环境DNA技术在水生入侵生物监测中的应用
Application of Environmental DNA Technologies in Monitoring Aquatic Invasive Species
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摘要: 生物入侵严重威胁入侵地的生态系统平衡及社会经济发展和公众健康，已日益成为全球性最重大的生态环境问题之一。外来生物的早期监测和预警对防控外来生物入侵、维护生态系统平衡和保护环境具重要意义。但外来水生生物，得益于其形体微小、形态多变等生理生态特性，与陆生外来生物相比隐蔽性更强、更易扩散，通常难以及时监测和有效防控，正严重威胁着水生生态系统的健康与稳定，其早期监测和预警更加迫切也更具技术挑战。环境DNA（environmental DNA，eDNA）技术通过检测环境样品中的DNA来解析生物物种组成及丰度，可实现生物物种的高效鉴别及多生物群落监测，与耗时费力的传统形态学生物监测相比，具低耗、高效、高灵敏度及对生物体无损伤等特点，其在外来水生生物监测方面具有十分广阔的应用前景。本文总结了eDNA技术在水生入侵生物监测研究中的应用实例；从eDNA的获取、条形码区域的PCR扩增和数据分析3个方面探讨了eDNA技术实施的方案、关键步骤；最后对促进其在水生生物入侵风险预警应用的方向及前景进行了展望。Abstract: Biological invasion has become one of the most serious environmental problems in the world, which severely destroy the balance of ecosystem, and affect the socioeconomic development and public health. Early monitoring and warning of aquatic invasive species are of great significance for preventing and controlling biological invasions, maintaining the balance of ecosystem and protecting the environment. Aquatic invasive species, however, due to its physiological and ecological characteristics such as small size, changeable forms, are easier to conceal and spread compared with terrestrial species, which will threat the health and stability of aquatic ecosystem. Hence, monitoring aquatic invasive species is urgent and challenging. Environmental DNA (eDNA) technologies detect the existence and abundance of species and monitor biodiversity efficiently through analyzing the DNA in environmental samples. Compared with routine monitoring using traditional methods, eDNA monitoring has the characteristics of low consumption, high efficiency, high sensitivity and no damage to organisms, and has a very broad application prospect in the monitoring of aquatic invasive species. In this review, the applications of eDNA technologies in monitoring aquatic invasive species are summarized firstly. Then, the implementation scheme and key steps of eDNA technologies are discussed, including acquisition of eDNA, PCR amplification of barcoding region and data analysis. Finally, the directions of promoting its application in early monitoring and warning of aquatic invasive species are prospected.
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Key words:
- eDNA /
- monitoring of aquatic invasive species /
- (meta)barcoding /
- implementation scheme
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Perrings C, Dehnen-Schmutz K, Touza J, et al. How to manage biological invasions under globalization[J]. Trends in Ecology & Evolution, 2005, 20(5):212-215 Banks N C, Paini D R, Bayliss K L, et al. The role of global trade and transport network topology in the human-mediated dispersal of alien species[J]. Ecology Letters, 2015, 18(2):188-199 Havel J E, Kovalenko K E, Thomaz S M, et al. Aquatic invasive species:Challenges for the future[J]. Hydrobiologia, 2015, 750(1):147-170 Gallardo B, Clavero M, Sánchez M I, et al. Global ecological impacts of invasive species in aquatic ecosystems[J]. Global Change Biology, 2016, 22(1):151-163 章家恩, 赵本良, 罗明珠, 等. 外来生物福寿螺入侵的生态风险及其评价探讨[J]. 佛山科学技术学院学报:自然科学版, 2010, 28(5):1-6 Zhang J E, Zhao B L, Luo M Z, et al. The ecological risk analysis and assessment on the invasion of golden apple snails[J]. Journal of Foshan University:Natural Science Edition, 2010, 28(5):1-6(in Chinese)
中国新闻网. 生物入侵酿逾2000亿损失专家称控制源头是关键[EB/OL] (2017-11-20 )[2021-01-22]. https://www.chinanews.com.cn/sh/2017/11-20/8381370.shtml
王朝晖, 陈菊芳, 杨宇峰. 船舶压舱水引起的有害赤潮藻类生态入侵及其控制管理[J]. 海洋环境科学, 2010, 29(6):920-922 , 934 Wang Z H, Chen J F, Yang Y F. Control and management of harmful algal bloom species induced by ballast water[J]. Marine Environmental Science, 2010, 29(6):920-922, 934(in Chinese)
木辛. 从巴西龟看入侵物种放生问题[J]. 环境教育, 2016(11):50-53 陈洁君, 王晶. 我国外来入侵生物防控科技进展[J]. 生物安全学报, 2018, 27(1):16-19 Chen J J, Wang J. Progress in prevention and control of invasive species in China[J]. Journal of Biosafety, 2018, 27(1):16-19(in Chinese)
Turbelin A J, Malamud B D, Francis R A. Mapping the global state of invasive alien species:Patterns of invasion and policy responses[J]. Global Ecology and Biogeography, 2017, 26(1):78-92 Juanes F. Visual and acoustic sensors for early detection of biological invasions:Current uses and future potential[J]. Journal for Nature Conservation, 2018, 42:7-11 Jarić I, Heger T, Castro Monzon F, et al. Crypticity in biological invasions[J]. Trends in Ecology & Evolution, 2019, 34(4):291-302 Taberlet P, Coissac E, Hajibabaei M, et al. Environmental DNA[J]. Molecular Ecology, 2012, 21(8):1789-1793 Ficetola G F, Miaud C, Pompanon F, et al. Species detection using environmental DNA from water samples[J]. Biology Letters, 2008, 4(4):423-425 Doi H, Uchii K, Takahara T, et al. Use of droplet digital PCR for estimation of fish abundance and biomass in environmental DNA surveys[J]. PLoS One, 2015, 10(3):e0122763 Zhang X W. Environmental DNA shaping a new era of ecotoxicological research[J]. Environmental Science & Technology, 2019, 53(10):5605-5612 李晗溪, 黄雪娜, 李世国, 等. 基于环境DNA-宏条形码技术的水生生态系统入侵生物的早期监测与预警[J]. 生物多样性, 2019, 27(5):491-504 Li H X, Huang X N, Li S G, et al. Environmental DNA (eDNA)-metabarcoding-based early monitoring and warning for invasive species in aquatic ecosystems[J]. Biodiversity Science, 2019, 27(5):491-504(in Chinese)
Deiner K, Bik H M, Mächler E, et al. Environmental DNA metabarcoding:Transforming how we survey animal and plant communities[J]. Molecular Ecology, 2017, 26(21):5872-5895 Jerde C L, Mahon A R, Chadderton W L, et al. "Sight-unseen" detection of rare aquatic species using environmental DNA[J]. Conservation Letters, 2011, 4(2):150-157 Piaggio A J, Engeman R M, Hopken M W, et al. Detecting an elusive invasive species:A diagnostic PCR to detect Burmese python in Florida waters and an assessment of persistence of environmental DNA[J]. Molecular Ecology Resources, 2014, 14(2):374-380 Ardura A, Zaiko A, Martinez J L, et al. eDNA and specific primers for early detection of invasive species-A case study on the bivalve Rangia cuneata, currently spreading in Europe[J]. Marine Environmental Research, 2015, 112:48-55 Serrao N R, Steinke D, Hanner R H. Calibrating snakehead diversity with DNA barcodes:Expanding taxonomic coverage to enable identification of potential and established invasive species[J]. PLoS One, 2014, 9(6):e99546 Takahara T, Minamoto T, Doi H. Using environmental DNA to estimate the distribution of an invasive fish species in ponds[J]. PLoS One, 2013, 8(2):e56584 Goldberg C S, Sepulveda A, Ray A, et al. Environmental DNA as a new method for early detection of New Zealand mudsnails (Potamopyrgus antipodarum)[J]. Freshwater Science, 2013, 32(3):792-800 Nathan L M, Simmons M, Wegleitner B J, et al. Quantifying environmental DNA signals for aquatic invasive species across multiple detection platforms[J]. Environmental Science & Technology, 2014, 48(21):12800-12806 Jo T, Fukuoka A, Uchida K, et al. Multiplex real-time PCR enables the simultaneous detection of environmental DNA from freshwater fishes:A case study of three exotic and three threatened native fishes in Japan[J]. Biological Invasions, 2020, 22(2):455-471 宋伦, 刘卫东, 吴景, 等. 有害甲藻Stoeckeria algicida在辽东湾的时空分布[J]. 生态学报, 2017, 37(4):1339-1345 Song L, Liu W D, Wu J, et al. Distribution of the toxic dinoflagellate Stoeckeria algicida in Liaodong Bay[J]. Acta Ecologica Sinica, 2017, 37(4):1339-1345(in Chinese)
Muha T P, Skukan R, Borrell Y J, et al. Contrasting seasonal and spatial distribution of native and invasive Codium seaweed revealed by targeting species-specific eDNA[J]. Ecology and Evolution, 2019, 9(15):8567-8579 von Ammon U, Wood S A, Laroche O, et al. Linking environmental DNA and RNA for improved detection of the marine invasive fanworm Sabella spallanzanii[J]. Frontiers in Marine Science, 2019, 6:621 Ardura A, Zaiko A, Borrell Y J, et al. Novel tools for early detection of a global aquatic invasive, the zebra mussel Dreissena polymorpha[J]. Aquatic Conservation:Marine and Freshwater Ecosystems, 2017, 27(1):165-176 Blackman R C, Ling K K S, Harper L R, et al. Targeted and passive environmental DNA approaches outperform established methods for detection of quagga mussels, Dreissena rostriformis bugensis in flowing water[J]. Ecology and Evolution, 2020, 10(23):13248-13259 马竹欣. 利用环境DNA技术调查入侵种克氏原螯虾在元阳梯田的分布[D]. 昆明:云南大学, 2016:33-34 Ma Z X. Distribution of invasive crayfish Procambarus clarkii in Yuanyang terrace revealed by eDNA[D]. Kunming:Yunnan University, 2016:33 -34(in Chinese)
Lin M X, Zhang S, Yao M. Effective detection of environmental DNA from the invasive American bullfrog[J]. Biological Invasions, 2019, 21(7):2255-2268 Brown E A, Chain F J J, Zhan A B, et al. Early detection of aquatic invaders using metabarcoding reveals a high number of non-indigenous species in Canadian ports[J]. Diversity and Distributions, 2016, 22(10):1045-1059 Rey A, Basurko O C, Rodriguez-Ezpeleta N. Considerations for metabarcoding-based port biological baseline surveys aimed at marine nonindigenous species monitoring and risk assessments[J]. Ecology and Evolution, 2020, 10(5):2452-2465 Westfall K M, Therriault T W, Abbott C L. A new approach to molecular biosurveillance of invasive species using DNA metabarcoding[J]. Global Change Biology, 2020, 26(2):1012-1022 Chen J W, Chen Z, Liu S S, et al. Revealing an invasion risk of fish species in Qingdao underwater world by environmental DNA metabarcoding[J]. Journal of Ocean University of China, 2021, 20(1):124-136 Rey A, Carney K J, Quinones L E, et al. Environmental DNA metabarcoding:A promising tool for ballast water monitoring[J]. Environmental Science & Technology, 2019, 53(20):11849-11859 Ardura A, Borrell Y, Fernández S, et al. Nuisance algae in ballast water facing international conventions. Insights from DNA metabarcoding in ships arriving in bay of Biscay[J]. Water, 2020, 12(8):2168 Lin Y, Zhan A, Hernandez M R, et al. Can chlorination of ballast water reduce biological invasions?[J]. Journal of Applied Ecology, 2019, 57(2):331-343 Barnes M A, Turner C R. The ecology of environmental DNA and implications for conservation genetics[J]. Conservation Genetics, 2016, 17(1):1-17 Goldberg C S, Turner C R, Deiner K, et al. Critical considerations for the application of environmental DNA methods to detect aquatic species[J]. Methods in Ecology and Evolution, 2016, 7(11):1299-1307 Harper L R, Buxton A S, Rees H C, et al. Prospects and challenges of environmental DNA (eDNA) monitoring in freshwater ponds[J]. Hydrobiologia, 2019, 826(1):25-41 Strickland G J, Roberts J H. Utility of eDNA and occupancy models for monitoring an endangered fish across diverse riverine habitats[J]. Hydrobiologia, 2019, 826(1):129-144 张丽娟, 徐杉, 赵峥, 等. 环境DNA宏条形码监测湖泊真核浮游植物的精准性[J]. 环境科学, 2021, 42(2):796-807 Zhang L J, Xu S, Zhao Z, et al. Precision of eDNA metabarcoding technology for biodiversity monitoring of eukaryotic phytoplankton in lakes[J]. Environmental Science, 2021, 42(2):796-807(in Chinese)
Zhang Y, Pavlovska M, Stoica E, et al. Holistic pelagic biodiversity monitoring of the Black Sea via eDNA metabarcoding approach:From bacteria to marine mammals[J]. Environment International, 2020, 135:105307 Stoof-Leichsenring K R, Dulias K, Biskaborn B K, et al. Lake-depth related pattern of genetic and morphological diatom diversity in boreal Lake Bolshoe Toko, Eastern Siberia[J]. PLoS One, 2020, 15(4):e0230284 Minamoto T, Naka T, Moji K, et al. Techniques for the practical collection of environmental DNA:Filter selection, preservation, and extraction[J]. Limnology, 2016, 17(1):23-32 Shu L, Ludwig A, Peng Z G. Standards for methods utilizing environmental DNA for detection of fish species[J]. Genes, 2020, 11(3):296 杨江华. 太湖流域浮游动物物种多样性与环境污染群落生态效应研究[D]. 南京:南京大学, 2017:50-68 Yang J H. Biodiversity of zooplankton and community effects of environmental pollution in Tai lake basin[D]. Nanjing:Nanjing University, 2017:50 -68(in Chinese)
Kumar G, Eble J E, Gaither M R. A practical guide to sample preservation and pre-PCR processing of aquatic environmental DNA[J]. Molecular Ecology Resources, 2020, 20(1):29-39 Piper A M, Batovska J, Cogan N O I, et al. Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance[J]. GigaScience, 2019, 8(8):giz092 Song H, Buhay J E, Whiting M F, et al. Many species in one:DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified[J]. PNAS, 2008, 105(36):13486-13491 Piñol J, Mir G, Gomez-Polo P, et al. Universal and blocking primer mismatches limit the use of high-throughput DNA sequencing for the quantitative metabarcoding of arthropods[J]. Molecular Ecology Resources, 2015, 15(4):819-830 李小闯, 霍守亮, 张含笑, 等. 环境DNA宏条形码技术在蓝藻群落监测中的应用[J]. 环境科学研究, 2021, 34(2):372-381 Li X C, Huo S L, Zhang H X, et al. Applications of environmental DNA metabarcoding in monitoring of cyanobacterial community[J]. Research of Environmental Sciences, 2021, 34(2):372-381(in Chinese)
Li X C, Yang Y M, Cai F F, et al. New insights into the taxonomy of the genus Sphaerospermopsis (Nostocales, Cyanobacteria) with the description of Sphaerospermopsis crassa sp. Nov[J]. Phycologia, 2017, 56(2):147-158 Hebert P D N, Ratnasingham S, DeWaard J R. Barcoding animal life:Cytochrome C oxidase subunit 1 divergences among closely related species[J]. Proceedings Biological Sciences, 2003, 270(Suppl.1):S96-S99 Leray M, Yang J Y, Meyer C P, et al. A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity:Application for characterizing coral reef fish gut contents[J]. Frontiers in Zoology, 2013, 10:34 Avó A P, Daniell T J, Neilson R, et al. DNA barcoding and morphological identification of benthic nematodes assemblages of estuarine intertidal sediments:Advances in molecular tools for biodiversity assessment[J]. Frontiers in Marine Science, 2017, 4:66 Aglieri G, Baillie C, Mariani S, et al. Environmental DNA effectively captures functional diversity of coastal fish communities[J]. Molecular Ecology, 2021, 30(13):3127-3139 Xiang X L, Xi Y L, Wen X L, et al. Patterns and processes in the genetic differentiation of the Brachionus calyciflorus complex, a passively dispersing freshwater zooplankton[J]. Molecular Phylogenetics and Evolution, 2011, 59(2):386-398 Brannock P M, Ortmann A C, Moss A G, et al. Metabarcoding reveals environmental factors influencing spatio-temporal variation in pelagic micro-eukaryotes[J]. Molecular Ecology, 2016, 25(15):3593-3604 Zhan A B, Bailey S A, Heath D D, et al. Performance comparison of genetic markers for high-throughput sequencing-based biodiversity assessment in complex communities[J]. Molecular Ecology Resources, 2014, 14(5):1049-1059 马鸿娟, Stewart Kathryn, 马利民, 等. 环境DNA及其在水生生态系统保护中的应用[J]. 生态学杂志, 2016, 35(2):516-523 Ma H J, Kathryn S, Ma L M, et al. Environmental DNA and its application in protecting aquatic ecosystems[J]. Chinese Journal of Ecology, 2016, 35(2):516-523(in Chinese)
陈炼, 吴琳, 刘燕, 等. 环境DNA metabarcoding及其在生态学研究中的应用[J]. 生态学报, 2016, 36(15):4573-4582 Chen L, Wu L, Liu Y, et al. Application of environmental DNA metabarcoding in ecology[J]. Acta Ecologica Sinica, 2016, 36(15):4573-4582(in Chinese)
李苗, 单秀娟, 王伟继, 等. 中国对虾生物量评估的环境DNA检测技术的建立及优化[J]. 渔业科学进展, 2019, 40(1):12-19 Li M, Shan X J, Wang W J, et al. Establishment and optimization of environmental DNA detection techniques for assessment of Fenneropenaeus chinensis biomass[J]. Progress in Fishery Sciences, 2019, 40(1):12-19(in Chinese)
秦传新, 左涛, 于刚, 等. 环境DNA在水生生态系统生物量评估中的研究进展[J]. 南方水产科学, 2020, 16(5):123-128 Scott R, Zhan A B, Brown E A, et al. Optimization and performance testing of a sequence processing pipeline applied to detection of nonindigenous species[J]. Evolutionary Applications, 2018, 11(6):891-905 Callahan B J, McMurdie P J, Holmes S P. Exact sequence variants should replace operational taxonomic units in marker-gene data analysis[J]. The ISME Journal, 2017, 11(12):2639-2643 Marshall N T, Stepien C A. Invasion genetics from eDNA and thousands of larvae:A targeted metabarcoding assay that distinguishes species and population variation of zebra and quagga mussels[J]. Ecology and Evolution, 2019, 9(6):3515-3538 Duarte S, Vieira P E, Lavrador A S, et al. Status and prospects of marine NIS detection and monitoring through (e)DNA metabarcoding[J]. Science of the Total Environment, 2021, 751:141729 Weigand H, Beermann A J, Čiampor F, et al. DNA barcode reference libraries for the monitoring of aquatic biota in Europe:Gap-analysis and recommendations for future work[J]. Science of the Total Environment, 2019, 678:499-524 李飞龙, 杨江华, 杨雅楠, 等. 环境DNA宏条形码监测水生态系统变化与健康状态[J]. 中国环境监测, 2018, 34(6):37-46 Li F L, Yang J H, Yang Y N, et al. Using environmental DNA metabarcoding to monitor the changes and health status of aquatic ecosystems[J]. Environmental Monitoring in China, 2018, 34(6):37-46(in Chinese)
Sepulveda A J, Nelson N M, Jerde C L, et al. Are environmental DNA methods ready for aquatic invasive species management?[J]. Trends in Ecology & Evolution, 2020, 35(8):668-678 Zhou X, Li Y Y, Liu S L, et al. Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification[J]. GigaScience, 2013, 2(1):2047 -
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