留言板

尊敬的读者、作者、审稿人, 关于本刊的投稿、审稿、编辑和出版的任何问题, 您可以本页添加留言。我们将尽快给您答复。谢谢您的支持!

姓名
邮箱
手机号码
标题
留言内容
验证码

基于环境DNA技术的夏季东海鱼类物种多样性研究

李晓玲 刘洋 王丛丛 俞晔伟 李纲

李晓玲,刘洋,王丛丛,等. 基于环境DNA技术的夏季东海鱼类物种多样性研究[J]. 海洋学报,2022,44(4):74–84 doi: 10.12284/hyxb2022088
引用本文: 李晓玲,刘洋,王丛丛,等. 基于环境DNA技术的夏季东海鱼类物种多样性研究[J]. 海洋学报,2022,44(4):74–84 doi: 10.12284/hyxb2022088
Li Xiaoling,Liu Yang,Wang Congcong, et al. Study on fish species diversity in the East China Sea in summer based on environmental DNA technology[J]. Haiyang Xuebao,2022, 44(4):74–84 doi: 10.12284/hyxb2022088
Citation: Li Xiaoling,Liu Yang,Wang Congcong, et al. Study on fish species diversity in the East China Sea in summer based on environmental DNA technology[J]. Haiyang Xuebao,2022, 44(4):74–84 doi: 10.12284/hyxb2022088

基于环境DNA技术的夏季东海鱼类物种多样性研究

doi: 10.12284/hyxb2022088
基金项目: 国家重点研发计划(2019YFD0901404);国家自然科学基金(31702312)。
详细信息
    作者简介:

    李晓玲(1997-),女,江苏省海安市人,主要从事环境DNA的研究。E-mail: 1103198570@qq.com

    通讯作者:

    王丛丛,女,讲师,主要从事环境DNA、种群遗传进化的研究。E-mail: ccwang@shou.edu.cn

    李纲,男,副教授,主要从事渔业资源评估的研究。E-mail: g-li@shou.edu.cn

  • 中图分类号: S932.4

Study on fish species diversity in the East China Sea in summer based on environmental DNA technology

  • 摘要: 为了解东海海域主要鱼类群落的种类组成,监测和保护其多样性,本研究利用环境DNA技术对东海鱼类进行物种多样性分析。通过海水样本的采集,环境DNA提取、扩增和高通量测序分析,从东海14个站点的环境DNA样本中共检测出2纲,23目,29科,42属,44种海水鱼类,大部分种类在东海传统渔业资源调查中均有出现。其中,相对丰度较高的物种为赤鼻棱鳀(Thryssa kammalensis)、蓝点马鲛(Scomberomorus niphonius)、日本鲐(Scomber japonicus)、小黄鱼(Larimichthys polyactis)和鲻(Mugil cephalus)。站点间α多样性差异较大,总体上呈现近海站点生物多样性高,远海站点生物丰度高的特点。研究结果表明,环境DNA技术可以作为传统渔业资源调查的补充,也可以对东海海域鱼类物种多样性及空间分布进行快速检测。
  • 图  1  2020年9月东海采样站点

    Fig.  1  Sampling stations in the East China Sea in September 2020

    图  2  东海鱼类OTU划分和分类地位鉴定结果

    Fig.  2  Result of OTU division and classification taxon identification of fish in the East China Sea

    图  3  各采样站点优势鱼类物种组成

    Fig.  3  The composition of dominant fish species at each sampling station

    图  4  东海不同采样站点(每条线代表一个站点)物种α多样性指数稀疏曲线

    Fig.  4  Sparse curve of species alpha diversity index at different sampling stations (each line represents a different station) in the East China Sea

    图  5  东海水域不同采样站点共有OTU的花瓣图

    Fig.  5  Petal map of OTU shared by different sampling stations in the East China Sea

    图  6  各优势鱼种在不同采样站点的相对丰度

    Fig.  6  Relative abundance of dominant fish species at different sampling stations

    图  7  环境DNA检出的东海鱼类物种组成热图

    样本按照物种组成数据的欧式距离进行UPGMA聚类,并根据聚类结果排列;物种按照其组成数据的Pearson相关性系数矩阵进行UPGMA聚类,并根据聚类结果排列;不同色标代表不同物种在不同样本中的表达量,色标数值通过物种丰度数据取Z值获得,由绿到棕表示对应样本中该种丰度逐渐降低

    Fig.  7  Heat map of fish species composition in the East China Sea detected by eDNA

    Samples are clustered by UPGMA according to the euclidean distance of species composition data, and arranged according to the clustering results; UPGMA clustering is carried out according to Pearson correlation coefficient matrix of species composition data, and arranged according to the clustering results; different color codes represent the expression of different species in different samples, and the value of color codes is obtained by taking Z value of species abundance data, and from green to brown, the abundance in corresponding samples gradually decreases

    表  1  各站点的序列量(eDNA)结果

    Tab.  1  Sequence quantity (eDNA) results of each station

    样本
    编号
    输入
    拼接
    过滤
    去除嵌合体
    去除稀有个体
    ES149 78344 71444 39142 43242 408
    ES246 90141 39340 86138 84038 805
    ES340 02532 22631 83628 59428 582
    ES451 37246 71446 34244 58444 577
    ES548 36842 88842 56938 71138 693
    ES640 21136 32336 04535 21535 191
    ES745 53637 14836 89633 50433 477
    ES842 89438 35037 91636 22236 206
    ES939 90535 71835 36533 79433 779
    ES1036 89434 16633 86633 02933 025
    ES1147 79842 48342 02540 46340 452
    ES1248 21244 93044 40542 82742 818
    ES1357 78252 82952 12650 61250 594
    ES1461 18252 15451 31448 60848 582
      注:表中第二列为原始数据中能同时匹配到正向和反向引物的序列量;第三列为拼接后的序列量;第四列为去除低质量序列后的数据量;第五列为聚类后去除嵌合体后序列量,即为高质量序列量;第六列为去除singleton OTUs(在所有样本中绝对丰度为1的OTU)后的序列量。
    下载: 导出CSV

    表  2  东海环境DNA检出的鱼类物种

    Tab.  2  Fish species detected by eDNA in the East China Sea

    AnguilliformesMuraenesocidaeMuraenesox褐海鳗 Muraenesox bagio
    海鳗 Muraenesox cinereus
    AulopiformesSynodontidaeHarpadon龙头鱼 Harpadon nehereus
    CarangariaPolynemidaePolydactylus黑斑多指马鲅 Polydactylus sextarius
    CarangiformesCarangidaeTrachurus日本竹筴鱼 Trachurus japonicus
    CentrarchiformesTerapontidaeRhynchopelates尖突吻䱨 Rhynchopelates oxyrhynchus
    ClupeiformesClupeidaeKonosirus斑鰶 Konosirus punctatus
    Sardinops远东拟沙丁鱼 Sardinops melanostictus
    EngraulidaeEncrasicholina银灰半棱鳀 Encrasicholina punctifer
    Engraulis日本鳀 Engraulis japonicus
    Setipinna太的黄鲫 Setipinna taty
    Thryssa赤鼻棱鳀Thryssa kammalensis
    黄吻棱鳀 Thryssa vitrirostris
    PristigasteridaeIlishaIlisha elongata
    ElopiformesElopidaeElops夏威夷海鲢 Elops hawaiensis
    EupercariaSciaenidaeChrysochir尖头黄鳍牙鱛 Chrysochir aureus
    Larimichthys小黄鱼 Larimichthys polyactis
    Pennahia银姑鱼 Pennahia argentata
    LabriformesLabridaeScarus青点鹦嘴鱼 Scarus ghobban
    MugiliformesMugilidaeMugilMugil cephalus
    MyctophiformesMyctophidaeBenthosema七星底灯鱼 Benthosema pterotum
    Diaphus帕尔眶灯鱼 Diaphus parri
    OphidiiformesOphidiidaeHoplobrotula棘鼬鳚 Hoplobrotula armata
    PempheriformesLateolabracidaeLateolabrax中国花鲈 Lateolabrax maculatus
    PerciformesPholidaePholis方氏锦鳚 Pholis fangi
    TriglidaeChelidonichthys棘绿鳍鱼 Chelidonichthys spinosus
    PleuronectiformesCynoglossidaeCynoglossus焦氏舌鳎 Cynoglossus joyneri
    Paraplagusia日本须鳎 Paraplagusia japonica
    PleuronectidaePleuronichthys木叶鲽 Pleuronichthys cornutus
    PriacanthiformesPriacanthidaePolydactylus长尾大眼鲷 Priacanthus tayenus
    ScombriformesCentrolophidaeHyperoglyphe日本栉鲳 Hyperoglyphe japonica
    Psenopsis刺鲳 Psenopsis anomala
    ScombridaeAuxis双鳍舵鲣 Auxis rochei
    Scomber日本鲐 Scomber japonicus
    Scomberomorus蓝点马鲛 Scomberomorus niphonius
    Thunnus长鳍金枪鱼 Thunnus alalunga
    TrichiuridaeTrichiurus日本带鱼 Trichiurus japonicus
    SpariformesSparidaeAcanthopagrus黑棘鲷 Acanthopagrus schlegelii
    StomiiformesSternoptychidaePolyipnus闪电烛光鱼 Polyipnus stereope
    SyngnathiformesCallionymidaeRepomucenus饰鳍斜棘鴨 Repomucenus ornatipinnis
    TetraodontiformesBalistidaeCanthidermis疣鳞鲀 Canthidermis maculata
    UranoscopiformesUranoscopidaeUranoscopus日本 Uranoscopus japonicus
    Xenocephalus青 Xenocephalus elongatus
    CarcharhiniformesCarcharhinidaeCarcharhinus镰状真鲨 Carcharhinus falciformis
    下载: 导出CSV

    表  3  东海鱼类物种相对丰度的α多样性指数

    Tab.  3  Alpha diversity index of relative abundance of fish species in the East China Sea

    样本编号
    α多样性指数
    Chao1
    指数
    Observed
    species指数
    Pielou
    均匀度指数
    Shannon
    多样性指数
    Simpson
    多样性指数
    ES1136.067110.90.114 6030.778 4470.146 170
    ES2141.298118.80.194 1341.338 0000.279 125
    ES366.30652.50.155 5470.888 8070.210 343
    ES487.05870.40.076 4280.469 0340.087 745
    ES5180.581158.00.179 9191.313 9800.260 339
    ES6146.008131.10.103 2140.726 0420.137 918
    ES7179.801156.10.120 0150.874 4470.159 080
    ES8123.483104.20.055 2190.370 1400.060 713
    ES996.78973.40.052 5000.325 3720.055 633
    ES1052.62841.30.031 3020.168 0190.028 676
    ES11128.553113.00.174 2761.188 4900.266 132
    ES1276.65265.10.240 0041.445 6800.358 558
    ES1397.96784.70.085 1210.545 0440.099 298
    ES14155.352140.80.396 2112.827 7300.644 819
    下载: 导出CSV
  • [1] Edlinger A, Saghaï A, Herzog C, et al. Towards a multidimensional view of biodiversity and ecosystem functioning in a changing world[J]. New Phytologist, 2020, 228(3): 820−822. doi: 10.1111/nph.16881
    [2] Noor N M, Das S K. Effects of elevated carbon dioxide on marine ecosystem and associated fishes[J]. Thalassas: An International Journal of Marine Sciences, 2019, 35(2): 421−429. doi: 10.1007/s41208-019-00161-3
    [3] Worm B, Barbier E B, Beaumont N, et al. Impacts of biodiversity loss on ocean ecosystem services[J]. Science, 2006, 314(5800): 787−790. doi: 10.1126/science.1132294
    [4] 李圣法, 程家骅, 严利平. 东海大陆架鱼类群落的空间结构[J]. 生态学报, 2007, 27(11): 4377−4386. doi: 10.3321/j.issn:1000-0933.2007.11.001

    Li Shengfa, Cheng Jiahua, Yan Liping. Spatial structures of fish communities on the continental shelf of the East China Sea[J]. Acta Ecologica Sinica, 2007, 27(11): 4377−4386. doi: 10.3321/j.issn:1000-0933.2007.11.001
    [5] Liu J Y. Status of marine biodiversity of the China Seas[J]. PLoS One, 2013, 8(1): e50719. doi: 10.1371/journal.pone.0050719
    [6] Takayanagi K, Nishiuchi K, Yokouchi K, et al. A possible collaboration with China on marine ecosystem research in the East China Sea[J]. Japan Agricultural Research Quarterly: JARQ, 2006, 40(1): 59−64. doi: 10.6090/jarq.40.59
    [7] 林龙山, 程家骅, 李惠玉. 东海底拖网渔业资源现状[J]. 现代渔业信息, 2006, 21(9): 13−15.

    Lin Longshan, Cheng Jiahua, Li Huiyu. Recent status of bottom trawl fishery resources in the East China Sea[J]. Modern Fisheries Information, 2006, 21(9): 13−15.
    [8] 刘勇, 程家骅. 东海及黄海南部渔业资源水文环境类群划分及其相关特征的初步分析[J]. 中国水产科学, 2019, 26(4): 796−810.

    Liu Yong, Cheng Jiahua. Preliminary analysis on the division of fishery resources based on hydrological environment factors in the East China Sea and south of the Yellow Sea[J]. Journal of Fishery Sciences of China, 2019, 26(4): 796−810.
    [9] 戴芳群, 朱玲, 陈云龙. 黄、东海渔业资源群落结构变化研究[J]. 渔业科学进展, 2020, 41(1): 1−10.

    Dai Fangqun, Zhu Ling, Chen Yunlong. Variations of fishery resource structure in the Yellow Sea and East China Sea[J]. Progress in Fishery Sciences, 2020, 41(1): 1−10.
    [10] 高天翔, 陈治, 王晓艳. 近海鱼类多样性调查新方法—环境DNA分析技术[J]. 浙江海洋大学学报(自然科学版), 2018, 37(1): 1−7.

    Gao Tianxiang, Chen Zhi, Wang Xiaoyan. Environmental DNA, a new method for fish diversity investigation in the coastal waters[J]. Journal of Zhejiang Ocean University (Natural Science Edition), 2018, 37(1): 1−7.
    [11] 张辉, 线薇薇. 环境DNA技术在生态保护和监测中的应用[J]. 海洋科学, 2020, 44(7): 96−102. doi: 10.11759/hykx20200119002

    Zhang Hui, Xian Weiwei. Application of environmental DNA technology in ecological conservation and monitoring[J]. Marine Science, 2020, 44(7): 96−102. doi: 10.11759/hykx20200119002
    [12] 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. doi: 10.3724/SP.J.1118.2019.18133

    Wu Yunsheng, Tang Yongkai, Li Jianlin, 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. doi: 10.3724/SP.J.1118.2019.18133
    [13] Lear G, Dickie I, Banks J, et al. Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples[J]. New Zealand Journal of Ecology, 2018, 42(1): 10.
    [14] 单秀娟, 李苗, 王伟继. 环境DNA(eDNA)技术在水生生态系统中的应用研究进展[J]. 渔业科学进展, 2018, 39(3): 23−29.

    Shan Xiujuan, Li Miao, Wang Weiji. Application of environmental DNA technology in aquatic ecosystem[J]. Progress in Fishery Sciences, 2018, 39(3): 23−29.
    [15] 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. doi: 10.1007/s00227-017-3147-4
    [16] Fraija-Fernández N, Bouquieaux M C, Rey A, et al. Marine water environmental DNA metabarcoding provides a comprehensive fish diversity assessment and reveals spatial patterns in a large oceanic area[J]. Ecology and Evolution, 2020, 10(14): 7560−7584. doi: 10.1002/ece3.6482
    [17] 凌建忠, 姜亚洲, 孙鹏, 等. 环境DNA技术在象山港水域鱼类多样性调查中的应用与评估[J]. 中国水产科学, 2021, 28(2): 205−214.

    Ling Jianzhong, Jiang Yazhou, Sun Peng, et al. Application and evaluation of environmental DNA technology in fish diversity research in Xiangshan Bay[J]. Journal of Fishery Sciences of China, 2021, 28(2): 205−214.
    [18] 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. doi: 10.7541/2020.125

    Shu Lu, Lin Jiayan, Xu Yuan, et al. Investigating the fish diversity in Erhai Lake based on environmental DNA metabarcoding[J]. Acta Hydrobiologica Sinica, 2020, 44(5): 1080−1086. doi: 10.7541/2020.125
    [19] Wang Xiaoyan, Lu Guoqing, Zhao Linlin, 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. doi: 10.1371/journal.pone.0244495
    [20] 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. doi: 10.1098/rsos.150088
    [21] Bolyen E, Rideout J R, Dillon M R, et al. Author correction: reproducible, interactive, scalable and extensible microbiome data science using QIIME 2[J]. Nature Biotechnology, 2019, 37(9): 1091.
    [22] Whittaker R H. Evolution and measurement of species diversity[J]. Taxon, 1972, 21(2/3): 213−251.
    [23] Chao Anne. Nonparametric estimation of the number of classes in a population[J]. Scandinavian Journal of Statistics, 1984, 11(4): 265−270.
    [24] Shannon C E. A mathematical theory of communication part I: discrete noiseless systems[J]. The Bell System Technical Journal, 1948, 27(3): 379−423. doi: 10.1002/j.1538-7305.1948.tb01338.x
    [25] Shannon C E. A mathematical theory of communication part II: the discrete channel with noise[J]. The Bell System Technical Journal, 1948, 27(3): 623−656.
    [26] Simpson E H. Measurement of diversity[J]. Nature, 1949, 163(4148): 688. doi: 10.1038/163688a0
    [27] Pielou E C. The measurement of diversity in different types of biological collections[J]. Journal of Theoretical Biology, 1966, 13: 131−144. doi: 10.1016/0022-5193(66)90013-0
    [28] 赵淑江, 吕宝强, 李汝伟, 等. 物种灭绝背景下东海渔业资源衰退原因分析[J]. 中国科学: 地球科学, 2015, 45(11): 1628−1640.

    Zhao Shujiang, Lü Baoqiang, Li Ruwei, et al. A preliminary analysis of fishery resource exhaustion in the context of biodiversity decline[J]. Science China: Earth Sciences, 2015, 45(11): 1628−1640.
    [29] Bergman P S, Schumer G, Blankenship S, et al. Detection of adult green sturgeon using environmental DNA analysis[J]. PLoS One, 2016, 11(4): e0153500. doi: 10.1371/journal.pone.0153500
    [30] Lugg W H, Griffiths J, Van Rooyen A R, et al. Optimal survey designs for environmental DNA sampling[J]. Methods in Ecology and Evolution, 2018, 9(4): 1049−1059. doi: 10.1111/2041-210X.12951
    [31] 刘勇, 李圣法, 陈学刚, 等. 东、黄海2000年冬季底层鱼类群落结构及其多样性[J]. 海洋科学, 2007, 31(10): 19−24. doi: 10.3969/j.issn.1000-3096.2007.10.009

    Liu Yong, Li Shengfa, Chen Xuegang, et al. The structure and diversity of demersal fish communities in winter 2000 in the East China Sea and the Yellow Sea[J]. Marine Science, 2007, 31(10): 19−24. doi: 10.3969/j.issn.1000-3096.2007.10.009
    [32] 宫亚运, 章群, 曹艳, 等. 基于线粒体COⅠ基因的中国近海棱鳀属鱼类DNA条形码[J]. 水产学报, 2016, 40(10): 1513−1520.

    Gong Yayun, Zhang Qun, Cao Yan, et al. DNA barcoding of Thryssa in coastal waters of China based on the mitochondrial cytochrome oxidase subunit I sequence[J]. Journal of Fisheries of China, 2016, 40(10): 1513−1520.
    [33] 马春艳, 马凌波, 倪勇, 等. 基于形态特征和线粒体16S rRNA基因序列探讨棱鳀属的系统进化[J]. 中国水产科学, 2010, 17(3): 471−477.

    Ma Chunyan, Ma Lingbo, Ni Yong, et al. Phylogenetic relationship of Thryssa inferred from morphologic characteristic and mitochondrial 16S rRNA gene sequences[J]. Journal of Fishery Sciences of China, 2010, 17(3): 471−477.
    [34] 程家骅, 张秋华, 李圣法, 等. 东黄海渔业资源利用[M]. 上海: 上海科学技术出版社, 2006.

    Cheng Jiahua, Zhang Qiuhua, Li Shengfa, et al. Fishery Resource Utilization in the Yellow Sea and East China Sea[M]. Shanghai: Shanghai Science and Technology Press, 2006.
    [35] 杜萍, 陈全震, 李尚鲁, 等. 东海带鱼资源变动及其栖息地驱动因子研究进展[J]. 广东海洋大学学报, 2020, 40(1): 126−132. doi: 10.3969/j.issn.1673-9159.2020.01.017

    Du Ping, Chen Quanzhen, Li Shanglu, et al. Advances in the Trichiurus lepturus changes and habitat driving factors in the East China Sea[J]. Journal of Guangdong Ocean University, 2020, 40(1): 126−132. doi: 10.3969/j.issn.1673-9159.2020.01.017
    [36] 杨青, 李宏俊, 李洪波, 等. 海洋生物多样性评价方法综述[J]. 海洋环境科学, 2013, 32(1): 157−160.

    Yang Qing, Li Hongjun, Li Hongbo, et al. Review on assessment methods of marine biodiversity[J]. Marine Environmental Science, 2013, 32(1): 157−160.
    [37] 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.

    Zhao Mengdi. Analysis of the fish diversity of the East China Sea and the Yellow Sea in winter using environmental DNA[D]. Shanghai: Shanghai Ocean University, 2017.
    [38] 周永东, 李圣法. 东海区主要经济种类三场一通道及保护区图集[M]. 北京: 海洋出版社, 2018.

    Zhou Yongdong, Li Shengfa. Atlas of Spawning Grounds, Feeding Grounds, Overwintering Grounds, Migratory Channels and Protected Areas of the Main Economic Species in the East China Sea[M]. Beijing: China Ocean Press, 2018.
    [39] 李圣法, 程家骅, 李长松, 等. 东海中部鱼类群落多样性的季节变化[J]. 海洋渔业, 2005, 27(2): 113−119. doi: 10.3969/j.issn.1004-2490.2005.02.005

    Li Shengfa, Cheng Jiahua, Li Changsong, et al. Seasonal changes on fish community diversity in the middle part of the East China Sea[J]. Marine Fisheries, 2005, 27(2): 113−119. doi: 10.3969/j.issn.1004-2490.2005.02.005
  • 加载中
图(7) / 表(3)
计量
  • 文章访问数:  530
  • HTML全文浏览量:  207
  • PDF下载量:  114
  • 被引次数: 0
出版历程
  • 收稿日期:  2021-07-21
  • 修回日期:  2021-12-17
  • 刊出日期:  2022-04-14

目录

    /

    返回文章
    返回