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Li X, Xu Q, Xia R, Zhang N, Wang S, Ding S, Gao X, Jia X, Shang G, Chen X. Stochastic process is main factor to affect plateau river fish community assembly. ENVIRONMENTAL RESEARCH 2024; 254:119083. [PMID: 38735377 DOI: 10.1016/j.envres.2024.119083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/03/2024] [Accepted: 05/04/2024] [Indexed: 05/14/2024]
Abstract
Plateau river ecosystems are often highly vulnerable and responsive to environmental change. The driving mechanism of fish diversity and community assembly in plateau rivers under changing environments presents a significant complexity to the interdisciplinary study of ecology and environment. This study integrated molecular biological techniques and mathematical models to identify the mechanisms influencing spatial heterogeneity of freshwater fish diversity and driving fish community assembly in plateau rivers. By utilizing environmental-DNA metabarcoding and the null model, this study revealed the impact of the stochastic process on fish diversity variations and community assembly in the Huangshui Plateau River of the Yellow River Basin (YRB) in China. This research identified 30 operational taxonomic units (OTUs), which correspond to 20 different fish species. The findings of this study revealed that the fish α-diversity in the upstream region of Xining is significantly higher than in the middle-lower reach (Shannon index: P = 0.017 and Simpson: P = 0.035). This pattern was not found to be related to any other environmental factors besides altitude (P = 0.023) that we measured. Further, the study indicated that the assembly of fish communities in the Huangshui River primarily depends on stochastic ecological processes. These findings suggested that elevation was not the primary factor impacting the biodiversity patterns of fish in plateau rivers. In plateau rivers, spatial heterogeneity of fish community on elevation is mainly determined by stochastic processes under habitat fragmentation, rather than any other physicochemical environmental factors. The limitations of connectivity in the downstream channel of the river could be taken the mainly responsibility for stochastic processes of fish community in Huangshui River. Incorporating ecological processes in the eDNA approach holds great potential for future monitoring and evaluation of fish biodiversity and community assembly in plateau rivers.
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Affiliation(s)
- Xiaoxuan Li
- State Environmental Protection Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Science, Beijing, China
| | - Qigong Xu
- State Environmental Protection Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Science, Beijing, China
| | - Rui Xia
- State Environmental Protection Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Science, Beijing, China.
| | - Nan Zhang
- College of Water Science, Beijing Normal University, Beijing, China
| | - Shuping Wang
- State Environmental Protection Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Science, Beijing, China
| | - Sen Ding
- State Environmental Protection Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Science, Beijing, China
| | - Xin Gao
- State Environmental Protection Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Science, Beijing, China
| | - Xiaobo Jia
- State Environmental Protection Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Science, Beijing, China
| | - Guangxia Shang
- State Environmental Protection Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Science, Beijing, China
| | - Xiaofei Chen
- State Environmental Protection Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Science, Beijing, 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; 67:1368-1384. [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] [MESH Headings] [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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Hu H, Liu L, Wei XY, Duan JJ, Deng JY, Pei DS. Revolutionizing aquatic eco-environmental monitoring: Utilizing the RPA-Cas-FQ detection platform for zooplankton. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 929:172414. [PMID: 38631624 DOI: 10.1016/j.scitotenv.2024.172414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/15/2024] [Accepted: 04/10/2024] [Indexed: 04/19/2024]
Abstract
The integration of recombinase polymerase amplification (RPA) with CRISPR/Cas technology has revolutionized molecular diagnostics and pathogen detection due to its unparalleled sensitivity and trans-cleavage ability. However, its potential in the ecological and environmental monitoring scenarios for aquatic ecosystems remains largely unexplored, particularly in accurate qualitative/quantitative detection, and its actual performance in handling complex real environmental samples. Using zooplankton as a model, we have successfully optimized the RPA-CRISPR/Cas12a fluorescence detection platform (RPA-Cas-FQ), providing several crucial "technical tips". Our findings indicate the sensitivity of CRISPR/Cas12a alone is 5 × 109 copies/reaction, which can be dramatically increased to 5 copies/reaction when combined with RPA. The optimized RPA-Cas-FQ enables reliable qualitative and semi-quantitative detection within 50 min, and exhibits a good linear relationship between fluorescence intensity and DNA concentration (R2 = 0.956-0.974***). Additionally, we developed a rapid and straightforward identification procedure for single zooplankton by incorporating heat-lysis and DNA-barcode techniques. We evaluated the platform's effectiveness using real environmental DNA (eDNA) samples from the Three Gorges Reservoir, confirming its practicality. The eDNA-RPA-Cas-FQ demonstrated strong consistency (Kappa = 0.43***) with eDNA-Metabarcoding in detecting species presence/absence in the reservoir. Furthermore, the two semi-quantitative eDNA technologies showed a strong positive correlation (R2 = 0.58-0.87***). This platform also has the potential to monitor environmental pollutants by selecting appropriate indicator species. The novel insights and methodologies presented in this study represent a significant advancement in meeting the complex needs of aquatic ecosystem protection and monitoring.
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Affiliation(s)
- Huan Hu
- Chongqing Jiaotong University, Chongqing 400074, China; Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing 400714, China
| | - Li Liu
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xing-Yi Wei
- Chongqing Jiaotong University, Chongqing 400074, China; Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing 400714, China
| | - Jin-Jing Duan
- Chongqing Miankai Biotechnology Research Institute Co., Ltd., Chongqing 400025, China; School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Jiao-Yun Deng
- School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - De-Sheng Pei
- School of Public Health, Chongqing Medical University, Chongqing 400016, China.
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Bhendarkar M, Rodriguez-Ezpeleta N. Exploring uncharted territory: new frontiers in environmental DNA for tropical fisheries management. ENVIRONMENTAL MONITORING AND ASSESSMENT 2024; 196:617. [PMID: 38874640 DOI: 10.1007/s10661-024-12788-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 06/06/2024] [Indexed: 06/15/2024]
Abstract
Tropical ecosystems host a significant share of global fish diversity contributing substantially to the global fisheries sector. Yet their sustainable management is challenging due to their complexity, diverse life history traits of tropical fishes, and varied fishing techniques involved. Traditional monitoring techniques are often costly, labour-intensive, and/or difficult to apply in inaccessible sites. These limitations call for the adoption of innovative, sensitive, and cost-effective monitoring solutions, especially in a scenario of climate change. Environmental DNA (eDNA) emerges as a potential game changer for biodiversity monitoring and conservation, especially in aquatic ecosystems. However, its utility in tropical settings remains underexplored, primarily due to a series of challenges, including the need for a comprehensive barcode reference library, an understanding of eDNA behaviour in tropical aquatic environments, standardized procedures, and supportive biomonitoring policies. Despite these challenges, the potential of eDNA for sensitive species detection across varied habitats is evident, and its global use is accelerating in biodiversity conservation efforts. This review takes an in-depth look at the current state and prospects of eDNA-based monitoring in tropical fisheries management research. Additionally, a SWOT analysis is used to underscore the opportunities and threats, with the aim of bridging the knowledge gaps and guiding the more extensive and effective use of eDNA-based monitoring in tropical fisheries management. Although the discussion applies worldwide, some specific experiences and insights from Indian tropical fisheries are shared to illustrate the practical application and challenges of employing eDNA in a tropical context.
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Affiliation(s)
- Mukesh Bhendarkar
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), 48395, Sukarrieta, Bizkaia, Spain.
- ICAR-National Institute of Abiotic Stress Management, Baramati, 413 115, Maharashtra, India.
| | - Naiara Rodriguez-Ezpeleta
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), 48395, Sukarrieta, Bizkaia, Spain
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Rund H, Wanzenböck J, Dobrovolny S, Kurmayer R. Relating target fish DNA concentration to community composition analysis in freshwater fish via metabarcoding. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172281. [PMID: 38588740 DOI: 10.1016/j.scitotenv.2024.172281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 03/04/2024] [Accepted: 04/05/2024] [Indexed: 04/10/2024]
Abstract
Metabarcoding has been widely accepted as a useful tool for biodiversity assessment based on eDNA. The method allows for the detection of entire groups of organisms in a single sample, making it particularly applicable in aquatic habitats. The high sensitivity of the molecular approaches is especially beneficial in detecting elusive and rare fish species, improving biodiversity assessments. Numerous biotic and abiotic factors that affect the persistence and availability of fish DNA in surface waters and therefore affecting species detectability, have been identified. However, little is known about the relationship between the total fish DNA concentration and the detectability of differential abundant species. In this study three controlled mock-community DNA samples (56 individual samples) were analyzed by (i) metabarcoding (MiSeq) of 12S rDNA (175 bp) and by (ii) total freshwater fish DNA quantification (via qPCR of 12S rDNA). We show that the fish DNA quantity affects the relative abundance of species-specific sequences and the detectability of rare species. In particular we found that samples with a concentration between 1000 pg/μL down to 10 pg/μL of total fish DNA revealed a stable relative frequency of DNA sequences obtained for a specific fish species, as well as a low variability between replicates. Additionally, we observed that even in complex mock-community DNA samples, a total fish DNA concentration of 23 pg/μL was sufficient to reliably detect all species in every replicate, including three rare species with proportions of ≤0.5 %. We also found that the DNA barcode similarity between species can affect detectability, if evenness is low. Our data suggest that the total DNA concentration of fish is an important factor to consider when analyzing and interpreting relative sequence abundance data. Therefore, the workflow proposed here will contribute to an ecologically and economically efficient application of metabarcoding in fish biodiversity assessment.
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Affiliation(s)
- Hans Rund
- Research Department for Limnology, Mondsee, Universität Innsbruck, Mondseestraße 9, 5310 Mondsee, Austria.
| | - Josef Wanzenböck
- Research Department for Limnology, Mondsee, Universität Innsbruck, Mondseestraße 9, 5310 Mondsee, Austria
| | - Stefanie Dobrovolny
- Department for Molecular Biology and Microbiology, Institute for Food Safety Vienna, Austrian Agency for Health and Food Safety, Spargelfeldstraße 191, 1220 Vienna, Austria
| | - Rainer Kurmayer
- Research Department for Limnology, Mondsee, Universität Innsbruck, Mondseestraße 9, 5310 Mondsee, Austria
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Schenekar T, Baxter J, Phukuntsi MA, Sedlmayr I, Weckworth B, Mwale M. Optimizing waterborne eDNA capture from waterholes in savanna systems under remote field conditions. Mol Ecol Resour 2024; 24:e13942. [PMID: 38390664 DOI: 10.1111/1755-0998.13942] [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: 07/27/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/24/2024]
Abstract
Environmental DNA (eDNA) is used for biodiversity assessments in a variety of ecosystems across the globe, whereby different eDNA concentration, preservation and extraction methods can outperform others depending on the sampling conditions and environment. Tropical and subtropical ecosystems in Africa are among the less studied systems concerning eDNA-based monitoring. Waterholes in arid parts of southern Africa represent important agglomeration points for terrestrial mammals, and the eDNA shed into such waterbodies provides a powerful source of information for monitoring mammalian biodiversity in the surrounding area. However, the applied methods for eDNA sampling, preservation and filtering in different freshwater systems vary greatly, and rigorous protocol testing in African freshwater systems is still lacking. This study represents the first attempt to examine variations in eDNA concentration, preservation and extraction methods under remote field conditions using waterborne eDNA in a savanna system. Collected samples were heavily affected by microalgal and bacterial growth, impeding eDNA capture and PCR success. We demonstrate clear effects of the methodological choices, which also depend on the state of eDNA. A preliminary metabarcoding run showed little taxonomic overlap in mammal species detection between two metabarcoding primers tested. We recommend water filtering (using filters with pore sizes >1 μm) over centrifugation for eDNA concentration, Longmire's solution for ambient temperature sample preservation and Qiagen's DNeasy PowerSoil Pro Kit for DNA extraction of these inhibitor-prone samples. Furthermore, at least two independent metabarcoding markers should be utilized in order to maximize species detections in metabarcoding studies.
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Affiliation(s)
| | - Janine Baxter
- South African National Biodiversity Institute, National Zoological Gardens, Pretoria, South Africa
| | - Metlholo Andries Phukuntsi
- South African National Biodiversity Institute, National Zoological Gardens, Pretoria, South Africa
- South African Environmental Observation Network, Egagasini Node, South African Environmental Observation Network, Cape Town, South Africa
| | | | | | - Monica Mwale
- South African National Biodiversity Institute, National Zoological Gardens, Pretoria, South Africa
- NRF-South African Institute for Aquatic Biodiversity, Makhanda (Grahamstown), South Africa
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7
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Pont D. Predicting downstream transport distance of fish eDNA in lotic environments. Mol Ecol Resour 2024; 24:e13934. [PMID: 38318749 DOI: 10.1111/1755-0998.13934] [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: 07/31/2023] [Revised: 01/21/2024] [Accepted: 01/26/2024] [Indexed: 02/07/2024]
Abstract
Environmental DNA (eDNA) is an effective tool for describing fish biodiversity in lotic environments, but the downstream transport of eDNA released by organisms makes it difficult to interpret species detection at the local scale. In addition to biophysical degradation and exchanges at the water-sediment interface, hydrological conditions control the transport distance. A new eDNA transport model described in this paper considers downstream retention and degradation processes in combination with hydraulic conditions and assumes that the sedimentation rate of very fine particles is a correct estimate of the eDNA deposition rate. Based on meta-analyses of available studies, the particle size distribution of fish eDNA (PSD), the relationship between the sedimentation rate and the size of very fine particles in suspension, and the influence of temperature on the degradation rate of fish eDNA were successively modelled. After combining the results in a mechanistic-based model, the eDNA uptake distances (distance required to retain 63.21% of the eDNA particles in the riverbed) observed in a compilation of previous experimental studies were correctly simulated. eDNA degradation is negligible at low flow and temperature but has a comparable influence to background transfer when hydraulic conditions allow a long uptake distance. The wide prediction intervals associated with the simulations reflect the complexity of the processes acting on eDNA after shedding. This model can be useful for estimating eDNA detection distance downstream from a source point and discussing the possibility of false positive detection in eDNA samples, as shown in an example.
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Affiliation(s)
- Didier Pont
- Institute of Hydrobiology and Aquatic Ecosystem Management (IHG), University of Natural Resources and Life Sciences, Vienna, Austria
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Rishan ST, Kline RJ, Rahman MS. New prospects of environmental RNA metabarcoding research in biological diversity, ecotoxicological monitoring, and detection of COVID-19: a critical review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:11406-11427. [PMID: 38183542 DOI: 10.1007/s11356-023-31776-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 12/26/2023] [Indexed: 01/08/2024]
Abstract
Ecosystems are multifaceted and complex systems and understanding their composition is crucial for the implementation of efficient conservation and management. Conventional approaches to biodiversity surveys can have limitations in detecting the complete range of species present. In contrast, the study of environmental RNA (eRNA) offers a non-invasive and comprehensive method for monitoring and evaluating biodiversity across different ecosystems. Similar to eDNA, the examination of genetic material found in environmental samples can identify and measure many species, including ones that pose challenges to traditional methods. However, eRNA is degraded quickly and therefore shows promise in detection of living organisms closer to their actual location than eDNA methods. This method provides a comprehensive perspective on the well-being of ecosystems, facilitating the development of focused conservation approaches to save at-risk species and uphold ecological equilibrium. Furthermore, eRNA has been recognized as a valuable method for the identification of COVID-19 in the environment, besides its established uses in biodiversity protection. The SARS-CoV-2 virus, which is accountable for the worldwide epidemic, releases RNA particles into the surrounding environment via human waste, providing insights into the feasibility of detecting it in wastewater and other samples taken from the environment. In this article, we critically reviewed the recent research activities that use the eRNA method, including its utilization in biodiversity conservation, ecological surveillance, and ecotoxicological monitoring as well as its innovative potential in identifying COVID-19. Through this review, the reader can understand the recent developments, prospects, and challenges of eRNA research in ecosystem management and biodiversity conservation.
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Affiliation(s)
- Sakib Tahmid Rishan
- Biochemistry and Molecular Biology Program, School of Integrative Biological and Chemical Sciences, University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Richard J Kline
- Biochemistry and Molecular Biology Program, School of Integrative Biological and Chemical Sciences, University of Texas Rio Grande Valley, Brownsville, TX, USA
- School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Md Saydur Rahman
- Biochemistry and Molecular Biology Program, School of Integrative Biological and Chemical Sciences, University of Texas Rio Grande Valley, Brownsville, TX, USA.
- School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Brownsville, TX, USA.
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Wang Z, Li F, Wu F, Guo F, Gao W, Zhang Y, Yang Z. Environmental DNA and remote sensing datasets reveal the spatial distribution of aquatic insects in a disturbed subtropical river system. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 351:119972. [PMID: 38159308 DOI: 10.1016/j.jenvman.2023.119972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 12/04/2023] [Accepted: 12/25/2023] [Indexed: 01/03/2024]
Abstract
Biodiversity datasets with high spatial resolution are critical prerequisites for river protection and management decision-making. However, traditional morphological biomonitoring is inefficient and only provides several site estimates, and there is an urgent need for new approaches to predict biodiversity on fine spatial scales throughout the entire river systems. Here, we combined the environmental DNA (eDNA) and remote sensing (RS) technologies to develop a novel approach for predicting the spatial distribution of aquatic insects with high spatial resolution in a disturbed subtropical Dongjiang River system of southeast China. First, we screened thirteen RS-based vegetation indices that significantly correlated with the eDNA-inferred richness of aquatic insects. In particular, the green normalized difference vegetation index (GNDVI) and normalized difference red-edge2 (NDRE2) were closely related to eDNA-inferred richness. Second, using the gradient boosting decision tree, our data showed that the spatial pattern of eDNA-inferred richness could achieve a high spatial resolution to 500 m reach and accurate prediction of more than 80%, and the prediction efficiency of the headwater streams (Strahler stream order = 1) was slightly higher than the downstream (Strahler stream order >1). Third, using the random forest algorithm, the spatial distribution of aquatic insects could reach a prediction rate of over 70% for the presence or absence of specific genera. Overall, this study provides a new approach to achieving high spatial resolution prediction of the distribution of aquatic insects, which supports decision-making on river diversity protection under climate changes and human impacts.
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Affiliation(s)
- Zongyang Wang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China
| | - Feilong Li
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China.
| | - Feifei Wu
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China
| | - Fen Guo
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China
| | - Wei Gao
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China
| | - Yuan Zhang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China.
| | - Zhifeng Yang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
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Li Z, Li F, Qin S, Guo F, Wang S, Zhang Y. Environmental DNA biomonitoring reveals the human impacts on native and non-native fish communities in subtropical river systems. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 349:119595. [PMID: 37979384 DOI: 10.1016/j.jenvman.2023.119595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 10/30/2023] [Accepted: 11/10/2023] [Indexed: 11/20/2023]
Abstract
Subtropical rivers are one of the hotspots of global biodiversity, facing increased risks of fish diversity changes and species extinction. However, until now, human impacts on native and non-native fish communities in subtropical rivers still lack sufficient effort. Here, we used the environmental DNA (eDNA) approach to investigate fish communities in the Dongjiang River of southeast China, a typical subtropical river, and explored the effects of regional land use and local water pollution on fish taxonomic and functional diversity. Our data showed that 90 species or genera of native fish and 15 species or genera of non-native fish were detected by the eDNA approach, and there was over 85% overlap between eDNA datasets and historical records. The taxonomic and functional diversity of all, native and non-native fish communities showed consistent spatial patterns, that is, the upstream of the tributary was significantly higher than that of the mainstream and downstream. Land use and water pollution such as COD and TP were the determinants in shaping the spatial structure of fish communities, and water pollution explained 31.56%, 29.88%, and 27.80% of the structural variation in all, native and non-native fish communities, respectively. The Shannon diversity and functional richness of native fish showed a significant downward trend driven by COD (pShannon = 0.0374; pfunctional = 0.0215) and land use (pShannon = 0.0159; pfunctional = 0.0441), but they did not have significant impacts on non-native fish communities. Overall, this study emphasizes the inconsistent response of native and non-native fish communities to human impacts in subtropical rivers, and managers need to develop strategies tailored to specific fish species to effectively protect water security and rivers.
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Affiliation(s)
- Zhen Li
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China
| | - Feilong Li
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China.
| | - Shan Qin
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China
| | - Fen Guo
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China
| | - Shuping Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Yuan Zhang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China
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11
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Duarte S, Simões L, Costa FO. Current status and topical issues on the use of eDNA-based targeted detection of rare animal species. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166675. [PMID: 37647964 DOI: 10.1016/j.scitotenv.2023.166675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/26/2023] [Accepted: 08/27/2023] [Indexed: 09/01/2023]
Abstract
Animal detection through DNA present in environmental samples (eDNA) is a valuable tool for detecting rare species, that are difficult to observe and monitor. eDNA-based tools are underpinned by molecular evolutionary principles, key to devising tools to efficiently single out a targeted species from an environmental sample. Here, we present a comprehensive review of the use of eDNA-based methods for the detection of targeted animal species, such as rare, endangered, or invasive species, through the analysis of 549 publications (2008-2022). Aquatic ecosystems have been the most surveyed, in particular, freshwaters (74 %), and to a less extent marine (14 %) and terrestrial systems (10 %). Vertebrates, in particular, fish (38 %), and endangered species, have been the focus of most of these studies, and Cytb and COI are the most employed markers. Among invertebrates, assays have been mainly designed for Mollusca and Crustacea species (21 %), in particular, to target invasive species, and COI the most employed marker. Targeted molecular approaches, in particular qPCR, have been the most adopted (75 %), while eDNA metabarcoding has been rarely used to target single or few species (approx. 6 %). However, less attention has been given in these studies to the effects of environmental factors on the amount of shed DNA, the differential amount of shed DNA among species, or the sensitivity of the markers developed, which may impact the design of the assays, particularly to warrant the required detection level and avoid false negatives and positives. The accuracy of the assays will also depend on the availability of genetic data and vouchered tissue or DNA samples from closely related species to assess both marker and primers' specificity. In addition, eDNA-based assays developed for a particular species may have to be refined for use in a new geographic area taking into account site-specific populations, as well as any intraspecific variation.
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Affiliation(s)
- Sofia Duarte
- Centre of Molecular and Environmental Biology (CBMA) and ARNET-Aquatic Research Network, Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
| | - Luara Simões
- Centre of Molecular and Environmental Biology (CBMA) and ARNET-Aquatic Research Network, Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Filipe O Costa
- Centre of Molecular and Environmental Biology (CBMA) and ARNET-Aquatic Research Network, Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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Baletaud F, Lecellier G, Gilbert A, Mathon L, Côme JM, Dejean T, Dumas M, Fiat S, Vigliola L. Comparing Seamounts and Coral Reefs with eDNA and BRUVS Reveals Oases and Refuges on Shallow Seamounts. BIOLOGY 2023; 12:1446. [PMID: 37998045 PMCID: PMC10669620 DOI: 10.3390/biology12111446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/13/2023] [Accepted: 11/13/2023] [Indexed: 11/25/2023]
Abstract
Seamounts are the least known ocean biome. Considered biodiversity hotspots, biomass oases, and refuges for megafauna, large gaps exist in their real diversity relative to other ecosystems like coral reefs. Using environmental DNA metabarcoding (eDNA) and baited video (BRUVS), we compared fish assemblages across five environments of different depths: coral reefs (15 m), shallow seamounts (50 m), continental slopes (150 m), intermediate seamounts (250 m), and deep seamounts (500 m). We modeled assemblages using 12 environmental variables and found depth to be the main driver of fish diversity and biomass, although other variables like human accessibility were important. Boosted Regression Trees (BRT) revealed a strong negative effect of depth on species richness, segregating coral reefs from deep-sea environments. Surprisingly, BRT showed a hump-shaped effect of depth on fish biomass, with significantly lower biomass on coral reefs than in shallowest deep-sea environments. Biomass of large predators like sharks was three times higher on shallow seamounts (50 m) than on coral reefs. The five studied environments showed quite distinct assemblages. However, species shared between coral reefs and deeper-sea environments were dominated by highly mobile large predators. Our results suggest that seamounts are no diversity hotspots for fish. However, we show that shallower seamounts form biomass oases and refuges for threatened megafauna, suggesting that priority should be given to their protection.
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Affiliation(s)
- Florian Baletaud
- ENTROPIE, Institut de Recherche pour le Développement (IRD), UR, UNC, IFREMER, CNRS, Centre IRD de Nouméa, 98848 Noumea, New Caledonia, France; (F.B.); (G.L.); (L.M.); (M.D.); (S.F.)
- GINGER SOPRONER, 98000 Noumea, New Caledonia, France;
- GINGER BURGEAP, 69000 Lyon, France;
- MARBEC, University of Montpellier, CNRS, IFREMER, 34000 Montpellier, France
| | - Gaël Lecellier
- ENTROPIE, Institut de Recherche pour le Développement (IRD), UR, UNC, IFREMER, CNRS, Centre IRD de Nouméa, 98848 Noumea, New Caledonia, France; (F.B.); (G.L.); (L.M.); (M.D.); (S.F.)
- ISEA, University of New Caledonia, 98800 Noumea, New Caledonia, France
| | | | - Laëtitia Mathon
- ENTROPIE, Institut de Recherche pour le Développement (IRD), UR, UNC, IFREMER, CNRS, Centre IRD de Nouméa, 98848 Noumea, New Caledonia, France; (F.B.); (G.L.); (L.M.); (M.D.); (S.F.)
- CEFE, University of Montpellier, CNRS, EPHE-PSL, IRD, 34000 Montpellier, France
| | | | | | - Mahé Dumas
- ENTROPIE, Institut de Recherche pour le Développement (IRD), UR, UNC, IFREMER, CNRS, Centre IRD de Nouméa, 98848 Noumea, New Caledonia, France; (F.B.); (G.L.); (L.M.); (M.D.); (S.F.)
| | - Sylvie Fiat
- ENTROPIE, Institut de Recherche pour le Développement (IRD), UR, UNC, IFREMER, CNRS, Centre IRD de Nouméa, 98848 Noumea, New Caledonia, France; (F.B.); (G.L.); (L.M.); (M.D.); (S.F.)
| | - Laurent Vigliola
- ENTROPIE, Institut de Recherche pour le Développement (IRD), UR, UNC, IFREMER, CNRS, Centre IRD de Nouméa, 98848 Noumea, New Caledonia, France; (F.B.); (G.L.); (L.M.); (M.D.); (S.F.)
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13
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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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Burian A, Bruce K, Tovela E, Bakker J, Balcells L, Bennett R, Chordekar S, Costa HM, Crampton-Platt A, de Boer H, Ross-Gillespie V, de Sacramento A, Sidat N, Simbine L, Ready J, Tang C, Mauvisseau Q. Merging two eDNA metabarcoding approaches and citizen-science-based sampling to facilitate fish community monitoring along vast Sub-Saharan coastlines. Mol Ecol Resour 2023; 23:1641-1655. [PMID: 37464467 DOI: 10.1111/1755-0998.13839] [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: 06/22/2022] [Revised: 06/29/2023] [Accepted: 07/06/2023] [Indexed: 07/20/2023]
Abstract
The coastline of Sub-Saharan Africa hosts highly diverse fish communities of great conservation value, which are also key resources for local livelihoods. However, many costal ecosystems are threatened by overexploitation and their conservation state is frequently unknown due to their vast spatial extent and limited monitoring budgets. Here, we evaluated the potential of citizen science-based eDNA surveys to alleviate such chronic data deficiencies and assessed fish communities in Mozambique using two 12S metabarcoding primer sets. Samples were either collected by scientific personnel or trained community members and results from the two metabarcoding primers were combined using a new data merging approach. Irrespective of the background of sampling personnel, a high average fish species richness was recorded (38 ± 20 OTUs per sample). Individual sections of the coastline largely differed in the occurrence of threatened and commercially important species, highlighting the need for regionally differentiated management strategies. A detailed comparison of the two applied primer sets revealed an important trade-off in primer choice with MiFish primers amplifying a higher number of species but Riaz primers performing better in the detection of threatened fish species. This trade-off could be partly resolved by applying our new data-merging approach, which was especially designed to increase the robustness of multiprimer assessments in regions with poor reference libraries. Overall, our study provides encouraging results but also highlights that eDNA-based monitoring will require further improvements of, for example, reference databases and local analytical infrastructure to facilitate routine applications in Sub-Saharan Africa.
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Affiliation(s)
- Alfred Burian
- Department of Computational Landscape Ecology, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany
- Marine Ecology Department, Lurio University, Nampula, Mozambique
| | | | - Erica Tovela
- Natural History Museum, University Eduardo Mondlane, Maputo, Mozambique
| | | | | | | | | | - Hugo M Costa
- Wildlife Conservation Society, Maputo, Mozambique
| | | | - Hugo de Boer
- Natural History Museum, University of Oslo, Oslo, Norway
| | | | | | | | - Luisa Simbine
- Instituto Oceanográfico de Moçambique, Ministério do Mar, Águas Interiores e Pescas, Maputo, Mozambique
| | - Jonathan Ready
- Universidade Federal do Pará, Grupo de Investigação Biológica Integrada, Centro de Estudos Avançados da Biodiversidade, Belem, Brazil
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15
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Diao C, Wang M, Zhong Z, Li Y, Xian W, Zhang H. Biodiversity exploration of Formosa Ridge cold seep in the South China Sea using an eDNA metabarcoding approach. MARINE ENVIRONMENTAL RESEARCH 2023; 190:106109. [PMID: 37506653 DOI: 10.1016/j.marenvres.2023.106109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/12/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023]
Abstract
The Formosa Ridge, also named Site F, is an active cold seep marine ecosystem site that has been studied since it was discovered on the continental slope of the northeast South China Sea (SCS). However, few studies have focused on the eukaryotic diversity at Site F. Environmental DNA (eDNA) technology is a non-invasive method applied in biodiversity surveys with a high species detection probability. In the present study, we identified multi-trophic biodiversity using eDNA metabarcoding combined with multiple ribosomal RNA gene (rDNA) markers. We detected 142 phytoplankton, 90 invertebrates, and 64 fish species by amplifying the 18S rRNA gene V4 region, the 18S rRNA gene V9 region, and the 12S rRNA gene. The results elucidated dissimilar trends of different assemblages with depth. The diversity of phytoplankton and invertebrate assemblages markedly decreased with depth, whereas little change was observed within the fish assemblage. We comprehensively assessed the relationship between the three assemblages and environmental factors (temperature, salinity, depth, dissolved oxygen, and chlorophyll a). These factors strongly impacted on phytoplankton and invertebrates, but only slightly on fish. We inferred the finding might be due to fish having a strong migration capacity and wide distribution. This study indicates that eDNA metabarcoding with multiple markers is a powerful tool for marine biodiversity research that is able to provide technical support and knowledge for resource management and biodiversity protection efforts.
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Affiliation(s)
- Caoyun Diao
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Minxiao Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Deep Sea Research Center, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Zhaoshan Zhong
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Deep Sea Research Center, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Yuan Li
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, 361005, China
| | - Weiwei Xian
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China
| | - Hui Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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16
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Zhang M, Zou Y, Xiao S, Hou J. Environmental DNA metabarcoding serves as a promising method for aquatic species monitoring and management: A review focused on its workflow, applications, challenges and prospects. MARINE POLLUTION BULLETIN 2023; 194:115430. [PMID: 37647798 DOI: 10.1016/j.marpolbul.2023.115430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 08/10/2023] [Accepted: 08/15/2023] [Indexed: 09/01/2023]
Abstract
Marine and freshwater biodiversity is under threat from both natural and manmade causes. Biological monitoring is currently a top priority for biodiversity protection. Given present limitations, traditional biological monitoring methods may not achieve the proposed monitoring aims. Environmental DNA metabarcoding technology reflects species information by capturing and extracting DNA from environmental samples, using molecular biology techniques to sequence and analyze the DNA, and comparing the obtained information with existing reference libraries to obtain species identification. However, its practical application has highlighted several limitations. This paper summarizes the main steps in the environmental application of eDNA metabarcoding technology in aquatic ecosystems, including the discovery of unknown species, the detection of invasive species, and evaluations of biodiversity. At present, with the rapid development of big data and artificial intelligence, certain advanced technologies and devices can be combined with environmental DNA metabarcoding technology to promote further development of aquatic species monitoring and management.
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Affiliation(s)
- Miaolian Zhang
- MOE Key Laboratory of Resources and Environmental Systems Optimization, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Yingtong Zou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shan Xiao
- MOE Key Laboratory of Resources and Environmental Systems Optimization, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Jing Hou
- MOE Key Laboratory of Resources and Environmental Systems Optimization, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China.
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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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Jo TS. Utilizing the state of environmental DNA (eDNA) to incorporate time-scale information into eDNA analysis. Proc Biol Sci 2023; 290:20230979. [PMID: 37253423 PMCID: PMC10229230 DOI: 10.1098/rspb.2023.0979] [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: 05/01/2023] [Accepted: 05/10/2023] [Indexed: 06/01/2023] Open
Abstract
Environmental DNA (eDNA) analysis allows cost-effective and non-destructive biomonitoring with a high detection sensitivity in terrestrial and aquatic environments. However, the eDNA results can sometimes include false-positive inferences of target organisms owing to the detection of aged eDNA that has long since been released from the individual and is more likely to be detected at a site further away from its source. In order to address the issue, this manuscript focuses on the state of eDNA, proposing new methodologies to estimate the age of eDNA: (1) DNA damage rate, (2) eDNA particle size distribution, and (3) viable cell-derived eDNA. In addition, the manuscript also focuses on the shorter persistence of environmental RNA (eRNA) compared with eDNA, highlighting the application of eRNA and environmental nucleic acid ratio for assessing the age of the genetic materials in water. Although substantial further research is essential to support the feasibility of these methodologies, incorporating time-scale information into eDNA analysis would update current eDNA analysis, improve the accuracy and reliability of eDNA-based monitoring, and further refine eDNA analysis as a useful monitoring tool in ecology, fisheries and various environmental sciences.
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Affiliation(s)
- Toshiaki S. Jo
- Research Fellow of Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan
- Ryukoku Center for Biodiversity Science, Ryukoku University, 1-5, Yokotani, Oe-cho, Seta, Otsu City, Shiga 520-2194, Japan
- Faculty of Advanced Science and Technology, Ryukoku University, 1-5, Yokotani, Oe-cho, Seta, Otsu City, Shiga 520-2194, Japan
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McDonald R, Bateman PW, Cooper C, van der Heyde M, Mousavi‐Derazmahalleh M, Hedges BA, Guzik MT, Nevill P. Detection of vertebrates from natural and artificial inland water bodies in a semi-arid habitat using eDNA from filtered, swept, and sediment samples. Ecol Evol 2023; 13:e10014. [PMID: 37113520 PMCID: PMC10126312 DOI: 10.1002/ece3.10014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 03/21/2023] [Accepted: 03/24/2023] [Indexed: 04/29/2023] Open
Abstract
Biomonitoring is vital for establishing baseline data that is needed to identify and quantify ecological change and to inform management and conservation activities. However, biomonitoring and biodiversity assessment in arid environments, which are predicted to cover 56% of the Earth's land surface by 2100, can be prohibitively time consuming, expensive, and logistically challenging due to their often remote and inhospitable nature. Sampling of environmental DNA (eDNA) coupled with high-throughput sequencing is an emerging biodiversity assessment method. Here we explore the application of eDNA metabarcoding and various sampling approaches to estimate vertebrate richness and assemblage at human-constructed and natural water sources in a semi-arid region of Western Australia. Three sampling methods: sediment samples, filtering through a membrane with a pump, and membrane sweeping in the water body, were compared using two eDNA metabarcoding assays, 12S-V5 and 16smam, for 120 eDNA samples collected from four gnammas (gnamma: Australian Indigenous Noongar language term-granite rock pools) and four cattle troughs in the Great Western Woodlands, Western Australia. We detected higher vertebrate richness in samples from cattle troughs and found differences between assemblages detected in gnammas (more birds and amphibians) and cattle troughs (more mammals, including feral taxa). Total vertebrate richness was not different between swept and filtered samples, but all sampling methods yielded different assemblages. Our findings indicate that eDNA surveys in arid lands will benefit from collecting multiple samples at multiple water sources to avoid underestimating vertebrate richness. The high concentration of eDNA in small, isolated water bodies permits the use of sweep sampling that simplifies sample collection, processing, and storage, particularly when assessing vertebrate biodiversity across large spatial scales.
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Affiliation(s)
- Rupert McDonald
- Trace and Environmental DNA Laboratory, School of Life and Molecular SciencesCurtin UniversityPerthAustralia
| | - Philip W. Bateman
- Trace and Environmental DNA Laboratory, School of Life and Molecular SciencesCurtin UniversityPerthAustralia
- Behavioural Ecology Lab, School of Molecular and Life SciencesCurtin UniversityPerthAustralia
| | - Christine Cooper
- School of Molecular and Life SciencesCurtin UniversityPerthAustralia
| | - Mieke van der Heyde
- Trace and Environmental DNA Laboratory, School of Life and Molecular SciencesCurtin UniversityPerthAustralia
| | - Mahsa Mousavi‐Derazmahalleh
- Trace and Environmental DNA Laboratory, School of Life and Molecular SciencesCurtin UniversityPerthAustralia
| | - Brock A. Hedges
- School of Biological SciencesThe University of AdelaideAdelaideAustralia
| | - Michelle T. Guzik
- School of Biological SciencesThe University of AdelaideAdelaideAustralia
| | - Paul Nevill
- Trace and Environmental DNA Laboratory, School of Life and Molecular SciencesCurtin UniversityPerthAustralia
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Yan ZG, Zheng X, Zhang YZ, Yang ZH, Zhou Q, Men SH, Du JZ. Chinese Technical Guideline for Deriving Water Quality Criteria for Protection of Freshwater Organisms. TOXICS 2023; 11:toxics11020194. [PMID: 36851068 PMCID: PMC9960927 DOI: 10.3390/toxics11020194] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/18/2023] [Accepted: 02/17/2023] [Indexed: 05/29/2023]
Abstract
In recent years, China has determined the national goal of "developing national environmental criteria", thereby promoting the rapid development of environmental quality criteria research in China. In 2017, the Ministry of Ecology and Environment of China (MEEC, formerly the Ministry of Environmental Protection of China) issued the technical guideline for deriving water quality criteria (WQC) for protection of freshwater organisms (HJ 831-2017), and in 2022, they organized the guideline revision and issued an updated version (HJ 831-2022). The primary contents of the revision included the following. The minimum toxicity data requirements were upgraded from 6 to 10, and the species mean toxicity value was replaced by the same effect toxicity value for the criteria calculation. It is now required that the tested organisms must be distributed in China's natural fresh waters, and the toxicity data of non-native model species will no longer be used. The list of freshwater invasive species in China that cannot be used as test species was added into the guideline. The acute/chronic ratio (ACR) method for the criteria derivation and the extreme value model were deleted, and the provisions for testing the toxicity data distribution were also deleted. The exposure time of the toxicity test of various tested organisms was refined, and the priority of the toxicity data was clearly specified. This paper introduces the framework and specific technical requirements of HJ 831-2022 in detail, including data collection, pre-processing of toxicity data, criteria derivation, fitting models, and quality control. This introduction is helpful for international peers to understand the latest research progress of China's WQC.
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Affiliation(s)
- Zhen-Guang Yan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Xin Zheng
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Yi-Zhang Zhang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Zhan-Hong Yang
- Environmental Standards Institute of Ministry of Ecology and Environment of the People’s Republic of China, Beijing 100012, China
| | - Quan Zhou
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Shu-Hui Men
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Jin-Zhe Du
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266061, China
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21
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Yan ZG, Zhu XM, Zhang SW, Jiang H, Wang SP, Wei C, Wang J, Shao Y, Liu C, Wang H. Environmental DNA sequencing reveals the regional difference in diversity and community assembly mechanisms of eukaryotic plankton in coastal waters. Front Microbiol 2023; 14:1132925. [PMID: 36846757 PMCID: PMC9956185 DOI: 10.3389/fmicb.2023.1132925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 01/26/2023] [Indexed: 02/12/2023] Open
Abstract
The diversity and community assembly mechanisms of eukaryotic plankton in coastal waters is so far not clear. In this study, we selected the coastal waters of Guangdong-Hong Kong-Macao Greater Bay Area, which is a highly developed region in China, as the research area. By use of high-throughput sequencing technologies, the diversity and community assembly mechanisms of eukaryotic marine plankton were studied in which a total of 7,295 OTUs were obtained, and 2,307 species were annotated by doing environmental DNA survey of 17 sites consist of surface and bottom layer. Ultimately, the analysis reveals that the species abundance of bottom layer is, by and large, higher than that in the surface layer. In the bottom, Arthropoda is the first largest group, accounting for more than 20% while Arthropoda and Bacillariophyta are dominant groups in surface waters accounting for more than 40%. It is significant of the variance in alpha-diversity between sampling sites, and the difference of alpha-diversity between bottom sites is greater than that of surface sites. The result suggests that the environmental factors that have significant influence on alpha-diversity are total alkalinity and offshore distance for surface sites, and water depth and turbidity for bottom sites. Likewise, the plankton communities obey the typical distance-decay pattern. Analysis about community assembly mechanisms reveals that, overall, dispersal limitation is the major pattern of community formation, which accounts for more than 83% of the community formation processes, suggesting that stochastic processes are the crucial assembly mechanism of the eukaryotic plankton community in the study area.
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Affiliation(s)
- Zhen-Guang Yan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China,Frontiers Research Center, Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China,*Correspondence: Zhen-Guang Yan, ✉
| | - Xue-Ming Zhu
- Frontiers Research Center, Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Shou-Wen Zhang
- Frontiers Research Center, Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Hua Jiang
- Marine Climate Prediction and Assessment Center, National Marine Environmental Forecasting Center, Beijing, China
| | - Shu-Ping Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China,Frontiers Research Center, Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Chao Wei
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China,Frontiers Research Center, Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Jie Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China,Frontiers Research Center, Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Yun Shao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China,Frontiers Research Center, Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Chen Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China,Frontiers Research Center, Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Hui Wang
- Frontiers Research Center, Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China,Marine Climate Prediction and Assessment Center, National Marine Environmental Forecasting Center, Beijing, China
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22
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Gonzalez Colmenares GM, Gonzalez Montes AJ, Harms-Tuohy CA, Schizas NV. Using eDNA sampling for species-specific fish detection in tropical oceanic samples: limitations and recommendations for future use. PeerJ 2023; 11:e14810. [PMID: 36751629 PMCID: PMC9899429 DOI: 10.7717/peerj.14810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 01/06/2023] [Indexed: 02/05/2023] Open
Abstract
Background Over the past decade, environmental DNA (eDNA) has become a resourceful tool in conservation and biomonitoring. Environmental DNA has been applied in a variety of environments, but the application to studies of marine fish, particularly at tropical latitudes, are limited. Since many commercially important Caribbean fishes are overexploited, these species are optimal candidates to explore the use of this method as a biomonitoring tool. Specifically, for many of these species, the formation of fish spawning aggregations (FSAs) marks a critical life history event where fishes will gather in large numbers for reproduction. These FSAs are ephemeral in nature, lasting only a few days, but are predictable in time and space which makes them susceptible to overfishing. Methods In this study, we test the feasibility of using an eDNA sampling approach (water and sediment collection) to detect the presence of known FSAs off the west coast of Puerto Rico, with cytochrome c oxidase subunit 1 (CO1) and 12S rRNA (12S) primers designed to target specific species. A total of 290 eDNA samples were collected and, of those, 206 eDNA samples were processed. All eDNA samples varied in DNA concentration, both between replicates and collection methods. A total of 12 primer sets were developed and tested using traditional PCR and qPCR. Results Despite validation of primer accuracy and sample collection during known peak spawning times, the use of traditional PCR and qPCR with both molecular markers failed to produce species-specific amplification. Thus, a trial test was conducted using the CO1 primers in which target fish DNA was 'spiked' at various concentrations into the respective eDNA samples to determine the target species DNA concentration limit of detection. Upon successful amplification of the trial, results indicated that eDNA samples were below the detection threshold of our methods, suggesting that the number of fish present at the spawning aggregations was inadequate for single-species detection methods. In addition, elements such as the unavoidable presence of non-target DNA, oceanic environmental conditions, shedding rates of target fish, among other biotic and abiotic factors could have affected DNA persistence and degradation rates at the sites. Conclusion We provide recommendations for species-specific fish detection in lower latitudes, and suggestions for studies aiming to monitor or detect fish spawning aggregations using eDNA sampling.
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Affiliation(s)
| | | | | | - Nikolaos V. Schizas
- Department of Marine Sciences, Universidad de Puerto Rico, Recinto de Mayagüez, Mayagüez, Puerto Rico
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23
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Pont D, Meulenbroek P, Bammer V, Dejean T, Erős T, Jean P, Lenhardt M, Nagel C, Pekarik L, Schabuss M, Stoeckle BC, Stoica E, Zornig H, Weigand A, Valentini A. Quantitative monitoring of diverse fish communities on a large scale combining eDNA metabarcoding and qPCR. Mol Ecol Resour 2023; 23:396-409. [PMID: 36151931 DOI: 10.1111/1755-0998.13715] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 07/21/2022] [Accepted: 09/15/2022] [Indexed: 01/04/2023]
Abstract
Environmental DNA (eDNA) metabarcoding is an effective method for studying fish communities but allows only an estimation of relative species abundance (density/biomass). Here, we combine metabarcoding with an estimation of the total abundance of eDNA amplified by our universal marker (teleo) using a quantitative (q)PCR approach to infer the absolute abundance of fish species. We carried out a 2850-km eDNA survey within the Danube catchment using a spatial integrative sampling protocol coupled with traditional electrofishing for fish biomass and density estimation. Total fish eDNA concentrations and total fish abundance were highly correlated. The correlation between eDNA concentrations per taxon and absolute specific abundance was of comparable strength when all sites were pooled and remained significant when the sites were considered separately. Furthermore, a nonlinear mixed model showed that species richness was underestimated when the amount of teleo-DNA extracted from a sample was below a threshold of 0.65 × 106 copies of eDNA. This result, combined with the decrease in teleo-DNA concentration by several orders of magnitude with river size, highlights the need to increase sampling effort in large rivers. Our results provide a comprehensive description of longitudinal changes in fish communities and underline our combined metabarcoding/qPCR approach for biomonitoring and bioassessment surveys when a rough estimate of absolute species abundance is sufficient.
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Affiliation(s)
- Didier Pont
- Institute of Hydrobiology and Aquatic Ecosystem Management, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Paul Meulenbroek
- Institute of Hydrobiology and Aquatic Ecosystem Management, University of Natural Resources and Life Sciences, Vienna, Austria
- WasserCluster Lunz -Biologische Station GmbH, Lunz am See, Austria
| | - Vincenz Bammer
- Bundesamt für Wasserwirtschaft, Institut für Gewässerökologie und Fischereiwirtschaft, Abteilung Gewässerökologie, Mondsee, Austria
| | | | - Tibor Erős
- Balaton Limnological Research Institute, Eötvös Lor'and Research Network (ELKH), Tihany, Hungary
| | | | - Mirjana Lenhardt
- Institute for Multidisciplinary Research, Institute for Biological Research "Siniša Stanković," National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Christoffer Nagel
- Technical University of Munich, Chair of Aquatic Systems Biology, Freising-Weihenstephan, Germany
| | - Ladislav Pekarik
- Plant Science and Biodiversity Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | | | - Bernhard C Stoeckle
- Technical University of Munich, Chair of Aquatic Systems Biology, Freising-Weihenstephan, Germany
| | - Elena Stoica
- National Institute for Marine Research and Development "Grigore Antipa,", Constanţa, Romania
| | - Horst Zornig
- PRO FISCH OG Ecological Consultants, Vienna, Austria
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24
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Xu X, Yuan Y, Wang Z, Zheng T, Cai H, Yi M, Li T, Zhao Z, Chen Q, Sun W. Environmental DNA metabarcoding reveals the impacts of anthropogenic pollution on multitrophic aquatic communities across an urban river of western China. ENVIRONMENTAL RESEARCH 2023; 216:114512. [PMID: 36208790 DOI: 10.1016/j.envres.2022.114512] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 09/29/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Anthropogenic activities are intensively affecting the structure and function of biological communities in river ecosystems. The effects of anthropogenic pollution on single-trophic community have been widely explored, but their effects on the structures and co-occurrence patterns of multitrophic communities remain largely unknown. In this study, we collected 13 water samples from the Neijiang River in Chengdu City of China, and identified totally 2352 bacterial, 207 algal, 204 macroinvertebrate, and 33 fish species based on the eDNA metabarcoding to systematically investigate the responses of multitrophic communities to environmental stressors. We observed significant variations in bacterial, algal, and macroinvertebrate community structures (except fish) with the pollution levels in the river. Network analyses indicated a more intensive interspecific co-occurrence pattern at high pollution level. Although taxonomic diversity of the multitrophic communities varied insignificantly, phylogenetic diversities of fish and algae showed significantly positive and negative associations with the pollution levels, respectively. We demonstrated the primary role of environmental filtering in driving the structures of bacteria, algae, and macroinvertebrates, while the fish was more controlled by dispersal limitation. Nitrogen was identified as the most important factor impacting the multitrophic community, where bacterial composition was mostly associated with NO3--N, algal spatial differentiation with TN, and macroinvertebrate and fish with NH4+-N. Further partial least-squares path model confirmed more important effect of environmental variables on the relative abundance of bacteria and algae, while macroinvertebrate and fish communities were directly driven by the algae-mediated pathway in the food web. Our study highlighted the necessity of integrated consideration of multitrophic biodiversity for riverine pollution management, and emphasized the importance of controlling nitrogen inputs targeting a healthy ecosystem.
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Affiliation(s)
- Xuming Xu
- College of Environmental Sciences and Engineering, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing, 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing, 100871, China
| | - Yibin Yuan
- College of Water Resource & Hydropower, Sichuan University, Chengdu, 610065, China; Chengdu Research Academy of Environmental Protection Science, Chengdu, 610072, China
| | - Zhaoli Wang
- Chengdu Research Academy of Environmental Protection Science, Chengdu, 610072, China
| | - Tong Zheng
- State Environmental Protection Key Laboratory of Environmental Pollution Health Risk Assessment, South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou, 510655, China
| | - Hetong Cai
- College of Environmental Sciences and Engineering, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing, 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing, 100871, China
| | - Malan Yi
- Tianjin Research Institute for Water Transport Engineering, M. O. T, Tianjin, 300000, China
| | - Tianhong Li
- College of Environmental Sciences and Engineering, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing, 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing, 100871, China
| | - Zhijie Zhao
- College of Environmental Sciences and Engineering, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing, 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing, 100871, China
| | - Qian Chen
- College of Environmental Sciences and Engineering, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing, 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing, 100871, China.
| | - Weiling Sun
- College of Environmental Sciences and Engineering, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing, 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing, 100871, China
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25
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Goethel DR, Omori KL, Punt AE, Lynch PD, Berger AM, de Moor CL, Plagányi ÉE, Cope JM, Dowling NA, McGarvey R, Preece AL, Thorson JT, Chaloupka M, Gaichas S, Gilman E, Hesp SA, Longo C, Yao N, Methot RD. Oceans of plenty? Challenges, advancements, and future directions for the provision of evidence-based fisheries management advice. REVIEWS IN FISH BIOLOGY AND FISHERIES 2023; 33:375-410. [PMID: 36124316 PMCID: PMC9476434 DOI: 10.1007/s11160-022-09726-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 08/18/2022] [Indexed: 05/19/2023]
Abstract
UNLABELLED Marine population modeling, which underpins the scientific advice to support fisheries interventions, is an active research field with recent advancements to address modern challenges (e.g., climate change) and enduring issues (e.g., data limitations). Based on discussions during the 'Land of Plenty' session at the 2021 World Fisheries Congress, we synthesize current challenges, recent advances, and interdisciplinary developments in biological fisheries models (i.e., data-limited, stock assessment, spatial, ecosystem, and climate), management strategy evaluation, and the scientific advice that bridges the science-policy interface. Our review demonstrates that proliferation of interdisciplinary research teams and enhanced data collection protocols have enabled increased integration of spatiotemporal, ecosystem, and socioeconomic dimensions in many fisheries models. However, not all management systems have the resources to implement model-based advice, while protocols for sharing confidential data are lacking and impeding research advances. We recommend that management and modeling frameworks continue to adopt participatory co-management approaches that emphasize wider inclusion of local knowledge and stakeholder input to fill knowledge gaps and promote information sharing. Moreover, fisheries management, by which we mean the end-to-end process of data collection, scientific analysis, and implementation of evidence-informed management actions, must integrate improved communication, engagement, and capacity building, while incorporating feedback loops at each stage. Increasing application of management strategy evaluation is viewed as a critical unifying component, which will bridge fisheries modeling disciplines, aid management decision-making, and better incorporate the array of stakeholders, thereby leading to a more proactive, pragmatic, transparent, and inclusive management framework-ensuring better informed decisions in an uncertain world. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s11160-022-09726-7.
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Affiliation(s)
- Daniel R. Goethel
- Auke Bay Laboratories, Marine Ecology and Stock Assessment (MESA) Program, Alaska Fisheries Science Center, NOAA Fisheries, Juneau, AK 99801 USA
| | - Kristen L. Omori
- Virginia Institute of Marine Science, William & Mary, Gloucester Point, VA 23062 USA
| | - André E. Punt
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA 98195-5020 USA
| | - Patrick D. Lynch
- Office of Science and Technology, NOAA Fisheries, Silver Spring, MD 20910 USA
| | - Aaron M. Berger
- Fisheries Resource, Analysis, and Monitoring (FRAM) Division, Northwest Fisheries Science Center, NOAA Fisheries, Newport, OR 97365 USA
| | - Carryn L. de Moor
- Marine Resource Assessment and Management (MARAM) Group, Department of Mathematics and Applied Mathematics, University of Cape Town, Rondebosch, 7701 South Africa
| | | | - Jason M. Cope
- Fisheries Resource, Analysis, and Monitoring (FRAM) Division, Northwest Fisheries Science Center, NOAA Fisheries, Seattle, WA 98112 USA
| | | | | | - Ann L. Preece
- CSIRO Oceans and Atmosphere, Hobart, TAS 7001 Australia
| | - James T. Thorson
- Habitat and Ecological Process Research (HEPR) Program, Alaska Fisheries Science Center, NOAA Fisheries, Seattle, WA 98115 USA
| | - Milani Chaloupka
- Ecological Modelling Services Pty Ltd & Marine Spatial Ecology Lab, University of Queensland, St Lucia, QLD 4067 Australia
| | - Sarah Gaichas
- Resource Evaluation and Assessment Division, Northeast Fisheries Science Center, NOAA Fisheries, Woods Hole, MA 02543 USA
| | | | - Sybrand A. Hesp
- Western Australian Fisheries and Marine Research Laboratories, Department of Primary Industries and Regional Development, Government of Western Australia, North Beach, WA 6920 Australia
| | - Catherine Longo
- Science & Standards, Marine Stewardship Council, EC1A 2DH London, U.K
| | - Nan Yao
- Oceanic Fisheries Programme, The Pacific Community (SPC), B.P. D5, 98848 Nouméa, New Caledonia
| | - Richard D. Methot
- Northwest Fisheries Science Center, NOAA Fisheries, Seattle, WA 98112 USA
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26
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Rusch JC, Strand DA, Laurendz C, Andersen T, Johnsen SI, Edsman L, Vrålstad T. Exploring the eDNA dynamics of the host-pathogen pair Pacifastacus leniusculus (Decapoda) and Aphanomyces astaci (Saprolegniales) under experimental conditions. NEOBIOTA 2022. [DOI: 10.3897/neobiota.79.82793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The oomycete Aphanomyces astaci causes crayfish plague, a disease threatening native European crayfish. It is carried and transmitted by American crayfish species, which are the original hosts of A. astaci. In recent years, environmental DNA (eDNA) methods have been successfully implemented to monitor the spread of both A. astaci and its hosts. However, still little is known about how population density and other environmental factors influence the detectability of this host-pathogen complex. In a mesocosm experiment, we tested the influence of crayfish density, temperature and food availability on the detectability of eDNA for A. astaci and its host, signal crayfish Pacifastacus leniusculus. We also compared eDNA results with crayfish population density measured by catch per unit effort (CPUE) from two lakes with varying crayfish density and A. astaci prevalence. The mesocosm experiment revealed that a limited set of controlled factors can substantially change the detectable amount of eDNA, even though the physical presence of the target organisms remains the same. In cold, clear water, eDNA quantities of both targets increased far more than in a linear fashion with increased crayfish density. However, the presence of food decreased the detectability of crayfish eDNA, presumably through increased microbial-induced eDNA degradation. For A. astaci, where eDNA typically represents living spores, food did not affect the detectability. However, high water temperature strongly reduced it. The increased complexity and variability of factors influencing eDNA concentration under natural conditions, compared to a controlled experimental environment, suggests that establishing a reliable relationship between eDNA quantities and crayfish density is difficult to achieve. This was also supported by field data, where we found minimal correspondence between eDNA quantity and CPUE data. A comparison between quantitative real-time PCR (qPCR) analysis and droplet-digital PCR (ddPCR) analysis revealed higher detection success of the targets in field samples when using qPCR. Overall, our results support eDNA as an effective tool for presence-absence monitoring, but it seems less suited for biomass quantification and population density estimates. Detection of A. astaci and P. leniusculus is not influenced uniformly by respective environmental factors. Consequently, we recommend a strategy of monitoring both targets, where the detection of one may point towards the presence of the other.
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27
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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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28
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Yao M, Zhang S, Lu Q, Chen X, Zhang SY, Kong Y, Zhao J. Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward. Mol Ecol 2022; 31:5132-5164. [PMID: 35972241 DOI: 10.1111/mec.16659] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 07/20/2022] [Accepted: 07/27/2022] [Indexed: 12/15/2022]
Abstract
Vast global declines of freshwater and marine fish diversity and population abundance pose serious threats to both ecosystem sustainability and human livelihoods. Environmental DNA (eDNA)-based biomonitoring provides robust, efficient, and cost-effective assessment of species occurrences and population trends in diverse aquatic environments. Thus, it holds great potential for improving conventional surveillance frameworks to facilitate fish conservation and fisheries management. However, the many technical considerations and rapid developments underway in the eDNA arena can overwhelm researchers and practitioners new to the field. Here, we systematically analysed 416 fish eDNA studies to summarize research trends in terms of investigated targets, research aims, and study systems, and reviewed the applications, rationales, methodological considerations, and limitations of eDNA methods with an emphasis on fish and fisheries research. We highlighted how eDNA technology may advance our knowledge of fish behaviour, species distributions, population genetics, community structures, and ecological interactions. We also synthesized the current knowledge of several important methodological concerns, including the qualitative and quantitative power eDNA has to recover fish biodiversity and abundance, and the spatial and temporal representations of eDNA with respect to its sources. To facilitate ecological applications implementing fish eDNA techniques, recent literature was summarized to generate guidelines for effective sampling in lentic, lotic, and marine habitats. Finally, we identified current gaps and limitations, and pointed out newly emerging research avenues for fish eDNA. As methodological optimization and standardization improve, eDNA technology should revolutionize fish monitoring and promote biodiversity conservation and fisheries management that transcends geographic and temporal boundaries.
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Affiliation(s)
- Meng Yao
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Shan Zhang
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Qi Lu
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Xiaoyu Chen
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Si-Yu Zhang
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Yueqiao Kong
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Jindong Zhao
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
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29
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Zainal Abidin DH, Mohd Nor SA, Lavoué S, A Rahim M, Mohammed Akib NA. Assessing a megadiverse but poorly known community of fishes in a tropical mangrove estuary through environmental DNA (eDNA) metabarcoding. Sci Rep 2022; 12:16346. [PMID: 36175455 PMCID: PMC9523059 DOI: 10.1038/s41598-022-19954-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 09/07/2022] [Indexed: 11/18/2022] Open
Abstract
Biodiversity surveys are crucial for monitoring the status of threatened aquatic ecosystems, such as tropical estuaries and mangroves. Conventional monitoring methods are intrusive, time-consuming, substantially expensive, and often provide only rough estimates in complex habitats. An advanced monitoring approach, environmental DNA (eDNA) metabarcoding, is promising, although only few applications in tropical mangrove estuaries have been reported. In this study, we explore the advantages and limitations of an eDNA metabarcoding survey on the fish community of the Merbok Estuary (Peninsular Malaysia). COI and 12S eDNA metabarcoding assays collectively detected 178 species from 127 genera, 68 families, and 25 orders. Using this approach, significantly more species have been detected in the Merbok Estuary over the past decade (2010–2019) than in conventional surveys, including several species of conservation importance. However, we highlight three limitations: (1) in the absence of a comprehensive reference database the identities of several species are unresolved; (2) some of the previously documented specimen-based diversity was not captured by the current method, perhaps as a consequence of PCR primer specificity, and (3) the detection of non-resident species—stenohaline freshwater taxa (e.g., cyprinids, channids, osphronemids) and marine coral reef taxa (e.g., holocentrids, some syngnathids and sharks), not known to frequent estuaries, leading to the supposition that their DNA have drifted into the estuary through water movements. The community analysis revealed that fish diversity along the Merbok Estuary is not homogenous, with the upstream more diverse than further downstream. This could be due to the different landscapes or degree of anthropogenic influences along the estuary. In summary, we demonstrated the practicality of eDNA metabarcoding in assessing fish community and structure within a complex and rich tropical environment within a short sampling period. However, some limitations need to be considered and addressed to fully exploit the efficacy of this approach.
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Affiliation(s)
- Danial Hariz Zainal Abidin
- Centre for Global Sustainability Studies (CGSS), Level 5, Hamzah Sendut Library, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Siti Azizah Mohd Nor
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Terengganu, Malaysia.
| | - Sébastien Lavoué
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | | | - Noor Adelyna Mohammed Akib
- Centre for Global Sustainability Studies (CGSS), Level 5, Hamzah Sendut Library, Universiti Sains Malaysia, 11800, Penang, Malaysia. .,School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia.
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30
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Lavery TH, Lindenmayer DB, Allan H, Southwell D, Woinarski JCZ, Lintermans M. Monitoring populations and threats to range‐restricted freshwater fishes: A case study of the Stocky Galaxias (
Galaxias tantangara
). ECOLOGICAL MANAGEMENT & RESTORATION 2022. [DOI: 10.1111/emr.12562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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31
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Hervé A, Domaizon I, Baudoin JM, Dejean T, Gibert P, Jean P, Peroux T, Raymond JC, Valentini A, Vautier M, Logez M. Spatio-temporal variability of eDNA signal and its implication for fish monitoring in lakes. PLoS One 2022; 17:e0272660. [PMID: 35960745 PMCID: PMC9374266 DOI: 10.1371/journal.pone.0272660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 07/24/2022] [Indexed: 11/18/2022] Open
Abstract
Environmental DNA (eDNA) metabarcoding is revolutionizing the monitoring of aquatic biodiversity. The use of eDNA has the potential to enable non-invasive, cost-effective, time-efficient and high-sensitivity monitoring of fish assemblages. Although the capacity of eDNA metabarcoding to describe fish assemblages is recognised, research efforts are still needed to better assess the spatial and temporal variability of the eDNA signal and to ultimately design an optimal sampling strategy for eDNA monitoring. In this context, we sampled three different lakes (a dam reservoir, a shallow eutrophic lake and a deep oligotrophic lake) every 6 weeks for 1 year. We performed four types of sampling for each lake (integrative sampling of sub-surface water along transects on the left shore, the right shore and above the deepest zone, and point sampling in deeper layers near the lake bottom) to explore the spatial variability of the eDNA signal at the lake scale over a period of 1 year. A metabarcoding approach was applied to analyse the 92 eDNA samples in order to obtain fish species inventories which were compared with traditional fish monitoring methods (standardized gillnet samplings). Several species known to be present in these lakes were only detected by eDNA, confirming the higher sensitivity of this technique in comparison with gillnetting. The eDNA signal varied spatially, with shoreline samples being richer in species than the other samples. Furthermore, deep-water samplings appeared to be non-relevant for regularly mixed lakes, where the eDNA signal was homogeneously distributed. These results also demonstrate a clear temporal variability of the eDNA signal that seems to be related to species phenology, with most of the species detected in spring during the spawning period on shores, but also a peak of detection in winter for salmonid and coregonid species during their reproduction period. These results contribute to our understanding of the spatio-temporal distribution of eDNA in lakes and allow us to provide methodological recommendations regarding where and when to sample eDNA for fish monitoring in lakes.
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Affiliation(s)
- Alix Hervé
- SPYGEN, Le Bourget du Lac, France
- Pole R&D ECLA, Le Bourget-du-Lac, France
- INRAE, Aix Marseille Université, RECOVER, Aix-en-Provence, France
| | - Isabelle Domaizon
- Pole R&D ECLA, Le Bourget-du-Lac, France
- INRAE, UMR CARRTEL, Thonon-les-Bains, France
| | - Jean-Marc Baudoin
- Pole R&D ECLA, Le Bourget-du-Lac, France
- OFB, Direction de la Recherche et de l’Appui Scientifique, Route Cézanne, Aix-en-Provence, France
| | | | - Pierre Gibert
- Pole R&D ECLA, Le Bourget-du-Lac, France
- INRAE, Aix Marseille Université, RECOVER, Aix-en-Provence, France
| | | | - Tiphaine Peroux
- Pole R&D ECLA, Le Bourget-du-Lac, France
- INRAE, Aix Marseille Université, RECOVER, Aix-en-Provence, France
| | - Jean-Claude Raymond
- Pole R&D ECLA, Le Bourget-du-Lac, France
- OFB, DR AURA, Thonon-les-Bains, France
| | | | - Marine Vautier
- Pole R&D ECLA, Le Bourget-du-Lac, France
- INRAE, UMR CARRTEL, Thonon-les-Bains, France
| | - Maxime Logez
- Pole R&D ECLA, Le Bourget-du-Lac, France
- INRAE, Aix Marseille Université, RECOVER, Aix-en-Provence, France
- INRAE, UR RIVERLY, Villeurbanne, France
- * E-mail:
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32
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Chen X, Kong Y, Zhang S, Zhao J, Li S, Yao M. Comparative Evaluation of Common Materials as Passive Samplers of Environmental DNA. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:10798-10807. [PMID: 35856738 DOI: 10.1021/acs.est.2c02506] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Environmental DNA (eDNA) technology has revolutionized biomonitoring in recent years; however, eDNA collection from aquatic environments generally relies on the time-consuming and equipment-dependent process of water filtration. Passive eDNA sampling deploys sorbent materials to capture eDNA from water, circumventing many problems associated with active filtration; yet, very few candidate materials have been systematically evaluated for this purpose. Here, we evaluated the ability of 12 different types of common loose sorbents and filter membranes to capture eDNA in laboratory and field experiments compared with conventional water filtration. Glass fiber filters (GF) outperformed all other materials in laboratory experiments with respect to their quantitative capacity to recover amphibian eDNA, with the eDNA yield increasing linearly with submersion time up to 72 h. Furthermore, GF rapidly (within 0.5 h) captured the eDNA of up to 71% of the total fish species in a lake, in addition to detecting the entire fish community by 8 h, as assessed by metabarcoding analysis. Our results demonstrate that GF could passively capture aqueous eDNA with a similar or greater efficiency than conventional methods, thus paving the way for convenient, effective, and eco-friendly eDNA sampling in aquatic environments.
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Affiliation(s)
- Xiaoyu Chen
- School of Life Sciences, Peking University, Beijing 100871, China
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Yueqiao Kong
- School of Life Sciences, Peking University, Beijing 100871, China
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Shan Zhang
- School of Life Sciences, Peking University, Beijing 100871, China
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Jindong Zhao
- School of Life Sciences, Peking University, Beijing 100871, China
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Sheng Li
- School of Life Sciences, Peking University, Beijing 100871, China
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Meng Yao
- School of Life Sciences, Peking University, Beijing 100871, China
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
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33
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Fukuzawa T, Kameda Y, Nagata H, Nishizawa N, Doi H. Filtration extraction method using microfluidic channel for measuring environmental DNA. Mol Ecol Resour 2022; 22:2651-2661. [PMID: 35652737 DOI: 10.1111/1755-0998.13657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 05/09/2022] [Accepted: 05/26/2022] [Indexed: 11/28/2022]
Abstract
The environmental DNA (eDNA) method, which is widely applied in biomonitoring, is limited to laboratory analysis and processing. In this study, we developed a filtration/extraction component using a microfluidic channel, the Biryu-Chip (BC), and a filtration/extraction method, the BC method, to minimize the volume of the sample necessary for DNA extraction and subsequent PCR amplification. We tested the performance of the BC method and compared it with that of the Sterivex filtration/extraction method using aquarium and river water samples. We observed that using the BC method, the same concentration of extracted DNA was obtained with 1/20-1/40 of the filtration volume of the Sterivex method, suggesting that the BC method can be widely used for eDNA measurement. In addition, we performed on-site measurements of eDNA within 30 min using a mobile PCR device, demonstrating that filtration and extraction can be performed easily and quickly using the BC method. The PCR results obtained using the BC method were similar to those obtained using the Sterivex method. The BC method requires fewer steps; therefore, the risk of DNA contamination can be reduced. When combined with mobile PCR, the BC method can be applied to easily detect eDNA within 30 min from the collection of water sample, even on-site.
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Affiliation(s)
| | - Yuichi Kameda
- GO!FOTON INC., Tsukuba, Japan.,Department of Anthropology, National Museum of Nature and Science, Tsukuba, Japan
| | | | | | - Hideyuki Doi
- Graduate School of Information Science, University of Hyogo, Kobe, Japan
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34
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Diao C, Jia H, Guo S, Hou G, Xian W, Zhang H. Biodiversity exploration in autumn using environmental DNA in the South China sea. ENVIRONMENTAL RESEARCH 2022; 204:112357. [PMID: 34774836 DOI: 10.1016/j.envres.2021.112357] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/30/2021] [Accepted: 11/06/2021] [Indexed: 06/13/2023]
Abstract
The South China Sea (SCS) is an important part of the Indo-Pacific convergence zone, with high biodiversity and abundant marine resources. Traditional methods are primarily used to monitor biodiversity. However, a few studies have used environmental DNA (eDNA) metabarcoding to research the assemblage structure of the SCS. This study used eDNA metabarcoding to survey the SCS assemblage and its relationship with environmental factors over a month-long time-series (August 30th to September 30th, 2020) of seawater samples from the central part of the SCS (9°-20°86' N, 113°-118°47' E). 32 stations were divided into six groups (A, B, C, D, E, F) according to longitude. We collected water samples, extracted eDNA, and amplified 18S rRNA gene V4 region (18S V4), 18S rRNA gene V9 region (18S V9), and 12S rRNA gene (12S). Krona diagrams were used to show species composition. We identified 192 phytoplankton, 104 invertebrate, and 61 fish species from 18S V4, 18S V9, and 12S, respectively. Generally, the three assemblage structures exhibited an increase in species diversity with increasing longitude. Group E had the highest fish diversity. Groups F and C had the highest phytoplankton and invertebrate diversity, respectively. Canonical correspondence analysis showed that four factors (chlorophyll a, depth, salinity, and temperature) were correlated with assemblage structure. Chlorophyll a was the main environmental factor that affected fish, phytoplankton, and invertebrate assemblage structures; salinity was strongly correlated with fish and invertebrate assemblage structures; temperature was a key factor that impacted fish and invertebrate assemblage structures; and depth was strongly correlated with invertebrate assemblage structure. Our results revealed that eDNA metabarcoding is a powerful tool for improving detection rate and using multiple markers is an effective approach for monitoring biodiversity. This study provided information that can be used to enhance biodiversity protection efforts in the SCS.
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Affiliation(s)
- Caoyun Diao
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hui Jia
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; China School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Shujin Guo
- Jiaozhou Bay National Marine Ecosystem Research Station, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Gang Hou
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524000, China
| | - Weiwei Xian
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
| | - Hui Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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35
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Miya M. Environmental DNA Metabarcoding: A Novel Method for Biodiversity Monitoring of Marine Fish Communities. ANNUAL REVIEW OF MARINE SCIENCE 2022; 14:161-185. [PMID: 34351788 DOI: 10.1146/annurev-marine-041421-082251] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Environmental DNA (eDNA) is genetic material that has been shed from macroorganisms. It has received increased attention as an indirect marker for biodiversity monitoring. This article reviews the current status of eDNA metabarcoding (simultaneous detection of multiple species) as a noninvasive and cost-effective approach for monitoring marine fish communities and discusses the prospects for this growing field. eDNA metabarcoding coamplifies short fragments of fish eDNA across a wide variety of taxa and, coupled with high-throughput sequencing technologies, allows massively parallel sequencing to be performed simultaneously for dozens to hundreds of samples. It can predict species richness in a given area, detect habitat segregation and biogeographic patterns from small to large spatial scales, and monitor the spatiotemporal dynamics of fish communities. In addition, it can detect an anthropogenic impact on fish communities through evaluation of their functional diversity. Recognizing the strengths and limitations of eDNA metabarcoding will help ensure that continuous biodiversity monitoring at multiple sites will be useful for ecosystem conservation and sustainable use of fishery resources, possibly contributing to achieving the targets of the United Nations' Sustainable Development Goal 14 for 2030.
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Affiliation(s)
- Masaki Miya
- Natural History Museum and Institute, Chiba, Chiba 260-8682, Japan;
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36
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Ritterbusch D, Blabolil P, Breine J, Erős T, Mehner T, Olin M, Peirson G, Volta P, Poikane S. European fish-based assessment reveals high diversity of systems for determining ecological status of lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 802:149620. [PMID: 34461474 DOI: 10.1016/j.scitotenv.2021.149620] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 08/05/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
Triggered by the adoption of the Water Framework Directive, a variety of fish-based systems were developed throughout Europe to assess the ecological status of lakes. This paper provides a comprehensive overview of all existing systems and summarizes sampling methods, fish community traits (metrics) and the relevant anthropogenic pressures assessed by them. Twenty-one European countries developed fish-based assessment systems. Three countries each developed two distinct systems to approach different ecoregions, either to use different data, or to assess different lake types leading to a total number of 24 systems. The most common approach for the setting of reference conditions, used in seventeen systems, was the utilisation of fish communities in comparably undisturbed natural lakes as reference. Eleven used expert judgment, nine historical data and eight modelled relationships. Fourteen systems combined at least two approaches. The most common fish sampling method was a standardized fishing procedure with multimesh-gillnets. Many countries applied combinations of fishing methods, e.g. non-standard gillnets, fyke nets and electrofishing. Altogether 177 metrics were used for index development and each system combined 2-13 metrics. The most common ones were total standardized catches of number and biomass, relative abundance of Perca fluviatilis, Rutilus rutilus, and Abramis brama, feeding preferences, sensitive species, and non-natives. The pressure-response-relationships for these metrics were supported with both correlations established during system development and scientific publications. However, the metrics and their combinations were highly diverse and no metric was applied universally. Our analysis reveals that most fish-based assessment systems address multiple pressures (eutrophication, hydromorphological alterations, fishery pressure and occurrence of non-natives), whilst few are pressure-specific, tackling only eutrophication or acidification. We argue that the value of fish-based systems for lakes lies in their capacity to capture the effect of many different pressures and their interactions which is lacking for most assessment systems based on other biota.
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Affiliation(s)
- David Ritterbusch
- Institute for Inland Fisheries, Im Königswald 2, D-14469 Potsdam, Germany.
| | - Petr Blabolil
- Biology Centre of the Czech Academy of Sciences, Na Sádkách 7, 37005 České Budějovice, Czech Republic.
| | - Jan Breine
- Research Institute for Nature and Forest (INBO), Dwersbos 28, B-1630 Linkebeek, Belgium.
| | - Tibor Erős
- Balaton Limnological Research Institute, Klebelsberg K. u. 3, H-8237 Tihany, Hungary.
| | - Thomas Mehner
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 310, D-12587 Berlin, Germany.
| | - Mikko Olin
- Natural Resources Institute Finland, P. O. Box 2, FI-00791 Helsinki, Finland.
| | - Graeme Peirson
- Environment Agency, Research, Analysis and Evaluation, Air, Land and Water Team, Worcester Road, Kidderminster DY11 RA, United Kingdom.
| | - Pietro Volta
- CNR Water Research Institute (IRSA), L.go Tonolli 50, 28922 Verbania Pallanza, Italy.
| | - Sandra Poikane
- European Commission Joint Research Centre (JRC), Via Enrico Fermi 274, 21027 Ispra, VA, Italy.
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Rivera SF, Rimet F, Vasselon V, Vautier M, Domaizon I, Bouchez A. Fish eDNA metabarcoding from aquatic biofilm samples: Methodological aspects. Mol Ecol Resour 2021; 22:1440-1453. [PMID: 34863036 DOI: 10.1111/1755-0998.13568] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 10/22/2021] [Accepted: 11/25/2021] [Indexed: 01/04/2023]
Abstract
Fish eDNA metabarcoding is usually performed from filtered water samples. The volume of filtered water depends on the study scope and can rapidly become time consuming according to the number of samples that have to be processed. To avoid time allocated to filtration, passive DNA samplers have been used to recover fish eDNA from marine environments faster. In freshwater ecosystems, aquatic biofilms were used to catch eDNA from macroinvertebrates. Here, we test the capacity of aquatic biofilms to entrap fish eDNA in a large lake and, therefore, the possibility to perform fish eDNA metabarcoding from this matrix compared to the traditional fish eDNA approach from filtered water samples. Methodological aspects of the use of aquatic biofilms for fish eDNA metabarcoding (e.g. PCR replicates, biological replicates, bioinformatics pipeline, reference database and taxonomic assignment) were validated against a mock community. When using biofilms from habitats sheltered from wind and waves, biofilm and water approach provided similar inventories. Richness and diversity were comparable between both approaches. Approaches differed only for rare taxa. Our results illustrate the capacity of aquatic biofilms to act as passive eDNA samplers of fish eDNA and, therefore, the possibility to use biofilms to monitor fish communities efficiently from biofilms. Furthermore, our results open up avenues of research to study a diversity of biological groups (among which bioindicators as diatoms, macroinvertebrates and fish) from eDNA isolated from a single environmental matrix reducing sampling efforts, analysis time and costs.
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Affiliation(s)
- Sinziana F Rivera
- INRA, UMR CARRTEL, Université Savoie Mont-Blanc, Thonon-les-Bains, France
| | - Frédéric Rimet
- INRA, UMR CARRTEL, Université Savoie Mont-Blanc, Thonon-les-Bains, France
| | | | - Marine Vautier
- INRA, UMR CARRTEL, Université Savoie Mont-Blanc, Thonon-les-Bains, France
| | - Isabelle Domaizon
- INRA, UMR CARRTEL, Université Savoie Mont-Blanc, Thonon-les-Bains, France
| | - Agnès Bouchez
- INRA, UMR CARRTEL, Université Savoie Mont-Blanc, Thonon-les-Bains, France
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Banerjee P, Dey G, Antognazza CM, Sharma RK, Maity JP, Chan MWY, Huang YH, Lin PY, Chao HC, Lu CM, Chen CY. Reinforcement of Environmental DNA Based Methods ( Sensu Stricto) in Biodiversity Monitoring and Conservation: A Review. BIOLOGY 2021; 10:biology10121223. [PMID: 34943137 PMCID: PMC8698464 DOI: 10.3390/biology10121223] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/15/2021] [Accepted: 11/18/2021] [Indexed: 12/02/2022]
Abstract
Simple Summary Worldwide biodiversity loss points to a necessity of upgrading to a fast and effective monitoring method that can provide quick conservation action. Newly developed environmental DNA (eDNA) based method found to be more cost-effective, non-invasive, quick, and accurate than traditional monitoring (spot identification, camera trapping). Although the eDNA based methods are proliferating rapidly, as a newly developed branch, it needs more standardization and practitioner adaptation. The present study aims to evaluate the eDNA based methods, and their potential achievements in biodiversity monitoring, and conservation for quick practitioners’ adaption. The investigation shows that the eDNA technique is applicable largely in (i) early detection of invasive species, (ii) species detection for conservation, (iii) community-level biodiversity monitoring, (iv) ecosystem health monitoring, (v) study on trophic interactions, etc. Thus, the eDNA technique shows a great promise with its high accuracy and authenticity, and will be applicable alone or alongside other methods in the near future. Abstract Recently developed non-invasive environmental DNA-based (eDNA) techniques have enlightened modern conservation biology, propelling the monitoring/management of natural populations to a more effective and efficient approach, compared to traditional surveys. However, due to rapid-expansion of eDNA, confusion in terminology and collection/analytical pipelines can potentially jeopardize research progression, methodological standardization, and practitioner adoption in several ways. Present investigation reflects the developmental progress of eDNA (sensu stricto) including highlighting the successful case studies in conservation management. The eDNA technique is successfully relevant in several areas of conservation research (invasive/conserve species detection) with a high accuracy and authentication, which gradually upgrading modern conservation approaches. The eDNA technique related bioinformatics (e.g., taxon-specific-primers MiFish, MiBird, etc.), sample-dependent methodology, and advancement of sequencing technology (e.g., oxford-nanopore-sequencing) are helping in research progress. The investigation shows that the eDNA technique is applicable largely in (i) early detection of invasive species, (ii) species detection for conservation, (iii) community level biodiversity monitoring, (iv) ecosystem health monitoring, (v) study on trophic interactions, etc. Thus, the eDNA technique with a high accuracy and authentication can be applicable alone or coupled with traditional surveys in conservation biology. However, a comprehensive eDNA-based monitoring program (ecosystem modeling and function) is essential on a global scale for future management decisions.
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Affiliation(s)
- Pritam Banerjee
- Department of Biomedical Science, Graduate Institute of Molecular Biology, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County, Jiayi 62102, Taiwan; (P.B.); (G.D.); (M.W.Y.C.)
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County, Jiayi 62102, Taiwan; (R.K.S.); (J.P.M.); (Y.-H.H.); (H.-C.C.)
| | - Gobinda Dey
- Department of Biomedical Science, Graduate Institute of Molecular Biology, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County, Jiayi 62102, Taiwan; (P.B.); (G.D.); (M.W.Y.C.)
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County, Jiayi 62102, Taiwan; (R.K.S.); (J.P.M.); (Y.-H.H.); (H.-C.C.)
| | - Caterina M. Antognazza
- Department of Theoretical and Applied Science, University of Insubria, Via J.H. Dunant, 3, 21100 Varese, Italy;
| | - Raju Kumar Sharma
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County, Jiayi 62102, Taiwan; (R.K.S.); (J.P.M.); (Y.-H.H.); (H.-C.C.)
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County, Jiayi 62102, Taiwan;
| | - Jyoti Prakash Maity
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County, Jiayi 62102, Taiwan; (R.K.S.); (J.P.M.); (Y.-H.H.); (H.-C.C.)
- Department of Chemistry, School of Applied Sciences, KIIT Deemed to be University, Bhubaneswar 751024, India
| | - Michael W. Y. Chan
- Department of Biomedical Science, Graduate Institute of Molecular Biology, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County, Jiayi 62102, Taiwan; (P.B.); (G.D.); (M.W.Y.C.)
| | - Yi-Hsun Huang
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County, Jiayi 62102, Taiwan; (R.K.S.); (J.P.M.); (Y.-H.H.); (H.-C.C.)
| | - Pin-Yun Lin
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County, Jiayi 62102, Taiwan;
| | - Hung-Chun Chao
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County, Jiayi 62102, Taiwan; (R.K.S.); (J.P.M.); (Y.-H.H.); (H.-C.C.)
| | - Chung-Ming Lu
- Department of Chemical Engineering, National Chung Cheng University, 168 University Road, Ming-Shung, Chiayi County, Jiayi 62102, Taiwan;
| | - Chien-Yen Chen
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County, Jiayi 62102, Taiwan; (R.K.S.); (J.P.M.); (Y.-H.H.); (H.-C.C.)
- Correspondence: or ; Tel.: +886-5-2720411 (ext. 66220); Fax: +886-5-2720807
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39
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Karr JR, Larson ER, Chu EW. Ecological integrity is both real and valuable. CONSERVATION SCIENCE AND PRACTICE 2021. [DOI: 10.1111/csp2.583] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
| | - Eric R. Larson
- Department of Natural Resources and Environmental Sciences University of Illinois Urbana Illinois USA
| | - Ellen W. Chu
- Ecologist and Editor Port Townsend Washington USA
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40
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Ríos-Castro R, Romero A, Aranguren R, Pallavicini A, Banchi E, Novoa B, Figueras A. High-Throughput Sequencing of Environmental DNA as a Tool for Monitoring Eukaryotic Communities and Potential Pathogens in a Coastal Upwelling Ecosystem. Front Vet Sci 2021; 8:765606. [PMID: 34805343 PMCID: PMC8595318 DOI: 10.3389/fvets.2021.765606] [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: 08/27/2021] [Accepted: 10/08/2021] [Indexed: 12/04/2022] Open
Abstract
The marine environment includes diverse microeukaryotic organisms that play important functional roles in the ecosystem. With molecular approaches, eukaryotic taxonomy has been improved, complementing classical analysis. In this study, DNA metabarcoding was performed to describe putative pathogenic eukaryotic microorganisms in sediment and marine water fractions collected in Galicia (NW Spain) from 2016 to 2018. The composition of eukaryotic communities was distinct between sediment and water fractions. Protists were the most diverse group, with the clade TSAR (Stramenopiles, Alveolata, Rhizaria, and Telonemida) as the primary representative organisms in the environment. Harmful algae and invasive species were frequently detected. Potential pathogens, invasive pathogenic organisms as well as the causative agents of harmful phytoplanktonic blooms were identified in this marine ecosystem. Most of the identified pathogens have a crucial impact on the aquacultural sector or affect to relevant species in the marine ecosystem, such as diatoms. Moreover, pathogens with medical and veterinary importance worldwide were also found, as well as pathogens that affect diatoms. The evaluation of the health of a marine ecosystem that directly affects the aquacultural sector with a zoonotic concern was performed with the metabarcoding assay.
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Affiliation(s)
- Raquel Ríos-Castro
- Inmunology and Genomics, Marine Research Institute (IIM-CSIC), Vigo, Spain
| | - Alejandro Romero
- Inmunology and Genomics, Marine Research Institute (IIM-CSIC), Vigo, Spain
| | - Raquel Aranguren
- Inmunology and Genomics, Marine Research Institute (IIM-CSIC), Vigo, Spain
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Trieste, Italy
- Division of Oceanography, National Institute of Oceanography and Applied Geophysics, Trieste, Italy
| | - Elisa Banchi
- Department of Life Sciences, University of Trieste, Trieste, Italy
- Division of Oceanography, National Institute of Oceanography and Applied Geophysics, Trieste, Italy
| | - Beatriz Novoa
- Inmunology and Genomics, Marine Research Institute (IIM-CSIC), Vigo, Spain
| | - Antonio Figueras
- Inmunology and Genomics, Marine Research Institute (IIM-CSIC), Vigo, Spain
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Inoue J. ORTHOSCOPE*: a phylogenetic pipeline to infer gene histories from genome-wide data. Mol Biol Evol 2021; 39:6400256. [PMID: 34662403 PMCID: PMC8763121 DOI: 10.1093/molbev/msab301] [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] [Indexed: 11/13/2022] Open
Abstract
Comparative genome-scale analyses of protein-coding gene sequences are employed to examine evidence for whole-genome duplication and horizontal gene transfer. For this purpose, an orthogroup should be delineated to infer evolutionary history regarding each gene, and results of all orthogroup analyses need to be integrated to infer a genome-scale history. An orthogroup is a set of genes descended from a single gene in the last common ancestor of all species under consideration. However, such analyses confront several problems: (1) analytical pipelines to infer all gene histories with methods comparing species and gene trees are not fully developed, and (2) without detailed analyses within orthogroups, evolutionary events of paralogous genes in the same orthogroup cannot be distinguished for genome-wide integration of results derived from multiple orthogroup analyses. Here I present an analytical pipeline, ORTHOSCOPE* (star), to infer evolutionary histories of animal/plant genes from genome-scale data. ORTHOSCOPE* estimates a tree for a specified gene, detects speciation/gene duplication events that occurred at nodes belonging to only one lineage leading to a species of interest, and then integrates results derived from gene trees estimated for all query genes in genome-wide data. Thus, ORTHOSCOPE* can be used to detect species nodes just after whole genome duplications as a first step of comparative genomic analyses. Moreover, by examining the presence or absence of genes belonging to species lineages with dense taxon sampling available from the ORTHOSCOPE web version, ORTHOSCOPE* can detect genes lost in specific lineages and horizontal gene transfers. This pipeline is available at https://github.com/jun-inoue/ORTHOSCOPE_STAR.
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Affiliation(s)
- Jun Inoue
- Center for Earth Surface System Dynamics, Atmosphere and Ocean Research Institute, University of Tokyo, Kashiwa, Japan
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Boulanger E, Loiseau N, Valentini A, Arnal V, Boissery P, Dejean T, Deter J, Guellati N, Holon F, Juhel JB, Lenfant P, Manel S, Mouillot D. Environmental DNA metabarcoding reveals and unpacks a biodiversity conservation paradox in Mediterranean marine reserves. Proc Biol Sci 2021; 288:20210112. [PMID: 33906403 PMCID: PMC8080007 DOI: 10.1098/rspb.2021.0112] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/29/2021] [Indexed: 12/17/2022] Open
Abstract
Although we are currently experiencing worldwide biodiversity loss, local species richness does not always decline under anthropogenic pressure. This conservation paradox may also apply in protected areas but has not yet received conclusive evidence in marine ecosystems. Here, we survey fish assemblages in six Mediterranean no-take reserves and their adjacent fishing grounds using environmental DNA (eDNA) while controlling for environmental conditions. We detect less fish species in marine reserves than in nearby fished areas. The paradoxical gradient in species richness is accompanied by a marked change in fish species composition under different managements. This dissimilarity is mainly driven by species that are often overlooked by classical visual surveys but detected with eDNA: cryptobenthic, pelagic, and rare fishes. These results do not negate the importance of reserves in protecting biodiversity but shed new light on how under-represented species groups can positively react to fishing pressure and how conservation efforts can shape regional biodiversity patterns.
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Affiliation(s)
- Emilie Boulanger
- CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Nicolas Loiseau
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | | | - Véronique Arnal
- CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
| | - Pierre Boissery
- Agence de l'Eau Rhône-Méditerranée-Corse, Délégation de Marseille, Marseille, France
| | | | | | - Nacim Guellati
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | | | | | | | - Stéphanie Manel
- CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
| | - David Mouillot
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France
- Institut Universitaire de France, Paris, France
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