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Everts T, Van Driessche C, Neyrinck S, Haegeman A, Ruttink T, Jacquemyn H, Brys R. Phenological mismatches mitigate the ecological impact of a biological invader on amphibian communities. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2024; 34:e3017. [PMID: 39118362 DOI: 10.1002/eap.3017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 05/23/2024] [Indexed: 08/10/2024]
Abstract
Horizon scans have emerged as a valuable tool to anticipate the incoming invasive alien species (IAS) by judging species on their potential impacts. However, little research has been conducted on quantifying actual impacts and assessing causes of species-specific vulnerabilities to particular IAS due to persistent methodological challenges. The underlying interspecific mechanisms driving species-specific vulnerabilities therefore remain poorly understood, even though they can substantially improve the accuracy of risk assessments. Given that interspecific interactions underlying ecological impacts of IAS are often shaped by phenological synchrony, we tested the hypothesis that temporal mismatches in breeding phenology between native species and IAS can mitigate their ecological impacts. Focusing on the invasive American bullfrog (Lithobates catesbeianus), we combined an environmental DNA (eDNA) quantitative barcoding and metabarcoding survey in Belgium with a global meta-analysis, and integrated citizen-science data on breeding phenology. We examined whether the presence of native amphibian species was negatively related to the presence or abundance of invasive bullfrogs and whether this relationship was affected by their phenological mismatches. The field study revealed a significant negative effect of increasing bullfrog eDNA concentrations on native amphibian species richness and community structure. These observations were shaped by species-specific vulnerabilities to invasive bullfrogs, with late spring- and summer-breeding species being strongly affected, while winter-breeding species remained unaffected. This trend was confirmed by the global meta-analysis. A significant negative relationship was observed between phenological mismatch and the impact of bullfrogs. Specifically, native amphibian species with breeding phenology differing by 6 weeks or less from invasive bullfrogs were more likely to be absent in the presence of bullfrogs than species whose phenology differed by more than 6 weeks with that of bullfrogs. Taken together, we present a novel method based on the combination of aqueous eDNA quantitative barcoding and metabarcoding to quantify the ecological impacts of biological invaders at the community level. We show that phenological mismatches between native and invasive species can be a strong predictor of invasion impact regardless of ecological or methodological context. Therefore, we advocate for the integration of temporal alignment between native and IAS's phenologies into invasion impact frameworks.
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Affiliation(s)
- Teun Everts
- Genetic Diversity, Research Institute for Nature and Forest, Geraardsbergen, Belgium
- Department of Biology, Plant Conservation and Population Biology, KU Leuven, Heverlee, Belgium
| | - Charlotte Van Driessche
- Genetic Diversity, Research Institute for Nature and Forest, Geraardsbergen, Belgium
- Terrestrial Ecology Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Sabrina Neyrinck
- Genetic Diversity, Research Institute for Nature and Forest, Geraardsbergen, Belgium
| | - Annelies Haegeman
- Plant Science Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Melle, Belgium
| | - Tom Ruttink
- Plant Science Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Melle, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Hans Jacquemyn
- Department of Biology, Plant Conservation and Population Biology, KU Leuven, Heverlee, Belgium
| | - Rein Brys
- Genetic Diversity, Research Institute for Nature and Forest, Geraardsbergen, Belgium
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2
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Parsley MB, Crespi EJ, Rittenhouse TAG, Brunner JL, Goldberg CS. Environmental DNA concentrations vary greatly across productive and degradative conditions, with implications for the precision of population estimates. Sci Rep 2024; 14:17392. [PMID: 39075085 PMCID: PMC11286860 DOI: 10.1038/s41598-024-66732-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 07/03/2024] [Indexed: 07/31/2024] Open
Abstract
Population size is an important metric to inform the conservation and management of species. For aquatic species, environmental DNA (eDNA) concentration has been suggested for non-invasively estimating population size. However, many biotic and abiotic factors simultaneously influence the production and degradation of eDNA which can alter the relationship between population size and eDNA concentration. We investigated the influence of temperature, salinity, and ranavirus infection on eDNA concentrations using tadpole mesocosms. Using linear regression models, we tested the influence of each experimental treatment on eDNA concentrations at three time points before and during epidemics. Prior to infection, elevated temperatures lowered eDNA concentrations, indicating that degradation was the driving force influencing eDNA concentrations. During early epidemics, no treatments strongly influenced eDNA concentrations and in late epidemics, productive forces dominated as ranavirus intensity and dead organisms increased eDNA concentrations. Finally, population size was only an important predictor of eDNA concentration in late epidemics and we observed high levels of variation between samples of replicate mesocosms. We demonstrate the complexities of several interacting factors influencing productive and degradative forces, variation in influences on eDNA concentration over short time spans, and examine the limitations of estimating population sizes from eDNA with precision in semi-natural conditions.
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Affiliation(s)
- Meghan B Parsley
- School of the Environment, Washington State University, Pullman, WA, USA.
| | - Erica J Crespi
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Tracy A G Rittenhouse
- Department of Natural Resources and the Environment, University of Connecticut, Storrs, CT, USA
| | - Jesse L Brunner
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Caren S Goldberg
- School of the Environment, Washington State University, Pullman, WA, USA
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3
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Scriver M, von Ammon U, Youngbull C, Pochon X, Stanton JAL, Gemmell NJ, Zaiko A. Drop it all: extraction-free detection of targeted marine species through optimized direct droplet digital PCR. PeerJ 2024; 12:e16969. [PMID: 38410796 PMCID: PMC10896080 DOI: 10.7717/peerj.16969] [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: 12/01/2023] [Accepted: 01/29/2024] [Indexed: 02/28/2024] Open
Abstract
Molecular biomonitoring programs increasingly use environmental DNA (eDNA) for detecting targeted species such as marine non-indigenous species (NIS) or endangered species. However, the current molecular detection workflow is cumbersome and time-demanding, and thereby can hinder management efforts and restrict the "opportunity window" for rapid management responses. Here, we describe a direct droplet digital PCR (direct-ddPCR) approach to detect species-specific free-floating extra-cellular eDNA (free-eDNA) signals, i.e., detection of species-specific eDNA without the need for filtration or DNA extraction, with seawater samples. This first proof-of-concept aquarium study was conducted with three distinct marine species: the Mediterranean fanworm Sabella spallanzanii, the ascidian clubbed tunicate Styela clava, and the brown bryozoan Bugula neritina to evaluate the detectability of free-eDNA in seawater. The detectability of targeted free-eDNA was assessed by directly analysing aquarium marine water samples using an optimized species-specific ddPCR assay. The results demonstrated the consistent detection of S. spallanzanii and B. neritina free-eDNA when these organisms were present in high abundance. Once organisms were removed, the free-eDNA signal exponentially declined, noting that free-eDNA persisted between 24-72 h. Results indicate that organism biomass, specimen characteristics (e.g., stress and viability), and species-specific biological differences may influence free-eDNA detectability. This study represents the first step in assessing the feasibility of direct-ddPCR technology for the detection of marine species. Our results provide information that could aid in the development of new technology, such as a field development of ddPCR systems, which could allow for automated continuous monitoring of targeted marine species, enabling point-of-need detection and rapid management responses.
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Affiliation(s)
- Michelle Scriver
- Biosecurity Group, Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Ulla von Ammon
- Biosecurity Group, Cawthron Institute, Nelson, New Zealand
| | - Cody Youngbull
- Nucleic Sensing Systems, LCC, Saint Paul, Minnesota, United States
| | - Xavier Pochon
- Biosecurity Group, Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Jo-Ann L Stanton
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Anastasija Zaiko
- Biosecurity Group, Cawthron Institute, Nelson, New Zealand
- Sequench Ltd, Nelson, New Zealand
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4
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Sun X, Guo N, Gao J, Xiao N. Using eDNA to survey amphibians: Methods, applications, and challenges. Biotechnol Bioeng 2024; 121:456-471. [PMID: 37986625 DOI: 10.1002/bit.28592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 11/22/2023]
Abstract
In recent years, environmental DNA (eDNA) has received attention from biologists due to its sensitivity, convenience, labor and material efficiency, and lack of damage to organisms. The extensive application of eDNA has opened avenues for the monitoring and biodiversity assessment of amphibians, which are frequently small and difficult to observe in the field, in areas such as biodiversity survey assessment and detection of specific, rare and threatened, or alien invasive species. However, the accuracy of eDNA can be influenced by factors such as ambient temperature, pH, and false positives or false negatives, which makes eDNA an adjunctive tool rather than a replacement for traditional surveys. This review provides a concise overview of the eDNA method and its workflow, summarizes the differences between applying eDNA for detecting amphibians and other organisms, reviews the research progress in eDNA technology for amphibian monitoring, identifies factors influencing detection efficiency, and discusses the challenges and prospects of eDNA. It aims to serve as a reference for future research on the application of eDNA in amphibian detection.
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Affiliation(s)
- Xiaoxuan Sun
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Ningning Guo
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Jianan Gao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
- Collage of Forestry, Shanxi Agricultural University, Jinzhong, China
| | - Nengwen Xiao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
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Ip YCA, Chang JJM, Tun KPP, Meier R, Huang D. Multispecies environmental DNA metabarcoding sheds light on annual coral spawning events. Mol Ecol 2023; 32:6474-6488. [PMID: 35852023 DOI: 10.1111/mec.16621] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 06/27/2022] [Accepted: 07/14/2022] [Indexed: 11/28/2022]
Abstract
Synchronous multispecific coral spawning generally occurs annually and forms an integral part of the coral life cycle. Apart from spawning times and species participation, however, much else remains unknown. Here, we applied environmental DNA (eDNA) metabarcoding to study two tropical reef sites of contrasting coral cover before, during and after coral spawning. Using coral-ITS2 and vertebrate-12S markers, we evaluated eDNA as an alternative monitoring tool by assessing its capabilities in detecting spawning species and tracking relative abundances of coral and fish eDNA. Over 3 years, elevated eDNA coral signals during the event (proportional read increase of up to five-fold) were observed, detecting a total of 38 coral and 133 fish species with all but one of the coral species visually observed to be spawning. This is also the first demonstration that eDNA metabarcoding can be used to infer the diurnal partitioning of night- and day-time spawning, spawning in coral species overlooked by visual surveys, and the associated changes in fish trophic structures as an indicator of spawning events. Our study paves the way for applied quantitative eDNA metabarcoding approaches to better study ephemeral and important biological events.
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Affiliation(s)
- Yin Cheong Aden Ip
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Jia Jin Marc Chang
- Department of Biological Sciences, National University of Singapore, Singapore
| | | | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, Singapore
- Tropical Marine Science Institute, National University of Singapore, Singapore
| | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, Singapore
- Tropical Marine Science Institute, National University of Singapore, Singapore
- Centre for Nature-based Climate Solutions, National University of Singapore, Singapore
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore
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6
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Zhang M, Zou Y, Xiao S, Hou J. Environmental DNA metabarcoding serves as a promising method for aquatic species monitoring and management: A review focused on its workflow, applications, challenges and prospects. MARINE POLLUTION BULLETIN 2023; 194:115430. [PMID: 37647798 DOI: 10.1016/j.marpolbul.2023.115430] [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: 04/23/2023] [Revised: 08/10/2023] [Accepted: 08/15/2023] [Indexed: 09/01/2023]
Abstract
Marine and freshwater biodiversity is under threat from both natural and manmade causes. Biological monitoring is currently a top priority for biodiversity protection. Given present limitations, traditional biological monitoring methods may not achieve the proposed monitoring aims. Environmental DNA metabarcoding technology reflects species information by capturing and extracting DNA from environmental samples, using molecular biology techniques to sequence and analyze the DNA, and comparing the obtained information with existing reference libraries to obtain species identification. However, its practical application has highlighted several limitations. This paper summarizes the main steps in the environmental application of eDNA metabarcoding technology in aquatic ecosystems, including the discovery of unknown species, the detection of invasive species, and evaluations of biodiversity. At present, with the rapid development of big data and artificial intelligence, certain advanced technologies and devices can be combined with environmental DNA metabarcoding technology to promote further development of aquatic species monitoring and management.
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Affiliation(s)
- Miaolian Zhang
- MOE Key Laboratory of Resources and Environmental Systems Optimization, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Yingtong Zou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shan Xiao
- MOE Key Laboratory of Resources and Environmental Systems Optimization, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Jing Hou
- MOE Key Laboratory of Resources and Environmental Systems Optimization, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China.
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Van Driessche C, Everts T, Neyrinck S, Halfmaerten D, Haegeman A, Ruttink T, Bonte D, Brys R. Using environmental DNA metabarcoding to monitor fish communities in small rivers and large brooks: Insights on the spatial scale of information. ENVIRONMENTAL RESEARCH 2023; 228:115857. [PMID: 37059322 DOI: 10.1016/j.envres.2023.115857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/28/2023] [Accepted: 04/04/2023] [Indexed: 05/16/2023]
Abstract
Monitoring fish communities is central to the evaluation of ecological health of rivers. Both presence/absence of fish species and their relative quantity in local fish assemblages are crucial parameters to measure. Fish communities in lotic systems are traditionally monitored via electrofishing, characterized by a known limited efficiency and high survey costs. Analysis of environmental DNA could serve as a non-destructive alternative for detection and quantification of lotic fish communities, but this approach still requires further insights in practical sampling schemes incorporating transport and dilution of the eDNA particles; optimization of predictive power and quality assurance of the molecular detection method. Via a controlled cage experiment, we aim to extend the knowledge on streamreach of eDNA in small rivers and large brooks, as laid out in the European Water Framework Directive's water typology. Using a high and low source biomass in two river transects of a species-poor river characterized by contrasting river discharge rates, we found strong and significant correlations between the eDNA relative species abundances and the relative biomass per species in the cage community. Despite a decreasing correlation over distance, the underlying community composition remained stable from 25 to 300 m, or up to 1 km downstream of the eDNA source, depending on the river discharge rate. Such decrease in similarity between relative source biomass and the corresponding eDNA-based community profile with increasing distance downstream from the source, might be attributed to variation in species-specific eDNA persistence. Our findings offer crucial insights on eDNA behaviour and characterization of riverine fish communities. We conclude that water sampled from a relatively small river offers an adequate eDNA snapshot of the total fish community in the 300-1000 m upstream transect. The potential application for other river systems is further discussed.
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Affiliation(s)
- Charlotte Van Driessche
- Research Institute for Nature and Forest (INBO), Genetic Diversity, Geraardsbergen, Belgium; Ghent University, Department of Biology, Terrestrial Ecology Unit, Ghent, Belgium.
| | - Teun Everts
- Research Institute for Nature and Forest (INBO), Genetic Diversity, Geraardsbergen, Belgium; KU Leuven, Department of Biology, Plant Conservation and Population Biology, Leuven, Belgium
| | - Sabrina Neyrinck
- Research Institute for Nature and Forest (INBO), Genetic Diversity, Geraardsbergen, Belgium
| | - David Halfmaerten
- Research Institute for Nature and Forest (INBO), Genetic Diversity, Geraardsbergen, Belgium
| | - Annelies Haegeman
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Melle, Belgium
| | - Tom Ruttink
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Melle, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Dries Bonte
- Ghent University, Department of Biology, Terrestrial Ecology Unit, Ghent, Belgium
| | - Rein Brys
- Research Institute for Nature and Forest (INBO), Genetic Diversity, Geraardsbergen, Belgium
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8
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Verhelst P, Verreycken H. First record in Europe of the Asian gobiid, shimofuri (marbled) goby Tridentiger bifasciatus Steindachner, 1881. JOURNAL OF FISH BIOLOGY 2023; 102:1253-1255. [PMID: 36855906 DOI: 10.1111/jfb.15362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 02/23/2023] [Indexed: 05/13/2023]
Abstract
In November 2022, two shimofuri (marbled) gobies Tridentiger bifasciatus Steindachner, 1881 were caught in the Gent-Terneuzen shipping canal, Belgium. It is the first record of the species in Europe. Outside its native distribution area in Japan, China and South Korea, thus far the shimofuri goby has been observed only on the West Coast of the USA, where established populations exist. The introduction vector potentially was ballast water exchange.
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Affiliation(s)
- Pieterjan Verhelst
- Team Aquatic Management, Research Institute for Nature and Forest (INBO), Brussels, Belgium
| | - Hugo Verreycken
- Team Monitoring and Restoration of Aquatic Fauna, Research Institute for Nature and Forest (INBO), Linkebeek, Belgium
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Environmental DNA Assay for the Detection of the American Bullfrog ( Lithobates catesbeianus) in the Early Stages of the Invasion in the Ebre Delta. Animals (Basel) 2023; 13:ani13040683. [PMID: 36830468 PMCID: PMC9952411 DOI: 10.3390/ani13040683] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/06/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
The American bullfrog (Lithobates catesbeianus) is considered to be one of the most harmful invasive species. In the Iberian Peninsula, this species had been cited occasionally until the year 2018, when L. catesbeianus appeared in the Ebre Delta, and, for the first time, it started breeding in a territory of the Peninsula. Using environmental DNA (eDNA) analysis and visual surveys, the American bullfrog invasion in the Ebre Delta was monitored across two consecutive years (2019-2020). No specimens were observed in 2019, and results for the eDNA survey also failed to detect this species in the Delta. In 2020, two individuals were captured and, under the most conservative criteria to constrain the number of positive detections, eDNA analyses detected the presence of the American bullfrog in at least five locations. Performing an eDNA assay yielded a higher sensitivity with a lower sampling effort than traditional methods. Although the American bullfrog does not appear to still be well-established in the Ebre Delta, only a few bullfrog individuals could be enough for their establishment in suitable habitats. In this context, eDNA assays are essential tools to facilitate the detection, control, and eradication of this species in the first stage of the invasion process.
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Chen Y, Tournayre O, Tian H, Lougheed SC. Assessing the breeding phenology of a threatened frog species using eDNA and automatic acoustic monitoring. PeerJ 2023; 11:e14679. [PMID: 36710869 PMCID: PMC9879156 DOI: 10.7717/peerj.14679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 12/13/2022] [Indexed: 01/25/2023] Open
Abstract
Background Climate change has driven shifts in breeding phenology of many amphibians, causing phenological mismatches (e.g., predator-prey interactions), and potentially population declines. Collecting data with high spatiotemporal sensitivity on hibernation emergence and breeding times can inform conservation best practices. However, monitoring the phenology of amphibians can be challenging because of their cryptic nature over much of their life cycle. Moreover, most salamanders and caecilians do not produce conspicuous breeding calls like frogs and toads do, presenting additional monitoring challenges. Methods In this study, we designed and evaluated the performance of an environmental DNA (eDNA) droplet digital PCR (ddPCR) assay as a non-invasive tool to assess the breeding phenology of a Western Chorus Frog population (Pseudacris maculata mitotype) in Eastern Ontario and compared eDNA detection patterns to hourly automatic acoustic monitoring. For two eDNA samples with strong PCR inhibition, we tested three methods to diminish the effect of inhibitors: diluting eDNA samples, adding bovine serum albumin to PCR reactions, and purifying eDNA using a commercial clean-up kit. Results We recorded the first male calling when the focal marsh was still largely frozen. Chorus frog eDNA was detected on April 6th, 6 days after acoustic monitoring revealed this first calling male, but only 2 days after males attained higher chorus activity. eDNA signals were detected at more sampling locales within the marsh and eDNA concentrations increased as more males participated in the chorus, suggesting that eDNA may be a reasonable proxy for calling assemblage size. Internal positive control revealed strong inhibition in some samples, limiting detection probability and quantification accuracy in ddPCR. We found diluting samples was the most effective in reducing inhibition and improving eDNA quantification. Conclusions Altogether, our results showed that eDNA ddPCR signals lagged behind male chorusing by a few days; thus, acoustic monitoring is preferable if the desire is to document the onset of male chorusing. However, eDNA may be an effective, non-invasive monitoring tool for amphibians that do not call and may provide a useful complement to automated acoustic recording. We found inhibition patterns were heterogeneous across time and space and we demonstrate that an internal positive control should always be included to assess inhibition for eDNA ddPCR signal interpretations.
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Huang S, Yoshitake K, Watabe S, Asakawa S. Environmental DNA study on aquatic ecosystem monitoring and management: Recent advances and prospects. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 323:116310. [PMID: 36261997 DOI: 10.1016/j.jenvman.2022.116310] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Environmental DNA (eDNA) is organismal DNA that can be detected in the environment and is derived from cellular material of organisms shed into aquatic or terrestrial environments. It can be sampled and monitored using molecular methods, which is important for the early detection of invasive and native species as well as the discovery of rare and cryptic species. While few reviews have summarized the latest findings on eDNA for most aquatic animal categories in the aquatic ecosystem, especially for aquatic eDNA processing and application. In the present review, we first performed a bibliometric network analysis of eDNA studies on aquatic animals. Subsequently, we summarized the abiotic and biotic factors affecting aquatic eDNA occurrence. We also systematically discussed the relevant experiments and analyses of aquatic eDNA from various aquatic organisms, including fish, molluscans, crustaceans, amphibians, and reptiles. Subsequently, we discussed the major achievements of eDNA application in studies on the aquatic ecosystem and environment. The application of eDNA will provide an entirely new paradigm for biodiversity conservation, environment monitoring, and aquatic species management at a global scale.
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Affiliation(s)
- Songqian Huang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, 201306, China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, 201306, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 200120, China; Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo, 113-8657, Japan.
| | - Kazutoshi Yoshitake
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Shugo Watabe
- School of Marine Biosciences, Kitasato University, Minami-ku, Sagamihara, Kanagawa, 252-0313, Japan
| | - Shuichi Asakawa
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo, 113-8657, Japan.
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Ogata S, Doi H, Igawa T, Komaki S, Takahara T. Environmental
DNA
methods for detecting two invasive alien species (American bullfrog and red swamp crayfish) in Japanese ponds. Ecol Res 2022. [DOI: 10.1111/1440-1703.12341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shigeki Ogata
- Graduate School of Life and Environmental Sciences Shimane University Matsue Shimane Japan
| | - Hideyuki Doi
- Graduate School of Information Science University of Hyogo Kobe Hyogo Japan
| | - Takeshi Igawa
- Amphibian Research Center Hiroshima University Higashi‐Hiroshima, Hiroshima Japan
- Graduate School of Integrated Sciences for Life Hiroshima University Higashi‐Hiroshima, Hiroshima Japan
| | - Shohei Komaki
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center Iwate Medical University Iwate Japan
| | - Teruhiko Takahara
- Faculty of Life and Environmental Sciences Shimane University Matsue Japan
- Estuary Research Center Shimane University Matsue Japan
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