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Mu Y, Zhang J, Yang J, Wu J, Zhang Y, Yu H, Zhang X. Enhancing amphibian biomonitoring through eDNA metabarcoding. Mol Ecol Resour 2024; 24:e13931. [PMID: 38345249 DOI: 10.1111/1755-0998.13931] [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: 05/08/2023] [Revised: 01/03/2024] [Accepted: 01/10/2024] [Indexed: 02/17/2024]
Abstract
Surveying biodiversity has taken a quantum leap with environmental DNA (eDNA) metabarcoding, an immensely powerful approach lauded for its efficiency, sensitivity, and non-invasiveness. This approach emerges as a game-changer for the elusive realm of endangered and rare species-think nocturnal, environmentally elusive amphibians. Here, we have established a framework for constructing a reliable metabarcoding pipeline for amphibians, covering primer design, performance evaluation, laboratory validation, and field validation processes. The Am250 primer, located on the mitochondrial 16S gene, was optimal for the eDNA monitoring of amphibians, which demonstrated higher taxonomic resolution, smaller species amplification bias, and more extraordinary detection ability compared to the other primers tested. Am250 primer exhibit an 83.8% species amplification rate and 75.4% accurate species identification rate for Chinese amphibians in the in silico PCR and successfully amplified all tested species of the standard samples in the in vitro assay. Furthermore, the field-based mesocosm experiment showed that DNA can still be detected by metabarcoding even days to weeks after organisms have been removed from the mesocosm. Moreover, field mesocosm findings indicate that eDNA metabarcoding primers exhibit different read abundances, which can affect the relative biomass of species. Thus, appropriate primers should be screened and evaluated by three experimental approaches: in silico PCR simulation, target DNA amplification, and mesocosm eDNA validation. The selection of a single primer set or multiple primers' combination should be based on the monitoring groups to improve the species detection rate and the credibility of results.
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Affiliation(s)
- Yawen Mu
- State Key Laboratory of Pollution Control & Resource, School of the Environment, Nanjing University, Nanjing, China
- Jiangsu Provincial Environmental Monitoring Center, Nanjing, China
| | - Jingwen Zhang
- State Key Laboratory of Pollution Control & Resource, School of the Environment, Nanjing University, Nanjing, China
| | - Jianghua Yang
- State Key Laboratory of Pollution Control & Resource, School of the Environment, Nanjing University, Nanjing, China
- School of Marine Science and Engineering, Nanjing Normal University, Nanjing, China
| | - Jun Wu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Nanjing, China
| | - Yong Zhang
- Jiangsu Provincial Environmental Monitoring Center, Nanjing, China
| | - Hongxia Yu
- State Key Laboratory of Pollution Control & Resource, School of the Environment, Nanjing University, Nanjing, China
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource, School of the Environment, Nanjing University, Nanjing, China
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Lu S, Zeng H, Xiong F, Yao M, He S. Advances in environmental DNA monitoring: standardization, automation, and emerging technologies in aquatic ecosystems. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2493-5. [PMID: 38512561 DOI: 10.1007/s11427-023-2493-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 10/30/2023] [Indexed: 03/23/2024]
Abstract
Environmental DNA (eDNA) monitoring, a rapidly advancing technique for assessing biodiversity and ecosystem health, offers a noninvasive approach for detecting and quantifying species from various environmental samples. In this review, a comprehensive overview of current eDNA collection and detection technologies is provided, emphasizing the necessity for standardization and automation in aquatic ecological monitoring. Furthermore, the intricacies of water bodies, from streams to the deep sea, and the associated challenges they pose for eDNA capture and analysis are explored. The paper delineates three primary eDNA survey methods, namely, bringing back water, bringing back filters, and bringing back data, each with specific advantages and constraints in terms of labor, transport, and data acquisition. Additionally, innovations in eDNA sampling equipment, including autonomous drones, subsurface samplers, and in-situ filtration devices, and their applications in monitoring diverse taxa are discussed. Moreover, recent advancements in species-specific detection and eDNA metabarcoding are addressed, highlighting the integration of novel techniques such as CRISPR-Cas and nanopore sequencing that enable precise and rapid detection of biodiversity. The implications of environmental RNA and epigenetic modifications are considered for future applications in providing nuanced ecological data. Lastly, the review stresses the critical role of standardization and automation in enhancing data consistency and comparability for robust long-term biomonitoring. We propose that the amalgamation of these technologies represents a paradigm shift in ecological monitoring, aligning with the urgent call for biodiversity conservation and sustainable management of aquatic ecosystems.
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Affiliation(s)
- Suxiang Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Honghui Zeng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Fan Xiong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Meng Yao
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China.
- School of Life Sciences, Peking University, Beijing, 100871, China.
| | - Shunping He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
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Quilumbaquin W, Carrera-Gonzalez A, Van der heyden C, Ortega-Andrade HM. Environmental DNA and visual encounter surveys for amphibian biomonitoring in aquatic environments of the Ecuadorian Amazon. PeerJ 2023; 11:e15455. [PMID: 37456876 PMCID: PMC10348306 DOI: 10.7717/peerj.15455] [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: 07/04/2022] [Accepted: 05/03/2023] [Indexed: 07/18/2023] Open
Abstract
Background The development of anthropogenic activities has generated a decline in aquatic fauna populations, and amphibians have been the most affected. The decline of batrachofauna is concerning, as 41% of all species worldwide are endangered. For this reason, rapid, efficient, and non-invasive biodiversity monitoring techniques are needed, and environmental DNA (eDNA) is one such tool that has been sparsely applied in Ecuador. This technique has allowed scientists generates information on species diversity and amphibian community composition from a water sample. This study applied eDNA-based biomonitoring analyses and visual encounter surveys (VES) as inventory techniques to identify the diversity of aquatic amphibians in the Tena River micro-basin (TRMB). Methods The experimental design was divided into three components: (1) fieldwork: all amphibians were recorded by the VES technique and water samples were collected; (2) laboratory work: DNA isolation from amphibian tissue samples and eDNA-containing filters, amplification, electrophoresis, and sequencing were performed; (3) Data analysis: a local DNA reference database was constructed, and eDNA sequence data were processed for classification, taxonomic assignment, and ecological interpretation. Results Using both eDNA and VES, we detected 33 amphibian species (13 with eDNA only, five with VES only, and 15 with both methods). These species belonged to six amphibian families: Hylidae being the richest with 14 species (three eDNA, one VES, and 10 with both methods), followed by Strabomantidae with nine species (six eDNA, one VES, and two with both methods). All families were detected with both methods, except for the Aromobatidae, having one single record (Allobates aff. insperatus) by VES. Individually, eDNA detected 28 species and had a detection probability (DP) of 0.42 CI [0.40-0.45], while VES recorded 20 species with a DP of 0.17 CI [0.14-0.20]. Similarly, using VES, Cochranella resplendens was detected for the first time in TRMB, while with eDNA, four mountain frogs Pristimantis acerus, Pristimantis eriphus, Pristimantis mallii, and Pristimantis sp. (INABIO 15591) previously recorded at 1,518 m.a.s.l. at altitudes below 600 m.a.s.l. were detected. Conclusions Results obtained in this study showed that eDNA-based detection had a greater capacity to detect amphibians in aquatic environments compared to VES. The combination of VES and eDNA improves the sensitivity of species detection and provides more reliable, robust, and detailed information. The latter is essential for developing conservation strategies in the Ecuadorian Amazon.
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Affiliation(s)
- Walter Quilumbaquin
- Biogeography and Spatial Ecology Research Group, Universidad Regional Amazónica Ikiam, Tena, Napo, Ecuador
| | - Andrea Carrera-Gonzalez
- Biogeography and Spatial Ecology Research Group, Universidad Regional Amazónica Ikiam, Tena, Napo, Ecuador
- Molecular Biology and Biochemistry Lab, Universidad Regional Amazónica Ikiam, Tena, Napo, Ecuador
| | - Christine Van der heyden
- Health and Water Technology Research Centre, Department of Biosciences and Industrial Technology, HOGENT–Univesity of Applied Sciences and arts, Gent, Belgium
| | - H. Mauricio Ortega-Andrade
- Biogeography and Spatial Ecology Research Group, Universidad Regional Amazónica Ikiam, Tena, Napo, Ecuador
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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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Sakata MK, Kawata MU, Kurabayashi A, Kurita T, Nakamura M, Shirako T, Kakehashi R, Nishikawa K, Hossman MY, Nishijima T, Kabamoto J, Miya M, Minamoto T. Development and evaluation of PCR primers for environmental DNA (eDNA) metabarcoding of Amphibia. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.76534] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Biodiversity monitoring is important for the conservation of natural ecosystems in general, but particularly for amphibians, whose populations are pronouncedly declining. However, amphibians’ ecological traits (e.g. nocturnal or aquatic) often prevent their precise monitoring. Environmental DNA (eDNA) metabarcoding – analysis of extra-organismal DNA released into the environment – allows the easy and effective monitoring of the biodiversity of aquatic organisms. Here, we developed and tested the utility of original PCR primer sets. First, we conducted in vitro PCR amplification tests with universal primer candidates using total DNA extracted from amphibian tissues. Five primer sets successfully amplified the target DNA fragments (partial 16S rRNA gene fragments of 160–311 bp) from all 16 taxa tested (from the three living amphibian orders Anura, Caudata and Gymnophiona). Next, we investigated the taxonomic resolution retrieved using each primer set. The results revealed that the universal primer set “Amph16S” had the highest resolution amongst the tested sets. Finally, we applied Amph16S to the water samples collected in the field and evaluated its detection capability by comparing the species detected using eDNA and physical survey (capture-based sampling and visual survey) in multiple agricultural ecosystems across Japan (160 sites in 10 areas). The eDNA metabarcoding with Amph16S detected twice as many species as the physical surveys (16 vs. 8 species, respectively), indicating the effectiveness of Amph16S in biodiversity monitoring and ecological research for amphibian communities.
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