Bacterial and archaeal communities in deep sea waters near the Ninetyeast Ridge in Indian Ocean

Ping GAO; Lingyun QU; Guangxun DU; Qinsheng WEI; Xuelei ZHANG; Guang YANG

doi:10.1007/s00343-020-9343-y

Your Location：

Home >

Browse articles >

Bacterial and archaeal communities in deep sea waters near the Ninetyeast Ridge in Indian Ocean

Ecology | Updated：2023-06-06

- Bacterial and archaeal communities in deep sea waters near the Ninetyeast Ridge in Indian Ocean
- Journal of Oceanology and Limnology Vol. 39, Issue 2, Pages: 582-597(2021)
- Affiliations：
  
  1.Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources (MNR), Qingdao 266061, China
  2.Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
  3.Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
- Author bio：
  
  Lingyun QU, E-mail: qly@fio.org.cn
- Funds：
- DOI：10.1007/s00343-020-9343-y
  CLC：
- Received：06 January 2020，
  
  Accepted：19 February 2020，
  
  Online First：24 April 2020，
  
  Published：2021-03
- Accepted：
Scan QR Code
Ping GAO, Lingyun QU, Guangxun DU, et al. Bacterial and archaeal communities in deep sea waters near the Ninetyeast Ridge in Indian Ocean[J]. Journal of Oceanology and Limnology, 2021, 39(2): 582-597.
DOI：

Ping GAO, Lingyun QU, Guangxun DU, et al. Bacterial and archaeal communities in deep sea waters near the Ninetyeast Ridge in Indian Ocean[J]. Journal of Oceanology and Limnology, 2021, 39(2): 582-597. DOI： 10.1007/s00343-020-9343-y.

摘要

Abstract

Depth-dependent distribution patterns of bacterial and archaeal communities in deep sea water column around the Ninetyeast Ridge in the Indian Ocean were investigated using 16S rRNA gene profiling. Sampling was conducted at the northern Ninetyeast Ridge (1°59.89'N-9°59.70'S

87°58.90'E-88°00.03'E) from September to November 2016 where samples were collected from the bathyal (1 000 m) to bathypelagic depths (

4 000 m) in four different stations. A total of 1 565 405 clean data falling into 6 712 bacterial OTUs and 1 452 727 clean data falling into 806 archaeal OTUs based on 97% similarity level were analyzed. Most of the bacterial 16S rRNA gene sequences were affiliated with Gammaproteobacteria

followed by Alphaproteobacteria and Bacteroidia. The archaeal 16S rRNA gene sequences mostly affiliated to Nitrososphaeria (Thaumarchaeota) dominated with relative abundances ranging from 52.68% to 97.2%

followed by Thermoplasmata (Euryarchaeota). Vertical partitioning of bacterial and archaeal communities among different water layers was observed. Canonical correspondence analysis (CCA) and Spearman's correlations revealed that depth (

=0.003)

dissolved oxygen (

=0.019)

and nitrite (

=0.033) were the main environmental factors affecting bacterial community structure at genus level in the Ninetyeast Ridge. On the other hand

the first two CCA axes accounted for 74.4% of the explained total variance

it seems that the archaeal communities at genus level were heavily influenced by the environmental variables including depth

dissolved oxygen (DO)

nitrite

salinity

phosphate

ammonia

nitrate

and silicate

but none of them exhibited any significant correlation on the structuring (

0.1).

关键词

Keywords

references

AgoguéH,LamyD,NealPR,SoginML,HerndlGJ.2011.Watermass-specificityofbacterialcommunitiesintheNorthAtlanticrevealedbymassivelyparallelsequencing. Molecular Ecology , 20 (2):258-274..

BandekarM,RamaiahN,JainA,MeenaRM.2018.Seasonalanddepth-wisevariationsinbacterialandarchaealgroupsintheArabianSeaoxygenminimumzone. Deep Sea Research Part Ⅱ: Topical Studies in Oceanography , 156 :4-18..

BarlettMA,LeffLG.2010.TheeffectsofN:Pratioandnitrogenformonfourmajorfreshwaterbacterialtaxainbiofilms. Canadian Journal of Microbiology , 56 (1):32-43..

BemanJM,CarolanMT.2013.Deoxygenationaltersbacterialdiversityandcommunitycompositionintheocean'slargestoxygenminimumzone. Nature Communications , 4 :2705..

BiddandaB,OgdahlM,CotnerJ.2001.Dominanceofbacterialmetabolisminoligotrophicrelativetoeutrophicwaters. Limnology and Oceanography , 46 (3):730-739..

BouvierTC,deGiorgioPA.2002.Compositionalchangesinfree-livingbacterialcommunitiesalongasalinitygradientintwotemperateestuaries. Limnology and Oceanography , 47 (2):453-470..

BrinLD,GiblinAE,RichJJ.2014.EnvironmentalcontrolsofanammoxanddenitrificationinSouthernNewEnglandestuarineandshelfsediments. Limnology and Oceanography , 59 (3):851-860..

Brochier-ArmanetC,BoussauB,GribaldoS,ForterreP.2008.Mesophiliccrenarchaeota:proposalforathirdarchaealphylum,theThaumarchaeota. Nature Reviews Microbiology , 6 (3):245-252..

ChaoA,MaM-C,YangMCK.1993.Stoppingrulesandestimationforrecapturedebuggingwithunequalfailurerates. Biometrika , 80 (1):193-201..

ChaoA.1984.Nonparametricestimationofthenumberofclassesinapopulation. Scandinavian Journal of Statistics , 11 (4):265-270..

ChoJCC,GiovannoniSJ.2004.CultivationandgrowthcharacteristicsofadiversegroupofoligotrophicmarineGammaproteobacteria. Applied and Environmental Microbiology , 70 (1):432-440..

ChristnerBC,PriscuJC,AchbergerAM,BarbanteC,CarterSP,ChristiansonK,MichaudAB,MikuckiJA,MitchellAC,SkidmoreML,Vick-MajorsTJ,theWISSARDScienceTeam.2014.AmicrobialecosystembeneaththeWestAntarcticicesheet. Nature , 512 (7514):310-313..

CottrellMT,WaidnerLA,YuLY,KirchmanDL.2005.BacterialdiversityofmetagenomicandPCRlibrariesfromtheDelawareRiver. Environmental Microbiology , 7 (12):1883-1895..

CunliffeM,Upstill-GoddardRC,MurrellJC.2011.Microbiologyofaquaticsurfacemicrolayers. FEMS Microbiology Reviews , 35 (2):233-246..

DongY,ZhaoY,ZhangWY,LiY,ZhouF,LiuCG,WuY,LiuSM,ZhangWC,XiaoT.2014.BacterialdiversityandcommunitystructureintheEastChinaSeaby454sequencingofthe16SrRNAgene. Chinese Journal of Oceanology and Limnology , 32 (3):527-541..

EdgarRC,HaasBJ,ClementeJC,QuinceC,KnightR.2011.UCHIMEimprovessensitivityandspeedofchimeradetection. Bioinformatics , 27 (16):2194-2200..

EdgarRC.2013.UPARSE:highlyaccurateOTUsequencesfrommicrobialampliconreads. Nature Methods , 10 (10):996-998..

FengBW,LiXR,WangJH,HuZY,MengH,XiangLY,QuanZX.2009.BacterialdiversityofwaterandsedimentintheChangjiangestuaryandcoastalareaoftheEastChinaSea. FEMS Microbiology Ecology , 70 (2):236-248..

FreedmanZ,ZakDR.2014.AtmosphericNdepositionincreasesbacteriallaccase-likemulticopperoxidases:implicationsfororganicmatterdecay. Applied and Environmental Microbiology , 80 (14):4460-4468..

GuoXP,LuDP,NiuZS,FengJN,ChenYR,TouFY,LiuM,YangY.2018.BacterialcommunitystructureinresponsetoenvironmentalimpactsintheintertidalsedimentsalongtheYangtzeEstuary,China. Marine Pollution Bulletin , 126 :141-149..

GuoXP,NiuZS,LuDP,FengJN,ChenYR,TouFY,LiuM,YangY.2017.BacterialcommunitystructureintheintertidalbiofilmalongtheYangtzeestuary,China. Marine Pollution Bulletin , 124 (1):314-320..

HaasBJ,GeversD,EarlAM,FeldgardenM,WardDV,GiannoukosG,CiullaD,TabbaaD,HighlanderSK,SodergrenE,MethéB,DeSantisTZ,HumanMicrobiomeConsortium,PetrosinoJF,KnightR,BirrenBW.2011.Chimeric16SrRNAsequenceformationanddetectioninSangerand454-pyrosequencedPCRamplicons. Genome Research , 21 (3):494-504..

HaggertyJM,DinsdaleEA.2017.Distinctbiogeographicalpatternsofmarinebacterialtaxonomyandfunctionalgenes. Global Ecology and Biogeography , 26 (2):177-190..

HanD,HaHK,HwangCY,LeeBY,HurHG,LeeYK.2015.BacterialcommunitiesalongstratifiedwatercolumnsattheChukchiBorderlandinthewesternArcticOcean. Deep Sea Research Part Ⅱ: Topical Studies in Oceanography , 120 :52-60..

HugoniM,DomaizonI,TaibN,Biderre-PetitC,AgoguéH,GalandPE,DebroasD,MaryI.2015.TemporaldynamicsofactiveArchaeainoxygen-depletedzonesoftwodeeplakes. Environmental Microbiology Reports , 7 (2):321-329..

JamiesonRE,HeywoodJL,RogersAD,BillettDSM,PearceDA.2013.Bacterialbiodiversityindeep-seasedimentsfromtworegionsofcontrastingsurfacewaterproductivityneartheCrozetIslands,SouthernOcean. Deep Sea Research Part Ⅰ: Oceanographic Research Papers , 75 :67-77..

KirchmanDL.2016.Growthratesofmicrobesintheoceans. Annual Review of Marine Science , 8 :285-309..

KönnekeM,BernhardAE,delaTorreJR,WalkerCB,WaterburyJB,StahlDA.2005.Isolationofanautotrophicammonia-oxidizingmarinearchaeon. Nature , 437 (7058):543-546..

KönnekeM,LippSJ,HinrichsKU.2012.Carbonisotopefractionationbythemarineammonia-oxidizingarchaeon Nitrosopumilus maritimus . Organic Geochemistry , 48 (7):21-24..

KrishnaKS,RaoDG,RajuLVS,ChaubeyAK,ShcherbakovVS,PilipenkoAI,MurthyIVR.1999.Paleoceneonspreading-axishotspotvolcanismalongtheNinetyeastRidge:aninteractionbetweentheKerguelenhotspotandtheWhartonspreadingcenter. Proceedings of the Indian Academy of Sciences-Earth and Planetary Sciences , 108 (4):255-267..

KruskalJB.1964.Nonmetricmultidimensionalscaling:Anumericalmethod. Psychometrika , 29 (2):115-129..

KumarR,MishraA,JhaB.2019.BacterialcommunitystructureandfunctionaldiversityinsubsurfaceseawaterfromthewesterncoastalecosystemoftheArabianSea,India. Gene , 701 :55-64..

KumarSP,NarvekarJ,NuncioM,GaunsM,SardesaiS.2009.WhatdrivesthebiologicalproductivityofthenorthernIndianOcean? In :WiggertJD,HoodRR,NaqviSWA,BrinkKH,SmithSLeds.IndianOceanBiogeochemicalProcessesandEcologicalVariability,Volume185.Washington:AmericanGeophysicalUnion.

LiJL,LiN,LiFC,ZouT,YuSX,WangYC,QinS,WangGY.2014.SpatialdiversityofbacterioplanktoncommunitiesinsurfacewaterofnorthernSouthChinaSea. PLoS One , 9 (11):e113014..

LiYJ,XuLY.2007.Improvementforunweightedpairgroupmethodwitharithmeticmeananditsapplication. Journal of Beijing University of Technology , 33 (12):1333-1339.(inChinesewithEnglishabstract).

LinXJ,HandleyKM,GilbertJA,KostkaJE.2015.MetabolicpotentialoffattyacidoxidationandanaerobicrespirationbyabundantmembersofThaumarchaeotaandThermoplasmataindeepanoxicpeat. The ISME Journal , 9 (12):2740-2744..

LiuJW,LiuXS,WangM,QiaoYL,ZhengYF,ZhangXH.2015.BacterialandarchaealcommunitiesinsedimentsoftheNorthChinesemarginalseas. Microbial Ecology , 70 (1):105-117..

LiuJW,ZhengYF,LinHY,WangXC,LiM,LiuY,YuM,ZhaoMX,PedentchoukN,Lea-SmithDJ,ToddJD,MagillCR,ZhangWJ,ZhouS,SongDL,ZhongHH,XinY,YuM,TianJW,ZhangXH.2019.Proliferationofhydrocarbon-degradingmicrobesatthebottomoftheMarianaTrench. Microbiome , 7 :47..

Martens-HabbenaW,BerubePM,UrakawaH,delaTorreJR,StahlDA.2009.AmmoniaoxidationkineticsdeterminenicheseparationofnitrifyingArchaeaandBacteria. Nature , 461 (7266):976-979..

MartinM.2011.Cutadaptremovesadaptersequencesfromhigh-throughputsequencingreads. EMBnet. Journal , 17 (1):10-12..

McArthurJV.2013.ProcessesinMicrobialEcologybyDavidL.Kirchman. Quarterly Review of Biology , 88 (2):143-144..

MenezesLD,FernandesGL,MullaAB,MeenaRM,DamareSR.2018.Diversityofculturablesulphur-oxidisingbacteriaintheoxygenminimumzonesofthenorthernIndianOcean. Journal of Marine Systems ,https://doi.org/10.1016/j.jmarsys.2018.05.007.

MichaelL,KrishnaKS.2011.Datingofthe85°ERidge(northeasternIndianOcean)usingmarinemagneticanomalies. Current Science , 100 (9):1314-1322..

MichelsenCF,PedasP,GlaringMA,SchjoerringJK,StougaardP.2013.BacterialdiversityinGreenlandicsoilsasaffectedbypotatocroppingandinorganicversusorganicfertilization. Polar Biology , 37 (1):61-71..

NaqviSWA.2006.OxygendeficiencyintheNorthIndianOcean. Gayana , 70 (S1):53-58..

OffreP,SpangA,SchleperC.2013.Archaeainbiogeochemicalcycles. Annual Review of Microbiology , 67 :437-457..

ParsonsTR,MaitaY,LalliCM.1984.AManualofChemicalandBiologicalMethodsforSeawaterAnalysis.PergamonPress,Oxford,UK.

PaulmierA,Ruiz-PinoD.2009.Oxygenminimumzones(OMZs)inthemodernocean. Progress in Oceanography , 80 (3-4):113-128..

QianG,WangJ,KanJJ,ZhangXD,XiaZQ,ZhangXC,MiaoYY,SunJ.2018.DiversityanddistributionofanammoxbacteriainwatercolumnandsedimentsoftheEasternIndianOcean. International Biodeterioration & Biodegradation , 133 :52-62..

QuastC,PruesseE,YilmazP,GerkenJ,SchweerT,YarzaP,PepliesJ,GlöcknerFO.2012.TheSILVAribosomalRNAgenedatabaseproject:improveddataprocessingandweb-basedtools. Nucleic Acids Research , 41 (D1):D590-D596..

RysgaardS,GludRN,Risgaard-PetersenN,DalsgaardT.2004.Denitrificationandanammoxactivityinarcticmarinesediments. Limnology and Oceanography , 49 (5):1493-1502..

SheikCS,MitchellTW,RizviFZ,RehmanY,FaisalM,HasnainS,McInerneyMJ,KrumholzLR.2012.Exposureofsoilmicrobialcommunitiestochromiumandarsenicalterstheirdiversityandstructure. PLoS One , 7 (6):e40059..

ShulseCN,MaillotB,SmithCR,ChurchMJ.2017.Polymetallicnodules,sediments,anddeepwatersintheequatorialNorthPacificexhibithighlydiverseanddistinctbacterial,archaeal,andmicroeukaryoticcommunities. Microbiology , 6 (2):e00428..

SoginML,MorrisonHG,HuberJA,MarkWelchD,HuseSM,NealPR,ArrietaJM,HerndlGJ.2006.Microbialdiversityinthedeepseaandtheunderexplored"rarebiosphere". Proceedings of the National Academy of Sciences of the United States of America , 103 (32):12115-12120..

StahlDA,delaTorreJR.2012.Physiologyanddiversityofammonia-oxidizingArchaea. Annual Review of Microbiology , 66 :83-101..

TeraharaT,YamadaK,NakayamaJ,IgarashiY,KobayashiT,ImadaC.2016.Bacterialcommunitystructuresofdeepseawaterinvestigatedbymolecularbiologicaltechniques. Gene , 576 (2):696-700..

WilliamsTJ,WilkinsD,LongE,EvansF,DeMaereMZ,RafteryMJ,RicardoC.2013.TheroleofplanktonicFlavobacteriainprocessingalgalorganicmatterincoastalEastAntarcticarevealedusingmetagenomicsandmetaproteomics. Environmental Microbiology , 15 (5):1302-1317..

XieLS,XuL,HeY,ZhangY,WangJH,XuJ.2017.ArchaealdiversityintheeuphoticseawaterataslopeinthenorthernSouthChinaSea. Chinese Journal of Applied & Environmental Biology , 23 (1):22-27.(inChinesewithEnglishabstract).

ZhangLK,KangMY,XuJJ,XuJ,ShuaiYJ,ZhouXJ,YangZH,MaKS.2016.Bacterialandarchaealcommunitiesinthedeep-seasedimentsofinactivehydrothermalventsintheSouthwestIndiaRidge. Scientific Reports , 6 :25982..

ZhengYL,HouLJ,NewellS,LiuM,ZhouJL,ZhaoH,YouLL,ChengXL.2014.Communitydynamicsandactivityofammonia-oxidizingprokaryotesinintertidalsedimentsoftheYangtzeestuary. Applied and Environmental Microbiology , 80 (1):408-419..

Views

Downloads

CSCD

Alert me when the article has been cited

Submit

Tools

Publicity Resources

Description of two new species of Pseudoaliinostoc (Nostocales, Cyanobacteria) from China based on the polyphasic approach

Bacterial community composition in gut content and ambient sediment of two tropical wild sea cucumbers (Holothuria atra and H. leucospilota)

Characterization of microbial communities in sediments of the South Yellow Sea

High-throughput sequencing of 16S rRNA amplicons characterizes gut microbiota shift of juvenile sea cucumber Apostichopus japonicus feeding with three antibiotics

Taxonomic and metabolic shifts in the Coorong bacterial metagenome driven by salinity and external inputs

Related Author

Renhui LI

Gongliang YU

Fangfang CAI

Yue ZHANG

Aimin WANG

Linwen HE

Fei GAO

Peilin WU

Related Institution

School of Life and Environmental Sciences, Wenzhou University

Key Laboratory of Algal Biology, State Key Laboratory of Freshwater Ecology and Biotechnology of China, Institute of Hydrobiology, Chinese Academy of Sciences

Hubei Key Laboratory of Animal Nutrition and Feed Science, Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan Polytechnic University

Ocean College, Hainan University

State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University

Address：Editorial Office of JOL, 88 Haijun Rd. Qingdao, 266000, China
Tel：+86-532-82898754 Email：jol@qdio.ac.cn
Technical support is provided by Beijing Founder electronics co., LTD 京ICP备09064830号-19 京公网安备11010802024621
It is recommended to read the content of this site in Chrome&IE9+. Please switch to extreme mode in browser 360.
Cookies We use cookies to help provide and enhance our service and tailor content. By continuing, you agree to the use of cookies.

⁰