eDNA Samples Research Articles

The Foster method: rapid and non-invasive detection of clinically significant American Foulbrood disease levels using eDNA sampling and a dual-target qPCR assay, with its potential for other hive pathogens

Clinical signs of American Foulbrood (AFB) can be difficult to diagnose and thus disease is often missed and leads to further spread. Diagnosis is centred on the beekeeper’s skill in recognising clinical symptoms – a highly subjective and time-consuming activity. Previous testing methods have relied on sampling that necessitates dismantling the hive and/or requires multiple visits to retrieve passive samples. The Foster method is a novel environmental DNA (eDNA) sampling method using colony entrance swabs together with a dual-target qPCR for Paenibacillus larvae: the causative bacteria of AFB disease. The quantification data generated can be used to detect hives with clinically significant infections, even before visual symptoms are apparent. The testing method shows promise for other bee pathogens and incursion pests.

Spatial analysis of demersal food webs through integration of eDNA metabarcoding with fishing activities

The evaluation of the status of marine communities, and especially the monitoring of those heavily exploited by fisheries, is a key, challenging task in marine sciences. Fishing activities are a major source of disruption to marine food webs, both directly, by selectively removing components at specific trophic levels (TL), and indirectly, by altering habitats and production cycles. Food web analysis can be very useful in the context of an Ecosystem Approach to Fisheries, but food web reconstructions demand large and expensive data sets, which are typically available only for a small fraction of marine ecosystems. Recently, new technologies have been developed to easily, quickly and cost-effectively collect environmental DNA (eDNA) during fishing activities. By generating large, multi-marker metabarcoding data from eDNA samples obtained from commercial trawlers, it is possible to produce exhaustive taxonomic inventories for the exploited ecosystems, which are suitable for food-web reconstructions. Here, we integrate and re-analyse the data of a recent study in which the α diversity was investigated using the eDNA opportunistically collected during fishing operations. Indeed, we collect highly resolved information on species feeding relationships to reconstruct the food webs at different sites in the Strait of Sicily (Mediterranean Sea) from eDNA and catch data. After observing that the trophic networks obtained from eDNA metabarcoding data are more consistent with the available knowledge, a set of food web indicators (species richness, number of links, direct connectance and generality) is computed and analysed to unravel differences in food webs structure through different areas (spatial variations). Species richness, number of links and generality (positively) and direct connectance (negatively) are correlated with increasing distance from the coast and fishing effort intensity. The combined effects of environmental gradients and fishing effort on food web structure at different study sites are then examined and modelled. Taken together, these findings indicate the suitability of eDNA metabarcoding to assist and food web analysis, obtain several food web-related ecological indicators, and tease out the effect of fishing intensity from the environmental gradients of marine ecosystems.

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.

Environmental DNA captures diurnal fluctuations of surface eukaryotes on a tropical coral reef

AbstractEnvironmental DNA (eDNA) metabarcoding has been widely employed to describe biological communities in the marine environment and to compare the richness and diversity of sites across large spatial scales. However, fine‐scale temporal eDNA dynamics are poorly understood and the time of eDNA sample collection is rarely reported in publications. Here, we collected surface eDNA samples every 6 h, for 3 days, at two coral reef sites to assess fine‐scale changes in the eukaryotic communities detected. Distinct eukaryotic communities were detected at two sites within the same lagoon. Sampling time was found to have a significant effect on ESV and class richness, both peaking during the 1 p.m. sampling time at both sites. Sampling time also had a significant effect on the detection of eukaryotic taxa, with relative read frequency showing clear diurnal patterns in line with the migratory behavior of planktonic groups. Other groups of organisms showed considerable variation in read frequency, highlighting the dynamic nature of marine eukaryotic communities and potential stochasticity of eDNA detections. For eukaryotic communities, eDNA samples can provide a “snapshot” of contemporary biodiversity and provide information on short‐term community dynamics on hyperdiverse coral reefs. However, our findings add to growing evidence that sampling time should be clearly considered and reported in marine eDNA studies and that multiple samples from the same site are needed to facilitate more robust comparisons across sites.

EDNA metabarcoding reveals riverine fish community structure and climate associations in northeastern Canada

AbstractClimate change is a critical threat to northern freshwater ecosystems, yet many remote areas are data deficient in terms of biodiversity information. Generating community composition data through collection of environmental DNA (eDNA) is less labor‐intensive than traditional sampling methods and is being increasingly used in areas that have been historically difficult to sample such as northern freshwater habitats. Here, we employed eDNA metabarcoding using three mitochondrial markers at 174 coastal river sites, sampled over three years (2019–2021) across a broad region in northeastern North America, Newfoundland and Labrador. We characterized current riverine fish community composition, compared it to traditional sampling records, and quantified the influence of climate on variation in fish community composition. The analysis detected 33 fish species across the region (1–13 per location), including three non‐native species, as well as several new possible range expansions. Variance partitioning with redundancy analysis indicated ~56% of the variation in community composition could be explained by spatial and climate factors (~21% and ~7%, respectively, with an additional ~28% shared). A temporal comparison across a subset of locations with both eDNA and historical records (1965–1985) revealed that more species were detected on average with eDNA sampling, and that sampling method explained a small portion of the variation (~4%) in comparison with space (~10%) and climate (~7%). Ultimately, this work is the most complete survey of freshwater and diadromous fishes present in Newfoundland and Labrador to date, highlights new detections of non‐native species including previously unknown diversity for the region, and provides future direction for the application of eDNA analysis in northern riverine habitats.

Exploring freshwater snail diversity and community structure in china's largest lake using eDNA technology

Freshwater snails are a crucial benthic animal group that plays a pivotal role in algae regulation and ecosystems while serving as intermediate hosts for certain parasites. Environmental DNA (eDNA) technology offers numerous advantages for biodiversity assessment. However, the utilization of eDNA techniques for freshwater snail monitoring remains limited. In this study, we screened primers for assessing freshwater snail diversity using eDNA technology and constructed a comprehensive database for Poyang Lake. Using eDNA technology, a total of 21 species of snails were detected in Poyang Lake, while traditional methods detected only 11 species. Notably, all species collected by traditional methods were also detected by eDNA technology. Additionally, environmental DNA methods detected the invasive snail Pomacea canaliculata, while traditional methods did not. In this study, eleven intermediate host snail species for parasitic disease were identified using eDNA methods, while six were detected through traditional sampling techniques. The eDNA metabarcoding analysis showed that the α and β diversity levels of snails in Poyang Lake did not vary significantly, indicating that results obtained by eDNA sampling are not influenced by the season in which samples were collected. The correlation analysis between the community structure of snails and environmental factors in Poyang Lake revealed significant impacts of total nitrogen, chlorophyll a, water depth, and water temperature on the snail community structure. These results confirm that eDNA technology can be exploited to monitor freshwater snail biodiversity.

Putting eDNA to the test: A field comparison of eDNA metabarcoding to established protocols for assessing biodiversity in Missouri's Ozark Highland streams

AbstractAquatic biodiversity monitoring to inform conservation and management efforts in‐stream systems has increasingly begun to incorporate environmental DNA (eDNA)‐based sampling methods. We conducted a comparison of eDNA metabarcoding to a traditional protocol of combined seining and electrofishing methods to assess fish biodiversity of wadeable stream sites in six separate drainages in the Ozark Highlands of Missouri (USA). The study further focused on the headwaters of the Meramec River, which included 11 sites and seasonal sampling (summer and winter). We compared estimates of diversity across sampling methods, assessed the influences of water flow (depth, velocity, and discharge) and season, and tested the effects of sampling method and site locality on fish assemblage composition. eDNA sampling detected approximately double the number of species compared to traditional methods, providing higher diversity estimates while maintaining the relative ranking of sites. eDNA detection probabilities were positively associated with stream depth and velocity and were generally higher in summer than in winter but not for all species. Estimated species richness was positively associated with discharge for both methods but the relationship was stronger with eDNA sampling. Assemblage differences between tributary and mainstem sites were attributable to a small number of species that were found predominantly in one stream size category or the other, indicating that eDNA was sensitive to within‐drainage assemblage structure relationships. We highlight improved species detection, a more comprehensive understanding of assemblage structural dynamics, and the potential ability to integrate data across sampling methods as important benefits that encourage the use of eDNA metabarcoding as a primary collection method in future stream biodiversity assessment and monitoring programs.

CRISPR‐based environmental DNA detection for a rare endangered estuarine species

AbstractEnvironmental DNA (eDNA) methods complement traditional aquatic monitoring surveys and are especially advantageous for rare and listed species to detect spatial and temporal distribution patterns. However, improvements in ease of use and portability could increase the utility of eDNA methods, leading to more widespread application, including expanding its role in management decision‐making processes. We describe the development of an eDNA detection assay for delta smelt (Hypomesus transpacificus), an endangered fish in the San Francisco Estuary, using SHERLOCK (Specific High‐Sensitivity Enzymatic Reporter Unlocking). SHERLOCK is a clustered regularly interspaced short palindromic repeats (CRISPR)‐based diagnostic tool with the ability to detect species‐specific genetic variants, making it ideal for genetic‐based taxonomic identification of any organism. Because of its high sensitivity and specificity, SHERLOCK is adaptable to eDNA detection in water samples. Here, we describe adaptation of a delta smelt SHERLOCK assay for use with estuarine water eDNA samples. This version of the assay exhibits increased sensitivity compared to the original delta smelt SHERLOCK protocol (new limit of detection approximately three copies per reaction compared to ~300 in original assay) and successfully detected delta smelt eDNA in both experimental and natural contexts. Overall, our results demonstrate that SHERLOCK eDNA detection offers managers an alternative, isothermal methodology, and highlights some challenges for detection of rare, endangered species at low abundance.

Enumeration potential of environmental DNA for Pacific salmon stock assessments

AbstractThe field of environmental DNA (eDNA) has advanced over the past decade, with multiple approaches available for a variety of sampling media and species. While using eDNA for the purpose of simply detecting species is becoming a routine process, the utility of eDNA to estimate species abundance is not well understood. Here, we quantify salmon environmental DNA upstream of a fish counting fence along with river velocity, and together, use these values to determine the correlation between the number of salmon passing by the fish fence daily with daily eDNA rates in water before, during, and after the salmon spawning season for four Pacific salmonids (Oncorhynchus gorbuscha, O. kisutch, O. tshawytscha, and O. nerka; pink, coho, chinook, and sockeye, respectively). Throughout the spawning season, approximately 182,000 salmon were counted passing through the fence, of which >98% were pink salmon. Pink salmon exhibited strong correlation between human counts (effect size = 0.65, SE = 0.040) to eDNA rates in the present study and exhibited day‐to‐day variation and a unimodal profile rising and falling with human fish counts. However, the salmon species observed in much lower numbers exhibited a much weaker correlation with eDNA levels higher during the pre‐migratory period than during the migratory period for sockeye, coho, and chinook. Thus, for salmon spawning runs with less than ~1000 adults and daily counts of less than ~100, the juvenile and/or prior seasons eDNA signal appears to be indistinguishable from the adult spawning eDNA signal in our river system. However, for the large pink salmon run, eDNA rates appeared to reflect a local signal of salmon in space and time, essentially tracking these fish within days of passing through the eDNA sampling site.

Environmental DNA reveals patterns of biological invasion in an inland sea.

Non-native species have the potential to cause ecological and economic harm to coastal and estuarine ecosystems. Understanding which habitat types are most vulnerable to biological invasions, where invasions originate, and the vectors by which they arrive can help direct limited resources to prevent or mitigate ecological and socio-economic harm. Information about the occurrence of non-native species can help guide interventions at all stages of invasion, from first introduction, to naturalization and invasion. However, monitoring at relevant scales requires considerable investment of time, resources, and taxonomic expertise. Environmental DNA (eDNA) metabarcoding methods sample coastal ecosystems at broad spatial and temporal scales to augment established monitoring methods. We use COI mtDNA eDNA sampling to survey a diverse assemblage of species across distinct habitats in the Salish Sea in Washington State, USA, and classify each as non-native, native, or indeterminate in origin. The non-native species detected include both well-documented invaders and species not previously reported within the Salish Sea. We find a non-native assemblage dominated by shellfish and algae with native ranges in the temperate western Pacific, and find more-retentive estuarine habitats to be invaded at far higher levels than better-flushed rocky shores. Furthermore, we find an increase in invasion level with higher water temperatures in spring and summer across habitat types. This analysis contributes to a growing understanding of the biotic and abiotic factors that influence invasion level, and underscores the utility of eDNA surveys to monitor biological invasions and to better understand the factors that drive these invasions.

Environmental DNA reflects spatial distribution of a rare turtle in a lentic wetland assisted colonization site

AbstractConservation translocations require robust post‐release monitoring to evaluate their success, which can be challenging to implement and maintain. Monitoring techniques that can account for the dispersal and cryptic nature of translocated animals are necessary to provide critical information on persistence and distribution. In this study, we developed a highly sensitive environmental DNA (eDNA) assay specific to the critically endangered western swamp turtle (Pseudemydura umbrina), a species currently undergoing trials of assisted colonization. Actively filtering sufficient volumes of water in lentic systems is difficult due to high concentrations of clogging particulates, therefore we assessed the viability of passive sampling in a controlled environment by submerging filter membranes and directly extracting DNA. Active sampling detected P. umbrina with a 97.6% detection rate, whereas passive sampling resulted in an 8.3% detection rate. We then used a fine‐scale eDNA sampling design and radio‐tracked translocated P. umbrina at the assisted colonization wetland to investigate eDNA dispersal and spatial monitoring resolution. We detected P. umbrina at 42% (7/17) of eDNA sample sites, and the probability of a positive eDNA detection was negatively associated with the distance of P. umbrina from the sampling site, indicating limited eDNA dispersal from the source. Systems with low natural mixing and limited eDNA dispersal provide an opportunity for high‐resolution spatial and temporal monitoring via targeted eDNA approaches. This is beneficial for monitoring rare species in these systems, as such high‐resolution results can provide insights into species presence, distribution, and microhabitat use.

Individual genotypes from environmental DNA: Fingerprinting snow tracks of three large carnivore species.

Continued advancements in environmental DNA (eDNA) research have made it possible to access intraspecific variation from eDNA samples, opening new opportunities to expand non-invasive genetic studies of wildlife populations. However, the use of eDNA samples for individual genotyping, as typically performed in non-invasive genetics, still remains elusive. We present successful individual genotyping of eDNA obtained from snow tracks of three large carnivores: brown bear (Ursus arctos), European lynx (Lynx lynx) and wolf (Canis lupus). DNA was extracted using a protocol for isolating water eDNA and genotyped using amplicon sequencing of short tandem repeats (STR), and for brown bear a sex marker, on a high-throughput sequencing platform. Individual genotypes were obtained for all species, but genotyping performance differed among samples and species. The proportion of samples genotyped to individuals was higher for brown bear (5/7) and wolf (7/10) than for lynx (4/9), and locus genotyping success was greater for brown bear (0.88). The sex marker was typed in six out of seven brown bear samples. Results for three species show that reliable individual genotyping, including sex identification, is now possible from eDNA in snow tracks, underlining its vast potential to complement the non-invasive genetic methods used for wildlife. To fully leverage the application of snow track eDNA, improved understanding of the ideal species- and site-specific sampling conditions, as well as laboratory methods promoting genotyping success, is needed. This will also inform efforts to retrieve and type nuclear DNA from other eDNA samples, thereby advancing eDNA-based individual and population-level studies.

English

Abstract For the stone crayfish, a threatened species listed in the Habitats Directive in Annex II and V, three monitoring methods were evaluated: hand capture by day, hand capture by night and eDNA sampling respectively. The lack of a standardized sampling method in Austria and the simultaneous obligation to monitor and report on the status of protected species requires therefore an evaluation of the different techniques. However, data show that day sampling massively favored the observation of juveniles whereas night sampling obtained higher shares of adults and males. Moreover, organic layer primarily determines the applicability of hand capturing methods. If the share of organic layer exceeded 40%, night sampling was more effective. In brooks with low amount of organic layer, no notable divergences were found. eDNA sampling provided reliable presence-absence data but cannot fully replace hand capturing methods. Data indicate that eDNA detectability depends probably on the discharge level. Below 1.5 L·s-1 eDNA detection failed but provided reliable results in sections with a higher discharge regime. In summary, all three methods are appropriate for crayfish surveillance programs, but must be applied according to the sampling design appropriate for the research questions and with an awareness of their strengths and weaknesses.

Assessing mesopelagic fish diversity and diel vertical migration with environmental DNA

Mesopelagic fishes are an important component of the world’s oceans in terms of their abundance, biomass, and ecosystem function. These fishes are important contributors to the biological carbon pump via their feeding and behaviors, whereby they facilitate the transfer of carbon from shallow waters to the deep sea. Several species undertake diel vertical migration, feeding in shallower waters at night and moving to deeper waters during the day. This process actively expedites the downward flux of carbon. However, carbon budgets and climate models require accurate information regarding the depth distributions and migration patterns of these fishes, and environmental DNA (eDNA) analyses can provide this information. Here, we utilize eDNA approaches, generating taxonomically-informative COI and 12S reference barcodes for 80 species of mesopelagic fishes, which can be used for species-level identification of eDNA sequences. Using these, along with a publicly available barcodes database, we compare results from eDNA analysis with traditional net sampling, and explore the ability of eDNA techniques to detect diel vertical migration in fishes from samples collected in Northwest Atlantic Slope Water. We found that eDNA and net samples often resulted in different species identifications, demonstrating that eDNA can detect species that would otherwise be missed with traditional methods. In our eDNA samples, we also detected more species (12) in our shallowest depth category (0 - 100 m) from night samples than from day samples (3). This is consistent with increased diversity in shallow waters at night due to diel vertical migration. Based on the variability observed in sample duplicates, we suggest that future mesopelagic eDNA studies incorporate larger sample volumes and scaled-up sampling efforts. We also note the potential applications of eDNA analysis in addressing ecological questions related to predator-prey relationships identification of foraging hotspots, and carbon flow through the ocean’s midwaters.

Detection of African swine fever virus and wild boar eDNA in soil and turbid water samples: towards environmental surveillance

Since 2007, an ongoing African swine fever (ASF) pandemic has significantly impacted Eurasia. Extensive field evidence and modeling confirm the central role of wild boar in ASF epidemiology. To effectively control and eradicate the infection, rapid detection of the ASF virus (ASFV) is crucial for prompt intervention in areas of recent viral introduction or ongoing outbreaks. Environmental DNA (eDNA) is a cost-effective and non-invasive technique that has shown promising results in monitoring animal species and their pathogens and has the potential to be used for wildlife disease surveillance. In this study, we designed and evaluated an eDNA sampling method for highly turbid water and soil samples to detect ASFV and wild boar (Sus scrofa) DNA as a control using qPCR while ensuring biosafety measures and evaluating ASF epidemiology. To validate our method, we obtained samples from La Mandria Regional Park (LMRP) in northwestern Italy, an area free of ASFV, and spiked them in a laboratory setting with an ASFV’s synthetic DNA template. Our findings highlight the potential of eDNA monitoring as a reliable, rapid, and safe method for early detection of ASFV from soil and turbid water samples.

Conventional net tow versus environmental DNA for metabarcoding-based analysis of plankton-environment interactions in polluted aquatic ecosystems

Human societal development has caused rapid degradation of freshwater ecosystems, resulting in significant biodiversity decline globally. The conservation of aquatic ecosystems, particularly the management of biodiversity in urban areas, has become an increasingly significant issue for ensuring the sustainability of these ecosystems. The restoration of degraded aquatic ecosystems relies on a comprehensive understanding of the interactions between biological communities and multiple stressors derived from human activities. Environmental DNA (eDNA)-based methods have emerged as effective tools for dissecting complex community-environment interactions. Nevertheless, potential causes for technical disparities and conclusions drawn from conventional sampling versus eDNA-based methods remain inadequately evaluated. In this study, we conducted a comprehensive survey of plankton communities along the environmental gradient of the North Canal River in Northern China to assess causes and consequences for any disparities between conventional plankton net tow and eDNA sampling for metabarcoding-based analysis of plankton-environment interactions. Our findings demonstrated that eDNA-metabarcoding was effective for characterizing both biodiversity and geographical distribution. Both methods exhibited general consistency in elucidating community structure and identifying the key environmental factors influencing geographical distribution of both zooplankton and phytoplankton. As we explored lower taxonomic ranks, we found inconsistent patterns at certain levels (e.g., phylum or order) within some taxa (e.g., Bacillariophyta and Rotifera), even substantial variability for several taxonomic groups (e.g., Euglenozoa and Apicomplexa). The varied environmental prevalence and persistence of eDNA, biological and ecological characteristics of diverse taxa in plankton, and sampling efficiency of both methods likely contributed to the observed disparities. Given its higher biodiversity recovery capacity, efficiency, sampling convenience, and capability to identify influential factors driving the geographical distribution of biodiversity, eDNA-based metabarcoding is recommended for studying plankton-environment interactions, particularly in studies involving a large number of samples at extended geographical scales.

Batrachochytrium dendrobatidis in the Arid and Thermally Extreme Sonoran Desert.

Batrachochytrium dendrobatidis (Bd), the causative agent of the devastating global amphibian disease chytridiomycosis, was not projected to threaten amphibians in hot and arid regions due to its sensitivity to heat and desiccation. However, Bd is being detected more frequently than ever in hot and arid regions of Australia and the USA, challenging our current understanding of the environmental tolerances of the pathogen under natural conditions. We surveyed for Bd in an extremely hot and arid portion of the Sonoran Desert, where the pathogen is not projected to occur, and related presence and prevalence of the pathogen to local environmental conditions. We collected eDNA samples from isolated desert water sites including six tinajas and 13 catchments in June and August of 2020 and swabbed a total of 281 anurans of three species (red-spotted toad Anaxyrus punctatus, Couch's spadefoot Scaphiopus couchii, and the Sonoran Desert toad Incillius alvarius) across five catchments and six tinajas from June to September of 2020. Overall, Bd occurred at 68.4% of sites, despite extreme heat and aridity routinely exceeding tolerances established in laboratory studies. Average summer maximum air and water temperatures were 40.7°C and 30.7°C, respectively, and sites received an average of just 16.9mm of precipitation throughout the summer monsoon season. Prevalence was low (5.7%) across species and life stage. Our results demonstrate that Bd is capable of persisting and infecting amphibians beyond its projected range, indicating a need to account for higher thermal tolerances when quantifying risk of Bd presence and infection.

Performance of environmental DNA metabarcoding to identify and quantify benthic organisms in river ecosystems

Our lack of fundamental knowledge about species occurrence, abundance, distribution, threats, and habitat requirements makes it challenging to conserve biodiversity in the face of rising human pressure. To obtain this information, practical and sensitive methods are required to identify and quantify the occurrence and diversity of rare, cryptic, and elusive species. Environmental DNA (eDNA) is a new technology that can help to discover and quantify biodiversity by addressing some of the limitations of conventional surveys. This study aimed to evaluate the biodiversity and composition of benthic species in the Lower Ciliwung River, Jakarta, Indonesia. The investigation was conducted from upstream to downstream of the river at the three sites during the dry season (July 2022). The DNA read sequences were used to examine the composition, relative abundance, and diversity of the samples. In this study, 1,492,975 initial reads were filtered down to 1,265,307 reads belonging to 27 species of benthic organisms. The taxa identified from the eDNA samples revealed that the most frequently detected species belonged to the family Siboglinidae, order Sabellida, and class Polychaeta. The composition of benthic species discovered in the eDNA water samples varied substantially (p ≤ 0.05). Osedax sp. (class Polychaeta) was the most prevalent species across all locations. The diversity index (H) ranged from low to moderate. eDNA offers potential advantages, but is hampered by DNA degradation, primer sensitivity, and the inability to distinguish between dead and living organisms.

Do aquatic fungal environmental DNA assemblages reflect the surrounding terrestrial sporocarp communities?

The relationship between aquatic environmental DNA (eDNA) assemblages in rivers and the surrounding terrestrial fungal communities has been poorly investigated. Here, we focused on fungi that form soft sporocarps (soft fungi). Two years of sporocarp and aquatic eDNA sampling were conducted at a fragmented forest site, and the soft-fungal assemblages and their temporal dynamics were compared between these two sample types. Aquatic eDNA yielded approximately 1.5 times the operational taxonomic units (OTUs) compared to sporocarps and covered approximately half of the OTUs from sporocarp samples. Lineages that seldom form sporocarps or form inconspicuous sporocarps were successfully detected from aquatic eDNA. Although the OTU composition differed between sporocarp and aquatic eDNA, their temporal dynamics were similar, with both showing a 1-year periodicity. Aquatic eDNA provides insights into fungal diversity and temporal dynamics, but does not fully reflect terrestrial fungi diversity.

Comparing eDNA metabarcoding and conventional pelagic netting to inform biodiversity monitoring in deep ocean environments

Abstract The performance of environmental DNA (eDNA) metabarcoding has rarely been evaluated against conventional sampling methods in deep ocean mesopelagic environments. We assessed the biodiversity patterns generated with eDNA and two co-located conventional methods, oblique midwater trawls and vertical multinets, to compare regional and sample-level diversity. We then assessed the concordance of ecological patterns across water column habitats and evaluated how DNA markers and the level of sampling effort influenced the inferred community. We found eDNA metabarcoding characterized regional diversity well, detecting more taxa while identifying similar ecological patterns as conventional samples. Within sampling locations, eDNA metabarcoding rarely detected taxa across more than one replicate. While more taxa were found in eDNA than oblique midwater trawls within sample stations, fewer were found compared to vertical multinets. Our simulations show greater eDNA sampling effort would improve concordance with conventional methods. We also observed that using taxonomic data from multiple markers generated ecological patterns most similar to those observed with conventional methods. Patterns observed with Exact Sequence Variants were more stable across markers suggesting they are more powerful for detecting change. eDNA metabarcoding is a valuable tool for identifying and monitoring biological hotspots but some methodological adjustments are recommended for deep ocean environments.