Physiology and Diversity of Ammonia-Oxidizing Archaea

21 Pages·2012·0.41 MB·English

MI66CH05-Stahl ARI 14August2012 13:53
Physiology and Diversity of
Ammonia-Oxidizing Archaea
David A. Stahl1 and Jose´ R. de la Torre2
g
or 1DepartmentofCivilandEnvironmentalEngineeringandDepartmentofMicrobiology,
ws. UniversityofWashington,Seattle,Washington98195-2700;email:[email protected]
alreviee only. e2Dmeapila:[email protected],SanFranciscoStateUniversity,SanFrancisco,California94132-1722;
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012.6State Annu.Rev.Microbiol.2012.66:83–101 Keywords
Microbiol. 2n Francisco mTThhiciersoAa.rantnnicnuluaela’slRrdeevoviiie:ewwso.foMrgicrobiologyisonlineat TAhbasutmraacrcthaeota,ammoniaoxidation,nitrification,nitrogencycle
u. Rev. by Sa 1C0o.p11yr4i6g/hatn(cid:2)ncur2e0v1-2mbicyroA-n0n9u2a6l1R1-e1v5ie0w1s2.8 Tnihzeeddtiosceoxveerrtyporifmaamrymcoonnitar-oolxoidviezrinamgmarochnaiaeaox(AidOatAio)n,ninowtergreensterriaalll,ymraercionge-,
Ann Allrightsreserved andgeothermalhabitats,necessitatesareassessmentofthenitrogencycle.
0066-4227/12/1013-0083$20.00 Inparticular,theunusuallyhighaffinityofmarineandterrestrialAOAfor
ammonia indicates that this group may determine the oxidation state of
nitrogen available to associated micro- and macrobiota, altering our cur-
rentunderstandingoftrophicinteractions.Initialcomparativegenomicsand
physiologicalstudieshaverevealedanovel,andasyetunresolved,primarily
copper-basedpathwayforammoniaoxidationandrespirationdistinctfrom
thatofknownammonia-oxidizingbacteriaandpossiblyrelevanttothepro-
ductionofatmosphericallyactivenitrogenoxides.Comparativestudiesalso
providecompellingevidencethatthelineageofArchaeawithwhichtheAOA
affiliateissufficientlydivergenttojustifythecreationofanovelphylum,the
Thaumarchaeota.
83
MI66CH05-Stahl ARI 14August2012 13:53
Contents
INTRODUCTION............................................................... 84
ABRIEFHISTORYOFDISCOVERY............................................ 85
PHYLOGENETICDIVERSITY.................................................. 86
THAUMARCHAEOTA:ANEWDIVISIONWITHINTHEARCHAEA........... 87
HABITATRANGE............................................................... 87
PHYSIOLOGICALPROPERTIES............................................... 88
KineticsandStoichiometryofAmmoniaOxidation............................... 88
EvidenceforAutotrophic,Mixotrophic,andHeterotrophicGrowth............... 90
COMPARATIVEGENOMICSPOINTSTOUNUSUAL
BIOCHEMISTRYANDCELLBIOLOGY..................................... 90
TheBiochemistryofArchaealAmmoniaOxidation............................... 91
g
or CellCycleandtheMachineryofCellDivision................................... 93
s.
w POTENTIALEFFECTSONATMOSPHERICCHEMISTRY................... 95
alreviee only. FUTURERESEARCH........................................................... 96
us
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83-101. Downloadniversity on 09/24/ ioatpcomrragondmactinenloysiinsstmariialont-gemomerxeneaidddngiiyizaanitnsninabgvtgoiuaatrahratnchl1haes9eayre9asoo9tnebnamaimcn(sAdmasOmu2ocA0xmh0)ro5aewn.saaicTtashtihoepoexunBibydliaelasicastknrihooeS1nwde9a(9(7r39ae26nc)m)do,.agacArnneknrideztaadeeiindrntoht2mboe0iac0fibr5redinsettaechfooemomxrfiaympjrgosoaertsln,iddt-iifemeossnncicnorroiitipmpfdttuiaiooommmnnmizoonooffannnaaeitnnas,
6:U (38,39).Themorerecentrevisioninourunderstandingofthenitrogencyclefollowedtheiso-
012.6State lationofthefirstAOA,Nitrosopumilusmaritimus[nitrosus(Latin):nitrous;pumilus(Latin):dwarf;
Rev. Microbiol. 2by San Francisco mobbfyaacprmHtlieatoorinmilwokeuctpeosuvlanle(anLirrc,kattmttoyhinpnae)ri:n(bin3ogio4efo)gta,fherhoc1eahc6sdhaSeeearrame]R,mfiiaNcraassiAtmlniseagdidgleelnnnmmietfiyisafics.rteaiendnreciioenouortshgfuaemnn1iat9sirml9ind0ecasltboaayrsfcerFhloyuamerrhaem,lmacataoernmidnetpetormaiasl.nein(t2aaggb12e)u0nan–nod4mda0nDe%tsepeLooqfopunumelgnaactr(i1iionn7nge)
u. AOA: ammonia- reportedanarchaealopen-readingframecodingforaproteindistantlyrelatedtomonooxygenases
n
n oxidizingarchaea
A ofammonia-oxidizingbacteria(AOB)andmethanotrophs(77).Inthesebacteriathemonooxyge-
Monooxygenase: naseactivateseitherammoniaormethaneforfurthermetabolictransformationbyinsertingone
anenzymethat
atomfrommolecularoxygenintothesubstrate,yieldinghydroxylamineormethanol.Ahomolo-
incorporatesoneatom
gousgenewassubsequentlydescribedinanarchaealfosmidclonederivedfromasoilmetagenome
ofmolecularoxygen
intoitssubstrateasa study (75). And, more recently, a related but functionally distinct monooxygenase, functioning
hydroxylgroup inthehydroxylationofbutane,wasdescribedforabacterialbutaneoxidizer(64).Thepresump-
AOB: ammonia- tiveannotationofthearchaealhomologsservedforspeculationthatsomemarinearchaeamay
oxidizingbacteria functionasammoniaoxidizers(77).
MMO: methane Interestingly,thealternativepossibilitythatthesedivergentmonooxygenasesfrommarineand
monooxygenase soilarchaeaservedanalternativecatabolicfunctionwassurprisinglynotformallyconsidered.The
AMO: ammonia bacterialparticulatemethanemonooxygenase(pMMO)andbacterialammoniamonooxygenase
monooxygenase (AMO)shareanaminoacidsimilarityofapproximately74%(64).Incontrast,theputativearchaeal
AMOwasonlydistantlyrelatedtothebacterialpMMOandAMO.Thus,afunctionalassignment
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toammoniaoxidationwasbasedononly∼40%aminoacidsimilarity.Forperspective,theBmoA
subunitoftherecentlydescribedputativebutanemonooxygenasefromagram-positivebacterium
(Nocardioidessp.strainCF8)ismorecloselyrelatedtoproteobacterialPmoAandAmoAsequences
AmoA,AmoB,
(37–38%averageaminoacididentity)thantotheputativearchaealAmoAsequence(20%average
AmoC: threeprotein
aminoacididentity)(64).However,giventheimportanceofammoniaoxidationincontributing subunitscomposing
tobothpositiveandnegativeenvironmentalimpacts,andthepossibilitythatamajorplayerinthe theammonia
nitrogencyclehadbeenoverlookedsincethepioneeringworkofSergeiWinogradskyinthelate monooxygenase
nineteenthcentury(81),themetagenomeannotationdidengendersomeattention.Nonetheless,
it was only the isolation of a representative microorganism that conclusively demonstrated the
physiologicalcapacityofammoniaoxidationandthatfullycaughttheattentionofoceanographers,
limnologists,andsoilscientists(36).Numerousstudiesandreviewspublishedinthepastfiveyears
nowprovidepersuasivedatainsupportofthegeneraldominanceofarchaeaincontrollingthe
fateofammoniainbothsoilandaquaticsystems(42,57,76,84).
g
or
s.
w
alreviee only. ABRIEFHISTORYOFDISCOVERY
us
nu The paths to discovery are rarely direct, and the backstories generally not published nor at-
anal
w.on tributabletoanindividualeffort.ThediscoveryofAOAisnoexception,andwerelateeventsthat
ws
wer ledtotheisolationofN.maritimus.Ourinitialindicationofanovelgroupofammoniaoxidizers
d from 2. For p creaamcetofrrosymsteomurssutsueddietositnretahtewlaatteer1i9n9t0hsealasrpgaerstaoltfwaacteernasuqsuaorfiabaactttehreiaSlhdeidvedrAsiqtyuainriuthme(nCithriicfyaignog,
e1
83-101. Downloadniversity on 09/24/ Ia&rleqlsiuDnuAalo.rtAifissea.)ww.SfaePtyiraCleeheaRdlp,rustuaotmnlaapytpsiueiledriblfi,edlicsstisahometeiqboidulenaeorrnobeofcsvbeebissrsaeivcctratelvteodiarso.tieanilolysn1).rs6eBSwlearectReraeduNsmteAoaPgkdCenenoRiewnsanmafrbsoptamlucifidtDecyraNiotaifloAtnahrmehecmamosoviintecsrriaeoadsbosifxooriclodoimiagzteyetrdhosebf(isnJaa.isLltetrw.so,Fagttlheaenexr
6:U processinginPlumIslandSound(Massachusetts)estuarysediments(36).Again,generalandspe-
012.6State cificprimersforbacterialammoniaoxidizersfailedtoamplifytheexpectedsequencetypesfrom
Rev. Microbiol. 2by San Francisco ngrcthRhriteaaNrpeinfhoAiyttiicrangi,fgeIrynneeisnelntagirtsteieuficdqthlitusmoreeanqnet.inucoHeetnssnodcsfwyreeossvetmevwelemoerapr,seecbadflytaoitdunehenxecpdooSaftlhnloamedbbdianoedrrgiaaAnbtteqiuhouneanardrPcwaihCuniatmtRehian-(ibn3ttah6vhse)eee.sndteTiskgshtnacuotroasoerwereysnnrseaeasttdoustilhmmteesneasWcnrtoiitnmmoeeounpdGlraaissctrsHehodamuorpalceehfn1oOatlseclcoaraeelwnan1dn-a6uoirnSp--
u. studyofnitrifyingfiltrationsystemsattheSeattleAquarium,whichalsorevealedhighrepresenta-
n
n
A tionofthesamesequencetype(36).Thus,anarchaealpopulationcloselyrelatedtotheabundant
Group1crenarchaeotawasclearlyimplicatedinammoniaoxidation.Subsequentdevelopmentof
enrichmentculturesusingthesaltwateraquariamaterialasinoculant,andamediumcontaininga
muchlowerconcentrationofammoniathantypicallyusedtoenrichbacterialammoniaoxidizers,
yieldedanactiveammonia-oxidizingculturehighlyenrichedinanarchaealpopulationaffiliated
with the Group 1 crenarchaeota. Following another year or so of painstaking end-point dilu-
tions,combinedwithselectionbysizeandantibioticresistance,thefirstpurecultureofanAOA,
N.maritimusstrainSCM1,wasdescribed(36).
Inaresearchenvironmentwheremetagenomicsandextensiveenvironmentalgenesequence
surveysareincreasinglycommon,thisstoryoffersacounterpoint.Anorganismrelevanttoamajor
environmentalprocesswastrackeddownusingculture-independentmethodstofirstassociatethe
process(ammoniaoxidation)withaphylotype(Group1crenarchaeota)asapreludetoinvesting
thesignificanteffortnecessaryforisolationinculture.SincetheisolationofN.maritimusin2005,
www.annualreviews.org • PhysiologyandDiversityofAmmonia-OxidizingArchaea 85
MI66CH05-Stahl ARI 14August2012 13:53
a 53 concatenated ribosomal proteins b 16S rRNA c amoA
Nitrosoarchaeum koreensis Marine group 1.1a
Nitrosoarchaeum limnia SAGMCG−1 Marine group 1.1a
Nitrosopumilus maritimus
Soil group 1.1b
Cenarchaeum symbiosum Nitrosotalea cluster
HWCG−III
Nitrososphaera gargensis
Nitrosocaldus yellowstonii pSL12 Soil group 1.1b
Caldiarchaeum subterraneum MCG Nitrosocaldus cluster
Korarchaeum cryptofilum OPF8 Marine benthic group B 0.10
Crenarchaeota
Crenarchaeota
HWCG−I
Nanoarchaeum equitans
Euryarchaeota
Euryarchaeota Nanoarchaeota
g Korarchaeota
or 0.10
ws. 0.10
alreviee only. Figure1
nuus Phylogenyofammonia-oxidizingarchaea.(a)Maximum-likelihoodanalysisof53concatenatedconservedribosomalproteins
anal constructedusing6,138aminoacidpositions.Eukaryoticsequenceswereusedasanoutgroup.ThetreewasconstructedusingPhyML
ww.son withanLGmodelwithgammacorrection(foursitecategoriesandusingestimatedproportionofinvariablesites).(b)Maximum-
d from w2. For per lgoiaukmetglmirhoaouocpdo.r(trcr)eecMetiooafxniam(rfcouhumare-asliilkt1ee6lciShatoreiogbdoorstiroeemseaaonlfdraRurNcshinAagesaeelqsatuimmenoaActeegsd,epcnarelocspueoqlarutteeiondncueossif,nicgnavl5ca9ur4ilaapbteoledsisutiistoeinns)gs.a1En,u2dk6aa5rHpyooatssiiectgisoaenwqsau-aeKnndicsehasiHnwoae-srYeegauanswoeadm-Kaosidsaehnlinwoit-h
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83-101. Downloadniversity on 09/24/ gMYsweoaiqCtlnhduoGeamnm,bcimnoleoedsicsewccklreedewlrlnoaeitatnhu.recBsogheluaduamseeaocmsbrtaiaeaccnnckgaoogrrurrcorohtueguapcrento1oiduo;tpnibHc.o(gWIxfnoreousCaurilGnlpsdt.i-rtiIeec,eachstae,otnteligownodeareatisegeressuscaprbnepednoloaurrntsceignhdiganbegeyosttbtoiicomtoghatretsoetTurdaphppaIruv;omaHplauoWrerctshiCoganGeroeto-aaItf.IeiIArn,bvthhaborartineawvb8iala0ett%eisoritnc(e1srs:e0)Sn.0BAarraGeccphMtlaeicerCiaoatGtleicsa-)m1ga,rorSoAeouiaupnntdIhdIicIAp;amftreoidcAan
6:U thesamegeneralapproachtoenrichmentandisolationhasbeenusedsuccessfullytoculturenew
012.6State AOAfromsoilsandgeothermalenvironments(5,16,24,30,41,74).
Rev. Microbiol. 2by San Francisco PTseHhqrueYeenLcmOeasjGoasrEalNinperEoaTgxyeIsfCoorfDrmeIasVorilnvEienRagSrcgIheTaneYeatiwcaelrlyedidisetninticfitepdoipnutlahteiolnatse(p1h99yl0ost,yupseins)g(1176,S2r1R,N48A).gOennee
u. lineage(Group1)wasproposedtobeaffiliatedwiththekingdomCrenarchaeotaandtheremain-
n
n
A ingtwogroupsaffiliatedwiththekingdomEuryarchaeota.Subsequentextensive16SrRNAgene
surveysofbothsoilandaquaticsystemsrevealedthatGroup1archaeawerewidelydistributedin
moderatehabitats.Theywereabundantthroughoutthemarinewatercolumn(34),representing
thedominantdeepmarinemicrobialpopulation,andcommoninestuaries(3,4,14),sediments
(26,44,65,79),andsoils(31).Asadditionalsequenceswerecompiled,additionaldivisionsrelated
totheGroup1crenarchaeotaweredefined(Figure1).Themajorityofsoilandmarinesequences
couldbeassignedtotwoclades,definedasGroup1.1a(marine)andGroup1.1b(soil).Because
noorganismwasavailableinculture,insightsintothebiogeochemicalsignificanceoftheseglob-
allydistributedandabundantmicroorganismswereinitiallyinferredfrominsitumeasurements
ofnaturalisotopiccompositionofdiagnosticetherlipids(27,55)andfromincorporationofra-
diolabeledorganicandinorganicsubstrates(25,53,82).Theseanalysessuggestedasignificant
inorganiccarbonsourceofcellularcarbonbythedeep-watermarineGroup1populationbutalso
establishedacapacitytoassimilateorganicmaterial.Thephysiologicalbasisfortheseassimilation
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86 Stahl delaTorre
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propertiesremainedunknownuntiltheisolationoftheAOAandtheanalysisoftheirgenomes
(23,80).
Thaumarchaeota:
arecentlydefined
THAUMARCHAEOTA:ANEWDIVISIONWITHINTHEARCHAEA division(phylum)
withintheArchaea
SincethedescriptionofN.maritimus,thephylogeneticdiversityofAOAhasbeenunderconstant
encompassingall
revision as new organisms are described. The current census reveals an assemblage that spans knownammonia-
tremendous depth within the Archaea, affiliated with marine and soil groups initially assigned oxidizingarchaea,
to the Crenarchaeota on the basis of comparative 16S rRNA sequence comparisons (Figure 1), includingorganisms
previouslyclassifiedas
andmoredivergentcladesderivedfromgeothermalenvironments.Phylogeneticinferencebased
Group1crenarchaeota
on larger sets of phylogenetically informative genes (including concatenated ribosomal protein
Crenarchaeol:
sequencealignments)nowmadeavailablebycompletegenomesequenceshasprovidedsupportfor
aglyceroldialkyl
thecreationofanewdivisionwithintheArchaea,theThaumarchaeota,withwhichallcharacterized
g glyceroltetraether
or AOAaffiliate(7,71). containingfour
s.
w The current understanding of phylogenetic and physiological diversity within the cyclopentanemoieties
ualreviese only. Tdihvaeursmitayr.chTaheoetafewGrcouultpur1esmoafrAinOeAancadnsboeiluasrecdhtaoeaphisysbioasloedgicparlilmyaarniclyhoornso1m6SeorfRtNheAclsaedqeuseinncie- pcylucsloahnexaadndeitimonoiaelty,
nu associatedspecifically
ww.ansonal tmiaelmlybinefresrorfedthfirsonmewenkviinrogdnommenhtaavlleybdeeernivebdro1u6gShrtRinNtoAcsuelqtuuerencoews.inHgotwoeavnera,bbileictyautosegarloldwevsciariabmed- withThaumarchaeota
wer
d from 2. For p mchoanraiactoexriidstaitcioonf,thwiesnareewlleyftdwefiitnhedthdeivuinsiuosnu,aalsimispmreestshioannotgheanteasmismaodneifianoixnigdacthioarnacistetrhiestdicefiofnitnhge
e1 Euryarchaeota. The possibility that a deeply diverging group within the Archaea split from the
6:83-101. DownloadUniversity on 09/24/ bemaamglyeaecaimnotnrofalointennhrieaoeabfccwociocolenluppotltehwdomyirrnspaiwgooisoldreouaegrflvudyye,nnlsoadeinptaerdmmmoegeetaennornttlaryocleyfdqqcetuulhveieeer.selDtcoiaapoepnmneapsecealicnytroytldynoticvonfeeorgrrenngrsopiipnnwhiggroabtcbtoylooatretdryhxoetpsstryhhawsceitictetoihmsnroiginsugeutrinhncseiseenroAoggffryoctOhxhayan2eged(Aae1enar1lcre)ahe.csadtearoaotmenarnsimndfariottnhemadel
012.6State
Rev. Microbiol. 2by San Francisco HTdthehaApteeBoonftIdhcTeuenrAlttruTteermecRdhanrbAkiaqaNcubteelGersipEiasilctathmuermeexeotmnriaeaororgdxiniidngiazfrreyorsmr.aAnthgbeeuncoodfaahlneacsbecietaanntcdseodocifvcceuurpslitietuydrepb-ayitnttdehreenpsAehnOadAveen,tbfaaerneendxiccnuefleetdrurirneedg-
u. primarilyfromsequencingandquantificationofthegenecodingfortheputativearchaealamoA
n
n
A (2,20),ameasuregenerallywellcorrelatedwiththeabundanceofauniqueglyceroldialkylglycerol
tetraether,crenarchaeol,firstassociatedwithmarineGroup1archaeaandnowrecognizedtobe
madebybothmesophilicandthermophilicAOA(15,16,42,54).AOAappeartobethedominant
archaeal clade in soils (generally comprising 1–5% of all prokaryotes) (40, 51), are a dominant
marinegroup(comprising20–40%ofallmarinebacterioplankton)(12,34),andappeartobea
majorammonia-oxidizingpopulationingeothermalhabitats(16,19,60,83).Thus,theirhabitat
rangefarexceedsthatoftheirknownbacterialcounterparts.
Those AOA now available in culture grow at temperatures as high as 74◦C (Nitrosocaldus
yellowstonii) (16) and at pH values as low as 4 (Nitrosotalea devanaterra) (41). The existence of
thermophilic representatives of AOA was initially indicated by the recovery of the diagnostic
glyceroldialkylglyceroltetraetherlipid(crenarchaeol)previouslyassociatedonlywiththemarine
Group1.1aandbytheamplificationofthearchaealhomologofamoAfromhotsprings(54).The
moderatethermophileNitrososphaeragargensis[nitrosus(Latin):nitrous;sphaera(Latin):spherical;
www.annualreviews.org • PhysiologyandDiversityofAmmonia-OxidizingArchaea 87
MI66CH05-Stahl ARI 14August2012 13:53
gargensis(Latin):fromGargaspring],enrichedfromaSiberianhotspring,hasanoptimumgrowth
temperatureofabout46◦C(24).
Continuedsurveysofgeothermalhabitatsbasedonbothnitrificationratemeasurementsand
Half-saturation
selectiveamplificationofthearchaealamoAandgenetranscriptssuggesttheirdistributionincludes
tchoencsotanncten(KtrmatioornKosf)a: hot springs with temperatures as high as 97◦C and pH values as low as 2.5, but with greater
limitingnutrient diversity and abundance trending to springs with temperatures below 75◦C (29, 60, 85). This
supportingone-half broadhabitatrangeisalsoreflectedbythetremendousphylogeneticdiversityofmajorarchaeal
themaximumgrowth
lineages defined by 16S rRNA sequence types recognized to have ammonia-oxidizing affiliates
rateofanorganism
andthecorrespondingdiversityofputativearchaealamoAsequences(Figure1).
PHYSIOLOGICALPROPERTIES
KineticsandStoichiometryofAmmoniaOxidation
g
or InitialphysiologicalstudiesofN.maritimusstrainSCM1,theonlyavailablemarineisolate,have
s.
w
alreviee only. pstrooivcihdieodmiemtrpyourtsainngtimnsicigrohrtessipnitroomtheetrbyastiosmfoeratshuereeocoxyloggeincaalnsducacmemssoonfiAaOcoAn.suSmtupdtiieosnorferlaetaicvteiotno
us nitriteproductionshowedthattheoverallstoichiometryofammoniaoxidationbyN.maritimus
nu
anal isindistinguishablefromthatofAOB(46):
w.on
wwers 1NH +1.5O ⇒1NO−+H O+H+.
d from 2. For p Studiesofammoniaoxidationkin3eticssubse2quentlyde2monst2ratedthatthismarineisolateisanex-
e1
83-101. Downloadniversity on 09/24/ atmtporcleuitntmishvgiaeetmpyoaodlmciodogloiuo.tnltiFdroiaounb)pretoohhffe,elho1ircna3miv2etoientnrdegeMab,asyNpn(o∼ta.hopm3enpanaaordrMifedtcniimtNotinouhHcnsael3cfone-aftsltrla2satn0tude0eriadadnrta-MinnomoenamtumcttooormnanlelisourtpnaamHntiuet)hm(ay(Km4dtm6orm))o.rfxoeoMinsdrtioetianortaegtoattclacheanoalmlnnOsmc.5elTyo0nmhn%triipsaaitoi(cisafomsemniqzsmauesxioisvignwmaniliuueimfinmm--t
6:U cantlyabove1mM.SimilarobservationshavebeenmadewiththemoderatelythermophilicAOA
012.6State N.gargensis(24).Incontrast,characterizedAOBhaveKmvaluesthataremorethan200-foldhigher
Microbiol. 2n Francisco tt6hi9va,i0nty0t0ohfeliNtKe.mrmgvaa[rlwuiteeimtouwfseNcigo.hnmtt]ar−irb1ituihmt−eu1t.soT(4ah6si)ps.eTicsihfiaemceoaxfntfirgneimtthyeelfyohrilgoahwmesmatpospunabiraestn(rVtamtKeamxa·Kfafinmnd−it1hy)igorehfpamoprpatxreoidmxifumomrataaenclyy-
Rev. by Sa mheitcerroootrrgoapnhissman,dnomtaorninlyefpohryotorgpalannicktsounbsftorratceesllbuulatraglsroowfotrha(s1s0im,4il6a)t.ioAnsoexftarmemmeoonliiagobpyhbialecst,erthiael
u. marinepopulationsareplausiblyresponsibleformaintainingoceanicconcentrationsofammonia
n
n
A inthelownanomolarrange,effectivelyoutcompetingthebacterialammoniaoxidizersinaccess-
ing ammonia (46). In contrast to the very low ammonium concentrations required for growth,
N.maritimushasanaffinityforoxygenthatismoretypicalofaerobicmicroorganisms(∼4μM)
andisunabletogrowanaerobicallyundercultureconditionssofarevaluated(D.A.Stahl&J.R.
delaTorre,unpublishedobservations).BecauseAOAhavebeenimplicatedinprovidingtheni-
triteusedbyanaerobicammoniaoxidizersinoxygen-minimumzones,suchorganismsmayhave
significantlyhigheroxygenaffinitiesthanN.maritimus.
The soil AOA have been only more recently brought into culture and there is less direct
physiologicaldataavailable.Nitrososphaeraviennensis[nitrosus(Latin):nitrous(nitriteproducer);
sphaera(Latin):sphericallyshaped;viennensis(Latin):fromVienna],isolatedfromgardensoilin
Vienna, Austria, tolerates higher concentrations of ammonia than does N. maritimus, demon-
stratingcompleteconversionofammoniaatinitialammoniaconcentrationsashighas3mM(74).
Growthcanbeinitiatedathigherconcentrations(greaterthan10mMammonia)butstoppedwhen
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88 Stahl delaTorre
MI66CH05-Stahl ARI 14August2012 13:53
nitriteoriginatingfromammoniaoxidationexceeds∼3mM(74).Nitritealoneisnotassociated
withgrowthinhibition,as growthcanbe initiatedinfreshculturemediumsupplementedwith
10-mM nitrite. Thus, an unknown metabolite or intermediate was invoked as inhibitory (74).
Theseculture-basedobservationsaregenerallyconsistentwithinsitustudiesshowingthatAOA
populationsgrowoverawiderangeofammoniaconcentrationsincontrasttoAOBthatrequire
significantlyhigherammoniaconcentrationstoinitiategrowth(57,78,84).Amorerecentlyde-
scribedAOAenrichedfromlowpHsoils,Nitrosotaleadevanaterra[nitrosus(Latin):nitrous(nitrite
producer);talea(Latin):slenderrod;devana(Latin):Aberdeen;terra(Latin):soil],hasanoptimum
pHbetween4and5(41).Thismarkedthefirstdescriptionofanacidophilicammoniaoxidizer
and provided a clear microbiological explanation for significant nitrification rates measured in
acidicsoils,eventhoughnosuchcapacitywasknownforAOB(6).TheabilityofN.devanaterra
to grow at extremely low pH values is also suggestive that ammonium, rather than un-ionized
ammonia, is the substrate for growth. One explanation for the failure of AOB to grow at pH
g valuessignificantlybelowpH7istheirrequirementfortheun-ionizedformasgrowthsubstrate
or
s. (1, 8). Because the concentration of the un-ionized ammonia form decreases 10-fold for every
w
alreviee only. 1ex-aumniptlree,dinucatisoynstienmpcHo,ntthaienAinOgBatwootaullcdobnecceonmtreatrioapnidolfyasmumbsotrnaitae/almimmitoedniausmpoHf1is0l0omwegretodt.aFloNr
nuus liter−1(28◦C),thereis7mgNH -Nliter−1atpH8andonly0.0007mgNH -Nliter−1atpH4.A
anal 3 3
w.on preference,orrequirement,forammoniummayalsobetrueofthemarinepopulations,becauseat
ws
wer ahalf-saturationvalueof100nMforN.maritimus,theconcentrationofun-ionizedammonianear
d from 2. For p pcoHlle7citsioonnolyfaapmpmrooxnimiaaftoerlyox1i–d3atnioMn.(Wcateabthoelirsemfo)reenstuirsepleycdtitfhfeartetnhtefrAoOmAthuasteuasemdefcohraansissimmifloartitohne.
e1
83-101. Downloadniversity on 09/24/ aIsufymlannrmItonhptoerssnsoooiisxi,al.iaseaT,hslsshitsogueuhsdac-ephiaepdfsafieaslnatianraistmkpyitoonocAiagnpttangrbtoeiotonvrliieaidficneacpnaosatdvoiteoihtllnrwAparanhOaysytcAwesrisooiwptluootiltgdahtyhbiameuanncnpdodiotamvrsniuepficrpeeeipstsrhi)otairhabvtnaeiunvnaaegnddasbavubniaogonccgeltihaecaegsnptmeedadoitsahvttcwrehtyriaa.vytAithuOyisgB(euhd.sIfianonffigrgncmeeintloyleulreflaocal-rr,
6:U AOBtendtodominateinsystemsreceivinghighdirectadditionsofinorganicammonia(28,57),
012.6State whereassystemssustainedbymineralization(ammonification)oforganicmaterialselectforAOA
Rev. Microbiol. 2by San Francisco (ooimm1rxa8gipdr,alia5ninct2ieiaso)tm.eniTons,nvhgpisureroesnf,onseuwrmrmaittelhlhanyebtrlsceyg.oplNfnoruesbinistaderclenitfiirntoecaindattritvoaitoeosgsneabtnshkeeaecrttyyvhfecevulsaenrlacavatteknieoei-dnynlimfnafousiirtntericxitnfitrtgirocoepasnmtthieioiepncnoitilbnnhigyteneocrnittoariroctnirtfiptoirochgoanselt,lsniitonhincngey.stcbeThloecehthbhiresaymtthepeaorrosarofeusvsitaigtodmrntiirnamifiolgopcatanhnhniideact
u. oxidizedspeciesofnitrogen(nitriteandnitrate)thatareessentialsubstratesforbothdenitrification
n
n
A andanaerobicammoniaoxidation,activitiesthatservetoreturnfixednitrogentotherelatively
inert atmospheric form of molecular nitrogen. The recognition of archaeal groups adapted to
extremelylowammoniaconcentrations,acidicpH,andhightemperaturesnowpointstoafully
functionalnitrogencycleinamuchgreaterrangeofhabitatsthanpreviouslyrecognized.Inturn,
ifAOAeffectivelycompetewithphytoplankton,heterotrophs,andotherautotrophsintheocean,
or with plants and other microorganisms in soils, this may mean that assimilation of ammonia
isaminorpathwayforthemetabolismofammoniareleasedthroughmineralizationoforganic
material.Thus,theAOAmaybeammoniathievesandconceivablyforceothergroupstoinvest
reducingpowerinthereductionofnitrate/nitritetoammoniaforbiosynthesis.Resolutionofthe
majoroperativepathway,assimilationversusoxidationofammoniareleasedthroughmineraliza-
tion,isthenofgreatsignificancetodevelopingabetterunderstandingofmicrobialcontrolsof
nitrogenformandavailabilitytoassociatedmicro-andmacrobiotainbothmarineandterrestrial
systems.
www.annualreviews.org • PhysiologyandDiversityofAmmonia-OxidizingArchaea 89
MI66CH05-Stahl ARI 14August2012 13:53
EvidenceforAutotrophic,Mixotrophic,andHeterotrophicGrowth
AvailabledatasuggestthattheAOAaregenerallycapableoffixingCO .Inadditiontotheclear
2
demonstrationofautotrophicgrowthbyN.maritimus,CO fixationwaspreviouslyinferredfrom
2
environmentalstudiesoftheisotopiccompositionofsignaturelipidsandmicroautoradiographic
imagingofnaturalsamplesincubatedwithlabeledorganicorinorganiccarbon(37,53,55).These
dataalsosuggestedsomeabilityfortheincorporationoforganiccarbon(27).Thelatteriscon-
sistentwithgenomesequenceannotationofN.maritimus,pointingtothepresenceofanumber
oftransportersfororganicmolecules.Recentstudiesinourlaboratorieshavedemonstratedsome
stimulation of N. maritimus growth by the addition of central metabolism intermediates (e.g.,
pyruvateandα-ketoglutarate)(47).Alargersetoftestsubstrates(includingaminoacidsandfatty
acids) did not stimulate growth. N. viennensis is also capable of chemolithoautotrophic growth.
Althoughgrowthwasobligatelycoupledtoammoniaoxidation,itcouldbesignificantlyenhanced
byincludingpyruvateinthegrowthmedium(74).
g
or InadditiontoacapacityformixotrophicgrowthbythemarineAOA,arecentpublicationfrom
s.
w theWagnerandHeadlaboratories(50)suggeststhatsomeThaumarchaeota,althoughexpressingan
alreviee only. oamxiodAizgeeanmemcloonseialy.TrehlaistesdtutdoytheaxtamofitnheedGarpoouppu1la.1tibonsooilfcplraedseu,mlapcktivtheeAcOapAacinityatpoeetritohleeurmfixrCefiOn2eoryr
us
nu
anal wastewatertreatmentsystem.Initiallyidentifiedbycombined16SrRNAgeneandamoAsequence
ww.son characterization,stimulationoftheammoniaoxidizersinthisreactorbyammoniaadditionfailed
wer
ed from 12. For p tisnoycsstoetrimmpocurolaautteledliaancbcceool.rupMnotrofaodtreiolainlnlgaomfstrmuaddoiineoislaasobuxegildgeaedtsitCoendO.t2Thbhaytustth,haeeltAhAOoOuBAgh,eneavcuetminveetrhtarotaeundgschinricptohtrieoesnsiadomefntehtteAraeOractBhmadeeniadtl
83-101. Downloadniversity on 09/24/ ascpoulmofogphosgueAyelldysawrttreoaieodsxlnycatlothaefnausdtefin,strcaomotsibfoehadpnac,esstttebhrirneoeiealretnlehuAwremeMacb-sedOinnoeodtgalerenyagvdrdiredpaipnedMognarctMbtieoeaOodncftfe(aoo6rfcri4aoao).n,nrTttghorahirebngeuAisactenMiomidsOnamattt-aoelhirfkaaiumaerrblmt,moharoeoirnnnwogieeaomlaolx-pbyxchiguhdaetaaasnrtinaaizoesceentmet.ohrTofieznthehdoediiossfefixfayucarguuncelhtcthntayioaeoisrannesl
6:U
012.6State aasnsdigfnuinncgtifounnacltliyonwesolll-eclhyaornacttheeribzeadsiseonfzyhmome.oMloogrye,egveennerwahlleyn,tthhiesgreaniseescothdeesqfuoersatioclnosoeflywrheelathteedr
Microbiol. 2n Francisco tshheoualbdubnedadnirceectolyf aasmsooAciagteednewsiothrngietnriefictraatinosnc.ripts in marine or terrestrial systems can or even
Rev. by Sa
u. COMPARATIVEGENOMICSPOINTSTOUNUSUAL
n
n BIOCHEMISTRYANDCELLBIOLOGY
A
The completion of the genome sequence (1.64 Mbp circular chromosome) of the first isolated
AOA,N.maritimus,revealedthreemajordeviationsfromthecanonicalbacterialsystemofammo-
niaoxidationandcarbonfixation:(a)aroleforcopper(ratherthaniron)asthemajorredoxactive
metalinelectrontransferreactions,(b)theabsenceofanyhomologtothebacterialoxidoreductase
(hydroxylamineoxidoreductase,HAO)responsiblefortheoxidationofhydroxylaminetonitrite,
and(c)avariantofthe3-hydroxypropionate/4-hydroxybutyratecycleforCO fixation(asopposed
2
tofixationbytheribulosebisphosphatecarboxylase/oxygenaseoftheCalvin-Bassham-Bensoncy-
cleemployedbycharacterizedbacterialammoniaoxidizers)(80).Thus,thecurrentpictureofcar-
bonmetabolismsuggeststhattheserepresentativesofthemarineandsoilAOAderiveenergyand
electronsprimarilyfromtheoxidationofammoniabutcansupplementcarbonfromCO fixation
2
usingalimitedsetofsimplecompoundsthatfeeddirectlyintocentralmetabolism.Thecombined
·
90 Stahl delaTorre
MI66CH05-Stahl ARI 14August2012 13:53
propertiesofhavingselectiveorganicmaterialuptake,CO fixationbythe3-hydroxypropionate/
2
4-hydroxybutyratepathway,andthepresenceofabranched(incomplete)tricarboxylicacid(TCA)
cyclenowpointtoarelativelysimplemetabolicarchitectureofcarbonassimilationandanabolism.
Phosphonate:
Otherdistinctlynovelfeaturesindicatedbythegenomesequencesincludedanunusualsystemof
organiccompound
celldivisionandthecapacitytosynthesizenovelphosphonatecompounds(80). containingadirect
C-Pbond
Nitroxyl(HNO): the
TheBiochemistryofArchaealAmmoniaOxidation
oneelectronreduced
The most glaring problem presented by annotation of available genome sequences of AOA is andprotonated
congenerofnitric
theabsenceofthecanonicalbacterialpathwayforammoniaoxidation(Figure2).Theavailable
oxideisahighly
sequenceinformationindicatesthattheAOAaremissingallelementsofthebacterialpathway
reactivenitrogen
otherthangenescodingforthepresumptiveAMO.Nitrosopumiluslacksahomologofthebacterial speciesimplicatedin
HAOandthecapacityforsynthesisofc-typecytochromes(23,80).Bacterialc-typecytochromes mammaliancell
g composetheredox-activecentersoftheHAOandmediaterespiratorytransferofelectronsfrom signalingandasa
or possibleintermediate
s. HAOtotheterminaloxidase(Figure2).Thesedistinctivefeatureshadbeenpreviouslysuggested
w inarchaealoxidation
alreviee only. fsrpoomngteh,eCaennnaortcahtaieounmofsyammbeiotsaugmen(o2m3)i.cAselqthuoeungcehatshseempbhlyesdioflroogmyaoGf trhoautpu1nscyumltubrioendtaorfcahameoarninies ofammonia
us
nu unknown, the general genome features are similar to that of N. maritimus and suggestive of a
anal
w.on capacityforammoniaoxidationthatmayfunctionindetoxificationofspongenitrogenouswaste.
ws
wer As yet there is no evidence that the product of ammonia oxidation by the archaeal AMO is
d from 2. For p hnyitdroroxxyyll(aHmNinOe.)AcnoualltderbneattihveepparothdwucatyopfrotphoesaerdchbyaeKalloAtzM,AOrp(6,a6n)d(Fciogllueraegu2e)s.(S8o0m)seugclgaersitfiecdattihoant
e1
83-101. Downloadniversity on 09/24/ doiiasscifosrctntooahssnnesotsaleafylrrelvcrvlheeiondlalaeeutaaaetmlgidoepontsaon.atgrNhtihwliAyetarOdmyosiAovafcoera(irrslngduaeeucmnsahtnymeasdlsoplosneaowciiaisnletootosyn.vxpieAiidelsisasCs,tuniauomno-nbwdinaiagsstsheaadsenunmtHcoihcovAisepaOtlagdtc)oe,oivodsreduetrcogcphaeadnntfehedtrawiridtveauaepyrtreeffesrofsooresmrhnaotsmaugutmcelidhvnoeobcnmooeiafmectoophcxnaeoirdsmAieasrpOotvianoeArsnd-.,
6:U AsshowninFigure 3,thegenescodingforthepresumptiveAMOremainthemostdiagnostic
012.6State featureofanammoniaoxidationpathwaycommontoallavailablegenomesequences.However,
Rev. Microbiol. 2by San Francisco itpionpolraaitfnstuietaiortlirtcnhcoyoexaemrynlelci)pcnotat-norrloasiakttnriemvatpeirnearamontnhtsbnefereionarbtnsaifoetrai-ocrobhemnoesumohthnfaiedrstehturedeylnebNkocyntfirtoaarolwrolncsnAohtcOraapaelrdAnaouls.dsfaTeuamrchntmcedhosoeNafnirainitemard(oFomosoxixopgi-dunuaamciratteiiiolovu2nexs)i..cdgIoaenptniapoodemndrei(ptesir.ogohn.ta,e,shionnynsodltmyroytaxewyytolpsaeasmrrmvtiinaeclde-l
u. Althoughthearchaealpathwayforammoniaoxidationhasnotbeenresolvedbycomparative
n
n
A genomics,recentstudiesusingnitricoxide(NO)sensitivemicroelectrodesaresuggestivethatNO
mayfunctioninthebiochemistry(47).MeasurableamountsofNOareproducedduringammonia
oxidation. This has led to speculation that NO may be an intermediate or function as a redox
shuttle, for instance, delivering electrons to the AMO (Figure 2). In contrast, the AOB draw
electronsrequiredbythemonooxygenasefromthemembrane-associatedquinonepool.Either
theformationofnitroxylasthefirstproductofammoniaoxidationortheuseofNOasanelectron
redoxshuttleforhydroxylaminegenerationwouldeliminatetheneedtodrawelectronsdirectly
from the quinone pool, either by obviating a requirement for reductant through formation of
nitroxylorbydrawingelectronsfromalowerpotentialdonorinthereductionofnitritetoNO
(Figure 2).Equations1and2showpossiblerecyclingofanNOredoxshuttle.Theassociated
thermodynamic calculations assume that electrons for nitrite reduction originate from a donor
specieswithanelectricalpotential(230mV)approximatelythatofac -typecytochromeandin
1
www.annualreviews.org • PhysiologyandDiversityofAmmonia-OxidizingArchaea 91
MI66CH05-Stahl ARI 14August2012 13:53
theknownrangeofplastocyanins.
2NO−+2e−+4H+→2NO+2H O 1.
2 2
2NO+O +NH +H O →NH OH+2NO−+2H+ 2.
2 3 2 2 2
Rx2(cid:2)Go(cid:5) =−103.4 KJ
moleNH
3
Rx1(cid:2)Go(cid:5) =−12.5 KJ .
−
moleNO
2
Because the formation of hydroxylamine as the immediate product of the presumptive AMO
hasnotbeendemonstratedyet,thearchaealpathwayforammoniaoxidationmustbeconsidered
unresolvedatthistime.
g
s.or a AOB (Nitrosomonas europaea)
w
alreviee only. meOmubterarne
us
nu
anal
ww.son HAO 2H+ + HNO2
wer Periplasm
d from 2. For p NH3 + O2 H2O + NH2OH cyt c5544e– cyt cM552 2H+ H+ 4H+
012.66:83-101. DownloadeState University on 09/24/1 AMO 2e– QQH2 2e– cyt c25e5–3 2e–0.C5o Om24apHal3+exH I2VO QQNHA2D+ C+ oHNm+DHpH+le NIxA DIHADPC +o mPi4pHl+eAxmAT TVePPImnasnbeerarne
Microbiol. 2n Francisco b AOA (Nitrosopumilus maritimus) (cytochrome aa3) (NoAxDidHo:ruebdiuqcutiansoen)e (ATP synthase)
Rev. by Sa
u. Electron shuttling to AMO via nitric oxide
n
An 2H+ + 2HNO2 CuNIR 2NO + 2H2O
NXOR 2H+ + HNO2
H2O + HNO CuHAO 4H+ + HNO2 pcy
H2O + NH2OH 4e– 2e– H+ H+ 2H+ 4H+
NH3 + O2 3 pcy pcy Cell
2e– 2 1 pcy pcy membrane
Q Q Q
AMO QH2 QRED QH2 NDH I QH2 aa3 ATPase
NAD+ + H+ NADH 0.5 O2 H2O
2H+ H+ H+ 4H+ ADP + Pi ATP
4H+
QRED Complex I Complex III Complex IV Complex V
(quinone (NADH:ubiquinone (cytochrome bb6)(cytochrome aa3)(ATP synthase)
reductase) oxidoreductase)
·
92 Stahl delaTorre