Bacterial Community Responses to Soils along a Latitudinal and Vegetation Gradient on the Loess ...

17 Pages·2016·3.17 MB·English

RESEARCHARTICLE
Bacterial Community Responses to Soils
along a Latitudinal and Vegetation Gradient
on the Loess Plateau, China
QuanchaoZeng1,YanghongDong1,ShaoshanAn1,2*
1 CollegeofNaturalResourcesandEnvironment,NorthwestA&FUniversity,Yangling,Shaanxi,P.R.China,
2 StateKeyLaboratoryofSoilErosionandDryLandFarmingonLoessPlateau,NorthwestA&FUniversity,
Yangling,Shaanxi,P.R.China
a11111 *[email protected]
Abstract
Soilbacterialcommunitiesplayanimportantroleinnutrientrecyclingandstorageinterres-
trialecosystems.Loesssoilsareoneofthemostimportantsoilresourcesformaintaining
OPENACCESS
thestabilityofvegetationecosystemsandaremainlydistributedinnorthwestChina.Esti-
Citation:ZengQ,DongY,AnS(2016)Bacterial
matingthedistributionsandaffectingfactorsofsoilbacterialcommunitiesassociatedwith
CommunityResponsestoSoilsalongaLatitudinal
andVegetationGradientontheLoessPlateau, varioustypesofvegetationwillinformourunderstandingoftheeffectofvegetationrestora-
China.PLoSONE11(4):e0152894.doi:10.1371/ tionandclimatechangeontheseprocesses.Inthisstudy,wecollectedsoilsamplesfrom
journal.pone.0152894
15sitesfromnorthtosouthontheLoessPlateauofChinathatrepresentdifferentecosys-
Editor:JohnJ.Kelly,LoyolaUniversityChicago, temtypesandanalyzedthedistributionsofsoilbacterialcommunitiesbyhigh-throughput
UNITEDSTATES
454pyrosequencing.Theresultsshowedthatthe142444sequencesweregroupedinto
Received:December22,2015 36816operationaltaxonomicunits(OTUs)basedon97%similarity.Theresultsoftheanal-
Accepted:March21,2016 ysisshowedthatthedominanttaxonomicphylaobservedinallsampleswereActinobac-
teria,Proteobacteria,Chloroflexi,AcidobacteriaandPlanctomycetes.Actinobacteriaand
Published:April5,2016
Proteobacteriawerethetwomostabundantgroupsinallsamples.Therelativeabundance
Copyright:©2016Zengetal.Thisisanopen
ofActinobacteriaincreasedfrom14.73%to40.22%astheecosystemchangedfromforest
accessarticledistributedunderthetermsofthe
CreativeCommonsAttributionLicense,whichpermits tosandy,whiletherelativeabundanceofProteobacteriadecreasedfrom35.35%to
unrestricteduse,distribution,andreproductioninany 21.40%.ActinobacteriaandProteobacteriahadsignificantcorrelationswithmeanannual
medium,providedtheoriginalauthorandsourceare
precipitation(MAP),pH,andsoilmoistureandnutrients.MAPwassignificantlycorrelated
credited.
withsoilchemicalandphysicalproperties.TherelativeabundanceofActinobacteria,Pro-
DataAvailabilityStatement:Allrelevantdataare
teobacteriaandPlanctomycetescorrelatedsignificantlywithMAP,suggestingthatMAP
withinthepaperanditsSupportingInformationfile.
wasakeyfactorthataffectedthesoilbacterialcommunitycomposition.However,along
Funding:ThisstudywassupportedbytheNational
withtheMAPgradient,Chloroflexi,BacteroidetesandCyanobacteriahadnarrowranges
NaturalSciencesFoundationofChina(41171226,
thatdidnotsignificantlyvarywiththesoilandenvironmentalfactors.Overall,weconclude
41101254),theProgramforNewCenturyExcellent
TalentsinUniversity(NCET-12-0479)andthe thattheedaphicpropertiesand/orvegetationtypesaredrivingbacterialcommunitycompo-
DemonstrationofKeyTechnologiesforSoiland sition.MAPwasakeyfactorthataffectsthecompositionofthesoilbacteriaontheLoess
WaterConservationandRestoringandEco-
PlateauofChina.
restructingforDamagedRegionalEcosystemofthe
Shanxi-Shaanxi-InnerMongoliaenergysourcebase
(KZCX2-XB3-13).AllthefundingwereShaoshan
An'sandheconceivedanddesignedthe
experiments.
PLOSONE|DOI:10.1371/journal.pone.0152894 April5,2016 1/17
BacterialCommunityVariedwithVegetationEcosystems
CompetingInterests:Theauthorshavedeclared Introduction
thatnocompetinginterestsexist.
TheLoessPlateauinChinaisoneofthemosterodedareasintheworld.Accordingly,the
“Grain-for-GreenProgram”wasimplementedonalargescalebythecentralgovernment
beginningin1999inwhichvegetationrestorationwasimplementedinthisareatoremediate
thesoildegradationproblem.Bacteriaareadominantgroupofsoilorganisms[1]andplayan
essentialroleinecosystemrecovery[2].Overthepastfewdecades,anincreasingnumberof
researchershavebeeninvestigatingthebacterialdiversityindifferentsoils,particularlyduring
theprocessofvegetationrestoration.Bacteriahavestrongeffectsonsoilprocesses,andman-
agementandlanduseshaveeffectsonthesoilbacterialdiversity[3].However,thereislittle
informationregardingthelong-termeffectsofvegetationrestorationonthesoilbacterialcom-
munitiesontheLoessPlateauinChina.Vegetationtypeshavelargedirectorindirecteffectson
soilcommunitycompositionanddiversity.Theeffectsofalterationsinthevegetationtypeson
thesoilphysicalandchemicalpropertieshavebeenwell-studied.Duetothechangesinplant
speciescomposition,vegetationtypescanhavesignificantandlong-lastingeffectsonsoilcar-
bonandnutrientcontents,soiltexture,andpH[4–6].Theeffectsofthevegetationtypesand
soilpropertiesaffectthegroupsofsoilorganisms[7].
Previousstudieshavefocusedexclusivelyonplantandanimaltaxa,showingthatmacroor-
ganismssuchastreesandanimalsexhibitbiogeographicaldistributions[8].However,itisnot
knownwhetherthemicroorganismssuchasfungiandbacteriavaryalongalatitudinalgradi-
ent.Steganetal.[9]foundthatthemicrobialspecieswerewidelydistributedandthatthe
microbialcommunitycompositionwasgovernedbyecologicalDriftandSelection.Fiereretal.
[10]suggestedthatgeographicdistanceshouldbethebestpredictorofgeneticdivergence
amongcommunities.Liuetal.[11]usedahigh-throughputsequencingmethodtoexplore
thediversityintheblacksoilsinnortheastChina.Theresultssuggestedthatalatitudinaldiver-
sitygradientofthebacterialcommunitiesmightbepresentintheblackagriculturesoilzone.
Sofar,similarstudiesonalargescaleindisturbedecosystemsintheLoessPlateauarestill
limited.
Soilisacomplexenvironment,withinwhichthetypesofmicroorganismsareassociated
withthesoilproperties,latitude,vegetationtypes,andotherfactors.Therefore,understanding
thediversityofsoilmicroorganismsalongalatitudinalgradienthasimportantecologicalsig-
nificance.Thedevelopmentofhigh-throughputsequencingtechnologiessuchas454pyrose-
quencingcurrentlyoffersanopportunitytoeffectivelysequenceDNAfragments,which
substantiallyimprovestheresearcher’sabilitytodetectnon-dominantmicrobialcommunities.
Next-generationsequencingtechnologieshavemadehigh-throughputsequencingeasyand
inexpensivetoimplement[12].
Inthisstudy,weselectedfivevegetationzones(forest,forest-grass,grass,sandanddesert
ecosystems)assubjects,whichrepresentedthevegetationecosystemsfromsouthtonorthin
theLoessPlateau.Ourobjectivesweretodeterminetheeffectsofedaphicpropertiesandsoil
propertiesonthediversityofsoilmicrobialcommunitiesusinghigh-throughput454pyrose-
quencingtechnology.
Ourobjectivesforthisstudywere(i)todeterminetheabundance,taxonomicdiversityand
compositionofthebacterialcommunitiesacrossthe600kmgeodistanceoftheLoessPlateau
inShaanxiprovince;(ii)todirectlycomparethevariabilityinthebacterialcommunitiesacross
this600kmgeodistancewiththevariabilityamongsoilscollectedfromthewiderangeofmean
annualprecipitationfromNorthtoSouth;and(iii)todeterminewhichfactorsmoststrongly
affectthesoilbacterialcommunities.
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BacterialCommunityVariedwithVegetationEcosystems
MaterialsandMethods
Experimentaldesignandsoilsampling
ThisstudywasperformedinYulinCity,JingbianCity,LiandaowanCitiy,AnsaiCityandFux-
0 00 0 00 0 00
ianCityinthenorthernLoessPlateau(108°4140.27 -109°5810 E,36°0337.16 -38°
0 00
559.63 N),China.Theseareasrepentedfivevegetationstagesaftertheimplementationof
“Grain-for-GreenProgram”.Thestudyareasarecharacterizedbyasemi-aridclimateanda
deeplyincisedhilly-gullyLoesslandscape.Theslopesarebetween0°and20°.Sitesstabilized
throughvegetationrestorationfordifferentvegetationecosystemsprovideanidealopportunity
tounderstandvegetationtypesinextremeenvironments.
AsandyecosystemislocatedinthecityofJingbian,andadesertecosystemislocatedinthe
cityofYulin.Thesetworegionshavesimilardominantplantspecies,includingArtemisiaordo-
sica,HedysarumscopariumandHedysarumleaveandotherherbspecies.Thesoilsinthetwo
ecosystemaresandsoilwithlessvegetation,andthesoilsintheforest,forest-grassandgrass
ecosystemsareloess-derived.Intheforestecosystem,Platycladusorientalis,Quercuswutaisha-
nicaandRobiniapseudoacaciapredominate.ThegrassecosystemisdominatedbyArtemisia
giraldii,ArtemisiavestitaandStipabungeana.However,theforest-grassecosystemhastrees,
shrubsandgrasses,includingRobiniapseudoacacia,ArtemisiavestitaandSophora
moorcroftiana.
Alongthelatitudinalgradientfrom36°to39°,themeanannualtemperature(MAT)
decreasesfrom11°Cto8°Candthemeanannualprecipitation(MAP)decreasesfrom560mm
to390mm.Fromsouthtonorth,therewerefivetypesofvegetationecosystems(forest,forest-
grass,grass,sandyanddesertecosystems).Thefieldsitesdonotcontainendangeredorpro-
tectedspeciesanddidnotrequireresearchpermission.
InAugust2013,whenthevegetationcommunitybiomasshadpeaked,15siteswereselected
onthebasisoffivevegetationecosystems(forest,forest-grass,grass,sandyanddesertecosys-
tems).Thesesiteswereseparatedby2to2.5km(Table1andFig1).Ateachsite,wesetupfive
plotsof20m×20m.Plotsinbothsiteswereatleast1000mapart.Ineachplot,fivequadrants
(1m×1m)wereindividuallychosen,oneineachofthefourcornersandoneinthecenterof
Table1. Thedescriptionsofsoilsamplingsites.
Ecosystem Locations MAT MAP Longitude Latitude Altitude Dominantplantspecies
type (°C) (mm) (°) (°) (m)
109.75 38.92 1192 Artemisiaordosica,Hedysarumscoparium,Hedysarumlaeve
Desert Yulin 8.7 390.3 109.65 38.82 1192 Artemisiaordosica,Hedysarumscoparium,Hedysarumlaeve
109.7 38.38 1120 Artemisiaordosica,Hedysarumscoparium,Hedysarumlaeve
108.75 37.65 1333 Artemisiaordosica,Hedysarumscoparium,Hedysarumlaeve
Sandy Jingbian 9.4 412.6 108.69 37.64 1349 Artemisiaordosica,Hedysarumscoparium,Hedysarumlaeve
109.08 37.86 1229 Artemisiaordosica,Hedysarumscoparium,Hedysarumlaeve
108.97 37.24 1463 Artemisiagiraldii,Artemisiavestita
Grass Liandaowan 9.1 499.2 108.99 37.18 1341 Artemisiagiraldii,Artemisiavestitaa
108.97 37.25 1406 Artemisiagiraldii,Artemisiavestita
109.25 36.75 1166 Sophoramoorcroftiana,Artemisiagiraldii
Forest-Grass Ansai 10.3 501.8 109.26 36.75 1153 Robiniapseudoacacia,Artemisiagiraldii
109.31 36.86 1192 Artemisiavestita,Artemisiagiraldii
109.15 36.06 1333 Platycladusorientalis,Artemisiagiraldii
Forest Fuxian 9.5 518.3 109.15 36.06 1327 Quercuswutaishanica,Artemisiagiraldii
109.17 36.08 1193 Robiniapseudoacacia,Artemisiagiraldii
doi:10.1371/journal.pone.0152894.t001
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BacterialCommunityVariedwithVegetationEcosystems
theplot.Soilsamplesweretakenatfivepointsinthequadrantsofeachplot,andsoilsamples
in0–10cmsoillayerwerecollected.Aftercarefullyremovingthesurfaceorganicmaterialsand
fineroots,eachmixedsoilsamplewasdividedintotwoparts.Onepartofthesoilsamplewas
air-driedfortheevaluationofthesoilproperties.Theotherpartwasfrozenat-80°C(liquid
nitrogen)forsubsequenthigh-throughput454pyrosequencinganalysis.Thecollectedsamples
wereanalyzedforphysicochemicalpropertiesorusedforDNAextraction.
Selectedsoilproperties
ThesoilpHwasdeterminedontheair-driedsamples(sievedto1mm)usingaglasselectrode
meterinasuspensionof1:2.5soil/waterratio(w/v).Soilmoisturewasdeterminedgravimetri-
callyinfreshsoilsat105°Covernight,andthewatercontentwasexpressedasapercentageof
thedryweight.Thesoilbulkdensity(BD)wasdeterminedusingtheauger-holemethod[13].
Thefumigation-extractionmethodwasusedtodeterminethesoilmicrobialbiomass(MBC)
[14].Theorganicmatter(SOM)contentwasanalyzedusingdichromateoxidation[15].Total
N(TN)wasmeasuredusingtheKjeldahlmethod[16].Totalphosphorus(TP)wasmeasured
spectrophotometricallyafterwetdigestionwithH SO andHClO [17].AvailableP(AP)was
2 4 4
extractedusingtheOlsenbicarbonatemethod.NH +-N(AN)andNO −-N(NN)weremea-
4 3
suredusingaSealAutoAnalyzer3.
DNAextractionandsequencingPCR
SoilDNAwasextractedfrom0.5gofthemixedsoilsamplesusingaSoilDNAkit(OMEGA,
Bio-Tek,GA,USA)accordingtothemanufacturer’sinstructions.Analiquotoftheextracted
DNAfromeachsamplewasusedasatemplateforamplification.TheV1-V3hypervariable
regionsofthebacterial16SrRNAgenewereamplifiedwithprimers27F(50-AGAGTTTG
ATCCTGGCTCAG-30)and533R(50-TTACCGCGGCTGCTGGCAC-30)containingtheA
andBsequencingadapters(454LifeSciences)[11].
The20μlPCRreactionsystemcontained4μl5×FastPfuBuffer,2.5μlmMdNTPs,0.8μl
forwardandreverseprimers(5μM),0.4μlFastPfupolymerase(TransStartFastpfuDNAPoly-
merase,TransGen)and10ngofthetemplateDNA.ThePCRamplificationwasperformed
usinganABIGeneAmp9700instrument.ThePCRconditionsusedfortheamplificationof
the16SrRNAgenewereasfollows:2minat95°C;25cyclesof30secondsat95°Cfordenatur-
ation,30secondsat55°Cforannealingand30secondsat72°Cforextension;and5minat
72°C.Foreachsample,20parallelPCRs(includingtwonegativecontrolreactions)wereper-
formed,andthePCRproductswereevaluatedbyanalyzing2μloftheproductona2%agarose
gel.Next,allofthePCRproductsfromthesamesamplewerepooled,andPCRproductsofan
approximatesizeof400bpwerepurifiedusingaPCRPurificationkit(AxygenBio,USA).
AfterpurificationandquantificationusingQuantiFluor™-ST(Promega,U.S.),amixtureofthe
amplifiedproductswasusedforpyrosequencingonaRoche454GSFLX+Titaniumplatform
(Roche454LifeSciences,Branford,CT,U.S.)accordingtostandardprotocols[18].Pyrose-
quencingwascarriedoutona454LifeSciencesGenomeSequenceFLX(Roche)attheShang-
haiMajorbioBioPharmTechnologyCo.,Ltd.,Shanghai,China.
Statisticalandbioinformaticsanalysis
Severalstatisticalanalyseswereperformedseparatelyonthesoilpropertydatasetsusingthe
statisticalpackageforthesocialsciences(SPSSversion20.0forWindows),includingone-way
ANOVAandS-K-Nmultiplerangecomparison(P=0.05).Therelationshipsbetweensoilbac-
terialcompositionandtheenvironmentalfactorsweretestedusinglinearregressionanalyses
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BacterialCommunityVariedwithVegetationEcosystems
Fig1.Thedescriptionsofsoilsamplesites.
doi:10.1371/journal.pone.0152894.g001
usingSPSS20.0forWindows.Therelationshipsbetweenthesoilbacterialcompositionand
propertieswereevaluatedusingR.
TheresultingsequenceswereprocessedusingMothursoftware[19].Briefly,therawreads
werefirstassignedtosamplesaccordingtotheirtagsandthenthestandardprimersandbar-
codesweretrimmedoff,afterwhichreadswithlengthlessthan200bporwithambiguous
characterswereremoved.Thechimericsequenceswerealsoexcludedbythechimera.uchime
commandwithdefaultparameters.Afterremovingthebarcodeandprimersequences,the
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uniquesequenceswerealignedagainstthereferencesequencedatabase(Silvadatabase).The
remainingreadswerepre-clustered(http://www.mothur.org/wiki/Pre.cluster)andthenclus-
teredusinguncorrectedpairwisealgorithm.Inaddition,Operationaltaxonomicunits(OTUs)
weredefinedassharing>97%sequenceidentityusingFurthestneighbormethod(http://www.
mothur.org/wiki/Cluster).AnOTU-basedanalysiswasperformedtocalculatetherichnessand
diversityindices(Ace,Coverage,Chao,SimpsonandShannon)withacutoffof3%dissimilar-
ity.RawsequencedatainFASTQformatareaccessiblefromtheNCBISRAstudynumber
SRP070625,accessionnumbersSRX1602057-SRX16072.
Results
EffectsofMAPonsoilbiogeochemicalproperties
Theecosystemtypeshadsignificantlydifferentsoilproperties(Table2).ThesoilpHandBD
variedfrom7.95to8.36andfrom0.94to1.66g/cm3,respectively.ThesoilpHandBDwere
thelowestintheforestecosystemandhighestinthedesertecosystem.SOMcontentofthe
soilsdifferedasafunctionofthevegetationtypes.TheconcentrationofSOMintheforesteco-
systemweresignificantlyhigherthantheotherecosystems.TNcontentinsamplesfromthe
forestecosystemwasthehighest,whereasthisvaluewaslowestinthesandyecosystem.TP
contentwashighestintheforestandforest-grassecosystemsandlowestinthesandyecosys-
tem.TheratioofC/Ninthedesertecosystemwassignificanthigherthanthatingrassandfor-
estecosystem,andtheratioofN/Pintheforestandforest-grassecosystemswassignificant
higherthanthatinotherecosystems.MBCrangedfrom552.05mg/kgintheforestecosystem
to20.18mg/kginthesandyecosystem,anditconsistentlydecreasedasMAPincreased.Over-
all,theforestecosystemwithhigherMAPhadthehighestlevelofnutrients,whilesandyand
desertecosystemshadthelowest.Overall,fromsouthtonorth,alongtheincreasingMAPgra-
dient,soilpHandBDincreasedandSM,SOM,TN,TP,NN,AN,AP,AKandMBCdecreased.
Table2. Biogeochemicalpropertiesofsoilsunderdifferentvegetationtypes.
Vegetationecosystems Forest Forest-grass Grass Sandy Desert
pH 7.95±0.12c 8.13±0.05b 8.22±0.03ab 8.33±0.06a 8.36±0.14a
BD(g/cm3) 0.94±0.05c 1.14±0.06bc 1.19±0.04b 1.50±0.10a 1.66±0.05a
SM 0.18±0.04a 0.14±0.03a 0.06±0.01b 0.02±0.02b 0.01±0.01b
SOM(g/kg) 37.66±16.93a 15.76±5.83b 8.41±0.49b 2.14±1.23b 3.62±1.21b
TN(g/kg) 1.91±0.72a 1.14±0.52ab 0.51±0.06bc 0.09±0.03c 0.13±0.04c
TP(g/kg) 0.57±0.04a 0.55±0.01a 0.47±0.02b 0.15±0.03c 0.22±0.05c
NN(mg/kg) 5.11±3.26bc 9.34±2.75a 6.13±1.57ab 3.21±0.14bc 1.50±0.58c
AN(mg/kg) 9.33±2.78a 7.81±2.67a 6.01±1.30a 5.84±3.63a 3.42±0.77a
AP(mg/kg) 2.27±0.17a 2.58±0.27a 1.76±0.24b 1.17±0.14c 2.42±0.26a
AK(mg/kg) 530.45±25.02a 328.88±64.74b 325.09±39.70b 173.56±14.70c 209.99±26.42bc
MBC(mg/kg) 552.05±178.91a 310.05±105.37b 161.27±60.2bc 20.18±6.43c 22.64±3.04c
C/N 11.14±1.62b 8.33±0.87b 9.59±0.73b 12.81±3.83ab 16.07±2.48a
C/P 38.58±17.32a 16.67±5.97b 10.28±0.34b 7.75±3.21b 9.51±1.19b
N/P 3.36±1.20a 2.08±0.92ab 1.08±0.1bc 0.59±0.08c 0.60±0.04c
Soilbulkdensity,BD;Soilorganicmatter,SOM;SM,Soilmoisture;TN,Totalnitrogen;TP,Totalphosphorus;NN,Nitratenitrogen;AN,Ammonium
nitrogen;AP,Availablephosphorus;AK,Availablepotassium;MBC,Soilmicrobialbiomasscarbon;C/N,Theratiooftotalorganiccarbontototalnitrogen;
C/P,Theratiooftotalorganiccarbontototalphosphorus;N/P,Theratiooftotalnitrogentototalphosphorus.Differentlowercaselettersshowed
significantdifferencesunderdifferentvegetationecosystemsinthesamephyla(P<0.05).
doi:10.1371/journal.pone.0152894.t002
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Table3. Characteristicsofsoilbacteriarichnessanddiversityindicesunderdifferentvegetationtypes(Means±SD,n=3).
Vegetationsystems Reads 0.97
OTU Ace Chao Coverage Shannon Simpson
Desert 9462±1167a 2392±186a 3326±271a 3184±237a 0.90±0.01a 7.12±0.07a 0.0018±0.0005a
Sandy 9364±1641a 2243±578a 3204±868a 3123±829a 0.91±0.02a 6.90±0.42a 0.0031±0.0021a
Grass 10062±604a 2810±27a 4033±114a 3909±112a 0.89±0.01a 7.31±0.03a 0.0014±0.0001a
Forest-grass 9190±1680a 2589±306a 3863±494a 3709±469a 0.88±0.02a 7.21±0.10a 0.0015±0.0002a
Forest 9404±956a 2238±233a 3194±404a 3138±350a 0.90±0.01a 6.90±0.13a 0.0028±0.0008a
Differentlowercaselettersshowedsignificantdifferencesunderdifferentvegetationecosystemsinthesamephyla(P<0.05).
doi:10.1371/journal.pone.0152894.t003
Bacterialcommunitycomposition
Acrossallofthesoilsamples,weobtainedatotalof36816OTUswith1593–2829OTUsper
sample(mean2454).Inthegrassecosystem,Shannon’sdiversityindex,ChaoindexandAce
indexwerehighest,andtheSimpsondiversityindexwaslowest.Incontrast,theSimpsondiver-
sityindexwasthehighestinthesandyecosystem(Table3).Vegetationecosystemshadnosig-
nificanteffectonShannon’sdiversityindex,ChaoindexandAceindex(P>0.05).
AsshowninFig2A,atthephylumlevel,thestructuresofthemicrobialcommunitiesdif-
feredintermsofboththepredominantphylumandtherelativeabundanceofeachphylum.
Actinobacteria(12.66–42.96%),Proteobacteria(17.45–40.33%),Chloroflexi(9.25–16.25%),
Acidobacteria(7.10–20.21%),Planctomycetes(4.70–10.01%),Bacteroidetes(1.52–4.47%),Gem-
matimonadetes(1.17–6.29%),Armatimonadetes(1.17–6.29%)andCyanobacteria(0.32–
2.98%)werethe9mostabundantphyla.Inallsamples,ActinobacteriaandProteobacteriawere
themostabundantphyla,whichtogetheraccountedfor46.89–67.23%ofallbacterialsequences
obtainedfromallofthesoilsamples.TherelativeabundanceofActinobacteriawasmuch
higherinthesandyecosystemthaninotherecosystems.Proteobacteriawerethesecondhighest
bacterialabundancefoundinallsamples.Therelativeabundanceofthesebacteriawashighest
(35.35%)intheforestecosystemandlowestinthesandyecosystem(21.40%).TheANOVA
testindicatedthatActinobacteria,ProteobacteriaandPlanctomycetesdifferedsignificantly
underdifferentecosystems(P<0.05)andthatPlanctomycetesweresignificantlymoreabun-
dantinforestandgrassecosystemsoils(P<0.05).ComparedwiththeActinobacteriaandPro-
teobacteria,Chloroflexi,Plantctomyceteshadnarrowranges,whichaccountedfor10.90–
13.86%,2.05–2.88%and0.34–1.65%,respectively(Fig2C).Andforthethreephyla,therewas
nosignificantdifferencesbetweendifferentvegetationecosystems(P>0.05).
Attheclasslevel,Actinobacteria,Alphaproteobacteria,Acidobacteria,ChloroflexiaandBeta-
proteobacteriaweredominantcommunities.Vegetationecosystemshadsignificanteffectson
soilbacterialcommunities(P<0.05).TherelativeabundanceofActinobacteriaforsandyeco-
systemwassignificanthigherthangrass,forest-grassandforestsystems(Fig2B).Nosignifi-
cantdifferencesforAlphaprotebacteria,Acidobacteria,Ktedonobacteria,Anaerolineaeand
Gemmatimonadetesweredetectedindifferentecosystems.
Ofalloftheedaphicandclimatevariablesexamined,onlyaltitudeandMAThadnosignifi-
cantassociationwithsoilbacterialcommunities(Table4).Therewasasignificantnegativecor-
relationofActinobacteriawithSM,MAP,SOM,TN,TP,NN,AN,AP,AK,MBC,C/PandN/P
andasignificantpositivecorrelationbetweenpHandBD.However,Proteobacteriahadthe
oppositecorrelationswiththeedaphicandclimatevariables.Meanwhile,therewerenosignifi-
cantcorrelationsbetweenChloroflex,BacteroidetesandCyanobacteriaandedaphicandclimate
variables(Table4).
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Fig2.Relativeabundanceinthebacterialcommunitycompositionatthephylumlevel(AandC)andattheclasslevel(BandD)withinthedifferent
ecosystems.Valuesdesignatedbydifferentlowercaselettersshowedsignificantdifferencesunderdifferentvegetationecosystemsinthesamephyla,the
sameasfollowings(P<0.05).
doi:10.1371/journal.pone.0152894.g002
Whentheedaphicandclimatevariableswereusedtoconstraintheordinationofthesoil
bacterial(atthephylumlevel)withtheRDA(Fig3),thereweredistinctdifferencesinbacterial
communitycompositionsunderdifferentecosystems.WefoundthatMAP,totalP,SOM,TN,
SMandC/Pwerethekeyfactorsthataffectedthesoilbacterialcompositions.TheRDAanaly-
sisshowedthattherewereclearsoilbacteriacommunitydifferencesbetweensamplesites,with
desertandsandyecosystemsclustersdifferingfromthegrassandforestvegetationecosystems
(Fig3).Indesertandsandyecosystems,Actinobacteriawasthedominantphylumandaffected
bysoilpH.InGrassandforest-grassecosystems,Proteobacteriawerethemostabundantand
thesoilhadthehighestsoilnutrientsandMAP.
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ri
e
act 88 24 01 84 52 60 95 95 05 47 82 67 18 77 98 32 35 al
ob 0.0 0.2 0.4 0.3 0.2 0.4 0.3 0.3 0.1 0.1 0.1 0.1 0.3 0.3 0.0 0.4 0.4 tot
n - - - - - - - - - - - - - e o
Cya ailabl bont
s Av car
ete AP, nic
monad 467 255 036**640*574**748**768**754 463 175*616 200**648**740 127**772**763 ogen; alorga
ati -0. -0. 0. 0. 0. -0. -0. -0. -0. -0. -0. -0. -. -. 0. -. -. nitr tot
m m of
sAr moniu eratio
e m h
et A T
entfactors. mmatimonad **0.651 0.336 -0.101 -0.387 -0.463*0.535 0.288 0.413**0.672*0.619 0.063 0.365 0.459 0.362*-0.553 0.211 0.388 nitrogen;AN, nitrogen;C/P,
phylaandenvironm BacteroidetesGe 0.291 0.121 0.176 -0.307 -0.391 0.366 0.274 0.231 0.218 0.302 0.084 0.177*0.500 0.372 -0.184 0.300 0.266 sphorus;NN,Nitrate ganiccarbontototal
al ho or
bacteri ycetes ** * * ** ** * ** ** * * ** * Totalp oftotal
ant om 890 533 023 567 770 668 451 562 889 676 442 372 533 609 634 356 527 TP, atio
Table4.ThePearsoncorrelationsbetweentherelativeabundancesofthe9domin flActinobacteriaProteobacteriaChloroexiAcidobacteriaPlanct ****MAP-0.8170.666-0.4560.2470. MAT-0.4330.484-0.3790.0110. Altitude0.175-0.184-0.2410.0230.******pH0.794-0.7330.515-0.553-0.****BD0.781-0.6110.444-0.516-0.*****SM-0.9160.804-0.4300.5800.******SOM-0.8000.769-0.4700.6310.******TN-0.8690.862-0.5030.5230.****TP-0.8710.747-0.3810.1640.**-N-0.5830.551-0.244-0.1130.NO3***-N-0.5620.656-0.1830.1960.NH4***AP-0.6200.644-0.1400.040.****AK-0.7960.702-0.4180.4120.*****MBC-0.8930.835-0.460.5980. C/N0.410-0.3600.4590.020-0.******C/P-0.7520.712-0.4240.7160.******N/P-0.8580.836-0.4980.6020. *<IndicatesP0.05;**<IndicatesP0.01. Soilbulkdensity,BD;Soilorganicmatter,SOM;SM,Soilmoisture;TN,Totalnitrogen; phosphorus;AK,Availablepotassium;MBC,Soilmicrobialbiomasscarbon;C/N,Ther phosphorus;N/P,Theratiooftotalnitrogentototalphosphorus. doi:10.1371/journal.pone.0152894.t004
PLOSONE|DOI:10.1371/journal.pone.0152894 April5,2016 9/17
BacterialCommunityVariedwithVegetationEcosystems
Fig3.OrdinationplotsoftheresultsfromtheRDAtoexaminetherelationshipbetweenbacterialpopulations(shownintheblue)andselected
environmentfactors(showninred),includingpH,TP,TN,MAP,MAT,MBC,SOM,SMandC/Pinthefivedifferentecosystems.Site1,2and3were
inthedesertecosystem;Site4,5and6wereinthesandyecosystem;site7,8and9wereinthegrassecosystem;site10,11and12wereintheforest-grass
ecosystem;site13,14and15wereintheforestecosystem.
doi:10.1371/journal.pone.0152894.g003
PLOSONE|DOI:10.1371/journal.pone.0152894 April5,2016 10/17