Environmental DNA最新文献

Biodiversity surveys are critical for detecting environmental change; however, undertaking them at scale and capturing all available diversity through observation is challenging and costly. This study evaluated the potential of soil-extracted eDNA to describe plant communities and compared these findings to traditional, observation-based field surveys. We analyzed 789 soil samples using high-throughput amplicon sequencing and compared DNA-based diversity metrics, indicator taxa, predicted vegetation class, and plant cover in a comparison with co-located field survey data. The results indicated that taxonomically aggregated (genus) eDNA-derived data, while showing slightly reduced Shannon's diversity scores, yielded remarkably similar overall richness and composition estimates. However, the DNA indicator taxa and predictive power for vegetation community classification were also lower overall than those recorded by the field survey. In many cases, plant cover could be inferred from amplicon abundance data with some accuracy despite widely differing scales of sampling—0.25 g crumb of soil versus a 1 m² quadrat. Overall, results from eDNA demonstrated lower sensitivity but were broadly in accordance with traditional surveys, with our findings revealing comparable taxonomic resolution at the genus level. We demonstrate the potential and limitations of a simple molecular method to inform landscape-scale plant biodiversity surveys, a vital tool in the monitoring of land use and environmental change.

Environmental DNA (eDNA) analysis faces challenges regarding sensitivity and quantification accuracy, particularly in areas with low target species densities or during seasons when eDNA release decreases. Multi-copy markers such as mitochondrial genomic DNA and ribosomal DNA (rDNA) have been widely used in eDNA analysis to address this issue. However, the copy number of the DNA markers per cell remains a potential bottleneck for eDNA sensitivity. In this study, we aimed to increase the sensitivity of eDNA assays by using retrotransposons, which are abundant in the genome, as novel target markers. We developed an assay targeting UnaSINE1, a short interspersed nucleotide element (SINE) characteristic of Anguilla eels, and compared its sensitivity and accuracy with that of an established mitochondrial 16S rRNA marker. Our results demonstrated that UnaSINE1 was detected at over 100 times the copy number of the mitochondrial marker in both genomic and eDNA samples. In the river surveys, the 16S marker was positive in 32 of the 81 samples, whereas the UnaSINE1 marker was positive in 62 samples, indicating that the use of the SINE marker remarkably reduced false negatives. Furthermore, both biological and technical replicates exhibited improved positive consistency and reduced variability in quantification, leading to more robust presence/absence determination and quantitative results. Utilizing retrotransposon sequences as markers requires additional effort for sequence acquisition and organization and may limit taxonomic resolution to the genus level. However, this approach significantly improves sensitivity without increasing the labor or cost of sampling and PCR analysis, making it highly practical for eDNA studies.

Tetracapsuloides bryosalmonae, the causative agent of Proliferative Kidney Disease (PKD), affects salmonid populations in the northern hemisphere. In Switzerland, PKD monitoring to date has been conducted irregularly using invasive sampling. However, non-invasive detection protocols based on environmental DNA (eDNA) have been established, and there is still a lack of knowledge about environmental parameters that may influence detection. In this study, we evaluated which sampling period would be best for eDNA-based monitoring of T. bryosalmonae and which environmental parameters might influence the outcome by regularly sampling water from six Swiss rivers over an entire year and testing for presence of T. bryosalmonae DNA by droplet digital PCR (ddPCR). The T. bryosalmonae infection status of bryozoans from all investigated rivers was also assessed. Water temperature, precipitation, and air temperature were examined as environmental parameters. We found T. bryosalmonae DNA in all rivers by ddPCR. Positive results were almost exclusively retrieved between late spring and early autumn (mid-April until end of October). 98.3% of T. bryosalmonae positive water samples were collected when average daily water temperatures were above 8°C, and 71.9% of the positive samples when average daily water temperatures were above 14°C. Occupancy modeling corroborated the influence of water and air temperature on detecting T. bryosalmonae eDNA. Precipitation caused early clogging of filters in some cases and reduced detection by reducing sample volumes, suggesting when sampling for eDNA should be avoided. Finally, recommendations for a future eDNA-based monitoring of T. bryosalmonae are provided.

The Ross Sea is characterized by a significant export of particulate organic carbon, with up to 50% of surface primary production being transferred to deep water layers. On their way to the ocean's interior, these particles undergo a remineralization process mainly carried out by prokaryotic communities through a complex set of hydrolytic enzymes. In this study, we used a metagenomic approach to explore the genetic repertoire of free-living and total prokaryotic communities at surface and in deep water masses of the Ross Sea. We focused on genes involved in the production of hydrolytic enzymes, including carbohydrate-active enzymes (CAZymes), proteases, and lipases. Our analysis revealed that the genetic profile of prokaryotes reflects different strategies for optimizing the degradation of organic substrates, adapting to variations in the quantity and quality of particulate organic matter along the water column, and at different locations. These results suggested that Ross Sea surface communities were strongly influenced by the dynamics of phytoplankton at different sampling sites, exhibiting greater variability in their enzymatic repertoire in respect to bottom communities. Deep-sea microbes, on the other hand, rely on a broader and more diverse set of enzymes compared to surface communities, being more adapted to a particle-bound lifestyle and playing a critical role in the remineralization of complex polysaccharides, such as algal cell wall components.

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.