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Microbialmetabolism
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Microbialmetabolismisthemeansbywhichamicrobeobtainstheenergyandnutrients(e.g.carbon)itneedstoliveandreproduce.Microbesusemanydifferenttypesof
metabolicstrategiesandspeciescanoftenbedifferentiatedfromeachotherbasedonmetaboliccharacteristics.Thespecificmetabolicpropertiesofamicrobearethemajor
factorsindeterminingthatmicrobesecologicalniche,andoftenallowforthatmicrobetobeusefulinindustrialprocessesorresponsibleforbiogeochemicalcycles.

Contents
1
2
3
4

Typesofmicrobialmetabolism
Heterotrophicmicrobialmetabolism
Fermentation
Specialmetabolicproperties
4.1 Methylotrophy
4.2 Syntrophy
5 Anaerobicrespiration
5.1 Denitrificationnitrateaselectronacceptor
5.2 Sulfatereductionsulfateaselectronacceptor
5.2.1 Electrondonors
5.2.2 Energyforreduction
5.3 Acetogenesiscarbondioxideaselectronacceptor
5.4 Otherinorganicelectronacceptors
5.5 Organicterminalelectronacceptors
6 Chemolithotrophy
6.1 Hydrogenoxidation
6.2 Sulfuroxidation
6.3 Ferrousiron(Fe2+)oxidation
6.4 Nitrification
6.5 Anammox
7 Phototrophy
8 Nitrogenfixation
9 Seealso
10 References
11 Furtherreading

Typesofmicrobialmetabolism
Allmicrobialmetabolismscanbearrangedaccordingtothreeprinciples:
1.Howtheorganismobtainscarbonforsynthesisingcellmass:
autotrophiccarbonisobtainedfromcarbondioxide(CO2)
heterotrophiccarbonisobtainedfromorganiccompounds
mixotrophiccarbonisobtainedfrombothorganiccompoundsandbyfixingcarbondioxide
2.Howtheorganismobtainsreducingequivalentsusedeitherinenergyconservationorinbiosynthetic
reactions:
lithotrophicreducingequivalentsareobtainedfrominorganiccompounds
organotrophicreducingequivalentsareobtainedfromorganiccompounds
3.Howtheorganismobtainsenergyforlivingandgrowing:
chemotrophicenergyisobtainedfromexternalchemicalcompounds
phototrophicenergyisobtainedfromlight

Flowcharttodeterminethemetaboliccharacteristicsof
microorganisms

Inpractice,thesetermsarealmostfreelycombined.Typicalexamplesareasfollows:
chemolithoautotrophsobtainenergyfromtheoxidationofinorganiccompoundsandcarbonfromthefixationofcarbondioxide.Examples:Nitrifyingbacteria,
Sulfuroxidizingbacteria,Ironoxidizingbacteria,Knallgasbacteria
photolithoautotrophsobtainenergyfromlightandcarbonfromthefixationofcarbondioxide,usingreducingequivalentsfrominorganiccompounds.Examples:
Cyanobacteria(water(H2O)asreducingequivalentdonor),Chlorobiaceae,Chromatiaceae(hydrogensulfide(H2S)asreducingequivalentdonor),Chloroflexus
(hydrogen(H2)asreducingequivalentdonor)
chemolithoheterotrophsobtainenergyfromtheoxidationofinorganiccompounds,butcannotfixcarbondioxide(CO2).Examples:someThiobacilus,some
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Beggiatoa,someNitrobacterspp.,Wolinella(withH2asreducingequivalentdonor),someKnallgasbacteria,somesulfatereducingbacteria
chemoorganoheterotrophsobtainenergy,carbon,andreducingequivalentsforbiosyntheticreactionsfromorganiccompounds.Examples:mostbacteria,e.g.
Escherichiacoli,Bacillusspp.,Actinobacteria
photoorganoheterotrophsobtainenergyfromlight,carbonandreducingequivalentsforbiosyntheticreactionsfromorganiccompounds.Somespeciesarestrictly
heterotrophic,manyotherscanalsofixcarbondioxideandaremixotrophic.Examples:Rhodobacter,Rhodopseudomonas,Rhodospirillum,Rhodomicrobium,
Rhodocyclus,Heliobacterium,Chloroflexus(alternativelytophotolithoautotrophywithhydrogen)

Heterotrophicmicrobialmetabolism
Somemicrobesareheterotrophic(morepreciselychemoorganoheterotrophic),usingorganiccompoundsasbothcarbonandenergysources.Heterotrophicmicrobesliveoff
ofnutrientsthattheyscavengefromlivinghosts(ascommensalsorparasites)orfindindeadorganicmatterofallkind(saprophages).Microbialmetabolismisthemain
contributionforthebodilydecayofallorganismsafterdeath.Manyeukaryoticmicroorganismsareheterotrophicbypredationorparasitism,propertiesalsofoundinsome
bacteriasuchasBdellovibrio(anintracellularparasiteofotherbacteria,causingdeathofitsvictims)andMyxobacteriasuchasMyxococcus(predatorsofotherbacteria
whicharekilledandlysedbycooperatingswarmsofmanysinglecellsofMyxobacteria).Mostpathogenicbacteriacanbeviewedasheterotrophicparasitesofhumansor
theothereukaryoticspeciestheyaffect.Heterotrophicmicrobesareextremelyabundantinnatureandareresponsibleforthebreakdownoflargeorganicpolymerssuchas
cellulose,chitinorligninwhicharegenerallyindigestibletolargeranimals.Generally,thebreakdownoflargepolymerstocarbondioxide(mineralization)requiresseveral
differentorganisms,withonebreakingdownthepolymerintoitsconstituentmonomers,oneabletousethemonomersandexcretingsimplerwastecompoundsasby
products,andoneabletousetheexcretedwastes.Therearemanyvariationsonthistheme,asdifferentorganismsareabletodegradedifferentpolymersandsecrete
differentwasteproducts.Someorganismsareevenabletodegrademorerecalcitrantcompoundssuchaspetroleumcompoundsorpesticides,makingthemusefulin
bioremediation.
Biochemically,prokaryoticheterotrophicmetabolismismuchmoreversatilethanthatofeukaryoticorganisms,althoughmanyprokaryotessharethemostbasicmetabolic
modelswitheukaryotes,e.g.usingglycolysis(alsocalledEMPpathway)forsugarmetabolismandthecitricacidcycletodegradeacetate,producingenergyintheformof
ATPandreducingpowerintheformofNADHorquinols.Thesebasicpathwaysarewellconservedbecausetheyarealsoinvolvedinbiosynthesisofmanyconserved
buildingblocksneededforcellgrowth(sometimesinreversedirection).However,manybacteriaandarchaeautilizealternativemetabolicpathwaysotherthanglycolysis
andthecitricacidcycle.Awellstudiedexampleissugarmetabolismviatheketodeoxyphosphogluconatepathway(alsocalledEDpathway)inPseudomonas.Moreover,
thereisathirdalternativesugarcatabolicpathwayusedbysomebacteria,thepentosephosphatepathway.Themetabolicdiversityandabilityofprokaryotestousealarge
varietyoforganiccompoundsarisesfromthemuchdeeperevolutionaryhistoryanddiversityofprokaryotes,ascomparedtoeukaryotes.Itisalsonoteworthythatthe
mitochondrion,thesmallmembraneboundintracellularorganellethatisthesiteofeukaryoticenergymetabolism,arosefromtheendosymbiosisofabacteriumrelatedto
obligateintracellularRickettsia,andalsotoplantassociatedRhizobiumorAgrobacterium.Therefore,itisnotsurprisingthatallmitrochondriateeukaryotessharemetabolic
propertieswiththeseProteobacteria.Mostmicrobesrespire(useanelectrontransportchain),althoughoxygenisnottheonlyterminalelectronacceptorthatmaybeused.
Asdiscussedbelow,theuseofterminalelectronacceptorsotherthanoxygenhasimportantbiogeochemicalconsequences.

Fermentation
Fermentationisaspecifictypeofheterotrophicmetabolismthatusesorganiccarboninsteadofoxygenasaterminalelectronacceptor.Thismeansthattheseorganismsdo
+
notuseanelectrontransportchaintooxidizeNADHtoNAD andthereforemusthaveanalternativemethodofusingthisreducingpowerandmaintainingasupplyof
+

NAD fortheproperfunctioningofnormalmetabolicpathways(e.g.glycolysis).Asoxygenisnotrequired,fermentativeorganismsareanaerobic.Manyorganismscanuse
fermentationunderanaerobicconditionsandaerobicrespirationwhenoxygenispresent.Theseorganismsarefacultativeanaerobes.ToavoidtheoverproductionofNADH,
obligatelyfermentativeorganismsusuallydonothaveacompletecitricacidcycle.InsteadofusinganATPsynthaseasinrespiration,ATPinfermentativeorganismsis
producedbysubstratelevelphosphorylationwhereaphosphategroupistransferredfromahighenergyorganiccompoundtoADPtoformATP.Asaresultoftheneedto
producehighenergyphosphatecontainingorganiccompounds(generallyintheformofCoenzymeAesters)fermentativeorganismsuseNADHandothercofactorsto
producemanydifferentreducedmetabolicbyproducts,oftenincludinghydrogengas(H2).Thesereducedorganiccompoundsaregenerallysmallorganicacidsand
alcoholsderivedfrompyruvate,theendproductofglycolysis.Examplesincludeethanol,acetate,lactate,andbutyrate.Fermentativeorganismsareveryimportant
industriallyandareusedtomakemanydifferenttypesoffoodproducts.Thedifferentmetabolicendproductsproducedbyeachspecificbacterialspeciesareresponsiblefor
thedifferenttastesandpropertiesofeachfood.
Notallfermentativeorganismsusesubstratelevelphosphorylation.Instead,someorganismsareabletocoupletheoxidationoflowenergyorganiccompoundsdirectlyto
theformationofaproton(orsodium)motiveforceandthereforeATPsynthesis.Examplesoftheseunusualformsoffermentationincludesuccinatefermentationby
PropionigeniummodestumandoxalatefermentationbyOxalobacterformigenes.Thesereactionsareextremelylowenergyyielding.Humansandotherhigheranimalsalso
usefermentationtoproducelactatefromexcessNADH,althoughthisisnotthemajorformofmetabolismasitisinfermentativemicroorganisms.

Specialmetabolicproperties
Methylotrophy
MethylotrophyreferstotheabilityofanorganismtouseC1compoundsasenergysources.Thesecompoundsincludemethanol,methylamines,formaldehyde,andformate.
Severalotherlesscommonsubstratesmayalsobeusedformetabolism,allofwhichlackcarboncarbonbonds.Examplesofmethylotrophsincludethebacteria
MethylomonasandMethylobacter.Methanotrophsareaspecifictypeofmethylotrophthatarealsoabletousemethane(CH4)asacarbonsourcebyoxidizingitsequentially

tomethanol(CH3OH),formaldehyde(CH2O),formate(HCOO ),andcarbondioxideCO2initiallyusingtheenzymemethanemonooxygenase.Asoxygenisrequiredfor
thisprocess,all(conventional)methanotrophsareobligateaerobes.ReducingpowerintheformofquinonesandNADHisproducedduringtheseoxidationstoproducea
protonmotiveforceandthereforeATPgeneration.Methylotrophsandmethanotrophsarenotconsideredasautotrophic,becausetheyareabletoincorporatesomeofthe
oxidizedmethane(orothermetabolites)intocellularcarbonbeforeitiscompletelyoxidizedtoCO2(atthelevelofformaldehyde),usingeithertheserinepathway
(Methylosinus,Methylocystis)ortheribulosemonophosphatepathway(Methylococcus),dependingonthespeciesofmethylotroph.
Inadditiontoaerobicmethylotrophy,methanecanalsobeoxidizedanaerobically.Thisoccursbyaconsortiumofsulfatereducingbacteriaandrelativesofmethanogenic
Archaeaworkingsyntrophically(seebelow).Littleiscurrentlyknownaboutthebiochemistryandecologyofthisprocess.
Methanogenesisisthebiologicalproductionofmethane.Itiscarriedoutbymethanogens,strictlyanaerobicArchaeasuchasMethanococcus,Methanocaldococcus,
Methanobacterium,Methanothermus,Methanosarcina,MethanosaetaandMethanopyrus.Thebiochemistryofmethanogenesisisuniqueinnatureinitsuseofanumberof
unusualcofactorstosequentiallyreducemethanogenicsubstratestomethane,suchascoenzymeMandmethanofuran.[1]Thesecofactorsareresponsible(amongother
things)fortheestablishmentofaprotongradientacrosstheoutermembranetherebydrivingATPsynthesis.Severaltypesofmethanogenesisoccur,differinginthestarting
compoundsoxidized.Somemethanogensreducecarbondioxide(CO2)tomethane(CH4)usingelectrons(mostoften)fromhydrogengas(H2)chemolithoautotrophically.
Thesemethanogenscanoftenbefoundinenvironmentscontainingfermentativeorganisms.Thetightassociationofmethanogensandfermentativebacteriacanbe
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consideredtobesyntrophic(seebelow)becausethemethanogens,whichrelyonthefermentorsforhydrogen,relievefeedbackinhibitionofthefermentorsbythebuildup
ofexcesshydrogenthatwouldotherwiseinhibittheirgrowth.Thistypeofsyntrophicrelationshipisspecificallyknownasinterspecieshydrogentransfer.Asecondgroupof
methanogensusemethanol(CH3OH)asasubstrateformethanogenesis.Thesearechemoorganotrophic,butstillautotrophicinusingCO2asonlycarbonsource.The
biochemistryofthisprocessisquitedifferentfromthatofthecarbondioxidereducingmethanogens.Lastly,athirdgroupofmethanogensproducebothmethaneandcarbon

dioxidefromacetate(CH3COO )withtheacetatebeingsplitbetweenthetwocarbons.Theseacetatecleavingorganismsaretheonlychemoorganoheterotrophic
methanogens.AllautotrophicmethanogensuseavariationofthereductiveacetylCoApathwaytofixCO2andobtaincellularcarbon.

Syntrophy
Syntrophy,inthecontextofmicrobialmetabolism,referstothepairingofmultiplespeciestoachieveachemicalreactionthat,onitsown,wouldbeenergetically
unfavorable.Thebeststudiedexampleofthisprocessistheoxidationoffermentativeendproducts(suchasacetate,ethanolandbutyrate)byorganismssuchas
Syntrophomonas.Alone,theoxidationofbutyratetoacetateandhydrogengasisenergeticallyunfavorable.However,whenahydrogenotrophic(hydrogenusing)
methanogenispresenttheuseofthehydrogengaswillsignificantlylowertheconcentrationofhydrogen(downto105atm)andtherebyshifttheequilibriumofthe
butyrateoxidationreactionunderstandardconditions(G)tononstandardconditions(G).Becausetheconcentrationofoneproductislowered,thereactionis"pulled"
towardstheproductsandshiftedtowardsnetenergeticallyfavorableconditions(forbutyrateoxidation:G=+48.2kJ/mol,butG'=8.9kJ/molat105atmhydrogen
andevenlowerifalsotheinitiallyproducedacetateisfurthermetabolizedbymethanogens).Conversely,theavailablefreeenergyfrommethanogenesisisloweredfrom
G=131kJ/molunderstandardconditionstoG'=17kJ/molat105atmhydrogen.Thisisanexampleofintraspecieshydrogentransfer.Inthisway,lowenergy
yieldingcarbonsourcescanbeusedbyaconsortiumoforganismstoachievefurtherdegradationandeventualmineralizationofthesecompounds.Thesereactionshelp
preventtheexcesssequestrationofcarbonovergeologictimescales,releasingitbacktothebiosphereinusableformssuchasmethaneandCO2.

Anaerobicrespiration
Whileaerobicorganismsduringrespirationuseoxygenasaterminalelectronacceptor,anaerobicorganismsuseotherelectronacceptors.Theseinorganiccompoundshave
alowerreductionpotentialthanoxygen,meaningthatrespirationislessefficientintheseorganismsandleadstoslowergrowthratesthanaerobes.Manyfacultative
anaerobescanuseeitheroxygenoralternativeterminalelectronacceptorsforrespirationdependingontheenvironmentalconditions.
Mostrespiringanaerobesareheterotrophs,althoughsomedoliveautotrophically.Alloftheprocessesdescribedbelowaredissimilative,meaningthattheyareusedduring
energyproductionandnottoprovidenutrientsforthecell(assimilative).Assimilativepathwaysformanyformsofanaerobicrespirationarealsoknown.

Denitrificationnitrateaselectronacceptor
Denitrificationistheutilizationofnitrate(NO3)asaterminalelectronacceptor.ItisawidespreadprocessthatisusedbymanymembersoftheProteobacteria.Many
3+

facultativeanaerobesusedenitrificationbecausenitrate,likeoxygen,hasahighreductionpotential.Manydenitrifyingbacteriacanalsouseferriciron(Fe )andsome
organicelectronacceptors.Denitrificationinvolvesthestepwisereductionofnitratetonitrite(NO2),nitricoxide(NO),nitrousoxide(N2O),anddinitrogen(N2)bythe
enzymesnitratereductase,nitritereductase,nitricoxidereductase,andnitrousoxidereductase,respectively.Protonsaretransportedacrossthemembranebytheinitial
NADHreductase,quinones,andnitrousoxidereductasetoproducetheelectrochemicalgradientcriticalforrespiration.Someorganisms(e.g.E.coli)onlyproducenitrate
reductaseandthereforecanaccomplishonlythefirstreductionleadingtotheaccumulationofnitrite.Others(e.g.ParacoccusdenitrificansorPseudomonasstutzeri)reduce
nitratecompletely.Completedenitrificationisanenvironmentallysignificantprocessbecausesomeintermediatesofdenitrification(nitricoxideandnitrousoxide)are
importantgreenhousegasesthatreactwithsunlightandozonetoproducenitricacid,acomponentofacidrain.Denitrificationisalsoimportantinbiologicalwastewater
treatmentwhereitisusedtoreducetheamountofnitrogenreleasedintotheenvironmenttherebyreducingeutrophication.

Sulfatereductionsulfateaselectronacceptor
DissimilatorysulfatereductionisarelativelyenergeticallypoorprocessusedbymanyGramnegativebacteriafoundwithintheProteobacteria,Grampositiveorganisms
relatingtoDesulfotomaculumorthearchaeonArchaeoglobus.Hydrogensulfide(H2S)isproducedasametabolicendproduct.Forsulfatereductionelectrondonorsand
energyareneeded.
Electrondonors
Manysulfatereducersareorganotrophic,usingcarboncompoundssuchaslactateandpyruvate(amongmanyothers)aselectrondonors,[2]whileothersarelithotrophic,
usinghydrogengas(H2)asanelectrondonor.[3]Someunusualautotrophicsulfatereducingbacteria(e.g.Desulfotignumphosphitoxidans)canusephosphite(HPO3)asan
electrondonor[4]whereasothers(e.g.Desulfovibriosulfodismutans,Desulfocapsathiozymogenes,Desulfocapsasulfoexigens)arecapableofsulfurdisproportionation
(splittingonecompoundintotwodifferentcompounds,inthiscaseanelectrondonorandanelectronacceptor)usingelementalsulfur(S0),sulfite(SO2
3 ),andthiosulfate
2 [5]
(S2O2
3 )toproducebothhydrogensulfide(H2S)andsulfate(SO4 ).
Energyforreduction
Allsulfatereducingorganismsarestrictanaerobes.Becausesulfateisenergeticallystable,beforeitcanbemetabolizeditmustfirstbeactivatedbyadenylationtoformAPS
(adenosine5phosphosulfate)therebyconsumingATP.TheAPSisthenreducedbytheenzymeAPSreductasetoformsulfite(SO2
3 )andAMP.Inorganismsthatuse
carboncompoundsaselectrondonors,theATPconsumedisaccountedforbyfermentationofthecarbonsubstrate.Thehydrogenproducedduringfermentationisactually
whatdrivesrespirationduringsulfatereduction.

Acetogenesiscarbondioxideaselectronacceptor
Acetogenesisisatypeofmicrobialmetabolismthatuseshydrogen(H2)asanelectrondonorandcarbondioxide(CO2)asanelectronacceptortoproduceacetate,thesame
electrondonorsandacceptorsusedinmethanogenesis(seeabove).Bacteriathatcanautotrophicallysynthesizeacetatearecalledhomoacetogens.Carbondioxidereduction
inallhomoacetogensoccursbytheacetylCoApathway.Thispathwayisalsousedforcarbonfixationbyautotrophicsulfatereducingbacteriaandhydrogenotrophic
methanogens.Oftenhomoacetogenscanalsobefermentative,usingthehydrogenandcarbondioxideproducedasaresultoffermentationtoproduceacetate,whichis
secretedasanendproduct.

Otherinorganicelectronacceptors
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3+

Ferriciron(Fe )isawidespreadanaerobicterminalelectronacceptorbothforautotrophicandheterotrophicorganisms.Electronflowintheseorganismsissimilartothose
inelectrontransport,endinginoxygenornitrate,exceptthatinferricironreducingorganismsthefinalenzymeinthissystemisaferricironreductase.Modelorganisms
includeShewanellaputrefaciensandGeobactermetallireducens.Sincesomeferricironreducingbacteria(e.g.G.metallireducens)canusetoxichydrocarbonssuchas
tolueneasacarbonsource,thereissignificantinterestinusingtheseorganismsasbioremediationagentsinferricironrichcontaminatedaquifers.
Althoughferricironisthemostprevalentinorganicelectronacceptor,anumberoforganisms(includingtheironreducingbacteriamentionedabove)canuseother
inorganicionsinanaerobicrespiration.Whiletheseprocessesmayoftenbelesssignificantecologically,theyareofconsiderableinterestforbioremediation,especially
whenheavymetalsorradionuclidesareusedaselectronacceptors.Examplesinclude:
4+

2+

Manganicion(Mn )reductiontomanganousion(Mn )
2
0
Selenate(SeO2
4 )reductiontoselenite(SeO3 )andselenitereductiontoinorganicselenium(Se )
3
3
Arsenate(AsO4 )reductiontoarsenite(AsO3 )
Uranylionion(UO2+
2 )reductiontouraniumdioxide(UO2)

Organicterminalelectronacceptors
Anumberoforganisms,insteadofusinginorganiccompoundsasterminalelectronacceptors,areabletouseorganiccompoundstoacceptelectronsfromrespiration.
Examplesinclude:
Fumaratereductiontosuccinate
TrimethylamineNoxide(TMAO)reductiontotrimethylamine(TMA)
Dimethylsulfoxide(DMSO)reductiontoDimethylsulfide(DMS)
Reductivedechlorination
TMAOisachemicalcommonlyproducedbyfish,andwhenreducedtoTMAproducesastrongodor.DMSOisacommonmarineandfreshwaterchemicalwhichisalso
odiferouswhenreducedtoDMS.Reductivedechlorinationistheprocessbywhichchlorinatedorganiccompoundsarereducedtoformtheirnonchlorinatedendproducts.
Aschlorinatedorganiccompoundsareoftenimportant(anddifficulttodegrade)environmentalpollutants,reductivedechlorinationisanimportantprocessin
bioremediation.

Chemolithotrophy
Chemolithotrophyisatypeofmetabolismwhereenergyisobtainedfromtheoxidationofinorganiccompounds.Mostchemolithotrophicorganismsarealsoautotrophic.
Therearetwomajorobjectivestochemolithotrophy:thegenerationofenergy(ATP)andthegenerationofreducingpower(NADH).

Hydrogenoxidation
Manyorganismsarecapableofusinghydrogen(H2)asasourceofenergy.Whileseveralmechanismsofanaerobichydrogenoxidationhavebeenmentionedpreviously
(e.g.sulfatereducingandacetogenicbacteria),hydrogencanalsobeusedasanenergysourceaerobically.Intheseorganisms,hydrogenisoxidizedbyamembranebound
hydrogenasecausingprotonpumpingviaelectrontransfertovariousquinonesandcytochromes.Inmanyorganisms,asecondcytoplasmichydrogenaseisusedtogenerate
reducingpowerintheformofNADH,whichissubsequentlyusedtofixcarbondioxideviatheCalvincycle.Hydrogenoxidizingorganisms,suchasCupriavidusnecator
(formerlyRalstoniaeutropha),ofteninhabitoxicanoxicinterfacesinnaturetotakeadvantageofthehydrogenproducedbyanaerobicfermentativeorganismswhilestill
maintainingasupplyofoxygen.

Sulfuroxidation
Sulfuroxidationinvolvestheoxidationofreducedsulfurcompounds(suchassulfideH2S),inorganicsulfur(S0),andthiosulfate(S2O2
3 )toformsulfuricacid(H2SO4).A
classicexampleofasulfuroxidizingbacteriumisBeggiatoa,amicrobeoriginallydescribedbySergeiWinogradsky,oneofthefoundersofenvironmentalmicrobiology.
AnotherexampleisParacoccus.Generally,theoxidationofsulfideoccursinstages,withinorganicsulfurbeingstoredeitherinsideoroutsideofthecelluntilneeded.This
twostepprocessoccursbecauseenergeticallysulfideisabetterelectrondonorthaninorganicsulfurorthiosulfate,allowingforagreaternumberofprotonstobe
translocatedacrossthemembrane.SulfuroxidizingorganismsgeneratereducingpowerforcarbondioxidefixationviatheCalvincycleusingreverseelectronflow,an
energyrequiringprocessthatpushestheelectronsagainsttheirthermodynamicgradienttoproduceNADH.Biochemically,reducedsulfurcompoundsareconvertedto
2
[6]
sulfite(SO2
3 )andsubsequentlyconvertedtosulfate(SO4 )bytheenzymesulfiteoxidase. Someorganisms,however,accomplishthesameoxidationusingareversalof
theAPSreductasesystemusedbysulfatereducingbacteria(seeabove).InallcasestheenergyliberatedistransferredtotheelectrontransportchainforATPandNADH
production.[6]Inadditiontoaerobicsulfuroxidation,someorganisms(e.g.Thiobacillusdenitrificans)usenitrate(NO3)asaterminalelectronacceptorandthereforegrow
anaerobically.
2+

Ferrousiron(Fe )oxidation
Forfurtherinformation,seeAcidophilesinacidminedrainage
FerrousironisasolubleformofironthatisstableatextremelylowpHsorunderanaerobicconditions.Underaerobic,moderatepHconditionsferrousironisoxidized
3+

spontaneouslytotheferric(Fe )formandishydrolyzedabioticallytoinsolubleferrichydroxide(Fe(OH)3).Therearethreedistincttypesofferrousironoxidizing
microbes.Thefirstareacidophiles,suchasthebacteriaAcidithiobacillusferrooxidansandLeptospirillumferrooxidans,aswellasthearchaeonFerroplasma.These
microbesoxidizeironinenvironmentsthathaveaverylowpHandareimportantinacidminedrainage.Thesecondtypeofmicrobesoxidizeferrousironatcirumneutral
pH.Thesemicroorganisms(forexampleGallionellaferruginea,Leptothrixochracea,orMariprofundusferrooxydans)liveattheoxicanoxicinterfacesandare
microaerophiles.ThethirdtypeofironoxidizingmicrobesareanaerobicphotosyntheticbacteriasuchasRhodopseudomonas,[7]whichuseferrousirontoproduceNADH
forautotrophiccarbondioxidefixation.Biochemically,aerobicironoxidationisaveryenergeticallypoorprocesswhichthereforerequireslargeamountsofirontobe
oxidizedbytheenzymerusticyanintofacilitatetheformationofprotonmotiveforce.Likesulfuroxidation,reverseelectronflowmustbeusedtoformtheNADHusedfor
carbondioxidefixationviatheCalvincycle.

Nitrification

Nitrificationistheprocessbywhichammonia(NH )isconvertedtonitrate(NO).Nitrificationisactuallythenetresultoftwodistinctprocesses:oxidationofammoniato4/6
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Nitrificationistheprocessbywhichammonia(NH3)isconvertedtonitrate(NO3).Nitrificationisactuallythenetresultoftwodistinctprocesses:oxidationofammoniato
nitrite(NO2)bynitrosifyingbacteria(e.g.Nitrosomonas)andoxidationofnitritetonitratebythenitriteoxidizingbacteria(e.g.Nitrobacter).Bothoftheseprocessesare
extremelyenergeticallypoorleadingtoveryslowgrowthratesforbothtypesoforganisms.Biochemically,ammoniaoxidationoccursbythestepwiseoxidationofammonia
tohydroxylamine(NH2OH)bytheenzymeammoniamonooxygenaseinthecytoplasm,followedbytheoxidationofhydroxylaminetonitritebytheenzymehydroxylamine
oxidoreductaseintheperiplasm.
Electronandprotoncyclingareverycomplexbutasanetresultonlyoneprotonistranslocatedacrossthemembranepermoleculeofammoniaoxidized.Nitritereductionis
muchsimpler,withnitritebeingoxidizedbytheenzymenitriteoxidoreductasecoupledtoprotontranslocationbyaveryshortelectrontransportchain,againleadingtovery
lowgrowthratesfortheseorganisms.Oxygenisrequiredinbothammoniaandnitriteoxidation,meaningthatbothnitrosifyingandnitriteoxidizingbacteriaareaerobes.As
insulfurandironoxidation,NADHforcarbondioxidefixationusingtheCalvincycleisgeneratedbyreverseelectronflow,therebyplacingafurthermetabolicburdenon
analreadyenergypoorprocess.
In2015,twogroupsindependentlyshowedthemicrobialgenusNitrospiraiscapableofcompletenitrification(Comammox).[8][9]

Anammox
Anammoxstandsforanaerobicammoniaoxidationandtheorganismsresponsiblewererelativelyrecentlydiscovered,inthelate1990s.[10]Thisformofmetabolismoccurs
inmembersofthePlanctomycetes(e.g.CandidatusBrocadiaanammoxidans)andinvolvesthecouplingofammoniaoxidationtonitritereduction.Asoxygenisnot
requiredforthisprocess,theseorganismsarestrictanaerobes.Amazingly,hydrazine(N2H4rocketfuel)isproducedasanintermediateduringanammoxmetabolism.To
dealwiththehightoxicityofhydrazine,anammoxbacteriacontainahydrazinecontainingintracellularorganellecalledtheanammoxasome,surroundedbyhighlycompact
(andunusual)ladderanelipidmembrane.Theselipidsareuniqueinnature,asistheuseofhydrazineasametabolicintermediate.Anammoxorganismsareautotrophs
althoughthemechanismforcarbondioxidefixationisunclear.Becauseofthisproperty,theseorganismscouldbeusedtoremovenitrogeninindustrialwastewater
treatmentprocesses.[11]Anammoxhasalsobeenshownhavewidespreadoccurrenceinanaerobicaquaticsystemsandhasbeenspeculatedtoaccountforapproximately
50%ofnitrogengasproductionintheocean.[12]

Phototrophy
Manymicrobes(phototrophs)arecapableofusinglightasasourceofenergytoproduceATPandorganiccompoundssuchascarbohydrates,lipids,andproteins.Ofthese,
algaeareparticularlysignificantbecausetheyareoxygenic,usingwaterasanelectrondonorforelectrontransferduringphotosynthesis.[13]Phototrophicbacteriaarefound
inthephylaCyanobacteria,Chlorobi,Proteobacteria,Chloroflexi,andFirmicutes.[14]Alongwithplantsthesemicrobesareresponsibleforallbiologicalgenerationof
oxygengasonEarth.BecausechloroplastswerederivedfromalineageoftheCyanobacteria,thegeneralprinciplesofmetabolismintheseendosymbiontscanalsobe
appliedtochloroplasts.[15]Inadditiontooxygenicphotosynthesis,manybacteriacanalsophotosynthesizeanaerobically,typicallyusingsulfide(H2S)asanelectrondonor
2+
toproducesulfate.Inorganicsulfur(S0),thiosulfate(S2O2
3 )andferrousiron(Fe )canalsobeusedbysomeorganisms.Phylogenetically,alloxygenicphotosynthetic
bacteriaareCyanobacteria,whileanoxygenicphotosyntheticbacteriabelongtothepurplebacteria(Proteobacteria),Greensulfurbacteria(e.g.Chlorobium),Greennon
sulfurbacteria(e.g.Chloroflexus),ortheheliobacteria(Low%G+CGrampositives).Inadditiontotheseorganisms,somemicrobes(e.g.theArchaeonHalobacteriumor
thebacteriumRoseobacter,amongothers)canutilizelighttoproduceenergyusingtheenzymebacteriorhodopsin,alightdrivenprotonpump.However,therearenoknown
Archaeathatcarryoutphotosynthesis.[14]
Asbefitsthelargediversityofphotosyntheticbacteria,therearemanydifferentmechanismsbywhichlightisconvertedintoenergyformetabolism.Allphotosynthetic
organismslocatetheirphotosyntheticreactioncenterswithinamembrane,whichmaybeinvaginationsofthecytoplasmicmembrane(Proteobacteria),thylakoidmembranes
(Cyanobacteria),specializedantennastructurescalledchlorosomes(Greensulfurandnonsulfurbacteria),orthecytoplasmicmembraneitself(heliobacteria).Different
photosyntheticbacteriaalsocontaindifferentphotosyntheticpigments,suchaschlorophyllsandcarotenoids,allowingthemtotakeadvantageofdifferentportionsofthe
electromagneticspectrumandtherebyinhabitdifferentniches.Somegroupsoforganismscontainmorespecializedlightharvestingstructures(e.g.phycobilisomesin
CyanobacteriaandchlorosomesinGreensulfurandnonsulfurbacteria),allowingforincreasedefficiencyinlightutilization.
Biochemically,anoxygenicphotosynthesisisverydifferentfromoxygenicphotosynthesis.Cyanobacteria(andbyextension,chloroplasts)usetheZschemeofelectronflow
inwhichelectronseventuallyareusedtoformNADH.Twodifferentreactioncenters(photosystems)areusedandprotonmotiveforceisgeneratedbothbyusingcyclic
electronflowandthequinonepool.Inanoxygenicphotosyntheticbacteria,electronflowiscyclic,withallelectronsusedinphotosynthesiseventuallybeingtransferred
backtothesinglereactioncenter.Aprotonmotiveforceisgeneratedusingonlythequinonepool.Inheliobacteria,Greensulfur,andGreennonsulfurbacteria,NADHis
formedusingtheproteinferredoxin,anenergeticallyfavorablereaction.Inpurplebacteria,NADHisformedbyreverseelectronflowduetothelowerchemicalpotentialof
thisreactioncenter.Inallcases,however,aprotonmotiveforceisgeneratedandusedtodriveATPproductionviaanATPase.
Mostphotosyntheticmicrobesareautotrophic,fixingcarbondioxideviatheCalvincycle.Somephotosyntheticbacteria(e.g.Chloroflexus)arephotoheterotrophs,meaning
thattheyuseorganiccarboncompoundsasacarbonsourceforgrowth.Somephotosyntheticorganismsalsofixnitrogen(seebelow).

Nitrogenfixation
Nitrogenisanelementrequiredforgrowthbyallbiologicalsystems.Whileextremelycommon(80%byvolume)intheatmosphere,dinitrogengas(N2)isgenerally
biologicallyinaccessibleduetoitshighactivationenergy.Throughoutallofnature,onlyspecializedbacteriaandArchaeaarecapableofnitrogenfixation,converting
dinitrogengasintoammonia(NH3),whichiseasilyassimilatedbyallorganisms.[16]Theseprokaryotes,therefore,areveryimportantecologicallyandareoftenessentialfor
thesurvivalofentireecosystems.Thisisespeciallytrueintheocean,wherenitrogenfixingcyanobacteriaareoftentheonlysourcesoffixednitrogen,andinsoils,where
specializedsymbiosesexistbetweenlegumesandtheirnitrogenfixingpartnerstoprovidethenitrogenneededbytheseplantsforgrowth.
Nitrogenfixationcanbefounddistributedthroughoutnearlyallbacteriallineagesandphysiologicalclassesbutisnotauniversalproperty.Becausetheenzymenitrogenase,
responsiblefornitrogenfixation,isverysensitivetooxygenwhichwillinhibititirreversibly,allnitrogenfixingorganismsmustpossesssomemechanismtokeepthe
concentrationofoxygenlow.Examplesinclude:
heterocystformation(cyanobacteriae.g.Anabaena)whereonecelldoesnotphotosynthesizebutinsteadfixesnitrogenforitsneighborswhichinturnprovideitwith
energy
rootnodulesymbioses(e.g.Rhizobium)withplantsthatsupplyoxygentothebacteriaboundtomoleculesofleghaemoglobin
anaerobiclifestyle(e.g.Clostridiumpasteurianum)
veryfastmetabolism(e.g.Azotobactervinelandii)

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Theproductionandactivityofnitrogenasesisveryhighlyregulated,bothbecausenitrogenfixationisanextremelyenergeticallyexpensiveprocess(1624ATPareusedper
N2fixed)andduetotheextremesensitivityofthenitrogenasetooxygen.

Seealso
Lipophilicbacteria,aminorityofbacteriawithlipidmetabolism

References
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Annu.Rev.Biochem.59:35594.doi:10.1146/annurev.bi.59.070190.002035.
PMID2115763.
2.IshimotoM,KoyamaJ,NagaiY(September1954)."BiochemicalStudiesonSulfate
ReducingBacteria:IV.TheCytochromeSystemofSulfateReducingBacteria".J
Biochem41(6):76370.
3.MizunoO,LiYY,NoikeT(May1998)."Thebehaviorofsulfatereducingbacteriain
acidogenicphaseofanaerobicdigestion".WaterResearch32(5):162634.
doi:10.1016/S00431354(97)003722.
4.SchinkB,ThiemannV,LaueH,FriedrichMW(May2002)."Desulfotignum
phosphitoxidanssp.nov.,anewmarinesulfatereducerthatoxidizesphosphiteto
phosphate".ArchMicrobiol177(5):38191.doi:10.1007/s002030020402x.
PMID11976747.
5.JacksonBE,McInerneyMJ(August2000)."ThiosulfateDisproportionationby
Desulfotomaculumthermobenzoicum".ApplEnvironMicrobiol66(8):36503.
doi:10.1128/AEM.66.8.36503653.2000.PMC92201.PMID10919837.
6.KapplerU,BennettB,RethmeierJ,SchwarzG,DeutzmannR,McEwanAG,DahlC
(May2000)."Sulfite:CytochromecOxidoreductasefromThiobacillusnovellus.
Purification,Characterization,andMolecularBiologyofaHeterodimericMemberof
theSulfiteOxidaseFamily".JBiolChem275(18):1320212.
doi:10.1074/jbc.275.18.13202.PMID10788424.
7.JiaoY,KapplerA,CroalLR,NewmanDK(August2005)."Isolationand
CharacterizationofaGeneticallyTractablePhotoautotrophicFe(II)Oxidizing
Bacterium,RhodopseudomonaspalustrisStrainTIE1".ApplEnvironMicrobiol71(8):
448796.doi:10.1128/AEM.71.8.44874496.2005.PMC1183355.PMID16085840.
8.vanKessel,MaartjeA.H.J.Speth,DaanR.Albertsen,MadsNielsen,PerH.Opden
Camp,HuubJ.M.Kartal,BoranJetten,MikeS.M.Lcker,Sebastian(20151224).
"Completenitrificationbyasinglemicroorganism".Nature528(7583):555559.
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9.Daims,HolgerLebedeva,ElenaV.Pjevac,PetraHan,PingHerbold,Craig

9.Daims,HolgerLebedeva,ElenaV.Pjevac,PetraHan,PingHerbold,Craig
Albertsen,MadsJehmlich,NicoPalatinszky,MartonVierheilig,Julia(20151224).
"CompletenitrificationbyNitrospirabacteria".Nature528(7583):504509.
doi:10.1038/nature16461.ISSN00280836.
10.StrousM,FuerstJA,KramerEH,etal.(July1999)."Missinglithotrophidentifiedas
newplanctomycete".Nature400(6743):4469.doi:10.1038/22749.PMID10440372.
11.ZhuG,PengY,LiB,GuoJ,YangQ,WangS(2008)."Biologicalremovalofnitrogen
fromwastewater".RevEnvironContamToxicol.ReviewsofEnvironmental
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ammoniumoxidizing(anammox)bacteria".BiochemSocTrans.34(Pt1):1748.
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Biol2(6):5139.doi:10.1016/S13695266(99)000254.PMID10607659.
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doi:10.1099/mic.0.273030.PMID15528644.

Furtherreading
Madigan,,MichaelT.Martinko,JohnM.(2005).BrockBiologyofMicroorganisms.PearsonPrenticeHall.
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