Identification of Microplankton in South China Sea with Image-Matching Individual PCR

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英文篇名：Identification of Microplankton in South China Sea with Image-Matching Individual PCR 作者：LI ; Si ; YANG ; Guanpin ; ZHU ; Baohua ; PAN ; Kehou 英文作者：LI Si;YANG Guanpin;ZHU Baohua;PAN Kehou;School of Chemical Engineering and Technology, Hebei University of Technology;Engineering Research Center of Seawater Utilization Technology of Chinese Ministry of Education, Hebei University of Technology;College of Marine Life Sciences, Ocean University of China;Key Laboratory of Mariculture of Chinese Ministry of Education, Ocean University of China; 英文关键词：image-matching individual PCR;;microplankton;;18S ribosomal RNA gene;;morphological identification;;molecular identification;;South China Sea 中文刊名：QDHB 英文刊名：中国海洋大学学报(英文版) 机构：School of Chemical Engineering and Technology, Hebei University of Technology;Engineering Research Center of Seawater Utilization Technology of Chinese Ministry of Education, Hebei University of Technology;College of Marine Life Sciences, Ocean University of China;Key Laboratory of Mariculture of Chinese Ministry of Education, Ocean University of China; 出版日期：2019-02-06 出版单位：Journal of Ocean University of China 年：2019 期：v.18 基金：supported by Hebei Province Natural Science Foundation for Youths (No. C2015202202);; Colleges and Universities in Hebei Province Science and Technology Research Project (No. QN20131082);; the National Natural Science Foundation of China (No. 51474084);; the National Key Research and Development Program of China (No. 2016YFB0601001) 语种：英文; 页：QDHB201901022 页数：8 CN：01 ISSN：37-1415/P 分类号：223-230

摘要

In this study, marine microplankton were identified by combining standard light microscopy with Sanger 18S rRNA gene sequencing. The image-matching individual PCR technique was applied to identify the image collectable unicellular microplankton to genera. Instead of pure strain culture and morphological identification, microplankton individual cells were isolated and fixed with glutaraldehyde, frozen and stored for months. Finally, they were imaged under a microscope and molecularly identified via phylogenetic analysis of their 18S ribosomal RNA gene(18S rDNA). Microplankton cells were collected at 30 locations in South China Sea, and were assigned to 21 known and 4 unidentified genera(2 uncultured fungi and 2 uncultured stramenopiles) with phylogenetic analysis in parallel to the morphological identification.
        In this study, marine microplankton were identified by combining standard light microscopy with Sanger 18S rRNA gene sequencing. The image-matching individual PCR technique was applied to identify the image collectable unicellular microplankton to genera. Instead of pure strain culture and morphological identification, microplankton individual cells were isolated and fixed with glutaraldehyde, frozen and stored for months. Finally, they were imaged under a microscope and molecularly identified via phylogenetic analysis of their 18S ribosomal RNA gene(18S rDNA). Microplankton cells were collected at 30 locations in South China Sea, and were assigned to 21 known and 4 unidentified genera(2 uncultured fungi and 2 uncultured stramenopiles) with phylogenetic analysis in parallel to the morphological identification.

引文

Andersen,R.A.,Brett,R.W.,Potter,D.,and Sexton,J.P.,1998.Phylogeny of the Eustigmatophyceae based upon 18S rDNA,with emphasis on Nannochloropsis.Protist,149:61-74.
    Coetzee,J.,and Merwe,C.F.V.D.,1985.Penetration rate of glutaraldehyde in various buffers into plant tissue and gelatin gels.Journal of Microscopy,137:129-136.
    Costa,S.,Carvalho,S.,Costa,C.,Coelho,P.,Silva,S.,Santos,L.S.,Gaspar,J.F.,Porto,B.,Laffon,B.,and Teixeira,J.P.,2015.Increased levels of chromosomal aberrations and DNAdamage in a group of workers exposed to formaldehyde.Mutagenesis,30:463.
    Das,T.,Sehar,S.,and Manefield,M.,2013.The roles of extracellular DNA in the structural integrity of extracellular polymeric substance and bacterial biofilm development.Environmental Microbiology Reports,5:778.
    Daste,P.,Neuville,D.,and Victor-Baptiste,B.,1983.A simple procedure for obtaining clonal isolation of diatoms.British Phycological Journal,18:1-3.
    Fenech,M.,Nersesyan,A.,and Knasmueller,S.,2016.A systematic review of the association between occupational exposure to formaldehyde and effects on chromosomal DNA damage measured using the cytokinesis-block micronucleus assay in lymphocytes.Mutation Research,770:46.
    Guindon,S.,Dufayard,J.F.,Lefort,V.,Anisimova,M.,Hordijk,W.,and Gascuel,O.,2010.New algorithms and methods to estimate maximum-likelihood phylogenies:Assessing the performance of PhyML 3.0.Systematic Biology,59:307-321.
    Huelsenbeck,J.P.,Ronquist,F.,Nielsen,R.,and Bollback,J.P.,2001.Bayesian inference of phylogeny and its impact on evolutionary biology.Science,294:2310-2314.
    Jeon,S.-O.,Bunge,J.,Stoeck,T.,Barger,K.J.-A.,Hong,S.-H.,and Epstein,S.S.,2006.Synthetic statistical approach reveals a high degree of richness of microbial eukaryotes in an anoxic water column.Applied and Environmental Mircobiology,72:6578-6583.
    Koppelstaetter,C.,Jennings,P.,Hochegger,K.,Perco,P.,Ischia,R.,Karkoszka,H.,and Mayer,G.,2005.Effect of tissue fixatives on telomere length determination by quantitative PCR.Mechanisms of Ageing&Development,126:1331-1333.
    Lefort,V.,Longueville,J.E.,and Gascuel,O.,2017.SMS:Smart Model Selection in PhyML.Molecular Biology&Evolution,34(9):2422
    Li,N.,Yu,S.X.,Wang,Y.C.,Li,J.L.,Li,F.C.,and Qin,S.,2015.Diversity of phototrophic phytoplankton in Northern South China Sea indicated by rbcL analysis.Journal of Applied Phycology,28:1-9.
    Li,S.,and Ismar,S.M.H.,2018.Transcriptome,biochemical and growth responses of the marine phytoplankter Phaeodactylum tricornutum Bohlin(Bacillariophyta)to copepod grazer presence.Cellular Physiology and Biochemistry,46:1091-1111.
    Li,T.,Liu,S.,and Wang,H.F.,2010.Species composition of phytoplankton and its distribution in the northern South China Sea in autumn 2004.Journal of Tropical Oceanography,29:65-73.
    Liu,H.,Song,X.,Huang,L.,Tan,Y.,and Zhang,J.,2011.Phytoplankton biomass and production in northern South China Sea during summer:Influenced by Pearl River discharge and coastal upwelling.Acta Ecologica Sinica,31:133-136.
    Massana,R.,Castresana,J.,Balagué,V.,Guillou,L.,Romari,K.,Groisillier,A.,Valentin,K.,and Pedrós-Alió,C.,2004.Phylogenetic and ecological analysis of novel marine stramenopiles.Applied and Environmental Microbiology,70:3528-3534.
    McManus,G.B.,and Katz,L.A.,2009.Molecular and morphological methods for identifying plankton:What makes a successful marriage?Journal of Plankton Research,31:1119-1129.
    Modigh,M.,and Castaldo,S.,2005.Effects of fixatives on ciliates as related to cell size.Journal of Plankton Research,27:845-849.
    Omori,M.,and Ikeda,T.,1985.Methods in marine zooplankton ecology.Quarterly Review of Biology,60(4):527-528.
    Parisi,M.,Merot,J.,and Bourguet,J.,1985.Glutaraldehyde fixation preserves the permeability properties of the ADH-induced water channels.Journal of Membrane Biology,86:239-245.
    Ronquist,F.,and Huelsenbeck,J.P.,2003.MrBayes 3:Bayesian phylogenetic inference under mixed models.Bioinformatics,19:1572-1574.
    Sal,S.,Lopezurrutia,A.,Irigoien,X.,Harbour,D.,and Harris,R.P.,2013.Marine microplankton diversity database.Ecology,94:1658-1658.
    Sch?fer,H.,Abbas,B.,Witte,H.,and Muyzer,G.,2002.Genetic diversity of‘satellite’bacteria present in cultures of marine diatoms.FEMS Microbiology Ecology,42:25-35.
    Sommer,U.,Paul,C.,and Moustakagouni,M.,2015.Warming and ocean acidification effects on phytoplankton-From species shifts to size shifts within species in a mesocosm experiment.PLo S One,10(5):e0125239.
    Sy,M.V.D.S.,De,W.R.,and Vaulot,D.,2001.Oceanic 18Sr DNA sequences from picoplankton reveal unsuspected eukaryotic diversity.Nature,409:607-610.
    Tamura,K.,Peterson,D.,Peterson,N.,Stecher,G.,Nei,M.,and Kumar,S.,2011.MEGA5:Molecular evolutionary genetics analysis using maximum likelihood,evolutionary distance,and maximum parsimony methods.Molecular Biology and Evolution,28:2731-2739.
    Thompson,J.D.,Gibson,T.J.,Plewniak,F.,Jeanmougin,F.,and Higgins,D.G.,1997.The CLUSTAL_X windows interface:Flexible strategies for multiple sequence alignment aided by quality analysis tools.Nucleic Acids Research,25:4876-4882.
    Xing,D.,Cheng,S.,Logan,B.E.,and Regan,J.M.,2010.Isolation of the exoelectrogenic denitrifying bacterium Comamonas denitrificans based on dilution to extinction.Applied Microbiology&Biotechnology,85:1575-1587.
    Zhang,P.,Li,X.,and Wang,B.G.,2016.Secondary metabolites from the marine algal-derived endophytic fungi:Chemical diversity and biological activity.Planta Medica,82:832-842.(Edited by Qiu Yantao)