Environmental DNA最新文献

Does environmental DNA (eDNA) concentration correlate with numerical abundance (N) or biomass in aquatic organisms? We hypothesize that eDNA can be adjusted to simultaneously reflect both. Building on frameworks developed from the Metabolic Theory of Ecology, we derive two equations to adjust eDNA data to simultaneously reflect both N and biomass using population size structure data and allometric scaling coefficients. We also demonstrate that these equations share model parameters, necessitating the joint estimation of regressions between adjusted eDNA, N, and biomass. Furthermore, our framework can be extended to model how other variables (temperature, taxa, diet, trophic level, etc.) might impact relationships between eDNA, N, and biomass in natural ecosystems. We applied our framework to data from two previously published studies correlating eDNA to Brook Trout (Salvelinus fontinalis) N and biomass. In both case studies, point estimates of the scaling coefficient (b) reflected allometric processes (b = 0.51 and 0.37 for Case Study 1 and 2, respectively), with credible intervals indicating that b likely differed from zero (i.e., eDNA scales with N) and one (i.e., eDNA scales with biomass). Directly estimating the value of b improved estimates of N and biomass relative to assuming b equals 0, which particularly affected the capacity to estimate biomass. However, models assuming eDNA production scaled with biomass (i.e., b = 1) were largely similar to estimating b, implying that assuming eDNA scales linearly with biomass might be a sufficient approximation for some systems. Nevertheless, the framework demonstrates that correlating eDNA directly with either N or biomass (as is commonly done in many studies) inherently necessitates an adjustment to infer the other metric if populations exhibit size structure variation. Collectively, we demonstrate that quantitative eDNA data is unlikely to correspond exactly to either population N or biomass but can be adjusted to simultaneously reflect both.

Invasive species, such as the freshwater crayfish Procambarus clarkii, reportedly negatively influence the abundance of various aquatic species. Moreover, these invaders are increasingly linked to ecological degradation of aquatic ecosystems, as invaded habitats show increased levels of turbidity, nitrogen, and organic matter concentration. P. clarkii has, among other impacts, been associated with eutrophication in invaded habitats. However, observations suggest that the presence of P. clarkii is often not accompanied by ecosystem degradation, raising the question of whether they are drivers of degradation or function as passive passengers, with the degradation being caused by other stressors. To investigate these contrasting hypotheses, we conducted a full factorial experiment in 24 mesocosms with P. clarkii and nutrient pollution (specifically N, P, and K), a ubiquitous stressor in aquatic ecosystems. Here, we assessed the effects on community compositions of morphologically identified macrophytes and chironomids, as well as the compositions of bacteria, phytoplankton, and diatoms identified using environmental DNA (eDNA) metabarcoding. Nutrient pollution induced significant shifts in macrophyte biomass and in the composition of the bacterial, diatom, and phytoplankton communities. All microbial communities exposed to nutrient pollution initially diverged from the control, after which the bacterial and phytoplankton communities converged back to the control in the final weeks. In contrast, we found only marginal effects of P. clarkii, rendering it unlikely as a significant short- to medium-term driver of the tested biodiversity. As microbial communities respond quickly to changes in the environmental conditions, these results signify that the mesocosms used in the study were relatively stable in spite of the presence of P. clarkii. The crayfish density and timeframe studied may be leveraged as threshold values in the design and execution of freshwater management strategies that aim to avert potential negative impacts of P. clarkii on ecosystem structure. Ultimately, the importance of nutrient pollution is reinforced as a driver of environmental change in aquatic ecosystems.

Increasing the success of invasive species management depends on the development, testing, and deployment of new tools. Environmental DNA (eDNA) is an effective tool for monitoring invasive species that can help identify presence/absence, geographical boundaries of invasion, risk pathways, and population connectivity. In particular, understanding the sensitivity of eDNA detection rates to target species density allows calibration of sampling rates. In this study, we take a lab-validated eDNA assay for Mus musculus (house mouse) and test its detection rates at different populations densities for wild-caught, free-ranging M. musculus in a controlled laboratory and an outdoor mesocosm. The goal was to understand both eDNA accumulation after M. musculus is introduced and the persistence of the accumulated eDNA signal in the environment after animals were removed. We found that eDNA signal was detectable within 1 h of a single mouse being introduced and that the signal was detectable for months after in the controlled environment but largely undetectable after 4 days in an outdoor mesocosm. We suggest sampling strategies for post-eradication deployment of eDNA and highlight other uses for this assay, which are important to the deployment of this tool for invasive M. musculus management.

Understanding the diversity and ecological roles of arthropods within tree-related microhabitats (TreMs) is crucial for forest ecosystem conservation and management. In our study, we aimed to identify the most effective environmental DNA (eDNA) metabarcoding approach for capturing ecologically important arthropod species primarily inhabiting the near-ground-level TreMs. We evaluated the use of COI and 16S primers for eDNA metabarcoding and compared direct and indirect eDNA sampling methods, including lying deadwood sediment sampling (LDS), standing deadwood sediment sampling (SDS), soil sampling (SS), and tree surface roller sampling (TSRS). Our results indicated significant biases and challenges, particularly in primer selection, with COI outperforming 16S in taxonomic resolution for most arthropod taxa. Our TSRS method effectively captured 408 OTUs at the species level, with the highest number of ecologically significant arthropods associated with TreMs compared to other approaches. Direct sampling from sediments revealed a higher abundance of fungi than arthropods, impacting diversity estimates. We also observed habitat-specific preferences among arthropods, with certain sampling methods capturing distinct taxa. Our findings underscore the importance of carefully selecting sampling methods and validating primers in eDNA metabarcoding studies and provide insights into the complexity of arthropod communities in TreMs. Optimized methods will advance monitoring techniques for forest ecosystems and inform conservation efforts to preserve arthropod diversity in TreMs.

Designing effective conservation plans to protect species from extinction requires a comprehensive understanding of their ecology. Conventional methods used to investigate habitat use are time-consuming, and the detectability of cryptic species is often insufficient. Environmental DNA (eDNA)-based approaches provide a complementary tool to traditional monitoring methods for ecosystem monitoring and assessment. Nevertheless, to our knowledge, such methods have rarely been applied to investigate habitat use at a fine scale in a continuous wetland environment. Here, we used an eDNA metabarcoding approach to characterize the breeding habitat use of local amphibian species in a wet meadow expanse along the southern shore of Lake Neuchâtel, Switzerland. We retrieved DNA from six out of the seven species expected to be present. We tested the influence of six abiotic environmental variables on overall species assemblages and individual species occurrences. We showed that the main factor structuring species assemblages was water temperature and that the distribution of three amphibian species was associated with several environmental variables. Our results indicate that the eDNA detection approaches are promising tools to study species' ecology at a small scale in continuous wetland habitats.

Environmental DNA (eDNA) is transforming the way aquatic ecosystems are monitored and managed by scientists, resource managers, ENGOs, First Nations communities, and citizen scientists alike. However, available sampling systems currently don't allow for combined high filtration volumes, rapid sample collection, and preservation in the field, thus far hindering broad scale eDNA studies in the ocean specifically for small and medium scale organizations. To overcome these challenges, several modular water sampling systems that utilize hollow-membrane (HM) filtration cartridges were developed by RKS laboratories and tested by the Fisheries and Oceans, Canada, Molecular Genetics Laboratory. Compared to Sterivex filters, an industry standard for eDNA filtration, the HM filtration cartridges allowed for a six-fold increase in filtration volume and threefold increase in filtration speed. The field sampling systems, which combine pumps, a programmable controller, an air pump, an ozone generator, and up to eight filters at once, enabled efficient direct eDNA filtration from diverse aquatic environments, from creeks to the open ocean. To evaluate ease of deployment, we present the results of a 3 day workshop where technical staff of an Indigenous resource management organization, without any prior knowledge in eDNA sampling, were trained and performed independent eDNA sample collection. The samples were analyzed by metabarcoding and qPCR to reveal the distributions of salmon and other species co-occurring in salmon ecosystems, from large ephemeral predators, to the planktonic prey of salmon, even including their pathogens. In this example study, we further observed a substantial shift in community composition in the vicinity of aquaculture facilities where marine species associated with aquaculture feed were detected in freshwater at high relative abundance. This study demonstrates how these sampling systems provide an efficient entry point for small and medium scale organizations to utilize eDNA to fulfill their research and monitoring objectives.

Metabarcoding of environmental DNA (eDNA) is becoming practically applied to fish monitoring and conservation surveys in estuaries. However, estuarine bays may be an unsuitable zone to use eDNA metabarcoding because they are affected by eDNA originating from upstream rivers. In this study, the transition of eDNA composition from river to bay was examined to investigate the influence of freshwater sources on the eDNA composition of the downstream bay. Samples were collected in a bay spanning around 1 km and an upstream river under high and low tide within 1 day in November and in January. The samples were analyzed by using eDNA metabarcoding for fish species and species-specific quantitative analysis for the freshwater fish Cyprinus carpio. Our findings reveal that the eDNA of freshwater fishes was drastically diluted in the model estuarine bay. As a result, the relative-read-based composition clearly changed from riverine to marine environments, and the freshwater inflow had little effect on the relative-read-based composition at those sites. However, eDNA from freshwater fishes was widely detected in the bay by species-specific and metabarcoding analysis, suggesting that fresh water may have a more significant impact when focusing on presence/absence-based composition. Our study also found that the transition zone for the concentration of freshwater eDNA fluctuated spatiotemporally with tides, indicating that the degree of influence from the river varies with tide. Therefore, prior measurement of the distribution of freshwater fish eDNA at low tide would help to conservatively determine better sampling sites and design more reliable sampling in estuaries.

Beaked redfishes (Sebastes fasciatus and Sebastes mentella) of the northwest Atlantic have recently reached record abundance levels in the estuary and northern Gulf of St. Lawrence, dominated by Sebastes mentella. Knowledge of their diet composition is essential to understand the trophic role that these groundfish play in the ecosystem. The objective of the present study was to compare the performance of visual examination and DNA metabarcoding of stomach contents of the same individual redfish caught in the estuary and northern Gulf of St. Lawrence. Using a universal metazoan mitochondrial cytochrome c oxidase subunit I (COI) marker, we identified a total of 24 taxonomic groups, composed of 22 species and two genera in the content of 185 stomachs with DNA metabarcoding. We compared these results to the 25 prey types, eight identified at the genus and nine at the species level, obtained with visual stomach content analysis (SCA). While both techniques revealed a similar diet composition, our results showed that the SCA and DNA metabarcoding perform differently for particular prey categories, both in terms of detectability and taxonomic resolution, as well as in the estimated relative importance of weight and occurrence in the diet. The use of DNA metabarcoding along with SCA validates and improves the taxonomic resolution of visually determined prey, which supports the concept that both techniques provide useful complementary information on the diet of redfish and likely other fish species.

Human activities severely impact biodiversity, particularly in freshwater lakes. These habitats provide critical ecosystem services and, at the same time, suffer from river inflow, agricultural runoff, and urban discharge. DNA-based techniques are preferred for monitoring biodiversity due to their effectiveness. However, pinpointing the causes of biodiversity decline across landscapes poses challenges due to the complex interactions between biodiversity and environmental drivers. In this study, we used an explainable multimodal machine learning approach that can integrate different types of data, such as biological, chemical, and physical data, to discover potential causes of biodiversity dynamics. This is done by identifying relationships between environmental drivers—plant protection products, physico-chemical parameters and typology- and community biodiversity changes in 52 lake ecosystems. By analyzing benthic and pelagic lake communities, we found significant correlations between biodiversity and environmental drivers, such as plant protection products. Furthermore, our analysis allowed us to identify factors within these drivers responsible for biodiversity dynamics. Specifically, insecticides and fungicides were identified as the most important factors, followed by 43 physico-chemical factors, including many heavy metals. Our holistic, data-driven approach provides insights into large-scale biodiversity changes and could inform conservation efforts and regulatory interventions to protect biodiversity from pollution.

Terrestrial vertebrates are experiencing worldwide population declines and species extinctions. To effectively conserve remaining populations and species, rapid, cost-effective, and scalable methods are needed to complement longstanding monitoring methods. Increasingly, environmental DNA (eDNA)-based approaches are being used for terrestrial vertebrate biomonitoring within a range of environments. However, as we move eDNA biomonitoring onto land, we are presented with a new set of challenges. This necessitates the development of “best-practice” eDNA sample collection guidelines for terrestrial systems with the purpose of detecting terrestrial vertebrates. To address these needs, we conducted a systematic literature review of 143 peer-reviewed papers applying eDNA to terrestrial vertebrate monitoring (excluding Lissamphibia) that were published between 2012 and 2023. We summarize the use of eDNA for terrestrial vertebrate biomonitoring, focusing on study design and field techniques. Over the decade we observe a steady growth in the annual number of publications, with 3 in 2012 and 33 in 2023. The majority of the reviewed studies targeted terrestrial mammals within temperate forest regions. While an equal number of studies focused on a metabarcoding approach to assess community taxon composition and/or species-specific eDNA detection methods, novel uses are increasingly published. These include studies of animal behavior and population genetics. We record three types of sampling strategies, eight different substrate types, and seven different preservation methods, suggesting that there is no “one size fits all” eDNA-based sampling methodology when detecting terrestrial vertebrates. With a multitude of study aims, across different environments, and target organisms with different ecologies, the standardization of eDNA sampling approaches in terrestrial systems is extremely challenging. We summarize in a table known factors influencing eDNA detection within terrestrial environments. Furthermore, we identify five key considerations to be addressed when sampling for eDNA studies targeting terrestrial vertebrate species, with the aim of guiding decision making.