Environmental DNA最新文献

Environmental DNA (eDNA) analysis is an effective and non-invasive technique for surveying and monitoring rare, threatened, or endangered (RTE) species. Compared to conventional capture-based sampling, eDNA analysis may offer a more cost-effective approach for surveying RTE species, yet few studies have compared their cost-efficiency—a critical consideration for conservation planning. We compared the costs, effort, and relative performance of aquatic eDNA sampling and conventional trapping for detecting the Alligator Snapping Turtle, Macrochelys temminckii Troost, 1835, in southwest Louisiana, United States. Environmental DNA was sampled quarterly over 1 year (2018–2019) at 19 streams, including three streams where M. temminckii presence had been previously confirmed via conventional trapping efforts (2012–2013). Water samples from each stream were analyzed using quantitative polymerase chain reaction (qPCR) to assess M. temminckii eDNA presence/absence. Time and costs (i.e., labor, travel, wages, and supplies) per detection via eDNA analysis and trapping were calculated and compared. Environmental DNA analysis documented the presence of M. temminckii DNA at two of the three streams where individuals had previously been trapped and yielded detections (qPCR amplifications) at 16 additional streams not previously sampled, expanding M. temminckii's documented distribution at our study sites by 84%. Environmental DNA analysis returned a detection rate (per site) 5.55 times higher than conventional trapping and was 18.7% less expensive. Our results provide evidence that strategically deployed eDNA surveys may be an effective and cost-efficient approach for detecting freshwater RTE species. With eDNA analysis, additional resources can be invested toward expanding survey coverage and increasing sampling frequency, allowing managers to more effectively target subsequent intensive monitoring efforts.

Aquatic invasive species are a serious and growing threat to biodiversity. Zebra and quagga mussels (Dreissena polymorpha and D. rostriformis bugensis) are freshwater invaders causing substantial ecological and economic damage across Europe and North America. Early detection of invasive mussels and other non-indigenous species is increasingly needed to prevent their establishment and spread. Environmental DNA (eDNA) techniques potentially offer higher sensitivity monitoring tools to complement more conventional methods for surveying adult and juvenile mussels and veliger larvae. eDNA assays are typically performed on small-volume (0.5–5 L) water samples that are concentrated by filtration prior to extraction and downstream processing. Sampling using a towed plankton net of a larger (64 μm) pore size can process orders of magnitude larger water volumes with the potential for increasing eDNA detection sensitivity. We compared the sensitivities of high-volume plankton tow net water sampling to filter sampling in three recently infested lakes in Canada and Minnesota, USA. Paired filtration and tow net samples were analyzed for Dreissena DNA using an established quantitative polymerase chain reaction assay for the genus. Higher yields of Dreissena eDNA (more DNA copies) were recovered from plankton tow than from filtered samples in all 33 paired comparisons. In some cases, plankton tow samples were positive for Dreissena eDNA while lower-volume filtering produced a false negative detection. Our results demonstrate the effectiveness of plankton tow net sampling for eDNA early detection of invasive mussels, a method that can be used exclusively or as a supplement to filter sampling. Our results further suggest that eDNA testing could be incorporated into monitoring programs that routinely use plankton tows for visual detection of invasive mollusk larvae, as well as other aquatic invasive and non-invasive species ranging from plankton to metazoans, including many fish.

Environmental RNA (eRNA) has the potential as a non-invasive tool for assessing the physiological status of macro-organisms, yet the quantitative method for relative gene expression analysis is still underexplored. To bridge this gap, this study introduces a relative quantification method for eRNA, employing quantitative PCR (qPCR) to evaluate the expression of the antioxidant gene, catalase (cat), in the Japanese medaka Oryzias latipes exposed to two toxic chemicals for 96 h: chlorpyrifos (CPS) and carbamazepine. Our results showed that, in eRNA, genes frequently used as a reference for tissue or cells in conventional expression analysis correlated with each other. Also, one of them (elfa) exhibited less variability, showing its potential suitability as a reference gene in eRNA analyses. Additionally, cat expression levels in eRNA increased with increasing CPS concentrations, in a concentration-response manner. These results suggest the promising potential of qPCR applications for eRNA in the monitoring of an organism's health and response to environmental changes. However, we observed disparities in gene expression levels of cat and beta-actin (actb) between eRNA and whole fish body, indicating eRNA might have a biased origin. Further research is needed to uncover the origin of eRNA and determine the limitations and applicability domain of eRNA analysis.

Environmental DNA (eDNA) is increasingly used to detect animals in aquatic habitats, but uncertainty remains about the relationship between the present location of an animal relative to eDNA detections. In marine environments, physical characteristics—such as tides and currents—can influence the distribution of eDNA. In this study, we make use of hatchery net pens containing >46 million juvenile chum salmon (Oncorhynchus keta) in nearshore Southeast Alaska to test for dispersion of eDNA and the effects of tide. Initially, we collected and filtered surface water every 80 m along a 2 km transect to test eDNA attenuation over surface distance during incoming and outgoing tides on a single day. The following year, we sampled at three depths (0 m, 5 m, and 10 m) every 500 m along the same transect as well as along a perpendicular transect, to understand dispersion by depth and in additional directions. Chum salmon eDNA was quantified using species-specific qPCR. We found that surface samples showed a consistent signal of decreasing chum salmon eDNA across the 2 km transect (R² = 0.665), with the majority of eDNA detections within 1.5 km of the net pens. Tide had a significant effect, resulting in higher concentrations of chum DNA throughout the transect during incoming tide and a steeper decline in eDNA over distance during outgoing tide (R² = 0.759). Depth affected chum salmon DNA concentration, with the majority of eDNA at the surface and a decreasing amount of DNA with increasing depth. This study addresses one of the critical knowledge gaps in applying eDNA to marine fisheries management by providing empirical evidence of eDNA dispersion and demonstrating that most eDNA detections are likely from nearby individuals that are either currently or recently present. Yet even at close proximity, eDNA signal strength fluctuates and depends on the physical environmental variables during a given sampling event.

Northern British Columbia has been identified as an important habitat for several coastal cetacean species, including humpback whales (Megaptera novaeangliae). This species is listed as being of “Special Concern” under Canada's Species at Risk Act, partly due to data deficiencies concerning genetic population structure and demographics in British Columbia. Anthropogenic activities threaten North Coast humpback whale populations, with particular concern for the impact of vessel noise, entanglement, and ship strikes. Current methodology (i.e., biopsy sampling) for obtaining cetacean genetic data is invasive, challenging, and costly; therefore, there is an urgency to develop effective and minimally invasive methodologies for efficiently collecting this data. Environmental DNA (eDNA) has been identified as an ideal tool for monitoring the presence and distribution of numerous species within marine ecosystems; however, the feasibility for cetaceans is not yet well established. In this study, we opportunistically collected targeted 1 L seawater eDNA samples from flukeprints when individual humpback whales were observed diving between the years of 2020 and 2022. A total of 93 samples were collected from individual humpback whales identified using a photographic identification catalogue. We successfully detected humpback whale eDNA in 28 samples using novel species-specific qPCR primers (~500 mL of sample), with relatively equal successful detection between immediate (0 days) and delayed (up to 10 days) sample filtration. Here, we have validated a qPCR assay for detecting humpback whale DNA from flukeprints and highlighted the future optimizations required to improve the potential application of flukeprint eDNA for conservation management.

Retrieval of modern and ancient environmental DNA (eDNA) from sediments has revolutionized our ability to study past and present ecosystems. Little emphasis has been placed, however, on the fundamentals of the DNA–sediment associations in environmental settings. Consequently, our understanding of mineralogic controls and geochemical processes that take place on the DNA–sediment interface, and its implications for eDNA taphonomy and provenance, remain extremely limited. Here, we apply interfacial geochemical principles to elucidate how depositional processes and the stability of DNA–sediment associations in different environments can influence our interpretation and identify possible interpretational biases arising from neglecting mineral and geochemical controls on eDNA taphonomy. We use atomic force microscopy to show how interfacial geochemical interactions drive DNA adsorption behavior and we outline how to increase the scope and resolution of ecological interpretations from eDNA by combining mineralogic composition information with experimental adsorption data. We bring the concepts together and propose how to integrate sediment provenance as well as mineralogic and geochemical principles in eDNA taphonomy analysis for improved reconstruction of past ecosystems and monitoring of modern ecosystems from eDNA data. We provide a conceptual understanding of how eDNA taphonomy and sediment provenance can be addressed and further applied to enhance the scope, resolution, and accuracy of modern and past ecological reconstructions based on eDNA data.

Marine biodiversity consists of a complex network of organisms responsible for keeping the ecosystem's balance. Fungi are an understudied group of organisms despite their recognized importance for ecosystem processes and diversity. How fungi respond to environmental change remains poorly understood, especially in marine benthic habitats. The Baltic Sea is a brackish coastal ecosystem with steep environmental gradients in a relatively limited geographical area and is therefore a particularly good system to investigate the impact of different abiotic factors on benthic fungal diversity. This study used environmental DNA (eDNA) metabarcoding to analyze the spatial dynamics of benthic fungal diversity in the Baltic Sea and quantify the environmental drivers that shape these dynamics. Based on 59 stations spreading over 1145 km the results showed that benthic fungal communities were dominated by the phylum Chytridiomycota, and the fungal species Alphamyces chaetifer and Operculomyces laminatus from this phylum were the main drivers of the community structure dissimilarities observed between regions. Water depth and salinity were the main predictors of the benthic fungal community composition. The impact of nutrient availability was also significant, possibly related to the known role of Chytridiomycota species such as A. chaetifer and O. laminatus in nutrient cycling. Our results indicate that the benthic fungal diversity of the Baltic Sea is shaped by salinity gradients and nutrient availability and highlights that the current fungal biodiversity is at risk of species shift or decline with predicted changes in salinity due to climate change and intensified eutrophication.

Effective management of biodiversity requires regular surveillance of multiple species. Analysis of environmental DNA (eDNA) by metabarcoding holds promise to achieve this relatively easily. However, taxonomy-focused eDNA surveys need suitable molecular reference data, which are often lacking, particularly at the species level and for remote locations. To evaluate the comparability of environmental DNA surveys and traditional surveys in a real-life case study in a marine area of high conservation value, we conducted a biodiversity survey of the fish in remote and pristine Te Wāhipounamu/Fiordland (Aotearoa/New Zealand), incorporating multiple data sources. We compared eDNA-derived species identifications against Baited Remote Underwater Video (BRUV) data collected at the same time and locations as eDNA. We also cross-referenced both eDNA and BRUV data against literature and the Ocean Biodiversity Information System (OBIS), with literature and OBIS data representing a summary of multiple traditional surveying approaches. In total, we found 116 fish species in our study area. Environmental DNA detected 43 species; however, only three of those species overlap with species known from the literature, OBIS, or our BRUV analyses. A total of 61 fish species were known from the region from the literature, while OBIS listed 28 species, and our BRUV analyses picked up 26 species. BRUV data coincided more strongly than eDNA data with literature and OBIS data. Twenty of the 26 species detected by BRUV were known from literature and OBIS. We argue that limitated DNA reference databases are the main cause of this discrepancy, and our results indicate that eDNA of rare and endangered species can be detected if matching reference data were available. Environmental DNA analyses can only identify species present among reference data and with relaxed taxonomic assignment parameters may converge on relatives of detected species if the actually existing species themselves are missing among reference data. However, the high number of species detected by our eDNA analyses confirms that eDNA could be a powerful tool for biodiversity surveys if suitable investments in local reference databases were made.

Molecular methods to understand host feeding patterns of arthropod vectors are critical to assess exposure risk to vector-borne disease and unveil complex ecological interactions. We build on our prior work discovering the utility of PCR-Sanger sequencing blood meal analysis that work well for soft ticks (Acari: Argasidae), unlike for hard ticks (Acari: Ixodidae), thanks to their unique physiology that retains prior blood meals for years. Here, we apply blood meal metabarcoding using amplicon deep sequencing to identify multiple host species in individual Ornithodoros turicata soft ticks collected from two natural areas in Texas, United States. Of 788 collected O. turicata, 394 were evaluated for blood meal source via metabarcoding, revealing 27 different vertebrate hosts (17 mammals, five birds, one reptile, and four amphibians) fed upon by 274 soft ticks. Information on multiple hosts was derived from 167 individual O. turicata (61%). Metabarcoding revealed mixed vertebrate blood meals in O. turicata while same specimens yielded only one vertebrate species using Sanger sequencing. These data reveal wide host range of O. turicata and demonstrate the value of blood meal metabarcoding for understanding the ecology for known and potential tick-borne pathogens circulating among humans, domestic animals, and wildlife such as relapsing fever caused by Borrelia turicatae. Our results also document evidence of prior feeding on wild pig from an off-host soft tick for the first time in North America; a critical observation in the context of enzootic transmission of African swine fever virus if it were introduced to the US. This research enhances our understanding of vector-host associations and offers a promising perspective for biodiversity monitoring and disease control strategies.

The Ogasawara Islands are a highly isolated oceanic archipelago in the Pacific Ocean that possess unique faunal and floral biodiversity with a high level of endemism. As historically more focus has been put on the terrestrial realm in examining diversification and evolutionary processes on oceanic islands, publicly accessible and spatially resolved data of marine reef ecosystems remain scarce. To address this issue, we conducted the first environmental DNA (eDNA) metabarcoding surveys of the actinopterygian (ray-finned) and elasmobranch fishes and of Scleractinia coral assemblages in the waters of the Ogasawara Islands. We detected a total of 124 unique taxa of fish and 38 unique taxa of scleractinian corals. Overall, our eDNA results confirmed that the Ogasawara Islands host a rich variety of coral and fish fauna and underline the strength of eDNA surveys in rapidly obtaining targeted multi-taxa data using seawater samples, requiring comparatively little effort and a lack of requirement for in situ taxonomic expertise. We anticipate that continued biomonitoring using eDNA with high sampling effort will add to and complement the body of knowledge regarding species distributions, invasive species, and biodiversity hotspots within oceanic archipelagos.