Research Article The Distribution Pattern of Sediment Archaea Community of ... - Semantic Scholar

12 Pages·2016·1.33 MB·English

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;[email protected];[email protected]
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
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