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Liu B, Wang F, Li S, Xiong W, Zhan A. Environmental DNA-Based Identification of Non-Native Fish in Beijing: Diversity, Geographical Distribution, and Interactions with Native Taxa. Animals (Basel) 2024; 14:2532. [PMID: 39272318 PMCID: PMC11393847 DOI: 10.3390/ani14172532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 08/22/2024] [Accepted: 08/29/2024] [Indexed: 09/15/2024] Open
Abstract
Rapid urbanization and its associated human activities have facilitated the colonization and spread of non-native species, rendering urban ecosystems, particularly in megacities such as Beijing, highly susceptible to biological invasions. This study employed environmental DNA (eDNA) metabarcoding to evaluate the biodiversity and geographical distribution of non-native fish, as well as their interactions with native fish species, across three river basins in Beijing pertaining to the Daqing River, the North Canal, and the Ji Canal. Across all the 67 sampling sites, we identified 60 fish taxa, representing 11 orders, 23 families, and 40 genera, with an average of 33.0 taxa per site. Of these, 40 taxa were native, accounting for only 47.1% of the historically recorded native fish species. Additionally, we detected 20 non-native fish taxa, spanning 11 orders, 13 families, and 17 genera. Native fish exhibited geographical homogenization across the basins, while non-native taxa displayed varied geographical distributions. Non-metric multidimensional scaling (NMDS) and analysis of similarities (ANOSIM) revealed no significant variation in the non-native communities across the river basins. Although most of the non-native taxa were widespread, some were restricted to specific sites or basins. The North Canal exhibited significantly lower non-native biodiversity compared with the Ji Canal across all alpha diversity indices. Simple linear regression analyses indicated positive correlations between the number of taxa and species richness for both native and non-native taxa. Interestingly, species co-occurrence analyses revealed predominantly positive interactions among both native and non-native species pairs, with only two negative relationships involving one native and two non-native taxa. This study provides insights into the biodiversity and geographical distribution of non-native fish in Beijing and establishes a baseline for future biomonitoring and conservation efforts. The findings underscore the need for further investigation into the mechanisms and dynamics of biological invasions within urban environments in Beijing.
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Affiliation(s)
- Bo Liu
- Beijing Hydrology Center, Beijing 100089, China
| | - Fuwen Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Shiguo Li
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Xiong
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China
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Chen Y, Bin Q, Liu H, Xie Y, Wang S, Lu J, Ou W, Zhang M, Wang L, Yu K. A novel biosensing strategy on the dynamic and on-site detection of Vibrio coralliilyticus eDNA for coral health warnings. Bioelectrochemistry 2024; 158:108697. [PMID: 38554560 DOI: 10.1016/j.bioelechem.2024.108697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 03/20/2024] [Accepted: 03/27/2024] [Indexed: 04/01/2024]
Abstract
Heat stress and coral diseases are the predominant factors causing the degradation of coral reef ecosystems. Over recent years, Vibrio coralliilyticus was identified as a temperature-dependent pathogen causing tissue lysis in Pocillopora damicornis and one of the primary pathogens causing bleaching and mortality in other corals. Yet current detection techniques for V. coralliilyticus rely primarily on qPCR and ddPCR, which cannot meet the requirements for non-invasive and real-time detection. Herein, we developed an effective electrochemical biosensor modified by an Au-MoS2/rGO (AMG) nanocomposites and a specific capture probe to dynamically detect V. coralliilyticus environment DNA (eDNA) in aquarium experiments, with a lower limit of detection (0.28 fM) for synthetic DNA and a lower limit of quantification (9.8 fg/µL, ∼0.86 copies/µL) for genomic DNA. Its reliability and accuracy were verified by comparison with the ddPCR method (P > 0.05). Notably, coral tissue started to lyse at only 29 °C when the concentration of V. coralliilyticus increased abruptly to 880 copies/µL, indicating the biosensor could reflect the types of pathogen and health risks of corals under heat stress. Overall, the novel and reliable electrochemical biosensing technology provides an efficient strategy for the on-site monitoring and early warning of coral health in the context of global warming.
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Affiliation(s)
- Yingzhan Chen
- School of Resources, Environment and Materials, School of Marine Sciences, School of Chemistry and Chemical Engineering, School of Life Science and Technology, Guangxi University, Nanning 530004, China; Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning 530004, China
| | - Qi Bin
- School of Resources, Environment and Materials, School of Marine Sciences, School of Chemistry and Chemical Engineering, School of Life Science and Technology, Guangxi University, Nanning 530004, China; Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning 530004, China
| | - Hongjie Liu
- School of Resources, Environment and Materials, School of Marine Sciences, School of Chemistry and Chemical Engineering, School of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Yuanyu Xie
- School of Resources, Environment and Materials, School of Marine Sciences, School of Chemistry and Chemical Engineering, School of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Shaopeng Wang
- School of Resources, Environment and Materials, School of Marine Sciences, School of Chemistry and Chemical Engineering, School of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Jie Lu
- School of Resources, Environment and Materials, School of Marine Sciences, School of Chemistry and Chemical Engineering, School of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Wenchao Ou
- School of Resources, Environment and Materials, School of Marine Sciences, School of Chemistry and Chemical Engineering, School of Life Science and Technology, Guangxi University, Nanning 530004, China; Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning 530004, China
| | - Man Zhang
- School of Resources, Environment and Materials, School of Marine Sciences, School of Chemistry and Chemical Engineering, School of Life Science and Technology, Guangxi University, Nanning 530004, China; Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning 530004, China.
| | - Liwei Wang
- School of Resources, Environment and Materials, School of Marine Sciences, School of Chemistry and Chemical Engineering, School of Life Science and Technology, Guangxi University, Nanning 530004, China; Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning 530004, China.
| | - Kefu Yu
- School of Resources, Environment and Materials, School of Marine Sciences, School of Chemistry and Chemical Engineering, School of Life Science and Technology, Guangxi University, Nanning 530004, China; Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning 530004, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
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3
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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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Wei Z, Zhang X, Chen Y, Liu H, Wang S, Zhang M, Ma H, Yu K, Wang L. A new strategy based on a cascade amplification strategy biosensor for on-site eDNA detection and outbreak warning of crown-of-thorns starfish. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172258. [PMID: 38583618 DOI: 10.1016/j.scitotenv.2024.172258] [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: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/09/2024]
Abstract
Population outbreaks of the crown-of-thorns starfish (COTS) seriously threaten the sustainability of coral reef ecosystems. However, traditional ecological monitoring techniques cannot provide early warning before the outbreaks, thus preventing timely intervention. Therefore, there is an urgent need for a more accurate and faster technology to predict the outbreaks of COTS. In this work, we developed an electrochemical biosensor based on a programmed catalytic hairpin assembly (CHA) and hybridization chain reaction (HCR) cyclic amplification strategy for sensitive and selective detection of COTS environmental DNA (eDNA) in water bodies. This biosensor exhibited excellent electrochemical characteristics, including a low limit of detection (LOD = 18.4 fM), low limit of quantification (LOQ = 41.1 fM), and wide linear range (50 fM - 10 nM). The biosensing technology successfully allowed the detection of COTS eDNA in the aquarium environment, and the results also demonstrated a significant correlation between eDNA concentration and COTS number (r = 0.990; P < 0.001). The reliability and accuracy of the biosensor results have been further validated through comparison with digital droplet PCR (ddPCR). Moreover, the applicability and accuracy of the biosensor were reconfirmed in field tests at the COTS outbreak site in the South China Sea, which has shown potential application in dynamically monitoring the larvae before the COTS outbreak. Therefore, this efficient electrochemical biosensing technology offers a new solution for on-site monitoring and early warning of the COTS outbreak.
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Affiliation(s)
- Zongwu Wei
- School of Resources, Environment and Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Xuzhe Zhang
- School of Resources, Environment and Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Yingzhan Chen
- School of Resources, Environment and Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Hongjie Liu
- School of Resources, Environment and Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Shaopeng Wang
- School of Resources, Environment and Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Man Zhang
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning 530004, China
| | - Honglin Ma
- Sansha Track Ocean Coral Reef Conservation Research Institute Co. Ltd., Qionghai 571499, China
| | - Kefu Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning 530004, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China.
| | - Liwei Wang
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning 530004, China.
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5
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Chen X, Li S, Zhao J, Yao M. Passive eDNA sampling facilitates biodiversity monitoring and rare species detection. ENVIRONMENT INTERNATIONAL 2024; 187:108706. [PMID: 38696978 DOI: 10.1016/j.envint.2024.108706] [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: 10/31/2023] [Revised: 04/09/2024] [Accepted: 04/25/2024] [Indexed: 05/04/2024]
Abstract
Environmental DNA (eDNA) technology has revolutionized biomonitoring, but challenges remain regarding water sample processing. The passive eDNA sampler (PEDS) represents a viable alternative to active, water filtration-based eDNA enrichment methods, but the effectiveness of PEDS for surveying biodiverse and complex natural water bodies is unknown. Here, we collected eDNA using filtration and glass fiber filter-based PEDS (submerged in water for 1 d) from 27 sites along the final reach of the Yangtze River and the coast of the Yellow Sea, followed by eDNA metabarcoding analysis of fish biodiversity and quantitative PCR (qPCR) for a critically endangered aquatic mammal, the Yangtze finless porpoise. We ultimately detected 98 fish species via eDNA metabarcoding. Both eDNA sampling methods captured comparable local species richness and revealed largely similar spatial variation in fish assemblages and community partitions between the river and sea sites. Notably, the Yangtze finless porpoise was detected only in the metabarcoding of eDNA collected by PEDS at five sites. Also, species-specific qPCR revealed that the PEDS captured porpoise eDNA at more sites (7 vs. 2), in greater quantities, and with a higher detection probability (0.803 vs. 0.407) than did filtration. Our results demonstrate the capacity of PEDS for surveying fish biodiversity, and support that continuous eDNA collection by PEDS can be more effective than instantaneous water sampling at capturing low abundance and ephemeral species in natural waters. Thus, the PEDS approach can facilitate more efficient and convenient eDNA-based biodiversity surveillance and rare species detection.
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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, China 100871
| | - Sheng Li
- School of Life Sciences, Peking University, Beijing 100871, China; Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China 100871
| | - Jindong Zhao
- School of Life Sciences, Peking University, Beijing 100871, China; Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China 100871
| | - Meng Yao
- School of Life Sciences, Peking University, Beijing 100871, China; Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China 100871.
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6
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Müller ND, Kirtane A, Schefer RB, Mitrano DM. eDNA Adsorption onto Microplastics: Impacts of Water Chemistry and Polymer Physiochemical Properties. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:7588-7599. [PMID: 38624040 DOI: 10.1021/acs.est.3c10825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Adsorption of biomacromolecules onto polymer surfaces, including microplastics (MPs), occurs in multiple environmental compartments, forming an ecocorona. Environmental DNA (eDNA), genetic material shed from organisms, can adsorb onto MPs which can potentially either (1) promote long-range transport of antibiotic resistant genes or (2) serve to gain insights into the transport pathways and origins of MPs by analyzing DNA sequences on MPs. However, little is known about the capacity of MPs to adsorb eDNA or the factors that influence sorption, such as polymer and water chemistries. Here we investigated the adsorption of extracellular linear DNA onto a variety of model MP fragments composed of three of the most environmentally prevalent polymers (polyethylene, polyethylene terephthalate, and polystyrene) in their pristine and photochemically weathered states. Batch adsorption experiments in a variety of water chemistries were complemented with nonlinear modeling to quantify the rate and extent of eDNA sorption. Ionic strength was shown to strongly impact DNA adsorption by reducing or inhibiting electrostatic repulsion. Polyethylene terephthalate exhibited the highest adsorption capacity when normalizing for MP specific surface area, likely due to the presence of ester groups. Kinetics experiments showed fast adsorption (majority adsorbed under 30 min) before eventually reaching equilibrium after 1-2 h. Overall, we demonstrated that DNA quickly binds to MPs, with pseudo-first- and -second-order models describing adsorption kinetics and the Freundlich model describing adsorption isotherms most accurately. These insights into DNA sorption onto MPs show that there is potential for MPs to act as vectors for genetic material of interest, especially considering that particle-bound DNA typically persists longer in the environment than dissolved DNA.
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Affiliation(s)
- Nicolas D Müller
- Department of Environmental Systems Science, ETH Zurich, Universitätstrasse 16, 8092 Zurich, Switzerland
| | - Anish Kirtane
- Department of Environmental Systems Science, ETH Zurich, Universitätstrasse 16, 8092 Zurich, Switzerland
| | - Roman B Schefer
- Department of Environmental Systems Science, ETH Zurich, Universitätstrasse 16, 8092 Zurich, Switzerland
| | - Denise M Mitrano
- Department of Environmental Systems Science, ETH Zurich, Universitätstrasse 16, 8092 Zurich, Switzerland
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7
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Sun X, Guo N, Gao J, Xiao N. Using eDNA to survey amphibians: Methods, applications, and challenges. Biotechnol Bioeng 2024; 121:456-471. [PMID: 37986625 DOI: 10.1002/bit.28592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 11/22/2023]
Abstract
In recent years, environmental DNA (eDNA) has received attention from biologists due to its sensitivity, convenience, labor and material efficiency, and lack of damage to organisms. The extensive application of eDNA has opened avenues for the monitoring and biodiversity assessment of amphibians, which are frequently small and difficult to observe in the field, in areas such as biodiversity survey assessment and detection of specific, rare and threatened, or alien invasive species. However, the accuracy of eDNA can be influenced by factors such as ambient temperature, pH, and false positives or false negatives, which makes eDNA an adjunctive tool rather than a replacement for traditional surveys. This review provides a concise overview of the eDNA method and its workflow, summarizes the differences between applying eDNA for detecting amphibians and other organisms, reviews the research progress in eDNA technology for amphibian monitoring, identifies factors influencing detection efficiency, and discusses the challenges and prospects of eDNA. It aims to serve as a reference for future research on the application of eDNA in amphibian detection.
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Affiliation(s)
- Xiaoxuan Sun
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Ningning Guo
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Jianan Gao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
- Collage of Forestry, Shanxi Agricultural University, Jinzhong, China
| | - Nengwen Xiao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
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Zhang L, Zhou W, Jiao M, Xie T, Xie M, Li H, Suo A, Yue W, Ding D, He W. Use of passive sampling in environmental DNA metabarcoding technology: Monitoring of fish diversity in the Jiangmen coastal waters. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168298. [PMID: 37939943 DOI: 10.1016/j.scitotenv.2023.168298] [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: 04/28/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/10/2023]
Abstract
Environmental DNA (eDNA) metabarcoding technology is proving to be the most up-to-date and promising method for monitoring marine fish diversity. Fish eDNA is usually collected on a filter membrane after the filtration of water. Not only does this require the use of specialized equipment, but the amount of filtered water needed is also difficult to meet. The recently proposed passive eDNA collection method can expand the sampling scale, providing new perspectives for monitoring marine biodiversity. The role of collection methods in eDNA surveys, however, remains unclear. In this study, a low-cost custom framework with two types of filter membrane materials was used to conduct passive submersion samplings at the north and south ends of Shangchuan Island, Jiangmen, China. After defined periods of submersion, the filter membranes were recovered and eDNA extracted. Metabarcoding techniques were applied to detect fish species information in the eDNA samples. A total of 106 marine fish species from 27 orders, 53 families, and 92 genera, including one cartilaginous fish, were identified in the samples. The majority of fish detected by active filtration were also found in the passively collected samples, within the same location. Both sampling methods, therefore, showed similar species richness. Passive sampling was effective in identifying fish species diversity and provided a higher spatial resolution owing to the sample replicates. Passive sampling was also more sensitive in detecting species that differ significantly in abundance (biomarkers) between different sampling depths. When active filtration is not possible, or when large-scale sampling is the purpose of the study, passive sampling methods certainly provide a promising alternative. The findings of our study provide guidance for fish surveys and continuous bio-stereoscopic monitoring in coastal waters.
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Affiliation(s)
- Li Zhang
- Marine Environmental Engineering Center, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiguo Zhou
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Mengyu Jiao
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tian Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Mujiao Xie
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Hanying Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Anning Suo
- Marine Environmental Engineering Center, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
| | - Weizhong Yue
- Marine Environmental Engineering Center, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
| | - Dewen Ding
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 51145, China
| | - Weihong He
- Marine Environmental Engineering Center, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
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Zhang Y, Zhang X, Li F, Altermatt F. Fishing eDNA in One of the World's Largest Rivers: A Case Study of Cross-Sectional and Depth Profile Sampling in the Yangtze. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:21691-21703. [PMID: 37878726 DOI: 10.1021/acs.est.3c03890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2023]
Abstract
The world's largest rivers are home to diverse, endemic, and threatened fish species. However, their sheer sizes make large-scale biomonitoring challenging. While environmental DNA (eDNA) metabarcoding has become an established monitoring approach in smaller freshwater ecosystems, its suitability for large rivers may be challenged by the sheer extent of their cross sections (>1 km wide and tens of meters deep). Here, we sampled fish eDNA from multiple vertical layers and horizontal locations from two cross sections of the lower reach of the Yangtze River in China. Over half of the ASVs (amplicon sequence variants) were detected in only a single combination of the vertical layers and horizontal locations, with ∼7% across all combinations. We estimated the need to sample >100 L of water across the cross-sectional profiles to achieve ASV richness saturation, which translates to ∼60 L of water at the species level. No consistent pattern emerged for prioritizing certain depth and horizontal samples, yet we underline the importance of sampling and integrating different layers and locations simultaneously. Our study highlights the significance of spatially stratified sampling and sampling volumes when using eDNA approaches. Specifically, we developed and tested a scalable and broadly applicable strategy that advances the monitoring and conservation of large rivers.
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Affiliation(s)
- Yan Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf 8600, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich 8006, Switzerland
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, 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
| | - Florian Altermatt
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf 8600, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich 8006, Switzerland
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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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11
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Wang L, Xu J, Liu H, Wang S, Ou W, Zhang M, Wei F, Luo S, Chen B, Zhang S, Yu K. Ultrasensitive and on-site eDNA detection for the monitoring of crown-of-thorns starfish densities at the pre-outbreak stage using an electrochemical biosensor. Biosens Bioelectron 2023; 230:115265. [PMID: 36996547 DOI: 10.1016/j.bios.2023.115265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 03/02/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023]
Abstract
The coral reef crisis has significantly intensified over the last decades, mainly due to severe outbreaks of crown-of-thorns starfish (COTS). Current ecological monitoring has failed to detect COTS densities at the pre-outbreak stage, thus preventing early intervention. In this work, we developed an effective electrochemical biosensor modified by a MoO2/C nanomaterial, as well as a specific DNA probe that could detect trace COTS environmental DNA (eDNA) at a lower detection limit (LOD = 0.147 ng/μL) with excellent specificity. The reliability and accuracy of the biosensor were validated against the standard methods by an ultramicro spectrophotometer and droplet digital PCR (p > 0.05). The biosensor was then utilized for the on-site analysis of seawater samples from SYM-LD and SY sites in the South China Sea. For the SYM-LD site suffering an outbreak, the COTS eDNA concentrations were 0.33 ng/μL (1 m, depth) and 0.26 ng/μL (10 m, depth), respectively. According to the ecological survey, the COTS density was 500 ind/hm2 at the SYM-LD site, verifying the accuracy of our measurements. At the SY site, COTS eDNA was also detected at 0.19 ng/μL, but COTS was not found by the traditional survey. Hence, larvae were possibly present in this region. Therefore, this electrochemical biosensor could be used to monitor COTS populations at the pre-outbreak stages, and potentially serve as a revolutionary early warning method. We will continue to improve this method for picomolar or even femtomolar detection of COTS eDNA.
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Affiliation(s)
- Liwei Wang
- School of Marine Sciences, Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, 530004, China; School of Resources, Environment and Materials, Guangxi, Key Laboratory of Processing for Non-ferrous Metallic and Featured Materials, Nanning, 530003, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519080, China
| | - Jiarong Xu
- School of Marine Sciences, Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, 530004, China; School of Resources, Environment and Materials, Guangxi, Key Laboratory of Processing for Non-ferrous Metallic and Featured Materials, Nanning, 530003, China
| | - Hongjie Liu
- School of Resources, Environment and Materials, Guangxi, Key Laboratory of Processing for Non-ferrous Metallic and Featured Materials, Nanning, 530003, China; School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China; College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Shaopeng Wang
- School of Marine Sciences, Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, 530004, China
| | - Wenchao Ou
- School of Marine Sciences, Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, 530004, China
| | - Man Zhang
- School of Marine Sciences, Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, 530004, China
| | - Fen Wei
- School of Marine Sciences, Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, 530004, China
| | - Songlin Luo
- School of Marine Sciences, Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, 530004, China
| | - Biao Chen
- School of Marine Sciences, Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, 530004, China
| | - Shaolong Zhang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Kefu Yu
- School of Marine Sciences, Coral Reef Research Center of China, Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, 530004, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519080, China.
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12
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Takahashi M, Saccò M, Kestel JH, Nester G, Campbell MA, van der Heyde M, Heydenrych MJ, Juszkiewicz DJ, Nevill P, Dawkins KL, Bessey C, Fernandes K, Miller H, Power M, Mousavi-Derazmahalleh M, Newton JP, White NE, Richards ZT, Allentoft ME. Aquatic environmental DNA: A review of the macro-organismal biomonitoring revolution. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 873:162322. [PMID: 36801404 DOI: 10.1016/j.scitotenv.2023.162322] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
Environmental DNA (eDNA) is the fastest growing biomonitoring tool fuelled by two key features: time efficiency and sensitivity. Technological advancements allow rapid biodiversity detection at both species and community levels with increasing accuracy. Concurrently, there has been a global demand to standardise eDNA methods, but this is only possible with an in-depth overview of the technological advancements and a discussion of the pros and cons of available methods. We therefore conducted a systematic literature review of 407 peer-reviewed papers on aquatic eDNA published between 2012 and 2021. We observed a gradual increase in the annual number of publications from four (2012) to 28 (2018), followed by a rapid growth to 124 publications in 2021. This was mirrored by a tremendous diversification of methods in all aspects of the eDNA workflow. For example, in 2012 only freezing was applied to preserve filter samples, whereas we recorded 12 different preservation methods in the 2021 literature. Despite an ongoing standardisation debate in the eDNA community, the field is seemingly moving fast in the opposite direction and we discuss the reasons and implications. Moreover, by compiling the largest PCR-primer database to date, we provide information on 522 and 141 published species-specific and metabarcoding primers targeting a wide range of aquatic organisms. This works as a user-friendly 'distillation' of primer information that was hitherto scattered across hundreds of papers, but the list also reflects which taxa are commonly studied with eDNA technology in aquatic environments such as fish and amphibians, and reveals that groups such as corals, plankton and algae are under-studied. Efforts to improve sampling and extraction methods, primer specificity and reference databases are crucial to capture these ecologically important taxa in future eDNA biomonitoring surveys. In a rapidly diversifying field, this review synthetises aquatic eDNA procedures and can guide eDNA users towards best practice.
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Affiliation(s)
- Miwa Takahashi
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia; Commonwealth Scientific and Industrial Research Organization, Indian Oceans Marine Research Centre, Environomics Future Science Platform, Crawley, Western Australia, Australia.
| | - Mattia Saccò
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia.
| | - Joshua H Kestel
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Georgia Nester
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Matthew A Campbell
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Mieke van der Heyde
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Matthew J Heydenrych
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia; Jarman Laboratory, Indian Ocean Marine Research Centre, School of Biological Sciences, University of Western Australia, Australia
| | - David J Juszkiewicz
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Paul Nevill
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Kathryn L Dawkins
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Cindy Bessey
- Commonwealth Scientific and Industrial Research Organization, Indian Oceans Marine Research Centre, Oceans and Atmosphere, Crawley, Western Australia, Australia
| | - Kristen Fernandes
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Haylea Miller
- Commonwealth Scientific and Industrial Research Organization, Indian Oceans Marine Research Centre, Environomics Future Science Platform, Crawley, Western Australia, Australia
| | - Matthew Power
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Mahsa Mousavi-Derazmahalleh
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Joshua P Newton
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Nicole E White
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Zoe T Richards
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia
| | - Morten E Allentoft
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA 6102, Australia; Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
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13
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Yang J, Zhang L, Mu Y, Wang J, Yu H, Zhang X. Unsupervised biological integrity assessment by eDNA biomonitoring of multi-trophic aquatic taxa. ENVIRONMENT INTERNATIONAL 2023; 175:107950. [PMID: 37182420 DOI: 10.1016/j.envint.2023.107950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 04/12/2023] [Accepted: 04/23/2023] [Indexed: 05/16/2023]
Abstract
The biological integrity of global freshwater ecosystems is threatened by ever-increasing environmental stressors due to increased human activities, such as land-use change, eutrophication, toxic pollutants, overfishing, and exploitation. Traditional ecological assessments of lake or riverine ecosystems often require human supervision of a pre-selected reference area, using the current state of the reference area as the expected state. However, selecting an appropriate reference area has become increasingly difficult with the expansion of human activities. Here, an unsupervised biological integrity assessment framework based on environmental DNA metabarcoding without a prior reference area is proposed. Taxon richness, species dominance, co-occurrence network density, and phylogenetic distance were used to assess the aquatic communities in the Taihu Lake basin. Multi-gene metabarcoding revealed comprehensive biodiversity at multiple trophic levels including algae, protists, zooplankton, and fish. Fish sequences were mainly derived from 12S, zooplankton mainly from mitochondrial cytochrome C oxidase subunit I, and algae and protists mainly from 18S. There were significant differences in community composition among lakes, rivers, and reservoirs but no significant differences in the four fundamental biological indicators. The algal and zooplankton integrities were positively correlated with protist and fish integrities, respectively. Additionally, the algal integrity of lakes was found to be significantly lower than that of rivers. The unsupervised assessment framework proposed in this study allows different ecosystems, including the same ecosystem in different seasons, to adopt the same indicators and assessment methods, which is more convenient for environmental management and decision-making.
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Affiliation(s)
- Jianghua Yang
- State Key Laboratory of Pollution Control & Resource, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Lijuan Zhang
- State Key Laboratory of Pollution Control & Resource, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Yawen Mu
- State Key Laboratory of Pollution Control & Resource, School of the Environment, Nanjing University, Nanjing 210023, China; Jiangsu Provincial Environmental Monitoring Center, Nanjing 210019, China
| | - Jiangye Wang
- State Key Laboratory of Pollution Control & Resource, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Hongxia Yu
- State Key Laboratory of Pollution Control & Resource, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource, School of the Environment, Nanjing University, Nanjing 210023, China.
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14
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Patin NV, Goodwin KD. Capturing marine microbiomes and environmental DNA: A field sampling guide. Front Microbiol 2023; 13:1026596. [PMID: 36713215 PMCID: PMC9877356 DOI: 10.3389/fmicb.2022.1026596] [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: 08/24/2022] [Accepted: 11/22/2022] [Indexed: 01/15/2023] Open
Abstract
The expanding interest in marine microbiome and eDNA sequence data has led to a demand for sample collection and preservation standard practices to enable comparative assessments of results across studies and facilitate meta-analyses. We support this effort by providing guidelines based on a review of published methods and field sampling experiences. The major components considered here are environmental and resource considerations, sample processing strategies, sample storage options, and eDNA extraction protocols. It is impossible to provide universal recommendations considering the wide range of eDNA applications; rather, we provide information to design fit-for-purpose protocols. To manage scope, the focus here is on sampling collection and preservation of prokaryotic and microeukaryotic eDNA. Even with a focused view, the practical utility of any approach depends on multiple factors, including habitat type, available resources, and experimental goals. We broadly recommend enacting rigorous decontamination protocols, pilot studies to guide the filtration volume needed to characterize the target(s) of interest and minimize PCR inhibitor collection, and prioritizing sample freezing over (only) the addition of preservation buffer. An annotated list of studies that test these parameters is included for more detailed investigation on specific steps. To illustrate an approach that demonstrates fit-for-purpose methodologies, we provide a protocol for eDNA sampling aboard an oceanographic vessel. These guidelines can aid the decision-making process for scientists interested in sampling and sequencing marine microbiomes and/or eDNA.
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Affiliation(s)
- Nastassia Virginia Patin
- Atlantic Oceanographic and Meteorological Laboratory, Ocean Chemistry and Ecosystems Division, National Oceanic and Atmospheric Administration, Miami, FL, United States,Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, United States,Stationed at Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, United States,*Correspondence: Nastassia Virginia Patin,
| | - Kelly D. Goodwin
- Atlantic Oceanographic and Meteorological Laboratory, Ocean Chemistry and Ecosystems Division, National Oceanic and Atmospheric Administration, Miami, FL, United States,Stationed at Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, United States
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15
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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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