Profile Changes in the Soil Microbial Community When Desert Becomes Oasis

15 Pages·2015·2.21 MB·English

RESEARCHARTICLE
Profile Changes in the Soil Microbial
Community When Desert Becomes Oasis
Chen-huaLi1,Li-songTang1,Zhong-junJia2,YanLi1*
1 StateKeyLaboratoryofDesertandOasisEcology,XinjiangInstituteofEcologyandGeography,Chinese
AcademyofSciences,Urumqi,Xinjiang,China,2 StateKeyLaboratoryofSoilandSustainableAgriculture,
NanjingInstituteofSoilScience,ChineseAcademyofSciences,Nanjing,China
*[email protected]
Abstract
Theconversionofvirgindesertintooasisfarmlandcreatestwocontrastingtypesofland-
cover.Duringoasisformationwithirrigationandfertilizerapplication,however,thechanges
inthesoilmicrobialpopulation,whichplaycriticalrolesintheecosystem,remainpoorly
OPENACCESS understood.Weappliedhigh-throughputpyrosequencingtoinvestigatebacterialand
archaealcommunitiesthroughouttheprofile(0–3m)inanexperimentalfield,whereirriga-
Citation:LiC-h,TangL-s,JiaZ-j,LiY(2015)Profile
ChangesintheSoilMicrobialCommunityWhen tionandfertilizationbeganin1990andcroppedwithwinterwheatsincethen.Toassessthe
DesertBecomesOasis.PLoSONE10(10): effectsofcultivation,thefollowingtreatmentswerecomparedwiththevirgindesert:CK(no
e0139626.doi:10.1371/journal.pone.0139626
fertilizer),PK,NK,NP,NPK,NPKR,andNPKM(R:strawresidue;M:manurefertilizer).Irri-
Editor:ZhiliHe,UniversityofOklahoma,UNITED gationhadagreaterimpactontheoverallmicrobialcommunitythanfertilizerapplication.
STATES Thegreatestimpactoccurredintopsoil(0–0.2m),e.g.,Cyanobacteria(25%totalabun-
Received:June8,2015 dance)weremostabundantindesertsoil,whileActinobacteria(26%)weremostabundant
Accepted:September14,2015 inoasissoil.Theproportionsofextremophilicandphotosyntheticgroups(e.g.,Deinococ-
cus-ThermusandCyanobacteria)decreased,whiletheproportionsofR-strategy(e.g.,
Published:October1,2015
GammaproteobacteriaincludingXanthomonadales),nitrifying(e.g.,Nitrospirae),and
Copyright:©2015Lietal.Thisisanopenaccess
anaerobicbacteria(e.g.,Anaerolineae)increasedthroughouttheoasisprofile.Archaea
articledistributedunderthetermsoftheCreative
CommonsAttributionLicense,whichpermits occurredonlyinoasissoil.Theimpactoffertilizerapplicationwasmainlyreflectedinthe
unrestricteduse,distribution,andreproductioninany non-dominantcommunitiesorfinertaxonomicdivisions.Oasisformationledtoadramatic
medium,providedtheoriginalauthorandsourceare
shiftinmicrobialcommunityandenhancedsoilenzymeactivities.Therapidlyincreasedsoil
credited.
moistureanddecreasedsaltcausedbyirrigationwereresponsibleforthisshift.Further-
DataAvailabilityStatement:Allrelevantdataare
more,differenceinfertilizationandcropgrowthalteredtheorganiccarboncontentsinthe
withinthepaperanditsSupportingInformationfiles.
soil,whichresultedindifferencesofmicrobialcommunitieswithinoasis.
Funding:Theworkwassupportedbythefollowing:
1)NationalNaturalScienceFoundationofChina
(grantno:41301102toCL);2)StrategicPriority
ResearchProgramoftheChineseAcademyof Introduction
Sciences(grantno:XDA05050405toLT);3)The
InternationalScience&TechnologyCooperation Soilmicrobesplayfundamentalrolesinsoilbiogeochemicalprocesses.Landuseandmanage-
ProgramofChina(grantno:2010DFA92720toYL); menthavesignificanteffectsonthemicrobialcommunitystructureandfunction,andthismay
and4)TheKnowledgeInnovationProjectofthe
subsequentlyinfluencesoilqualityandecologicalstability[1].Agriculturaluseofnaturalsoils
ChineseAcademyofSciences(grantno:KZCX2-
isconsideredtohaveproducednegativeeffects[2].Forexample,cultivationonforestor
YW-T09toYL).Thefundershadnoroleinstudy
meadowsoilscanchangethemicrobialcommunitystructureandrapidlydecreasesoilorganic
design,datacollectionandanalysis,decisionto
publish,orpreparationofthemanuscript. carbon(SOC)[3–5],andtheoveruseofnitrogen(N)fertilizercanresultinadecreasing
PLOSONE|DOI:10.1371/journal.pone.0139626 October1,2015 1/15
ProfileChangesinSoilMicrobialCommunityWhenDesertBecomesOasis
CompetingInterests:Theauthorshavedeclared microbialdiversityandlossofSOC[6–8].However,therearealsomanagementpracticesthat
thatnocompetinginterestsexist. areconsideredtohavepositiveeffectsonmicrobialdiversity,activityandSOCsequestration,
e.g.,thecombinedapplicationofchemicalandorganicfertilizer[9–10].
Aridlandsaccountfornearly30%ofglobalterrestrialecosystems.Thereisanincreasing
needforlarge-scalecultivationindesertregionstofeedhumanpopulations.Whenvirgindes-
ertiscultivatedintooasisfarmland,twocontrastinglandscapeorland-covertypesareformed
withinthearidland.Duetodroughtandlownutrientlevels,irrigationandfertilizationarenec-
essarytoensurecropyieldsandoasisformation.Thelargequantityofwaterandfertilizer
applicationsandthedramaticallyincreasedprimaryproductivityinevitablyleadstoremark-
ablechangesinthesoil.Furthermore,theimpactisnotlimitedtothetopsoilwherethewater
andfertilizerisdirectlyapplied,butthedeepsoilwhichisimpactedbyleachedsubstancesand
alteredrootsystems[11].Thesechangescanaltertheabundanceandcompositionofthe
microbialcommunityanditsfunction,andinturnsignificantlyinfluencethedynamicsofeco-
logicalprocessesinthetopsoilanddeepsoil[12–13].Previousstudieshavesuggestedthatcul-
tivationindesertsmayleadtothedisappearanceofsomeextremophilicbacterialgroups,but
wouldpromotebacterialdiversityandplanthealth[14].However,becauseoftheverylowlev-
elsofcultivablemicroorganismsandthemethodologicallimitationsinmicrobialecology,our
knowledgeofdesertsoilmicro-organismsremainsfragmentary.Furthermore,morecompre-
hensivestudiesofawiderrangeofsoilsandmanagementpracticesareneededtofullyunder-
standtheshiftinmicrobialcommunitiesduringoasisformation.
Themethodscurrentlyusedtostudysoilmicrobialcommunitiesaremainlybasedonfin-
gerprinttechnology[15]andsoilbiochemicaltechniques[16].However,thesemethodsdonot
providesufficientinformationtocomprehensivelyresolvethephylogeneticandtoxicological
responsesofmicrobialcommunitiestochangesinenvironmentalconditions.Thehigh-
throughputpyrosequencingtechniqueisbasedonhighresolutionsequencinganalysis.Itcan
obtainlargeamountsofinformationandprovidemoremeaningfulcomparisonsofmicrobial
communitiesthatmaybeaffectedbydifferentmanagementpractices[17–18].
ThisstudywasconductedatthesouthernperipheryoftheGurbantonggutDesert,whichis
characterizedbydryness,highsoilsalinity,lownutrientlevels,andintenseradiation[19].Asa
typicalaridregion,irrigatedfarmlandistheprevailingland-usetypeinagriculture.Ourpre-
cedingresearchshowedthatcultivationinthedesertsignificantlychangedsoilpropertiesand
increasedmicrobialbiomass[20].Inthecurrentstudy,wecomparedtheoasissoilsreceiving
differentfertilizerapplicationswiththevirgindeserttostudytheeffectsofcultivationonsoil
microbialcommunities,usinghigh-throughputpyrosequencing.Theobjectiveofthestudywas
toassessthechangesinmicrobialcommunitiesthroughoutthesoilprofileduringoasisforma-
tion,andtoevaluateanypossiblelinkagesbetweenthesecommunitiesandsoilproperties,
includingenzymeactivity.Wehypothesizedthat:(1)cultivationindesertregionshouldresult
inaremarkableshiftinthestructureofthemicrobialcommunity,notonlyinthetopsoilbut
alsointhedeepsoil.(2)Increasedsoilmoistureanddecreasedsaltcontentcausedbyirrigation
hadthemostsignificantinfluencesonmicrobialcommunitybecausethecorrespondingcondi-
tionsaresubstantiallyimprovedwhenanoasisiscreated.
MaterialsandMethods
Studydescriptionandexperimentaldesign
TheexperimentswereconductedattheFukangStationofDesertEcology,ChineseAcademy
0 0
ofSciences,whichislocatedinthehinterlandoftheEurasiacontinent(44°17N,87°56E).The
detaileddescriptionsofthestudysitecanbefoundin[11,20,21].Thisregioniscoveredby
sparsehalophytevegetation,whichisdominatedbyTamarixramosissima,Reaumuriasoongor,
PLOSONE|DOI:10.1371/journal.pone.0139626 October1,2015 2/15
ProfileChangesinSoilMicrobialCommunityWhenDesertBecomesOasis
Table1. Fertilizerapplicationratesunderdifferentfertilizertreatmentsinawinterwheatsystem.
Treatment Inorganicfertilizer(kgha-1yr-1) Organicfertilizer
Nitrogen(N) Phosphorus(P) Potassium(K) (tha-1yr-1)
CK 0 0 0 0
PK 0 33 50 0
NK 150 0 50 0
NP 150 33 0 0
NPK 150 33 50 0
NPKR 150 33 50 2.5(Straw)
NPKM 150 33 50 2.5(Manure)
doi:10.1371/journal.pone.0139626.t001
Nitrariasibirica,andSalsolacollina.Duetothelimitedavailabilityofwater,cultivationisonly
conductedinlimitedareas,thusoasisfarmsaregenerallysurroundedbynativedesert.
Along-termexperimentonsoilfertilitystartedin1990.Thecropwaswinterwheat,planted
inSeptembereachyear,andharvestedattheendofJuneorJulyofthenextyear.Thedetailed
descriptionfortheexperimentaldesigncanbefoundinWangetal.[21].Thetreatments
selectedinthisstudywere:(1)CK(nofertilizer),(2)PK,(3)NK,(4)NP,(5)NPK,(6)NPKR,
and(7)NPKM(R:strawresidueandM:manurefertilizer).Eachtreatmenthadthreereplicates
withaplotsizeof33m2.ThemeangrainyieldsfortheCK,PK,NK,NP,NPK,NPKR,and
NPKMtreatmentswere0.86,1.06,2.71,3.07,3.71,3.75,4.07tha-1yr-1.Therateoffertilizer
applicationineachtreatmentislistedinTable1.Thefertilizerapplicationandfloodirrigation
weredescribedindetailpreviously[11].
Soilsampling,soilproperties,microbialbiomass,andenzymeactivity
AfterthewinterwheatharvestinearlyJuly2011,soilsampleswerecollectedbothintheoasis
receivingdifferentfertilizerapplicationsandtheadjacentdesert.Intheseventreatmentsofthe
oasis,fivesamplepointswererandomlycollectedineachofthetreatmentplots.Soilsamples
weretakenverticallyusinganaugeratthefollowingdepthintervals:0–0.2,0.2–0.4,0.4–0.6,
0.6–1,1–1.5,1.5–2,2–2.5,and2.5–3m.Theundisturbeddesertsites(withoutirrigationand
fertilizerapplication),fromwhichtheoasissoilswerederived,weresampledusingapreviously
describedmethod[20].Briefly,threesamplingpointswereplacedrespectivelyinbaresoil,
undershrubsandundergrasscoverinthenativedesert,witheachoneamixedsampleoffive
locations.Theweightedaveragesofrelevantsoilparametersweredeterminedaccordingtothe
areaweightingofthesoilunderplantcanopiesandinbareland.
TheSOCandtotalNcontentweremeasuredusingaTotalOrganicCarbon/TotalNitrogen
analyzer(MultiC/N3100,AnalytikJena,Jena,Germany),andtotalPwasdeterminedbyacid
melt–molybdenum,antimony,andscandiumcolorimetry.Theelectricalconductivity(EC)
andpHweremeasuredusingtheconductivitymethodandpotentiometry,respectively(ata
soiltowaterratioof1:5).Soilwatercontentwasdeterminedbyagravimetricmethod.Micro-
bialbiomasscarbon(MBC)wasdeterminedbythefumigation-extractionmethodcombined
withtheTotalOrganicCarbon/TotalNitrogenanalyzer.Theactivitiesoffivesoilenzymesfor
severalmetaboliccycles(C,N,P)weredeterminedusingamethoddescribedbyGuan[22].
Invertaseactivity(EC3.2.1.26)wasdeterminedby3,5-dinitrosalicylicacidcolorimetry;urease
activity(EC3.5.1.5)wasdeterminedbyindophenolcolorimetry;proteaseactivity(EC:3.4.4.1)
wasdeterminedbyninhydrincolorimetry;alkalinephosphataseactivity(EC3.1.3.1.)was
determinedbyphenylphosphatesodiumtwocolorimetry;andcatalaseactivity(EC1.11.1.6)
wasdeterminedbypermanganatetitration.PhosphatebufferswithpHvaluesof5.5,6.7,7.4,
PLOSONE|DOI:10.1371/journal.pone.0139626 October1,2015 3/15
ProfileChangesinSoilMicrobialCommunityWhenDesertBecomesOasis
10,7.8wereusedtocontrolpHduringthemeasurementsofinvertase,urease,protease,alkaline
phosphatase,catalaseactivities,respectively.
SoilDNAextractionandpyrosequencing
SoilDNAwasextractedfromapproximately0.5gofsoil(ovendrybasisoffield-moistsoil)
usingaFastDNAspinkitforsoil(MPBiomedicals,Cleveland,OH,USA)accordingtothe
manufacturer’sinstructions.Thequality,quantity,andintegrityoftheDNAextractswere
checkedasdescribedby[11].DNAwasPCR-amplifiedintriplicateusingthe515Fand907R
primers,whichweredesignedtoamplifythehypervariableV3–V4regionofthe16SrRNA
genefrombacteriaandarchaea.Primersweretaggedwithuniquebarcodesforeachsample.
ThePCRreactions(Qiagen,Valencia,CA,USA)wereconductedasdescribedby[11].All
sampleswereamplifiedintriplicate.TheAandBadaptersrequiredfor454pyrosequencing
wereaddedtospecificendsofthePCRproductsaccordingto[23].Technicaltriplicateampli-
conswerepooledandpurifiedviathegelpurificationmethodandquantifiedusingPico-
1
Green dye(Invitrogen,Shanghai,China)aftertheywerecheckedby1.2%agarosegel
electrophoresis.TheconcentrationofpurifiedPCRampliconswasdetermined,andthey
werethencombinedinequimolarratiosintoasingletubeinpreparationforpyrosequencing
analysis.PyrosequencingwasperformedonaRoche454GSFLXTitaniumsequencer(Roche
DiagnosticsCorporation,Branford,CT,USA)accordingto[23–24].Inthisstudy,pyrose-
quencingproducedapproximately250,000high-qualitysequenceswithanaverageread
lengthofabout387bp.
The16SrRNAgenesequencereadswereprocessedusingribosomaldatabaseproject(RDP)
pyrosequencingpipeline(http://pyro.cme.msu.edu/)accordingto[25–27].Briefly,thereadings
werealignedbysecondary-structureawareinfernalalignerandthenclusteredintoOperational
TaxonomicUnits(OTU)byacustomcodethatimplementsthecomplete-linkageclustering
algorithm.ThetaxonomicidentityofeachphylotypewasdeterminedbytheRDPClassifier
withan80%bootstrapscore.ThediversityindicesShannon(H)andChao1wereestimated
usingMOTHUR[28]usingthegreengenes(http://greengenes.lbl.gov/)asthetargetdatabase.
Dataanalysisandstatistics
Asthetopsoilenvironmentwasverydistinctandthecompactionaftercultivationoccurredat
0–0.6maccordingtheprofilechangeofthesoilbulkdensityinthestudyarea[20],thetotal
profilewasdividedintothetopsoil(0–0.2m)andbelowtopsoil(0.2–0.6mand0.6–3m,or
0.2–3m),inordertomakecomparisonseasier.Theweightedmeansoftherelevantparameters
belowtopsoilwereobtainedbyassigningcorrespondingweighttoeachdepth.Statisticalanaly-
sesofdatawereconductedusingSPSS11.5forWindows(IBM,Endicott,NY,USA).Analysis
ofvariance(ANOVA)andleastsignificantdifference(LSD)testswereusedtoassessthesignif-
icanceoftheeffectsofirrigation,fertilizerapplication,andsoildepthonmicrobialcommunity
andsoilproperties.ThesignificancelevelwasP<0.05.
Canonicalcorrespondenceanalysis(CCA)canreflectqualitativechangesinspeciescompo-
sitionandmaximizetheseparationofspeciesoptimaalongsyntheticaxes[29–30].Theanaly-
siswasexecutedinCANOCO4.5todeterminetherelationshipbetweenmicrobialtaxaand
soilproperties,andtoassesstheeffectsofirrigationandfertilizerapplicationonthecomposi-
tionandstructureofthemicrobialcommunity.Themostinfluentialfactoronthemicrobial
communitywasselectedfromtheenvironmentalvariablesusingtheforwardselectionin
CANOCOforWindowsandaPvalueassociatedwiththeeffectoftheenvironmentalvariables
wasgivenbyMonteCarlotest.
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ProfileChangesinSoilMicrobialCommunityWhenDesertBecomesOasis
Results
Soilproperties,MBCandenzymeactivity
Fertilizerapplicationsnotonlyincreasedcropyield,butalsoincreasedSOCandTNcontents
intopsoil(0–0.2m),comparedtodesertsoilorplotswithnofertilizertreatment(S1Table).
AlltreatmentsintheoasissoilalsoincreasedthesoilMBCandenzymeactivity,including
invertase,prolease,catalase,urease,andphosphatasecomparedtodesertsoil(S2Table).The
combinedapplicationofchemicalandorganicfertilizerproducedthelargestchangesinsoil
biochemicalproperties.Inaddition,theSOCcontentdecreasedbelowthetopsoilintheplots
receivingfertilizertreatments,exceptforthetreatmentscombinedwithorganicfertilizer,and
theTNcontentincreasedslightlyinthedeepsoilforalltreatmentsintheoasis(S1Table).
SoilECandpHvaluessignificantlydecreasedandthesoilwatercontentsignificantly
increasedthroughoutthesoilprofile(0–3m)intheoasissoil(S1Table).Therewerenosig-
nificantdifferencesintheEC,watercontentandpHvalueamongthetreatmentswithinthe
oasis.
Effectsofirrigationontheabundanceofmicrobialtaxon
Irrigationhadasignificantimpactonthesoilmicrobialcommunityintopsoil(0–0.2m).In
thedeserttopsoil,themostabundantphylawereCyanobacteria(25%)andProteobacteria
(22%);whereasintheoasis,themostabundantphylawereActinobacteria(26%)andProteo-
bacteria(24%)(Fig1).ThedesertsoilhadahigherrelativeabundanceofCyanobacteria,Dei-
nococcus-Thermus,Firmicutes,Bacteroidetes(Fig1),andAlphaproteobacteria(α-
proteobacteria)(Fig2);whileintheoasissoil,foralltreatmentstherewerehigherrelative
abundancesofActinobacteria,Acidobacteria,Chloroflexi(Fig1),Gammaproteobacteria(γ-
proteobacteria),Betaproteobacteria(β-proteobacteria),Deltaproteobacteria(δ-proteobac-
teria),Gemmatimonadetes,andNitrospirae(Fig2).Moreover,archaea(includingCrenarch-
aeota)wereonlyfoundinoasissoils(Fig2).Changeswerealsoobservedatfinertaxonomic
divisions(Table2).Withintheα-proteobacteria,theproportionsofRhizobiales,Sphingomo-
nadales,Rhodobateraleswerelower,buttheRhodospirillaleswerehigherinalltreatmentsof
theoasissoil,comparedtothedesertsoil.WithintheActinobacteria,therelativeabundances
ofthesubclassesAcidimicrobidaeandActinobacteridaewerehigher,buttheRubrobacteridae
werelowerintheoasissoilsthanthedesertsoils.Inaddition,allofthetreatmentsintheoasis
alsoresultedinhigherproportionsoftheXanthomonadaleswithintheγ-phaproteobacteria,
AnaerolineaewithintheChloroflexi,ClostridialeswithintheFirmicutesandGp6withinthe
Acidobacteria,andlowerproportionsoftheBacillaleswithintheFirmicutesthaninthedesert
soil(Table2).
Assoildepthincreased,therelativeabundanceofCyanobacteriaandActinobacteriarap-
idlydecreased,buttheabundanceofProteobacteria,especiallyγ-proteobacteriasignificantly
increasedandbecametheoverwhelminglydominantpopulationinthedeepsoilforboth
desertandoasis(Fig3).Thefrequenciesandabundancesoffinertaxonomicdivisions(e.g.,
theordersPseudomonadales,Oceanospirillales,andEnterobacterialeswithintheγ-proteo-
bacteria)alsoincreasedcorrespondinglywithdepth(Table3).Irrigationalsohadasignifi-
cantimpactonthemicrobialcommunitiesbelowthetopsoil.Andtheresponseofmost
microbialtaxabelowthetopsoilwassimilartothatintopsoil(Table3andFig3).However,
theresponsesofsomemicrobialpopulationsweredifferent,e.g.,decreasesinthepropor-
tionsofActinobacteridae,Acidimicrobidae(Table3),andδ-proteobacteria(Fig3)below
thetopsoil,whichcontrastedwiththeirincreasesintopsoil,intheoasiscomparingtothe
desert.
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ProfileChangesinSoilMicrobialCommunityWhenDesertBecomesOasis
Fig1.Relativeabundancesofselectedbacterialphylaintopsoil(0–0.2m)fromdesertandoasiswithdifferentfertilizertreatments.
Deinococcus=Deinococcus-Thermus.Desert:theoriginalsoilfromwhichtheoasiswasderived.
doi:10.1371/journal.pone.0139626.g001
Effectsoffertilizationontheabundanceofmicrobialtaxon
Comparedtothetreatmentwithoutfertilizer(CK),thereweresignificanteffectsonthemicro-
bialcommunity,especiallyfinertaxonomicdivisionsornon-dominanttaxa,intreatments
wherefertilizerwasapplied(Fig2).Inthetopsoil,fertilizerapplicationsincreasedtherelative
abundancesofγ-proteobacteria(includingtheorderXanthomonadales),β-proteobacteria,Cre-
narchaeota,Nitrospirae,Firmicues,Rhizobiales,andBacillales(Fig2)andslightlydecreased
thatofδ-proteobacteriaandGp6(Table2).Belowthetopsoil,fertilizerapplicationincreased
theproportionsofγ-proteobacteria,Crenarchaeota,Rhizobiales,andBacillales,butdecreased
thatofδ-proteobacteriaandGp6(Table3andFig3),withhigherproportionsoftheEnterobac-
terialesandPseudomonadalesalsoobserved(Table3).Thecombinedtreatmentswithorganic
fertilizerproducedalargerincreaseofγ-proteobacteriaandNitrospirae.
Correlationsbetweensoilpropertiesandmicrobialtaxa
Giventhatthestrongestimpactofoasisformationonthemicrobialcommunityoccurredin
thetopsoilandmostcommunityresponsesweresimilarthroughoutthesoilprofile,wepresent
hereonlytheCCAordinationfortopsoil.Theordinationplotsdemonstratethecommunity
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ProfileChangesinSoilMicrobialCommunityWhenDesertBecomesOasis
Fig2.Relativeabundancesofselectedarchaeaandbacterialtaxaintopsoil(0–0.2m)fromdesertandoasiswithdifferentfertilizertreatments.
Desert:theoriginalsoilfromwhichtheoasiswasderived.Differentlettersatthetopofeachcolumnindicatethattreatmentmeansaresignificantlydifferentat
p<0.05.
doi:10.1371/journal.pone.0139626.g002
differentiationsbetweenthedesertandoasissoils(Fig4A),andbetweendifferentfertilizer
applications(Fig4B).InFig4A,thedesertsoilsarecenteredinareaswithlowsoilmoisture
andhighEC;whiletheseventreatmentsoftheoasissoilshadarelativelyconcentrateddistri-
butionintheoppositearea.Thisindicatesthatthemicrobialcommunitystructureinthedesert
soilwascompletelydifferentfromthatoftheoasissoil,whilealltreatmentsintheoasissoil
producedroughlysimilarcommunitystructures.However,intheplotwithoutthedesertsoil
(Fig4B),fertilizerapplicationsexertedsignificanteffectsonthemicrobialcommunity.These
treatmentsweredispersedindifferentareasoftheordinationplot.TheCK,PK,andNKtreat-
mentswerecenteredalongagradientwithrelativelyhighEC,pH,andrelativelylowSOCand
nutrientcontents.Thecombinedtreatmentswithorganicfertilizers(NPKRandNPKM)were
centeredontheareawithhighSOCandnutrientcontentsandlowECandpH.TheNPand
NPKtreatmentsweredistributedinanotherarea.
Accordingtotheforwardselectionoption,soilwatercontentandEChadsignificantinflu-
encesonthemicrobialcommunitystructureduringoasisformation(bothvaluesofPwere
0.002),whileSOCandEChadsignificantinfluencesduringfertilizerapplication(P=0.012
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ProfileChangesinSoilMicrobialCommunityWhenDesertBecomesOasis
Table2. Relativeabundancesofselectedbacterialtaxaintopsoil(0–0.2m)fromdesertandoasiswithdifferentfertilizertreatments.
Taxonomic Name Desert CK PK NK NP NPK NPKR NPKM
rank Relativeabundance(%)
Phylum Proteobacteria
Class α-proteobacteria
Order Rhizobiales 6.5a 3.2d 3.5cd 3.8c 3.8c 3.5cd 4.7b 4.0c
Order Sphingomonadales 1.3a 0.4bc 0.1c 0.5bc 0.4bc 0.1c 0.7b 0.3bc
Order Rhodobaterales 5.8a 0.2d 0.2d 0.7c 1.4b 0.7c 1.0bc 0.8c
Order Rhodospirillales 0.5d 2.5a 1.8b 1.8b 1.2c 1.1c 2.7a 2.9a
Class γ-proteobacteria
Order Xanthomonadales 0.1d 0.4c 1.2b 1.7a 0.8bc 1.1b 2.0a 2.1a
Order Pseudomonadales 0.0b 0.3ab 0.1b 0.2ab 0.1b 0.6a 0.4ab 0.3ab
Phylum Actinobacteria
Subclass Actinobacteridae 4.8e 15.2bc 17.6bc 12.8c 18.2b 18.8b 22.6a 8.9d
Subclass Acidimicrobidae 0.8d 1.1d 3.5a 2.3bc 1.9c 2.8b 1.1d 0.9d
Subclass Rubrobacteridae 3.3a 3.2a 1.8c 3.0ab 1.9c 2.6b 2.7b 0.7d
Phylum Chloroflexi
Class Anaerolineae 0.3c 0.8b 1.2ab 1.2ab 0.8b 1.2ab 0.8b 1.6a
Phylum Firmicuts
Order Bacillales 8.8a 1.6d 2.6bc 2.6bc 2.1c 2.2c 3.2b 2.9b
Order Clostridiales 0.0b 0.2a 0.6a 0.2a 0.4a 0.2a 0.2a 0.3a
Phylum Acidobacteria
Class Gp6 0.5c 2.9a 1.8b 2.4a 1.6b 2.5a 1.4b 1.3b
Differentletterswithineachlineindicatethattreatmentmeansaresignificantlydifferentatp<0.05.
doi:10.1371/journal.pone.0139626.t002
and0.04).Mostbacterialtaxa(e.g.,Cyanobacteria,Deinococcus-Thermus,Firmicutes,Bacteroi-
detes,andα-,β-,γ-proteobacteria)exhibitedsignificantcorrelationswiththesoilwaterandEC
(P<0.05).Somemicrobialgroups(e.g.,Deinococcus-Thermus,Acidobacteria,β-proteobacteria,
andCrenarchaeotaaeota)wereassociatedcloselywithsoilpH(P<0.05).Meanwhile,positive
correlationswerefoundbetweencertainmicrobialtaxa(e.g.,γ-proteobacteria,Nitrospirae,and
Crenarchaeota)andSOC,totalNcontents,MBC,andmostenzymeactivities(P<0.05).These
resultsdemonstratedthatirrigationhadstrongereffectsonthemicrobialcommunitythanfer-
tilizerapplication.
Discussion
Changesinmicrobialcommunityasaffectedbyoasisformation
Theresultsinthisstudyconfirmedourbasichypothesis.Itdemonstratedthatcultivationin
thedesertsoilresultedinastrongshiftinthemicrobialcommunitystructurethroughoutthe
soilprofile(0–3m)(Fig5).Thelargestchangeintheoverallmicrobialcommunitywas
observedinthetopsoil.Whileconvertingdesertintooasis,therelativeabundanceofCyano-
bacteriadecreasedfrom25.4to2.5%onaverage,andthatofActinobacteriaincreasedfrom
10.8to26.4%onaverage.TheCyanobacteriawerethereforethemostabundantgroupindesert
topsoilandtheActinobacteriabecamethemostabundantgroupinoasistopsoil(Fig1).Cyano-
bacteriaparticipateinbothcarbonandnitrogenfixation,andgenerallyoccurinharshdesert
environments[31–32].InadditiontoCyanobacteria,otherphotosyntheticgroups(e.g.,the
Rhizobiales,Sphingomonadales,andRhodobaterales)werealsopresentinlowerproportionsin
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ProfileChangesinSoilMicrobialCommunityWhenDesertBecomesOasis
Fig3.Relativeabundancesofselectedmicrobialtaxaat0.2–0.6and0.6–3mdepthsindesertandoasissoils.Desert:theoriginalsoilfromwhichthe
oasiswasderived;Nofertilizer:thecontrol(CK);Fertilizer:theaveragevaluesofsixfertilizertreatments(PK,NK,NP,NPK,NPKR,andNPKM).
Deinococcus=Deinococcus-Thermus.Valuesateachdepthareweightedmeans.Foreachmicrobialtaxon,valuesfordifferentdepthswithinsame
treatmentfollowedbythesameuppercaseletterarenotsignificantlydifferent(p>0.05);treatmentmeanswithinsamedepthfollowedbythesamelowercase
lettersarenotsignificantlydifferent(p>0.05).
doi:10.1371/journal.pone.0139626.g003
theoasis(Table2).Actinobacteriaparticipateinthedecompositionofligninandchitin[33].
Wheatcover/lackoflightandreturnofwheatresiduestothesoilintheoasismayexplain
above-mentionedcommunityshift.Meanwhile,therewerealsohigherproportionsoftheDei-
nococcus-Thermus,α-proteobacteria,andBacillalespresentindesertsoil(Figs1and2),allof
whichareextremophilicgroupsorantagonists,withastrongtolerancetodesiccation,radia-
tion,andhighlevelssalinity[34].TheoasissoilhadhigherproportionsoftheR-strategy(e.g.,
γ-,β-proteobacteria),facultativevegetative(e.g.,Rhodospirillales)andnitrifyingbacteria(e.g.,
Nitrospirae)(Table2andFig2).Archaeaoccurredonlyinoasissoil.Thereisincreasingevi-
denceshowingthatarchaeaareinvolvedinammonia-oxidizingprocess,andmayplaysignifi-
cantroleinthecarbonandnitrogencycles[24]
Unliketheremarkablechangeinthepredominantgroupintopsoil,theγ-proteobacteria
graduallybecametheoverwhelminglydominantgroupwiththeincreaseofsoildepthinboth
thedesertandoasissoils,emphasizingtheimportanceofsoildepthasanenvironmentalgradi-
entstructuringsoilmicrobialcommunities.Belowthetopsoil,mostmicrobialtaxaexhibited
similarresponsestocultivationtothatinthetopsoil.However,duetothemultiplefactors
involved(e.g.,soilmoisture,O ,saltcontent,pH,availablenutrients,andsoilparticlecomposi-
2
tion)andtheirinteractionsduringoasisformation,somebacterialtaxa,e.g.,Actinobacteria
PLOSONE|DOI:10.1371/journal.pone.0139626 October1,2015 9/15
ProfileChangesinSoilMicrobialCommunityWhenDesertBecomesOasis
Table3. Relativeabundancesofselectedbacterialtaxabelowtopsoil(0.2–3m)fromdesertandoasiswithdifferentfertilizertreatments.
Phyla Class/Order Desert Nofertilizer Fertilizer
Proteobacteria Rhizobiales 4.8a 3.7c 4.3b
Sphingomonadales 1.6a 1.6a 2.0a
Rhodobaterales 0.9a 0.2b 0.4b
Rhodospirillales 2.2b 3.0a 3.4a
Xanthomonadales 0.7c 1.2b 2.5a
Pseudomonadales 6.3b 6.6b 8.0a
Oceanospirillales 0.5b 3.1a 2.8a
Enterobacteriales 10.4a 2.8c 4.9b
Actinobacteria Actinobacteridae 4.9a 3.3b 2.6c
Acidimicrobidae 0.7a 0.6a 0.4a
Rubrobacteridae 2.0a 0.8b 0.7b
Chloroflexi Anaerolineae 0.1b 0.4a 0.4a
Firmicutes Bacillales 6.8b 6.8b 8.3a
Clostridiales 0.3b 1.8a 1.5a
Acidobacteria Gp6 1.4b 2.8a 1.6b
Desert:theoriginalsoilfromwhichtheoasiswasderived;Nofertilizer:thecontrol(CK);Fertilizer:theaveragevaluesofsixfertilizertreatments(PK,NK,
NP,NPK,NPKR,andNPKM).Valuesatthedepthareweightedmeans.Differentletterswithineachlineindicatethattreatmentmeansaresignificantly
differentatp<0.05.
doi:10.1371/journal.pone.0139626.t003
Fig4.Ordinationplotsoftheresultsfromcanonicalcorrespondenceanalysis(CCA)intopsoil(0–0.2m)toexploretherelationshipbetween
microbialpopulationsandsoilproperties,suchassoilorganiccarbon(SOC),totalnitrogen(TN),totalphosphorus(TP),soilpH,electric
conductivity(EC),andsoilwatercontent(SWC)fordifferentfertilizertreatments(CK,PK,NK,NP,NPK,NPKRandNPKM)with(A)andwithout
desertsoil(B).Cyanobacteria=Cya,Deinococcus-Thermus=Dei,Actinobacteria=Act,Alphaproteobacteria=Alp,Betaproteobacteria=Bet,
Gammaproteobacteria=Gam,Deltaproteobacteria=Del,Acidobacteria=Aci,Firmicutes=Fir,Chloroflexi=Chl,Gemmatimonadetes=Gem,
Nitrospirae=Nit,Planctomycetes=Pla,Bacteroidetes=Bac,Crenarchaeota=Cre.
doi:10.1371/journal.pone.0139626.g004
PLOSONE|DOI:10.1371/journal.pone.0139626 October1,2015 10/15