Environmental DNA最新文献

While the utility of environmental DNA (eDNA) metabarcoding surveys for biodiversity monitoring continues to be demonstrated, the spatial and temporal variability of eDNA, and thus the limits of the differentiability of an eDNA signal, remains under-characterized. In this study, we collected eDNA samples from distinct micro-habitats (~40 m apart) in a rocky intertidal ecosystem over their exposure period in a tidal cycle. During this period, the micro-habitats transitioned from being interconnected, to physically isolated, to interconnected again. Using a well-established eukaryotic (cytochrome oxidase subunit I) metabarcoding assay, we detected 415 species across 28 phyla. Across a variety of univariate and multivariate analyses, using exclusively taxonomically assigned data as well as all detected amplicon sequence variants (ASVs), we identified unique eDNA signals from the different micro-habitats sampled. This differentiability paralleled expected ecological gradients and increased as the sites became more physically disconnected. Our results demonstrate that eDNA biomonitoring can differentiate micro-habitats in the rocky intertidal only 40 m apart, that these differences reflect known ecology in the area, and that physical connectivity informs the degree of differentiation possible. These findings showcase the potential power of eDNA biomonitoring to increase the spatial and temporal resolution of marine biodiversity data, aiding research, conservation, and management efforts.

The range expansion of ticks to higher latitudes poses a severe threat to human health exposing human populations who had no prior contact with ticks to several harmful tick-borne diseases. Early detection of ticks in new areas is critical to help inform the public and medical professionals of the dangers associated with tick encounters. Environmental DNA represents a novel survey method that could provide reliable records of tick occurrences and timely warnings of their range expansions. In this study, we designed novel eDNA qPCR assays for three common North American tick species (Dermacentor variabilis, Amblyomma americanum, and Ixodes scapularis) and tested them on 51 samples of grasses and leaf litter collected from 12 grassland and forest sites in central and southern Illinois. We provide in silico and in vitro validation of all three assays; however, we were unable to generate any positive detections from field samples. Our lack of eDNA detections likely stems from low eDNA deposition rates coupled with rapid degradation in grasslands and forests, a problem exacerbated by terrestrial eDNA sampling methods limited by volume of substrate. We provide recommendations for improving sample collection methods to increase detection probability in future efforts. Continued research should focus on the viability of eDNA to detect small terrestrial invertebrates, like ticks, and it potential as early warning indicator of the spread of vector-borne diseases.

Although studies of insect decline have recently dominated headlines worldwide, their interpretation requires caution since for most species, we lack long-term population baselines. In the tropics, where most insect species thrive, our knowledge is even more limited and so reliable insect assessments must originate from well-established long-term monitoring efforts. Combining the extensive monitoring data from the Arthropod Program of the Smithsonian Tropical Research Institute (STRI) on Barro Colorado Island (BCI), Panama, we compare whether known arthropod diversity can be detected through metabarcoding of bulk insect samples obtained through automatic light-trapping. Our study detected 4402 species based on Barcode Index Numbers (BIN) and detected fine-scale differences between wet and dry seasons and sampling localities. We further refined our analysis to indicate which families and genera explained seasonal turnover. Using samples collected in parallel, but sorted manually as part of the ongoing arthropod monitoring program, we compared these methods. Out of 538 BINs recovered through manual sorting, there was a 70% overlap with the metabarcoding data; however, it represented 30% of the total BINs detected through metabarcoding. Expecting higher detection through metabarcoding, we also compare the results with the 14 years of sampling in BCI to better understand how well the monitoring program has captured the diversity of focal groups. Our results revealed a ~50% overlap between both methods and similar total catch. Barcode Index Numbers manually detected but not recovered by metabarcoding highlight some of the limitations of molecular detection methods such as primer bias. Contrastingly, BINs detected with metabarcoding, but not recovered by the traditional monitoring scheme, highlight the importance of local and regional barcode reference libraries.

Crowley et al.'s eDNA metabarcoding reveals riverine fish community structure and climate associations in northeastern Canada. Environ. DNA. 2024;6(1):517.

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Environmental DNA and RNA (eDNA/eRNA) can serve as molecular tools for biodiversity monitoring and biosecurity surveillance. However, uncertainties still exist regarding the persistence and dynamics of marine nucleic acids in the environment and the effects of post-sampling storage on species detectability. To bridge these gaps, an experiment was conducted in an Auckland marina, a known New Zealand entry point for marine non-indigenous species (NIS). We targeted a prominent invader, the Mediterranean fanworm Sabella spallanzanii, for eDNA/eRNA-based detection. Permeable dialysis bags filled with seawater collected near an S. spallanzanii colony were deployed in the marina to simulate environmental conditions, with a subset of bags stored on ice to mimic field storage conditions. Sabella spallanzanii eDNA/eRNA signal was quantified using droplet digital PCR on samples collected over 24 h of dialysis bag deployment. Results challenged traditional first-order decay models, showing inconsistent eDNA/eRNA signal patterns and no significant concentration changes between 0 and 24 h. Consequently, total eDNA fragmentation was assessed using the Agilent 2100 Bioanalyzer^® electrophoresis system, which revealed a rise in the number of total eDNA fragments and an unexpected increase in the median fragment size of total eDNA under field conditions over time, likely originating from the ambient microbiome. Additional analysis using long-read sequencing (Oxford Nanopore Technologies, UK) revealed an increase in microbial eDNA reads within the in-field samples, suggesting potential microbial growth within the dialysis bags. In contrast, the ice-stored samples exhibited no significant changes in the number of reads assigned to microbial taxa, implying limited microbial growth in cold storage. These findings provide insights into total eDNA dynamics and its potential impact on targeted eDNA concentration and detection. Further comprehensive research on eDNA/eRNA dynamics, particularly focused on eRNA, is essential, as this understanding is crucial for refining survey interpretation and sampling design for effective environmental management.

The Chicago Area Waterway System (CAWS) connects the Great Lakes watershed with the Mississippi watershed via canals that withdraw water from Lake Michigan. From 2009 through 2011, collaborators and I provided research, development, and application of eDNA to invasive species management in the CAWS in cooperation with the US Army Corps of Engineers (USACE). The research team's approach was a high-stakes test of a novel combination of proven technologies (field sampling techniques and laboratory genetics). In the first application of eDNA to a large scale, urgent management goal, we quickly discovered eDNA of two species of bigheaded carps in parts of the waterway where traditional tools had not captured fish. The central research question was whether the sensitivity (probability of detecting a fish when it was present) of eDNA was higher than that of traditional fish sampling tools (e.g., nets, electrofishing). The effort was part of what became a very large, complex, on-going initiative to reduce access by invasive species to Lake Michigan. This immediately garnered much attention, initiating a dialog about the reliability of eDNA, public discussion about the benefits and costs of the CAWS, and skepticism from industries that use the CAWS. Government agencies formed the Asian Carp Rapid Response Workgroup, which eventually became the Invasive Carp Regional Coordinating Committee (ICRCC). The ICRCC continues its coordinating role on the use of eDNA and other management responses in the CAWS. With the benefit of hindsight, I draw several lessons from the experience that may help in other settings where eDNA is now being deployed with increasing confidence and acceptance; evaluate the on-going CAWS surveillance and management effort; and recommend strengthening the current approach by broadening and deepening participation in a collaborative governance approach. Stronger public-private partnerships would accelerate research, development, commercialization, and application of eDNA analysis to the benefit of society.

Environmental DNA (eDNA) technology is an essential tool for monitoring living organisms in ecological research. The combination of eDNA methods with traditional methods of ecological observation can significantly improve the study of the ecology of rare species. Here, we present the development and application of an eDNA approach to identify rare sturgeons in the lower reaches of the Ural River (Zhaiyk) (~1084 km). The presence of representatives of the genus Sturgeon was detected at all sites in spring (nine sites) and autumn (ten sites) while they were absent during the summer period, consistent with their semi-anadromous ecology. Detection in spring and autumn indicates the passage of spring and winter forms to the lower and upper spawning grounds, respectively. This study confirms the difficulties of species-specific identification of Eurasian sturgeon and provides the first documented eDNA detection of specimens of the genus Sturgeon in the Ural River. It also provides a biogeographic snapshot of their distribution, experimentally confirming their seasonal migrations in the lower reaches of the river. The successful detection of sturgeon motivates further eDNA surveys of this and other fish species for accurate species identification and population assessment, opening up prospects for the management of these threatened species.

Proteinase K (ProK) is regarded as an essential ingredient in most DNA extraction protocols for protein-rich sample types such as tissue, blood, and mucus. However, ProK is expensive and may be unnecessary when samples are protein-limited, such as environmental DNA (eDNA) from oligotrophic seawater. To investigate this, we filtered seawater through Sterivex cartridges from a mesocosm receiving input from the adjacent coral reef slope at the Hawai‘i Institute of Marine Biology. We tested whether the addition of varying levels of ProK (0 μL, 25 μL, 50 μL, 100 μL, or 150 μL—20 mg/mL stock concentrations) to 1.8 mL of lysis buffer affected DNA yield and the diversity, community composition, and detection of known organisms within the mesocosm community based on zero-width operational taxonomic units (ZOTUs) obtained from DNA metabarcoding. We found no significant differences in diversity metrics among ProK quantities and dominant ZOTUs were consistent across concentrations. Over 50% of detected ZOTUs were shared among samples and only two ZOTUs were unique to samples of a particular ProK concentration. While the community composition among ProK quantities differed, pairwise community comparisons between quantities were not statistically significant and matched the known species composition of the mesocosm. These results suggest that rare ZOTUs and eDNA patchiness are driving overall community differences as opposed to extraction ingredients. Our data show that ProK is not essential when assessing communities from oligotrophic marine environments using eDNA and that the reduction or elimination of ProK can decrease sample preparation time and costs while maintaining data integrity.

Forests are threatened by many natural stressors intensified by climate change and anthropogenic activities, which tend to increase their susceptibility to pests and pathogens. Consequently, oomycete-related forest decline or dieback cases are increasing in natural, urban, and agricultural landscapes. It is in this context that Christmas tree growers from Southern Québec, Canada, are experiencing root rot problems, with reported incidences up to 25%. In a previous study, seven Phytophthora spp. were associated with this root rot problem, but the overall diversity of oomycetes has not yet been investigated. Hence, in this study, we use a metabarcoding approach to provide an overview of the diversity, richness, and composition of the oomycete community in fir plantations compared to surrounding natural forests. We showed that the P. cryptogea cluster, P. europaea cluster, P. sansomeana, and P. chlamydospora cluster were significantly more abundant in soils collected from plantations under diseased trees and confirmed that the P. europaea cluster (including P. abietivora) was most frequently associated with trees showing Phytophthora root rot-like symptoms. Finally, we report that land use (anthropogenic activities) shapes oomycete diversity, while plantations can act as a gateway for invading natural forests. In fact, the results presented here suggested that the P. europaea cluster might already have crossed this boundary and that other species might follow, advocating the importance of improved surveillance of oomycete diversity in various environments.

Globally, the diversity of arthropods and the plants upon which they rely are under increasing pressure due to a combination of biotic and abiotic anthropogenic stressors. Unfortunately, conventional survey methods used to monitor ecosystems are often challenging to conduct on large scales. Pan traps are a commonly used pollinator survey method and environmental DNA (eDNA) metabarcoding of pan trap water may offer a high-throughput alternative to aid in the detection of both arthropods and the plant resources they rely on. Here, we examined if eDNA metabarcoding can be used to identify arthropods and plant species from pan trap water, and investigated the effect of different DNA extraction methods. We then compared plant species identified by metabarcoding with observation-based floral surveys and also assessed the contribution of airborne plant DNA (plant DNA not carried by arthropods) using marble traps to reduce putative false positives in the pan trap dataset. Arthropod eDNA was only detected in 17% of pan trap samples and there was minimal overlap between the eDNA results and morphological identifications. In contrast, for plants, we detected 64 taxa, of which 53 were unique to the eDNA dataset, and no differences were identified between the two extraction kits. We were able to significantly reduce the contribution of airborne plant DNA to the final dataset using marble traps. This study demonstrates that eDNA metabarcoding of pan trap water can detect plant resources used by arthropods and highlights the potential for eDNA metabarcoding to be applied to investigations of arthropod-plant interactions.