Environmental DNA最新文献

Environmental DNA metabarcoding has found application in a range of research areas by simplifying the collection of high-quality field data in a cost-efficient way. In biodiversity studies, environmental DNA metabarcoding of filter feeders like mussels and sponges has recently gained attention. Due to their continuous filtering activity, they accumulate a high amount of genetic signatures from their environment in their tissue. However, it can be difficult to separate genetic signatures of ingested dietary taxa from endobiotic ones originating from parasites or commensals living within the host. This issue parallels a broader problem in environmental DNA-based biodiversity studies: the inability to differentiate between DNA derived from living and dead organisms. A recent attempt to address this problem is using environmental RNA metabarcoding, which is believed to specifically represent the live and active community of an ecosystem. Therefore, we tested whether endobionts, as metabolically active organisms, can be distinguished from dietary taxa, as the presumed dead community, in a parallel RNA and DNA metabarcoding approach. We targeted nuclear 18S rDNA and rRNA to amplify mussel-associated communities (dietary and endobiotic taxa) in samples of Dreissena polymorpha and Mytilus edulis. Our results do not reveal any presence/absence or abundance pattern in the RNA and DNA library that could be used to distinguish dietary from endobiotic signatures. However, we found that over 40% of all genetic signatures were detected by RNA only and that those accounted for < 4% of the total reads. This study thus demonstrates the outstanding sensitivity of RNA metabarcoding in comparison to DNA metabarcoding and suggests that using (environmental) RNA may be a way of capturing a larger proportion of the biodiversity in a given ecosystem.

Freshwater ecosystems are highly biodiverse and provide essential services that support both ecosystem health and economic sustainability. Despite their ecological significance, these ecosystems are disproportionately affected by the global biodiversity crisis. Large river floodplains constitute a fundamental component of freshwater ecosystems, sustaining fish biodiversity, growth, and reproduction. Yet, these floodplains face mounting threats from anthropogenic pressures, including physical modifications and land conversion for agriculture. In this context, there is an urgent need for scalable biomonitoring methods to more effectively assess floodplain ecosystems, which present methodological challenges due to their heterogeneous and dynamic nature. Traditional fish monitoring methods, however, are often invasive, costly, and resource-intensive. In contrast, environmental DNA (eDNA) metabarcoding presents a noninvasive, cost-effective, and scalable alternative. This study compares eDNA metabarcoding and electrofishing for fish community biomonitoring in the floodplain of Lake St. Pierre, the largest floodplain habitat along the St. Lawrence River. We assessed the effectiveness of these methods in monitoring fish community diversity and composition, as well as the influence of floodplain sectors and a gradient of land use from natural wetlands to annual (row) crops. eDNA metabarcoding detected a broader range of species than electrofishing, while both methods consistently identified abundant species. The two methods yielded uncorrelated diversity indices and distinct community compositions. Fish eDNA community composition was strongly associated with floodplain sectors, whereas land use within these sectors had a weaker influence on community diversity and composition. Our findings highlight eDNA metabarcoding as a valuable tool for characterizing broad patterns of fish communities in floodplain ecosystems. This method provides an additional tool to traditional methods for monitoring and conserving threatened floodplain habitats. However, careful consideration of study scale is essential to ensure effective conservation outcomes in these hydrologically dynamic environments.

There is increasing interest in using eDNA for deriving abundance indices for biodiversity monitoring and in support of fisheries management. However, eDNA concentrations are affected by animal behavior, such as diel vertical migration, which has repercussions for designing eDNA sampling strategies for deriving unbiased abundance indices. In this study, we investigated the potential impact of diel vertical migration or other diel activity variations on measured eDNA concentrations for European hake (Merluccius merluccius), European seabass (Dicentrarchus labrax) and blackspot seabream (Pagellus bogaraveo). For hake, in situ eDNA concentrations near the sea floor differed systematically between samples taken before sunrise and after sunset, with the average concentration in morning samples being 24% of the average evening samples. For the two other species, only a weak diel signal in eDNA concentrations was found. Modeling the dispersal and decay of eDNA particles through a Lagrangian approach revealed that eDNA concentrations might decrease to 21%–41% of their initial value during the absence of a species moving entirely up from the sea floor during the night. For M. merluccius, the coherence between observed diel variations in eDNA concentrations near the sea floor and modeling results indicates that diel vertical migration behavior needs to be accounted for when devising eDNA sampling plans. The necessity is less clear for D. labrax and P. bogaraveo.

Although environmental DNA (eDNA) metabarcoding has become a widespread tool used by ecologists to monitor wildlife diversity, there have been few applications of the approach for impact assessments. Here we use eDNA collected in a before–after, control-impact (BACI) experimental design to determine if the noise produced by a large-scale seismic survey modified the fish community on a tropical shelf. We compared abundance estimates of fishes calculated using metrics that included eDNA counts and an eDNA index of relative abundance (a proportional metric) with estimates sampled using baited remote underwater video stations (BRUVS). In total, we detected 102 different genera of fishes using the BRUVS and eDNA datasets combined, although there were more genera observed using BRUVS (n = 71) than with eDNA metabarcoding (n = 57). There was a weak positive relationship between the estimates of relative abundance sampled using BRUVS and eDNA counts when data from common genera were combined, although relationships at the genera level were inconsistent. We found no evidence of major change in the community structure of fishes at the high impact zone of the seismic survey compared to control zones. This result was confirmed using metrics across fish taxa within the BACI framework, suggesting no material impacts to species richness or abundance due to the seismic survey. The power to detect change in the fish community structure and abundance was high (99% probability) for detecting an 80% change in all metrics tested; however, it was considerably lower for detecting smaller changes. Our study highlights the utility and applicability of eDNA metabarcoding to assess point-source impacts on fish communities, particularly when used in parallel with other techniques such as BRUVS.

The symposium “New Approaches to Assessing the Environmental Impact of Chemicals: Bridging Ecotoxicology and Ecology through Environmental DNA/RNA Monitoring” was held on December 2, 2024 during the 7th annual meeting of The eDNA Society in Tsukuba, Japan. With increasing concerns about biodiversity loss and chemical pollution, the symposium aimed to explore innovative methodologies that assess ecological impacts from both chemical and biodiversity perspectives. Presentations addressed various applications of environmental DNA (eDNA) and RNA (eRNA) technologies, including ecological effect assessments of pesticides and metals as well as noninvasive biological stress profiling. This report summarizes the key discussions and insights from the symposium, highlighting the potential of eDNA and eRNA in integrating ecotoxicology with ecological assessments to achieve “Nature Positive” outcomes.

Biological invasions are a leading driver of biodiversity loss and generate significant economic costs, either through direct impact on native ecosystems or through repairs and remediation. Reducing the impact of invasive species is a key aspect of environmental management targets, necessitating early detection and comprehensive distribution data for effective management. Environmental DNA (eDNA) has been demonstrated to enable sensitive monitoring, able to infer the presence of a target organism without physical observations and is particularly advantageous in aquatic environments where invasive species detection is challenging. The Chinese mitten crab (Eriocheir sinensis) is amongst the world's top 100 invasive species and is considered amongst the most damaging invasive species globally, causing significant detriment to riverbanks, fishing practices, and native populations, for example, through generalist predation and as a carrier of crayfish plague. In the UK, its distribution remains poorly understood, with current management relying on reporting of ad hoc sightings. This study developed and validated a species-specific qPCR assay for detecting E. sinensis eDNA against a standardized scale. Primer design utilized genome skimming of E. sinensis and related species collected in the UK, with the final assay achieving a detection limit of 15.6 copies/μL. Field tests in the UK detected target species eDNA at three sites with historical sightings, despite no recent visual records. Overall, the assay shows potential as a tool to support environmental monitoring and offer insights into the distribution, population dynamics, and invasion pathways, to support informed management of E. sinensis.

Filtering water is currently the primary field method used for collecting aquatic environmental DNA (eDNA). One of the drawbacks of filtering is the need to transfer the filter from the filter housing to a preservative-filled container in the field. New products are being developed to avoid this handling step, but comparative studies are needed to ensure that new protocols are transferable within and across eDNA monitoring programs with requisite calibration. To meet this need, we evaluated two filter preservation methods (self-preserving vs. ethanol) of the 5.0 μm polyethersulfone (PES) filter membrane in a field trial typical of stream fisheries eDNA sampling. We compared eDNA detection rates and yield for free-swimming rainbow trout, Oncorhynchus mykiss (Walbaum, 1792), from streams in Washington, United States, and British Columbia, Canada, while accounting for the effects of three environmental covariates: stream discharge, water temperature, and target species abundance. Given these streams were part of an ongoing fisheries eDNA monitoring program, we also compared results against those generated from the original protocol, which used a 0.45-μm cellulose nitrate (CN) filter membrane and ethanol preservative. This secondary comparison allowed us to demonstrate the importance of calibration when changing sampling methods. We found no significant difference in rainbow trout detection rate and limited evidence for a difference in DNA yield between the self-preserving and ethanol-preserved 5.0 μm PES filters. DNA yield was higher in samples collected using the original protocol, possibly because of the smaller pore size or CN membrane material. Detection rate was not influenced by environmental covariates; however, DNA yield increased with increases in trout abundance and declined with increases in discharge and water temperature. These results could help inform fisheries eDNA monitoring programs that are considering switching to self-preserving filters.

In Quebec's James Bay region, mining activities pose significant risks to local aquatic biodiversity due to habitat disturbance and potential contaminant release. This study evaluates the efficacy of environmental DNA (eDNA) for detecting and monitoring fish species in areas affected by mining operations, specifically at an active gold mine and a prospective lithium mine. Over two sampling campaigns, eDNA analyses identified the presence of four target fish species, including species of ecological and cultural significance to the Cree communities. The eDNA method proved to be a sensitive and non-invasive tool, capable of detecting species across large aquatic ecosystems and providing insight into species distribution and abundance in relation to environmental changes. Results indicate that certain species, like lake sturgeon or sauger, may be absent or less detectable in mining-impacted areas, potentially due to habitat fragmentation and altered water quality parameters, including low pH and elevated heavy metal concentrations. Our findings support the integration of eDNA as a valuable monitoring tool for assessing biodiversity and establishing species presence baselines in sensitive ecosystems and highlight its potential for community-led environmental management initiatives in Indigenous territories.

In aquatic ecosystems, environmental DNA (eDNA) can be collected from water samples to produce species inventories. One method for this is passive eDNA sampling, whose development for aquatic biodiversity monitoring is in its early stages. While several materials have been successfully tested for passive eDNA samplers (PEDS), methodological advances are still needed to explore their versatility as a complement to the more common method of active filtration. This study tested for the first time a PEDS using human-crafted material in controlled marine mesocosms (1 m³) containing one species, the European seabass (Dicentrarchus labrax) in different conditions of fish density (1, 5, 10, 100 fish per m³) and exposure times (30 min, 2 h, 8 h, 24 h). We then tested the influence of another source of eDNA on the sampler's performance by introducing another species, the Pacific oyster (Magallana gigas). In addition, we compared the efficacy of the method with active filtration. The PEDS we produced consisted of a small electrospun polyacrylonitrile (PAN) membrane encapsulated in a custom-made 3D-printed frame. Each sampler is low-cost, easy to manipulate, highly replicable, and customizable. A specific quantitative polymerase chain reaction-based assay for the seabass was developed. Results were analyzed with multiscale occupancy modeling and continuous response variable modeling. We found that the PAN-PEDS efficiently collected eDNA in a large volume (1 m³) of renewed water (1 m³/h), with a clear positive effect of high fish density on fish detection. The introduction of oysters did not significantly influence detection. Regarding exposure times, a range of results were obtained that could be attributed to the unreached equilibrium between eDNA shedding and degradation. While active eDNA collection (30 L) outperformed PAN-PEDS, the ongoing development of passive methods can provide new insights in aquatic species monitoring when spatio-temporal eDNA collection is required.

Recording flower-associated taxa can be challenging in contexts where plant–arthropod interactions are limited, thereby constraining the assessment of their ecological responses. For example, forests typically provide fewer floral resources for pollinators than other ecosystems, such as grasslands, while understory microclimates influence the spatiotemporal dynamics of insect activity, further complicating their detection. In this study, we use environmental DNA (eDNA) to address these challenges and investigate the influence of forest microclimate, density, and tree composition on the diversity of flower-associated arthropods in a Swedish forest. We used two flowering plant species, Fragaria vesca and Trifolium pratense, as sentinel plants, translocating them to a mixed forest across 40 plots spanning a gradient of forest density and broadleaf tree dominance. The metabarcoding of flower eDNA documented a high diversity of arthropods with very specific communities in different forest plots. This high species turnover suggests either short eDNA persistence on flowers or unmeasured ecological factors structuring these communities. We found that forest structure, particularly light availability in broadleaf-dominated open plots, positively influenced species richness of arthropods detectable in flowers, while microclimate had a small impact. These effects varied between plant species, likely due to differences in flower visitor communities. Our study also offers significant methodological insights into using flower eDNA for detecting flower-associated taxa. We also emphasize the need for optimized sampling and DNA extraction processes to enhance the likelihood of successful amplification. We show that the number of flowers pooled in the same DNA extraction positively influences the number of taxa detected. By improving methods in flower eDNA sampling and analysis, future studies can more accurately assess the ecological interactions and conservation needs of forest environments and other ecosystems.