring can provide important information for the protection of endangered fish, sustainable use of fishery resources and management of alien species. Previous studies have attempted to monitor fish using non-invasive environmental DNA (eDNA) technology, generally employing quantitative PCR to quantify the eDNA concentration. However, the throughput was limited. High-throughput metabarcoding technology can detect the DNA of multiple species simultaneously in a single experiment but does not provide sufficient quantification. In this study, we applied a quantitative metabarcoding approach to simultaneously quantify the eDNA concentration of an entire fish assemblage in a small reservoir over two summer seasons. Traditional surveys were also conducted to investigate the individuals of fish. The eDNA concentrations were quantified using quantitative metabarcoding, and the fish species detected using this approach were highly consistent with the results of traditional fish monitoring. A significant positive relationship was observed between the eDNA concentration and fish species abundance. Seasonal changes in fish community structure were estimated using eDNA concentrations, which may reveal the activity seasons of different fish. The eDNA concentrations of different fish species peaked at different water temperatures, reflecting the differential responses of fish species to this environmental factor. Finally, by detecting outlier eDNA concentrations, the spawning activities of 13 fish species were estimated, 12 of which were roughly consistent with the current knowledge of fish spawning periods. These results indicate that quantitative eDNA metabarcoding with dozens of sampling times is useful for the simultaneous ecological monitoring of multiple fish species.

Non-invasive real-time genomic monitoring of the critically endangered kākāpō

We used non-invasive real-time genomic approaches to monitor one of the last surviving populations of the critically endangered kākāpō (Strigops habroptilus). We first established an environmental DNA metabarcoding protocol to identify the distribution of kākāpō and other vertebrate species in a highly localized manner using soil samples. Harnessing real-time nanopore sequencing and the high-quality kākāpō reference genome, we then extracted species-specific DNA from soil. We combined long read-based haplotype phasing with known individual genomic variation in the kākāpō population to identify the presence of individuals, and confirmed these genomically informed predictions through detailed metadata on kākāpō distributions. This study shows that individual identification is feasible through nanopore sequencing of environmental DNA, with important implications for future efforts in the application of genomics to the conservation of rare species, potentially expanding the application of real-time environmental DNA research from monitoring species distribution to inferring fitness parameters such as genomic diversity and inbreeding.