环境DNA技术在鱼类资源研究中的应用

doi:10.13560/j.cnki.biotech.bull.1985.2018-0580

摘要/Abstract

摘要： 环境DNA（Environmental DNA,eDNA）是指从生物体生活环境中直接提取到的不同物种DNA片段的总和,eDNA在鱼类资源研究上越来越热,主要是在鱼类的特异性基因识别片段的基础上,与利用分子手段检测eDNA所获得的识别片段进行比对,进而确定水环境中鱼类是否存在的一种技术,是一种新型的生物资源调查手段。与传统方法相比,eDNA技术具高灵敏、低成本、无损伤等优点,能够快速的检测出入侵种、濒危种及稀有种等种类,但也存在一些不足之处,如不能获得目标物种存在或不存在的实时数据、不能获得物种各生长阶段等的生物学特征以及种群结构、不能将“纯种”与杂交种区分开来。eDNA技术对于鱼类资源研究具有颠覆性意义,并展现出良好的发展势头。主要综述了基于eDNA技术在鱼类物种多样性研究、资源量估算和种群分布等研究中的应用进展,以期为渔业资源研究提供一些思考。可以预期,eDNA技术与传统调查方法相结合将成为鱼类资源研究的一个发展趋势。

关键词: 环境DNA, eDNA技术, 鱼类资源

Abstract: Environmental DNA（eDNA）refers to the sum of DNA fragments of different species extracted directly from the living environment of organisms,and eDNA is becoming more and more popular in the study of fish resources. It is a novel investigation approach for biological resources,i.e.,whether or not existence of fish species in a water environment can be determined,based on the identification of specific gene fragments of fish and by aligning with the identification fragments obtained via molecular methods to detect eDNA. Compared with traditional methods,eDNA technology has the advantages of high sensitivity,low cost,and no damage. It can quickly detect invasive species,endangered species,and rare species. However,there are some deficiencies for it,for instance,the real-time data whether target species exist or not cannot be acquired,biological characteristics such as the growth stages of species as well as population structure cannot be obtained,“purebreds” cannot be distinguished from hybrids. The eDNA technology is of subversive significance to the study of fish resources and shows a good momentum of development. This article mainly reviews the application of eDNA technology in the research of fish species diversity,resource estimation and population distribution,aiming at providing some ideas for the study of fishery resources. It can be expected that the combination of eDNA technology and traditional survey methods will become a development trend for fish resources research.

Key words: environmental DNA, eDNA technology, fish resources

郝雅宾, 张爱菊, 刘金殿, 顾志敏. 环境DNA技术在鱼类资源研究中的应用[J]. 生物技术通报, 2018, 34(12): 56-62.

HAO Ya-bin ZHANG Ai-ju LIU Jin-dian GU Zhi-min. Application of Environmental DNA Technology in the Study of Fish Resources[J]. Biotechnology Bulletin, 2018, 34(12): 56-62.

参考文献

[1] Coryd S, Stevenj C.Conservation of aquatic resources through the use of freshwater protected areas:opportunities and challenges[J]. Biodiversity & Conservation, 2007, 16(7):2015-2029.
[2] Dudgeon D, Arthington AH, Gessner MO, et al.Freshwater biodiversity:importance, threats, status and conservation challenges[J]Biological Reviews, 2006, 81(2):163-182.
[3] Revenga C, Campbell I, Abell R, et al.Prospects for monitoring freshwater ecosystems towards the 2010 targets[J]. Philosophical Transactions of the Royal Society of London, 2005, 360(1454):397-413.
[4] Order TO.Standard methods for sampling North American freshwater fishes:opportunities for international collaboration[J]. Fisheries, 2017, 42(3):7.
[5] Bohmann K, Evans A, Gilbert MTP, et al.Environmental DNA for wildlife biology and biodiversity monitoring[J]. Trends in Ecology & Evolution, 2014, 29(6):358-367.
[6] 姜维, 赵虎, 邓捷, 等. 环境DNA分析技术—一种水生生物调查新方法[J]. 水生态学杂志, 2016, 37(5):1-7.
[7] Evans NT, Shirey PD, Wieringa JG, et al.Comparative cost and effort of fish distribution detection via environmental DNA analysis and electrofishing[J]. Fisheries, 2017, 42(2):90-99.
[8] Laramie MB, Pilliod DS, Goldberg CS.Characterizing the distribution of an endangered salmonid using environmental DNA analysis[J]. Biol Conserv, 2015, 183:29-37.
[9] Mckelvey KS, Young MK, Knotek WL, et al.Sampling large geographic areas for rare species using environmental DNA:a study of bull trout Salvelinus confluentus occupancy in western Montana[J]. Journal of Fish Biology, 2016, 88(3):1215-1222.
[10] Rees HC, Maddison BC, Middleditch DJ, et al.The detection of aquatic animal species using environmental DNA - a review of eDNA as a survey tool in ecology[J]. Journal of Applied Ecology, 2014, 51:1450-1459.
[11] Taberlet P, Coissac E, Hajibabaei M, et al.Environmental DNA[J]. Molecular Ecology, 2012, 21:1789-1793.
[12] Evans NT, Olds BP, Renshaw MA, et al.Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding[J]. Molecular Ecology Resources, 2015, 16(1):29-41.
[13] Keskin E.Detection of invasive freshwater fish species using environmental DNA survey[J]. Biochemical Systematics & Ecology, 2014, 56:68-74.
[14] Thomsen PF, Kielgast J, Iversen LL, et al.Detection of a diverse marine fish fauna using environmental dNA from seawater samples[J]. PLoS One, 2012, 7:e41732.
[15] Thomsen PF, Kielgast J, Iversen LL, et al.Monitoring endangered freshwater biodiversity using environmental DNA[J]. Molecular Ecology, 2012, 21:2565.
[16] Lacoursière-Roussel A, Côté G, Leclerc V, et al.Quantifying relative fish abundance with eDNA:a promising tool for fisheries management[J]. Journal of Applied Ecology, 2016, 53(4):1148-1157.
[17] Takahara T, Minamoto T, Yamanaka H, et al.Estimation of fish biomass using environmental DNA[J]. PLoS One, 2012, 7:e35868.
[18] Yamanaka H, Minamoto T.The use of environmental DNA of fishes as an efficient method of determining habitat connectivity[J]. Ecological Indicators, 2016, 62(1):147-153.
[19] Jerde CL, Chadderton WL, Mahon AR, et al.Detection of asian carp DNA as part of a Great Lakes basin-wide surveillance program[J]. Canadian Journal of Fisheries & Aquatic Sciences, 2013, 70(4):522-526.
[20] Pilliod DS, Goldbergcaren S, Arklerobert S, et al.Estimating occupancy and abundance of stream amphibians using environmental DNA from filtered water samples[J]. Canadian Journal of Fisheries & Aquatic Sciences, 2013, 70(8):1123-1130.
[21] Turner CR, Uy KL, Everhart RC.Fish environmental DNA is more concentrated in aquatic sediments than surface water[J]. Biol Conserv, 2015, 183:93-102.
[22] Jerde CL, Mahon AR, Chadderton WL, et al.“Sight-unseen” detection of rare aquatic species using environmental DNA[J]. Conservation Letters, 2011, 4(2):150-157.
[23] Foote AD, Thomsen PF, Sveegaard S, et al.Investigating the potential use of environmental DNA(eDNA)for genetic monitoring of marine mammals[J]. PLoS One, 2012, 7(8):e41781.
[24] Wilcox TM, Mckelvey KS, Young MK, et al.Robust Detection of rare species using environmental DNA:the importance of primer specificity[J]. PLoS One, 2013, 8:e59520.
[25] Mahon AR, Jerde CL, Galaska M, et al.Validation of eDNA surveillance sensitivity for detection of Asian carps in controlled and field experiments[J]. PLoS One, 2013, 8(3):e58316.
[26] 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.
[27] Klymus KE, Richter CA, Chapman DC, et al.Quantification of eDNA shedding rates from invasive bighead carp Hypophthalmichthys nobilis and silver carp Hypophthalmichthys molitrix[J]. Biol Conserv, 2015, 183:77-84.
[28] Keskin E, Unal EM, Atar HH.Detection of rare and invasive freshwater fish species using eDNA pyrosequencing:Lake Iznik ichthyofauna revised[J]. Biochemical Systematics & Ecology, 2016, 67:29-36.
[29] 徐念, 常剑波. 长江中下游干流环境DNA样本鱼类物种检测的初步研究[J]. 水生态学杂志, 2016, 37(5):49-55.
[30] 赵梦迪. 利用环境DNA分析冬季中国东黄海水域的鱼类多样性[D]. 上海:上海海洋大学, 2017.
[31] Takahara T, Minamoto T, Doi H. Effects of sample processing on the detection rate of environmental DNA from the Common Carp(Cyprinus carpio)[J]. Biol Conserv, 2015, 183:64-69.
[32] Strickler KM, Fremier AK, Goldberg CS.Quantifying effects of UV-B, temperature, and pH on eDNA degradation in aquatic microcosms[J]. Biol Conserv, 2015, 183:85-92.
[33] Turner CR, Barnes MA, Xu CCY, et al.Particle size distribution and optimal capture of aqueous macrobial eDNA[J]. Methods in Ecology & Evolution, 2014, 5(7):676-684.
[34] 范圣第, 权春善. 环境DNA的提取和纯化方法的研究[J]. 大连民族大学学报, 2005, 7(5):1-4.
[35] Kristy D, Florian A.Transport distance of invertebrate enviro-nmental DNA in a Natural River[J]. PLoS One, 2014, 9(2):e88786.
[36] Renshaw MA, Olds BP, Jerde CL, et al.The room temperature preservation of filtered environmental DNA samples and assimilation into a phenol-chloroform-isoamyl alcohol DNA extraction[J]. Molecular Ecology Resources, 2015, 15(1):168-176.
[37] Goldberg CS, Pilliod DS, Arkle RS, et al.Molecular detection of vertebrates in stream water:ademonstration using rocky mountain tailed frogs and idaho giant salamanders[J]. PLoS One, 2011, 6(7):e22746.
[38] Collins RA, Armstrong KF, Holyoake AJ, et al.Something in the water:biosecurity monitoring of ornamental fish imports using environmental DNA[J]. Biological Invasions, 2013, 15(6):1209-1215.
[39] Olson ZH, Briggler JT, Williams RN.An eDNA approach to detect eastern hellbenders(Cryptobranchus a. alleganiensis)using samples of water[J]. Wildlife Research, 2012, 39(7):629.
[40] 刘军, 赵良杰, 凡迎春, 等. 鱼类环境DNA研究中通用引物的筛选验证[J]. 淡水渔业, 2016, 46(1):9-17.
[41] 马鸿娟, Stewart K, 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.
[42] Piaggio AJ, Engeman RM, Hopken MW, 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.
[43] Minamoto T, Yamanaka H, Takahara T, et al.Surveillance of fish species composition using environmental DNA[J]. Limnology, 2012, 13(2):193-197.
[44] Pyšek P, Richardson DM.Invasive species, environmental change and management, and health[J]. Annual Review of Environment & Resources, 2010, 35(1):25-46.
[45] Deiner K, Walser JC, Mächler E, et al.Choice of capture and extraction methods affect detection of freshwater biodiversity from environmental DNA[J]. Biol Conserv, 2015, 183(9):53-63.
[46] Eva B, Harmony P, Thomas G, et al.Trails of river monsters:detecting critically endangered mekong giant catfish pangasianodon gigas using environmental DNA[J]. Global Ecology & Conservation, 2016, 7(C):148-156.
[47] Song JW, Small MJ, Casman EA. Making sense of the noise:The effect of hydrology on silver carp eDNA detection in the Chicago area waterway system[J]. Science of the Total Environment, 2017, 15: 605-606, 713-720.
[48] Karahan A, Douek J, Paz G, et al.Employing DNA barcoding as taxonomy and conservation tools for fish species censuses at the southeastern Mediterranean, a hot-spot area for biological invasion[J]. Journal for Nature Conservation, 2017, 36:1-9.
[49] Yamamoto S, Masuda R, Sato Y, et al.Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea[J]. Scientific Reports, 2017, 7:40368.
[50] Briers R.Ecology:from individuals to ecosystems[J]. Freshwater Biology, 2006, 51(9):1787-1788.
[51] 卢珊. 常见水生动物与其环境DNA的定性与定量关系[D]. 南京:南京师范大学, 2015.
[52] Spear SF, Groves JD, , Williams LA, et al, Using environmental DNA methods to improve detectability in a hellbender(Cryptobranchus alleganiensis)monitoring program[J]. Biol Conserv, 2015, 183:38-45.
[53] Barnes MA, Turner CR.The ecology of environmental DNA and implications for conservation genetics[J]. Conservation Genetics, 2016, 17(1):1-17.
[54] Sigsgaard EE, Carl H, Møller PR, et al.Monitoring the near-extinct European weather loach in Denmark based on environmental DNA from water samples[J]. Biol Conserv, 2015, 183:46-52.
[55] 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.
[56] 徐浩, 罗茜, 李云, 等. 环境DNA研究技术及其在生态学领域的应用[J]. 生物技术通报, 2014(10):49-55.
[57] 于水强, 王文娟, Li BL, 等. 环境DNA技术在地下生态学中的应用[J]. 生态学报, 2015, 35(15):4968-4976.