Environmental DNA

Journal: Environmental DNA

Publisher

Wiley

ISSN

2637-4943

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Publications1 - 10 of 30

Introduction to special issue: Advancing disease ecology through eDNA monitoring of infectious agents
Childress, Jasmine; Faust, Christina L.; Deiner, Kristy (2024)
Environmental DNA
This special issue focuses on the applications of environmental DNA (eDNA) sequencing for the detection and monitoring of disease-causing agents, including viruses, bacteria, protozoans, myxozoans, fungi, trematodes, and arthropods. We explore the impact of eDNA technologies, such as metabarcoding and qPCR, in understanding the dynamics of pathogens in various environments as well as their implications for conservation, biosecurity, and veterinary and agricultural health under the “One Health” framework. This issue addresses how molecular sequencing provides innovative solutions to the challenges faced by conventional parasite and pathogen detection methods, enabling a more comprehensive understanding of the spatiotemporal dynamics of disease agents. Finally, we discuss the challenges in eDNA applications, such as primer development and taxonomic resolution, and the opportunities for future research in advancing eDNA methodologies for infectious disease studies. This issue highlights the growing importance of eDNA surveillance in understanding and managing the health of ecosystems and at-risk species.
Sensitive environmental DNA (eDNA) methods to detect hemlock woolly adelgid and its biological control predators Leucotaraxis silver flies and a Laricobius beetle
Kirtane, Anish; Dietschler, Nicholas J.; Bittner, Tonya D.; et al. (2022)
Environmental DNA
Environmental DNA (eDNA) analysis can be a powerful tool for the early detection of invasive organisms. However, research on terrestrial eDNA detection from foliage surfaces has been limited. In this study, we developed methods to capture and detect eDNA using qPCR from an invasive forest pest, hemlock woolly adelgid (Adelges tsugae), and three of its biological control predators Leucotaraxis piniperda, Leucotaraxis argenticollis, and Laricobius nigrinus. We designed four highly efficient qPCR assays with a low limit of detection (1–10 copies/reaction). The assay targeting A. tsugae was species-specific. The assays targeting Le. piniperda, and Le. argenticollis were biotype-specific in addition to being species-specific demonstrating applications of eDNA analysis beyond species-level detection. The La. nigrinus assay also detected DNA from closely related and hybridizing Laricobius rubidus. The eDNA methods were evaluated against traditional detection methods. We collected foliage samples from three strata (bottom, middle, and top) of eastern hemlock trees to detect the presence of A. tsugae. The detection of the biological control predators was evaluated using western hemlock foliage samples collected from the predators' native range in western Washington. The eDNA methods had significantly higher positive detection rates (2.8–4.5 times) than conventional methods of all target species. The strata of sampling were not significant in determining the presence of A. tsugae infestation. The eDNA concentration positively correlated with the observed density for all species. This study demonstrates the efficacy of eDNA analysis as a more sensitive tool for early detection of A. tsugae and to track the establishment of its biological control predators.
Environmental DNA highlights fish biodiversity in mesophotic ecosystems
Muff, Marion; Jaquier, Mélissa; Marques, Virginie; et al. (2023)
Environmental DNA
Mesophotic marine ecosystems are characterized by lower light penetration supporting specialized fish fauna. Due to their depths (−30–−150 m), accessibility is challenging, and the structure of mesophotic fish assemblages is generally less known than either shallow reefs or deep zones with soft bottoms which are generally trawled. Environmental DNA metabarcoding from seawater filtered in situ could improve our ability to monitor the diversity of mesophotic ecosystems. Here, we developed and tested a submersible standalone pumping device allowing targeted marine water filtering to explore the biodiversity of two mesophotic ecosystems, one temperate along the Provence coast in the North-Western Mediterranean Sea and one tropical at the seamount La Pérouse in the Western Indian Ocean. We filtered water samples from depths ranging between 0 and 200 m in the Mediterranean Sea and between 60 and 140 m in the Indian Ocean and applied a metabarcoding protocol using the teleo primer pair targeting the 12S mitochondrial rDNA (Actinopterygii and Chondrichthyes). For both study regions, our eDNA surveys were able to recover highly diverse fish assemblages, and the compositional analysis of eDNA samples showed both a marked signal of fish compositional turnover and overlapping taxa between depth zones. Further, we observed that a substantial number of species were found in samples collected in depths beyond their reported depth range suggesting an underestimation of species' depth tolerances. eDNA metabarcoding should thus complement existing knowledge of species' geographic distributions across space and depth. Overall, our results demonstrate the potential of eDNA metabarcoding for future mesophotic surveys as it allows fast and broad biodiversity assessment.
A validation scale to determine the readiness of environmental DNA assays for routine species monitoring
Thalinger, Bettina; Deiner, Kristy; Harper, Lynsey R.; et al. (2021)
Environmental DNA
The use of environmental DNA (eDNA) analysis for species monitoring requires rigorous validation—from field sampling to the analysis of PCR-based results—for meaningful application and interpretation. Assays targeting eDNA released by individual species are typically validated with no predefined criteria to answer specific research questions in one ecosystem. Hence, the general applicability of assays, as well as associated uncertainties and limitations, often remain undetermined. The absence of clear guidelines for assay validation prevents targeted eDNA assays from being incorporated into species monitoring and policy; thus, their establishment is essential for realizing the potential of eDNA-based surveys. We describe the measures and tests necessary for successful validation of targeted eDNA assays and the associated pitfalls to form the basis of guidelines. A list of 122 variables was compiled, consolidated into 14 thematic blocks (e.g., “in silico analysis”), and arranged on a 5-level validation scale from “incomplete” to “operational” with defined minimum validation criteria for each level. These variables were evaluated for 546 published single-species assays. The resulting dataset was used to provide an overview of current validation practices and test the applicability of the validation scale for future assay rating. Of the 122 variables, 20% to 76% were reported; the majority (30%) of investigated assays were classified as Level 1 (incomplete), and 15% did not achieve this first level. These assays were characterized by minimal in silico and in vitro testing, but their share in annually published eDNA assays has declined since 2014. The meta-analysis demonstrates the suitability of the 5-level validation scale for assessing targeted eDNA assays. It is a user-friendly tool to evaluate previously published assays for future research and routine monitoring, while also enabling the appropriate interpretation of results. Finally, it provides guidance on validation and reporting standards for newly developed assays.
Airborne environmental DNA metabarcoding for the monitoring of terrestrial insects—A proof of concept from the field
Roger, Fabian; Ghanavi, Hamid R.; Danielsson, Natalie; et al. (2022)
Environmental DNA
Biodiversity is in decline due to human-induced pressures on ecosystems around the world. To be able to counteract this alarming trend, it is paramount to closely monitor biodiversity at global scales. Because this is practically impossible with traditional methods, the last decade has seen a strong push for new solutions. In aquatic ecosystems, the monitoring of species from environmental DNA (eDNA) has emerged as one of the most powerful tools at our disposal, but in terrestrial ecosystems, the power of eDNA for monitoring has so far been hampered by the local scale of the samples. In this study, we report the successful detection of insects from airborne eDNA from samples taken in the field. We compare our results to two traditional insect monitoring methods (1) light traps for moth monitoring and (2) transect walks for the monitoring of butterflies and wild bees. Airborne eDNA metabarcoding revealed DNA from six classes of arthropods, and twelve order of insects—including representatives from the four largest orders: Diptera (flies), Lepidoptera (butterflies and moths), Coleoptera (beetles), and Hymenoptera (bees, wasps, and ants). We did not detect all species observed using traditional methods and suggest further directions for the development of airborne eDNA metabarcoding. We also recovered DNA from nine species of vertebrates, including frogs, birds, and mammals as well as from 12 other phyla. Airborne eDNA has the potential to become a powerful tool for terrestrial biodiversity monitoring, with many impactful applications including the monitoring of pests, invasive, or endangered species and disease vectors.
Homogeneity in terrestrial land cover is reflected in fish diversity patterns in a Chinese river system
Kirschner, Dominik; Zhang, Yan; Zhong, Wenjun; et al. (2023)
Environmental DNA
In river systems worldwide, land cover changes have been identified as major drivers of biodiversity change. Quantifying how terrestrial land cover impacts riverine diversity requires local biodiversity assessments. In this study, we investigated the association of terrestrial land cover and the corresponding riverine fish species communities using eDNA-metabarcoding in the Chinese Shaying River basin. This basin is home to about 37 million people and is largely dominated by a mix of intense agriculture and urban areas, creating a relatively homogeneous, intensely used landscape. We investigated whether the homogeneous landscape is mirrored in the composition and structure of fish communities in the river network. We sampled eDNA in spring and fall of 2018, amplified it with a primer designed for local fish species and used operational taxonomic units (OTU) assigned to fish as proxy for diversity. Furthermore, we used redundancy analysis, general linear models, and distance decay curves to assess the effects of land cover on fish communities. We found that the Shaying River showed relatively high basin-wide richness (63 OTU) and seasonal differences in local richness, but limited community differentiation. Variations in alpha- and beta-diversity, measured as local OTU richness and pairwise distance-decay across the basin were low. Redundancy analysis showed only a weak association between observed aquatic communities and their terrestrial surroundings in a 10 km buffer upstream. The lack of community differentiation assessed by eDNA metabarcoding reflects the homogeneous and intense land-use in this basin.
Investigating pelagic biodiversity and gelatinous zooplankton communities in the rapidly changing European Arctic: An eDNA metabarcoding survey
Murray, Ayla; Priest, Taylor; Antich, Adria; et al. (2024)
Environmental DNA
Fram Strait, the gateway between the Arctic and Atlantic Oceans, is undergoing major climate change-induced physical and biological transformations. In particular, rapid warming and ongoing "Atlantification" are driving species range shifts and altering food web structures in the Arctic. Understanding and predicting the consequences of these processes on future ecosystems requires detailed assessments of local and pelagic biodiversity. Gelatinous zooplankton (GZP) is an important component of pelagic communities, and recent evidence indicates that such communities are undergoing major changes in the Fram Strait. However, as sampling GZP is challenging, they are regularly underestimated in biodiversity, distribution, and abundance. To overcome this and address existing ecological knowledge gaps, we investigated patterns of pelagic metazoan diversity in Fram Strait using environmental DNA (eDNA) metabarcoding of the cytochrome c oxidase I (COI) gene. We successfully detected a broad range of taxa from the marine metazoan and GZP communities across sampling locations and ocean depth zones. We demonstrate the vertical structuring of diversity and elucidate relationships between taxa and water mass indicators, such as salinity and temperature. Furthermore, when comparing eDNA data with net and video transect data for GZP at the same period and location, we found that eDNA uncovered a higher number of taxa, including several that were not detected by the other methods. This study is a contribution to the formation of baseline Arctic GZP biodiversity datasets, as well as future research on changing marine metazoan biodiversity and community composition.
Evaluating bioinformatics pipelines for population-level inference using environmental DNA
Macé, Bastien; Hocdé, Régis; Marques, Virginie; et al. (2022)
Environmental DNA
Environmental DNA is mainly not only used at the interspecific level, to quantify species diversity in ecosystems, but can also be used to quantify intraspecific genetic variability, thus avoiding the need to sample individual tissue. However, errors in the amplification and sequencing of eDNA samples can blur this intraspecific signal and strongly over-estimate genetic diversity. Existing bioinformatics pipelines therefore need to be tested to evaluate whether reliable levels of intraspecific genetic variability can be derived from eDNA samples. Here, we compare the ability of twelve metabarcoding pipelines to detect intraspecific genetic variability combining five programs. All pipelines have common pre-processing steps, a processing data step using programs among obiclean; DADA2; SWARM; and LULU. An additional chimera removal step is also investigated based on two programs (VSEARCH or DADA2). The case study was the natural intraspecific variation within Mullus surmuletus in experimental settings. We developed specific primers for this species, located on the mitochondrial D-loop fragment (barcode MS-DL06). Thirty-nine individuals were collected from the Mediterranean Sea, placed into four aquariums, and their DNA was sequenced on this marker to build an intraspecific reference database. After filtering the aquarium water, DNA was extracted, amplified, and sequenced using the primer pair developed. We then quantified the number of true haplotypes returned by each pipeline and its capacity to eliminate most of the erroneous sequences. We show that the program DADA2 with a two-parent chimeric sequence removal step is the best tool to estimate intraspecific diversity from eDNA. Furthermore, our approach was also able to detect true M. surmuletus haplotypes in two eDNA samples collected in the Mediterranean Sea. We conclude that the combination of an appropriate intrapopulation barcode and a denoising pipeline like DADA2 with a chimeric sequence removal step is promising to make population-level inference using environmental DNA possible.
General principles for assignments of communities from eDNA: Open versus closed taxonomic databases
Blackman, Rosetta C.; Walser, Jean-Claude; Rüber, Lukas; et al. (2023)
Environmental DNA
Metabarcoding of environmental DNA (eDNA) is a powerful tool for describing biodiversity, such as finding keystone species or detecting invasive species in environmental samples. Continuous improvements in the method and the advances in sequencing platforms over the last decade have meant this approach is now widely used in biodiversity sciences and biomonitoring. For its general use, the method hinges on a correct identification of taxa. However, past studies have shown how this crucially depends on important decisions during sampling, sample processing, and subsequent handling of sequencing data. With no clear consensus as to the best practice, particularly the latter has led to varied bioinformatic approaches and recommendations for data preparation and taxonomic identification. In this study, using a large freshwater fish eDNA sequence dataset, we compared the frequently used zero-radius Operational Taxonomic Unit (zOTU) approach of our raw reads and assigned it taxonomically (i) in combination with publicly available reference sequences (open databases) or (ii) with an OSU (Operational Sequence Units) database approach, using a curated database of reference sequences generated from specimen barcoding (closed database). We show both approaches gave comparable results for common species. However, the commonalities between the approaches decreased with read abundance and were thus less reliable and not comparable for rare species. The success of the zOTU approach depended on the suitability, rather than the size, of a reference database. Contrastingly, the OSU approach used reliable DNA sequences and thus often enabled species-level identifications, yet this resolution decreased with the recent phylogenetic age of the species. We show the need to include target group coverage, outgroups and full taxonomic annotation in reference databases to avoid misleading annotations that can occur when using short amplicon sizes as commonly used in eDNA metabarcoding studies. Finally, we make general suggestions to improve the construction and use of reference databases for metabarcoding studies in the future.
Large‐scale eDNA monitoring of multiple aquatic pathogens as a tool to provide risk maps for wildlife diseases
Sieber, Natalie; King, Alex; Krieg, Raphael; et al. (2024)
Environmental DNA
Multiple parasites and pathogens cause disease in aquatic wildlife and in aquaculture species, generating a need for monitoring and management. Conventional disease monitoring methods involve laborious, costly, and invasive capture and examination of host species, and require specialized expertise for every host and pathogen of interest. Environmental DNA could provide simultaneous occurrence data for multiple pathogens across different host taxa, valuable for using parasite diversity as, for example, a bioindicator of ecosystem disturbance. Here, we tested the potential for simultaneous detection of four wildlife pathogens in water samples from 280, mainly riverine, sites across Switzerland. We targeted the crayfish pathogen Aphanomyces astaci, the amphibian pathogen Batrachochytrium dendrobatidis, and the fish pathogens Saprolegnia parasitica and Tetracapsuloides bryosalmonae. The eDNA detection showed a widespread distribution of A. astaci, S. parasitica, and T. bryosalmonae, although A. astaci and T. bryosalmonae were not detected in some alpine river catchments. B. dendrobatidis was detected only rarely, which was expected since the sampling did not target amphibian breeding sites. Co-detection rates were higher in rivers than in lakes, likely reflecting the habitat preferences and distributions of the host species. We discuss the advantages and limitations of eDNA-based pathogen monitoring and list a set of recommendations for managers. Our study illustrates how eDNA-based techniques can monitor several pathogen species concurrently, thus facilitating more comprehensive disease monitoring schemes. Combined with metabarcoding approaches in the future, eDNA-based sampling and detection can facilitate the incorporation of parasite and pathogen occurrence and diversity as an indicator for aquatic ecosystem health, and for revealing the hidden biodiversity and structure of parasite communities.

Publications1 - 10 of 30

Journal: Environmental DNA

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