1
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Adams AJ, Kamoroff C, Daniele NR, Grasso RL, Halstead BJ, Kleeman PM, Mengelt C, Powelson K, Seaborn T, Goldberg CS. From eDNA to decisions using a multi-method approach to restoration planning in streams. Sci Rep 2024; 14:14335. [PMID: 38906892 PMCID: PMC11192730 DOI: 10.1038/s41598-024-64612-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/11/2024] [Indexed: 06/23/2024] Open
Abstract
Reintroduction efforts are increasingly used to mitigate biodiversity losses, but are frequently challenged by inadequate planning and uncertainty. High quality information about population status and threats can be used to prioritize reintroduction and restoration efforts and can transform ad hoc approaches into opportunities for improving conservation outcomes at a landscape scale. We conducted comprehensive environmental DNA (eDNA) and visual encounter surveys to determine the distribution of native and non-native aquatic species in two high-priority watersheds to address key uncertainties-such as the distribution of threats and the status of existing populations-inherent in restoration planning. We then used these occurrence data to develop a menu of potential conservation actions and a decision framework to benefit an endangered vertebrate (foothill yellow-legged frog, Rana boylii) in dynamic stream systems. Our framework combines the strengths of multiple methods, allowing managers and conservation scientists to incorporate conservation science and site-specific knowledge into the planning process to increase the likelihood of achieving conservation goals.
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Affiliation(s)
- A J Adams
- School of the Environment, Washington State University, Pullman, WA, 99164, USA.
- Earth Research Institute, University of California, Santa Barbara, CA, 93106, USA.
| | - C Kamoroff
- Resource Management and Science, Yosemite National Park, El Portal, CA, 95318, USA
- Stillwater Sciences, Davis, CA, 95618, USA
| | - N R Daniele
- Resource Management and Science, Yosemite National Park, El Portal, CA, 95318, USA
| | - R L Grasso
- Resource Management and Science, Yosemite National Park, El Portal, CA, 95318, USA
| | - B J Halstead
- Western Ecological Research Center, Dixon Field Station, U.S. Geological Survey, Dixon, CA, 95620, USA
| | - P M Kleeman
- Western Ecological Research Center, Point Reyes Field Station, U.S. Geological Survey, Point Reyes Station, CA, 94956, USA
| | - C Mengelt
- Ecosystems Mission Area, U.S. Geological Survey, Modoc Hall, Sacramento, CA, 95819, USA
| | - K Powelson
- Tahoe National Forest, U.S. Forest Service, Nevada City, CA, 94949, USA
| | - T Seaborn
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
- School of Natural Resource Sciences, North Dakota State University, Fargo, ND, 58047, USA
| | - C S Goldberg
- School of the Environment, Washington State University, Pullman, WA, 99164, USA
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2
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Parsley MB, Goldberg CS. Environmental RNA can distinguish life stages in amphibian populations. Mol Ecol Resour 2024; 24:e13857. [PMID: 37593778 DOI: 10.1111/1755-0998.13857] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 07/19/2023] [Accepted: 08/08/2023] [Indexed: 08/19/2023]
Abstract
Applications of environmental DNA (eDNA) analysis methods for biomonitoring have grown exponentially over the last decade and provide a wealth of new information on the distribution of species. However, eDNA methods have limited application for estimating population-level metrics. Environmental RNA (eRNA) has the potential to address ecological questions by gathering population demographic information from environmental media but may be challenging to detect and analyze. We developed gene-specific eRNA assays targeting keratin-associated genes in two focal species, American bullfrogs (Lithobates catesbeianus) and tiger salamanders (Ambystoma mavortium) to answer an important question in amphibian management: whether species detections represent breeding populations versus transitory adults. We performed an extensive laboratory validation with amphibians housed across development stages, where we collected 95 and 127 environmental samples for bullfrogs and salamanders, respectively. Both assays were highly specific to the larval stage and amplified with high sensitivity (90% in bullfrog and 88.4% in tiger salamander samples). We then applied our validated assays to multiple natural systems. When larvae were present, we found 74.1% overall detection in bullfrog field samples and 70.8% and 48.5% overall detection in field samples from ponds with A. macrodactylum and A. californiense larvae, correlating with eDNA detection rates. When only adults were present, we did not detect larvae-specific eRNA in A. macrodactylum ponds, despite high eDNA detection rates. Although much work is ahead for optimizing assay design, sampling and filtering methods, we demonstrate that eRNA can successfully be used to discern life stages with direct application for ecology and conservation management.
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Affiliation(s)
- Meghan B Parsley
- School of the Environment, Washington State University, Pullman, Washington, USA
| | - Caren S Goldberg
- School of the Environment, Washington State University, Pullman, Washington, USA
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3
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Vanderpool DD, Wilcox TM, Young MK, Pilgrim KL, Schwartz MK. Simultaneous species detection and discovery with environmental DNA metabarcoding: A freshwater mollusk case study. Ecol Evol 2024; 14:e11020. [PMID: 38371866 PMCID: PMC10870330 DOI: 10.1002/ece3.11020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/11/2023] [Accepted: 01/03/2024] [Indexed: 02/20/2024] Open
Abstract
Environmental DNA (eDNA) sampling is a powerful tool for rapidly characterizing biodiversity patterns for specious, cryptic taxa with incomplete taxonomies. One such group that are also of high conservation concern are North American freshwater gastropods. In particular, springsnails of the genus Pyrgulopsis (Family: Hydrobiidae) are prevalent throughout the western United States where >140 species have been described. Many of the described species are narrow endemics known from a single spring or locality, and it is believed that there are likely many additional species which have yet to be described. The distribution of these species across the landscape is of interest because habitat loss and degradation, climate change, groundwater mining, and pollution have resulted in springsnail imperilment rates as high as 92%. Determining distributions with conventional sampling methods is limited by the fact that these snails are often <5 mm in length with few distinguishing morphological characters, making them both difficult to detect and to identify. We developed an eDNA metabarcoding protocol that is both inexpensive and capable of rapid, accurate detection of all known Pyrgulopsis species. When compared with conventional collection techniques, our pipeline consistently resulted in detection at sites previously known to contain Pyrgulopsis springsnails and at a cost per site that is likely to be substantially less than the conventional sampling and individual barcoding that has been done historically. Additionally, because our method uses eDNA extracted from filtered water, it is non-destructive and suitable for the detection of endangered species where "no take" restrictions may be in effect. This effort represents both a tool which is immediately applicable to taxa of high conservation concern across western North America and a case study in the broader application of eDNA sampling for landscape assessments of cryptic taxa of conservation concern.
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Affiliation(s)
- Daniel D. Vanderpool
- USDA Forest Service Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish ConservationMissoulaMontanaUSA
| | - Taylor M. Wilcox
- USDA Forest Service Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish ConservationMissoulaMontanaUSA
| | - Michael K. Young
- USDA Forest Service Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish ConservationMissoulaMontanaUSA
| | - Kristine L. Pilgrim
- USDA Forest Service Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish ConservationMissoulaMontanaUSA
| | - Michael K. Schwartz
- USDA Forest Service Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish ConservationMissoulaMontanaUSA
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4
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Holmes AE, Baerwald MR, Rodzen J, Schreier BM, Mahardja B, Finger AJ. Evaluating environmental DNA detection of a rare fish in turbid water using field and experimental approaches. PeerJ 2024; 12:e16453. [PMID: 38188170 PMCID: PMC10768661 DOI: 10.7717/peerj.16453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 10/23/2023] [Indexed: 01/09/2024] Open
Abstract
Detection sensitivity of aquatic species using environmental DNA (eDNA) generally decreases in turbid water but is poorly characterized. In this study, eDNA detection targeted delta smelt (Hypomesus transpacificus), a critically endangered estuarine fish associated with turbid water. eDNA sampling in the field was first paired with a trawl survey. Species-specific detection using a Taqman qPCR assay showed concordance between the methods, but a weak eDNA signal. Informed by the results of field sampling, an experiment was designed to assess how turbidity and filtration methods influence detection of a rare target. Water from non-turbid (5 NTU) and turbid (50 NTU) estuarine sites was spiked with small volumes (0.5 and 1 mL) of water from a delta smelt tank to generate low eDNA concentrations. Samples were filtered using four filter types: cartridge filters (pore size 0.45 μm) and 47 mm filters (glass fiber, pore size 1.6 μm and polycarbonate, pore sizes 5 and 10 μm). Prefiltration was also tested as an addition to the filtration protocol for turbid water samples. eDNA copy numbers were analyzed using a censored data method for qPCR data. The assay limits and lack of PCR inhibition indicated an optimized assay. Glass fiber filters yielded the highest detection rates and eDNA copies in non-turbid and turbid water. Prefiltration improved detection in turbid water only when used with cartridge and polycarbonate filters. Statistical analysis identified turbidity as a significant effect on detection probability and eDNA copies detected; filter type and an interaction between filter type and prefilter were significant effects on eDNA copies detected, suggesting that particulate-filter interactions can affect detection sensitivity. Pilot experiments and transparent criteria for positive detection could improve eDNA surveys of rare species in turbid environments.
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Affiliation(s)
- Ann E. Holmes
- Genomic Variation Laboratory, University of California, Davis, Davis, California, United States
- Graduate Group in Ecology, University of California, Davis, Davis, California, United States
| | - Melinda R. Baerwald
- California Department of Water Resources, West Sacramento, California, United States
| | - Jeff Rodzen
- Genetics Research Laboratory, California Department of Fish and Wildlife, Sacramento, California, United States
| | - Brian M. Schreier
- California Department of Water Resources, West Sacramento, California, United States
| | - Brian Mahardja
- Bureau of Reclamation, US Department of the Interior, Sacramento, California, United States
| | - Amanda J. Finger
- Genomic Variation Laboratory, University of California, Davis, Davis, California, United States
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5
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Jo TS. Pooling of intra-site measurements inflates variability of the correlation between environmental DNA concentration and organism abundance. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:936. [PMID: 37436641 DOI: 10.1007/s10661-023-11539-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 06/19/2023] [Indexed: 07/13/2023]
Abstract
Environmental DNA (eDNA) analysis can promote efficient ecosystem monitoring and resource management. However, limited knowledge of the factors affecting the relationship between eDNA concentration and organism abundance causes uncertainty in relative abundance estimates based on eDNA concentration. Pooling of data points obtained from multiple locations within a site has been used to mitigate intra-site variation in eDNA and abundance estimates, but decreases the sample size used for estimating the relationship. I here assessed how the pooling of intra-site measurements of eDNA concentration and organism abundance impacted the reliability of the correlative relationship between eDNA concentration and organism abundance. Mathematical models were developed to simulate measurements of eDNA concentrations and organism abundances from multiple locations in a given survey site, and the CVs (coefficient of variability) of the correlations were compared depending on whether data points from different locations were individually treated or pooled. Although the mean and median values of the correlation coefficients were similar between the scenarios, the CVs of the simulated correlations were substantially higher under the pooled scenario than the individual scenario. Additionally, I re-analyzed two empirical studies conducted in lakes, both showing higher CVs of the correlations by pooling intra-site measurements. This study suggests that it would make eDNA-based abundance estimation more reliable and reproducible to individually analyze target eDNA concentrations and organism abundance estimates.
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Affiliation(s)
- Toshiaki S Jo
- Research Fellow of Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo, 102-0083, Japan.
- Ryukoku Center for Biodiversity Science, 1-5, Yokotani, Oe-cho, Seta, Otsu City, Shiga, 520-2194, Japan.
- Faculty of Advanced Science and Technology, Ryukoku University, 1-5, Yokotani, Oe-cho, Seta, Otsu City, Shiga, 520-2194, Japan.
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6
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Zanovello L, Girardi M, Marchesini A, Galla G, Casari S, Micheletti D, Endrizzi S, Fedrigotti C, Pedrini P, Bertorelle G, Hauffe HC. A validated protocol for eDNA-based monitoring of within-species genetic diversity in a pond-breeding amphibian. Sci Rep 2023; 13:4346. [PMID: 36928612 PMCID: PMC10020426 DOI: 10.1038/s41598-023-31410-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/11/2023] [Indexed: 03/18/2023] Open
Abstract
In light of the dramatic decline in amphibian biodiversity, new cost-efficient tools to rapidly monitor species abundance and population genetic diversity in space and time are urgently needed. It has been amply demonstrated that the use of environmental DNA (eDNA) for single-species detection and characterization of community composition can increase the precision of amphibian monitoring compared to traditional (observational) approaches. However, it has been suggested that the efficiency and accuracy of the eDNA approach could be further improved by more timely sampling; in addition, the quality of genetic diversity data derived from the same DNA has been confirmed in other vertebrate taxa, but not amphibians. Given the availability of previous tissue-based genetic data, here we use the common frog Rana temporaria Linnaeus, 1758 as our target species and an improved eDNA protocol to: (i) investigate differences in species detection between three developmental stages in various freshwater environments; and (ii) study the diversity of mitochondrial DNA (mtDNA) haplotypes detected in eDNA (water) samples, by amplifying a specific fragment of the COI gene (331 base pairs, bp) commonly used as a barcode. Our protocol proved to be a reliable tool for monitoring population genetic diversity of this species, and could be a valuable addition to amphibian conservation and wetland management.
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Affiliation(s)
- Lucia Zanovello
- Conservation Genomics Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, TN, Italy
- Conservation Biology Unit, MUSE - Science Museum Trento, Trento, Italy
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Matteo Girardi
- Conservation Genomics Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, TN, Italy
| | - Alexis Marchesini
- Institute for Sustainable Plant Protection (IPSP), The National Research Council of Italy (CNR), Sesto Fiorentino, Florence, Italy
| | - Giulio Galla
- Conservation Genomics Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, TN, Italy
| | - Stefano Casari
- Conservation Genomics Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, TN, Italy
| | - Diego Micheletti
- Computational Biology Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, TN, Italy
| | - Sonia Endrizzi
- Conservation Biology Unit, MUSE - Science Museum Trento, Trento, Italy
| | - Chiara Fedrigotti
- Conservation Biology Unit, MUSE - Science Museum Trento, Trento, Italy
| | - Paolo Pedrini
- Conservation Biology Unit, MUSE - Science Museum Trento, Trento, Italy
| | - Giorgio Bertorelle
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Heidi Christine Hauffe
- Conservation Genomics Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, TN, Italy.
- National Biodiversity Future Center, S.c.a.r.l., Palermo, Italy.
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7
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Detection of the Endangered Siamese Bat Catfish ( Oreoglanis siamensis Smith, 1933) in Doi Inthanon National Park Using Environmental DNA. Animals (Basel) 2023; 13:ani13030538. [PMID: 36766427 PMCID: PMC9913137 DOI: 10.3390/ani13030538] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 01/04/2023] [Accepted: 01/16/2023] [Indexed: 02/05/2023] Open
Abstract
Siamese bat catfish (Oreoglanis siamensis Smith, 1993) has been listed as an endangered species, and its abundance has been severely declining due to habitat degradation and overfishing. To establish an appropriate management strategy, it is crucial to gain information about the distribution of this endangered species. As O. siamensis live under rocks in streams, detecting their presence is difficult. Recently, environmental DNA (eDNA)-based detection has been demonstrated to be a valid tool for monitoring rare species, such as O. siamensis. Therefore, this study developed an eDNA assay targeting a 160 bp fragment of the COI region to detect the presence of this species in its natural habitat. An amount of 300 mL of water samples (0.7 μm filtered) were collected from 15 sites in the Mae Klang sub-basin, where this fish species was visually detected at two locations. O. siamensis eDNA was detected at 12 of the 15 sites sampled with varying concentrations (0.71-20.27 copies/mL), including at the sites where this species was visually detected previously. The developed O. siamensis eDNA assay was shown to be effective for detecting the presence of this endangered species in the Klang Phat and Klang Rivers within the Doi Inthanon National Park.
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8
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Yao M, Zhang S, Lu Q, Chen X, Zhang SY, Kong Y, Zhao J. Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward. Mol Ecol 2022; 31:5132-5164. [PMID: 35972241 DOI: 10.1111/mec.16659] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 07/20/2022] [Accepted: 07/27/2022] [Indexed: 12/15/2022]
Abstract
Vast global declines of freshwater and marine fish diversity and population abundance pose serious threats to both ecosystem sustainability and human livelihoods. Environmental DNA (eDNA)-based biomonitoring provides robust, efficient, and cost-effective assessment of species occurrences and population trends in diverse aquatic environments. Thus, it holds great potential for improving conventional surveillance frameworks to facilitate fish conservation and fisheries management. However, the many technical considerations and rapid developments underway in the eDNA arena can overwhelm researchers and practitioners new to the field. Here, we systematically analysed 416 fish eDNA studies to summarize research trends in terms of investigated targets, research aims, and study systems, and reviewed the applications, rationales, methodological considerations, and limitations of eDNA methods with an emphasis on fish and fisheries research. We highlighted how eDNA technology may advance our knowledge of fish behaviour, species distributions, population genetics, community structures, and ecological interactions. We also synthesized the current knowledge of several important methodological concerns, including the qualitative and quantitative power eDNA has to recover fish biodiversity and abundance, and the spatial and temporal representations of eDNA with respect to its sources. To facilitate ecological applications implementing fish eDNA techniques, recent literature was summarized to generate guidelines for effective sampling in lentic, lotic, and marine habitats. Finally, we identified current gaps and limitations, and pointed out newly emerging research avenues for fish eDNA. As methodological optimization and standardization improve, eDNA technology should revolutionize fish monitoring and promote biodiversity conservation and fisheries management that transcends geographic and temporal boundaries.
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Affiliation(s)
- Meng Yao
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Shan Zhang
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Qi Lu
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Xiaoyu Chen
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Si-Yu Zhang
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Yueqiao Kong
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Jindong Zhao
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
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9
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Moss WE, Harper LR, Davis MA, Goldberg CS, Smith MM, Johnson PTJ. Navigating the trade‐offs between environmental
DNA
and conventional field surveys for improved amphibian monitoring. Ecosphere 2022. [DOI: 10.1002/ecs2.3941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Wynne E. Moss
- Department of Ecology & Evolutionary Biology University of Colorado Boulder Colorado USA
| | - Lynsey R. Harper
- Illinois Natural History Survey Prairie Research Institute, University of Illinois at Urbana‐Champaign Champaign Illinois USA
- NatureMetrics Ltd, CABI Site Egham UK
| | - Mark A. Davis
- Illinois Natural History Survey Prairie Research Institute, University of Illinois at Urbana‐Champaign Champaign Illinois USA
| | - Caren S. Goldberg
- School of the Environment Washington State University Pullman Washington USA
| | - Matthew M. Smith
- School of the Environment Washington State University Pullman Washington USA
| | - Pieter T. J. Johnson
- Department of Ecology & Evolutionary Biology University of Colorado Boulder Colorado USA
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10
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Zhao B, van Bodegom PM, Trimbos K. The particle size distribution of environmental DNA varies with species and degradation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 797:149175. [PMID: 34303977 DOI: 10.1016/j.scitotenv.2021.149175] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 07/15/2021] [Accepted: 07/17/2021] [Indexed: 06/13/2023]
Abstract
Environmental DNA (eDNA) analysis is frequently used as a non-invasive method to investigate species and biodiversity in ecosystems. However, such eDNA may represent both organisms currently present as well as species that released their DNA some point in the past, thereby representing a mix of current and historic biodiversity. This may lead to a false-positive detection of organisms' presence. As the eDNA particle size distribution (PSD) changes along with the decay process, it may facilitate solving the above problem. Here, we set up tank experiments with snails, zebrafish and daphnids, respectively, to monitor the change in eDNA PSD and eDNA degradation through time after removing organisms. We found that zebrafish eDNA decays more slowly for larger particle sizes. Across all species tested, the percentage of large size ranges tended to increase over time while the smaller sizes showed relatively fast decay rates. As a result, PSD changed consistently with eDNA decay, although initial PSD varied between species. In combination, we propose that eDNA PSD can be used to assess the current prevalence of organisms at an eDNA sampling location while avoiding false-positives on the presence of species. Our findings expand the applicability of eDNA for monitoring target species in freshwater ecosystems.
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Affiliation(s)
- Beilun Zhao
- Department of Environmental Biology, Institute of Environmental Sciences, Leiden University, Einsteinweg 2, 2333 CC Leiden, Netherlands.
| | - Peter M van Bodegom
- Department of Environmental Biology, Institute of Environmental Sciences, Leiden University, Einsteinweg 2, 2333 CC Leiden, Netherlands
| | - Krijn Trimbos
- Department of Environmental Biology, Institute of Environmental Sciences, Leiden University, Einsteinweg 2, 2333 CC Leiden, Netherlands
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11
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Villacorta-Rath C, Hoskin CJ, Strugnell JM, Burrows D. Long distance (>20 km) downstream detection of endangered stream frogs suggests an important role for eDNA in surveying for remnant amphibian populations. PeerJ 2021; 9:e12013. [PMID: 34692243 PMCID: PMC8483009 DOI: 10.7717/peerj.12013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/28/2021] [Indexed: 01/04/2023] Open
Abstract
Background Globally, amphibian species have suffered drastic population declines over the past 40 years. Hundreds of species are now listed as Critically Endangered, with many of these considered "possibly extinct". Most of these species are stream-dwelling frogs inhabiting remote, montane areas, where remnant populations are hard to find using traditional surveys. Environmental DNA (eDNA) could revolutionize surveys for 'missing' and endangered amphibian populations by screening water samples from downstream sections to assess presence in the upstream catchments. However, the utility of this survey technique is dependent on quantifying downstream detection probability and distances. Methods Here we tested downstream detection distances in two endangered stream frogs (Litoria lorica and L. nannotis) that co-occur in a remote stream catchment in north-east Australia, and for which we know precise downstream distributional limits from traditional surveys. Importantly, the two last populations of L. lorica persist in this catchment: one small (~1,000 frogs) and one very small (~100 frogs). We conducted eDNA screening at a series of sites kilometers downstream from the populations using precipitation from two fixed water volumes (15 and 100 mL) and via water filtering (mean 1,480 L). Results We detected L. nannotis and the small L. lorica population (~1,000 frogs) at most sampling sites, including 22.8 km downstream. The filtration method was highly effective for far-downstream detection, as was precipitation from 100 mL water samples, which also resulted in consistent detections at the far-downstream sites (including to 22.8 km). In contrast, we had limited downstream detection success for the very small L. lorica population (~100 frogs). Discussion The ecological aspects of our study system, coupled with thorough traditional surveys, enabled us to measure downstream eDNA detection distances with accuracy. We demonstrate that eDNA from a small population of approximately 1,000 frogs can be detected as far as 22.8 km downstream from the population. Water filtration is considered best for eDNA detection of rare aquatic species-indeed it was effective in this study-but we also achieved far-downstream detections when precipitating eDNA from 100 mL water samples. Collecting small water volumes for subsequent precipitation in the lab is more practical than filtration when surveying remote areas. Our downstream detection distances (>20 km) suggest eDNA is a valuable tool for detecting rare stream amphibians. We provide recommendations on optimal survey methods.
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Affiliation(s)
- Cecilia Villacorta-Rath
- Centre for Tropical Water and Aquatic Ecosystem Research (TropWATER), James Cook University, Townsville, QLD, Australia
| | - Conrad J Hoskin
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - Jan M Strugnell
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - Damien Burrows
- Centre for Tropical Water and Aquatic Ecosystem Research (TropWATER), James Cook University, Townsville, QLD, Australia
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12
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Bedwell ME, Hopkins KVS, Dillingham C, Goldberg CS. Evaluating Sierra Nevada Yellow‐Legged Frog Distribution Using Environmental DNA. J Wildl Manage 2021. [DOI: 10.1002/jwmg.22053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
| | | | - Colin Dillingham
- U.S. Forest Service R5, 39696 State Highway 70 Quincy CA 95971 USA
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13
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Woodell JD, Neiman M, Levri EP. Matching a snail's pace: successful use of environmental DNA techniques to detect early stages of invasion by the destructive New Zealand mud snail. Biol Invasions 2021; 23:3263-3274. [PMID: 34093071 PMCID: PMC8166578 DOI: 10.1007/s10530-021-02576-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 05/13/2021] [Indexed: 12/27/2022]
Abstract
Early detection of invasive species allows for a more rapid and effective response. Restoration of the native ecosystem after an invasive population has established is expensive and difficult but more likely to succeed when invasions are detected early in the invasion process. Containment efforts to prevent the spread of known invasions also benefit from earlier knowledge of invaded sites. Environmental DNA (eDNA) techniques have emerged as a tool that can identify invasive species at a distinctly earlier time point than traditional methods of detection. Here, we focus on whether eDNA techniques can be successfully applied to detect new invasions by the destructive New Zealand Mud Snail Potamopyrgus antipodarum (NZMS). It is an opportune time to apply eDNA-based detection in P. antipodarum, which is currently expanding its invasive range across eastern North America. We collected water samples from eight sites in central Pennsylvania that prior evidence indicated were not yet invaded by the NZMS but were part of the same watershed as other previously documented invaded sites. We found evidence for NZMS invasion at five of the eight sites, with subsequent physical confirmation of mud snails at one of these sites. This study is the first example of successful application of eDNA to detect a previously unidentified invasive population of NZMS, setting the stage for further monitoring of at-risk sites to detect and control new invasions of this destructive snail. This study also shows potential opportunities for invasion monitoring offered by using low-cost efforts and methods that are adaptable for citizen science.
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Affiliation(s)
- James D. Woodell
- Department of Biology & Department of Gender, Women’s, and Sexuality Studies, University of Iowa, 129 E Jefferson Street, Iowa City, IA 52242 USA
| | - Maurine Neiman
- Department of Biology & Department of Gender, Women’s, and Sexuality Studies, University of Iowa, 129 E Jefferson Street, Iowa City, IA 52242 USA
| | - Edward P. Levri
- Division of Mathematics and Natural Sciences, Penn State - Altoona, 3000 Ivyside Park, Altoona, PA 16601 USA
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Dual Detection of the Chytrid Fungi Batrachochytrium spp. with an Enhanced Environmental DNA Approach. J Fungi (Basel) 2021; 7:jof7040258. [PMID: 33808405 PMCID: PMC8065926 DOI: 10.3390/jof7040258] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 03/23/2021] [Accepted: 03/26/2021] [Indexed: 01/24/2023] Open
Abstract
Environmental DNA (eDNA) is becoming an indispensable tool in biodiversity monitoring, including the monitoring of invasive species and pathogens. Aquatic chytrid fungi Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal) are major threats to amphibians. However, the use of eDNA for detecting these pathogens has not yet become widespread, due to technological and economic obstacles. Using the enhanced eDNA approach (a simple and cheap sampling protocol) and the universally accepted qPCR assay, we confirmed the presence of Bsal and Bd in previously identified sites in Spain, including four sites that were new for Bsal. The new approach was successfully tested in laboratory conditions using manufactured gene fragments (gBlocks) of the targeted DNA sequence. A comparison of storage methods showed that samples kept in ethanol had the best DNA yield. Our results showed that the number of DNA copies in the Internal Transcribed Spacer region was 120 copies per Bsal cell. Eradication of emerging diseases requires quick and cost-effective solutions. We therefore performed cost-efficiency analyses of standard animal swabbing, a previous eDNA approach, and our own approach. The procedure presented here was evaluated as the most cost-efficient. Our findings will help to disseminate information about efforts to prevent the spread of chytrid fungi.
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15
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Sepulveda AJ, Hoegh A, Gage JA, Caldwell Eldridge SL, Birch JM, Stratton C, Hutchins PR, Barnhart EP. Integrating Environmental DNA Results With Diverse Data Sets to Improve Biosurveillance of River Health. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.620715] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Autonomous, robotic environmental (e)DNA samplers now make it possible for biological observations to match the scale and quality of abiotic measurements collected by automated sensor networks. Merging these automated data streams may allow for improved insight into biotic responses to environmental change and stressors. Here, we merged eDNA data collected by robotic samplers installed at three U.S. Geological Survey (USGS) streamgages with gridded daily weather data, and daily water quality and quantity data into a cloud-hosted database. The eDNA targets were a rare fish parasite and a more common salmonid fish. We then used computationally expedient Bayesian hierarchical occupancy models to evaluate associations between abiotic conditions and eDNA detections and to simulate how uncertainty in result interpretation changes with the frequency of autonomous robotic eDNA sample collection. We developed scripts to automate data merging, cleaning and analysis steps into a chained-step, workflow. We found that inclusion of abiotic covariates only provided improved insight for the more common salmonid fish since its DNA was more frequently detected. Rare fish parasite DNA was infrequently detected, which caused occupancy parameter estimates and covariate associations to have high uncertainty. Our simulations found that collecting samples at least once per day resulted in more detections and less parameter uncertainty than less frequent sampling. Our occupancy and simulation results together demonstrate the advantages of robotic eDNA samplers and how these samples can be combined with easy to acquire, publicly available data to foster real-time biosurveillance and forecasting.
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