Environmental DNA最新文献

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.

A large number of marker typologies have been developed for the metabarcoding of environmental DNA (eDNA). Generalist markers have been advocated for their ability to amplify many taxa simultaneously and produce exhaustive biodiversity assessments, while more specific markers have been proposed for their higher ability to detect and discriminate taxa within a more restricted group. Quantitative comparisons between generalist and specific markers are needed to assess their relative efficiency depending on study targets. Here we compared the performance of one generalist (Euka02, amplifying all eukaryotic groups), one intermediate (Arth02, amplifying arthropods), and two specific markers (Coll01 and Inse01, amplifying springtails and insects, respectively) for the assessment of springtails and insects diversity using eDNA metabarcoding. The four markers were used to analyze eDNA extracted from > 1200 soil samples collected in recently deglaciated terrains. We then assessed whether the different markers were able to detect community responses to key environmental drivers (soil temperature, time since glacier retreat, plant productivity, and topographic wetness). The two specific markers detected more taxa of both springtails and insects than the generalist markers; still the taxonomic richness and community dissimilarity were well correlated between generalist and specific markers. There was good overlap between the taxa identified by the specific markers and those identified by the generalist ones, but the specific markers often detected the taxa identified by the generalist markers, plus several additional ones. Both generalist and specific markers detected the impact of key environmental drivers on arthropods; still the specific markers showed the strongest power to detect relationships, and the most generalist marker was unable to identify the weaker relationships. Generalist markers efficiently provide an overall view of soil biodiversity; nevertheless complementing them with specific markers allows more detailed biodiversity measures, and provides a clearer picture of its response to environmental stressors.

Environmental DNA (eDNA) metabarcoding is widely used in biodiversity monitoring, and its popularity is also growing because of its potential to simultaneously detect multiple taxonomic groups, allowing holistic community assessments. When working with water samples, the choice of the filter type is one of the key methodological factors influencing community characterization, with 0.22 μm pore size filters typically used for microbial communities and larger filters for eDNA of larger organisms. However, as holistic community assessments are increasingly adopted, the use of a single filter pore size would help to optimize sampling and experimental efforts. Yet, it remains unclear whether filters with large pore sizes can effectively capture both microbial and macro-organism eDNA. This study evaluates the use of 0.45 μm filters, commonly used for metazoan eDNA metabarcoding, in assessing microbial diversity across different coastal environments. Replicates of water samples from the Venice Lagoon and nearby waters were filtered independently using both 0.45 μm and the standard 0.22 μm pore size filters and analyzed through 16S rRNA gene metabarcoding. Both filters capture a shared core microbial community, but they also retain distinct taxa. Alpha diversity was significantly higher in samples collected with the 0.45 μm filters, which also showed a more effective recovery of particle-associated microbes. Our work contributes to optimizing eDNA-based methodologies for large-scale multi-taxa biodiversity monitoring, demonstrating that 0.45 μm filters can effectively capture microbial diversity and supporting their use in holistic studies in aquatic environments.

Environmental DNA (eDNA)-based detection is a valuable biomonitoring tool that is well-developed for water, soil, and scat substrates. Emergent research is focusing on air as a new substrate, including opportunistically collected natural spiderwebs which may have negative impacts on local spider diversity. Here, we design novel artificial spiderwebs and compare their effectiveness with natural spiderwebs and aquatic eDNA approaches for biomonitoring of terrestrial taxa. A total of 33 eDNA samples (18 water, 6 natural spiderwebs, 9 artificial spiderwebs) were collected from a rural property in Palmerston North (Aotearoa New Zealand). Three amplicons (COI, 16S, and ITS) were sequenced for each sample to evaluate the performance of each collection method for detecting invertebrates, vertebrates, and plant/algal taxa. The 16S amplicon performed best in terms of sequencing output and consistency, as well as species accumulation curves, with the COI dataset performing worst for all eDNA collection methods. Alpha diversity varied by amplicon and collection method in both value and consistency among samples, with 16S and ITS retrieving higher diversity for water samples and both artificial and natural webs outperforming water in fungal COI diversity recovery. Ordination plots showed clear differences in sample similarity across biomes, with all three amplicons showing differentiation between water and either web type. However, specialist species were recovered by each of the two web types, with artificial webs consistently recovering more unique diversity than natural webs. Our results suggest that artificial spiderwebs could be a promising new method in the eDNA biomonitoring toolbox, providing biodiversity data that complements water-based collections and, depending on the research question, may serve as a sufficient proxy for natural spiderweb studies.