Hindawi Publishing Corporation Archaea Volume 2016, Article ID 9278929, 12 pages http://dx.doi.org/10.1155/2016/9278929 Research Article The Distribution Pattern of Sediment Archaea Community of the Poyang Lake, the Largest Freshwater Lake in China YantianMa,1FangpengLiu,1ZhaoyuKong,1JianhuaYin,1WenboKou,1 LanWu,1andGangGe1,2 1KeyLaboratoryofPoyangLakeEnvironmentandResource,MinistryofEducation,SchoolofLifeSciences, NanchangUniversity,Nanchang330022,China 2CollaborativeInnovationCenterforPoyangLakeBasinGreenDevelopmentandWaterSecurity, NanchangUniversity,Nanchang330031,China CorrespondenceshouldbeaddressedtoLanWu;wl690902@hotmail.comandGangGe;gge@ncu.edu.cn Received26May2016;Revised23July2016;Accepted9August2016 AcademicEditor:WilliamB.Whitman Copyright©2016YantianMaetal.ThisisanopenaccessarticledistributedundertheCreativeCommonsAttributionLicense, whichpermitsunrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalworkisproperlycited. Archaeaplaysanimportantroleintheglobalgeobiochemicalcirculationofvariousenvironments.However,muchlessisknown about the ecological role of archaea in freshwater lake sediments. Thus, investigating the structure and diversity of archaea communityisvitaltounderstandthemetabolicprocessesinfreshwaterlakeecosystems.Inthisstudy,sedimentphysicochemical propertieswerecombinedwiththeresultsfrom16SrRNAclonelibrary-sequencingtoexaminethesedimentarchaeadiversity andtheenvironmentalfactorsdrivingthesedimentarchaeacommunitystructures.SevensiteswerechosenfromPoyangLake, includingtwositesfromthemainlakebodyandfivesitesfromtheinflowriverestuaries.Ourresultsrevealedhighdiversearchaea communityinthesedimentofPoyangLake,includingBathyarchaeota(45.5%),Euryarchaeota(43.1%),Woesearchaeota(3.6%), Pacearchaeota(1.7%),Thaumarchaeota(1.4%),suspendedLokiarchaeota(0.7%),Aigarchaeota(0.2%),andUnclassifiedArchaea (3.8%).Thearchaeacommunitycompositionsdifferedamongsites,andsedimentpropertyhadconsiderableinfluenceonarchaea communitystructuresanddistribution,especiallytotalorganiccarbon(TOC)andmetallead(Pb)(𝑝<0.05).Thisstudyprovides primary profile of sediment archaea distribution in freshwater lakes and helps to deepen our understanding of lake sediment microbes. 1.Introduction Lakesedimentisanactiveplacewithahighabundance of microorganisms, which is subjected to the changes of Asthethirddomainoflife,archaeawasonceconsideredas organicmatterdegradation,resuspension,andredeposition significanthabitantofextremeenvironments,butincreasing of various chemicals [9]. Compared to bacteria, the diver- evidencerevealstheirwidespreadpresenceinvariousnonex- sity and community distribution of sediment archaea have treme environments, including soil, ocean, and freshwaters receivedmuchlessattentioninfreshwaterlakeenvironments. [1].Archaeaisfoundhavinganimportantroleinglobalbio- Few previous studies indicated the variation of archaea geochemicalprocesses,suchasmethanogenesisandmethane communitystructureanddiversitywithseveralfactors,such oxidation[2],sulphatereduction[3],andammoniaoxidation as sediment depth, sampling sites, and contamination [10– [4,5].Infreshwaterenvironments,activearchaeacommunity 12].Archaeacommunityislessinfluencedbyenvironmental is responsible for methane release and nitrogen transfor- factors compared with bacteria [13]; several parameters are mation, especially in benthonic water and sediments [6]. found to affect the distribution of archaea in lake sedi- It is supposed that lacustrine ecosystems contribute nearly ments. The salinity played an important role in controlling 6–16% of the total natural methane emission on a global diversityanddistributionofarchaeainestuarinesediments scale[7].Consequently,theinvestigatingofsedimentarchaea [14, 15], particle sizes and water O2 saturation also shaped communityisvitaltounderstandthemetabolicprocessesin the sediment archaea distribution [16]. However, subject freshwaterlakeecosystems[8]. to the poor culturability and limited isolates of archaea 2 Archaea Table1:PhysicochemicalcharacteristicofsedimentsamplesfromPoyangLakeinthisstudy. 1,2 Longitudeand Waterdepth TOC TN TP Sites AFDM(%) SM(%) pH C:N N:P latitude (m) (g⋅kg−1) (g⋅kg−1) (g⋅kg−1) NP 116∘11󸀠E,29∘12󸀠N 5.5 3.4±0.4b 27.7±2.6a 6.2±0.3a 9.3±0.8a 0.9±0.2a 0.6±0.1a 11.3±1.6a 1.4±0.1a XH 116∘00󸀠E,29∘11󸀠N 1.5 4.8±0.8b 37.1±1.4ab 6.4±0.2a 7.9±0.5a 0.9±0.1a 0.5±0.0a 10.6±1.5a 1.4±0.1a RH 116∘40󸀠E,28∘59󸀠N 3.5 6.0±0.2a 48.2±2.4b 6.5±0.1a 11.9±0.5a 1.1±0.1a 1.0±0.0b 10.2±1.8a 1.5±0.3a SP 116∘16󸀠E,28∘55󸀠N 1.0 6.7±0.6a 35.5±4.8ab 6.5±0.3a 11.2±3.5a 1.0±0.5a 0.5±0.1a 9.5±1.3a 1.6±0.2a FH 116∘09󸀠E,28∘39󸀠N 4.5 4.8±0.6b 33.0±0.9ab 6.0±0.1a 6.6±1.2a 0.4±0.1a 0.4±0.1a 9.7±1.3a 1.5±0.3a XJ 116∘24󸀠E,28∘43󸀠N 1.0 6.5±0.6a 48.1±2.2b 6.3±0.1a 12.3±0.7a 0.9±0.1a 1.0±0.0b 11.1±0.1a 1.2±0.2a GJ 116∘22󸀠E,28∘48󸀠N 11.5 5.1±0.1ab 52.6±8.6b 6.4±0.1a 9.9±0.6a 0.8±0.1a 0.7±0.0a 10.9±0.2a 1.1±0.1a AFDM:ash-freedrymass;SM:sedimentmoisture;TOC:totalorganiccarbon;TN:totalnitrogen;TP:totalphosphorus;C:Nmeanstheratiooftotalorganic carbontonitrogen. 1Allthedatawasshowninthemean±SDformat. 2Thesignificantlydifferentvaluesamongsitesweremarkedwithdifferentletters(ANOVAbasedonTukeytest,𝑝<0.05). members, the taxonomy was obscured in many previous 2.MaterialsandMethods studies.Theconventionalaffiliationofsomearchaeagroups 2.1. Description of Sampling Sites. Both central lake and wasnamedaftertheirenvironmentalcharacteristicsorfind- tributary estuaries are included in this study. Although the ingordersandoftenscatteredseveraldifferentphylogenetic water area of Poyang Lake is very huge, two parts could taxa identified by molecular evolution methods. Moreover, be divided depending on the hydrographic conditions. The investigation on archaea communities in sediments from north part is a water channel with deep and quick current, a number of lakes has not been concerned, and fewer while the south part has vast water area and slow current. studies have been carried out to elucidate the spatial dis- Sevensamplingsiteswereselectedforstudy(Figure1):two tribution and environmental impact of sediment archaea siteswerefromthenorthandsouthcentraldistrictofPoyang communities. Lake,namedNP(NorthPoyangLake)andSP(SouthPoyang As one of the largest freshwater reservoirs of China, Lake),andtheotherfivesiteswerefromtributaryestuaries, Poyang Lake plays a vital role in the regional climate namedXH(XiuRiver),RH(RaoRiver),XJ(XinRiver),FH regulation, ecological keeping, and economic development. (FuRiver),andGJ(GanRiver),respectively.Thecoordinates PoyangLakeisatypicalthroughputlakethatmainlyreceives andwaterdepthoftheseselectedsamplingsitesareshownin water from five tributaries (Gan River, Fu River, Xiu River, Table1. Xin River, and Rao River) and finally flows into Yangtze River.However,thehydrologicalconditionsofPoyangLake 2.2. Sample Collection and Pretreatment. Surface sediment changed dramatically in recent years, and the overall water samples(0–5cm)werecollectedfromselectedsitesofPoyang areas also decreased. Meanwhile, the eutrophication and Lake in May 2014. Three samples were collected at each pollution caused by agriculture, aquiculture, and industrial site under aseptic conditions and put on ice in a con- activities threatened the water safety [17–19]. The inflow tainer and transported to the lab immediately. For each river has made an important contribution to the eutrophi- site,threesamplesweremixedtogetherforhomogenization. cation and contamination of Poyang Lake; among the five Afterwards,samplesweredividedintotwohalves.One-half tributaries, Gan, Xin, and Rao Rivers were polluted by was processed immediately for measurements of sediment industrial plants discharges (copper and phosphate mines physicochemicalparameters;andtheotherhalfwasstoredin in the upstream of Rao and Xin Rivers) and urban wastes sterilepolypropylenetubesat−80∘Cformolecularanalysis. (Nanchang City in the upstream of Gan River) [20]. Many studieshavebeenconductedtoinvestigatethehydrological 2.3.PhysicochemicalAnalyses. ThepHvaluesweremeasured regime,waterqualityandbiodiversityoffishes,birds,plants, using pH meter (Sartorius PB-10, Germany) with 1:2.5 andbacterioplanktoncommunitiesofPoyangLake[21–25]. (wt/vol)ofsedimenttowater.Sedimentmoisture(SM)was Thedistributionofarchaeacommunityanditsecologicalrole obtainedastheweightlossof30gsamplesafter70∘Cbakefor is not well concerned in Poyang Lake. The objective of the 12–24htoachieveaconstantweight.Sedimentash-freedry presentstudyistocharacterizethearchaeacommunitystruc- mass(AFDM)wascalculatedbytheweightlossof5gsamples tureinsedimentsofPoyangLakeandestimatetheinfluence after 4h at 550∘C in a BF51800 muffle furnace (Thermal ofsurfacesedimentpropertiesonthespatialdistributionof Fisher, USA). Sediment samples were timely freeze-dried archaea community. This study was the primary attempt to to detect geochemical characteristics. Total organic carbon unscramblethetotalarchaeacommunityinthePoyangLake (TOC), total nitrogen (TN), and total phosphorus (TP) sediment. contents were, respectively, analyzed by the Walkley-Black Archaea 3 116∘0󳰀0󳰀󳰀E 116∘20󳰀0󳰀󳰀E 116∘40󳰀0󳰀󳰀E 80∘0󳰀0󳰀󳰀E 90∘0󳰀0󳰀󳰀E 110∘0󳰀0󳰀󳰀E 130∘0󳰀0󳰀󳰀E Yangtze River N N N N ∘󳰀󳰀󳰀6000 ∘󳰀󳰀󳰀6000 N 󳰀󳰀󳰀400 JiuJiang ∘󳰀󳰀󳰀5000N ∘󳰀󳰀󳰀5000N 󳰀󳰀󳰀400 ∘9 N N ∘9 2 ∘󳰀󳰀󳰀4000 ∘󳰀󳰀󳰀4000 2 N N Poyang Lake N ∘󳰀󳰀󳰀3000 ∘󳰀󳰀󳰀3000 N N ∘󳰀󳰀󳰀2000 ∘󳰀󳰀󳰀2000 N N 󳰀󳰀0N ∘󳰀󳰀󳰀1000 80∘0󳰀0󳰀󳰀E 90∘0󳰀0󳰀󳰀E 110∘0󳰀0󳰀󳰀E 130∘0󳰀0󳰀󳰀E ∘󳰀󳰀󳰀1000 󳰀󳰀0N 󳰀0 󳰀0 2 2 ∘9 ∘9 2 2 XH NP Xiu River N N 󳰀󳰀0 RH 󳰀󳰀0 󳰀0 󳰀0 ∘9 ∘9 2 2 SP Rao River GJ Gan River Gan River XJ N N 󳰀󳰀0 Fu River Xin River 󳰀󳰀0 󳰀0 󳰀0 ∘84 Nan Chang FH ∘84 2 2 116∘0󳰀0󳰀󳰀E 116∘20󳰀0󳰀󳰀E 116∘40󳰀0󳰀󳰀E Figure1:LocationofsamplingsitesinPoyangLakeanditstributaries. wetoxidationprocedure,themicro-Kjeldahlmethod,andthe Isolation Kit (MoBio, USA) following the manufacturer’s phosphomolybdicacidbluecolormethod[26].Theconcen- instructions. The obtained DNA was used as templates trations of heavy metals including copper (Cu), zinc (Zn), to amplify archaeal 16S rRNA genes using a universal 󸀠 lead(Pb),andcadmium(Cd)werequantifiedbymicrowave primerset,thatis,Arch109F(5-ACKGCTCAGTAACACGT- 󸀠 󸀠 󸀠 digestionmethod.Briefly,0.5gofsievedanddriedsediment 3 )andArch915R(5 -GTGCTCCCCCGCCAATTCCTT-3 ) wasaddedin9mLconcentratednitricacidplus3mLconcen- [27]. The PCR reaction mixture (25𝜇L) consisted of 1 unit ∘ tratedhydrochloricacidat175 Cfor10min(USEPA2007). of Taq polymerase (Tiangen Co., Beijing, China), 0.16mM Aftercooling,theextractswerecentrifugedat3,000rpmfor ofdNTPs,2.5𝜇Lof10xPCRbuffer,3mMofMgCl2,0.1𝜇M 5min; supernatant was analyzed using an AA800 atomic of each primer, and 2.5𝜇L (approximately 10ng) of DNA absorptionspectrophotometer(PerkinElmer). template.ThePCRamplificationprogramincludedaninitial ∘ ∘ denaturation at 95 C for 5min, 30 cycles of 95 C for 1min, ∘ ∘ 2.4. Microbiological Analyses. Genomic DNA was extracted annealing at 56 C for 1min, extension at 72 C for 1.5min, from0.5gsediment(wet-weight)usingaPowerSoil(cid:2)DNA and a final extension for 10min at 72∘C. PCR amplicons 4 Archaea Table2:Summarystatisticsofarchaeaphylogeneticdiversityinthisstudy. NumberofOTUs Numberofclones Dominance Shannonindex Simpsonindex Evenness Coverage Chao1 ACE NP 13 23 0.12 2.34 0.88 0.80 0.61 23.50 28.31 XH 30 56 0.06 3.15 0.94 0.77 0.66 62.67 100.76 RH 33 66 0.06 3.19 0.94 0.73 0.68 88.00 137.42 SP 46 66 0.04 3.59 0.96 0.78 0.44 179.00 402.13 FH 56 90 0.04 3.74 0.96 0.75 0.53 116.57 299.74 XJ 34 62 0.05 3.24 0.95 0.75 0.63 70.50 141.78 GJ 46 59 0.03 3.69 0.97 0.87 0.34 163.17 162.00 were checked by electrophoresis in 1% agarose gels and the program for Windows 5.0. A heatmap was produced in R lengthofamplicons(about800bp)wasconfirmed.ThePCR project(R-3.0.2)withthe“heatmap”package.Furthermore, amplicons were finally purified using a Gel Extraction Kit Pearson coefficient correlations between the major archaea (TiangenCo.,Beijing,China). taxa,diverseindices,andsedimentvariableswerecalculated ThepurifiedPCRampliconswereusedforclonelibrary usingSPSS19.0. constructionusingapMD18-TVectorSystem(Takara,Japan) followingthemanufacturer’sprotocol.Theligationproducts were subsequently transformed into Escherichia coli DH5𝛼 3.Result cells,whichallowedforblue–whitescreening.Transformants 3.1. Sediment Physicochemical Characteristics. The physic- were plated on LB medium containing ampicillin (100mg −1 −1 −1 ochemical properties of sediment samples from Poyang mL ), X-Gal (20mgmL ) and IPTG (200mgmL ). Lake were heterogeneous among sites. The most obvious Positive clones were confirmed by PCR amplification with 󸀠 difference was revealed by AFDM (ash-free dry mass), SM primers M13-47 (5 -CGCCAGGGTTTTCCCAGTCAC- 󸀠 󸀠 (sediment moisture), and TP (total phosphorus) (ANOVA, GAC-3 ) and RV-M (5 -GAGCGGATAACAATTTCA- 󸀠 𝑝 < 0.05), while other parameters including TOC (total CACAGG-3 ). The screened positive clones were used for organiccarbon),TN(totalnitrogen),pH,andC:NandN:P sequencingbyBeijingGenomicsInstitution(BGI). weresimilaramongsites(Table1).Notably,siteNPhadthe The obtained raw sequences were analyzed using lowestvaluesoftheseparametersanddifferedobviouslywith Bellerophon(http://comp-bio.anu.edu.au/bellerophon/belle- sitesRHandXJ. rophon.pl)toremovechimericsequences.Then,theremain- Compared with the regional background values of ing sequences were clustered into operational taxonomic Poyang Lake [30], higher contents of four metals were units(OTUs)at3%divergenceimplementedintheMothur revealedbythisstudy.ThecontentofZnfromallsevensites software package v1.36.1 [28]. Then, the representative remarkablyexceededthebackgroundvalue,andPbcontent sequences were queried using Blast program (http://blast from most sites also exceeded the background value except .ncbi.nlm.nih.gov/Blast.cgi) in NCBI (National Center for forsitesNPandGJ.TheprofileofCuandCdcontentsamong Biotechnology Information) and Classifier (http://rdp.cme siteswassimilar,andthesignificantlyhighervaluesoccurred .msu.edu/classifier/classifier.jsp) in RDB (Ribosomal Data- in sites RH, XJ, and GJ (Figure 2). These results suggested base Project). The most similar sequences were extracted potentialmetalpollutionintheregionofPoyangLake. from the GeneBank database. The phylogenetic neighbor- joining tree, including the obtained sequences and their closestrelatives,wereconstructedusingtheMEGAsoftware 3.2. Diversity of Archaea Community. In this study, seven 5.0(http://www.megasoftware.net/)[29]. clone libraries of archaea 16S rRNA gene from sediments The recovered 16S rRNA sequences were deposited into of Poyang Lake were constructed and characterized. The the EMBL (European Nucleotide Archive) database under obtained422cloneswereconductedforsequencing,andthen accessionnumbersLN896486–LN896691. theresultingsequenceswereclusteredinto206OTUsusinga 97% sequence similarity cutoff. The OTU numbers of each 2.5. Statistical Analyses. Differences of sediment environ- clonelibraryvariedfrom13to56,andpositiveclonesvaried mental variables among sampling sites were assessed using from 23 to 90. Shannon and Simpson index showed high one-way ANOVA by SPSS 19.0 software package. The level archaea diversity in all samples, except for Site 1 (Table 2). of statistical significance was reported when 𝑝 < 0.05. To The Coverage, Chao 1, and ACE values all demonstrated construct rarefaction curves and calculate diversity indices, the underestimated archaea diversity (Table 2). However, sequenceswereclusteredintoOTUsat3%divergenceusing both dominance and evenness showed diverse and stable theMothurprogram.TheLIBSHUFFcomparisonsofdiffer- structuresofarchaeacommunityfromsedimentsamples. entclonelibrarieswerealsoconductedinMothur.Toinves- AllOTUscouldbeaffiliatedtosevenphylaandanUnclas- tigate relationships between sediment archaea community sified Archaea. The seven phyla included Bathyarchaeota and environmental variables, redundancy analysis (RDA) (45.5%), Euryarchaeota (43.1%), Woesearchaeota (3.6%), with Monte Carlo tests was carried out using the Canoco Pacearchaeota (1.7%), Thaumarchaeota (1.4%), suspended Archaea 5 450 5 b b 360 4 b b b ) 270 b 3 −1·gg −1g) 𝜇Zn ( 180 a a a a 𝜇·d (g 2 C 90 1 a a a a 0 0 NP XH RH SP FH XJ GJ NP XH RH SP FH XJ GJ Sites Sites 125 b 200 100 a b 150 a −1𝜇·gCu (g) 100 b −1𝜇·gPb (g) 5705 a a a a 50 a 25 a a a a 0 0 NP XH RH SP FH XJ GJ NP XH RH SP FH XJ GJ Sites Sites Figure2:ThemetalcontentsofZn,Cd,Cu,andPbamongdifferentsites.Thedottedlinesstandfortheenvironmentalbackgroundvalues ofPoyangLake.Thedifferentletters“a”and“b”inthisfiguremeansignificantdifference(𝑝<0.05). Table3:∫-LIBSHUFFcomparisonsofclonelibrariesconstructedinthisstudy. NP XH RH SP FH XJ GJ NP 0.0235 0.0071 0.0024 0.0406 0.0057 0.0074 XH 0.0625 0.0410 0.0137 0.0077 0.0364 0.0101 RH 0.0195 0.0247 0.0132 0.0238 0.0091 0.0084 SP 0.0096 0.0098 0.0082 0.0344 0.0063 0.0029 FH 0.0597 0.0123 0.0366 0.0146 0.0409 0.0157 XJ 0.0057 0.0251 0.0037 0.0019 0.0161 0.0016 GJ 0.0090 0.0061 0.0025 0.0019 0.0161 0.0014 Withanexperiment-wiseerrorrateof0.05,thelibrarieswereconsideredsignificantlydifferent(markedinbold)ifeitherofthetwo𝑝valuesgeneratedforan individualpairwisecomparisonwaslowerthan0.007. Lokiarchaeota(0.7%),andAigarchaeota(0.2%).TheUnclas- could be deeply divided into six orders, Methanomicro- sifiedArchaeastillrepresented3.8%oftotalclones(Figure3). biales (20.4%), Methanosarcinales (16.6%), Thermoplas- The phylum Bathyarchaeota mainly had three topological matales (3.1%), Methanocellales (1.7%), Methanobacteriales different clusters, including (Miscellaneous Crenarchaeotal (1.2%), and Halobacteriales (0.2%) were all included (Fig- Group,MCG)MCG-1(21.6%),MCG-2(20.9%),andMCG- ure3). 3 (3.1%). Some previously described groups were included, such as MCG group 5b, group 8, group 4, group 11, group 3.3. Distribution of Archaea Community. The sediment 5a, and group 15 (Figure 3). The phylum Euryarchaeota archaea community showed diverse distribution patterns 6 Archaea 99A625 [LN896520] KC926305.1 Uncultured archaeon Arch_M2_22 87 A759 [LN896579] 92 KC926108.1 Uncultured archaeon Arch_J1_27 FN432650.1 Uncultured archaeon LBatata_rib_14 A1024 [LN896667] 99KM463057.1 Uncultured archaeon RICE_18 EU681927 Uncultured archaeon SMTZArch9 HM998444 Uncultured archaeon M2-1Ar03 99A855 [LN896607] KC926407.1 Uncultured archaeon Arch_M1_61 A739 [LN896566] 99 A1059 [LN896545] 98AM503290.1 Uncultured archaeon LL_ADT_34 99 A995 [LN896660] FJ479781.1 Uncultured archaeon clone 8–10 A1011 [LN896663] MCG-Cluster 1 (91) A1019 [LN896665] 88 EF680201.1 Uncultured archaeon MidArch53 A1062 [LN896673] 78 A664 [LN896534] 99KM463018.1 Uncultured archaeon clone MAIZE_10 69 KC661717 Uncultured crenarchaeote clone BC-M-Sd-S1-G8 FN424304 Uncultured archaeon clone 12CSRZ-A20 72 92JFA718097705 [2L.1N U89n6cu68lt6u]red crenarchaeote clone EP091-2.41 A716 [LN896558] 68 A1030 [LN896670] 86 GAU911315 4[L92N.18 9U6n6c3u9l]tured crenarchaeote clone Pav-sed-512 MBaCthGyarchaeota MCG group 5b (15) A808 [LN896593] JF309328.1 Uncultured archaeon clone Sapric2 79 MCG-group 8 (3) 99 MCG group 4 (5) 91 A863 [LN896622] KC926357.1 Uncultured archaeon Arch_M1_04 92 AB161334.1 Uncultured archaeon clone:ASC33 A980 [LN896654] 67 JF431831.1 Uncultured archaeon clone 45-10-T32 MCG group 11 (12) 66A8A181815 [ L[LNN889966662360]] MCG-Cluster 2 (88) 97 A891 [LN896632] AM076831.1 Uncultured archaeon clone B10 84A8108 [LN896604] JX576139.1 Uncultured archaeon clone g18-3 A840 [LN896609] 82 JF431870.1 Uncultured archaeon clone 15-10-C17 64 AA886811 [[LLNN889966662208]] 97KC926412.1 Uncultured archaeon Arch_M1_66 HM244281.1 Uncultured archaeon HWA5257-3-26 A824 [LN896599] MCG group 5a (2) MCG-Cluster 3 (13) MCG group 15 (11) 99 A873 [LN896600] AB301872.1 Uncultured crenarchaeote A873 77 A899 [LN896634] A884 [LN896621] A749 [LN896572] Unclassified archaea group 1 80 A709 [LN896554] 99 A715 [LN896557] 77 GU257282.1 Uncultured crenarchaeote A749 JX984865.1 Uncultured archaeon A884 67 A764 [LN896583] 99 HM187496.1 Uncultured archaeon A764 A846 [LN896615] 20.38% 16.59% 99HQ614230.1 Uncultured soil archaeon A846 A1029 [LN896669] Unclassified archaea group 2 99 KP308663.1 Uncultured archaeon A1029 A535 [LN896515] 3.55% 99 GU135484.1 Uncultured crenarchaeote A535 3.08% 99 Aigarchaeota (1) 1.66% 98 Thaumarchaeota (6) 1.66% DQ300334.1 Uncultured archaeon A812 Suspected Lokiarchaeota (3) A539 [LN896518] Unclassified archaea group 3 1.42% X90479 Sulfolobus metallicus 01..7118%% 9395 M21087N PRy 0ro4d4i6c8ti3u Thm eorcmcuoltpurmote us tenax strain Kra 1 4.003.2%4% 98 M36474 Desulfurococcus mobilisl 91 X99560 Staphylothermus marinus 45.5% Methanobacteriales (5) NR 042736 Thermococcus celer Bathyarchaeota Methanocellales Methanomassiliicoccales (13) 64 97 Woesearchaeota (15) Methanomicrobiales Thaumarchaeota 81 A305 [LN8964P8a8ce]archaeota (7) Methanosarcinales Methanobacteriales A556 [LN896552] Unclassified archaea group 4 Woesearchaeota Lokiarchaeota A99983 [LNA8Y9569625469]1.1 UUnncculalstsuirfieedd a arrcchhaaeeoan g Aro5u5p6 5 Thermoplasmata Aigarchaeota Pacearchaeota Unclassified Archaea Methanosarcinales (70) Halobacteriales (1) 90 Methanocellales (7) Methanomicrobiales (86) M83548.2 Aquifex pyrophilus 0.05 Figure 3: Neighbor-joining phylogenetic trees of archaeal 16S rRNA gene sequences derived from Poyang Lake sediments. Bootstrap values greater than 50% of 1000 resamplings are shown near the nodes. Numbers in parentheses indicate the number of sequences affiliatedtothebranches(adetailedphylogenetictreewasavailableinsupportingmaterialsinSupplementaryMaterialavailableonlineat http://dx.doi.org/10.1155/2016/9278929).Themaincompositionofthewholearchaealcommunitywasalsoshowninthepiechart. Archaea 7 1.0 Pb XJ RH TOC Methanomicrobiales Thermoplasmata Methanosarcinales Methanomicrobiales MCG-2 MCG-1 Methanocellales MCG-1 Thermoplasmata MCG-3 XH SP Unclassified_Archaea 11.26% Pacearchaeota MCG-3 Methanobacteriales MCG-2 Woesearchaeota Woesearchaeota FH Pacearchaeota Methanosarcinales Methanobacteriales Thaumarchaeota Unclassified Archaea Methanocellales GJ Thaumarchaeota NP Lokiarchaeota −1.0 Aigarchaeota −1.0 61.69% 1.0 Halobacteriales XH FH NP SP XJ RH GJ Fdiimguernesio5n:sThofethReDaArchoaredaindaitsitorinbuptliootns(fsoormteherafirersgtrotwupospwreinrecinpoatl included(clones<5))andenvironmentalfactorsamongdifferent 0 1 2 3 4 5 0. 0. 0. 0. 0. sites. Figure 4: The heatmap profile showing the sediment archaea communitycompositionsfromsevensamplingsitesofPoyangLake. negatively correlated to the levels of metal Pb (𝑝 < 0.05). The ACE values of archaea community showed remarkable among seven sampling sites. Based on the analysis of ∫- negative correlations to the ratio of C:N (𝑝 < 0.01). LIBSHUFF,allsitescouldbedividedintotwogroupsdueto The distribution of Bathyarchaeota was positively affected their archaea community structures; XH and FH were one by several factors, including AFDM, TOC, TP, and Cu. group,andallothersiteswereanothergroup(Table3).Based The distribution of Methanomicrobiales illustrated highly on the heatmap analysis of archaea community on order significant correlations with TOC, TP, Cu, and Cd, while levelaffiliation,allsamplingsitescouldbedividedintothree PacearchaeotaillustratedpositivecorrelationswithC:N.The groups:sitesXHandFHfromXiuRiverandFuRiverwere distributionpatternofUnclassifiedArchaeashowednegative onegroup;sitesNPandSPfromnorthandsouthcentrallake correlationwithTP,Cu,andZn. constitutedagroup;sitesRH,XJ,andGJfromRaoRiver,Xin The confined influence was confirmed by the RDA River,andGanRiverwereonegroup(Figure4). results,althoughthephysicochemicalfactorsinthefirsttwo SitesXHandFHwerebothdominatedbyMCG-2(46.4% RDA axes, respectively, explained 61.69% and 11.26% of the and51.1%)andMCG-1(16.1%and25.6%)ofBathyarchaeota. total variance in sediment archaea composition (Figure 5). MCG-3ofBathyarchaeotaalsohadaquitelargeproportion However,onlyTOCandPbpassedthesignificancetests(𝑝< in site XH (10.7%), but only a small proportion in site 0.05).ThearchaeacommunitydistributioninXHandFHwas FH (3.3%). For sites NP and SP from the central lake, the obviouslydifferentthanothersites,andlowcontentofTOC mostabundantarchaeabothbelongedtoMethanosarcinales wasthemaincause.TheRDAresultsalsoexhibitedextensive (52.2%and37.9%)andMethanomicrobialesofEuryarchaeota influenceofPbonthearchaeacommunitydistributionofXH, (30.4% and 19.7%). Although the taxa MCG-1 and MCG- RH,andXJ. 2 also had considerable proportions in site SP (10.6% and 15.2%),onlyasmallpercentagewasfoundinsiteNP(4.4% 4.Discussion and 0). The archaea community from sites RH, XJ, and GJ were consistently dominated by MCG-1 (34.9%, 19.4%, and Aquaticsedimentsareimportantsitesformattertransforma- 27.6%),Methanomicrobiales(25.8%,50.0%,and18.6%),and tionandenergymetabolisms.Therefore,informationonthe Methanosarcinales(15.2%,14.5%,and22.0%),andtheirtotal microbialcommunitycompositionisofvitalimportancefor coverageshiftedbetween68.3%and83.9%(Figure4). better understanding of the metabolic processes in aquatic ecosystems. Up to now, the archaea community found in 3.4. Influential Factors on Archaea Communities. Pearson’s freshwater lake sediments was not so diverse as bacterial correlationcoefficientswereusedtoinvestigatethecorrela- community. Phylogenetic analysis of the sediment archaea tionsbetweenthelakesedimentpropertiesandthearchaea 16S rRNA gene libraries revealed high diversity in Poyang communities(Table4).However,onlyafewdatadramatically Lake, and the majority of archaea community belonged correlated with others. The sediment archaea community to common groups of river and lake sediments. Similar evenness was positively correlated to the water depth but to previous reports, the most frequently found archaea 8 Archaea Cd−1𝜇⋅gg)0.7170.4920.4290.258−0.1940.7140.620−0.1380.035∗0.7650.2800.476−0.0030.213∗∗0.882 ( − roperties. Pb−1𝜇⋅(gg)0.1210.013−0.005∗−0.8220.1650.671−0.324−0.725−0.0620.081−0.370−0.1630.644−0.461−0.171 p al c ntchemi Zn−1𝜇⋅(gg)0.5030.5380.580−0.065−0.1720.6650.315−0.0290.1920.4790.4020.3550.3960.003∗∗−0.936 e m di pthandse Cu−1𝜇⋅)(gg0.5330.3260.293−0.201−0.274∗0.8340.484−0.2440.042∗∗0.8560.2410.1860.285−0.150∗∗−0.869 e d water pH 0.4420.6610.7280.1310.0760.373−0.1320.5620.6240.353−0.079−0.3380.5480.148−0.387 h <5))wit N:P −0.589−0.289−0.147−0.4950.554−0.104−0.4380.1670.317−0.408−0.205−0.1350.238−0.4750.492 s e n ed(clo C:N 0.040−0.163−0.2390.362∗∗0.887−0.108∗0.855−0.169−0.5100.2770.636−0.308−0.0890.019−0.481 d − u cl n werenoti TP−1⋅(gkg)0.2760.1240.128−0.238−0.342∗0.8220.593−0.024−0.040∗0.7990.5060.0050.313−0.350∗∗−0.904 s p u meraregro TN−1⋅(gkg)0.0880.2910.395−0.064−0.0220.3950.1740.4120.4570.4950.376−0.3830.516−0.234−0.545 vel. o le munities(s TOC−1⋅(gkg)0.3280.3110.371−0.045−0.011∗0.7710.4520.3490.551∗0.7980.352−0.0830.125−0.218−0.716 ntatthe0.01 m a c robialco SM ∗∗0.881∗0.7580.7010.435−0.090−0.2300.308−0.3210.1370.6020.0250.5770.2060.409∗−0.807 nissignifi analysisofmic Waterdepth(m)0.3550.3660.323∗0.778−0.276−0.3350.3340.158−0.243−0.2890.3200.747−0.4080.719−0.267∗∗vel;correlatio 4:Statistical AFDM 0.5280.4800.499−0.2120.538∗0.833−0.166−0.2090.7280.321−0.4180.0800.171−0.060−0.268 ntatthe0.05le Table Pearsoncorrelation TaxaSShannonSimpsonEvennessACEBathyarchaeotaPacearchaeotaMethanosarcinalesMethanocellalesMethanomicrobialesMethanobacterialesWoesearchaeotaThermoplasmataThaumarchaeotaUnclassifiedarchaea∗Correlationissignifica Archaea 9 of this study was composed of Bathyarchaeota (MCG), [45, 46]. This point was also validated in this study where Thaumarchaeota, Methanosarcinales, Methanomicrobiales, the abundance of Methanomicrobiales was positively cor- Methanobacteriales, and Thermoplasmatales [31]. The sed- related with TOC content. Moreover, Methanomicrobiales iment archaea community from 13 plateau freshwater lakes and Methanobacteriales can use H2/CO2 as a substrate for comprised16classifiedphylaandclasses;MCGandThermo- methanogenesis,whileMethanosarcinalescanutilizeanum- plasmata were the most predominant groups [13]. Liu et al. berofdifferentsubstrates(e.g.,H2/CO2,methylcompounds, reportedthesedimentarchaeacommunityfromLakeTaihu and acetate) [47]. Thus, the abundance of Methanosarcina, with DGGE-sequencing method and found that most of Methanobacteriales, and Methanomicrobiales in this study archaealsequenceswereaffiliatedwithMethanosarcinaceae may suggest that their growth substrate was not limited, and Methanocorpusculaceae, while a small proportion was andtheelevationoforganiccarbonfromeutrophicationor affiliatedwithCrenarchaeota[32].InsedimentsofLakeKivu terrestrial organic carbon influx may change methanogen andLakeBled,Methanobacteriales,Methanosarcinales,and abundanceaswellasCH4productionrates[48]. Thermoplasmata all played a big part in the whole archaea The sediment properties (AFDM, SM, TP, Cu, and Cd) community;CrenarchaeotaandThaumarchaeotacollectively fromRH,XJ,andGJweresignificantlyhigherthanothersites take a small proportion compared with Euryarchaeota [33, (Figure 4); meanwhile, the archaea community structures 34]. fromthesethreesitesweresimilar.MCG-1,Methanomicro- Our study revealed spatial heterogeneity of archaea biales, and Methanosarcinales were the most predominant community in the sediment of Poyang Lake. The archaea archaeagroupsinthesethreesites,Thermoplasmatalesalso community structure of XH and FH was different than showedpreferenceinXJ,GJ,andRH,andThaumarchaeota that from other sites, which were dominated by MCG-2 wasmainlydistributedinGJ.MCG-1,Methanomicrobiales, and MCG-1 of Bathyarchaeota (Figure 5). Bathyarchaeota and Methanosarcinales all have a wide habitat in various (MCG)comprisedalargenumberofphylotypesfromanoxic waterenvironments.Thermoplasmataleswasoftenrelatedto environments and can be divided up to 17 subgroups [35]. methanogenic activities [49, 50] and was timely found in The broad range of habitats was an obvious feature for freshwater lake sediment [33, 51]. Thermoplasmatales has a Bathyarchaeotamembers,andthispointmaybethereason notableproportioninthePoyangLakesedimentofthisstudy, fortheirdominatinginmanyenvironments.Bathyarchaeota which might emphasis the active methanogenesis. The new was believed to have an organic heterotrophic lifestyle and genomereadingofThermoplasmatalescellshasrevealedthe can degrade buried organic carbon and detrital proteins genes that encode extracellular protein-degrading enzymes in subsurface sediments [36, 37]. This point was consistent and which could enable them to survive on sedimentary with the observation of this study that the distribution detrital proteins [37]. Other reports suggested that some of Bathyarchaeota was significantly correlated with AFDM members of the Thermoplasmatales may represent a new and TOC. Bathyarchaeota was also found having methyl- order of methanogens that can utilize methylamine [52, coenzyme M reductase (MCR) complex and involved in 53].TherecentlyproposedphylumThaumarchaeotainlake methanemetabolismrecentlyandwastheonlygroupoutside sedimentarchaeacommunityhasbeensporadicallyreported the phylum Euryarchaeota for methane metabolism [38]. [54–56]. The presence of Thaumarchaeota in this study Other groups like Aigarchaeota, suspended Lokiarchaeota, mainly contained Nitrososphaerales (previously Thaumar- and Unclassified Archaea also have higher proportions in chaea Soil Group I.1b) and Nitrosopumilales (previously sites XH and FH. As the most presently proposed phyla, MGI, Thaumarchaea Marine Group I.1a), which demon- Aigarchaeota and suspended Lokiarchaeota may both be stratedtheactiveammoxidationinsedimentofPoyangLake, involved in anaerobic carbon cycling [39]. Pacearchaeota andarchaeacommunityhasanimportantroleintheglobal and Woesearchaeota were previously reported from saline biogeochemicalnitrogencycle[57]. sediments,butinsurfacewatersofsomelakestheywerealso The sediment microbial community is often affected by detected[40]. sediment properties, and the community composition is ThearchaeacommunityofNPandSPbothfromcentral structured by both nutrient availability and environmental lakes showed similar structures; the most abundant clones pressuresfromsediment. Butmanystudiesshowedoutthat belonged to Methanosarcinales and Methanomicrobiales of sediment archaea community was less affected by environ- Euryarchaeota.MethanosarcinalesandMethanomicrobiales mental factors in comparison to bacterial community [13]. werethemostabundantEuryarchaeotagroupsinfreshwater Still some researchers also reported the variety of sediment sediments,andbothmethanogenicandmethanotrophicphy- archaeacommunitywithenvironmentalvariables.Thecom- lotypes (ANME-2a, 2b) were included [15]. The dominance munity structure of sediment archaea could be influenced ofMethanomicrobialesandMethanosarcinalesinsedimental bypollution[58],sedimentdepth[34,53],andsalinity[59]. archaeacommunityofthisstudywasnotasingleevent,and Archaeacommunitydistributionwasremarkablyaffectedby similar results have also been reported in other freshwater sedimentpropertiesinthisstudy.Thecommunityevenness lakes, such as Lake Biwa [41], Lake Soyang [42], and Lake was affected by both water depth and Pb, while ACE was Dagow [43]. Methanosarcinales and Methanomicrobiales affected by C:N. Water depth may influence the precip- usually draw energy from anaerobic oxidation of methane itation process of sediment and affected many sediment (AOM) and are coupled with bacterial sulphate reduction parameters[34,53],whilethepressureofPbselectedspecial [44]. Thus, the proportion of these orders often increased archaeagroupsandreducedtheevenness.TheeffectofC:N with the necessary sulphate and organic carbon availability reflectedtheshortageofnitrogeninsedimentandrestricted 10 Archaea the archaeal diversity. The contents of TOC and Pb could [7] M.Rahalkar,J.Deutzmann,B.Schink,andI.Bussmann,“Abun- shapethedistributionpatternofarchaeacommunityamong dance and activity of methanotrophic bacteria in littoral and differentsitesofPoyangLake.TheeffectofTOConarchaea profundal sediments of Lake Constance (Germany),” Applied community could be explained by the notion that TOC andEnvironmentalMicrobiology,vol.75,no.1,pp.119–126,2009. affectedtheabundanceofpredominantarchaeagroups,like [8] S. Spring, R. Schulze, J. Overmann, and K.-H. Schleifer, MethanomicrobialesandMethanocellales(Figure5,Table3). “Identificationandcharacterizationofecologicallysignificant The low content of Pb in sites NP and GJ may be also due prokaryotesinthesedimentoffreshwaterlakes:molecularand cultivationstudies,”FEMSMicrobiologyReviews,vol.24,no.5, to the presence of Halobacteriales, which had the capacity pp.573–590,2000. toreducetheconcentrationofPb,Cr,Zn,andNiionsfrom [9] R.G.Wetzel,Limnology:LakeandRiverEcosystems,GulfPro- mediawithhighsalinity[60]. fessionalPublishing,SanDiego,Calif,USA,2001. In conclusion, high diverse archaea community was foundinsedimentsofPoyangLake,andconsiderableinflu- [10] J. Lim, J. Woodward, S. Tulaczyk, P. Christoffersen, and S. P. Cummings, “Analysis of the microbial community and geo- ence was observed on archaea distribution patterns by chemistryofasedimentcorefromGreatSlaveLake,Canada,” TOC and metal Pb. Bathyarchaeota (MCG) and Euryar- AntonieVanLeeuwenhoek,vol.99,no.2,pp.423–430,2011. chaeota (especially Methanomicrobiales and Methanosarci- [11] A.R.Lucheta,X.L.Otero,F.Mac´ıas,andM.R.Lambais,“Bac- nales) were the most dominant phyla in Poyang Lake sedi- terialandarchaealcommunitiesintheacidpitlakesediments ments,buttheirproportionsdifferedamongsamples.Other ofachalcopyritemine,”Extremophiles,vol.17,no.6,pp.941–951, components of archaea community were Woesearchaeota, 2013. Pacearchaeota, Thaumarchaeota, suspended Lokiarchaeota, [12] A.Bhattacharyya,N.S.Majumder,P.Basaketal.,“Diversityand Aigarchaeota,andUnclassifiedArchaea. distribution of archaea in the mangrove sediment of sundar- bans,”Archaea,vol.2015,ArticleID968582,14pages,2015. CompetingInterests [13] J.Zhang,Y.Yang,L.Zhao,Y.Li,S.Xie,andY.Liu,“Distribution of sediment bacterial and archaeal communities in plateau The authors declare that there is no conflict of interests freshwaterlakes,”AppliedMicrobiologyandBiotechnology,vol. regardingthepublicationofthispaper. 99,no.7,pp.3291–3302,2015. [14] A. Baricz, A. Cristea, V. Muntean et al., “Culturable diversity of aerobic halophilic archaea (Fam. Halobacteriaceae) from Acknowledgments hypersaline, meromictic Transylvanian lakes,” Extremophiles, vol.19,no.2,pp.525–537,2015. This work was supported by the National Natural Science [15] G.Webster,L.A.O’Sullivan,Y.Mengetal.,“Archaealcommu- FoundationofChina(no.31060082andno.31260110)andthe nitydiversityandabundancechangesalonganaturalsalinity Open Foundation of MOE Key Laboratory of Poyang Lake gradientinestuarinesediments,”FEMSMicrobiologyEcology, EnvironmentandResource(PYH2015-13). vol.91,no.2,pp.1–18,2015. [16] E.Billard,I.Domaizon,N.Tissot,F.Arnaud,andE.Lyautey, References “Multi-scale phylogenetic heterogeneity of archaea, bacteria, methanogensandmethanotrophsinlakesediments,”Hydrobi- [1] R.Cavicchioli,“Archaea—timelineofthethirddomain,”Nature ologia,vol.751,no.1,pp.159–173,2015. ReviewsMicrobiology,vol.9,no.1,pp.51–61,2011. [17] Q.Zhang,P.Sun,X.Chen,andT.Jiang,“Hydrologicalextremes [2] N.K.Ahila,E.Kannapiran,J.Ravindran,andV.S.Ramkumar, inthePoyangLakebasin,China:changingproperties,causes “Studiesonmethanogenicconsortiaassociatedwithmangrove andimpacts,”HydrologicalProcesses,vol.25,no.20,pp.3121– sedimentsofennore,”JournalofEnvironmentalBiology,vol.35, 3130,2011. no.4,pp.649–654,2014. [18] L. Wu, G. Ge, G. Zhu, S. Gong, S. Li, and J. Wan, “Diversity [3] W.P.Hocking,R.Stokke,I.Roalkvam,andI.H.Steen,“Iden- and composition of the bacterial community of Poyang Lake tificationofkeycomponentsintheenergymetabolismofthe (China)asdeterminedby16SrRNAgenesequenceanalysis,” hyperthermophilic sulfate-reducing archaeon Archaeoglobus WorldJournalofMicrobiologyandBiotechnology,vol.28,no.1, fulgidusbytranscriptomeanalyses,”FrontiersinMicrobiology, pp.233–244,2012. vol.5,article95,2014. [19] L. Zhen, F. Li, H. Huang et al., “Households’ willingness to [4] Y.Liu,J.Zhang,X.Zhang,andS.Xie,“Depth-relatedchanges reducepollutionthreatsinthePoyangLakeregion,southern of sediment ammonia-oxidizing microorganisms in a high- China,”JournalofGeochemicalExploration,vol.110,no.1,pp. altitudefreshwaterwetland,”AppliedMicrobiologyandBiotech- 15–22,2011. nology,vol.98,no.12,pp.5697–5707,2014. [20] G.-L.Yuan,C.Liu,L.Chen,andZ.Yang,“Inputtinghistoryof [5] X.Zhou,Y.Li,J.Zhangetal.,“Diversity,abundanceandcom- heavymetalsintotheinlandlakerecordedinsedimentprofiles: munity structure of ammonia-oxidizing archaea and bacteria PoyangLakeinChina,”JournalofHazardousMaterials,vol.185, in riparian sediment of Zhenjiang ancient canal,” Ecological no.1,pp.336–345,2011. Engineering,vol.90,pp.447–458,2016. [21] P.Sheng,Y.Yu,G.Zhang,J.Huang,L.He,andJ.Ding,“Bacterial [6] Y. Liu, J. Zhang, L. Zhao, Y. Li, Y. Yang, and S. Xie, “Aerobic diversityanddistributioninsevendifferentestuarinesediments and nitrite-dependent methane-oxidizing microorganisms in ofPoyangLake,China,”EnvironmentalEarthSciences,vol.75, sedimentsoffreshwaterlakesontheYunnanPlateau,”Applied article479,2016. Microbiology and Biotechnology, vol. 99, no. 5, pp. 2371–2381, [22] Y.Liang,H.Xiao,X.Liu,J.Xiong,andW.Li,“Spatialandtem- 2015. poral water quality characteristics of Poyang Lake Migratory

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