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Li W, Hou X, Zhu Y, Du J, Xu C, Yang J, Li Y. eDNA Metabarcoding Reveals the Species-Area Relationship of Amphibians on the Zhoushan Archipelago. Animals (Basel) 2024; 14:1519. [PMID: 38891566 PMCID: PMC11171295 DOI: 10.3390/ani14111519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/10/2024] [Accepted: 05/14/2024] [Indexed: 06/21/2024] Open
Abstract
The species-area relationship is important for understanding species diversity patterns at spatial scales, but few studies have examined the relationship using environmental DNA (eDNA) techniques. We investigated amphibian diversity on 21 islands of the Zhoushan Archipelago and nearby mainland areas in China using the combination of eDNA metabarcoding and the traditional line transect method (TLTM) and identified the species-area relationship for amphibians on the islands. The mean detection probability of eDNA is 0.54, while the mean detection probability of TLTM is 0.24. The eDNA metabarcoding detected eight amphibian species on the islands and nine species in the mainland areas, compared with seven species on the islands and nine species in the mainland areas that were identified by TLTM. Amphibian richness on the islands increased with island area and habitat diversity. The species-area relationship for amphibians in the archipelago was formulated as the power function (S = 0.47A0.21) or exponential function (S = 2.59 + 2.41 (logA)). Our results suggested that eDNA metabarcoding is more sensitive for the detection of amphibian species. The combined use of eDNA metabarcoding and the traditional line transect method may optimize the survey results for amphibians.
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Affiliation(s)
- Wenhao Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xianglei Hou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunlong Zhu
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiacong Du
- School of Life Sciences, Hebei University, Baoding 071002, China
| | - Chunxia Xu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingyuan Yang
- Shengnongjia National Park Administration, Huibei Provincial Key Laboratory on Conservation Biology of the Shennongjia Golden Snub-Nosed Monkey, Shennongjia 442421, China
| | - Yiming Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, Hebei University, Baoding 071002, China
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Wu D, Lee P, Chen H, Yan F, Huang J, He Y, Wu R, Yuan Z. Validation and development of eDNA metabarcoding primers for comprehensive assessment of Chinese amphibians. Integr Zool 2024. [PMID: 38730493 DOI: 10.1111/1749-4877.12832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2024]
Abstract
Environmental DNA (eDNA) metabarcoding has emerged as a powerful, non-invasive tool for biodiversity assessments. However, the accuracy and limitations of these assessment techniques are highly dependent on the choice of primer pairs being used. Although several primer sets have been used in eDNA metabarcoding studies of amphibians, there are few comparisons of their reliability and efficiency. Here, we employed lab- and field-tested sets of publicly available and de novo-designed primers in amplifying 83 species of amphibian from all three orders (Anura, Caudata, and Gymnophiona) and 13 families present in China to evaluate the versatility and specificity of these primers sets in amphibian eDNA metabarcoding studies. Three pairs of primers were highly effective, as they could successfully amplify all the major clades of Chinese amphibians in our study. A few non-amphibian taxa were also amplified by these primers, which implies that further optimization of amphibian-specific primers is still needed. The simultaneous use of three primer sets can completely cover all the species obtained by conventional survey methods and has even effectively distinguished quite a number of species (n = 20) in the Wenshan National Nature Reserve. No single primer set could individually detect all of the species from the studied region, indicating that multiple primers might be necessary for a comprehensive survey of Chinese amphibians. Besides, seasonal variations in amphibian species composition were also revealed by eDNA metabarcoding, which was consistent with traditional survey methods. These results indicate that eDNA metabarcoding has the potential to be a powerful tool for studying spatial and temporal community changes in amphibian species richness.
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Affiliation(s)
- Dongyi Wu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing, China
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, China
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming, Yunnan, China
| | - Pingshin Lee
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Hongman Chen
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Fang Yan
- School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Jiayue Huang
- Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Yanhong He
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, China
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming, Yunnan, China
| | - Ruiyao Wu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing, China
| | - Zhiyong Yuan
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing, China
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, China
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming, Yunnan, China
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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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Weber S, Stothut M, Mahla L, Kripp A, Hirschler L, Lenz N, Junker A, Künzel S, Krehenwinkel H. Plant-derived environmental DNA complements diversity estimates from traditional arthropod monitoring methods but outperforms them detecting plant-arthropod interactions. Mol Ecol Resour 2024; 24:e13900. [PMID: 38010630 DOI: 10.1111/1755-0998.13900] [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: 06/10/2023] [Revised: 09/29/2023] [Accepted: 10/26/2023] [Indexed: 11/29/2023]
Abstract
Our limited knowledge about the ecological drivers of global arthropod decline highlights the urgent need for more effective biodiversity monitoring approaches. Monitoring of arthropods is commonly performed using passive trapping devices, which reliably recover diverse communities, but provide little ecological information on the sampled taxa. Especially the manifold interactions of arthropods with plants are barely understood. A promising strategy to overcome this shortfall is environmental DNA (eDNA) metabarcoding from plant material on which arthropods leave DNA traces through direct or indirect interactions. However, the accuracy of this approach has not been sufficiently tested. In four experiments, we exhaustively test the comparative performance of plant-derived eDNA from surface washes of plants and homogenized plant material against traditional monitoring approaches. We show that the recovered communities of plant-derived eDNA and traditional approaches only partly overlap, with eDNA recovering various additional taxa. This suggests eDNA as a useful complementary tool to traditional monitoring. Despite the differences in recovered taxa, estimates of community α- and β-diversity between both approaches are well correlated, highlighting the utility of eDNA as a broad scale tool for community monitoring. Last, eDNA outperforms traditional approaches in the recovery of plant-specific arthropod communities. Unlike traditional monitoring, eDNA revealed fine-scale community differentiation between individual plants and even within plant compartments. Especially specialized herbivores are better recovered with eDNA. Our results highlight the value of plant-derived eDNA analysis for large-scale biodiversity assessments that include information about community-level interactions.
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Affiliation(s)
- Sven Weber
- Department of Biogeography, Trier University, Trier, Germany
| | - Manuel Stothut
- Department of Biogeography, Trier University, Trier, Germany
| | - Lisa Mahla
- Department of Biogeography, Trier University, Trier, Germany
| | - Alanah Kripp
- iES Landau, Institute for Environmental Sciences, University of Kaiserslautern-Landau, Landau in der Pfalz, Germany
| | - Lena Hirschler
- Department of Biogeography, Trier University, Trier, Germany
| | - Nina Lenz
- Department of Biogeography, Trier University, Trier, Germany
| | - Anneke Junker
- Department of Biogeography, Trier University, Trier, Germany
| | - Sven Künzel
- Max Planck Institute for Evolutionary Biology, Plön, Germany
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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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Papaioannou C, Geladakis G, Kommata V, Batargias C, Lagoumintzis G. Insights in Pharmaceutical Pollution: The Prospective Role of eDNA Metabarcoding. TOXICS 2023; 11:903. [PMID: 37999555 PMCID: PMC10675236 DOI: 10.3390/toxics11110903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 11/25/2023]
Abstract
Environmental pollution is a growing threat to natural ecosystems and one of the world's most pressing concerns. The increasing worldwide use of pharmaceuticals has elevated their status as significant emerging contaminants. Pharmaceuticals enter aquatic environments through multiple pathways related to anthropogenic activity. Their high consumption, insufficient waste treatment, and the incapacity of organisms to completely metabolize them contribute to their accumulation in aquatic environments, posing a threat to all life forms. Various analytical methods have been used to quantify pharmaceuticals. Biotechnology advancements based on next-generation sequencing (NGS) techniques, like eDNA metabarcoding, have enabled the development of new methods for assessing and monitoring the ecotoxicological effects of pharmaceuticals. eDNA metabarcoding is a valuable biomonitoring tool for pharmaceutical pollution because it (a) provides an efficient method to assess and predict pollution status, (b) identifies pollution sources, (c) tracks changes in pharmaceutical pollution levels over time, (d) assesses the ecological impact of pharmaceutical pollution, (e) helps prioritize cleanup and mitigation efforts, and (f) offers insights into the diversity and composition of microbial and other bioindicator communities. This review highlights the issue of aquatic pharmaceutical pollution while emphasizing the importance of using modern NGS-based biomonitoring actions to assess its environmental effects more consistently and effectively.
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Affiliation(s)
- Charikleia Papaioannou
- Department of Biology, University of Patras, 26504 Patras, Greece; (C.P.); (G.G.); (V.K.)
| | - George Geladakis
- Department of Biology, University of Patras, 26504 Patras, Greece; (C.P.); (G.G.); (V.K.)
| | - Vasiliki Kommata
- Department of Biology, University of Patras, 26504 Patras, Greece; (C.P.); (G.G.); (V.K.)
| | - Costas Batargias
- Department of Biology, University of Patras, 26504 Patras, Greece; (C.P.); (G.G.); (V.K.)
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Osathanunkul M, Suwannapoom C. Sustainable fisheries management through reliable restocking and stock enhancement evaluation with environmental DNA. Sci Rep 2023; 13:11297. [PMID: 37438384 DOI: 10.1038/s41598-023-38218-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 07/05/2023] [Indexed: 07/14/2023] Open
Abstract
The practise of restocking and stock improvement as a means of managing fisheries and aquaculture has been widely used. However, it is difficult to claim that fish stocking is effective due to a number of challenges. One of those is the lack of suitable monitoring and assessment methods, although all assessment approaches have their strengths and weaknesses. If the full benefits of fisheries and their long-term sustainability are to be realised, it is necessary to examine the effectiveness of restocking and stock enhancement. Therefore, effective, rapid, and dependable monitoring techniques are necessary. In this study, we used an eDNA-based method to identify G. cambodgiensis at 14 sites throughout Thailand's restocking and stock enhancement programme. eDNA from this species was identified in water samples using quantitative polymerase chain reaction (qPCR) tests with primers and a probe specific to G. cambodgiensis. A successful stocking would show positive eDNA results in water samples collected from the studied sites. Only five of the studied sites returned positive eDNA readings, which could be considered a successful stocking. The locations that contained G. cambodgiensis eDNA were either confirmed to be natural habitats or were regularly stocked with a large number of hatchery fish. In this study, we demonstrated that eDNA is a reliable, fast and accurate alternative method for measuring stock improvement.
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Affiliation(s)
- Maslin Osathanunkul
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand.
| | - Chatmongkon Suwannapoom
- School of Agriculture and Natural Resources, University of Phayao, Muang District, Phayao, 56000, Thailand.
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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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9
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Pragmatic applications of DNA barcoding markers in identification of fish species – a review. ANNALS OF ANIMAL SCIENCE 2023. [DOI: 10.2478/aoas-2022-0073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Abstract
DNA barcoding and mini barcoding involve Cytochrome Oxidase Subunit I (COI) gene in mitochondrial genome and is used for accurate identification of species and biodiversity. The basic goal of the current study is to develop a complete reference database of fishes. It also evaluates the applicability of COI gene to identify fish at the species level with other aspects i.e., as Kimura 2 parameter (K2P) distance. The mean observed length of the sequence was ranging between 500 to 700 base pairs for fish species in DNA barcoding and 80 to 650 base pairs for DNA mini barcoding. This method describes the status of known to unknown samples but it also facilitates the detection of previously un-sampled species at distinct level. So, mini-barcoding is a method focuses on the analysis of short-length DNA markers has been demonstrated to be effective for species identification of processed food containing degraded DNA. While DNA meta-barcoding refers to the automated identification of multiple species from a single bulk sample. The may contain entire organisms or a single environmental sample containing degraded DNA. Despite DNA barcoding, mini barcoding and meta-barcoding are efficient methods for species identification which are helpful in conservation and proper management of biodiversity. It aids researchers to take an account of genetic as well as evolutionary relationships by collecting their morphological, distributional and molecular data. Overall, this paper discusses DNA barcoding technology and how it has been used to various fish species, as well as its universality, adaptability, and novel approach to DNA-based species identification.
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10
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Johnson MD, Freeland JR, Parducci L, Evans DM, Meyer RS, Molano-Flores B, Davis MA. Environmental DNA as an emerging tool in botanical research. AMERICAN JOURNAL OF BOTANY 2023; 110:e16120. [PMID: 36632660 DOI: 10.1002/ajb2.16120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/03/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Over the past quarter century, environmental DNA (eDNA) has been ascendant as a tool to detect, measure, and monitor biodiversity (species and communities), as a means of elucidating biological interaction networks, and as a window into understanding past patterns of biodiversity. However, only recently has the potential of eDNA been realized in the botanical world. Here we synthesize the state of eDNA applications in botanical systems with emphases on aquatic, ancient, contemporary sediment, and airborne systems, and focusing on both single-species approaches and multispecies community metabarcoding. Further, we describe how abiotic and biotic factors, taxonomic resolution, primer choice, spatiotemporal scales, and relative abundance influence the utilization and interpretation of airborne eDNA results. Lastly, we explore several areas and opportunities for further development of eDNA tools for plants, advancing our knowledge and understanding of the efficacy, utility, and cost-effectiveness, and ultimately facilitating increased adoption of eDNA analyses in botanical systems.
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Affiliation(s)
- Mark D Johnson
- Engineering Research and Development Center, Construction Engineering Research Laboratory (CERL), Champaign, IL, USA
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL, USA
| | - Joanna R Freeland
- Department of Biology, Trent University, 1600 West Bank Drive, Peterborough, ON, K9L 0G2, Canada
| | - Laura Parducci
- Department of Environmental Biology, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18D, SE-75236, Uppsala, Sweden
| | - Darren M Evans
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Rachel S Meyer
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Brenda Molano-Flores
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL, USA
| | - Mark A Davis
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL, USA
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11
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Koroiva R, Santana DJ. Evaluation of partial 12S rRNA, 16S rRNA, COI and Cytb gene sequence datasets for potential single DNA barcode for hylids (Anura: Hylidae). AN ACAD BRAS CIENC 2022; 94:e20200825. [PMID: 36477987 DOI: 10.1590/0001-3765202220200825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 05/19/2021] [Indexed: 12/09/2022] Open
Abstract
We evaluated the extent of intraspecific and interspecific genetic distances and the effectiveness of predefined threshold values using the main genes for estimates of biodiversity and specimens' identification in anurans. Partial sequences of the mitochondrial genes for small (12S) and large (16S) ribosomal subunits, cytochrome c oxidase subunit I (COI) and Cytochrome b (Cytb) of the family Hylidae were downloaded from GenBank and curated for length, coverage, and potential contaminations. We performed analyses for all sequences of each gene and the same species present in these datasets by distance and tree (monophyly)-based evaluations. We also evaluated the ability to identify specimens using these datasets applying "nearest neighbor" (NN), "best close match" (BCM) and "BOLD ID" tests. Genetic distance thresholds were generated by the function 'threshVal' and "localMinima" from SPIDER package and traditional threshold values (1%, 3%, 6% and 10%) were also evaluated. Coding genes, especially COI, had a better identification capacity than non-coding genes on barcoding gap and monophyly analysis and NN, BCM, BOLD ID tests. Considering the multiple factors involved in global DNA barcoding evaluations, we present a critical assessment of the use of these genes for biodiversity estimation and specimens' identification in anurans (e.g. hylids).
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Affiliation(s)
- Ricardo Koroiva
- Universidade Federal da Paraíba, Departamento de Sistemática e Tecnologia, Centro de Ciências Exatas e da Natureza, Laboratório Multiusuário do Programa de Pós-Graduação em Ciências Biológicas/Zoologia, Castelo Branco, Campus Universitário, s/n, 58051900 João Pessoa, PB, Brazil.,Universidade Federal de Mato Grosso do Sul, Instituto de Biociências, Laboratório Mapinguari, Cidade Universitária, Avenida Costa e Silva, s/n, 79070900 Campo Grande, MS, Brazil
| | - Diego José Santana
- Universidade Federal de Mato Grosso do Sul, Instituto de Biociências, Laboratório Mapinguari, Cidade Universitária, Avenida Costa e Silva, s/n, 79070900 Campo Grande, MS, Brazil
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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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13
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Pratomo A, Bengen DG, Zamani NP, Lane C, Humphries AT, Borbee E, Subhan B, Madduppa H. Diversity and distribution of Symbiodiniaceae detected on coral reefs of Lombok, Indonesia using environmental DNA metabarcoding. PeerJ 2022; 10:e14006. [PMID: 36312748 PMCID: PMC9610659 DOI: 10.7717/peerj.14006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 08/14/2022] [Indexed: 01/19/2023] Open
Abstract
Background Dinoflagellates of family Symbiodiniaceae are important to coral reef ecosystems because of their contribution to coral health and growth; however, only a few studies have investigated the function and distribution of Symbiodiniaceae in Indonesia. Understanding the distribution of different kinds of Symbiodiniaceae can improve forecasting of future responses of various coral reef systems to climate change. This study aimed to determine the diversity of Symbiodiniaceae around Lombok using environmental DNA (eDNA). Methods Seawater and sediment samples were collected from 18 locations and filtered to obtain fractions of 0.4-12 and >12 µm. After extraction, molecular barcoding polymerase chain reaction was conducted to amplify the primary V9-SSU 18S rRNA gene, followed by sequencing (Illumina MiSeq). BLAST, Naïve-fit-Bayes, and maximum likelihood routines were used for classification and phylogenetic reconstruction. We compared results across sampling sites, sample types (seawater/sediment), and filter pore sizes (fraction). Results Phylogenetic analyses resolved the amplicon sequence variants into 16 subclades comprising six Symbiodiniaceae genera (or genera-equivalent clades) as follows: Symbiodinium, Breviolum, Cladocopium, Durusdinium, Foraminifera Clade G, and Halluxium. Comparative analyses showed that the three distinct lineages within Cladocopium, Durusdinium, and Foraminifera Clade G were the most common. Most of the recovered sequences appeared to be distinctive of different sampling locations, supporting the possibility that eDNA may resolve regional and local differences among Symbiodiniaceae genera and species. Conclusions eDNA surveys offer a rapid proxy for evaluating Symbiodiniaceae species on coral reefs and are a potentially useful approach to revealing diversity and relative ecological dominance of certain Symbiodiniaceae organisms. Moreover, Symbiodiniaceae eDNA analysis shows potential in monitoring the local and regional stability of coral-algal mutualisms.
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Affiliation(s)
- Arief Pratomo
- Raja Ali Haji Maritime University, Tanjungpinang, Indonesia,Department of Marine Science and Technology, Institut Pertanian Bogor, Bogor, Indonesia
| | - Dietriech G. Bengen
- Department of Marine Science and Technology, Institut Pertanian Bogor, Bogor, Indonesia
| | - Neviaty P. Zamani
- Department of Marine Science and Technology, Institut Pertanian Bogor, Bogor, Indonesia
| | - Christopher Lane
- Department of Biological Sciences, University of Rhode Island, Rhode Island, United States of America
| | - Austin T. Humphries
- Department of Fisheries, Animal and Veterinary Sciences, University of Rhode Island, Rhode Island, United States of America
| | - Erin Borbee
- Department of Biological Sciences, University of Rhode Island, Rhode Island, United States of America
| | - Beginer Subhan
- Department of Marine Science and Technology, Institut Pertanian Bogor, Bogor, Indonesia
| | - Hawis Madduppa
- Department of Marine Science and Technology, Institut Pertanian Bogor, Bogor, Indonesia,Oceanogen Research Center, Bogor, Indonesia
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14
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Schmidt A, Schneider C, Decker P, Hohberg K, Römbke J, Lehmitz R, Bálint M. Shotgun metagenomics of soil invertebrate communities reflects taxonomy, biomass, and reference genome properties. Ecol Evol 2022; 12:e8991. [PMID: 35784064 PMCID: PMC9170594 DOI: 10.1002/ece3.8991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 05/11/2022] [Accepted: 05/17/2022] [Indexed: 12/03/2022] Open
Abstract
Metagenomics - shotgun sequencing of all DNA fragments from a community DNA extract - is routinely used to describe the composition, structure, and function of microorganism communities. Advances in DNA sequencing and the availability of genome databases increasingly allow the use of shotgun metagenomics on eukaryotic communities. Metagenomics offers major advances in the recovery of biomass relationships in a sample, in comparison to taxonomic marker gene-based approaches (metabarcoding). However, little is known about the factors which influence metagenomics data from eukaryotic communities, such as differences among organism groups, the properties of reference genomes, and genome assemblies.We evaluated how shotgun metagenomics records composition and biomass in artificial soil invertebrate communities at different sequencing efforts. We generated mock communities of controlled biomass ratios from 28 species from all major soil mesofauna groups: mites, springtails, nematodes, tardigrades, and potworms. We shotgun sequenced these communities and taxonomically assigned them with a database of over 270 soil invertebrate genomes.We recovered over 95% of the species, and observed relatively high false-positive detection rates. We found strong differences in reads assigned to different taxa, with some groups (e.g., springtails) consistently attracting more hits than others (e.g., enchytraeids). Original biomass could be predicted from read counts after considering these taxon-specific differences. Species with larger genomes, and with more complete assemblies, consistently attracted more reads than species with smaller genomes. The GC content of the genome assemblies had no effect on the biomass-read relationships. Results were similar among different sequencing efforts.The results show considerable differences in taxon recovery and taxon specificity of biomass recovery from metagenomic sequence data. The properties of reference genomes and genome assemblies also influence biomass recovery, and they should be considered in metagenomic studies of eukaryotes. We show that low- and high-sequencing efforts yield similar results, suggesting high cost-efficiency of metagenomics for eukaryotic communities. We provide a brief roadmap for investigating factors which influence metagenomics-based eukaryotic community reconstructions. Understanding these factors is timely as accessibility of DNA sequencing and momentum for reference genomes projects show a future where the taxonomic assignment of DNA from any community sample becomes a reality.
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Affiliation(s)
- Alexandra Schmidt
- Senckenberg Biodiversity Climate Research CenterFrankfurt am MainGermany
- Biology DepartmentJ.W. Goethe UniversityFrankfurt am MainGermany
- Loewe Center for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Limnological Institute (Environmental Genomics)University of KonstanzKonstanzGermany
| | - Clément Schneider
- Loewe Center for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Soil Zoology DepartmentSenckenberg Museum of Natural History GörlitzGörlitzGermany
| | - Peter Decker
- Loewe Center for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Blumenstr. 5GörlitzGermany
| | - Karin Hohberg
- Loewe Center for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Soil Zoology DepartmentSenckenberg Museum of Natural History GörlitzGörlitzGermany
| | - Jörg Römbke
- ECT Oekotoxikologie GmbHFlörsheim am MainGermany
| | - Ricarda Lehmitz
- Loewe Center for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Soil Zoology DepartmentSenckenberg Museum of Natural History GörlitzGörlitzGermany
| | - Miklós Bálint
- Senckenberg Biodiversity Climate Research CenterFrankfurt am MainGermany
- Loewe Center for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Institute for Insect BiotechnologyJustus Liebig UniversityGießenGermany
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15
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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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16
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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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17
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First extraction of eDNA from tree hole water to detect tree frogs: a simple field method piloted in Madagascar. CONSERV GENET RESOUR 2021. [DOI: 10.1007/s12686-021-01245-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
AbstractEnvironmental DNA (eDNA) is becoming an increasingly used tool for monitoring cryptic species within terrestrial and aquatic systems. We present the first method for extracting water from tree holes for eDNA studies of tree-dwelling frogs, and the first use of eDNA for amphibian monitoring in Madagascar. This pilot study expands on a previously developed method and aims to provide a simple field protocol for DNA extraction from very small water samples, using a relatively inexpensive kit compared to other collection methods. We collected 20 ml of water from tree holes in Ambohitantely Special Reserve in Madagascar, with the aim to survey for the Critically Endangered tree frog Anodonthyla vallani, and we developed species specific cytochrome c oxidase 1 primers for this species. While our two samples did not detect A. vallani, we successfully extracted up to 16.6 ng/µl of eDNA from the samples and using 16S rRNA primers barcoded the tree frog Plethodontohyla mihanika in one of the samples. Despite just two samples being collected, we highlight the future potential of eDNA from tree holes for investigating cryptic habitat specialist amphibians given we extracted frog eDNA from just 20 ml of water. The method provides a rapid, simple, and cost-effective method which can assist cryptic species monitoring in challenging and time-consuming field conditions and should be developed further for frog surveying in Madagascar and beyond. The newly developed primers can be used for further work using this eDNA method to survey threatened Anodonthyla frog species.
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18
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Charvoz L, Apothéloz-Perret-Gentil L, Reo E, Thiébaud J, Pawlowski J. Monitoring newt communities in urban area using eDNA metabarcoding. PeerJ 2021; 9:e12357. [PMID: 34900410 PMCID: PMC8628619 DOI: 10.7717/peerj.12357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 09/30/2021] [Indexed: 12/12/2022] Open
Abstract
Newts are amphibians commonly present in small ponds or garden pools in urban areas. They are protected in many countries and their presence is monitored through visual observation and/or trapping. However, newts are not easy to spot as they are small, elusive and often hidden at the bottom of water bodies. In recent years, environmental DNA (eDNA) has become a popular tool for detecting newts, with a focus on individual species using qPCR assays. Here, we assess the effectiveness of eDNA metabarcoding compared to conventional visual surveys of newt diversity in 45 ponds within urban areas of Geneva canton, Switzerland. We designed newt-specific mitochondrial 16S rRNA primers, which assign the majority of amplicons to newts, and were able to detect four species known to be present in the region, including the invasive subspecies Lissotriton vulgaris meridionalis, native to the Italian peninsula, that has been introduced in the Geneva area recently. The obtained eDNA results were congruent overall with conventional surveys, confirming the morphological observations in the majority of cases (67%). In 25% of cases, a species was only detected genetically, while in 8% of cases, the observations were not supported by eDNA metabarcoding. Our study confirms the usefulness of eDNA metabarcoding as a tool for the effective and non-invasive monitoring of newt community and suggests its broader use for the survey of newt diversity in urban area at larger scales.
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Affiliation(s)
- Léo Charvoz
- Department of Genetics and Evolution, University of Geneva, Geneva, Geneva, Switzerland
| | - Laure Apothéloz-Perret-Gentil
- Department of Genetics and Evolution, University of Geneva, Geneva, Geneva, Switzerland
- ID-Gene ecodiagnostics, Campus Biotech Innovation Park, Geneva, Switzerland
| | - Emanuela Reo
- Department of Genetics and Evolution, University of Geneva, Geneva, Geneva, Switzerland
| | - Jacques Thiébaud
- KARCH-GE (Swiss Coordination Center for the Protection of Amphibians and Reptiles)—Geneva Regional Branch, Switzerland, Geneva, Geneva, Switzerland
| | - Jan Pawlowski
- Department of Genetics and Evolution, University of Geneva, Geneva, Geneva, Switzerland
- ID-Gene ecodiagnostics, Campus Biotech Innovation Park, Geneva, Switzerland
- Polish Academy of Sciences, Institute of Oceanology, Sopot, Pomerania, Poland
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19
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Macher TH, Schütz R, Arle J, Beermann AJ, Koschorreck J, Leese F. Beyond fish eDNA metabarcoding: Field replicates disproportionately improve the detection of stream associated vertebrate species. METABARCODING AND METAGENOMICS 2021. [DOI: 10.3897/mbmg.5.66557] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Fast, reliable, and comprehensive biodiversity monitoring data are needed for environmental decision making and management. Recent work on fish environmental DNA (eDNA) metabarcoding shows that aquatic diversity can be captured fast, reliably, and non-invasively at moderate costs. Because water in a catchment flows to the lowest point in the landscape, often a stream, it can collect traces of terrestrial species via surface or subsurface runoff along its way or when specimens come into direct contact with water (e.g., when drinking). Thus, fish eDNA metabarcoding data can provide information on fish but also on other vertebrate species that live in riparian habitats. This additional data may offer a much more comprehensive approach for assessing vertebrate diversity at no additional costs. Studies on how the sampling strategy affects species detection especially of stream-associated communities, however, are scarce. We therefore performed an analysis on the effects of biological replication on both fish as well as (semi-)terrestrial species detection. Along a 2 km stretch of the river Mulde (Germany), we collected 18 1-L water samples and analyzed the relation of detected species richness and quantity of biological replicates taken. We detected 58 vertebrate species, of which 25 were fish and lamprey, 18 mammals, and 15 birds, which account for 50%, 22.2%, and 7.4% of all native species to the German federal state of Saxony-Anhalt. However, while increasing the number of biological replicates resulted in only 24.8% more detected fish and lamprey species, mammal, and bird species richness increased disproportionately by 68.9% and 77.3%, respectively. Contrary, PCR replicates showed little stochasticity. We thus emphasize to increase the number of biological replicates when the aim is to improve general species detections. This holds especially true when the focus is on rare aquatic taxa or on (semi-)terrestrial species, the so-called ‘bycatch’. As a clear advantage, this information can be obtained without any additional sampling or laboratory effort when the sampling strategy is chosen carefully. With the increased use of eDNA metabarcoding as part of national fish bioassessment and monitoring programs, the complimentary information provided on bycatch can be used for biodiversity monitoring and conservation on a much broader scale.
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20
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Mena JL, Yagui H, Tejeda V, Bonifaz E, Bellemain E, Valentini A, Tobler MW, Sánchez-Vendizú P, Lyet A. Environmental DNA metabarcoding as a useful tool for evaluating terrestrial mammal diversity in tropical forests. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2021; 31:e02335. [PMID: 33780592 DOI: 10.1002/eap.2335] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 11/04/2020] [Accepted: 01/14/2021] [Indexed: 06/12/2023]
Abstract
Innovative techniques, such as environmental DNA (eDNA) metabarcoding, are now promoting broader biodiversity monitoring at unprecedented scales, because of the reduction in time, presumably lower cost, and methodological efficiency. Our goal was to assess the efficiency of established inventory techniques (live-trapping grids, pitfall traps, camera trapping, mist netting) as well as eDNA for detecting Amazonian mammals. For terrestrial small mammals, we used 32 live-trapping grids based on Sherman and Tomahawk traps (total effort of 10,368 trap-nights); in addition to 16 pitfall traps (1,408 trap-nights). For bats, we used mist nets at 8 sites (4,800 net hours). For medium and large mammals, we used 72 camera trap stations (5,208 camera-days). We identified vertebrate and mammal taxa based on eDNA analysis (12S region, with V05 and Mamm01 markers) from water samples, including a total of 11 3-km transects for stagnant water sampling and seven small streams for running water sampling. A total of 106 mammal species were recorded. Building on sample-based rarefaction and extrapolation curves, both trapping grids and pitfall were successful, recording 91.16% and 82.1% of the expected species for these techniques (~22 and ~9 species), and 16.98% and 6.60% of the total recorded mammal species, respectively. Mist nets recorded 83.2% of the expected bat species (~48), and 34.91% of the total recorded species. Camera trapping recorded 99.2% of the predicted large- and medium-sized species (~31), and 33.02% of the total recorded species. eDNA recorded 75.4% of the expected mammal species for this technique (~68), and 47.0% of the total recorded species. eDNA resulted in a useful tool that saves on effort and reduces sampling costs. This study is among the first to show the large potential of eDNA metabarcoding for assessing Amazonian mammal communities, providing, in combination with conventional techniques, a rapid overview of mammal diversity with broad applications to monitoring, management and conservation. By including appropriate genetic markers and updated reference databases, eDNA metabarcoding method can be extended to the whole vertebrate community.
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Affiliation(s)
- José Luis Mena
- World Wildlife Fund-Perú, Trinidad Moran 853, Lima 14, Peru
| | | | - Vania Tejeda
- World Wildlife Fund-Perú, Trinidad Moran 853, Lima 14, Peru
- Museo de Historia Natural de la Universidad Nacional de San Agustín de Arequipa, Av. Alcides Carrión S/N, Arequipa, Peru
| | - Emilio Bonifaz
- Museo de Historia Natural Vera Alleman Haeghebaert, Universidad Ricardo Palma, Lima 33, Perú
| | - Eva Bellemain
- SPYGEN, 17 rue du Lac St André, Savoie Technolac, BP20274, Le Bourget du Lac, 73375, France
| | - Alice Valentini
- SPYGEN, 17 rue du Lac St André, Savoie Technolac, BP20274, Le Bourget du Lac, 73375, France
| | - Mathias W Tobler
- San Diego Zoo Global, Institute for Conservation Research, 15600 San Pasqual Valley Road, Escondido, California, 92027, USA
| | - Pamela Sánchez-Vendizú
- Facultad de Ciencias Biológicas de la Universidad Nacional Mayor de San Marcos, Ca. German Amezaga 375, Lima, Peru
| | - Arnaud Lyet
- World Wildlife Fund, 1250 24th Street NW, Washington, D.C., 20037, USA
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21
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Gumińska N, Łukomska-Kowalczyk M, Chaber K, Zakryś B, Milanowski R. Evaluation of V2 18S rDNA barcode marker and assessment of sample collection and DNA extraction methods for metabarcoding of autotrophic euglenids. Environ Microbiol 2021; 23:2992-3008. [PMID: 33830624 PMCID: PMC8359987 DOI: 10.1111/1462-2920.15495] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/17/2021] [Accepted: 03/26/2021] [Indexed: 12/13/2022]
Abstract
Even though the interest in metabarcoding in environmental studies is growing, euglenids are still underrepresented in both sea and freshwater bodies researches. The reason for this situation could be the unsuitability of universal eukaryotic DNA barcodes and primers as well as the lack of a verified protocol, suitable to assess euglenid diversity. In this study, using specific primers for the V2 hypervariable region of 18S rDNA for metabarcoding resulted in obtaining a high fraction (85%) of euglenid reads and species‐level identification of almost 90% of them. Fifty species were detected by the metabarcoding method, including almost all species observed using a light microscope. We investigated three biomass harvesting methods (filtering, centrifugation and scraping the side of a collection vessel) and determined that centrifugation and filtration outperformed scrapes, but the choice between them is not crucial for the reliability of the analysis. In addition, eight DNA extraction methods were evaluated. We compared five commercially available DNA isolation kits, two CTAB‐based protocols and a chelating resin. For this purpose, the efficiency of extraction, quality of obtained DNA, preparation time and generated costs were taken into consideration. After examination of the aforementioned criteria, we chose the GeneMATRIX Soil DNA Purification Kit as the most suitable for DNA isolation.
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Affiliation(s)
- Natalia Gumińska
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, ul. Żwirki i Wigury 101, PL-02-089, Warsaw, Poland
| | - Maja Łukomska-Kowalczyk
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, ul. Żwirki i Wigury 101, PL-02-089, Warsaw, Poland
| | - Katarzyna Chaber
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, ul. Żwirki i Wigury 101, PL-02-089, Warsaw, Poland
| | - Bożena Zakryś
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, ul. Żwirki i Wigury 101, PL-02-089, Warsaw, Poland
| | - Rafał Milanowski
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, ul. Żwirki i Wigury 101, PL-02-089, Warsaw, Poland
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22
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Li W, Hou X, Xu C, Qin M, Wang S, Wei L, Wang Y, Liu X, Li Y. Validating eDNA measurements of the richness and abundance of anurans at a large scale. J Anim Ecol 2021; 90:1466-1479. [PMID: 33694188 DOI: 10.1111/1365-2656.13468] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/17/2021] [Indexed: 02/06/2023]
Abstract
In some situations, environmental DNA (eDNA) metabarcoding is a more accurate tool for measuring species richness of a taxon than conventional methods. Whether this tool can reliably estimate the abundance of a taxon remains unresolved. We examined the reliability of metabarcoding for measuring anuran diversity compared to a commonly used traditional line transect method (TLTM) through the replicate sampling of three visits across 71 waterbodies (ponds or reservoirs) in Liuheng, China. We also investigated the relative contributions of species-specific characteristics and the physiochemical properties of a waterbody on the relative read count across species and waterbodies. We found that eDNA metabarcoding had a higher detection probability for each of seven anuran species found in the sampling region than TLTM. Furthermore, the relative read count estimated by metabarcoding was positively correlated with the density or relative density of individuals identified with the TLTM across waterbodies for every species. Species-specific characteristics of anurans, such as density, relative density, body mass, biomass and relative biomass, accounted for substantial variations in the read count across species and waterbodies, while physiochemical factors, including pH, temperature, water volume, vegetation and elevation, had little effect on the read count. Our results based on robust sampling suggest that metabarcoding enables more reliable and efficient measurements of anuran occurrence at a large scale during a short-term survey (within 15 days) than that obtained by the TLTM, and offers an alternative tool for quantifications of anuran abundance. Density or biomass is better and more reliable indicator of anuran abundance associated with read count than relative density or relative biomass.
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Affiliation(s)
- Wenhao Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, The Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xianglei Hou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, The Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Chunxia Xu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, The Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Mingshuo Qin
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, The Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Supen Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, The Chinese Academy of Sciences, Beijing, China
| | - Li Wei
- College of Ecology, Lishui University, Lishui, China
| | - Yanping Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, China
| | - Xuan Liu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, The Chinese Academy of Sciences, Beijing, China
| | - Yiming Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, The Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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Howell L, LaRue M, Flanagan SP. Environmental DNA as a tool for monitoring Antarctic vertebrates. NEW ZEALAND JOURNAL OF ZOOLOGY 2021. [DOI: 10.1080/03014223.2021.1900299] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Lucy Howell
- Gateway Antarctica, School of Earth and Environment, University of Canterbury, Christchurch, New Zealand
| | - Michelle LaRue
- Gateway Antarctica, School of Earth and Environment, University of Canterbury, Christchurch, New Zealand
- School of Earth and Environment, University of Canterbury, Christchurch, New Zealand
| | - Sarah P. Flanagan
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
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Mulero S, Toulza E, Loisier A, Zimmerman M, Allienne JF, Foata J, Quilichini Y, Pointier JP, Rey O, Boissier J. Malacological survey in a bottle of water: A comparative study between manual sampling and environmental DNA metabarcoding approaches. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2020.e01428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Lopes CM, Baêta D, Valentini A, Lyra ML, Sabbag AF, Gasparini JL, Dejean T, Haddad CFB, Zamudio KR. Lost and found: Frogs in a biodiversity hotspot rediscovered with environmental DNA. Mol Ecol 2020; 30:3289-3298. [PMID: 32786119 DOI: 10.1111/mec.15594] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 07/25/2020] [Accepted: 08/05/2020] [Indexed: 12/31/2022]
Abstract
Declines and extinctions are increasing globally and challenge conservationists to keep pace with biodiversity monitoring. Organisms leave DNA traces in the environment, e.g., in soil, water, and air. These DNA traces are referred to as environmental DNA (eDNA). The analysis of eDNA is a highly sensitive method with the potential to rapidly assess local diversity and the status of threatened species. We searched for DNA traces of 30 target amphibian species of conservation concern, at different levels of threat, using an environmental DNA metabarcoding approach, together with an extensive sequence reference database to analyse water samples from six montane sites in the Atlantic Coastal Forest and adjacent Cerrado grasslands of Brazil. We successfully detected DNA traces of four declined species (Hylodes ornatus, Hylodes regius, Crossodactylus timbuhy, and Vitreorana eurygnatha); two locally disappeared (Phasmahyla exilis and Phasmahyla guttata); and one species that has not been seen since 1968 (putatively assigned to Megaelosia bocainensis). We confirm the presence of species undetected by traditional methods, underscoring the efficacy of eDNA metabarcoding for biodiversity monitoring at low population densities, especially in megadiverse tropical sites. Our results support the potential application of eDNA in conservation biology, to evaluate persistence and distribution of threatened species in surveyed habitats or sites, and improve accuracy of red lists, especially for species undetected over long periods.
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Affiliation(s)
- Carla Martins Lopes
- Departamento de Biodiversidade e Centro de Aquicultura, I.B., Universidade Estadual Paulista (UNESP), Rio Claro, SP, Brazil
| | - Délio Baêta
- Departamento de Biodiversidade e Centro de Aquicultura, I.B., Universidade Estadual Paulista (UNESP), Rio Claro, SP, Brazil
| | | | - Mariana Lúcio Lyra
- Departamento de Biodiversidade e Centro de Aquicultura, I.B., Universidade Estadual Paulista (UNESP), Rio Claro, SP, Brazil
| | - Ariadne Fares Sabbag
- Departamento de Biodiversidade e Centro de Aquicultura, I.B., Universidade Estadual Paulista (UNESP), Rio Claro, SP, Brazil
| | - João Luiz Gasparini
- Núcleo em Ecologia e Desenvolvimento Socioambiental de Macaé, Universidade Federal do Rio de Janeiro (UFRJ), Macaé, RJ, Brazil
| | | | - Célio Fernando Baptista Haddad
- Departamento de Biodiversidade e Centro de Aquicultura, I.B., Universidade Estadual Paulista (UNESP), Rio Claro, SP, Brazil
| | - Kelly Raquel Zamudio
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
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McElroy ME, Dressler TL, Titcomb GC, Wilson EA, Deiner K, Dudley TL, Eliason EJ, Evans NT, Gaines SD, Lafferty KD, Lamberti GA, Li Y, Lodge DM, Love MS, Mahon AR, Pfrender ME, Renshaw MA, Selkoe KA, Jerde CL. Calibrating Environmental DNA Metabarcoding to Conventional Surveys for Measuring Fish Species Richness. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00276] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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Pabijan M, Palomar G, Antunes B, Antoł W, Zieliński P, Babik W. Evolutionary principles guiding amphibian conservation. Evol Appl 2020; 13:857-878. [PMID: 32431739 PMCID: PMC7232768 DOI: 10.1111/eva.12940] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 02/05/2020] [Accepted: 02/18/2020] [Indexed: 12/18/2022] Open
Abstract
The Anthropocene has witnessed catastrophic amphibian declines across the globe. A multitude of new, primarily human-induced drivers of decline may lead to extinction, but can also push species onto novel evolutionary trajectories. If these are recognized by amphibian biologists, they can be engaged in conservation actions. Here, we summarize how principles stemming from evolutionary concepts have been applied for conservation purposes, and address emerging ideas at the vanguard of amphibian conservation science. In particular, we examine the consequences of increased drift and inbreeding in small populations and their implications for practical conservation. We then review studies of connectivity between populations at the landscape level, which have emphasized the limiting influence of anthropogenic structures and degraded habitat on genetic cohesion. The rapid pace of environmental changes leads to the central question of whether amphibian populations can cope either by adapting to new conditions or by shifting their ranges. We gloomily conclude that extinction seems far more likely than adaptation or range shifts for most species. That said, conservation strategies employing evolutionary principles, such as selective breeding, introduction of adaptive variants through translocations, ecosystem interventions aimed at decreasing phenotype-environment mismatch, or genetic engineering, may effectively counter amphibian decline in some areas or for some species. The spread of invasive species and infectious diseases has often had disastrous consequences, but has also provided some premier examples of rapid evolution with conservation implications. Much can be done in terms of setting aside valuable amphibian habitat that should encompass both natural and agricultural areas, as well as designing protected areas to maximize the phylogenetic and functional diversity of the amphibian community. We conclude that an explicit consideration and application of evolutionary principles, although certainly not a silver bullet, should increase effectiveness of amphibian conservation in both the short and long term.
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Affiliation(s)
- Maciej Pabijan
- Institute of Zoology and Biomedical ResearchFaculty of BiologyJagiellonian UniversityKrakówPoland
| | - Gemma Palomar
- Institute of Environmental SciencesFaculty of BiologyJagiellonian UniversityKrakówPoland
| | - Bernardo Antunes
- Institute of Environmental SciencesFaculty of BiologyJagiellonian UniversityKrakówPoland
| | - Weronika Antoł
- Institute of Environmental SciencesFaculty of BiologyJagiellonian UniversityKrakówPoland
| | - Piotr Zieliński
- Institute of Environmental SciencesFaculty of BiologyJagiellonian UniversityKrakówPoland
| | - Wiesław Babik
- Institute of Environmental SciencesFaculty of BiologyJagiellonian UniversityKrakówPoland
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28
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Huerlimann R, Cooper MK, Edmunds RC, Villacorta‐Rath C, Le Port A, Robson HLA, Strugnell JM, Burrows D, Jerry DR. Enhancing tropical conservation and ecology research with aquatic environmental DNA methods: an introduction for non‐environmental DNA specialists. Anim Conserv 2020. [DOI: 10.1111/acv.12583] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- R. Huerlimann
- Centre for Sustainable Tropical Fisheries and Aquaculture College of Science and Engineering James Cook University Townsville QLD Australia
- Centre for Tropical Bioinformatics and Molecular Biology James Cook University Townsville QLD Australia
| | - M. K. Cooper
- Centre for Sustainable Tropical Fisheries and Aquaculture College of Science and Engineering James Cook University Townsville QLD Australia
- Centre for Tropical Bioinformatics and Molecular Biology James Cook University Townsville QLD Australia
| | - R. C. Edmunds
- Centre for Tropical Water and Aquatic Ecosystem Research (TropWATER) James Cook University Townsville QLD Australia
| | - C. Villacorta‐Rath
- Centre for Tropical Bioinformatics and Molecular Biology James Cook University Townsville QLD Australia
- Centre for Tropical Water and Aquatic Ecosystem Research (TropWATER) James Cook University Townsville QLD Australia
| | - A. Le Port
- Centre for Sustainable Tropical Fisheries and Aquaculture College of Science and Engineering James Cook University Townsville QLD Australia
| | - H. L. A. Robson
- Centre for Sustainable Tropical Fisheries and Aquaculture College of Science and Engineering James Cook University Townsville QLD Australia
| | - J. M. Strugnell
- Centre for Sustainable Tropical Fisheries and Aquaculture College of Science and Engineering James Cook University Townsville QLD Australia
- Centre for Tropical Bioinformatics and Molecular Biology James Cook University Townsville QLD Australia
| | - D. Burrows
- Centre for Tropical Water and Aquatic Ecosystem Research (TropWATER) James Cook University Townsville QLD Australia
| | - D. R. Jerry
- Centre for Sustainable Tropical Fisheries and Aquaculture College of Science and Engineering James Cook University Townsville QLD Australia
- Tropical Futures Institute James Cook University Singapore Singapore
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30
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Detection and Control of Invasive Freshwater Crayfish: From Traditional to Innovative Methods. DIVERSITY-BASEL 2019. [DOI: 10.3390/d11010005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Invasive alien species are widespread in freshwater systems compared to terrestrial ecosystems. Among crustaceans, crayfish in particular have been widely introduced and are considered a major threat to freshwater ecosystem functioning. New emerging techniques for detecting and controlling invasive crayfish and protecting endangered native species are; thus, now highly desirable and several are under evaluation. Important innovations have been developed in recent years for detection of both invasive and native crayfish, mainly through eDNA, which allows for the detection of the target species even at low abundance levels and when not directly observable. Forecasting models have also moved towards the creation of realistic invasion scenarios, allowing effective management plans to be developed in advance of invasions. The importance of monitoring the spread and impacts of crayfish and pathogens in developing national data and research networks is emphasised; here “citizen science” can also play a role. Emerging techniques are still being considered in the field of invasive crayfish control. Although for decades the main traditional techniques to manage invasive crayfish were solely based on trapping, since 2010 biological, biocidal, autocidal controls and sexual attractants, monosex populations, RNA interference, the sterile male release technique and oral delivery have all also been investigated for crayfish control. In this review, ongoing methodologies applied to the detection and management of invasive crayfish are discussed, highlighting their benefits and limitations.
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31
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eDNA-based crayfish plague detection as practical tool for biomonitoring and risk assessment of A. astaci-positive crayfish populations. Biol Invasions 2018. [DOI: 10.1007/s10530-018-1886-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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