基于环境DNA技术的长江上游重庆市江北段鱼类多样性研究
Study on Fish Diversity in Chongqing Jiangbei Section of Upper Reaches of Yangtze River Based on Environmental DNA Technology
-
摘要: 为了解长江上游重庆市江北段鱼类多样性，于2021年4月至2022年1月进行了为期一年的水样采集，使用环境DNA （environmental DNA，eDNA）技术对该江段进行了鱼类多样性分析。结果表明，长江上游重庆市江北段共检测出82种鱼类，包括未鉴别到种水平的罗非鱼属（Oreochromis），隶属7目19科63属，其中包括国家重点保护动物5种、长江上游特有种8种及外来物种8种。鱼类种类数在季节上呈现秋季>冬季>夏季>春季的趋势，其中鲤（Cyprinus carpio）、鳙（Hypophthalmichthys nobilis）、黄颡鱼（Pelteobagrus fulvidraco）、张氏（Hemiculter tchangi）和草鱼（Ctenopharyngodon idella）均在4个季度均被检测到且具有较高的序列丰度。Chao1指数和ACE指数在季节间差异显著（P<0.05），冬季的α多样性指数均高于其他3个季节。PCoA分析结果表明春季和夏季样本间异质性较低，物种组成相似，秋季和冬季鱼类种类组成差异显著，异质性较高。RDA分析表明水位、水流量和水温是鱼类群落季节分布的主要影响因子，春夏季与水温和水流量呈负相关，与水位呈正相关；冬季与水温和水流量呈负相关，与水位呈正相关。Spearman相关性检验表明水温与Shannon多样性、Chao1指数、ACE指数显著负相关（P<0.01）；电导率和Coverage多样性呈负相关（P<0.05），水温、水流量和Simpson多样性呈负相关（P<0.05）。总体上，本研究表明eDNA技术能够快速分析鱼类种类组成和分布，其在长江鱼类资源监测中是一种极具潜力和重要性的工具。Abstract: To understand the fish diversity in the upper reaches of the Yangtze River in Chongqing, environmental DNA (eDNA) technology was used to analyze the fish diversity during a one-year water body sampling period from April 2021 to January 2022. The results showed that a total of 82 fish species (including Oreochromis, which was not identified to species level). 7 orders and 19 families and 63 genera were detected in the Jiangbei Section of the upper Yangtze River in Chongqing including 5 species of national key protected animals, 8 species of endemic animals in the upper reaches of Yangtze River and 8 exotic species. The number of fish species showed a seasonal trend of autumn > winter > summer > spring, among which Cyprinus carpio, Hypophthalmichthys nobilis, Pelteobagrus fulvidraco, Hemiculter tchangi and Ctenopharyngodon idella were all detected in the four seasons and had high sequence abundance. The Chao1 and ACE indices differed significantly between seasons (P<0.05) and the alpha diversity index in winter was higher than the three other seasons. The PCoA results showed that the heterogeneity between spring and summer samples was low and the species composition was similar, while the fish species composition in autumn and winter were significantly different and the heterogeneity was high. RDA analysis showed that water level, water flow and water temperature were the main factors affecting the seasonal distribution of the fish community. They were negatively correlated with water temperature and water flow, positively correlated with water level in spring and summer, and negatively correlated with water temperature and flow and positively correlated with water level in winter. Spearman's correlation test showed that water temperature was significantly negatively correlated with Shannon diversity, Chao1 index and ACE index (P<0.01); conductivity was negatively correlated with Coverage index (P<0.05), and water temperature, water flow was negatively correlated with Simpson diversity (P<0.05). Overall, this study shows that eDNA technology can rapidly analyze fish species composition and distribution, and has great potential and importance in the monitoring fish resources in the Yangtze River.
-
-
Villéger S, Brosse S, Mouchet M, et al. Functional ecology of fish:Current approaches and future challenges [J]. Aquatic Sciences, 2017, 79(4):783-801 Zou K S, Chen J W, Ruan H T, et al. eDNA metabarco-ding as a promising conservation tool for monitoring fish diversity in a coastal wetland of the Pearl River Estuary compared to bottom trawling [J]. The Science of the Total Environment, 2020, 702:134704 Zhong W J, Zhang J Y, Wang Z H, et al. Holistic impact evaluation of human activities on the coastal fish biodiversity in the Chinese coastal environment [J]. Environmental Science & Technology, 2022, 56(10):6574-6583 Su G H, Logez M, Xu J, et al. Human impacts on global freshwater fish biodiversity [J]. Science, 2021, 371(6531):835-838 Barbarossa V, Schmitt R J P, Huijbregts M A J, et al. Impacts of current and future large dams on the geographic range connectivity of freshwater fish worldwide [J]. Proceedings of the National Academy of Sciences of the United States of America, 2020, 117(7):3648-3655 Reid A J, Carlson A K, Creed I F, et al. Emerging threats and persistent conservation challenges for freshwater biodiversity [J]. Biological Reviews of the Cambridge Philosophical Society, 2019, 94(3):849-873 Zhang S, Zhao J D, Yao M. A comprehensive and comparative evaluation of primers for metabarcoding eDNA from fish [J]. Methods in Ecology and Evolution, 2020, 11:1609-1625 Bonar S A, Mercado-Silva N, Hubert W A, et al. Standard methods for sampling freshwater fishes:Opportunities for international collaboration [J]. Fisheries, 2017, 42(3):150-156 Coble A A, Flinders C A, Homyack J A, et al. eDNA as a tool for identifying freshwater species in sustainable forestry:A critical review and potential future applications [J]. The Science of the Total Environment, 2019, 649:1157-1170 Hänfling B, Lawson Handley L, Read D S, et al. Environmental DNA metabarcoding of lake fish communities reflects long-term data from established survey methods [J]. Molecular Ecology, 2016, 25(13):3101-3119 Ruppert K M, Kline R J, Rahman M S. Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding:A systematic review in methods, monitoring, and applications of global eDNA [J]. Global Ecology and Conservation, 2019, 17:e00547 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 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 Thomsen P F, Kielgast J, Iversen L L, et al. Detection of a diverse marine fish fauna using environmental DNA from seawater samples [J]. PLoS One, 2012, 7(8):e41732 Kelly R P, Port J A, Yamahara K M, et al. Using environmental DNA to census marine fishes in a large mesocosm [J]. PLoS One, 2014, 9(1):e86175 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 Xu N, Chang J B. Preliminary study on fish species detection in the middle and lower Yangtze River using environmental DNA [J]. Journal of Hydroecology, 2016, 37(5):49-55(in Chinese)
蒋佩文, 李敏, 张帅, 等. 基于环境DNA宏条码和底拖网的珠江河口鱼类多样性[J]. 水生生物学报, 2022, 46(11):1701-1711 Jiang P W, Li M, Zhang S, et al. Investigating the fish diversity in Pearl River Estuary based on environmental DNA matebarcoding and bottom trawling [J]. Acta Hydrobiologica Sinica, 2022, 46(11):1701-1711(in Chinese)
舒璐, 林佳艳, 徐源, 等. 基于环境DNA宏条形码的洱海鱼类多样性研究[J]. 水生生物学报, 2020, 44(5):1080-1086 Shu L, Lin J Y, Xu Y, et al. Investigating the fish diversity in Erhai Lake based on environmental DNA metabarcoding [J]. Acta Hydrobiologica Sinica, 2020, 44(5):1080-1086(in Chinese)
Sigsgaard E E, Nielsen I B, Carl H, et al. Seawater environmental DNA reflects seasonality of a coastal fish community [J]. Marine Biology, 2017, 164(6):128 Thomsen P F, Willerslev E. Environmental DNA:An emerging tool in conservation for monitoring past and present biodiversity [J]. Biological Conservation, 2015, 183:4-18 Miya M. Environmental DNA metabarcoding:A novel method for biodiversity monitoring of marine fish communities [J]. Annual Review of Marine Science, 2022, 14:161-185 Antognazza C M, Britton R J, Read D S, et al. Application of eDNA metabarcoding in a fragmented lowland river:Spatial and methodological comparison of fish species composition [J]. Environmental DNA, 2021, 3(2):458-471 张先炳, 杨胜发, 杨威, 等. 长江上游宜宾-江津与涪陵-丰都江段鱼类早期资源分布研究[J]. 淡水渔业, 2021, 51(5):51-59 Zhang X B, Yang S F, Yang W, et al. The distribution of the early-stage fish resources between Yibin-Jiangjin and Fuling-Fengdu in the upper reaches of the Yangtze River [J]. Freshwater Fisheries, 2021, 51(5):51-59(in Chinese)
刘飞, 林鹏程, 黎明政, 等. 长江流域鱼类资源现状与保护对策[J]. 水生生物学报, 2019, 43(S1):144-156 Liu F, Lin P C, Li M Z, et al. Situations and conservation strategies of fish resources in the Yangtze River Basin [J]. Acta Hydrobiologica Sinica, 2019, 43(S1):144-156(in Chinese)
周园园. 基于能值生态足迹的微型城镇生态安全研究:以重庆市江北区为例[D]. 重庆:西南大学, 2016:17-20 Zhou Y Y. Study on the ecological security of miniature town based on the emergy-ecological footprint model [D]. Chongqing:Southwest University, 2016:17 -20(in Chinese)
刘玥. 嘉陵江中游鱼类资源与垂钓渔业现状研究[D]. 重庆:西南大学, 2021:1-7 Liu Y. The fish resources and angling fishery status in the middle reaches of Jialing River [D]. Chongqing:Southwest University, 2021:1 -7(in Chinese)
林婷. 御临河河岸带不同生境下植被组成特点研究[D]. 重庆:西南大学, 2020:13-20 Lin T. Study on the characteristics of vegetation composition in different habitats in the riparian zone of Yulin River [D]. Chongqing:Southwest University, 2020:13 -20(in Chinese)
曹文宣. 有关长江流域鱼类资源保护的几个问题[J]. 长江流域资源与环境, 2008, 17(2):163-164 Cao W X. Problems on the protection of fish resources in the Yangtze River Basin [J]. Resources and Environment in the Yangtze Basin, 2008, 17(2):163-164(in Chinese)
田辉伍, 何春, 刘明典, 等. 长江上游干流三层流刺网渔获物结构研究[J]. 淡水渔业, 2016, 46(5):37-42 Tian H W, He C, Liu M D, et al. Study on structure of gillnet catches in the upper reaches of the Yangtze River [J]. Freshwater Fisheries, 2016, 46(5):37-42(in Chinese)
Valentini A, Taberlet P, Miaud C, et al. Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding [J]. Molecular Ecology, 2016, 25(4):929-942 Zhang H. Physical habitat assessment of a remaining high-biodiversity reach of the Upper Yangtze River, China [J]. Applied Ecology and Environmental Research, 2016, 14(1):129-143 Shu L, Pan H M, Peng Z G. Collection and extraction of environmental DNA from lake water and amplification of fish genetic markers [J]. Bio-101, 2021:e1010673 Miya M, Sato Y, Fukunaga T, et al. MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes:Detection of more than 230 subtropical marine species [J]. Royal Society Open Science, 2015, 2(7):150088 高天珩, 田辉伍, 叶超, 等. 长江上游珍稀特有鱼类国家级自然保护区干流段鱼类组成及其多样性[J]. 淡水渔业, 2013, 43(2):36-42 Gao T H, Tian H W, Ye C, et al. Diversity and composition of fish in the mainstream of national nature reserve of rare and endemic fish in the Upper Yangtze River [J]. Freshwater Fisheries, 2013, 43(2):36-42(in Chinese)
危起伟. 长江上游珍稀特有鱼类国家级自然保护区科学考察报告[M]. 北京:科学出版社, 2012:1-251 Chao A. Nonparametric estimation of the number of classes in a population [J]. Scandinavian Journal of Statistics, 1984, 11:265-270 Shannon C E. A mathematical theory of communication [J]. The Bell System Technical Journal, 1948, 27(3):379-423 Simpson E H. Measurement of diversity [J]. Nature, 1949, 163(4148):688 Pielou E C. The measurement of diversity in different types of biological collections [J]. Journal of Theoretical Biology, 1966, 13:131-144 何滔, 魏耀东, 卢群, 等. 长江上游珍稀特有鱼类自然保护区重庆段渔业资源现状调查[J]. 水产研究, 2018(2):85-97 He T, Wei Y D, Lu Q, et al. Status study on fishery resources in rare and endemic fish national nature reserve in Chongqing of Yangtze River [J]. Fisheries Research, 2018 (2):85-97(in Chinese)
杨海乐, 沈丽, 何勇凤, 等. 长江水生生物资源与环境本底状况调查(2017-2021)[J]. 水产学报, 2023, 47(2):3-30 Yang H L, Shen L, He Y F, et al. Status of aquatic organisms resources and their environments in the Yangtze River system (2017-2021) [J]. Journal of Fisheries of China, 2023, 47(2):3-30(in Chinese)
Ficetola G F, Pansu J, Bonin A, et al. Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data [J]. Molecular Ecology Resources, 2015, 15(3):543-556 Anderson J T, Schumer G, Anders P J, et al. Confirmed observation:A North American green sturgeon Acipenser medirostris recorded in the Stanislaus River, California [J]. Journal of Fish and Wildlife Management, 2018, 9(2):624-630 Xu N, Zhu B, Shi F, et al. Monitoring seasonal distribution of an endangered anadromous sturgeon in a large river using environmental DNA [J]. Science of Nature, 2018, 105(11-12):62 Wang X Y, Lu G Q, Zhao L L, et al. Assessment of fishery resources using environmental DNA:Small yellow croaker (Larimichthys polyactis) in East China Sea [J]. PLoS One, 2020, 15(12):e0244495 Wang X Y, Lu G Q, Zhao L L, et al. Assessment of fishery resources using environmental DNA:The large yellow croaker (Larimichthys crocea) in the East China Sea [J]. Fisheries Research, 2021, 235:105813 Morita K, Fukuwaka M A, Tanimata N, et al. Size-dependent thermal preferences in a pelagic fish [J]. Oikos, 2010, 119(8):1265-1272 Sandersfeld T, Mark F C, Knust R. Temperature-depen-dent metabolism in Antarctic fish:Do habitat temperature conditions affect thermal tolerance ranges? [J]. Polar Biology, 2017, 40(1):141-149 王珂. 三峡库区鱼类时空分布特征及与相关因子关系分析[D]. 北京:中国水利水电科学研究院, 2013:47-74 王敏, 朱峰跃, 刘绍平, 等. 三峡库区汉丰湖鱼类群落结构的季节变化[J]. 湖泊科学, 2017, 29(2):439-447 Wang M, Zhu F Y, Liu S P, et al. Seasonal variations of fish community structure of Lake Hanfeng in Three Gorges Reservoir region [J]. Journal of Lake Sciences, 2017, 29(2):439-447(in Chinese)
董纯, 杨志, 龚云, 等. 三峡库区干流鱼类资源现状与物种多样性保护[J]. 水生态学杂志, 2019, 40(1):15-21 Dong C, Yang Z, Gong Y, et al. Fish resource status and biodiversity conservation in the main channel of Three Gorges Reservoir [J]. Journal of Hydroecology, 2019, 40(1):15-21(in Chinese)
蒋成勇. 长江重庆主城段河道碳同位素时空分布研究[D]. 重庆:重庆交通大学, 2021:8-11 Jiang C Y. Study on the spatial and temporal distribution of carbon isotope in the main city section of the Yangtze River in Chongqing [D]. Chongqing:Chongqing Jiaotong University, 2021:8 -11(in Chinese)
邬志红. 长江嘉陵江交汇口水力特性数值模拟研究[D]. 重庆:重庆交通大学, 2012:19-24 Wu Z H. Numerical simulation of hydraulic characteristics in confluence between Yangtze River and Jialing River [D]. Chongqing:Chongqing Jiaotong University, 2012:19 -24(in Chinese)
Barnes M A, Turner C R, Jerde C L, et al. Environmental conditions influence eDNA persistence in aquatic systems [J]. Environmental Science & Technology, 2014, 48(3):1819-1827 刘军, 曹文宣, 常剑波. 长江上游主要河流鱼类多样性与流域特征关系[J]. 吉首大学学报(自然科学版), 2004, 25(1):42-47 Liu J, Cao W X, Chang J B. The relationship between species diversity of fish and basin characteristics of main rivers in the upper reaches of the Yangtze River [J]. Journal of Jishou University (Natural Science Edition), 2004, 25(1):42-47(in Chinese) Tsuji S, Yamanaka H, Minamoto T. Effects of water pH and proteinase K treatment on the yield of environmental DNA from water samples [J]. Limnology, 2017, 18(1):1-7 Jo T, Murakami H, Yamamoto S, et al. Effect of water temperature and fish biomass on environmental DNA shedding, degradation, and size distribution [J]. Ecology and Evolution, 2019, 9(3):1135-1146 李苗. 基于eDNA技术对渤海中国对虾的定性与定量检测[D]. 上海:上海海洋大学, 2019:22-29 Li M. Qualitative and quantitative detection using eDNA technology:A case study of Fenneropenaeus chinensis in the Bohai [D]. Shanghai:Shanghai Ocean University, 2019:22 -29(in Chinese)
吴昀晟, 唐永凯, 李建林, 等. 环境DNA在长江江豚监测中的应用[J]. 中国水产科学, 2019, 26(1):124-132 Wu Y S, Tang Y K, Li J L, et al. The application of environmental DNA in the monitoring of the Yangtze finless porpoise, Neophocaena phocaenoides asaeorientalis [J]. Journal of Fishery Sciences of China, 2019, 26(1):124-132(in Chinese)
Zhang H, Yoshizawa S, Iwasaki W, et al. Seasonal fish assemblage structure using environmental DNA in the Yangtze Estuary and its adjacent waters [J]. Frontiers in Marine Science, 2019, 6:515 Strickler K M, Fremier A K, Goldberg C S. Quantifying effects of UV-B, temperature, and pH on eDNA degradation in aquatic microcosms [J]. Biological Conservation, 2015, 183:85-92 -
点击查看大图
计量
- 文章访问数: 1519
- HTML全文浏览数: 1519
- PDF下载数: 196
- 施引文献: 0
下载:
