ContentslistsavailableatScienceDirectSoilBiology&Biochemistryjournalhomepage:www.elsevier.com/locate/soilbioReviewpaperMicrobialhotspotsandhotmomentsinsoil:Concept&reviewYakovKuzyakova,c,d,*,EvgeniaBlagodatskayaa,b€ttingen,GermanyDept.ofSoilScienceofTemperateEcosystems,UniversityofGoInstituteofPhysicochemicalandBiologicalProblemsinSoilScience,RussianAcademyofSciences,Pushchino,Russiac€ttingen,GermanyDept.ofAgriculturalSoilScience,UniversityofGodInstituteofEnvironmentalSciences,KazanFederalUniversity,Kazan,RussiaabarticleinfoArticlehistory:Received5September2014Receivedinrevisedform21January2015Accepted22January2015Availableonline10February2015Keywords:CandNcyclesMicrobialactivitiesPrimingeffectsMicrobialsuccessionsSubsoilprocessesActivemicroorganismsMicrobiota-habitatinteractionsabstractSoilsarethemostheterogeneouspartsofthebiosphere,withanextremelyhighdifferentiationofpropertiesandprocesseswithinnano-tomacroscales.Thespatialandtemporalheterogeneityofinputoflabileorganicsbyplantscreatesmicrobialhotspotsovershortperiodsoftimeethehotmoments.Wedefinemicrobialhotspotsassmallsoilvolumeswithmuchfasterprocessratesandmuchmoreintensiveinteractionscomparedtotheaveragesoilconditions.Suchhotspotsarefoundintherhizosphere,detritusphere,biopores(includingdrilosphere)andonaggregatesurfaces,buthotspotsarefrequentlyofmixedorigin.Hotmomentsareshort-termeventsorsequencesofeventsinducingacceleratedprocessratesascomparedtotheaveragerates.Thus,hotspotsandhotmomentsaredefinedbydynamiccharacteristics,i.e.byprocessrates.Forthishotspotconceptweextensivelyreviewedandexaminedthelocalizationandsizeofhotspots,spatialdistributionandvisualizationapproaches,transportoflabileCtoandfromhotspots,lifetimeandprocessintensities,withaspecialfocusonprocessratesandmicrobialactivities.Thefractionofactivemicroorganismsinhotspotsis2e20timeshigherthaninthebulksoil,andtheirspecificactivities(i.e.respiration,microbialgrowth,mineralizationpotential,enzymeactivities,RNA/DNAratio)mayalsobemuchhigher.Thedurationofhotmomentsintherhizosphereislimitedandiscontrolledbythelengthoftheinputoflabileorganics.Itcanlastafewhoursuptoafewdays.Inthedetritusphere,however,thedurationofhotmomentsisregulatedbytheoutputebydecompositionratesoflittereandlastsforweeksandmonths.Hotmomentsinducesuccessioninmicrobialcommunitiesandintenseintra-andinterspecificcompetitionaffectingCuseefficiency,microbialgrowthandturnover.ThefasterturnoverandlowerCuseefficiencyinhotspotscounterbalancesthehighCinputs,leadingtotheabsenceofstrongincreasesinCstocks.Consequently,theintensificationoffluxesismuchstrongerthantheincreaseofpools.Maintenanceofstoichiometricratiosbyacceleratedmicrobialgrowthinhotspotsrequiresadditionalnutrients(e.g.NandP),causingtheirmicrobialminingfromsoilorganicmatter,i.e.primingeffects.Consequently,primingeffectsarelocalizedinmicrobialhotspotsandareconsequencesofhotmoments.Weestimatedthecontributionofthehotspotstothewholesoilprofileandsuggestedthat,irrespectiveoftheirvolume,thehotspotsaremainlyresponsiblefortheecologicallyrelevantprocessesinsoil.Bythisreview,weraisedtheimportanceofconceptsandecologicaltheoryofdistributionandfunctioningofmicroorganismsinsoil.©2015ElsevierLtd.Allrightsreserved.1.Introduction:definitionsandthemostimportanthotspots1.1.DefinitionsandconceptThemostecologicallyrelevantbiogeochemicalprocessesinsoilsaremicrobiallymediated.Despitetheenormousamountof*Correspondingauthor.Dept.ofSoilScienceofTemperateEcosystems,Univer-€ttingen,Germany.sityofGoE-mailaddress:kuzyakov@gwdg.de(Y.Kuzyakov).http://dx.doi.org/10.1016/j.soilbio.2015.01.0250038-0717/©2015ElsevierLtd.Allrightsreserved.microbialcells,i.e.107e1012inonegramsoil(Wattetal.,2006),theirlocalizationisrestrictedtoverysmallmicrohabitatscomprisingmuchlessthan1%oftotalsoilvolume(Youngetal.,2008)andgloballycoveringmerely10À6%ofthesoilsurfacearea(YoungandCrawford,2004).Manysoilmicroorganismstendtoformcoloniesandbiofilmsandtendtoaggregate(Hodgeetal.,1998;Ekschmittetal.,2005),formingmicrobialhotspots.Conse-quently,ecologicallyrelevantbiogeochemicalprocessesmainlyoccurinthesmallvolumeofsoilhotspots.WedefinemicrobialhotspotsassmallsoilvolumeswithmuchfasterprocessratesandY.Kuzyakov,E.Blagodatskaya/SoilBiology&Biochemistry83(2015)184e199185
muchmoreintensiveinteractions(betweenpools)comparedtotheaveragesoilconditions(Fig.1)(Kuzyakov,2009,2010).Asmicrobialactivityislimitedbyvariousenvironmentalfactorsandespeciallybycarbon(C)availability(Hodgeetal.,2000),microorganismsinsoilaremainlyinadormantstate(BlagodatskayaandKuzyakov,2013).Theybecomeactiveduringshorthotmomentsafterthelimitationsareremoved.Accordingly,wedefinemicrobialhotmomentsasshort-termeventsorsequencesofeventsthataccel-eratemicrobialprocessesascomparedtotheaveragerates.Thus,hotmomentsoccurinorleadtotheformationofhotspots,butthehotspotsdonotnecessarilydisappearattheendofhotmomentsandmaymaintainsomemicrobialactivityparametersathighleveloverlengthierperiodsevenaftersubstrateisdegraded(BlagodatskayaandKuzyakov,2013).Wethereforedefinethehot-spotsandhotmomentsbasedondynamicproperties,specificallytheintensityofprocesses,i.e.byprocessrates,notbytheconcentrationofthesubstancesoranyotherstaticproperties.Suchdefinitionsun-derlinethedynamicnatureofhotspotsandhotmoments.Thesedefinitionsconsidertheheterogeneityindistributionoflocationsandtheperiodsofmaximalactivityofmicroorganismsinspaceandtime.Notethatpreviousdefinitionsofhotspotsandhotmomentswerefocusedmainlyonabioticfluxes(rainfallorerosionevents)onmuchlargerscales,e.g.landscape(McClainetal.,2003;Vidonetal.,2010;Leonetal.,2014).Theheterogeneityofsoilpropertiesonthemeso-andmacroscaleshavebeenfrequentlydescribedandanalyzedstatisticallyearlier(Parkin,1993;Webster,2000;HeuvelinkandWebster,2001).However,meso-andmacroscalesandtherelatedpreviousdefinitionsofhotspotsandhotmomentswerenotfocusedonmicrobialprocessesandwerenotapplicableonthescalesfrommmtom-thescalesrelevantformicrobialac-tivitiesandfunctionsatthelevelofaggregatesuptosoilprofile.Therefore,newconceptanddefinitionofhotspotsandhotmo-mentsrelevantformicrobialprocessesisnecessary.Thisreviewisfocusedonthespatialandtemporalscalescomparablewiththesizeandlifeperiodsofmicroorganismsinsoil.ThehotspotsandhotmomentsarerelevantnotonlyfromtheperspectiveoforganicmatteravailabilityandClimitation,butalsofromtheperspectiveofotherspecificfactorslimitingmicrobialactivityorprocessratesunderparticularconditions,includingsoilmoisture,oxygenavailability,Nexcess.Thisaffectsmanyprocessessuchasdenitrification,methanogenesis(seebelow),nitrification,orweathering.LocalizedinputofhighNexcess(e.g.fertilizergrainsorurineofanimals)triggersNturnoverincludingstrongnitrifica-tion(Strongetal.,1997)anddenitrification.Therefore,thehotspotsandhotmomentsarenotconfinedtotheinputoflabileC(describedbelow)buthaveamuchbiggerimpactandbroaderperspectiveinvolvingtheremovalofanylimitationsofmicrobialprocesses.Fig.1.Conceptofmicrobialhotspotsinsoil:Hotspotsaresmallsoilvolumeswithmuchhigherprocessratesandintensiveinteractionscomparedtotheaveragesoilconditions.TheTableinsetrepresentstherelativevolumeandprocessratesinthehotspotsandbulksoil.“Mean”representstheweightedaverageprocessratesbysoilmixing.
Thesimultaneousoccurrenceofnumeroushotspotsinmicro-habitatscumulativelyaffectsthedynamicsofpoolsandfluxesandisthereforerelevantathigherscales,includingtheecosystemscale.Theimportanceofmicrobialhotspotsatthemicro-scalelevelisthereforedeterminedbytheirrelevancetothefunctionsatthehigherscales(BlagodatskyandSmith,2012).Thus,abundanthot-spotswithinasoilvolumetransformstheenvironmentandex-tendsthehotspotstothehotspheres(Beareetal.,1995)suchasrhizosphereordetritusphere,withahighimpactatthemacro-scale.Themechanisticunderstandingofsoilfunctioningatpro-file,ecosystemandlandscapelevelsisimpossiblewithoutquanti-fyingandlocalizingthehotspots,aswellasidentifyingtheiroriginandformation,theirspatialandtemporalorganization,processesandinteractions,alongwithcriticalthresholdsofintensitiesnecessaryforfunctionsathigherscales.1.2.ThemostimportantmicrobialhotspotsinsoilMicrobialactivityinallsoilsislimitedbylabileC(easilyavail-ableorganics)andenergy(Blagodatskyetal.,1998;Hodgeetal.,2000;SchimelandWeintraub,2003).Consequently,removingthislimitationetheinputoflabileCebooststheabundanceandactivityofmicroorganismsinsoilandproducesmicrobialhotspots.Basedonthesourcesofhighinput(notthecontent!)oflabileor-ganicsandtheirlocalizationinsoil,weemphasizethefollowinghotspotgroups(Fig.2,Table1):-Rhizosphere:inputoflabilerootexudatesandotherlessdecomposablerhizodepositsatvarioussoildepths(Jonesetal.,2004;Hinsingeretal.,2009).-Detritusphere:inputofmainlyrecalcitranthighlypolymeric(Kogel-Knabner,2002)(butalsosomelabile,lowmolecularweight)organicsaslitter,mainlyonthemineralsoilsurface,anduponrootdeathatvariousdepths.-Biopores:a)inputoflabileandrecalcitrantorganicspassedthroughandprocessedwithinthehindgutofearthworms(drilosphere)andothersoilorganisms(mainlyinvertebrates)atvariousdepthsor/andb)formedbydeep-growingrootsandmaintainedbyrootsandburrowinganimals(TiunovandScheu,1999,2004;Brownetal.,2000;Schraderetal.,2007).Alsoan-imalfecesinsoilwiththeinputoflabileandrecalcitrantor-ganicscanbegroupedtothebiopores.-Aggregatesurfaces:inputoforganicsleachedfromthedetri-tusphere(e.g.Ohorizon),fromtheCrichAhhorizonandpartlyfromtherhizosphere(KaiserandKalbitz,2012).Thishotspotgroupisespeciallyimportantindeepsoilhorizons(Fig.2).Otherlocationsinthesoilhavesometimesbeenmentionedasspotsofmicrobialactivities:biochar-sphere(Lehmannetal.,2011),porosphere,drilosphere,gutsofsoilanimals(MohrandTebbe,2006)etc.Theselocations,however,canbeincludedinoneoftheabove-mentionedhotspots(porosphereconsistsofbioporesandaggregatesurfaces,biochar-sphereispartlyrelatedtothedetritu-sphere),areofsecondaryimportanceandwillnotbereviewedhereseparately.Thedistributionandimportanceofthefourhotspotgroupsdependontheecosystemandsoildepth(Fig.2).Abovethemineralsoilsurface,thedetritusphereisthemostimportanthotspot.ThedensityoftherhizosphereisespeciallyhighinthetopoftheAh(orAp)horizon.TherelevanceofbioporesandaggregatesurfacesforCinputintopsoilismarginalcomparedtotheeffectsofthedetri-tusphereandrhizosphere,buttheirimportancestronglyincreaseswithdepth(Kautzetal.,2014).Thethreefirsthotspotsedetritu-sphere,rhizosphereandbioporesehaveabioticorigin.Onlyaggregatesurfaceshaveamainlyabioticorigin,especiallyinthe186Y.Kuzyakov,E.Blagodatskaya/SoilBiology&Biochemistry83(2015)184e199
Fig.2.Schemasandexamplesoffourmicrobialhotspotgroupsinsoil:Detritusphere(topright),Rhizosphere(middleright),Biopores(bottomright)andAggregatesurfaces(bottomleft)andtheirrelativeimportanceupto1mdepthalongasoilprofile(VoronicChernozem).Therelativeimportanceofhotspotsalongthedepthmaystronglydifferbetweensoilsundergrasslands,forestsorcrops,andstronglydependsonsoilparentmaterialandclimaticconditions.ThethinsectionexampleofdetritusphereiskindlyprovidedbyDr.OttoEhrmann(BildarchivBoden,http://www.bildarchiv-boden.de).TherhizosphereexampleisfromYaalon(2000).
subsoil.Therefore,aggregatesurfaceshavebeendisregardedorevenneglectedinmoststudiesofmicrobialhotspotsinsoil.1.3.TheroleofabioticandbioticfactorsinhotspotformationTheoccurrenceofhotspotsinsoil,whichisthemosthetero-geneousandcomplexcomponentofthebiosphere(YoungandCrawford,2004),isaresultofsoildevelopment.Theincreasingvariabilityofsoilpropertiesisakeycharacteristicofsoilformation,structuringtheenvironment.Suchpropertiesincludelocaldensityandporevolume,soilacidityandredoxpotential,organicmatterandnutrientcontents,microbialbiomassandcompositionofmi-crobialcommunities,andenzymeactivities.Remarkably,thevari-ationofallthesepropertiesinparentmaterialismuchlessthanindevelopedsoil.Theheterogeneityofthesoilenvironmentisresponsibleforhugediversitynotonlyofmicroorganismsbutalsoofvariousprocessesongoingatclosedistancesthatwouldbenotpossibleinahomogeneoussystem(Focht,1992).Consequently,increasingvariabilityisaprerequisiteforhotspotformation.Manypropertiesandespeciallyprocessratesinsoilsurroundinghotspotsvarybyordersofmagnitudewithinveryshortdistancesandwithinveryshortperiods.Thisisespeciallythecaseatscalescomparablewiththesizeofmicrobialcellsandtheircolonies,i.e.distancesrangingfrommmtomm.Examplesofsoilstructuring(verticalprofiledifferentiation,formationofaggregatesandvariouscon-cretions)reflectthatprocessesareongoinginspecificlocationswith(much)higherintensitycomparedtosurroundingsoil.Thus,theformationofhotspotsbydifferentiationofmorphologicalandbiochemicalsoilpropertiesisaconsequenceofcontrastingprocessrates.Soilstructuringstartsbyanoscillationofabioticfactors:freezing/thawing,drying/rewetting,waterpercolationevents,varyingoxic/anoxicconditions(Oades,1993)thatalterthephysicalenvironmentbyredistributingwater,dissolvednutrientsandlabileorganics.Thisincreasesthelocalconcentrationsofsubstancesnecessaryforbioticactivity(Rasaetal.,2012).Bioticfactorsfurtherstronglymodifythesurroundingphysicochemicalenvironment,leadingtothedevelopmentofspecificmicrobialcommunities(Feeneyetal.,2006).Thus,physicochemicalstructuringofsoilbyabioticandbioticfactorsandthesubsequentlocalremovaloflimitationareprerequisitesfortheformationofmicrobialhotspotsee.g.foraconcentrationoflifeinlocationswithlesslimitation.Theinputoflabilesubstratetothehotspotsremoveslimitation,triggersmicrobialactivityandthusdrivesthehotmoments.Thedurationandintensityoftheinputoflabileorganicsstimulatingmicrobialactivitiesarespecificforthehotspotgroups(Tables1and2).Dependingonthefactorsresponsibleforsubstrateinput/redistribution,thehotmomentscanbeofbioticorabioticnature.Themaindriversofbiotichotmomentsarerootexudation,litterfallandrootdeath,rootingrowthinanewsoilvolume,andac-tivitiesofburrowinganimals(Table1).ThesehotmomentsaredirectlylinkedwiththeinputoflabileorganicCintothesoil.Therefore,thebioticallyinducedhotmomentsalwaysleadtofor-mationormaintenanceofhotspots.Abioticprocessesalsochangethesoilenvironmentbecauselabileorganicsi)arereleasedandbecomeaccessibleformicroor-ganisms,orii)areredistributedtonewlocationsandthusproducehotspots.Freezing/thawinganddrying/rewettingdisruptsoilag-gregatesandreleaseencapsulatedparticulateanddissolvedor-ganics(BorkenandMatzner,2009).SuchhotspotsinducedbyY.Kuzyakov,E.Blagodatskaya/SoilBiology&Biochemistry83(2015)184e199
Table1Propertiesofthemostcommonhotspotgroupsinsoil.HotspotsOriginVolumerangeinsoil,%CommonvolumeinAh/Ap,%CommonvolumebelowAh/Ap-insubsoil,%Boundary,mmRelativeCavailabilityC/NratioRelevanceRegularityDurationofhotmomentsaa187
RhizospherePrimarybiotic;roots0…1005…10<52…10High~10WholesoilprofileOccasionalþregularDays(weeks)DetrituspherePrimarybiotic;litter0…1000…1000…<15…20High…medium>20Abovemineralsoilsurface,TopsoilRegularþoccasionalWeeks-monthsBioporesSecondarybiotic;burrowinganimals,roots0…101…51…21…3Medium…low?….BelowAh/Ap,subsoilOccasionalDays-weeksAggregatesurfaceSecondary(mainly)abiotic;swelling/shrinking0…101…31…50.1…1Low10…20BelowAh/Ap,subsoilOccasionalDaysThismeansonlythedurationofactiveprocessesaftertheCinput(nottheexistenceofthepropertythemselves).E.g.thelifetimeoftheaggregatesinsubsoilinBtcanbedecadesorevencenturies,butthemicrobialactivityontheaggregatesurfaceincreasesonlyforfewdays(toweeks)aftertheCinputfromthetopsoilbyrain.abioticdriversarerandomlydistributedinsoil.Theypersistovermuchshorterperiodsandaremuchlessactivecomparedtobio-ticallyinducedhotspots(Table2).Heavyrainsproducetwogroupsofhotspots:i)onaggregatesurfacesandinbioporesbyleachingofsolubleorganicsfromthedetritusphereintodeepersoil(KaiserandKalbitz,2012),andii)onthelandscapelevel1duetoerosion,i.e.runoffofparticulateanddissolvedorganics.Snowmeltingisanimportantfactorinteractingwiththedetritusphere.Becausemi-crobialprocessesremainactiveattemperaturesbelowzero(Panikovetal.,2006),thelitterwillbepartlydecomposedandaccumulateinthedetritusphereoverthewinter.Duringtheshortsnowmeltingperiod,thepartlydecomposedorganicswillberemovedandleachedintothebioporesandcracks(ifthesoilisnotfrozen)ormovedtolowerlandscapepositions,producinghotspotsthere.Generally,theabioticprocessesredistributetheavailableCalreadypresentinsoil(andpartlypreprocessedbymicroorgan-isms).Therefore,theintensityofprocessesinducedbyabioticdriversisgenerallylessandshorterthanthatinducedbiotically.1.4.TransportintoandfromhotspotsInitiationandformationofhotspotsrequireseitherdeliveryoflabileCorotherlimitingsubstancestothemicrobialcellsor,lessfrequently,transportofthemicroorganismstothesubstrate.Gener-ally,therearethreepotentialmechanismsforthetransportoflabileandsolubleCtomicroorganisms:1)directreleaseoforganicsatanalreadyexistinghotspot.Thisisverycommoninallthreehotspotsofbioticorigin.2)Transportoforganicsdissolvedinwaterbyadvectionemassflow.Thisiscommoninallfourhotspotgroups.3)Transportbydiffusion.Becausethediffusioncoefficientsoflabileorganicsareverylowandrangefrom(10À7e10À5cm2sÀ1)(Kuzyakovetal.,2003;Raynaud,2010),microbialutilizationismuchfasterthantheCde-liverybydiffusion.Therefore,thetransportbydiffusioncanbedis-regardedforhotspotproduction.ThismakesthedirectinputandadvectionwithwaterflowthemainwaysofCtransporttohotspots.Thesecondmechanismethetransportofmicroorganismstothesubstrateeisrelevantmainlyforbranch-andfilament-formingmi-croorganisms,mainlyfungi,somecyanobacteria,streptomycetesandotheractinobacteria.Proliferationoffungalhyphaeenablesreachingthesubstrateallocatedmanycmandevendmfromthemothercellsveryfast.FungihaveahugeadvantageoverbacteriatoreachdistantlocationswithexcesslabileC:theabilityofhyphaetopenetratewaterfilmsinsoilporesbecausehyphaereleasehydrophobinstronglydecreasingsurfacetension(Talbot,1999).Therefore,hyphaecommonlyshowingrowthsintothedetritusphere(Wardleetal.,2002),rhizosphere(Thorn,2002)(Rillig,2004)andbiopores(Athmannetal.,2013).Thetransportofcellsinsoilbyadvectionorbysoilanimals(Thorpeetal.,1996)isgenerallypossible,butdoesnotplayasignificantrolefortheoriginortriggeringofthefourhotspotgroupsunderaerobicconditions.Thistransportbyadvectionaswellasothertransportmechanisms(chemotaxis-inducedflagellarmotility,spinning,flexing,glidingoversurfacesetc.)aresufficienttobringindividualmicroorganismstotheCsourceandmayberelevanttostartnewcoloniesatspotsofexcesslabileC.Thehotspotsunderanaerobicconditions(seebelow)exhibitthereversesituation:theconsumptionofoxygenisfasterthanitsreplacementbydiffusion.ThismakestheoriginofanaerobichotspotsdependentonslowdiffusionofO2throughporesfilledbywater.Theremovalofmicrobialmetabolitesethetransportoftrans-formationproductsoutofthehotspotsehasneverbeeninvesti-gated.Somemetabolitesmaybetoxicformicroorganismsathotspotsduringhotmoments.Thecommonexamplesaretheproductionoforganicacidssuchasacetateorpropionate,orthereleaseofexcessHþstronglydecreasingthepH.Inouropinion,thetransportoftheseproductsoutofhotspotsismainlydrivenbydiffusion(aslowprocess).Consequently,hotmomentsinsomecasesmayterminateduenotonlytoexhaustionoflabileC,butalsotoaccumulationoftoxicproducts.2.Spatialandtemporalcharacteristicsofhotspotsandhotmoments2.1.ThesizeofmicrobialhotspotsEstimatingthesizeofhotspotsandtheproportionofthetotalsoilvolumethattheyrepresentisamajorchallengeinsoilecology.Table2Connectionbetweenhotspotsandhotmoments.HotmomentsHotspotsRhizosphereDetritusphereBioporesAggregatesurfacesBiotic-Litterfall-RootingrowthXXX-RootdeathX-AnimalactivitiesAbiotic-Heavyrains-Snowmelting-Freezing/thawing-Drying/rewettingX-ErosioneventsXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXThehotspotsonthelandscapescalearenotthefocusofthisreview.See(McClainetal.,2003;Vidonetal.,2010).1Thenumberof“X”presentstheintensityoftheeffect:X-smalleffect,XXX-verystrongeffect.Thisassessmentwasdonebasedon‘expertknowledge’.188Y.Kuzyakov,E.Blagodatskaya/SoilBiology&Biochemistry83(2015)184e199
Correctestimationisessential1)torelateprocessintensitiestotherealvolumeinwhichtheprocessesareongoinginsteadoftotalsoilvolume(seeFigs.1),2)toclarifytheregulationofmicrobialdensity,3)toanalyzethecommunicationbetweenmicrobialcoloniesinhotspots(Gantneretal.,2006)and4)toconsidercompetitiveandsynergicinteractionsbetweenkeymicrobialgroupsinhotspots(Kaiseretal.,2014).Hotspotvisualizationstudiesshowedthattheareaswiththehighestactivitiesofvariousenzymescover:<5%(SpohnandKuzyakov,2013;Spohnetal.,2013),<5%(15Nuptakebymicrobialcellsintherhizosphere(Clodeetal.,2009),~5%basedonO2releaseand~1%basedonpHchangesintherhizosphere(Blossfeldetal.,2011;Rudolphetal.,2013),~1%forlocationswithintensiverhizodeposition(PauschandKuzyakov,2011).Nannipierietal.(2003)concludedthatlessthan5%oftheavailablesoilspaceisoccupiedbymicroorganismsinhotspots.Thespaceoccupiedbybacteriainsubsoilisaboutoneorderofmagnitudelowerandamountsto<0.2%(Nunanetal.,2003).Thisconfirmsthatsoilisa‘desert’inwhichlifeisdiscretelydistributed,especiallyconsideringthatevenunicellularmicroorganismsperformtheirfunctionsincolonies(Hinsingeretal.,2009)thatrepresenthotspotsofactivity.Thisassessment,however,requiresrefinementandspecificationforhotspotgroupsdevelopedunderspecificconditions.Therangeofhotspotsizesisverybroadandtheuncertaintiesareveryhigh(Fig.3,notelogarithmicscaleofbothaxes).Individualmicrobialcellsareinsufficienttobeacceptedashotspotsbecausetheyfunctionsarenotrelevantonthehigherscales.Therefore,the(micro)colonies,biofilmsandothercellassemblagesshouldbeconsideredasrelevantmicrobialhotspotsinsoil(Panikov,2010).Consequently,thesizeofmicrobialhotspotsisatleastafewmm(Grundmannetal.,2001;Dechesneetal.,2003;EickhorstandTippkotter,2008b;RaynaudandNunan,2014).ThesoilvolumesinwhichlabileCisreleasedintherhizosphereordetrituspherearemuchlargerthanthisminimalsize.Accordingly,thesizeofmi-crobialhotspotsreachesuptoafewmm(Fig.3).Visualizationofexudateallocationatroottipsshowedthattherespectivemicrobialhotspotsareabout2e3mmindiameterandupto10mmlong(PauschandKuzyakov,2011).Similarsizeswereobtainedbyvisualizingoxygenconsumption,pHandredoxchangesintherhizosphere(Blossfeldetal.,2011;Schmidtetal.,2011;RudolphFig.3.Spatialandtemporalscalesofmicrobialhotspotsinsoil.Notethatthealloca-tionoftheareascorrespondstothesizeanddurationofmicrobialhotspotsandhotmoments,butnottothesizeofthepropertiesthemselves(e.g.aggregatesurfacesmayexistyearsanddecades,butthedurationofhotspotsontheaggregatesurfacesislimitedbydays).LogarithmicYscalecorrespondstoh:hours,d:days,w:weeks,m:months,y:years.TheintensityofgrayonshadedareasonXandYaxisrepresentsschematicallythespatialandtemporalprobabilityofmicrobialhotspots.
etal.,2013),orenzymeactivitiesintherhizosphereanddetritu-sphere(SpohnandKuzyakov,2013).H2-oxidizingbacteriaandtheiractivitywerelogarithmicallydistributedinthefewmmproximitytotherhizobianodulesurface(LafavreandFocht,1983).Microbialabundancechangeswithin1e2mmfromtherootanddetritussurface(Marschneretal.,2012)oruptoseveralmminthedetri-tusphere(Moritsukaetal.,2004;Haetal.,2007).Thiscorrespondsroughlytotheestimationsbasedondestructivecuttingapproachesinboththerhizosphere(Kandeleretal.,2002;Kuzyakovetal.,2003;Saueretal.,2006;Marschneretal.,2012)anddetritu-sphere(Kandeleretal.,2002;Marschneretal.,2012).Simulatingtherhizosphereextensionbytheratesofrootexudationrevealedexudatediffusionanddecayrates(Raynaud,2010)extendingfrom0.5upto~10mm.Basedonthestudiesreviewedhere,weconcludethatthesizeofmicrobialhotspotsrangesover3-4ordersofmagni-tude:fromafewmmuptoseveralmm(Fig.3).Thisverybroadrangeof3-4ordersofmagnitudereflectsnotonlythevariationanduncertaintiesinthespatialdistributionofpropertiesbutespeciallyoftheprocesses.Becausewedefinethehotspotsbyprocessrates(Fig.1),thesizeofhotspotscanalsobeviewedasgovernedbymetabolismandnotbyarbitrarydistance(Focht,1992).Themicrobialmetabolicpathwaysstronglydependontheamountsofsubstrate(DippoldandKuzyakov,2013).ThisiswhytheCutilizationpatternanditsstabilizationinhotspotsarealsodifferentfromthatinbulksoil.Thedistributionofmicrohabitats(themeandistancebetweenpatches)stronglydependsonmicrobialgroups,substrateinputandporedistributionandrangefrom50mmtoafewmm(Dechesneetal.,2003).Astrongincreaseoftheinputrateofsubstrates,e.g.byincreasingrootdensityingrassland,mayleadtooverlappingindividualhotspots.Theresultisthathotspotsaffecttheentiresoil(Raynaud,2010).Onlyveryfewstudiesareavailableonthisissue,andweexpectthatbroadrangeswillbepresentedinthenearfuture.2.2.DurationofhotmomentsTheprocessratesinmosthotspotsarenotconstant,butvarywithtime.Thehotmomentscanbeoccasionalorregularaspartofperiodicprocesses(Table1).Theregularityofhotmomentsde-pendsonnaturalvegetationcyclessuchasannuallitterfallinautumnorintensiverootgrowthinspring(Philippotetal.,2009),orevendiurnalcyclesofphotosynthesis(Herronetal.,2013).Theimportanceofhotmomentsisraisedespeciallybytheshortlifetimeofmanyhotspots.Itischallengingtoestimateexperi-mentallythelifetimeofhotspotsandthustodrawconclusionsaboutthedurationofhotmoments.Thedurationofhotmomentsdependson:i)durationoftheinputoflabileC,andii)ratesofmicrobialutilizationofthelabileC.Theinputoflabileorganicsinsoil,e.g.asexudatesbyrootsorreleaseofsolubleorganicsfromdecomposinglitterorfromearthwormcoprolites,isnotveryfastandusuallytakesatleastafewdays(Polletal.,2010;Pauschetal.,2013).Microbialuptakeandtheutilizationperiodoforganicsdependontheirqualityandareusuallyveryshortforlabilesub-stances.Asreviewedfrom155soils,thehalflifetime(T½)ofaminoacidsisabout2.9h(Jonesetal.,2005)withalmostimmediateuptakebymicroorganismswithinafewminutes(RouskandNadkarni,2009;Glanvilleetal.,2012;HobbieandHobbie,2012).Thisis(much)shorterthanthedurationoftheinputand,conse-quently,thedurationofhotmomentsintherhizospheredependsmainlyontheinput.Aftertheinputintothehotspotstops,theratesofmicrobialutilizationbecomesignificant.AssumingthatT½ofotherlowmo-lecularweightorganicsubstances(e.g.carboxylicacids,sugars)issimilartothatofaminoacids(Jonesetal.,2005),hotspotlifetimeisY.Kuzyakov,E.Blagodatskaya/SoilBiology&Biochemistry83(2015)184e199189
inthedetrituspherebytheoutput,namelybythedecompositionrateoflitter.2.3.TransitionbetweenthehotspotsofmultipleoriginsThehotspotsdescribedabove(Fig.2,Table1)frequentlyhavemixedorigin.VariousprocessesandCsourcescontributedtotheirdevelopmentsimultaneouslyorsuccessively.Inthesubsoil(becauseofhighbulkdensity),rootscommonlygrowincracks(Rasaetal.,2012)anddeveloptheirrhizospherebetweentheaggregates,i.e.ontheirsurface(Fig.5).Whenthematurerhizosphereisestablished(Jonesetal.,2004),therootsdie,developingthedetritusphere(Fig.5).Aftermicrobialutilizationofdetritus,theremainingroot-originatedbioporesmaybeusedbyburrowinganimals(anddevelopdrilosphere)becauseof:i)betteraerationandmoremoisturecomparedwiththesur-roundingsoil(TiunovandScheu,1999;Uteauetal.,2013),ii)richnessinnutrientsandlabileC(Athmannetal.,2013;Kautzetal.,2013),andiii)easierpossibilitytomovedown-andup-wardsbecauseoflowerbulkdensity(Bengoughetal.,2011)andhigherporosity(Feeneyetal.,2006).Suchbioporesmaybereusedrepeatedlybynewlygrowingroots(Fig.5).Consequently,thetransitionfromaggregatesurfacestorhizospherethroughdetritusphereandfurthertobioporesebetweenallfourhotspotgroupsemayundergocycles.Manyhotspots,especiallyinsubsoil,havenotonlyamixedoriginandmixeduse,butalsoamixedageetheyarereutilizedbecauseoftheirpreferredhabitatconditionsforrootsand(micro)organisms.So,liferepeatedlyconcentratesatthelocationswithbeneficialconditionscomparedwithbulksoil.Thisisoneoftheecosystemself-engineeringpropertiesresultinginsoilstructuringandecolog-icaldevelopmentof(micro)habitats.Fig.4.14Cimagingofrelative14Cactivityattheroottipsatincreasingtimeafterla-belingofLoliumperennein14CO2atmosphere:6h,2d,and11dafterthe14Clabeling.Thecolorscalepresentsthe14Cactivityasdigitallightunits(DLU)(fromPauschandKuzyakov,2011,changed).
restrictedto10e20hafterinputoflabileCceases.ConsideringthedynamicnatureofCinputs(e.g.diurnaldynamicsofrootexuda-tion)itischallengingtodeterminethislifetime.Thetime-resolved14Cimagingafter14CO2pulselabelingofLoliumperenneenableddeterminingthelifetime(1e3days)ofhotspotsatroottips(Fig.4)(PauschandKuzyakov,2011).Suchhotspots,however,existlongerifsubstrateinputiscontinuous.Rootdevelopmentanddeathtransformstherhizospheretoadetrituspherehotspot(seebelow)withmuchlongerlifetime.Thelifetimeofdetrituspherehotspotsatdyingroots(screenedbyzymographyofcellulase,chitinaseandphosphataseactivities)was10e30days(SpohnandKuzyakov,2014).Longerhotmomentsinthedetrituspherevs.rhizosphereareexplainedbyprolongedreleaseoflabileorganicsfromdecayinglitter(Bastianetal.,2009;Polletal.,2010)andtheirrelativerecalcitrance(Table1).Weconcludethatthedurationofhotmo-mentsintherhizosphereislimitedbytheinputoflabileorganics,butFig.5.Transitionbetweenthehotspotsofmultipleorigins:1)Crackbetweenaggregates,2)Juvenilerhizosphere:rootingrowinginthecrackbetweenaggregates,3)Developingrhizosphere,4)Maturerhizosphere,5)Detritusphere:dyingroot,6)Biopore:occupationofrhizosphere-detritusphereenvironmentbyearthworms,7)Reuseoftheexistinghotspots:/backtoingrowingrootandtherhizosphere.BlackarrowsshowtheCreleasebyrhizodeposition;weightarrowspresenttheuptakeofwaterandnutrients;blackdottedlinesreflectmycorrhizalhyphae.
190Y.Kuzyakov,E.Blagodatskaya/SoilBiology&Biochemistry83(2015)184e199
Change of the parameter in hotspotscompared to bulk soil(number of times)
0123456Microbial CMicrobial NBacteriaFungiErgosterolAmoebaeNematodes x 0.3dsDNARespirationPhosphataseβ-GlucosidaseDehydrohenaseUreasePeptidase02Rhizosphere4681012ErgosterolRespiration x 0.2Bacterial growthFungal growthMicrobial 13CPhosphataseUrease0Input of LMWOS123Funct.DiversityCiliates abundanceC utilizationNO3- leachingVarious enzymesβ-GlucosidasePhosphataseAmino-peptidaseGlucosaminidase0Detritusphere123456Microbial CMicrobial NBact.phylotypesArchaeal diversityErgosterolRespirationBacterial growthFungal growth0Input of HMWOS369Microbial CBacterial VolumeFungal VolumeBact.AbundanceRespirationqCO2Microbial growthLag periodBioporesFig.6.Changesofmicrobialparameters(means±SD)invarioushotspots:intheRhizosphere(top),aftertheinputofLowMolecularWeightOrganicSubstances(LMWOS)insoil(2ndfromtop),intheDetritusphere(middle),aftertheinputofHighMolecularWeightOrganicSubstances(HMWOS)insoil(2ndfrombottom),andinBiopores(bottom)comparedtobulkuntreatedsoil.TheXaxesshowthechangesinnumberoftimescomparedtobulksoil.Straightverticaldottedline(X¼1.0)correspondstotheabsenceofchanges.Foreach
Y.Kuzyakov,E.Blagodatskaya/SoilBiology&Biochemistry83(2015)184e199
Table3RelativechangesofPLFAcontentbyactivation/de-activationofsoilmicrobialcommunityduringhotmoments.EffectofRelativechangesinPLFAcontentTotalFungalBacterialGramþHotspotsincomparisontobulksoilPlantroots(rhizosphere)↑1.5e1.7↑1.8e3.4↑1.3-↓1.2Plantgrowth↑1.7Plantspecies↑1e1.7Detritusphere↑1.8e5.1Detritusphere↑1.1e1.4Detritusphere↑1.2ActivationduringhotmomentsRewetting↑1.4e1.6Availablenutrients↑2.4Wheatstraw&fertilizer↑1.7↑1.9↑1.3BarleystrawLeaflitter↑1.5e4.7Sorghumresidues↑1.7e2Changeincompetition↑2.3Hotspotsexpiration-endofhotmomentsOneyearincubation↓3.5e3.6Soildepth↓3↓7.5e26DecreasingpH↓2.1↓2.2Grazing↓1.1e1.3↑1.0e1.6↑↑↑↑1.4e211e682e2.32.5e4↑↓1.1↑↓1.3↑1.8↑1e1.2↑2.1-↓1.6↑1.5-↓1.3↑1.1e1.3Grame↑1.1e1.3Denefetal.,2009Rajaniemietal.,2009Marschneretal.,2012.Luetal.,2004HamerandMakeschin,2009Baldrianetal.,2010Marschneretal.,2012.RouskandBaath,2007.Source191
↑2↑1e1.3↑501.1↑1.41.0↑4↑2.3e3↑1.4e2Y6e10↓3.5↑1.3↓1.5↓2↑↑↑↑↑1.21.71.51.21.3↑5.5↑2.2↑1.2McIntyreetal.,2009Ehlersetal.,2010AciegoPietriandBrookes,2009↑1.5↓Y2.7e5↓1.5↓1.7↓2.1↑2↑2RouskandBaath,2007.McIntyreetal.,2009WhiteandRice,2009Demolingetal.,2009FengandSimpson,2009WhiteandRice,2009Schutzetal.,2009Djukiketal.,2010AciegoPietriandBrookes,2009Klumppetal.,2009↓2.9e6↓2.7↓4.5↑meansincreaseand↓meansdecreaseofPLFAcontentfornumberoftimes.Thepart:Hotspotsincomparisontobulksoil-showsjustthecomparisonofPLFAsbetweenhotspotandbulksoil.Thesecondpart:Activationduringhotmoments-showsthechangesofPLFAsattheincreasestartofthehotmoment.Thepart:Hotspotsexpiration-endofhotmoments-showsthedecreaseofPLFAsattheendofthehotmoment.3.Microbialactivityasadriverofhotspotfunctioning3.1.MicrobialabundanceandactivityasrelatedtoprocessratesinhotspotsHotspotsarecharacterizedbyhighermicrobialabundance,resultingin2e3timesgreatertotalbiomasscomparedwithbulksoil(Marschneretal.,2012).Thetotalbiomass,however,representsmainlydormantmicroorganisms,whereasactivemicroorganismsperformmostbiochemicalprocesses.Thefractionofactivemicro-organismsisupto2timesgreaterintherhizospherethaninbulksoil(Blagodatskayaetal.,2014a).Inthedetritusphere,however,whereCdeliveryislongerandmicrobialcompetitionwithrootsisweaker(seebelow)thanintherhizosphere,theactivebiomassis4e20timesgreaterthaninbulksoil(Blagodatskayaetal.,2009).Theportionofactivemicroorganismsremaininginaphysiologi-callyalertstage(DeNobilietal.,2001)ismuchhigherinhotspotswithhighsubstrateavailabilityandlongerhotmoments.Thisre-sultsinmuchfastermicrobialresponsestoCinputintherhizo-sphereanddetrituspherecomparedtobulksoil(Pattersonetal.,2008;Polletal.,2008).Highermicrobialactivity(andabundance)inhotspotsledtolitterdecompositionatratesuptothreetimesthoseofbulksoil,resultingin2e10timeshigherconcentrationsofsolubleproducts(Blagodatskayaetal.,2009).Theactivityofhy-drolyticenzymesintherhizospherewas3e5timeshigher(Marschneretal.,2012;SpohnandKuzyakov,2013;Leeetal.,2013b)andtheN2Oemissionsinthedetrituspherewere2e9timesmoreintensive(Blagodatskayaetal.,2010)thaninbulksoil.Consequently,notonlytotalmicrobialbiomass,butespeciallytheportionofactivemicroorganisms,ishigherinhotspots.Thisleadstomuchfasterprocessratesthaninbulksoil(seeFig.1).InFig.6wesummarizedseveralstudiesonthechangesofmi-crobialparametersinhotspotsandduringhotmomentsinducedbyadditionofloworhighmolecularweightorganicstosoil(Fig.6).Themostintensivehotmomentswereinducedbyaddinglowmolecularweightorganics.Furthermore,someactivityparameters,e.g.respirationandmicrobialgrowthrates,increasedmorethanthecontentparameters,e.g.microbialCandergosterol(Fig.6).3.2.MicrobialdiversityandcommunitystructureinhotspotsHotspotsarecharacterizedbyhighermicrobialdiversitycomparedtoindividuallyscatteredmicrobialcellsinmineralsoil(Marschneretal.,2012;Leeetal.,2013b).Highersubstrateavail-abilitystimulatesmicrobialgrowthandshapescommunitystruc-turespecifictothehotspotgroups.Theabundanceoffungalandbacterialspeciescomparedtobulksoilincreasesmoreinthedetrituspherethanintherhizosphere(Table3).ThehigherincreaseinfungalthaninbacterialPLFAsintherhizosphere(bythefactor1.4)andespeciallyinthedetritusphere(bythefactor4.7)resultedinhigherfungal-to-bacterialratiosinbothhotspotscomparedwithbulksoil(Marschneretal.,2012;Turneretal.,2013)(Table3).Nonetheless,theincreaseofindividualfungal(upto50times,Ehlersetal.,2010)andGram(À)bacterial(upto5.5times,Aciegosubfigure:theparametersabovethefreelinecorrespondtochangesofpools,andtheparametersbelowthefreelinereflectthechangesoffluxesorofmicrobialactivities.Vmaxvaluesarepresentedforchangesofenzymeactivities.NotedifferentXscalesforthe5subfigures.TheXscalesfor1st,2ndand4thsubfigureswerecutforbetterpresentationoftheaveragevalues.NotethatthehighincreaseofNematodedensity(top)andRespirationintensity(2ndfromtop)weremultipliedby0.3and0.2,respectively,tobringthevaluesonthescaleconvenientforotherparameters.Theresultswerecollectedfromthefollowingstudies:ForRhizosphere:(NortonandFirestone,1991;AppuhnandJoergensen,2006;Renellaetal.,2006;BergandSteinberger,2008;Marschneretal.,2012;Troxleretal.,2012;Turneretal.,2013);ForLMWOS:(Renellaetal.,2006;LemanskiandScheu,2014;Leonetal.,2014;Reischkeetal.,2014);ForDetritusphere:(Bonkowskietal.,2000b;BergandSteinberger,2008;Marschneretal.,2012;Leeetal.,2013a;Xiao,2014);ForHMWOS:(RouskandBaath,2007);ForBiopores:(TiunovandScheu,1999;Troxleretal.,2012).
192Y.Kuzyakov,E.Blagodatskaya/SoilBiology&Biochemistry83(2015)184e199
PietriandBrookes,2009)PLFAsinthedetrituspherecanstronglyexceedthetotalPLFAincrease(Table3).Thus,microbialcommunitystructureinhotspotsspecificallydependsonsubstratecompositionandinputduration.Microbialcommunitystructurewithinaparticularhotspotgroupisaffectedbysubstratequality.Microbialdiversitydiffersintherhizosphereofplantspecies(Kowalchuketal.,2002;Turneretal.,2013)orevenalongtheroots(SchmidtandEickhorst,2014)anditchangesduringrootdevelopment(Remenantetal.,2009;SchmidtandEickhorst,2014).Similarly,microbialcommunitiesinthedetritusphereareaffectedbylitterqualityanddecompositionstage(Bastianetal.,2009;Esperschutzetal.,2013).Fungidominatemorestronglyinthedetritusphereunderconiferousvs.deciduouslitter(BlagodatskayaandAnderson,1998).Thedeclineofthefungal-to-bacterialratiointhedetrituspherewithdepthismorepronouncedunderconiferousvs.deciduousforest(Baldrian,2009).Also,thecontributionofarchaeatothestructureandfunctioningofhotspotsisimportant(Leeetal.,2013b).Thehigheractivityofhydrolyticenzymesinthedetrituspherevs.mineralsoildependsmainlyonthediversityofbacteriaandarchaea,butislessaffectedbyfungi(Leeetal.,2013b).Despitedifferencesinmicrobialcommunitystructurebetweenandwithinhotspotsatthemicro-scale,microbialfunctioningatthehigherscales,i.e.atthesoilprofileorecosystemlevels,remainssimilar(Parkin,1993).Functionalredundancyandtheexcessivemicrobialpoolprinciple2(Morris,2007;Youngetal.,2008;Kuzyakovetal.,2009;Ruampsetal.,2013)leadtohighsimilar-itiesinthefunctionsofhotspotsdifferinginmicrobialcommunitystructure.Insoilunderdiverseplantcommunitiessuchasgrass-lands,microbialfunctioning(e.g.utilizationoforganicC,assimi-lationofrootexudates,enzymeactivity)remainsratherstableunlesstheplantdiversitydropsbelowathresholdof4species(Loranger-Mercirisetal.,2006;Sanaullahetal.,2011).Thus,mi-crobialfunctioningattheecosystemlevelismuchmorestablethanthemicrobialcommunitystructure.3.3.MicrobialstrategiesinhotspotsMicrobialfunctionsinthehotspotsdependstronglyonthedominanceoftheecologicalgroupssuchasr-andK-strategists(FontaineandBarot,2005;Nottinghametal.,2009).Thisdomi-nance,however,isnotdirectlyrelatedtophylogenicstructureofmicrobialcommunitybecausebothr-andK-strategistsareabun-dantwithinbacterialandfungalphylaaswellaswithinGramþandGram-bacteriagroups(Fiereretal.,2007).Thedominantstrategycanbedeterminedbythekineticsandefficiencyofmicrobialgrowth(Panikov,1995;Stenstr€om,1998;Nocentinietal.,2010).Accordingtothekineticparametersofmicrobialcommunities(carbonuseefficiency,CUEistheamountofCinmicrobialbiomasscomparedtotheCinthesubstrate;Km:Michaelisconstant;m:microbialgrowthrates,etc.),theinputofsmallamountsoflabilesubstratesactivatesfast-growingr-strategists(Blagodatskayaetal.,2009,2010).Thisiscommonintherhizosphere(Philippotetal.,2013),wheretheutilizationofsubstrateisatleast2timeslessefficient(CUE~0.2)thaninbulksoil(Blagodatskayaetal.,2007,2009).Dominationofslow-growingK-strategistsisattributedtomicrobialcommunitiesdecomposingplantresidues2Excessivepoolprinciple(or‘storageeffect’,MorrisandBlackwood,2007):soilshaveanexcessivepooloftotalmicrobialbiomass.Onlyasmallportionofmicro-organismsisactive,butaverylargedormantpoolwithabroadspectrumofpo-tentialmetabolicactivitiesprovidesaquickgrowthresponseafterinputofanylabilesubstrate.(Blagodatskayaetal.,2009),i.e.inthedetritusphere,whichwasconfirmedbyahighCUEof~0.6(Thietetal.,2006).Microbialfunctioninginhotspotscanbedistinguishedbythedynamicsofcatabolicandanabolicprocessesduringgrowth.Highsubstrateavailabilityintherhizosphereleadstoasimultaneousincreaseofcatabolic(detectedbyrespiration)andanabolic(detectedbyDNAincrease)activities(Blagodatskayaetal.,2014a).Inthedetritusphere,however,theincreaseofcellcomponentcontents(ergosterol,bacterialandfungalPLFAs)wasdelayedfor10dayscomparedtotheriseinrespiration(RouskandBaath,2007).Functionaldifferencesinthemicrobialcommunitiesinhotspotscanbeassessedbytheaffinityofenzymestosubstrates(Km):itislowerforr-strategists(theKmishigher).Inaccordancewithecologicalprinciples,theKmincreasedintherhizospherebutdecreasedinthedetrituspherecomparedtobulksoil(Blagodatskayaetal.,2009).Thisdemonstratesthedifferencesinfunctionaltraitsofmicroorganismsinhotspotsofvariousorigins.Specificmicrobialgrowthratesetheintrinsicfeatureofthedominantpopulation(Birganderetal.,2013)eareusefultodistinguishhotspots.Microbialgrowthrateswere1.5slowerinthedetrituspherethanintherhizosphere(Blagodatskayaetal.,2009).Slowgrowthrates,however,donotmeanlowactivity.Theactivebiomasswasca.10timesgreaterindetrituspherethanintherhizosphere.ThisillustratesthehigherinputoflabileCinthelatter,butlongerdurationintheformer.Therefore,theincreaseofmi-crobialactivityintherhizosphereismuchhigher,butthelifetimeoftherhizospherehotspotsismuchshorterthanthatinthedetritusphere(Fig.3).3.4.CompetitioninhotspotsThehighmicrobialactivity(andabundance)intherhizosphere(LynchandWhipps,1990),detritusphere(Kandeleretal.,1999;Polletal.,2008;Marschneretal.,2012)andbiopores(TiunovandScheu,1999,2000;TiunovandDobrovolskaya,2002)iswelldemonstrated,butlittleattentionhasbeenpaidtothecompetitionbetweenorganismsinthehotspots(Alpheietal.,1996;Bonkowskietal.,2000a;Marschneretal.,2012).ExcesslabileCinhotspotsleadstonutrientlimitation(Marschneretal.,2012).Rhizosphereanddetrituspheredifferintheircompetitionstructure.Whilecompetitioninthedetritusphereoccurswithinorbetweenmi-crobialspecies,intherhizosphereitoccursmainlybetweenplantsandmicroorganisms(KuzyakovandXu,2013).Thelatterisstronglyaffectedbynutrientuptakebyrootsandcanreducemicrobialgrowth,especiallyiftheplantisastrongcompetitorforN(Bonkowskietal.,2000a).Furthermore,protozoangrazingcandelaymicrobialdecompositionoforganicsinthedetritusphere(Bonkowskietal.,2000b;Blagodatskayaetal.,2014b).Thisresultsinfluctuationsofprocessrateseacceleratedactivityinhotspotsmaybefollowedbyretardationofmicrobialgrowth(Zelenevetal.,2006;vanBruggenetal.,2008)andenzymeactivities(Lavrent'evaetal.,2009).Inallhotspots,Cavailabilitycommonlydecreasesaftertheinputisfinished(Bastianetal.,2009;Polletal.,2010).Thisisbecausethemostlabilesubstratesarepreferentiallyutilizedatthestartofhotmomentsandlesslabilerecalcitrantorganicsremain(TheuerlandBuscot,2010).Therefore,thedeclineinactivitywithinthehotspotsisprolongedbecauseofthedecliningsubstratequality(andquantity).Thisboostscompetitionattheendofhotmoments.Thisisconfirmedbya3.5e26folddecreaseinthePLFAcontentintherhizosphereanddetritusphereattheendofhotmoments(FengandSimpson,2009;Schutzetal.,2009,Table3).ThePLFAsoffungiandGram(À)bacteriadecreasemorestronglythandoGram(þ)bacteria(AciegoPietriandBrookes,2009),probablybecauseofthelatter'shighercompetitiveabilitieswhenhotY.Kuzyakov,E.Blagodatskaya/SoilBiology&Biochemistry83(2015)184e199193
momentsterminate.Theexhaustionofsubstratesandboostedcompetitionattheendofhotmomentsfrequentlytriggerprimingeffects(Fontaineetal.,2003).3.5.SignalingpathwaysathotmomentsTheabilitytorapidlyswitchphysiologicalstates(i.e.fromac-tivitytodormancyandviceversa)dependingonsubstrateavail-abilityisanimportantmicrobialadaptationtodynamicenvironmentalconditionsinthehotspots.Besidesphysico-chemicaldrivers(e.g.moistureandtemperature)thatinduceashiftfromdormancytoactivityandback,theactivation/deactiva-tionmechanismsbasedonsignalingmoleculesareparticularlyimportant.Thetransitionofactivecellstodormancyasanoutcomeofquorumsensing,i.e.bysecretionofmoleculesinducingreduc-tionofpopulationdensity,isrelativelywellstudied(GrayandSmith,2005).Little,however,isknownaboutbiochemicalpath-waysoftheinverseprocesseactivationofdormantcellsinhot-spots.Theoriginofinducersesubstancesoreventsinitiatingmicrobialactivationeregulatesthedifferencesbetweenthetwoinversesignalings.Inhotspots,quorumsensingservestoauto-regulatepopulationdensitybysecretingsignalingmoleculesthatinducetheexpressionofgenesresponsibleforproducingantimi-crobialsubstancesandforcellmortality(Winsonetal.,1995;Redfield,2002;Ekschmittetal.,2005).Thus,theswitchfromac-tivitytodormancyisregulatedbyinternalsignals:autoinducermolecules(e.g.g-butyrolactones,gomoseryllacton)secretedbythemicrobialpopulation(Raffaetal.,2005).Incontrast,externalsignalsareoftenrequiredtowakemicrobesupfromdormancytoactivity.Suchexternaltriggeringsignalsoccuratthestartofhotmoments,whenlowamountsoflabileCsuchasglucose,aminoacidsoryeastextractserveasexternalinducersactivatingmicroorganisms(DeNobilietal.,2001).Thegeneralpatternsofsuchsignalingaredescribedforplant-growth-promotingbacteria,whereastherolesofinternalandexternalsignalsintheactivation/deactivationmechanismsofspecificmicrobialgroupsinthehotspotsremaintobeclarified(GrayandSmith,2005).4.Methodsforidentificationandspatialanalysisofhotspots4.1.ApproachesforhotspotidentificationIdentifyinghotspotsinsoilisverychallengingbecause:i)identificationshouldfocusonprocessintensities(andnotoncon-tentsorconcentrations),ii)theprocessesshouldbetracedinun-disturbedsoil,withoutmixingofhotspotswithbulksoil(Ruampsetal.,2011).Itisveryeasytopostulatetheexistenceofmicroen-vironmentswithanyrequiredpropertybutdifficulttoactuallydeterminetheirexistenceandsignificance(Prosser,1989).Thisisespeciallychallengingbecausenearlyallsoilanalysesusemixedsamples(Parkin,1993)andarefocusedondeterminingcontents(notintensities).Thefirstapproachestoidentifyhotspots(Lusteretal.,2009)involvedi)lightandelectronmicroscopy,ii)microelec-trodesor-sensors,iii)simpleseparationofsoiladheredtoroots(rhizosphere),iv)separationoftherootzonewithvariousgauzesand/orv)cuttingofsoilwithincreasingdistancefromtherootsurface(HelalandSauerbeck,1981;Kandeleretal.,2002).Theseapproaches,however,aredestructive,havemanyotherlimitations(Parkin,1993)andarethereforenotdiscussedhere.Thepre-requisitesforapproachestoidentifyhotspotsare:i)undisturbedsoilshouldbeanalyzed,ifpossiblebynon-invasiveapproaches,ii)theanalysisshouldbecompletedwithinashorttime(muchshorterthanthedurationofthehotmoments),iii)themethodshouldfocusonprocessintensities(notsolelyonanalyzingcontents),iv)thespatialresolutionofthemethodshouldbemuchsmallerthanhotspotsize.Onlyveryfewapproachesfulfilltheserequirements(Table4).Thefirsttrialstoidentifyhotspotsinvolvedidentifyingmicroor-ganismsinthinsections(Jones,1964)andautoradiography(Hendriksetal.,1981;Romheld,1986).pHchangeswerevisualizedingels(Hinsingeretal.,2009)orbyinstallingpHandredoxmi-croelectrodesclosetotheroots(FlessaandFischer,1992).Autora-diographyanditsfollow-upeimagingeenablelocalizationofrhizodeposits(Roslingetal.,2004;Wichernetal.,2011;Rasmussenetal.,2013)andofnutrientuptakezones(Rubioetal.,2004).Theselocalizations,however,donotnecessaryreflectmicrobialhotspots.Newlydevelopedplanaroptodesenabletheanalysisofthe2DdistributionofpH,O2andCO2partialpressures,temperatureandionconcentrationsinsoil(Blossfeld,2013;Rudolphetal.,2013).Theseparameterspartlyreflectmicrobialactivity(CO2/O2changes).Recentlyelaboratedsoilzymographyidentifieshotspotsofactiv-itiesofvariousenzymes:protease,amylase,acidandalkalinephosphatases,cellulaseandchitinase(SpohnandKuzyakov,2013;Spohnetal.,2013).Microbialhotspotshavebeenidentifiedandtheirdependenceonlocalenvironmentalconditionsbettervisu-alized(Rasaetal.,2012)bythin-sectionmicroscopyoffixedandpolishedsoilsamplesstainedwithrespectivedyes(Nunanetal.,2001,2002;EickhorstandTippkotter,2008a).Theothergroupofveryrapidlydevelopingapproachesisbasedonfluorescenceinsituhybridization(FISH),whichenablesidenti-fyingnotonlymicrobialhotspotsbutalsovariousmicrobialgroupswithinthehotspots(SchmidtandEickhorst,2014).CombinationsofFISHwithcatalyzedreporterdeposition(CARD-FISH(SchmidtandEickhorst,2013),withMicroAutoRadiography(MAR-FISH)(Teiraetal.,2004),withelectronmicroscopy(Gold-FISH,(Schmidtetal.,2012),ornanoscalesecondary-ionmassspectroscopy(MusatTable4Themostfrequentlyusednon-destructiveapproachesatoidentifymicrobialhotspotsinsoilandtherelevantparametersandprocesses.ApproachesbAutoradiography,PhosphorimagingMicroelectrodesPlanaroptodesZymographyComputertomographycFISH,CARD-FISH,Gold-FISHPolishedsoilsamplesThinsectionsmicroscopyBiologicalthinsectionsProcess/parameterRhizodeposition,nutrientuptake(P,K,Ca,…)pH,Eh3ÀO2,pH,CO2,NHþ4,PO4,Temperature,EhVariousenzymesPoredistributionandsizeVariousmicrobialgroupsBacterialgroupsBacterialgroups,couplingwithFISH,16S-rRNABacterialcellsConditionsLab,radioactiveisotopesonlyLab(field)LabLab(field)LabLabLab(field)LabLabResolution<100mmmm>100mm Thiscallsforrevisingtheratesofmanyprocessesinsoil.Thecommonopinionisthatmanyprocesses,especiallyrelatedtoCturnoverinsoil,areveryslow.Thisopinionoriginates1)fromthetraditionalsamplingandanalysisofmixedsamples,whereaverysmallhotspotvolumeismixedwiththeremaining95e99%volumeofbulksoil(Parkin,1993)and2)fromgreenhousegasemissionstudiesinfieldorlaboratoryincubations,wherethetotalfluxesareaveragedforasoilsurfaceorweight.Nonetheless,upto100-times-higherprocessratesinhotspotsclearlyshowthatsoilsareveryreactivesystems.EspeciallyCtransformationscanbeboostedbyremovingthelimitationbylabileorganicsandbyactivatingdormantmicroorganisms.Twogroupsofprocessesstartathotmoments:i)productionandreleaseofexoenzymesthatcandecomposeboththeorganicsreleasedbytheinputandtherecal-citrantsoilorganicmatter(SOM),and2)microbialgrowthtrig-geredbylabileCrequiresothernutrientsinstoichiometricratios,leadingtominingofthesenutrientsfromSOM.Accordingly,bothprocessgroupsaccelerateSOMdecompositioneleadingtoprimingeffects.ThefrequentlymeasuredacceleratedSOMdecomposition(priming)of20e50%comparedtothatinbulksoil(Chengetal.,2014)shouldthereforeberelatedtohotspotvolume(1e10%).Ourconclusionisthattherealintensityofprimingeffectswithinhotspotsisabout10e100timeshigherthanSOMdecompositioninbulksoil.SomeprocesseslocalizedinsmallsoilvolumesandongoingunderO2limitationcannotbeassociateddirectlytooneofthefourhotspotgroupsmentionedabove.Goodexamplesofsuchprocessesaredenitrification(Parkin,1987,1993;Grundmannetal.,2001;Groffmanetal.,2009;BlagodatskyandSmith,2012)orCH4pro-duction(Conrad,1996).TheseprocessesoccurinlocationswithlowO2level(<10%)andhighmoisture,e.g.withinaggregates,whereintensiveconsumptionofelectronacceptorsisnot(ortooslowly)replenishedbyO2diffusion(Focht,1992;Grundmannetal.,2001;BlagodatskyandSmith,2012).Thefourgroupsofhotspotsunderoxicconditions(Table1,Fig.2)arethusproducedbyfastinflowoflabileC.Incontrast,thehotspotsunderanoxicconditionsandrelateddenitrificationandCH4productionaretriggeredbyslowdiffusionofO2(Focht,1992).5.2.PoolsandconcentrationsdonotreflectthefluxesandprocessesMicroorganismsinsoilhotspotstakeupthelabileorganicsalmostimmediately(Fischeretal.,2010;RouskandJones,2010)andconsumethemwithinafewhours(Jonesetal.,2005).Suchquickuptakereflectstheexcessivepoolprinciple(Kuzyakovetal.,2009):thetinyfractionofmicroorganismsthatispermanentlyactivehasexcessuptakecapacity(highVmax)forlargeamountsoflabileC.Thisabilityforfastuptakeisespeciallypronouncedatlowsubstrateconcentrations(lowKm¼highsubstrateaffinity).Therefore,thesolubleCconcentrationsareusuallyverylowandvaryfromseveralmgtomaximally100e200mgCgÀ1soil(NguyenandHenry,2002;Bastidaetal.,2006;Waldropetal.,2006).Thehighinputoflabileorganicsinthehotspotsbyrootsordecomposedlitteriscompensatedbyveryfastmicrobialuptakeanddecompo-sition.Thehighinputoforganicsstimulatestheirfasterutilizationinthehotspots(Fig.6).Thus,theaccelerationoffluxes(highinputandoutput)ismuchhigherthantheincreaseofthestocks.Thiscomplicatestheanalysisofhotspotsbecausemostanalyticalmethodsinsoilscience(andinthemostotherenvironmentalsci-ences)focusoncontentandconcentrations,notonturnoverorfluxes.6.ConclusionsandoutlookThisreviewanalyzedtheorigin,propertiesandfunctionsofmicrobialhotspotsandhotmomentsinsoil,aimingtounderlinetheimportanceofspatialandtemporalbiologicalinhomogeneityofsoilsatthemicroscale.Soilphysicshasintensivelyinvestigatedthespatialinhomogeneityofsoilsatnano-andmicro-(butalsoatmeso-andmacro-)scalesoveratleastthelast3-4decades(Webster,2000;HeuvelinkandWebster,2001).Althoughspatialmicrobialinhomogeneityinsoilistacitlyaccepted,onlyveryfewstudieshavefocusedonmicrobialhotspotsandhotmomentsandonapproachesallowingtheirexperimentalanalysis,especiallyunderfieldconditions.Thisdiscrepancyintheprogressbetweensoilphysicsandbiologyisbecausevarioussoilphysicalparametersrepresenttheratesofabioticprocessesmuchbetterthantheydomicrobialtransformations.Thus,microbialbiomasscontentinnowayreflectsmicrobialactivity(BlagodatskayaandKuzyakov,2013).ThiscallsformeasuringmicrobialprocessesandCfluxes(whichismuchmoredifficult).Furthermore,themethodstoseparate,tosample,toanalyze,andtostatisticallyevaluatethespatialvari-abilityaremuchlessdevelopedinsoilbiologythaninsoilphysics.MostmicrobialhotspotsarecharacterizedbyahighinputoflabileCandenergy,temporarily(hotmoments)removingthelimitationcommonforbulksoil.ThemostimportanthotspotswithprimaryinputofCaretherhizosphereanddetrituspherebecauselabileCisreleasedbylivingrootsordecomposedlitter.Moststudiesonhotspotshaveconcentratedontherhizosphereanddetritusphere;fewresultsareavailableonmicrobialactivitiesandprocessesinotherhotspotgroups(bioporesanddrilosphere,aggregatesurfaces,animalfaecesandbodies).Althoughhotspotsoccupyonlyasmallportionofsoilvolume(usuallybetween1and5%,oreven0.2%insubsoil),theprocessratesareuptotwoordersofmagnitudefasterthaninbulksoil.Therefore,smallspatialsizeis(over)compensatedby(very)highprocessrates.Mostprocessesmeasuredinmixedsoilsamplesareprobablyactuallytakingplaceinhotspots.Thisshouldbespecifiedandquantifiedforthebroadrangeofmicrobialprocessesinsoil,aswasdoneearlierfordenitrification(Parkin,1987).Itisnecessarytodevelopapproachesforvisualizing,samplingandanalyzinghotspotsseparatelyfromthebulksoilinordertobetterunderstandsoilprocesses.Thisisverychallengingbecauseanysamplingleadstodisturbance,potentiallyalteringprocessin-tensitiesandevenprocessdirectionscomparedtoundisturbedconditions.Ourresearchtoolsshouldcorrespondtothespatialdistributionandtemporalfunctioningofmicroorganismsethemaindriversofbiogeochemicalprocessesinsoil.Thisisaprereq-uisiteforunderstandingmicrobialmechanismsandforprocess-basedmodelingofbiogeochemicalcycles.AcknowledgmentsWethanktwoanonymousreviewersforveryhelpfulsugges-tions.WearegratefulfortheorganizersandparticipantsoftheGermanSoilScienceSociety(DBG)workshop:‘Soilprocesseseisthewholesystemregulatedathotspots?eFrommicro-scalestothepedon”,whichunderlinedtheimportanceofhotspotsforsoilprocesses.ThecontributionofEBwassupportedbytheRussianScientificFoundation(projectN14-14-00625).WethankYueSunforpreparingthepicturesforFigs.2and5.ReferencesAciegoPietri,J.C.,Brookes,P.C.,2009.SubstrateinputsandpHasfactorscontrollingmicrobialbiomass,activityandcommunitystructureinanarablesoil.SoilBiology&Biochemistry41,1396e1405.http://dx.doi.org/10.1016/j.soilbio.2009.03.017.Alphei,J.,Bonkowski,M.,Scheu,S.,1996.Protozoa,NematodaandLumbricidaeintherhizosphereofHordelymuseuropaeus(Poaceae):faunalinteractions,responseofmicroorganismsandeffectsonplantgrowth.Oecologia106,111e126.196Y.Kuzyakov,E.Blagodatskaya/SoilBiology&Biochemistry83(2015)184e199 Appuhn,A.,Joergensen,R.G.,2006.Microbialcolonisationofrootsasafunctionofplantspecies.SoilBiology&Biochemistry38,1040e1051.Athmann,M.,Kautz,T.,Pude,R.,Koepke,U.,2013.Rootgrowthinbiopores-evaluationwithinsituendoscopy.PlantandSoil371,179e190.Baldrian,P.,2009.Microbialenzyme-catalyzedprocessesinsoilsandtheiranalysis.PlantSoilandEnvironment55,370e378.Baldrian,P.,Merhautova,V.,Cajthaml,T.,Petrankova,M.,Snajdr,J.,2010.Small-scaledistributionofextracellularenzymes,fungal,andbacterialbiomassinQuercuspetraeaforesttopsoil.BiologyandFertilityofSoils46,717e726.http://dx.doi.org/10.1007/s00374-010-0478-4.Bastian,F.,Bouziri,L.,Nicolardot,B.,Ranjard,L.,2009.Impactofwheatstrawdecompositiononsuccessionalpatternsofsoilmicrobialcommunitystructure.SoilBiology&Biochemistry41,262e275.Bastida,F.,Moreno,J.L.,Hernandez,T.,Garcia,C.,2006.Microbiologicalactivityinasoil15yearsafteritsdevegetation.SoilBiology&Biochemistry38,2503e2507.Beare,M.H.,Coleman,D.C.,Crossley,D.A.,Hendrix,P.F.,Odum,E.P.,1995.Ahierarchicalapproachtoevaluatingthesignificanceofsoilbiodiversitytobiogeochemicalcycling.PlantandSoil170,5e22.Bengough,A.G.,McKenzie,B.M.,Hallett,P.D.,Valentine,T.A.,2011.Rootelongation,waterstress,andmechanicalimpedance:areviewoflimitingstressesandbeneficialroottiptraits.JournalofExperimentalBotany62,59e68.Berg,N.,Steinberger,Y.,2008.RoleofperennialplantsindeterminingtheactivityofthemicrobialcommunityintheNegevDesertecosystem.SoilBiology&Biochemistry40,2686e2695.Birgander,J.,Reischke,S.,Jones,D.L.,Rousk,J.,2013.TemperatureadaptationofbacterialgrowthandC-14-glucosemineralisationinalaboratorystudy.SoilBiology&Biochemistry65,294e303.Blagodatskaya,E.,Blagodatsky,S.,Anderson,T.H.,Kuzyakov,Y.,2014a.Microbialgrowthandcarbonuseefficiencyintherhizosphereandroot-freesoil.PlosOne9.Blagodatskaya,E.,Dannenmann,M.,Gasche,R.,Butterbach-Bahl,K.,2010.Micro-climateandforestmanagementalterfungal-to-bacterialratioandN2O-emis-sionduringrewettingintheforestfloorandmineralsoilofmountainousbeechforests.Biogeochemistry97,55e70.Blagodatskaya,E.,Khomyakov,N.,Myachina,O.,Bogomolova,I.,Blagodatsky,S.,Kuzyakov,Y.,2014b.Microbialinteractionsaffectsourcesofpriminginducedbycellulose.SoilBiology&Biochemistry74,39e49.Blagodatskaya,E.,Kuzyakov,Y.,2013.Activemicroorganismsinsoil:criticalre-viewofestimationcriteriaandapproaches.SoilBiology&Biochemistry67,192e211.Blagodatskaya,E.V.,Anderson,T.H.,1998.InteractiveeffectsofpHandsubstratequalityonthefungal-to-bacterialratioandQCO(2)ofmicrobialcommunitiesinforestsoils.SoilBiology&Biochemistry30,1269e1274.Blagodatskaya,E.V.,Blagodatsky,S.A.,Anderson,T.H.,Kuzyakov,Y.,2007.PrimingeffectsinChernozeminducedbyglucoseandNinrelationtomicrobialgrowthstrategies.AppliedSoilEcology37,95e105.Blagodatskaya,E.V.,Blagodatsky,S.A.,Anderson,T.H.,Kuzyakov,Y.,2009.Con-trastingeffectsofglucose,livingrootsandmaizestrawonmicrobialgrowthkineticsandsubstrateavailabilityinsoil.EuropeanJournalofSoilScience60,186e197.Blagodatsky,S.,Smith,P.,2012.Soilphysicsmeetssoilbiology:towardsbettermechanisticpredictionofgreenhousegasemissionsfromsoil.SoilBiology&Biochemistry47,78e92.Blagodatsky,S.A.,Yevdokimov,I.V.,Larionova,A.A.,Richter,J.,1998.Microbialgrowthinsoilandnitrogenturnover:modelcalibrationwithlaboratorydata.SoilBiology&Biochemistry30,1757e1764.Blossfeld,S.,2013.Lightforthedarksideofplantlife:-Planaroptodesvisualizingrhizosphereprocesses.PlantandSoil369,29e32.Blossfeld,S.,Gansert,D.,Thiele,B.,Kuhn,A.J.,Losch,R.,2011.Thedynamicsofox-ygenconcentration,pHvalue,andorganicacidsintherhizosphereofJuncusspp.SoilBiology&Biochemistry43,1186e1197.Bonkowski,M.,Cheng,W.X.,Griffiths,B.S.,Alphei,G.,Scheu,S.,2000a.Microbial-faunalinteractionsintherhizosphereandeffectsonplantgrowth.EuropeanJournalofSoilBiology36,135e147.Bonkowski,M.,Griffiths,B.,Scrimgeour,C.,2000b.Substrateheterogeneityandmicrofaunainsoilorganic'hotspots'asdeterminantsofnitrogencaptureandgrowthofryegrass.AppliedSoilEcology14,37e53.Borisov,S.M.,Seifner,R.,Klimant,I.,2011.Anovelplanaropticalsensorforsimul-taneousmonitoringofoxygen,carbondioxide,pHandtemperature.AnalyticalandBioanalyticalChemistry400,2463e2474.Borken,W.,Matzner,E.,2009.ReappraisalofdryingandwettingeffectsonCandNmineralizationandfluxesinsoils.GlobalChangeBiology15,808e824.Brown,G.G.,Barois,I.,Lavelle,P.,2000.Regulationofsoilorganicmatterdynamicsandmicrobialactivityinthedrilosphereandtheroleofinteractionswithotheredaphicfunctionaldomains.EuropeanJournalofSoilBiology36,177e198.Carminati,A.,Kaestner,A.,Hassanein,R.,Ippisch,O.,Vontobel,P.,Fluhler,H.,2007.Infiltrationthroughseriesofsoilaggregates:neutronradiographyandmodeling.AdvancesinWaterResources30,1168e1178.Carminati,A.,Vetterlein,D.,Weller,U.,Vogel,H.J.,Oswald,S.E.,2009.Whenrootslosecontact.VadoseZoneJournal8,805e809.Carminati,A.,Zarebanadkouki,M.,2013.Commenton:“neutronimagingrevealsinternalplantwaterdynamics”.PlantandSoil369,25e27.Cheng,W.X.,Parton,W.J.,Gonzalez-Meler,M.A.,Phillips,R.,Asao,S.,McNickle,G.G.,Brzostek,E.,Jastrow,J.D.,2014.Synthesisandmodelingperspectivesofrhizo-spherepriming.NewPhytologist201,31e44.Christou,M.,Avramides,E.J.,Jones,D.L.,2006.DissolvedorganicnitrogendynamicsinaMediterraneanvineyardsoil.SoilBiology&Biochemistry38,2265e2277.Clode,P.L.,Kilburn,M.R.,Jones,D.L.,Stockdale,E.A.,Cliff,J.B.,Herrmann,A.M.,Murphy,D.V.,2009.InsitumappingofnutrientuptakeintherhizosphereusingnanoscalesecondaryionmassSpectrometry.PlantPhysiology151,1751e1757.Conrad,R.,1996.Soilmicroorganismsascontrollersofatmospherictracegases(H-2,CO,CH4,OCS,N2O,andNO).MicrobiologicalReviews60,609-þ.DeNobili,M.,Contin,M.,Mondini,C.,Brookes,P.C.,2001.Soilmicrobialbiomassistriggeredintoactivitybytraceamountsofsubstrate.SoilBiology&Biochem-istry33,1163e1170.Dechesne,A.,Pallud,C.,Debouzie,D.,Flandrois,J.P.,Vogel,T.M.,Gaudet,J.P.,Grundmann,G.L.,2003.Anovelmethodforcharacterizingthemicroscale3Dspatialdistributionofbacteriainsoil.SoilBiology&Biochemistry35,1537e1546.Demoling,L.A.,Baath,E.,Greve,G.,Wouterse,M.,Schmitt,H.,2009.Effectsofsulfa-methoxazoleonsoilmicrobialcommunitiesafteraddingsubstrate.SoilBiology&Biochemistry41,840e848.http://dx.doi.org/10.1016/j.soilbio.2009.02.001.Denef,K.,Roobroeck,D.,ManimelWadu,M.C.W.,Lootens,P.,Boeckx,P.,2009.Mi-crobialcommunitycompositionandrhizodeposit-carbonassimilationindifferentlymanagedtemperategrasslandsoils.SoilBiology&Biochemistry41,144e153.http://dx.doi.org/10.1016/j.soilbio.2008.10.008.Dippold,M.A.,Kuzyakov,Y.,2013.Biogeochemicaltransformationsofaminoacidsinsoilassessedbyposition-specificlabelling.PlantandSoil373,385e401.Djukic,I.,Zehetner,F.,Mentler,A.,Gerzabek,M.H.,2010.MicrobialcommunitycompositionandactivityindifferentAlpinevegetationzones.SoilBiology&Biochemistry42,155e161.http://dx.doi.org/10.1016/j.soilbio.2009.10.006.Eickhorst,T.,Tippkotter,R.,2008a.Detectionofmicroorganismsinundisturbedsoilbycombiningfluorescenceinsituhybridization(FISH)andmicropedologicalmethods.SoilBiology&Biochemistry40,1284e1293.Ehlers,K.,Bakken,L.R.,Frostegard,A.,Frossard,E.,Buenemann,E.K.,2010.Phos-phoruslimitationinaFerralsol:ImpactonmicrobialactivityandcellinternalPpools.SoilBiology&Biochemistry42,558e566.http://dx.doi.org/10.1016/j.soilbio.2009.11.025.Eickhorst,T.,Tippkotter,R.,2008b.Improveddetectionofsoilmicroorganismsus-ingfluorescenceinsituhybridization(FISH)andcatalyzedreporterdeposition(CARD-FISH).SoilBiology&Biochemistry40,1883e1891.Ekschmitt,K.,Liu,M.Q.,Vetter,S.,Fox,O.,Wolters,V.,2005.Strategiesusedbysoilbiotatoovercomesoilorganicmatterstability-whyisdeadorganicmatterleftoverinthesoil?Geoderma128,167e176.Esperschutz,J.,Zimmermann,C.,Dumig,A.,Welzl,G.,Buegger,F.,Elmer,M.,Munch,J.C.,Schloter,M.,2013.Dynamicsofmicrobialcommunitiesduringdecompositionoflitterfrompioneeringplantsininitialsoilecosystems.Bio-geosciences10,5115e5124.Feeney,D.S.,Crawford,J.W.,Daniell,T.,Hallett,P.D.,Nunan,N.,Ritz,K.,Rivers,M.,Young,I.M.,2006.Three-dimensionalmicroorganizationofthesoil-root-microbesystem.MicrobialEcology52,151e158.Feng,X.,Simpson,M.J.,2009.Temperatureandsubstratecontrolsonmicrobialphospholipidfattyacidcompositionduringincubationofgrasslandsoilscon-trastinginorganicmatterquality.SoilBiology&Biochemistry41,804e812.http://dx.doi.org/10.1016/j.soilbio.2009.01.020.Fierer,N.,Bradford,M.A.,Jackson,R.B.,2007.Towardanecologicalclassificationofsoilbacteria.Ecology88,1354e1364.Fischer,H.,Ingwersen,J.,Kuzyakov,Y.,2010.Microbialuptakeoflow-molecular-weightorganicsubstancesout-competessorptioninsoil.EuropeanJournalofSoilScience61,504e513.Flessa,H.,Fischer,W.R.,1992.Redoxprocessesintherhizosphereofterrestrialandpaludalplants.ZeitschriftFurPflanzenernahrungUndBodenkunde155,373e378.Focht,D.D.,1992.Diffusionalconstrainsonmicrobialprocessesinsoil.SoilScience154,300e307.Fontaine,S.,Barot,S.,2005.Sizeandfunctionaldiversityofmicrobepopulationscontrolplantpersistenceandlong-termsoilcarbonaccumulation.EcologyLetters8,1075e1087.Fontaine,S.,Mariotti,A.,Abbadie,L.,2003.Theprimingeffectoforganicmatter:aquestionofmicrobialcompetition?SoilBiology&Biochemistry35,837e843.Gantner,S.,Schmid,M.,Durr,C.,Schuhegger,R.,Steidle,A.,Hutzler,P.,Langebartels,C.,Eberl,L.,Hartmann,A.,Dazzo,F.B.,2006.Insituquantitationofthespatialscaleofcallingdistancesandpopulationdensity-independentN-acylhomoserinelactone-mediatedcommunicationbyrhizobacteriacolonizedonplantroots.FEMSMicrobiologyEcology56,188e194.Glanville,H.,Rousk,J.,Golyshin,P.,Jones,D.L.,2012.Mineralizationoflowmolec-ularweightcarbonsubstratesinsoilsolutionunderlaboratoryandfieldcon-ditions.SoilBiology&Biochemistry48,88e95.Gray,E.J.,Smith,D.L.,2005.IntracellularandextracellularPGPR:commonalitiesanddistinctionsintheplant-bacteriumsignalingprocesses.SoilBiology&Biochemistry37,395e412.Groffman,P.M.,Butterbach-Bahl,K.,Fulweiler,R.W.,Gold,A.J.,Morse,J.L.,Stander,E.K.,Tague,C.,Tonitto,C.,Vidon,P.,2009.Challengestoincorporatingspatiallyandtemporallyexplicitphenomena(hotspotsandhotmoments)indenitrificationmodels.Biogeochemistry93,49e77.Grundmann,G.L.,Dechesne,A.,Bartoli,F.,Flandrois,J.P.,Chasse,J.L.,Kizungu,R.,2001.Spatialmodelingofnitrifiermicrohabitatsinsoil.SoilScienceSocietyofAmericaJournal65,1709e1716.Ha,K.V.,Marschner,P.,Bunemann,E.K.,Smernik,R.,2007.Chemicalchangesandphosphorusreleaseduringdecompositionofpearesiduesinsoil.SoilBiology&Biochemistry39,2696e2699.Y.Kuzyakov,E.Blagodatskaya/SoilBiology&Biochemistry83(2015)184e199 197 Hamer,U.,Makeschin,F.,2009.Rhizospheresoilmicrobialcommunitystructureandmicrobialactivityinset-asideandintensivelymanagedarableland.PlantandSoil316,57e69.http://dx.doi.org/10.1007/s11104-008-9758-2.Helal,H.M.,Sauerbeck,D.,1981.Amethodforseparationofsoilzonesofvaryingrootdistance.ZeitschriftFurPflanzenernahrungUndBodenkunde144,524e527.Hendriks,L.,Claassen,N.,Jungk,A.,1981.Phosphate-depletionatthesoil-rootinterfaceandthephosphate-uptakeofmaizeandrape.ZeitschriftFurPflan-zenernahrungUndBodenkunde144,486e499.Herron,P.M.,Gage,D.J.,Pinedo,C.A.,Haider,Z.K.,Cardon,Z.G.,2013.Bettertolightacandlethancursethedarkness:illuminatingspatiallocalizationandtemporaldynamicsofrapidmicrobialgrowthintherhizosphere.FrontiersinPlantSci-ence4.Heuvelink,G.B.M.,Webster,R.,2001.Modellingsoilvariation:past,present,andfuture.Geoderma100,269e301.Hinsinger,P.,Bengough,A.G.,Vetterlein,D.,Young,I.M.,2009.Rhizosphere:biophysics,biogeochemistryandecologicalrelevance.PlantandSoil321,117e152.Hobbie,J.E.,Hobbie,E.A.,2012.Aminoacidcyclinginplanktonandsoilmicrobesstudiedwithradioisotopes:measuredaminoacidsinsoildonotreflectbioavailability.Biogeochemistry107,339e360.Hodge,A.,Paterson,E.,Grayston,S.J.,Campbell,C.D.,Ord,B.G.,Killham,K.,1998.Characterisationandmicrobialutilisationofexudatematerialfromtherhizo-sphereofLoliumperennegrownunderCO2enrichment.SoilBiology&Biochemistry30,1033e1043.Hodge,A.,Robinson,D.,Fitter,A.,2000.Aremicroorganismsmoreeffectivethanplantsatcompetingfornitrogen?TrendsinPlantScience5,304e308.Jones,D.G.,E,1964.Theuseofsoilthinsectionsforthestudyofsoilmicro-or-ganisms.PlantandSoil20,232e240.Jones,D.L.,Hodge,A.,Kuzyakov,Y.,2004.Plantandmycorrhizalregulationofrhi-zodeposition.NewPhytologist163,459e480.Jones,D.L.,Kemmitt,S.J.,Wright,D.,Cuttle,S.P.,Bol,R.,Edwards,A.C.,2005.Rapidintrinsicratesofaminoacidbiodegradationinsoilsareunaffectedbyagricul-turalmanagementstrategy.SoilBiology&Biochemistry37,1267e1275.Kaiser,C.,Franklin,O.,Dieckmann,U.,Richter,A.,2014.Microbialcommunitydy-namicsalleviatestoichiometricconstraintsduringlitterdecay.EcologyLetters17,680e690.Kaiser,K.,Kalbitz,K.,2012.Cyclingdownwards-dissolvedorganicmatterinsoils.SoilBiology&Biochemistry52,29e32.Kandeler,E.,Luxhoi,J.,Tscherko,D.,Magid,J.,1999.Xylanase,invertaseandpro-teaseatthesoil-litterinterfaceofaloamysand.SoilBiology&Biochemistry31,1171e1179.Kandeler,E.,Marschner,P.,Tscherko,D.,Gahoonia,T.S.,Nielsen,N.E.,2002.Mi-crobialcommunitycompositionandfunctionaldiversityintherhizosphereofmaize.PlantandSoil238,301e312.Kautz,T.,Amelung,W.,Ewert,F.,Gaiser,T.,Horn,R.,Jahn,R.,Javaux,M.,Kemna,A.,Kuzyakov,Y.,Munch,J.-C.,Paetzold,S.,Peth,S.,Scherer,H.W.,Schloter,M.,Schneider,H.,Vanderborght,J.,Vetterlein,D.,Walter,A.,Wiesenberg,G.L.B.,Koepke,U.,2013.Nutrientacquisitionfromarablesubsoilsintemperatecli-mates:areview.SoilBiology&Biochemistry57,1003e1022.Kautz,T.,Luesebrink,M.,Paetzold,S.,Vetterlein,D.,Pude,R.,Athmann,M.,Kuepper,P.M.,Perkons,U.,Koepke,U.,2014.Contributionofanecicearthwormstobioporeformationduringcultivationofperennialleycrops.Pedobiologia57,47e52.Klumpp,K.,Fontaine,S.,Attard,E.,LeRoux,X.,Gleixner,G.,Soussana,J.-F.,2009.Grazingtriggerssoilcarbonlossbyalteringplantrootsandtheircontrolonsoilmicrobialcommunity.JournalofEcology97,876e885.http://dx.doi.org/10.1111/j.1365-2745.2009.01549.x.Kogel-Knabner,I.,2002.Themacromolecularorganiccompositionofplantandmicrobialresiduesasinputstosoilorganicmatter.SoilBiology&Biochemistry34,139e162.Kowalchuk,G.A.,Buma,D.S.,deBoer,W.,Klinkhamer,P.G.L.,vanVeen,J.A.,2002.Effectsofabove-groundplantspeciescompositionanddiversityonthedi-versityofsoil-bornemicroorganisms.AntonieVanLeeuwenhoekInternationalJournalofGeneralandMolecularMicrobiology81,509e520.Kuzyakov,Y.,2009.Hotspotsintherhizosphere.GeophysicalResearchAbstracts11.EGU2009-7184-2001.Kuzyakov,Y.,2010.Primingeffects:Interactionsbetweenlivinganddeadorganicmatter.SoilBiology&Biochemistry42,1363e1371.Kuzyakov,Y.,Blagodatskaya,E.,Blagodatsky,S.,2009.CommentsonthepaperbyKemmittetal.(2008)‘Mineralizationofnativesoilorganicmatterisnotregulatedbythesize,activityorcompositionofthesoilmicrobialbiomasseanewperspective’SoilBiology&Biochemistry40,61e73:thebiologyoftheRegulatoryGate.SoilBiology&Biochemistry41,435e439.Kuzyakov,Y.,Raskatov,A.,Kaupenjohann,M.,2003.TurnoveranddistributionofrootexudatesofZeamays.PlantandSoil254,317e327.Kuzyakov,Y.,Xu,X.L.,2013.Competitionbetweenrootsandmicroorganismsfornitrogen:mechanismsandecologicalrelevance.NewPhytologist198,656e669.Lafavre,J.S.,Focht,D.D.,1983.ConservationinsoilofH2liberatedfromN2fixationbyHUP-nodules.AppliedandEnvironmentalMicrobiology46,304e311.Lavrent'eva,E.V.,Semenov,A.M.,Zelenev,V.V.,Chzhun,Y.,Semenova,E.V.,Semenov,V.M.,Namsaraev,B.B.,VanBruggen,A.H.C.,2009.Dailydynamicsofcellulaseactivityinarablesoilsdependingonmanagementpractices.EurasianSoilScience42,885e893.Lee,S.-H.,Jang,I.,Chae,N.,Choi,T.,Kang,H.,2013a.OrganiclayerservesasahotspotofmicrobialactivityandabundanceinArcticTundrasoils.MicrobialEcology65,405e414.Lee,S.H.,Jang,I.,Chae,N.,Choi,T.,Kang,H.,2013b.OrganiclayerservesasahotspotofmicrobialactivityandabundanceinArcticTundrasoils.MicrobialEcology65,405e414.Lehmann,J.,Rillig,M.C.,Thies,J.,Masiello,C.A.,Hockaday,W.C.,Crowley,D.,2011.Biochareffectsonsoilbiota-areview.SoilBiology&Biochemistry43,1812e1836.Lemanski,K.,Scheu,S.,2014.IncorporationofC-13labelledglucoseintosoilmi-croorganismsofgrassland:effectsoffertilizeradditionandplantfunctionalgroupcomposition.SoilBiology&Biochemistry69,38e45.Leon,E.,Vargas,R.,Bullock,S.,Lopez,E.,Panosso,A.R.,LaScala,N.,2014.Hotspots,hotmoments,andspatio-temporalcontrolsonsoilCO2effluxinawater-limitedecosystem.SoilBiology&Biochemistry77,12e21.Loranger-Merciris,G.,Barthes,L.,Gastine,A.,Leadley,P.,2006.Rapideffectsofplantspeciesdiversityandidentityonsoilmicrobialcommunitiesinexperimentalgrasslandecosystems.SoilBiology&Biochemistry38,2336e2343.Lu,Y.H.,Murase,J.,Watanabe,A.,Sugimoto,A.,Kimura,M.,2004.Linkingmicrobialcommunitydynamicstorhizospherecarbonflowinawetlandricesoil.FemsMicrobiologyEcology48,179e186.http://dx.doi.org/10.1016/j.femsec.2004.01.004.Luster,J.,Gottlein,A.,Nowack,B.,Sarret,G.,2009.Sampling,defining,characterisingandmodelingtherhizosphere-thesoilsciencetoolbox.PlantandSoil321,457e482.Lynch,J.M.,Whipps,J.M.,1990.Substrateflowintherhizosphere.PlantandSoil129,1e10.Marschner,H.,2011.MineralNutritionofHigherPlants,thirded.AcademicPress.Marschner,P.,Marhan,S.,Kandeler,E.,2012.Microscaledistributionandfunctionofsoilmicroorganismsintheinterfacebetweenrhizosphereanddetritusphere.SoilBiology&Biochemistry49,174e183.McClain,M.E.,Boyer,E.W.,Dent,C.L.,Gergel,S.E.,Grimm,N.B.,Groffman,P.M.,Hart,S.C.,Harvey,J.W.,Johnston,C.A.,Mayorga,E.,McDowell,W.H.,Pinay,G.,2003.Biogeochemicalhotspotsandhotmomentsattheinterfaceofterrestrialandaquaticecosystems.Ecosystems6,301e312.McIntyre,R.E.S.,Adams,M.A.,Ford,D.J.,Grierson,P.F.,2009.Rewettingandlitteradditioninfluencemineralisationandmicrobialcommunitiesinsoilsfromasemi-aridintermittentstream.SoilBiology&Biochemistry41,92e101.http://dx.doi.org/10.1016/j.soilbio.2008.09.021.Mohr,K.I.,Tebbe,C.C.,2006.Diversityandphylotypeconsistencyofbacteriainthegutsofthreebeespecies(Apoidea)atanoilseedrapefield.EnvironmentalMicrobiology8,258e272.Moradi,A.B.,Carminati,A.,Vetterlein,D.,Vontobel,P.,Lehmann,E.,Weller,U.,Hopmans,J.W.,Vogel,H.J.,Oswald,S.E.,2011.Three-dimensionalvisualizationandquantificationofwatercontentintherhizosphere.NewPhytologist192,653e663.Moritsuka,N.,Yanai,J.,Mori,K.,Kosaki,T.,2004.Bioticandabioticprocessesofnitrogenimmobilizationinthesoil-residueinterface.SoilBiology&Biochem-istry36,1141e1148.Morris,S.J.,Blackwood,C.B.,2007.Theecologyofsoilorganisms.In:E,P.(Ed.),SoilMicrobiology,Ecology,andBiochemistry.Elsevier,Amsterdam,pp.195e229.Musat,N.,Halm,H.,Winterholler,B.,Hoppe,P.,Peduzzi,S.,Hillion,F.,Horreard,F.,Amann,R.,Jorgensen,B.B.,Kuypers,M.M.M.,2008.Asingle-cellviewontheecophysiologyofanaerobicphototrophicbacteria.ProceedingsoftheNationalAcademyofSciencesoftheUnitedStatesofAmerica105,17861e17866.Nannipieri,P.,Ascher,J.,Ceccherini,M.T.,Landi,L.,Pietramellara,G.,Renella,G.,2003.Microbialdiversityandsoilfunctions.EuropeanJournalofSoilScience54,655e670.http://dx.doi.org/10.1046/j.1351-0754.2003.0556.x.Nguyen,C.,Henry,F.,2002.Acarbon-14-glucoseassaytocomparemicrobialactivitybetweenrhizospheresamples.BiologyandFertilityofSoils35,270e276.Nocentini,C.,Guenet,B.,DiMattia,E.,Certini,G.,Bardoux,G.,Rumpel,C.,2010.Charcoalmineralisationpotentialofmicrobialinoculafromburnedandun-burnedforestsoilwithandwithoutsubstrateaddition.SoilBiology&Biochemistry42,1472e1478.Norton,J.M.,Firestone,M.K.,1991.Metabolicstatusofbacteriaandfungiintherhizosphereofponderosapineseedlings.AppliedandEnvironmentalMicro-biology57,1161e1167.Nottingham,A.T.,Griffiths,H.,Chamberlain,P.M.,Stott,A.W.,Tanner,E.V.J.,2009.Soilprimingbysugarandleaf-littersubstrates:alinktomicrobialgroups.AppliedSoilEcology42,183e190.Nunan,N.,Ritz,K.,Crabb,D.,Harris,K.,Wu,K.J.,Crawford,J.W.,Young,I.M.,2001.Quantificationoftheinsitudistributionofsoilbacteriabylarge-scaleimagingofthinsectionsofundisturbedsoil.FEMSMicrobiologyEcology37,67e77.Nunan,N.,Wu,K.,Young,I.M.,Crawford,J.W.,Ritz,K.,2002.Insituspatialpatternsofsoilbacterialpopulations,mappedatmultiplescales,inanarablesoil.Mi-crobialEcology44,296e305.Nunan,N.,Wu,K.J.,Young,I.M.,Crawford,J.W.,Ritz,K.,2003.Spatialdistributionofbacterialcommunitiesandtheirrelationshipswiththemicro-architectureofsoil.FemsMicrobiologyEcology44,203e215.Oades,J.M.,1993.Theroleofbiologyintheformation,stabilizationanddagradationofsoilstructure.Geoderma56,377e400.Oswald,S.E.,Menon,M.,Carminati,A.,Vontobel,P.,Lehmann,E.,Schulin,R.,2008.Quantitativeimagingofinfiltration,rootgrowth,androotwateruptakevianeutronradiography.VadoseZoneJournal7,1035e1047.198Y.Kuzyakov,E.Blagodatskaya/SoilBiology&Biochemistry83(2015)184e199 Panikov,N.S.,1995.MicrobialGrowthKinetics.ChapmanandHall,London,Glasgow.Panikov,N.S.,2010.Microbialecology.Handbookofenvironmentalengineering.EnvironmentalBiotechnology10,121e191.Panikov,N.S.,Flanagan,P.W.,Oechel,W.C.,Mastepanov,M.A.,Christensen,T.R.,2006.Microbialactivityinsoilsfrozentobelow-39degreesC.SoilBiology&Biochemistry38,3520.Parkin,T.B.,1987.Soilmicrositesasassourceofdenitrificationvariability.SoilScienceSocietyofAmericaJournal51,1194e1199.Parkin,T.B.,1993.Spatialvariabilityofmicrobialprocessesinsoil-areview.JournalofEnvironmentalQuality22,409e417.Pausch,J.,Kuzyakov,Y.,2011.PhotoassimilateallocationanddynamicsofhotspotsinrootsvisualizedbyC-14phosphorimaging.JournalofPlantNutritionandSoilScience174,12e19.Pausch,J.,Tian,J.,Riederer,M.,Kuzyakov,Y.,2013.Estimationofrhizodepositionatfieldscale:upscalingofaC-14labelingstudy.PlantandSoil364,273e285.Peth,S.,Horn,R.,Beckmann,F.,Donath,T.,Fischer,J.,Smucker,A.J.M.,2008.Three-dimensionalquantificationofintra-aggregatepore-spacefeaturesusingsynchrotron-radiation-basedmicrotomography.SoilScienceSocietyofAmericaJournal72,897e907.Philippot,L.,Hallin,S.,Borjesson,G.,Baggs,E.M.,2009.Biochemicalcyclingintherhizospherehavinganimpactonglobalchange.PlantandSoil321,61e81.Philippot,L.,Raaijmakers,J.M.,Lemanceau,P.,vanderPutten,W.H.,2013.Goingbacktotheroots:themicrobialecologyoftherhizosphere.NatureReviewsMicrobiology11,789e799.Poll,C.,Brune,T.,Begerow,D.,Kandeler,E.,2010.Small-scalediversityandsuc-cessionoffungiinthedetritusphereofRyeresidues.MicrobialEcology59,130e140.Poll,C.,Marhan,S.,Ingwersen,J.,Kandeler,E.,2008.Dynamicsoflittercarbonturnoverandmicrobialabundanceinaryedetritusphere.SoilBiology&Biochemistry40,1306e1321.Prosser,J.I.,1989.Autotrophicnitrificationinbacteria.AdvancesinMicrobialPhysiology30,125e181.Raffa,R.B.,Iannuzzo,J.R.,Levine,D.R.,Saeid,K.K.,Schwartz,R.C.,Sucic,N.T.,Terleckyj,O.D.,Young,J.M.,2005.Bacterialcommunication(“Quorumsensing”)vialigandsandreceptors:anovelpharmacologictargetforthedesignofantibioticdrugs.JournalofPharmacologyandExperimentalTherapeutics312,417e423.Rajaniemi,T.K.,Turkington,R.,Goldberg,D.,2009.Community-levelconsequencesofspeciesinteractionsinanannualplantcommunity.JournalofVegetationScience20,836e846.Rasa,K.,Eickhorst,T.,Tippkotter,R.,Yli-Halla,M.,2012.Structureandporesystemindifferentlymanagedclayeysurfacesoilasdescribedbymicromorphologyandimageanalysis.Geoderma173,10e18.Rasmussen,J.,Kusliene,G.,Jacobsen,O.S.,Kuzyakov,Y.,Eriksen,J.,2013.BicarbonateastracerforassimilatedCandhomogeneityofC-14andN-15distributioninplantsbyalternativelabelingapproaches.PlantandSoil371,191e198.Raynaud,X.,2010.Soilpropertiesarekeydeterminantsforthedevelopmentofexudategradientsinarhizospheresimulationmodel.SoilBiology&Biochemistry42,210e219.Raynaud,X.,Nunan,N.,2014.Spatialecologyofbacteriaatthemicroscaleinsoil.PLoSOne9.Redfield,R.J.,2002.Isquorumsensingasideeffectofdiffusionsensing?TrendsinMicrobiology10,365e370.Reischke,S.,Rousk,J.,Baath,E.,2014.Theeffectsofglucoseloadingratesonbac-terialandfungalgrowthinsoil.SoilBiology&Biochemistry70,88e95.Remenant,B.,Grundmann,G.L.,Jocteur-Monrozier,L.,2009.Fromthemicro-scaletothehabitat:assessmentofsoilbacterialcommunitystructureasshownbysoilstructuredirectedsampling.SoilBiology&Biochemistry41,29e36.Renella,G.,Egamberdiyeva,D.,Landi,L.,Mench,M.,Nannipieri,P.,2006.MicrobialactivityandhydrolaseactivitiesduringdecompositionofrootexudatesreleasedbyanartificialrootsurfaceinCd-contaminatedsoils.SoilBiology&Biochem-istry38,702e708.Rillig,M.C.,2004.Arbuscularmycorrhizaeandterrestrialecosystemprocesses.EcologyLetters7,740e754.Romheld,V.,1986.pHchangesintherhizosphereofvariouscropplantsinrelationtothesupplyofplantnutrients.PotashReview12.Subject6,55thSuite.Rosling,A.,Lindahl,B.D.,Finlay,R.D.,2004.Carbonallocationtoectomycorrhizalrootsandmyceliumcolonisingdifferentmineralsubstrates.NewPhytologist162,795e802.Rousk,J.,Baath,E.,2007.FungalandbacterialgrowthinsoilwithplantmaterialsofdifferentC/Nratios.FEMSMicrobiologyEcology62,258e267.Rousk,J.,Jones,D.L.,2010.Lossoflowmolecularweightdissolvedorganiccarbon(DOC)andnitrogen(DON)inH2Oand0.5MK2SO4soilextracts.SoilBiology&Biochemistry42,2331e2335.Rousk,J.,Nadkarni,N.M.,2009.Growthmeasurementsofsaprotrophicfungiandbacteriarevealdifferencesbetweencanopyandforestfloorsoils.SoilBiology&Biochemistry41,862e865.Ruamps,L.S.,Nunan,N.,Chenu,C.,2011.Microbialbiogeographyatthesoilporescale.SoilBiology&Biochemistry43,280e286.Ruamps,L.S.,Nunan,N.,Pouteau,V.,Leloup,J.,Raynaud,X.,Roy,V.,Chenu,C.,2013.RegulationofsoilorganicCmineralisationattheporescale.FemsMicrobiologyEcology86,26e35.Rubio,G.,Sorgona,A.,Lynch,J.P.,2004.Spatialmappingofphosphorusinfluxinbeanrootsystemsusingdigitalautoradiography.JournalofExperimentalBot-any55,2269e2280.Rudolph,N.,Voss,S.,Moradi,A.B.,Nagl,S.,Oswald,S.E.,2013.Spatio-temporalmappingoflocalsoilpHchangesinducedbyrootsoflupinandsoft-rush.PlantandSoil369,669e680.Sanaullah,M.,Blagodatskaya,E.,Chabbi,A.,Rumpel,C.,Kuzyakov,Y.,2011.Droughteffectsonmicrobialbiomassandenzymeactivitiesintherhizo-sphereofgrassesdependonplantcommunitycomposition.AppliedSoilEcology48,38e44.Sauer,D.,Kuzyakov,Y.,Stahr,K.,2006.SpatialdistributionofrootexudatesoffiveplantspeciesasassessedbyC-14labeling.JournalofPlantNutritionandSoilScience-ZeitschriftFurPflanzenernahrungUndBodenkunde169,360e362.Schimel,J.P.,Weintraub,M.N.,2003.Theimplicationsofexoenzymeactivityonmicrobialcarbonandnitrogenlimitationinsoil:atheoreticalmodel.SoilBiology&Biochemistry35,549e563.Schmidt,H.,Eickhorst,T.,2013.Spatio-temporalvariabilityofmicrobialabundanceandcommunitystructureinthepuddledlayerofapaddysoilcultivatedwithwetlandrice(OryzasativaL.).AppliedSoilEcology72,93e102.Schmidt,H.,Eickhorst,T.,2014.Detectionandquantificationofnativemicrobialpopulationsonsoil-grownricerootsbycatalyzedreporterdeposition-fluorescenceinsituhybridization.FemsMicrobiologyEcology87,390e402.Schmidt,H.,Eickhorst,T.,Mussmann,M.,2012.Gold-FISH:anewapproachfortheinsitudetectionofsinglemicrobialcellscombiningfluorescenceandscanningelectronmicroscopy.SystematicandAppliedMicrobiology35,518e525.Schmidt,H.,Eickhorst,T.,Tippkotter,R.,2011.Monitoringofrootgrowthandredoxconditionsinpaddysoilrhizotronsbyredoxelectrodesandimageanalysis.PlantandSoil341,221e232.Schrader,S.,Rogasik,H.,Onasch,I.,Jegou,D.,2007.AssessmentofsoilstructuraldifferentiationaroundearthwormburrowsbymeansofX-raycomputedto-mographyandscanningelectronmicroscopy.Geoderma137,378e387.Schuetz,K.,Nagel,P.,Vetter,W.,Kandeler,E.,Ruess,L.,2009.Floodingforestedgroundwaterrechargeareasmodifiesmicrobialcommunitiesfromtopsoiltogroundwatertable.FemsMicrobiologyEcology67,171e182.http://dx.doi.org/10.1111/j.1574-6941.2008.00608.x.Spohn,M.,Carminati,A.,Kuzyakov,Y.,2013.Soilzymography-anovelinsitumethodformappingdistributionofenzymeactivityinsoil.SoilBiology&Biochemistry58,275e280.Spohn,M.,Kuzyakov,Y.,2013.Distributionofmicrobial-androot-derivedphos-phataseactivitiesintherhizospheredependingonPavailabilityandCalloca-tionecouplingsoilzymographywithC-14imaging.SoilBiology&Biochemistry67,106e113.Spohn,M.,Kuzyakov,Y.,2014.Spatialandtemporaldynamicsofhotspotsofenzymeactivityinsoilasaffectedbylivinganddeadroots-asoilzymographyanalysis.PlantandSoil379,67e77.Stenstr€om,J.,Stenberg,B.,Johansson,M.,1998.Kineticsofsubstrate-inducedrespiration(SIR):theory.Ambio27,35.Strobel,B.W.,2001.Influenceofvegetationonlow-molecular-weightcarboxylicacidsinsoilsolution-areview.Geoderma99,169e198.Strong,D.T.,Sale,P.W.G.,Helyar,K.R.,1997.InitialsoilpHaffectsthepHatwhichnitrificationceasesduetoself-inducedacidificationofmicrobialmicrosites.AustralianJournalofSoilResearch35,565e570.Talbot,N.J.,1999.Fungalbiologyecomingupforairandsporulation.Nature398,295e296.Teira,E.,Reinthaler,T.,Pernthaler,A.,Pernthaler,J.,Herndl,G.J.,2004.Combiningcatalyzedreporterdeposition-fluorescenceinsituhybridizationandmicro-autoradiographytodetectsubstrateutilizationbybacteriaandarchaeainthedeepocean.AppliedandEnvironmentalMicrobiology70,4411e4414.Theuerl,S.,Buscot,F.,2010.Laccases:towarddisentanglingtheirdiversityandfunctionsinrelationtosoilorganicmattercycling.BiologyandFertilityofSoils46,215e225.Thiet,R.K.,Frey,S.D.,Six,J.,2006.Dogrowthyieldefficienciesdifferbetweensoilmicrobialcommunitiesdifferinginfungal:bacterialratios?Realitycheckandmethodologicalissues.SoilBiology&Biochemistry38,837e844.Thorpe,I.S.,Prosser,J.I.,Glover,L.A.,Killham,K.,1996.TheroleoftheearthwormLumbricusterrestrisinthetransportofbacterialinoculathroughsoil.BiologyandFertilityofSoils23,132e139.Tippkotter,R.,Eickhorst,T.,Taubner,H.,Gredner,B.,Rademaker,G.,2009.DetectionofsoilwaterinmacroporesofundisturbedsoilusingmicrofocusX-raytubecomputerizedtomography(muCT).Soil&TillageResearch105,12e20.Tiunov,A.V.,Dobrovolskaya,T.G.,2002.FungalandbacterialcommunitiesinLumbricusterrestrisburrowwalls:alaboratoryexperiment.Pedobiologia46,595e605.Tiunov,A.V.,Scheu,S.,1999.Microbialrespiration,biomass,biovolumeandnutrientstatusinburrowwallsofLumbricusterrestrisL.(Lumbricidae).SoilBiology&Biochemistry31,2039e2048.Tiunov,A.V.,Scheu,S.,2000.Microbialbiomass,biovolumeandrespirationinLumbricusterrestrisL.castmaterialofdifferentage.SoilBiology&Biochem-istry32,265e275.Tiunov,A.V.,Scheu,S.,2004.Carbonavailabilitycontrolsthegrowthofdetritivores(Lumbricidae)andtheireffectonnitrogenmineralization.Oecologia138,83e90.Troxler,J.,Svercel,M.,Natsch,A.,Zala,M.,Keel,C.,Moenne-Loccoz,Y.,Defago,G.,2012.PersistenceofabiocontrolPseudomonasinoculantashighpopulationsofY.Kuzyakov,E.Blagodatskaya/SoilBiology&Biochemistry83(2015)184e199 199 culturableandnon-culturablecellsin200-cm-deepsoilprofiles.SoilBiology&Biochemistry44,122e129.Turner,T.R.,Ramakrishnan,K.,Walshaw,J.,Heavens,D.,Alston,M.,Swarbreck,D.,Osbourn,A.,Grant,A.,Poole,P.S.,2013.Comparativemetatranscriptomicsre-vealskingdomlevelchangesintherhizospheremicrobiomeofplants.IsmeJournal7,2248e2258.Uteau,D.,Pagenkemper,S.K.,Peth,S.,Horn,R.,2013.Rootandtimedependentsoilstructureformationanditsinfluenceongastransportinthesubsoil.Soil&TillageResearch132,69e76.vanBruggen,A.H.C.,Semenov,A.M.,Zelenev,V.V.,Semenov,A.V.,Raaijmakers,J.M.,Sayler,R.J.,deVos,O.,2008.Wave-likedistributionpatternsofGfp-markedPseudomonasfluorescensalongrootsofwheatplantsgrownintwosoils.Mi-crobialEcology55,466e475.Vidon,P.,Allan,C.,Burns,D.,Duval,T.P.,Gurwick,N.,Inamdar,S.,Lowrance,R.,Okay,J.,Scott,D.,Sebestyen,S.,2010.HotspotsandhotmomentsinRiparianzones:potentialforimprovedwaterqualitymanagement1.JournaloftheAmericanWaterResourcesAssociation46,278e298.Waldrop,M.P.,Zak,D.R.,Blackwood,C.B.,Curtis,C.D.,Tilman,D.,2006.Resourceavailabilitycontrolsfungaldiversityacrossaplantdiversitygradient.EcologyLetters9,1127e1135.Wardle,D.A.,Bonner,K.I.,Barker,G.M.,2002.Linkagesbetweenplantlitterdecomposition,litterquality,andvegetationresponsestoherbivores.Func-tionalEcology16,585e595.Watt,M.,Hugenholtz,P.,White,R.,Vinall,K.,2006.Numbersandlocationsofnativebacteriaonfield-grownwheatrootsquantifiedbyfluorescenceinsituhy-bridization(FISH).EnvironmentalMicrobiology8,871e884.Webster,R.,2000.Issoilvariationrandom?Geoderma97,149e163.White,P.A.,Rice,C.W.,2009.TillageEffectsonMicrobialandCarbonDynamicsduringPlantResidueDecomposition.SoilScienceSocietyofAmericaJournal73,138e145.http://dx.doi.org/10.2136/sssaj2007.0384.Wichern,F.,Andreeva,D.,Joergensen,R.G.,Kuzyakov,Y.,2011.StemlabelingresultsindifferentpatternsofC-14rhizorespirationandN-15distributioninplantscomparedtonaturalassimilationpathways.JournalofPlantNutritionandSoilScience174,732e741.Winson,M.K.,Camara,M.,Latifi,A.,Foglino,M.,Chhabra,S.R.,Daykin,M.,Bally,M.,Chapon,V.,Salmond,G.P.C.,Bycroft,B.W.,Lazdunski,A.,Stewart,G.,Williams,P.,1995.MultipleN-acyl-L-homoserinelactonesignalmoleculesregulatepro-ductionofvirulencedeterminantsandsecondarymetabolitesinPseudomonas-aeruginosa.ProceedingsoftheNationalAcademyofSciencesoftheUnitedStatesofAmerica92,9427e9431.Xiao,C.W.,Janssens,I.A.,Zhou,Y.,Su,J.Q.,Liang,Y.,Guenet,B.,2014.Strongstoi-chiometricresilienceafterlittermanipulationexperiments;acasestudyinaChinesegrassland.BiogeosciencesDiscussions11,10487e10512.Yaalon,D.H.,2000.Downtoearthewhysoil-andsoilscience-matters.Nature407.http://dx.doi.org/10.1038/35030260,301e301.Young,I.M.,Crawford,J.W.,2004.Interactionsandself-organizationinthesoil-microbecomplex.Science304,1634e1637.Young,I.M.,Crawford,J.W.,Nunan,N.,Otten,W.,Spiers,A.,2008.Microbialdistri-butioninsoils:physicsandscaling.In:Sparks,D.L.(Ed.),AdvancesinAgronomy,vol.100.ElsevierAcademicPressInc,SanDiego,pp.81e121.Zarebanadkouki,M.,Kim,Y.X.,Carminati,A.,2013.Wheredorootstakeupwater?Neutronradiographyofwaterflowintotherootsoftranspiringplantsgrowinginsoil.NewPhytologist199,1034e1044.Zelenev,V.V.,vanBruggen,A.H.C.,Leffelaar,P.A.,Bloem,J.,Semenov,A.M.,2006.Oscillatingdynamicsofbacterialpopulationsandtheirpredatorsinresponsetofreshorganicmatteraddedtosoil:thesimulationmodel'BACWAVE-WEB'.SoilBiology&Biochemistry38,1690e1711. 因篇幅问题不能全部显示，请点此查看更多更全内容