Environmental DNA最新文献

In the face of ongoing anthropogenic pressures on global biodiversity, effective monitoring strategies are essential for understanding species distributions and guiding conservation. Leptonycteris nivalis, L. yerbabuenae, and Choeronycteris mexicana are nectar-feeding bats of conservation concern that occur in the southwestern United States and Mexico. Leptonycteris nivalis and L. yerbabuenae are morphologically similar and difficult to differentiate in the field, making eDNA a particularly relevant monitoring tool. Since previous studies have shown that eDNA detection of these species is possible when swabs are taken from their dietary flowers, we sought to determine whether they can be detected from artificial feeders, which are commonly used on residential properties to attract hummingbirds and are a known supplemental food source for L. yerbabuenae. Between 2023 and 2024, citizen scientists (n = 12) in Arizona and New Mexico took 306 swabs of hummingbird feeders, which we tested with an existing qPCR assay for L. nivalis and newly-developed qPCR assays for L. yerbabuenae and C. mexicana. Leptonycteris yerbabuenae and C. mexicana showed the highest number of detections (300 and 274 swabs, respectively). Previously only known to occur in the U.S. in Texas and New Mexico, we detected L. nivalis near Portal, Arizona, within 50 km of documented foraging range in western New Mexico. Detections of this endangered species suggest its range extends beyond Hidalgo County, New Mexico and into neighboring Cochise County, Arizona, highlighting a need for increased surveillance of this species. Our work with artificial nectar feeders expands the eDNA detection method for nectar-feeding bats to the human-wildlife interface and shows that citizen science can be successfully used for eDNA surveys. Such methods provide an alternative to mist netting or acoustics, which can help monitor occupancy and clarify range extensions. This work corroborates other studies illustrating that eDNA can effectively detect and monitor terrestrial species.

In recent years, European countries have intensified efforts to control or limit the spread of invasive freshwater crayfish and the crayfish plague pathogen Aphanomyces astaci, while working to conserve native species such as the noble crayfish (Astacus astacus). Although crayfish shed relatively low amounts of DNA into their environment, environmental DNA (eDNA) approaches have proven effective for detecting their presence. A range of protocols and equipment is currently used in eDNA-based monitoring of freshwater crayfish. To evaluate how methodological variation influences detection accuracy, we conducted the first European interlaboratory ring test using eDNA to detect A. astacus, the invasive signal crayfish Pacifastacus leniusculus, a chronic carrier of A. astaci, and the pathogen itself. The aim is to harmonize monitoring methods for crayfish and disease surveillance across laboratories. Eleven teams from thirteen European countries participated, each using its own equipment and protocols to collect and filter water from indoor tanks and outdoor ponds where the presence of A. astacus and P. leniusculus had been experimentally manipulated, as well as from a natural lake containing a P. leniusculus population. The resulting samples were analyzed in each team's laboratory. Despite methodological differences, all teams successfully detected DNA from both crayfish species in indoor tanks (3–10 crayfish/m³). However, detection accuracy declined in outdoor ponds where crayfish density was an order of magnitude lower (0.32 crayfish/m³). Detection was most variable for A. astaci, likely due to its very low prevalence in the host stock. Our study demonstrates the challenges of achieving consistent eDNA results across laboratories and highlights the importance of interlaboratory comparisons. It also underscores the need to identify sources of variability and error, an essential step toward developing robust and standardized protocols. This multinational intercalibration and exchange of knowledge improved methodology and enhanced reliability in crayfish detection.

Dynamic heterogeneous metacommunities can be analyzed as complex networks. However, the interplay of species interactions, local environmental conditions, and spatiotemporal dispersal remains poorly understood. We assess the relative importance of these drivers in structuring river-floodplain metacommunities based on a spatiotemporal eDNA dataset. We applied Bayesian network learning to infer species interactions, spatiotemporal dynamics, and the importance of environmental factors, and used graph theory to summarize and analyze the patterns in the derived networks. Our analysis revealed distinct sub-communities linked by interacting species, spanning a gradient from environmentally filtered to dispersal-driven. Top predators and invasive species are identified as key connectors, being most important in regulating network dynamics and cohesion. Our findings highlight that combining Bayesian networks with graph theory has high potential to uncover the causal structure of metacommunities and provide a mechanistic understanding of community assembly in dynamic ecosystems, informing ecosystem management in dynamic landscapes.

Located in the southeast of Brazil, the Rio Santo Antônio basin, a tributary of the Rio Doce basin, has many preserved remnants of the Atlantic Forest, but is otherwise under imminent threats from several land use stressors. In this study, we used environmental DNA (eDNA) metabarcoding to assess vertebrate diversity in the headwaters of the Rio Santo Antônio basin, aiming to elucidate key ecological factors influencing its vertebrate richness. Additionally, we provide the first vertebrate species inventory for the basin. In 2023, water samples from 15 third- and fourth-order streams were collected and metabarcoding assays targeting the mitochondrial 12S rRNA gene were employed to detect the vertebrate community. We identified 119 vertebrate taxonomic units distributed across two distinct communities: one on the eastern slope and another on the western slope of the basin, both influenced by large-scale mining activities. We demonstrated that vertebrate richness was not correlated with forest cover or pH but was strongly associated with the water's oxidation–reduction potential (ORP). We interpret ORP as a reflection of local conditions, where sites with higher ORP values also exhibited greater taxonomic richness and were related to greater forest cover, lower air and water temperatures, and greater distance from mining activity. The vertebrate biodiversity and biogeographic distribution described here highlight the value of eDNA metabarcoding as a monitoring approach and support decision-making and conservation efforts aimed at preserving the remaining Atlantic Forest in the headwaters of the Rio Santo Antônio basin.

Changes in fire regimes and the introduction of invasive species are negatively impacting Northern Australia's biota, highlighting the need for reliable biodiversity monitoring data. Here we used mosquito-ingested DNA (iDNA) to detect birds and mammals within Kakadu National Park. Six sites were sampled on two occasions (wet and dry season), with three traps deployed for two consecutive nights of sampling at each site. Mosquitoes were processed in bulk samples per trap ranging from 31 to 1987 mosquitoes. Extracted DNA was amplified using primers targeting vertebrates (12SV5), mammals (16SMam1/2) and birds (Aves01) with iDNA-derived richness and composition measured. A total of 50 avian and 19 mammalian taxa were detected, including threatened species such as the white-throated grasswren (Amytornis woodwardi) and the ghost bat (Macroderma gigas), along with difficult-to-monitor groups such as small-bodied and arboreal mammals. Community composition was shown to be distinct between sampling events, and avian richness was higher during the dry season. Importantly for the management of the park, our findings suggest that fire regimes modified both bird and mammal communities during the dry season, with vegetation structure being correlated with avian and mammalian community composition during the wet season. This study highlights the capacity for iDNA metabarcoding to provide fine-scale ecologically relevant information within a large, dynamic and difficult-to-access landscape.

Global loss of biodiversity prioritizes the need for comprehensive and effective biomonitoring methods. Airborne environmental DNA (eDNA) has shown promise for monitoring terrestrial vertebrates but has not yet been rigorously compared to established biomonitoring methods. In a field-study in the Netherlands, this study aims to compare species detection from airborne eDNA with manual surveys, camera trapping and acoustic monitoring, focusing on birds and mammals. Monitoring was performed over the course of 4 weeks within an agroforestry ecosystem. Birds were monitored using eDNA, manual surveys and acoustic monitoring, while eDNA and camera trapping were used for mammals. This resulted in four mammal species, detected by both camera traps and eDNA, while eDNA identified an additional 16 species, primarily small-bodied, including two invasive species. A total of 74 bird species was detected, with varying degrees of overlap between methods and all three methods detected unique species. All but three bird and four mammal species detected were consistent with known occurrences near the study site. Rarefaction curves show that eDNA has the highest potential species diversity, but manual surveys are most efficient when limited time is available. Unique species can largely be explained by method characteristics or limitations; acoustic monitoring detections are limited to species that make sound, while eDNA requires further research on detection range and sensitivity. Our results indicate that for the studied agroforestry system, acoustic monitoring and airborne eDNA can detect a large proportion of birds and mammals detected by manual surveys, in addition to a range of species undetected by the latter, attesting to their effectiveness as biodiversity monitoring methods. This is the first study to compare airborne eDNA with manual surveys and acoustic data, further confirming the high potential of airborne eDNA for biodiversity monitoring.

Intensifying the management of grazed pasturelands can lead to higher greenhouse gas emissions, loss of biodiversity, and a general decline in ecosystem function. Yet, maintaining the abundance and activity of soil organisms, such as dung beetles, in pasturelands may improve soil ecosystem function. The tunneling dung beetle, Onthophagus taurus (Schreber 1759) buries dung in the soil, affecting soil physical properties, the soil microbial community, as well as nutrient cycling. However, few studies have examined links between dung-beetle-mediated changes in soil microbes and soil organic carbon. We used a 60-day enclosure experiment to examine how O. taurus affects the soil microbial community and soil organic carbon in pasturelands of California's Central Coast, and to examine whether any observed changes in the soil microbial community are beetle abundance-dependent. Using eDNA metabarcoding of the prokaryote 16S and fungal ITS1 loci, we find that dung beetles affect the soil bacterial community only within surface soils (top 0–1 cm), whereas their presence affects the fungal community in both surface soils and in 0–10 cm cores. We also found that the fungal taxa more likely to occur in the presence of dung beetles are associated with carbon cycling. Despite these relationships, neither the presence nor abundance of dung beetles in pastureland soils had an impact on soil carbon content in the time of this experiment. Our results illuminate the influences of dung beetles on the soil microbial community and nutrient cycling in pastureland soils which can have broad-reaching implications for ranchers and land managers.

Irrigated paddy fields provide alternative habitats for aquatic species amid degrading natural wetland habitats. Paddy field biodiversity depends on surrounding landscapes and agricultural practices, and biodiversity surveys are important in understanding it. However, its assessment is often time-consuming and depends on specialist skills. To overcome these limitations, we used environmental DNA (eDNA) metabarcoding of paddy water samples to detect species diversity of insects, fishes, and birds, and assessed the optimal sampling effort and sampling design. From each of seven paddy fields, we collected samples at each of eight positions. eDNA metabarcoding detected 118 insect, 14 fish, and 6 bird operational taxonomic units, most of them aquatic. Resampling analyzes suggested that four sampling replicates can recover all detectable operational taxonomic units of fishes and birds with > 50% probability, but the species accumulation curves suggested greater insect diversity than we detected, attributable to insufficient reference data. Samples collected near inlets included eDNA from irrigation channels, so inlets should be avoided in assessing biodiversity in paddy fields. Pooled samples could detect abundant species, but the samples detected fewer species than the total species diversity detected from eight sampling replications. Our findings are applicable to most paddies in Japan because the research was conducted in Japanese standard rectangular paddies. Moreover, given the prevalence of small agricultural fields in many Asian countries, our findings will promote the use of eDNA in biodiversity monitoring in paddy fields.

Environmental DNA (eDNA) metabarcoding is increasingly paired with electrofishing efforts for aquatic biomonitoring and it has been shown that aquatic eDNA and electrofishing can be complementary when used together. Sedimentary eDNA is also used when monitoring rivers but is infrequently paired with electrofishing. Additionally, the utility of capturing eDNA from suspended solids as an alternative sampling medium in freshwater systems has not been explored. In this study, we used a common universal 12S metabarcoding assay for fishes on three different eDNA sampling media (water, benthic surface sediments, and trapped suspended solids) to determine which most similarly estimated fish community diversity with paired electrofishing efforts in a recently restored creek in Guelph, Ontario, Canada. A mock community comprised of DNA extracts from fish inhabiting the system was used as a positive control for species detection. Estimates of species richness were most comparable between electrofishing and trapped suspended solids though water samples estimated the greatest overall species richness. However, all three eDNA sampling media were found to generate estimates of community diversity that were more similar to each other than they were to estimates from electrofishing. Differences in community diversity were associated most strongly with collection method, weakly with sampling site, and were not associated with sampling period. Additionally, an indicator species analysis revealed that the taxa discriminating between the eDNA and electrofishing methods were all taxa that could not be amplified from the mock community. These findings suggest that the dissimilarity in diversity and indicator species observed between eDNA and electrofishing sampling methods is being primarily driven by methodological limitations relating to primer specificity and resolution.

Healthy honey bees are critical in safeguarding our food supply, but monitoring their health presents a significant challenge to apiarists, biosecurity agencies and animal health experts. Our objective was to investigate the feasibility of using environmental DNA (eDNA) metabarcoding to characterize the arthropod, fungal and bacterial diversity of hives with a focus on taxa that contribute to hive health such as pests and pathogens, beneficials, and biocontrol agents. We collected hive debris from four hives approximately every 2 weeks during the pollination season, first at a research almond orchard and then at a small hobby farm. A single sample was also collected from a feral colony that was relocated to the hobby farm part way through the experiment. eDNA metabarcoding detected species from all the arthropod and microbial communities targeted in debris samples, including hive pests and pathogens as well as hive beneficials. Additionally, we detected DNA from other important agricultural pest and beneficial species not commonly associated with hives, as well as taxa that can impact human health. In total, 4480 unique amplicon sequence variants were recorded across the three taxonomic groups (arthropod, fungi and bacteria) considered in this study. Our results suggest that eDNA metabarcoding can be used to monitor different aspects of hive health, such as presence or absence of pests, pathogens, and beneficial organisms. Additionally, the whole community data collected could be used to detect and monitor agriculturally relevant species more broadly. Our findings contribute to a small but growing body of research laying the foundation for using hive diversity and indicator taxa as a measure of hive health.