Diversity and Habitat Preferences of Cultivated and Uncultivated Aerobic Methanotrophic Bacteria

38 Pages·2015·9.56 MB·English

by  Claudia Knief

REVIEW
published:15December2015
doi:10.3389/fmicb.2015.01346
Diversity and Habitat Preferences of
Cultivated and Uncultivated Aerobic
Methanotrophic Bacteria Evaluated
Based on pmoA as Molecular Marker
ClaudiaKnief*
InstituteofCropScienceandResourceConservation–MolecularBiologyoftheRhizosphere,UniversityofBonn,Bonn,
Germany
Methane-oxidizingbacteriaarecharacterizedbytheircapabilitytogrowonmethaneas
sole source of carbon and energy. Cultivation-dependent and -independent methods
have revealed that this functional guild of bacteria comprises a substantial diversity of
organisms.Inparticulartheuseofcultivation-independentmethodstargetingasubunitof
theparticulatemethanemonooxygenase(pmoA)asfunctionalmarkerforthedetectionof
aerobicmethanotrophshasresultedinthousandsofsequencesrepresenting“unknown
Editedby:
SvetlanaN.Dedysh, methanotrophic bacteria.” This limits data interpretation due to restricted information
WinogradskyInstituteofMicrobiology,
about these uncultured methanotrophs. A few groups of uncultivated methanotrophs
RussiaAcademyofScience,Russia
are assumed to play important roles in methane oxidation in specific habitats, while
Reviewedby:
MarcGregoryDumont, thebiologybehindothersequenceclustersremainsstilllargelyunknown.Thediscovery
UniversityofSouthampton,UK of evolutionary related monooxygenases in non-methanotrophic bacteria and of pmoA
LeventeBodrossy,
paralogs in methanotrophs requires that sequence clusters of uncultivated organisms
CSIROOceanandAtmosphere,
Australia have to be interpreted with care. This review article describes the present diversity
PaulBodelier,
of cultivated and uncultivated aerobic methanotrophic bacteria based on pmoA gene
NetherlandsInstituteofEcology,
Netherlands sequencediversity.Itsummarizescurrentknowledgeaboutcultivatedandmajorclusters
*Correspondence: of uncultivated methanotrophic bacteria and evaluates habitat specificity of these
ClaudiaKnief bacteria at different levels of taxonomic resolution. Habitat specificity exists for diverse
[email protected]
lineagesandatdifferenttaxonomiclevels.MethanotrophicgenerasuchasMethylocystis
Specialtysection: and Methylocaldum are identified as generalists, but they harbor habitat specific
Thisarticlewassubmittedto methanotrophs at species level. This finding implies that future studies should consider
TerrestrialMicrobiology,
thesedivergingpreferencesatdifferenttaxonomiclevelswhenanalyzingmethanotrophic
asectionofthejournal
FrontiersinMicrobiology communities.
Received:30September2015
Keywords:methanotrophicbacteria,pmoA,diversity,phylogeny,habitatspecificity,ecologicalniche
Accepted:16November2015
Published:15December2015
Citation: OCCURRENCE AND ROLE OF METHANE-OXIDIZING BACTERIA
KniefC(2015)DiversityandHabitat
PreferencesofCultivatedand Theactivityofmethane-oxidizingbacteriacontributessignificantlytotheglobalmethanebudget.
UncultivatedAerobicMethanotrophic
Methane is the second most abundant carbon compound in the atmosphere with a current
BacteriaEvaluatedBasedonpmoAas
concentrationof1.8ppmvanda26-foldstrongerradiativeefficiencycomparedtocarbondioxide
MolecularMarker.
Front.Microbiol.6:1346. (IPCC,2013).ThemajorsinkofatmosphericmethaneisitsoxidationbyOHradicals,butsoilsalso
doi:10.3389/fmicb.2015.01346 serveassinkbyabout5%duetotheactivityofmethanotrophicbacteria(IPCC,2013).Moreover,
FrontiersinMicrobiology|www.frontiersin.org 1 December2015|Volume6|Article1346
Knief DiversityandHabitatSpecificityofMethanotrophs
methanotrophs are of particular importance in attenuating net and Söhngen (1906) who reported for the first time the
fluxes of this greenhouse gas into the atmosphere in diverse existence of methane-oxidizing bacteria. The first isolates
ecosystemsthataresourcesofatmosphericmethane(DeVisscher were methanotrophic Gammaproteobacteria, among them
et al., 2007; Reeburgh, 2007; Conrad, 2009). Known sources Methylomonas methanica, initially referred to as “Bacillus
arefreshwaterandpermafrostecosystems,someanimalspecies methanicus” (Söhngen, 1906), and Methylococcus capsulatus
and termites, and the release of methane from geological (Foster and Davis, 1966). Extensive enrichment and isolation
processes, wildfires and hydrates. Another 50–65% of the total work by Whittenbury et al. (1970b) led to isolates of further
emissionsareduetoanthropogenicactivitiesincludingruminant Gammaproteobacteria and the genera Methylocystis and
husbandry,fossilfuelextractionanduse,ricepaddyagriculture Methylosinus,i.e.,thefirstmethanotrophicAlphaproteobacteria.
and emissions from landfills and waste, resulting in a current Duringthefollowingyearsandwiththeavailabilityofmolecular
elevationoftheatmosphericmethaneconcentrationbyafactor methodsfortherapididentificationandclassificationofbacteria,
of 2.5 compared to preindustrial times (IPCC, 2013). All these several existing strains were reclassified and new genera were
ecosystems with source function for atmospheric methane are described (e.g., Bowman et al., 1993, 1995; Bodrossy et al.,
typical habitats of methane-oxidizing bacteria. These include 1997). In particular the work of the last 10 years has resulted
freshwater and marine sediments and water columns, aquifers, in a doubling of the number of known genera and species.
floodplains,peatbogs,high-arctic,andtundrawetlands,upland Currently, 18 genera of cultivated aerobic methanotrophic
soils,ricepaddies,landfillcovers,andsewagesludge(Hansonand Gammaproteobacteria and 5 genera of Alphaproteobacteria are
Hanson,1996;Conrad,2007;Bowman,2014). known,representedbyapprox.60differentspecies(Table1).The
Besides their importance in the global methane cycle, numberofGammaproteobacteriaincreasesto20if“Candidatus
aerobic methanotrophic bacteria are of biotechnological Crenothrix polyspora” and “Candidatus Clonothrix fusca” are
interestsincealongtime.Theycanbeusedforbiodegradation included.Thesegeneradonotcontaincultivatedrepresentatives
processes of organic pollutants based on the fact that the key but were only studied in natural enrichments so far (Stoecker
enzyme for methanotrophy in these organisms, the methane et al., 2006; Vigliotta et al., 2007). To give an exact number of
monooxygenase, catalyzes diverse non-specific oxidation known methanotrophic taxa at species level is difficult because
reactions, e.g., of chlorinated solvents such as trichloroethylene the taxonomic status of some species, e.g., “Methylomonas
(Hanson and Hanson, 1996; Smith and Dalton, 2004; Dalton, rubra,” Methylococcus chroococcus, Methylococcus mobilis or
2005; Jiang et al., 2010; Semrau et al., 2010; Strong et al., Methylococcus thermophilus is unclear (Table2). In addition to
2015). Moreover, methanotrophs have been studied in the species considered in this review, more species have been
detail with regard to their potential to convert methane to describedinthe(early)literature,inparticularwithinthegenera
complex organic molecules of higher value. Since the 1970s, MethylomonasandMethylocystis(e.g.Whittenburyetal.,1970b;
methanotrophic bacteria have been studied for single cell Gal’chenkoetal.,1977),butthesewerenevervalidated.Several
protein production (Dalton, 2005). Besides, biopolymers such of them will probably be members of species that have been
as polyhydroxybutyrate, metabolic products such as organic described in the meantime. For an overview of non-validated
acids, vitamins, pigments or lipids (for biodiesel production) specieswithuncertaintaxonomicpositionthereaderisreferred
may be produced from methane by methanotrophs (Strong toGreen(1992)ortherelevantchaptersintaxonomictextbooks
et al., 2015). Further possible applications for biosynthesis (Bowman,2005a,b,2014).
processes are based on the co-metabolic activities of the Theknowndiversityofaerobicmethanotrophicbacteriawas
methane monooxygenase, e.g., for epoxide production via further expanded by the detection of methanotrophic bacteria
the conversion of propene to epoxypropane (Hanson and within the phylum Verrucomicrobia (Table3). Their existence
Hanson, 1996; Dalton, 2005). Moreover, researchers address was described in three independent studies in 2007 and 2008
the question to what extent methanotrophic bacteria can (Dunfield et al., 2007; Pol et al., 2007; Islam et al., 2008) and
be used to increase reduction of methane emissions from they were reported to represent distinct species of the genus
anthropogenicsourcessuchaslandfillsorcoalmines(Jiangetal., “Methylacidiphilum” (Op den Camp et al., 2009). Recently, a
2010). second genus within the newly formed methanotrophic family
Methylacidiphilaceae was proposed, “Methylacidimicrobium,”
alsoconsistingofthreespecies(vanTeeselingetal.,2014).
DIVERSITY AND ECOPHYSIOLOGY OF
Phylogenetically, the methanotrophic Alphaproteobacteria
CULTIVATED METHANOTROPHIC belongtotwofamilies,theMethylocystaceaeandBeijerinckiaceae
BACTERIA (Figure1, Table1). Both families include additional genera
of non-methanotrophic bacteria. Nearly all methanotrophic
Brief History About the Cultivation of Gammaproteobacteria are classified into the families
Methylococcaceae or the recently delineated Methylothermaceae
Aerobic Methanotrophic Bacteria and
(Hirayamaetal.,2014).Thesefamiliesdonotcontainanynon-
Current Diversity and Phylogeny of
methanotrophic bacteria. “Candidatus Crenothrix polyspora”
Cultivated Methanotrophs is the only exception as it belongs to a distinct family, the
Methanotrophicbacteriahavebeenstudiedsincethebeginning Crenotrichaceae,butthisclassificationwasputintoquestionby
of the last century, initiated by the work of Kaserer (1905) OpdenCampetal.(2009),whoproposedthatCrenothrixcould
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Knief DiversityandHabitatSpecificityofMethanotrophs
el
d
3; 3 3;
cReferences Belovaetal.,2013 Gal’chenkoetal.,1977;Bowmanetal.,1993 Dedyshetal.,2007 Lindneretal.,2007 Whittenburyetal.,1970b;Bowmanetal.,199Cerroetal.,2012 Wartiainenetal.,2006b Whittenburyetal.,1970b;Bowmanetal.,199 Whittenburyetal.,1970b;Bowmanetal.,199Steinetal.,2010 Dedyshetal.,2002;Tamasetal.,2014 Dunfieldetal.,2010 Dedyshetal.,2015a Dedyshetal.,2000 Dunfieldetal.,2003;Chenetal.,2010 Dedyshetal.,2004 Vorobevetal.,2011;Dedyshetal.,2015b
e
c
n
mmoXseque FN422005 Notdetected AM283545 DQ664498 Notdetected Notdetected DQ386732 X55394 Notdetected Notdetected Notdetected AJ458535 AJ491848 AJ555245 FR686346 ofthespecies.
n
ai
nt estr
e p
pres hety
t
MO for
pM Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes No No No No availableable.
Alphaproteobacteriaphic. (Eco-)physiology Facultativemethanotrophic,moderateacidophilic Facultativemethanotroph Facultativemethanotrophic,moderateacidophilic Moderateacidophilic Moderateacidophilic,facultativemethanotrophic Moderateacidophilic Moderateacidophilic,facultativemethanotrophic Moderateacidophilic,facultativemethanotrophic Moderateacidophilic Moderateacidophilic ain,sincethisinformationwasnotofthestrainasfarasalreadyavail
aerobicmethanotro Isolationbsource Peatboglake Sewagetreatmentplant Peatboglake Groundwater (Soilandfreshwatersediments) Arcticwetlandsoil Ricepaddy (Soil,freshwatersediments,groundwater) Peatbog Forestsoil Sphagnumfromapalsa Peatbog Forestsoil Tundrapeatland Peatbog asterisk.analysisofarelatedstrandgenomesequence
TABLE1|Taxonomicandphysiologicalcharacteristicsof aTypestrainCulturecollectionnumbersType Methylocystaceae MethylocystisbryophilaH2sIIaDSM21852,VKMB-2545 MethylocystisechinoidesIIa2IMET10491,LMG27198,NCIMB13100,UNIQEM25,VKMB-2128 MethylocystisheyeriH2IIaDSM16984,VKMB-2426 MethylocystishirsutaCSC1IIaATCCBAA-1344,DSM18500,LMG27832 MethylocystisparvusOBBPIIa*ACM3309,ATCC35066,IMET10483,NCIMB11129,UNIQEM38,VKMB-2129 MethylocystisroseaSV97IIaATCCBAA-1196,DSM17261,LMG27835 MethylosinussporiumIIa5ACM3306,ATCC35069,DSM17706,IMET10545,NCIMB11126,UNIQEM60 MethylosinustrichosporiumOB3bIIa*ACM3311,ATCC35070,IMET10543,NCIMB11131,UNIQEM75,VKMB-2117 Beijerinckiaceae MethylocapsaacidiphilaB2IIb*DSM13967,NCIMB13765 MethylocapsaaureaKYGIIbDSM22158,VKMB-2544 MethylocapsapalsarumNE2IIbLMG28715,VKMB-2945 MethylocellapalustrisKIIb*ATCC700799 MethylocellasilvestrisIIbBL2CIP108128,DSM15510,LMG27833,NCIMB13906 MethylocellatundraeT4IIbDSM15673,LMG27838,NCIMB13949 MethyloferulastellataAR4IIb*DSM22108,LMG25277,VKMB-2543 aTypespeciesrepresentingtherespectivegenusaremarkedwithanbInformationgiveninbracketsreferstoinformationobtainedfromthecListedpublicationsdescribetheinitialisolation,currentclassification
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Knief DiversityandHabitatSpecificityofMethanotrophs
cReferences Romanovskayaetal.,1978;Bowmanetal.,1993 Lidstrom,1988;Bowmanetal.,1993 Omelchenkoetal.,1996 Wartiainenetal.,2006a;Svenningetal.,2011 Romanovskayaetal.,1978;Bowmanetal.,1993 Poehleinetal.,2013;Deutzmannetal.,2014 Hirayamaetal.,2013 Whittenburyetal.,1970b;Bowmanetal.,1995;Hamiltonetal.,2015 Whittenburyetal.,1970b;Bowmanetal.,1995;Kitsetal.,2013 Khmeleninaetal.,1997;Kalyuzhnayaetal.,2008;Vuilleumieretal.,2012 Kaluzhnayaetal.,2001;Khmeleninaetal.,2013 Kalyuzhnayaetal.,2008 Kalyuzhnayaetal.,2008 Sieburthetal.,1987;Bowmanetal.,1995 Bowmanetal.,1990 Kitsetal.,2015 (Continued)
yi
m/basonym coccusluteus bacterbovis coccusbovis coccusfulvus monasmarinus bactercapsulatus coccuswhittenbur bactervinelandii coccusvinelandii monasagile bacteragilis monasalbusbacteralbus bacteralcaliphilus monaspelagica bacterpelagicus
y o o o o o o o o o o o oo o o o
on hyl hyl hyl hyl hyl hyl hyl hyl hyl hyl hyl hylhyl hyl hyl hyl
Syn Met Met Met Met Met Met Met Met Met Met Met MetMet Met Met Met
a.
maproteobacteri mmoXsequence Notanalyzed Notdetected Notanalyzed Notdetected Notanalyzed Notdetected Notdetected Notdetected Notdetected Notdetected AOTL00000000 AB253366 Notdetected Notdetected Notanalyzed Notdetected
m
a
Gcmethanotrophic (Eco-)physiology Psychrophilic Perferentiallymicroaerophilic Halophilic Moderatehalophilic,alkaliphilic Moderatehalophilic Slightlyhalophilic Moderatehalophilic,alkaliphilic Moderatehalophilic
bi
o
haracteristicsofaer bIsolationsource Sewage Seawatersediment Tundra Tundrasoil Lakesediment Lakesediment Marinehydrothermalsystem Sewage Soil Sodalake Sodalake Marinesediment Sodalake Marine Sewage Soil
c
al e
c p
ogi Ty Ia Ia Ia Ia Ia Ia Ia Ia Ia Ia Ia Ia Ia Ia Ia Ia
ol
si
y M
TABLE2|Taxonomy,isolationsource,andph aTypestrainCulturecollectionnumbers Methylococcaceae Methylobacterluteus53v*ACM3304,ATCC49878,IMET10584,NCIMB11914,UCM53B,VKM53B MethylobactermarinusA45ACM4717 MethylobacterpsychrophilusZ-0021VKMB-2103 MethylobactertundripaludumSV96ATCCBAA-1195,DSM17260 MethylobacterwhittenburyiYACM3310,ATCC51738,NCIMB11128 MethyloglobulusmorosusKoM1*DSM22980,JCM18850 MethylomarinumvadiIT-4*DSM18976,JCM13665 MethylomicrobiumagileA30*ACM3308,ATCC35068,NCIMB11124 MethylomicrobiumalbumBG8ACM3314,ATCC33003,NCIMB11123,VKM-BG8 Methylomicrobiumalcaliphilum20ZDSM19304,LMG27836,NCIMB14124,VKMB-2133 Methylomicrobiumburyatense5BVKMB-2245 MethylomicrobiumjapanenseNIFERMBP-5633,NBRC103677,VKMB-2462 MethylomicrobiumkenyenseAMO1DSM19305,NCCB97157,NCIMB13566,VKB-2464 MethylomicrobiumpelagicumAA-23ACM3505,NCIMB2265 MethylomonasaurantiacaJB103ACM3406,UQM3406 “Methylomonasdenitrificans”FJG
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2 d)
4 1 e
cReferences Bowmanetal.,1990 Ogisoetal.,2012 Hoefmanetal.,2014a Söhngen,1906;WhittenburyandKrieg,198 Danilovaetal.,2013 Whittenburyetal.,1970b;Romanovskayaetal.,2006 Kalyuzhnayaetal.,1999 Tavorminaetal.,2015 Wiseetal.,2001;Hamiltonetal.,2015 Kalyuzhnayaetal.,2005,2015 Wiseetal.,2001 Rahalkaretal.,2007 Bowmanetal.,1997 Iguchietal.,2011;Hamiltonetal.,2015 Romanovskayaetal.,1978;Bodrossyetal.,1997 Takeuchietal.,2014 Bodrossyetal.,1997 Bodrossyetal.,1997 FosterandDavis,1966;Kleivelandetal.,20 (Continu
a
c a
Synonym/basonym Bacillusmethanicus Methanomonasmethani Pseudomonasmethanic Methylomonasrubrum Methylomonasgracilis
0
0
0
d d d d d d d d d d d d d d d d 0
mmoXsequence Notanalyze Notdetecte Notdetecte Notdetecte Notdetecte Notanalyze Notdetecte Notdetecte Notdetecte Notdetecte Notdetecte Notdetecte Notdetecte AB501288 Notdetecte AB900160 Notdetecte Notdetecte AMCE0000
(Eco-)physiology Acid-tolerant Psychrotolerant Moderatehalophilic Microaerobic Psychrophilic,moderatehalophilic Thermotolerant Thermotolerant,moderatehalophilic Moderatethermophilic Thermotolerant Thermotolerant
bIsolationsource Coalminedrainagewater Ricepaddy Manure (Freshwatersediment,lake,pondwater,swamplysoil) Peatbog Coalminedrainagewater Groundwater Marinesediment Landfillcoversoil Lake Landfillcoversoil Lakesediment Lake Forestsoil Freshwatermud Marinesediment Waterfromhotspring Agriculturalsoil Sewagesludge
e
p
Ty Ia Ia Ia Ia Ia Ia Ia Ia Ia Ia Ia Ia Ia Ia Ib Ib Ib Ib Ib
B 2
M 6
TABLE2|Continued aTypestrainCulturecollectionnumbers MethylomonasfodinarumLD2ACM3268,UQM3268 MethylomonaskoyamaeFw12E-YJCM16701,LMG26899,NBRC105905,NCIMB14606 MethylomonaslentaR-45377LMG26260,JCM19378 MethylomonasmethanicaS*1ACM3307,ATCC35067,IMET10543,NCI11130,UNIQEM8,VKMB-2110 MethylomonaspaludisMG30DSM24973,VKMB-2745 d“Methylomonasrubra”15mACM3303,NCIMB11913,UCMB-3075,VKM-15m MethylomonasscandinavicaSR5VKMB-2140 MethyloprofundussedimentiWF1*ATCCBAA-2619,LMG28393 MethylosarcinafibrataAML-C10*ATCC700909,DSM13736 MethylosarcinalacusLW14ATCCBAA-1047,DSM16693,JCM13284 MethylosarcinaquisquiliarumAML-D4ATCC700908,DSM13737 MethylosomadifficileLC2*DSM18750,JCM14076 MethylosphaerahansoniiAM6*ACAM549 MethylovulummiyakonenseHT12*ATCCBAA-2070,DSM23269,NBRC1061 Methylocaldumgracile14LNCIMB11912,VKM-14L MethylocaldummarinumS8DSM27392,NBRC109686 MethylocaldumszegedienseOR2* MethylocaldumtepidumLK6 MethylococcuscapsulatusTexas*ACM1292,ATCC19069,NCIMB11853,UNIQEM1
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not be ore
TABLE2|Continued abcmmoXTypestrainCulturecollectionnumbersTypeIsolationsource(Eco-)physiologySynonym/basonymReferencessequence eMethylobacterMethylococcuschroococcus9NotanalyzedIb(Soil,freshwaterWhittenburyetal.,1970b;Romanovskayachroococcum?sediments,etal.,1978groundwater) eMethylococcusmobilisIbActivesiltNotanalyzedLMD77.28Hazeuetal.,1980NCCB77028 fMethylococcusthermophilusVKM-2YuIb(Mud,soils,pondThermophilicNotanalyzedMalashenkoetal.,1975ACM3585,IMV-B3037sediment) MethylogaeaoryzaeE10IbRicepaddyNotdetectedGeymonatetal.,2010*DSM23452,JCM16910 MethylomagnumishizawaiIbRicerhizosphereAB983338RS11D-PrKhalifaetal.,2015DSM29768,JCM18894,KCTC4681,NBRC109438 MethyloparacoccusmurrelliiR-49797IbPondwaterNotdetectedHoefmanetal.,2014b*LMG27482,JCM19379 g“CandidatusClonothrixfusca”DrinkingwaterNotanalyzedVigliottaetal.,2007(nopureculture) Methylothermaceae Methylohalobiuscrimeensis10KiIcHypersalinelakeModeratehalophilicNotdetectedHeyeretal.,2005;Sharpetal.,2015*ATCCBAA-967,DSM16011sediment MethylomarinovumcaldicuraliiNotdetectedIT-9IcMarinehydrothermalModerateHirayamaetal.,2014*DSM19749,JCM13666systemthermophilic,moderatehalophilic MethylothermussubterraneusHTM55IcHotaquiferModerateNotdetectedHirayamaetal.,2010DSM19750,JCM13664thermophilic MethylothermusthermalisNotdetectedMYHTIcHotspringModerateTsubotaetal.,2005*IPODFERMP-19714,VKMB-2345thermophilic,halotolerant Crenotrichaceae g“CandidatusDrinkingwaterFacultativeNotdetectedCrenothrixpolyspora”Stoeckeretal.,2006(nopureculture)methanotrophic aTypespeciesrepresentingtherespectivegenusaremarkedwithanasterisk.bInformationgiveninbracketsreferstoinformationobtainedfromtheanalysisofarelatedstrain,sincethisinformationwasnotavailableforthetypestrainofthespecies.cListedpublicationsdescribetheinitialisolation,currentclassificationandgenomesequenceofthestrainasfarasalreadyavailable.dThetypestrainofMethylomonasrubrawasreportedtobelongtothespecies“Methylomonasmethanica”(Bowmanetal.,1993),butlateritwasproposedtorepresentaseparatespecies(Romanovskayaetal.,2006);thishasbeenvalidatedyet.eAccordingtoBergey’smanualofsystematicbacteriology,strainsofthesespeciesdonotexistanymoreandthespeciesarenotconsideredasvalid(Bowman,2005a),butatleastforMethylococcusmobilis,thisappearsnottocorrect,asthetypestrainislistedintheNCCBcatalog.fBodrossyetal.(1997),thetypestrainisnolongeravailableandtheavailablestrainM.thermophilusstrainIMV-B3122(NCIMB13419)isactuallyastrainofMethylocaldumtepidum.AccordingtogParte,2014),therefCandidatusCrenothrixpolysporaandClonothrixfuscadonotcontainanyculturedtypestrainsandthegenusClonothrixisnotvalidatedaccordingtothelistofprokaryoticnameswithstandinginnomenclature(OpdenCampetal.(2009)thevalidatedfamilyCrenotrichaceaeisphylogeneticallyasubsetoftheMethylococcaceae.thesegeneraarereferredtoasCandidatus;accordingto
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009; Opden 2009; bgeenaepmheymlobgeernyof(FthigeuMree1th).ylococcaceae, based on its 16S rRNA
ampetal.,2 etal.,2008; Campetal.,15 CMleatshsaifincoatrtoiopnhiocfBCauclttievraitaeidnto Type I and
aReferences vanTeeselingetal.,2014 vanTeeselingetal.,2014 vanTeeselingetal.,2014 Poletal.,2007;OpdenCKhademetal.,2012 Dunfieldetal.,2007;HouCampetal.,2009 Islametal.,2008;OpdenErikstadandBirkeland,20 Ettwigetal.,2010 MTTitbcnwhahyaseoejpemtodhcreoemhtadoaIa1rxinIjas9ootcM7rnitn0peocshremgtiyizrtvasiaohcinetouidaolpcotnsnhrg,1aaio9ocirt8afatstyl0cr,sptsoeee(vrmWprieserohtIhsairucilpstlstahtn?eenoenbddwlebotugiwgnritceeyyaenptlnee,harenatuydIlocIptlrfeaaDsmmssItaireefiluatttcohhcnatnaadtunni,orooatnyttl1rrp9ooei8appnn1hhtI)dossI.
methanotrophs were the arrangement of internal membranes
olicum” m” ensis” acesllvepseirciuplharerdyis(ctysp(etyIpI)e,It)heorcaprabiorendfimxaetmiobnramneecshaalniginsmedvtioa tthhee
a. m umar noru chatk ribulose monophosphate pathway (type I) or serine cycle (type
Proteobacteriylum Synonym/basony “Acidimethylosilexf “Methylokorusinfer “Methyloacidakam (MfcIsuItthya)rua,pgtrrhetearhseec,IerltIlea),crdnafi2isadpff0ttai0tectbyr8hsie)laesn.ictutyipIicdnarhosteefdsa(doHsonmmitatfhnrreieoonsgmospatennrunecdasteyefiinepnxdoseca,feHttisIoyoappnfneme,rscioitebfiXhntuche,lamo1fCnos9ee1or9t6-mt6h1r;ao(,a5tnTpty-iohrbopotsinerstospbIoeph)afnhoskorseseorpdswhtaCieanonr1tndgee8
h
p e carboxylase, differences in nitrogen fixation capability or
e c
th en higher optimum growth temperatures (Green, 1992; Hanson
e u d d d d d d d
outsid oXseq detecte detecte detecte detecte detecte detecte detecte oanfd16HSanrRsoNnA, 1g9e9n6e; sBeoqwuemnacnes, 2c0o0n6fi)r.mPedhyltohgiesnectlaicssiafincaaltyiosens,
moA mm Not Not Not Not Not Not Not ble. whereby type I and type X methanotrophs correspond to the
p aila Gammaproteobacteria and type II to the Alphaproteobacteria.
ophicbacteriaharboring (Eco-)physiology Thermophilic,acidophilic Thermophilic,acidophilic Thermophilic,acidophilic Thermophilic,acidophilic Thermophilic,acidophilic Thermophilic,acidophilic Anaerobic enceofthestrainasfarasav ficoHdm(htux1oheaa)rnweritniarteMoicgogvntreenetortreh,hpiudestaapthncti:lcehraosiswctttrehaaoryayripereahaailcnirsactsroegsrhBetilaizloelysalinjtiegtinaoruetinrronndcoeqeiksxfuditcaseilnetsuhvtcssietipoisirvvenaeced.lliiyWensfsteefihwnoaaituclruegtneiretodenhn,neeiornsbmateavaaoscejnenoorddenarlsscooipadnorreetbchrttiohheeendeers
acteristicsofmethanotr Isolationsource Volcanicsoil Volcanicsoil Volcanicsoil Themalmudpod Soil,geothermalarea Hotspring Riversediment ssificationandgenomesequ 2athhgphse0aaaenv0rsttee2yiacrc,phau2vwia0lceMarea0satlil4leecc-,ttldthmee2yesry0pviel1seoetit5hclnioaecIas;pIlntlDeaeienmadutadmeennm,rtfiodhnebenaamluMonldtoboeemxrtttorahyeaonngymlpeell.,yohnb2fssraey0aMrss0ueant3seelea(,tmhD2msdy0.yeloo1sdFost0cyuetn;asrmVohptohts.ofaeeprStrtoomohpbasmealeso.mel,vressea2es,mr0tlautt0ahhcaml0ky.ee,,
calchar Type III III III III III III – urrentcla (2) 2A0ll11m).ethanotrophic Beijerinckia species lack the classical
TABLE3|Isolationsourceandphysiologi Typestrain Verrucomicrobia,Methylacidiphilaceae “Methylacidimicrobiumcyclopophantes”3B “Methylacidimicrobiumfagopyrum”3C “Methylacidimicrobiumtartarophylax”4AC “Methylacidiphilumfumariolicum”SolV “Methylacidiphiluminfernorum”V4 “Methylacidiphilumkamchatkense”Kam1 CANDIDATEDIVISIONNC10 “Candidatus”MethylomirabilisoxyferaNC10 aListedpublicationsdescribetheinitialisolation,c ((43)) fca21M(t2MdMahDrc080otieieeo1:0meted1titys09sdrhhωteo;)yyyen.8Vfasllmmnooochctosymctieairdeypsjmsoptaos,seitbgorarbiIisnleseon.svm,ahrffoea2steevseuMt0ytsttutor0eyyhameefrt0plathi.,hena,tpif2hycs2aoco0leit0aItodss0trI1ltysisdo2Mhg1e,ipnmes)cae2(s.hruaHtce0meSsthrist0uidaey(hum4wryDllasieo,eiiionet2ltrahfhfdo0acreyt1otel1rrtyst5tymn6oyhs,ap:uptM1a;aaeeabhωDciltct.ense,eia8u:tIadrhIlcne.r21y,Maa(fi0l8m2Bhnoe0s:e01asoelie5t0digvaωhdtn;7nheuyeeu7)aalstHl.csois,ntaeiuhsioglrrpar.anta,eomlrey2oarotfa0tbioaapuum0aintnhurmtl3dgy.aess,,
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Knief DiversityandHabitatSpecificityofMethanotrophs
FIGURE1|Phylogenetictreesshowingthephylogenyofmethanotrophictypestrainsbasedon16SrRNAgenesequences(lefttree)andPmoA
sequences(righttree).TheneighborjoiningtreeswerecalculatedusingtheARBsoftwarepackage(Ludwigetal.,2004)basedon1556nucleotidepositionswith
JukesCantorcorrectionor160aminoacidpositionswithKimuracorrection,respectively.PmoAsequencesofMethylobacterluteus,Methylobacterwhittenburyi,and
Methylomicrobiumpelagicumarenotavailablefromthetypestrains,butweretakenfromadifferentstrainrepresentingthespecies.The16SrRNAgenebasedtree
wasrootedwithsequencesofmethanogenicArchaea(AB301476,M60880,AB065296,AM114193,AB196288),thePmoAtreewithAmoAsequencesof
ammonia-oxidizingbacteria(NC_004757,X90822).Dotslabelbranchpointsthatwereconfirmedinmaximumlikelihoodtrees.Thescalebarsdisplay0.10changes
pernucleotideoraminoacidposition.
et al., 2010, 2014). The fourth member of this family, abandon it (Op den Camp et al., 2009; Semrau et al., 2010).
Methylothermus thermalis, contains 18:1ω9c, a C fatty Nevertheless, the terms are still frequently used and adapted
18
acidneitherabundantintheotherMethylothermaceaenor to the increasing diversity of methanotrophs, but should only
intypeIImethanotrophs(Tsubotaetal.,2005). be considered as synonyms for the phylogenetic groups of
(5) Methanotrophic Verrucomicrobia do not fit well into the methanotrophic Alpha- and Gammaproteobacteria. In this way
scheme as most of them lack the typical intracytoplasmic thetermswillbeusedinthisreview.
membranes (only exception “Methylacidimicrobium The methanotrophic Alphaproteobacteria were recently
fagopyrum”) and have distinct dominant fatty acids (i14:0, divided into type IIa (Methylocystaceae) and type IIb
a15:0)(OpdenCampetal.,2009;vanTeeselingetal.,2014). (Beijerinckiaceae) methanotrophs (Deng et al., 2013;
(6) Further differentiation criteria such as nitrogen fixation Dumont et al., 2014). Likewise, the methanotrophic
capability,theformationofrestingstages,ortheoptimum Gammaproteobacteria are frequently differentiated into
growth temperature, which were initially applied, are not subgroups. Often they are divided into two groups, whereby
indicativeforoneortheothertypeanymore. the genera Methylococcus, Methylocaldum, Methylogaea and
the Methylothermaceae form type 1b methanotrophs, while
Based on these exceptions, the initial concept of type I and the remaining gammaproteobacterial genera are grouped as
II methanotrophs is no longer useful to categorize all known type 1a methanotrophs (Chen et al., 2008; Deutzmann et al.,
aerobic methanotrophic bacteria and it has been proposed to 2011; Dumont et al., 2011; Siljanen et al., 2011; Krause et al.,
FrontiersinMicrobiology|www.frontiersin.org 8 December2015|Volume6|Article1346
Knief DiversityandHabitatSpecificityofMethanotrophs
2014). Some recent studies differentiated the methanotrophic on methane and methane monooxygenase expression is down-
Gammaproteobacteria into three type I subgroups, but this regulated in the presence of acetate (Dedysh et al., 2005;
categorization is not consistent among different publications. Theisen et al., 2005). In contrast, methane and propane are
A taxonomic review referred to the clade consisting of consumed simultaneously in this strain (Crombie and Murrell,
Methylococcus,Methylocaldum,Methylogaea,Methyloparacoccus 2014). A facultative lifestyle with a much narrower substrate
as type Ia and to members of the family Methylothermaceae as range has been reported for other members of the genus
type Ic, while the remaining Gammaproteobacteria represented Methylocella and for Methylocapsa aurea (Table1), but it is
type Ib methanotrophs (Bowman, 2014). In contrast, in some not a general feature of all methanotrophic Beijerinckiaceae.
cultivation independent studies the above mentioned frequent Moreover, several Methylocystis strains including diverse type
grouping into type Ia and Ib was applied and extended by strains are able to grow on acetate or ethanol, but with growth
introducingtypeIc,comprisingpmoAsequencesofuncultivated rates 3–10-fold lower compared to growth on methane (Belova
taxa (USCγ, JR2, JR3, OPU1) and the amoA sequence of et al., 2011; Im et al., 2011). Gene expression of methane
Nitrosococcus (Lüke and Frenzel, 2011; Henneberger et al., monooxygenase appears not to be regulated by acetate in
2012; Dumont et al., 2014). It is thus referring to a group of these methanotrophs (Belova et al., 2011; Yoon et al., 2011).
uncultivated methanotrophs. Such a further differentiation of It remains to be proven whether the capability to grow on
the methanotrophic Gammaproteobacteria appears useful to acetate is linked to phylogeny within this genus. Crenothrix
refer to the specific subgroups of cultivated and uncultivated polyspora is the only methanotrophic gammaproteobacterium
methanotrophs easily. In this review, the nomenclature of type for which uptake of acetate and, to lesser extent, glucose, has
Ia and Ib methanotrophs as applied in diverse cultivation- been reported (Stoecker et al., 2006), but besides evidence
independent studies is kept, while the Methylothermaceae are from fluorescence in situ hybridization experiments coupled
referred to as type Ic methanotrophs (Table2). The clade to microautoradiography (FISH-MAR) performed on natural
of Nitrosococcus and related uncultivated clusters represent enrichments, this phenomenon has not been further proven. It
type Id organisms when discussing diversity based on pmoA is obvious that a facultative lifestyle can provide a benefit for
phylogeny. Methanotrophic Verrucomicrobia are referred to as methanotrophic bacteria. However, the relevance of facultative
typeIII. methanotrophy in nature remains little understood, and linked
to this the question to what extent a facultative life style
Ecophysiology of Aerobic Methanotrophic
may influence methane emissions in the environment. Only
Bacteria few studies have analyzed the consumption of methane and
Aerobic methanotrophic bacteria occur in terrestrial, aquatic alternative substrates under in situ conditions so far. In
and marine ecosystems, typically at oxic-/anoxic interfaces, mire samples, acetate addition resulted in a reduction of
where oxygen is available as electron acceptor and methane as methaneemissionratesanddecreasedpmoAexpressionratesof
carbon and energy source, which is released as end product Methylocystis(Wieczoreketal.,2011).Likewise,acetateaddition
from the anaerobic degradation of organic matter. They are decreased methane oxidation rates and stimulated growth of
likewisepresentindiverseuplandsoilswheretheyareresponsible Methylocystis in paddy soil samples. Stable isotope probing
for atmospheric methane oxidation or become temporarily with 13C-labeled acetate under aerobic conditions resulted in a
active when higher concentrations of methane are available labelingofMethylocystisinthesesamples,demonstratingthatthe
(Knief et al., 2006; Dunfield, 2007; Kolb, 2009). The ecology of labeled carbon was somehow metabolized and incorporated by
methanotrophic bacteria has been reviewed in diverse articles thecells(Lengetal.,2015).
andwillnotbediscussedindetailhere(e.g.,HansonandHanson, Another aspect that has repeatedly been addressed is the
1996;Conrad,2007;Semrauetal.,2010;ChowdhuryandDick, adaptation to low methane concentrations. The observations
2013;Bowman,2014).Thefocusinthisarticleisonphysiological made in competition experiments with isolates grown in
adaptationstoparticularenvironmentalconditionsinrelationto continuous culture and in incubations with rice field soils
phylogeny. resulted in the frequently cited conclusion that type I
In terms of metabolic adaptations, some methanotrophic methanotrophs are more competitive under low methane
bacteria show higher versatility than initially thought. They concentrations compared to type II methanotrophs (Graham
are capable of growing on carbon compounds with C-C bond, et al., 1993; Henckel et al., 2000b; Macalady et al., 2002). This
whilemostmethanotrophicbacteriaareobligatemethanotrophs. seemstoapplytoecosystemsaslongasmethanesupplyremains
The existence of such facultative methanotrophs had been at a rather high level, but when methane concentrations drop
debated for a long time (reviewed in Theisen and Murrell, below 1000 or even 100ppmv for prolonged periods of time,
2005; Semrau et al., 2011), until it was rigorously proven Methylocystaceae have the better potential to remain active
for Methylocella silvestris BL2 (Dedysh et al., 2005). This (KniefandDunfield,2005).
strain has the broadest versatility currently known among Most methanotrophic bacteria are mesophilic and
methanotrophs; besides C -compounds, it can use a variety of neutrophilic organisms, but several isolates were obtained
1
organicacidsincludingacetate,pyruvate,propionate,succinate, from more extreme habitats and are specifically adapted to
malate,andgluconate,alcoholssuchasethanoland2-propanol lowerorhigherpH,temperature,saltoroxygenconcentrations
and the gaseous compounds ethane and propane (Crombie (Trotsenko and Khmelenina, 2002). Methanotrophic bacteria
and Murrell, 2014). Growth on acetate is more efficient than adaptedtowarmerorcoldertemperaturesarefoundinacouple
FrontiersinMicrobiology|www.frontiersin.org 9 December2015|Volume6|Article1346
Knief DiversityandHabitatSpecificityofMethanotrophs
of distinct genera of Gammaproteobacteria, often side by side limited to one phylogenetic lineage, but can often be found
with mesophilic species (Table2). Among the methanotrophic within different genera of methanotrophs side by side with
Alphaproteobacteria adaptations to temperatures outside the speciesthatshowdifferentadaptationsandhabitatpreferences.
mesophilic range appear to be uncommon. Outstanding are Thus, some genera have a broad ecological niche, though the
the verrucomicrobial methanotrophs, which represent the individual species or strains have smaller niches, while others
most thermophilic methanotrophs (optimum temperature arelessdiverseintermofecophysiologicaladaptationsandhave
55–60◦C) (Op den Camp et al., 2009). These are at the same a rather narrow niche. Habitat adaptation and specialization
time acidophiles, with pH optima for growth between 2.0 and appear to occur at different taxonomic levels. Consequently,
4.3. All isolates were obtained from geothermally influenced thedistributionofmethanotrophicbacteriaintheenvironment
environments (Op den Camp et al., 2009; van Teeseling shouldbeevaluatedatthesedifferenttaxonomiclevelsinorder
et al., 2014). The occurrence of these thermoacidophilic to better understand distribution and community composition.
methanotrophs appears to be largely restricted to such Such a detailed evaluation is undertaken in this review, based
geothermal environments, in particular to acidic conditions, on a meta-analysis including the large diversity of uncultivated
whiletheyseemtohaveabroadertemperaturerange,asrevealed methanotrophs(seeSectionsDescriptionofMajorUncultivated
by cultivation-dependent and -independent analyses (Sharp GroupsofMethanotrophicBacteriaandTheirHabitatSpecificity
etal.,2014;vanTeeselingetal.,2014). and Habitat Specificity of Methanotrophic Taxa Evaluated at
An adaptation to mildly acidic pH values (growth optima HigherTaxonomicResolution).
between 5.0 and 6.0) is characteristic for methanotrophic
Beijerinckiaceae and some Methylocystis strains, which were CULTIVATION-INDEPENDENT DETECTION
mostly isolated from acidic peatlands or forest soils (Table1).
OF AEROBIC METHANOTROPHIC
Cultivation-independentanalysessuggestthattheoccurrenceof
BACTERIA BASED ON MOLECULAR
Methylocellaisnotlimitedtotheseacidicenvironments(Rahman
et al., 2011). Less common are acidophilic methanotrophs MARKERS
among the Gammaproteobacteria. Members of the species
Methylomonas paludis have been described as acid-tolerant Tools for the cultivation-independent detection of aerobic
and are inhabitants of acidic peatlands (Danilova et al., 2013; methanotrophic bacteria exist since 20 years and have been
DanilovaandDedysh,2014).Methanotrophsthatareadaptedto used in diverse studies. The most frequently targeted gene in
high pH values are found within the Gammaproteobacteria, in environmental studies, the 16S rRNA gene, can be used for
particular within the genus Methylomicrobium. The occurrence the detection of methanotrophic bacteria using taxon specific
of alkaliphilic methanotrophs is not restricted to the class primersandprobesthatareavailableforseveraldifferentgroups
of Gammaproteobacteria, the isolation of an alkaliphilic (compiled by McDonald et al., 2008). While the analysis of
Methylocystis isolate has also been reported (Eshinimaev this gene provides valuable information about the phylogenetic
et al., 2008). Some alkaliphilic Gammaproteobacteria are at placementofmethanotrophicbacteriadetectedinenvironmental
the same time halophiles (Methylomicrobium alcaliphium samples, it does not allow the identification of methanotrophic
and Methylomicrobium kenyense), isolated from soda lakes bacteriabeyondthewell-knownfamilies.
(Kalyuzhnaya et al., 2008). Methanotrophic bacteria that were
Functional Marker Genes as Molecular
isolatedfrommarineecosystemsarealsoadaptedtohighersalt
concentrations and are likewise found among methanotrophic Markers
Gammaproteobacteria. High salt tolerance is not necessarily Suchalimitationisoflessrelevancewhenfunctionalgenesare
a characteristic of all members of a genus, as exemplified by usedasmarkers,suchasthemethanemonooxygenaseencoding
MethylocaldumandMethylomicrobium(Table2).Inthelastfew genes (McDonald et al., 2008). The methane monooxygenase
years, the first methanotrophic isolates were described that live is the key enzyme responsible for the initial conversion
preferentiallyunderloweroxygenconcentrations(Methylosoma step of methane to methanol. Two forms of this enzyme
difficile and Methyloglobulus morosus). They were enriched in are known, the soluble methane monooxygenase (sMMO)
systems with opposing gradients of methane and oxygen, thus and a membrane-bound enzyme, the particulate methane
mimicking the conditions in sediments (Rahalkar et al., 2007; monooxygenase (pMMO). The pmoA gene encoding the β-
Deutzmannetal.,2014). subunit of the particulate methane monooxygenase is the
In conclusion, a broad versatility in terms of adaptation most frequently used marker, as it is present in most
to different environmental conditions can be found among aerobic methanotrophic bacteria with exceptions among the
the methanotrophic Gammaproteobacteria (low and high Beijerinckiaceae (Table1). It is also present in anaerobic
temperatures, low and high pH, high salt, low oxygen), which denitrifying bacteria, represented by an enriched culture of
comes along with a high diversity of methanotrophs within “CandidatusMethylomirabilis,”abacteriumoftheNC10phylum
this group. Cultivated methanotrophic Alphaproteobacteria (Ettwigetal.,2010).
are less diverse and show less and different adaptations (low To include Beijerinckiaceae and to obtain a more complete
pH, low methane availability) based on current knowledge. At picture about the methanotrophs present in a sample, the
genuslevel,theoccurrenceofmethanotrophicbacteriathatare mmoX gene encoding the α-subunit of the soluble methane
adaptedtoaspecificenvironmentalconditionisnotnecessarily monooxygenase hydroxylase component has been used in
FrontiersinMicrobiology|www.frontiersin.org 10 December2015|Volume6|Article1346