Environmental Microbiology Reports (2009) 1(5), 285–292
Minireview
The global methane cycle: recent advances in
understanding the microbial processes involved
Ralf Conrad*
Max-Planck-Institute for Terrestrial Microbiology,
Karl-von-Frisch-Str.8, 35043 Marburg, Germany.
Summary
The global budget of atmospheric CH4, which is on
the order of 500–600 Tg CH4 per year, is mainly the
result of environmental microbial processes, such
as archaeal methanogenesis in wetlands, rice fields,
ruminant and termite digestive systems and of micro-
bial methane oxidation under anoxic and oxic condi-
tions. This review highlights recent progress in the
research of anaerobic CH4 oxidation, of CH4 pro-
duction in the plant rhizosphere, of CH4 serving as
substrate for the aquatic trophic food chain and
the discovery of novel aerobic methanotrophs. It also
emphasizes progress and deficiencies in our knowl-
edge of microbial utilization of low atmospheric CH4
concentrations in soil, CH4 production in the plant
canopy, intestinal methanogenesis and CH4 produc-
tion in pelagic water.
The global methane cycle
Methane is the second most important anthropogenic
greenhouse gas after CO2, contributing about 30% to
the total net anthropogenic radiative forcing of 1.6 W m-2
(IPCC WG I fourth assessment 2008; http://www.ipcc.
ch/pdf/assessment-report/ar4/syr/ar4_syr_spm.pdf). The
concentration of CH4 in the atmosphere has been increas-
ing from pre-industrial values of about 715 ppbv to cur-
rently about 1770 ppbv. The growth rate of atmospheric
CH4, which is determined by the balance of sources and
sinks, was about 12 ppb year-1 in the 1980s, but has
decreased since the early 1990s and with a value of about
4 ppb year-1 since 1999 (Bousquet et al., 2006). However,
there are indications of large year-to-year fluctuations
of sources and sinks, which eventually could result
in resumption of the growth of the atmospheric CH4
Received 1 April, 2009; accepted 18 May, 2009. *For correspon-
dence. E-mail conrad@mpi-marburg.mpg.de; Tel. (+49) 6421
178801; Fax (+49) 6421 178809.
© 2009 Society for Applied Microbiology and Blackwell Publishing Ltd
doi:10.1111/j.1758-2229.2009.00038.
emi4_038 285..292
concentration (Bousquet et al., 2006). The global budget
of atmospheric methane is on the order of 500–600 Tg
CH4 year-1 (Lelieveld et al., 1998; Wang et al., 2004). The
individual sources contributing to this budget are shown
as a pie chart in Fig. 1.
About 25% of all CH4 sources are associated with
mining and combustion of fossil fuels or with burning of
biomass. About 69% of the sources is the result of micro-
bial processes and another 6% is due to chemical pro-
duction of CH4 from plant material. This overview shows
that most of the atmospheric CH4 originates from micro-
bial metabolism, more precisely from CH4 production by
methanogenic archaea. Methanogenic archaea and CH4
production is typically found at those sites where organic
matter is decomposed in the absence of oxygen or of
other oxidants, such as nitrate, sulfate or ferric iron. Wet-
lands are the largest individual source of microbial CH4.
There is comparatively little direct influence of humans
on the CH4 source strength of wetlands, at least little in
comparison with flooded rice fields, which are anthro-
pogenic wetlands. Rumen fermentation in cattle, sheep
and other ruminants are another important individual CH4
source that is under human management. Further anthro-
pogenic sources are anaerobic digestion plants and land-
fills, in which waste materials are degraded to produce
large quantities of CH4. Intestinal fermentation in termites,
CH4 production in the water column of ocean and CH4
release from gas hydrates are comparatively minor but
significant sources of atmospheric CH4, all without much
direct human impact.
The global CH4 sources are balanced by sinks of similar
magnitude. In fact, the total sink strength has for long time
been a bit smaller than the total source strength, thus
causing the steady growth in atmospheric CH4 concen-
tration since pre-industrial times. Fortunately, the CH4 sink
strength increases proportionally with the increasing CH4
concentration in the atmosphere (quasi first-order reac-
tion) thus neutralizing changes in the source strength at
least partially. The lifetime of a CH4 molecule in the atmo-
sphere is only on the order of 8 years (Lelieveld et al.,
1998; Wang et al., 2004). The largest sink (> 80% of the
total) is the photochemical oxidation of CH4 initiated by
the reaction with OH radicals. The other two sinks are
286 R. Conrad
plants
6% wetlands
18%
termites natural
23% ocean
7% gas hydrates
microbial
rice fields
4% ruminants
7% 3% landfills
3% sewage treatment
17% 2% biomass burning
10% fossil fuel
Fig. 1. Global methane sources in per cent of the total budget of
about 500–600 Tg CH4 per year.
diffusion into the stratosphere and microbial CH4 oxidation
in soil.
It should be noted that the strengths of these sources or
sinks represent net fluxes between the planetary surface
and the atmosphere. Gross fluxes can be much larger.
In rice fields, for example, much (about 20%) of the pro-
duced CH4 is consumed by aerobic methanotrophs living
in the rhizosphere of the rice plants, thus attenuating the
net flux into the atmosphere (Schütz et al., 1989; Frenzel,
2000; Groot et al., 2003). For most CH4 sources shown in
Fig. 1, rates of CH4 production are usually much larger
than rates of CH4 emission since a large fraction of the
initially produced CH4 is consumed by microorganisms
before it can enter the atmosphere (Frenzel, 2000;
Reeburgh, 2003).
The quantitatively most important example is CH4
emission from gas hydrates, which presently constitutes
only about 1% of the total atmospheric CH4 budget or
about 5–6 Tg CH4 year-1. However, the total reservoir of
gas hydrates in the marine sediments of the continental
margins is huge, on the order of 500 000–10 000 000 Tg
CH4, or about 150–3000 the amount of CH4 in the atmo-
sphere (Reeburgh, 2007). In fact, mobilization of CH4 from
the gas hydrates is much larger than the net emission
into the atmosphere, but most of the mobilized CH4 is
fortunately consumed by anaerobic methane oxidizers,
which globally account for a consumption rate of about
70–300 Tg CH4 year-1 (Reeburgh, 2007). Without this
consumption activity, the atmospheric CH4 budget would
be higher by 10–60% resulting in dramatically higher
concentrations of atmospheric CH4.
There are several comprehensive reviews of the global
CH4 cycle and the environmental microbiology of metha-
nogenic and methanotrophic microorganisms (Reeburgh,
2003; Conrad, 2007; Dunfield, 2007; Reeburgh, 2007; Liu
and Whitman, 2008; Thauer and Shima, 2008; Trotsenko
and Murrell, 2008). In this minireview, I will therefore con-
centrate on some recent advances in the microbiology
of the CH4 cycle and discuss some problems that are still
unsolved.
© 2009 Society for Applied Microbiology and Blackwell Publishing Ltd, Environmental Microbiology Reports, 1, 285–292
Anaerobic methane oxidation
Existence of anaerobic oxidation of CH4 has been postu-
lated for a long time in order to explain concentration
gradients and isotopic signatures of CH4 in marine sedi-
ments. Furthermore, it has been possible for long time to
measure the conversion of 14CH4 to 14CO2 in environ-
mental samples, which usually were of marine origin. It
has been postulated that CH4 is oxidized by reduction
of sulfate and that this would possibly be carried out
by CH4-oxidizing H2-producing archaea syntrophically
associated with H2-consuming sulfate-reducing bacteria
(Valentine and Reeburgh, 2000; Reeburgh, 2007). Such
a process was shown to be consistent with the ther-
modynamic conditions in marine sediments, in particular
with the H2 partial pressures (Hoehler et al., 1994). The
microbes involved in such a process were for the first time
visualized by applying fluorescent in situ hybridization
(FISH) with nucleic acid probes specific for archaea and
for sulfate-reducing bacteria (Boetius et al., 2000). Using
FISH coupled to secondary ion mass spectrometry
(SIMS) it was possible to demonstrate that the archaea
indeed were highly depleted in 13C as expected when
utilizing CH4 as carbon source (Orphan et al., 2001).
It was shown that these consortia consist of archaea,
which form the phylogenetically distinct cluster ANME-2
within the methanogenic order Methanosarcinales, and
of sulfate-reducing bacteria from the Desulfosarcina–
Desulfococcus branch of Deltaproteobacteria. Subse-
quently similar consortia were found with archaea of the
clusters ANME-1, which is distantly related to Methanosa-
rcinales and Methanomicrobiales (Orphan et al., 2002;
Knittel et al., 2005), and ANME-3, which is related to
the genera Methanococoides and Methanolobus within
the Methanosarcinales (Lösekann et al., 2007). ANME
archaea contain gene homologues of the methyl-
coenzyme M reductase, the key enzyme of CH4 synthe-
sis, suggesting that a similar enzyme may be involved
in anaerobic oxidation of CH4 to CO2 (Hallam et al., 2004).
Indeed, two nickel proteins resembling cofactor 430 from
the methyl-coenzyme M reductase were isolated in rela-
tively high abundance (10% of total protein) from micro-
bial mats exhibiting anaerobic CH4 oxidation (Krüger
et al., 2003). However, the biochemical mechanism of
the enzymatic oxidation reaction is still unclear (Thauer
and Shima, 2008).
The CH4-oxidizing archaea of the ANME clusters have
so far only been grown in enrichment cultures with very
low growth rates (doubling times of weeks to months) and
low growth yields (only 1% of the CH4 oxidized is used
for biomass production), but have not yet been isolated
(Girguis et al., 2005; Nauhaus et al., 2007). It is also
debatable whether these archaea really need sulfate
reducers as syntrophic partners or can reduce sulfate by

themselves (Thauer and Shima, 2008). The idea of CH4
oxidation within one sole microbial species stems from
another recent discovery, the anaerobic oxidation of CH4
with nitrate as electron acceptor (Raghoebarsing et al.,
2006). Methane oxidation coupled to denitrification was
discovered in an anaerobic enrichment culture from a
canal sediment. This enrichment culture consisted of 10%
archaea of the order Methanosarcinales distantly related
to ANME-2, the rest being bacteria. Hence, it was plau-
sible to assume that anoxic CH4 oxidation with nitrate
would operate similarly as with sulfate, i.e. the archaea
oxidize CH4 to CO2 and transfer the electrons to the deni-
trifiers reducing nitrate or nitrite to N2. However, it turned
out that the oxidation of CH4 is catalysed exclusively by
the denitrifiers without participation of the archaea (Ettwig
et al., 2008). Hence, we may expect an interesting bio-
chemical mechanism for CH4 oxidation with oxidized nitro-
gen compounds. Interestingly, the analogous oxidation
of ammonia can also be initiated with NO2 instead of O2
(Schmidt and Bock, 1997; Schmidt et al., 2004). However,
it is unclear how NO2 could be formed in the absence of
O2. The mechanism of CH4 oxidation in the denitrifiers
is presently investigated by Jetten and co-workers.
Novel aerobic methanotrophs
Aerobic methanotrophic bacteria are widely distributed
in nature, typically at anoxic–oxic interfaces, such as sedi-
ments, where they attenuate the flux of CH4 into the
atmosphere. Canonical aerobic methanotrophs belong to
either the Gammaproteobacteria or type I methanotrophs
(10 different genera) or the Alphaproteobacteria or type
II methanotrophs (the genera Methylocystis, Methylo-
sinus, Methylocella, Methylocapsa). Type I methano-
trophs assimilate C via the ribulose monophosphate
pathway, while type II methanotrophs use the serine
pathway (Trotsenko and Murrell, 2008). A few years ago,
the filamentous bacterium Crenothrix polyspora was
found to be methanotrophic (Stoecker et al., 2006). Simi-
larly, Clonothrix fusca was described as a methanotroph
(Vigliotta et al., 2007). These were surprising discoveries,
since these filamentous bacteria had not been known to
be able to consume CH4. However, both species belong to
the Gammaproteobacteria and are closely related to the
type I methanotrophs. Molecular techniques useful to
detect these methanotrophs in the environment are based
on characteristic sequences of the 16S rRNA gene and
of functional genes coding for subunits of the particulate
(pMMO) or soluble methane monooxygenase (sMMO),
and have recently been reviewed (McDonald et al.,
2008). Very recently, methanotrophs within the phylum
Verrucomicrobia were discovered in hot environments
(Dunfield et al., 2007; Pol et al., 2007; Islam et al., 2008).
These isolates are thermoacidophilic (pH optimum
© 2009 Society for Applied Microbiology and Blackwell Publishing Ltd, Environmental Microbiology Reports, 1, 285–292
Global methane cycle 287
2.0–3.5, temperature optimum 55–60°C) and have
recently been placed into the new genus Methylacidi-
philum (OpdenCamp et al., 2009). This was the first dis-
covery that methanotrophic growth is not restricted to
the Proteobacteria, but also exists in another bacterial
phylum. Future research will show how broadly distributed
methanotrophy really is among prokaryotes.
It has been a paradigm that methanotrophic bacteria
are obligately methylotrophic, i.e. can only utilize C1 com-
pounds. This paradigm was recently disproved by the
discovery that Methylocella sp. are facultative hetero-
trophs, which can also utilize acetate as energy source
and actually prefer this substrate over CH4 (Dedysh et al.,
2005). Methylocella is the only methanotrophic genus,
which contains sMMO but no pMMO. Acetate was found
to suppress transcription of sMMO and thus CH4 oxidation
(Theisen et al., 2005). However, since acetate stimulates
growth of Methylocella, acetate may have a positive effect
on the longer term through increase of the population size
of methanotrophs. In fact, such effect has been observed
with atmospheric CH4 oxidation in alpine tundra soil,
but has been attributed to indirect stimulation through
CH4 production by acetoclastic methanogens (West and
Schmidt, 1999). It would be interesting to see whether
there exist more facultatively heterotrophic methanotro-
phs in nature and which effect this has on CH4 cycling.
Utilization of low methane concentrations
Soils act as a sink for atmospheric CH4. The atmospheric
concentrations of CH4 typically are 1.7 ppmv, after disso-
lution in water about 2 nM CH4. This is a very poor energy
source for methanotrophic bacteria and demands that
the enzymes of these bacteria have a high affinity for
the substrate (Conrad, 1984). Indeed, such high-affinity
methanotrophs actually exist in soil (Bender and Conrad,
1992), but their phylogenetic affiliation is not exactly
known. Uptake of CH4 from the atmosphere into the soil
is usually associated with the detection of particular
sequences of the pmoA gene (coding for a subunit of the
pMMO) (Holmes et al., 1999; Henckel et al., 2000; Knief
et al., 2003). Many of these sequences, e.g. those of
USCa, are closely related to the pmoA of Methylocapsa
acidiphila (Ricke et al., 2005), but isolates of these high-
affinity methanotrophs still do not exist.
Attempts to isolate high-affinity methanotrophs so far
resulted only in the retrieval of Methylocystis sp. (Dunfield
et al., 1999), which express high affinity for CH4 under
starvation conditions (Dunfield and Conrad, 2000). Many
of the Methylocystis species contain two types of pMMO,
the conventional enzyme and a second one (Ricke et al.,
2004). It has now been shown that the second pMMO
is specifically required for growth and maintenance
on low CH4 concentrations (10–100 ppmv), while the
288 R. Conrad
conventional pMMO is only active at high CH4 concentra-
tions (> 600 ppmv) (Baani and Liesack, 2008). Since the
apparent Km values (i.e. 0.11 mM) for CH4 of these Methy-
locystis species are at the higher end of those found in soil
environments, and since they have been found in hydro-
morphic soils in high abundance (Knief et al., 2006), it
is hypothesized that they may be specifically adapted to
environments where CH4 concentrations change between
high and low values.
Methane production in the rice rhizosphere
Rice fields and natural wetlands are an important source
in the global CH4 cycle. In rice fields, up to 60% of CH4
emission is due to decomposition of root exudates or
dead roots both originating from recently assimilated
CO2 (Watanabe et al., 1999). This was shown using pulse
labelling of rice plants with 13C-CO2 which resulted in the
production and emission of a proportional amount of 13C-
CH4. The same approach was used to label the metha-
nogenic archaea in the rhizosphere that incorporated
the photosynthetically fixed carbon into their cells using
the stable isotope probing technique (Radajewski et al.,
2000). As a result, Rice Cluster I methanogens were
identified as the major group responsible for CH4 produc-
tion in the rice rhizosphere (Lu and Conrad, 2005). These
methanogens, which produce CH4 by reduction of CO2,
seem to be specifically adapted to this environment, since
replacement of the rhizospheric population with Metha-
nomicrobiales resulted in lower population densities on
the roots and in much lower rates of CH4 production and
emission (Conrad et al., 2008). Rice Cluster I metha-
nogens have been known as a phylogenetic group of
Archaea since about 10 years ago (Grosskopf et al.,
1998), but attempts to isolate methanogens from this
cluster have not been successful until recently. Prior to
isolation, the entire genome sequence of a Rice Cluster I
methanogen has been retrieved from an enrichment
culture and reassembled by metagenomics (Erkel et al.,
2006). The sequence data indicated that these methano-
gens may be specifically adapted to the environmental
conditions in the rhizosphere, especially to the presence
of O2, by having a unique set of antioxidant and
O2-insensitive enzymes. Now, a first isolate of Rice
Cluster I methanogens exists (Sakai et al., 2007), which is
described as Methanocella paludicola representing the
new order of Methanocellales (Sakai et al., 2008).
Methane production and emission by plants
While microbial CH4 production in the rhizosphere of
aquatic plants is a common process, production within
the plant canopy is unexpected. Nevertheless, exactly this
was found recently during incubation experiments using
© 2009 Society for Applied Microbiology and Blackwell Publishing Ltd, Environmental Microbiology Reports, 1, 285–292
plant microcosms (Keppler et al., 2006). The resulting
emission of CH4 into the atmosphere, when extrapolated
to the global scale, is significant (Fig. 1) and could be
the additional CH4 source in tropical regions that had
been predicted from satellite measurements and model
calculations (Frankenberg et al., 2005). Keppler and
co-workers claimed that CH4 is produced by aerobic
chemical reactions in the plant leaves, for example by
degradation of pectin. The potential of plants to aerobi-
cally produce and emit CH4 has been discussed contro-
versially, in particular since some researchers were
unable to reproduce the original results (Dueck et al.,
2007; Beerling et al., 2008). However, the crucial factor
seems to be illumination of plant leaves with UV instead
of photosynthetically active radiation. UV radiation indeed
resulted in substantial CH4 production from leaf material
and also from pectin (McLeod et al., 2008; Vigano et al.,
2008).
Nevertheless, there are additional processes in
plants that can result in the emission of CH4 through the
plant canopy. The best characterized is the transport
of CH4 through the plant gas vascular (aerenchyma)
system, which accounts for most of the flux from anoxic
soils vegetated with aquatic plants (Schütz et al., 1989;
Frenzel, 2000). In addition, CH4 can be transported in the
dissolved state from the anoxic soil via the transpiration
stream into canopy. Such CH4 transport indeed exists, as
has been shown by studies on rice plants (Nouchi et al.,
1990) and trees (Rusch and Rennenberg, 1998; Ter-
azawa et al., 2007), but CH4 flux by transpiration is always
orders of magnitude lower than the CH4 transport through
the plant aerenchyma system. Finally, CH4 can be pro-
duced inside of living tree stems by anaerobic decom-
position of wetwood (Zeikus and Ward, 1974), which
involves a methanogenic community that degrades wood,
including pectin (Schink et al., 1981). The CH4 accumu-
lating inside of the stems is often under high pressure
(Zeikus and Ward, 1974), but it is not known to what
extent this CH4 can be emitted through the plant canopy.
The emission from plants by the transpiration stream or by
release from wetwood has never been studied explicitly
with respect to the role in the global CH4 budget.
Methane production in intestinal systems
Methane emission by ruminants and termites is a large
source in the budget of atmospheric CH4 (Fig. 1). The
microbiology and methanogenic processes in these habi-
tats have recently been reviewed in detail (Purdy, 2007;
Janssen and Kirs, 2008; Liu and Whitman, 2008; Brune,
2009). In both rumen and hindgut of insects (termites,
cockroaches, scarab beetles), CH4 seems to be exclu-
sively produced from H2 + CO2 and its activity seems to
be limited by the supply of H2. Methane production from

acetate has never been demonstrated and acetoclastic
methanogens are usually not detected in these environ-
ments. In the rumen, CH4 production largely occurs in the
gut lumen where it decreases H2 to concentrations that
are not permissive for acetogenesis. In the insect hindgut,
however, methanogenesis is restricted to the gut wall or
other gut structures, or is associated with gut flagellates,
while in the gut lumen acetogenesis is often the main
H2-consuming process. The reason for this difference in
localization of methanogens in the rumen versus the
insect hindgut is presently unknown. Why are methano-
gens in the insect gut restricted to the gut wall, where O2
partial pressures are uncomfortably high? Why do rumi-
nants not allow H2-dependent acetogenesis instead of
methanogenesis, although they would gain a significant
amount of additional energy [about 6–10% of the energy
value of food (Liu and Whitman, 2008)] which is lost as
CH4. The differences are possibly the result of an evolu-
tionary process, as methanogenesis is restricted to a few
animal taxa (Hackstein et al., 1996). In this context it
is important to ask in which respect animals benefit from
the methanogens in their gut system (Brune, 2009). Are
insects able to control their methanogenic populations
better than ruminants do?
Methane in the aquatic environment
Methane production in aquatic sediments is a common
feature, since these are anoxic environments. It was rec-
ognized early on that most of the CH4 produced is oxi-
dized at the sediment surface or in the water column by
aerobic methanotrophic bacteria so that little CH4 escapes
into the atmosphere (Rudd and Taylor, 1980). However,
since a substantial part (about 50%) of the primary pro-
duction of a lake can be returned to the water column in
the form of CH4 (Fallon et al., 1980), CH4 can provide an
important source of energy for the methanotrophic bacte-
rioplankton and the trophic food chain depending on these
bacteria. There is growing evidence that methanotrophic
bacteria indeed provide an important food source for
zooplankton and insect larvae (Bastviken et al., 2002;
Deines et al., 2007; Jones et al., 2008). Methanotrophs
apparently can also provide a food source for Myxo-
bacteria, amoebae, flagellates and ciliates (Murase and
Frenzel, 2007). However, a quantitative evaluation of the
CH4 flux through the trophic food chain is not yet avail-
able. It is worth mentioning that methanotrophs also serve
as symbionts in marine invertebrates (Cavanaugh, 1993)
and apparently also in Sphagnum moss (Raghoebarsing
et al., 2005).
Methane production in the oxic water column is a
paradox, but nevertheless exists (Reeburgh, 2007). In
lakes, supersaturation of oxic water bodies with CH4 can
sometimes be explained by lateral transport from the
© 2009 Society for Applied Microbiology and Blackwell Publishing Ltd, Environmental Microbiology Reports, 1, 285–292
Global methane cycle 289
littoral zone, where CH4 is produced in the anoxic sedi-
ment (Schmidt and Conrad, 1993). In the open ocean, on
the other hand, it can only be explained by in situ produc-
tion, albeit the conditions (high O2 and sulfate) are not
conducive for CH4 production. Therefore, the processes
discussed generally assume CH4 production in anoxic
microniches and from non-competitive substrates, such
as methylated compounds. Hence it was discussed that
CH4 is released from fish intestine, from zooplankton
or from organic particles (Oremland, 1979; Sieburth et al.,
1993; DeAngelis and Lee, 1994; Karl and Tilbrook, 1994;
Marty et al., 1997; Holmes et al., 2000; Damm et al.,
2008). However, anoxic aggregates may be only an
ephemeral phenomenon in the oxic water column (Ploug
et al., 1997), too short-lived to allow development of a
methanogenic population. It is also doubtful whether small
zooplankton can provide a permanently anoxic environ-
ment, since these animals are too small to prevent O2
diffusion into their interior. Hence, it is not really clear how
CH4 is produced in pelagic water.
Summary of key issues
Several key issues can be identified that need to be
addressed for better understanding of the ecology of CH4-
producing or -consuming microorganisms and for their
role in CH4 cycling:
i. Elucidation of the biochemical mechanisms respon-
sible for activation and oxidation of CH4 in the absence
of O2. This issue would be helped by isolation of
anaerobic methanotrophs into pure culture.
ii. Identification, isolation and biochemical characteri-
zation of high-affinity methanotrophs able to oxidize
atmospheric CH4 in soil.
iii. Identification, isolation and biochemical characteri-
zation of aero-tolerant methanogens thriving in the
pelagic zone of lakes and ocean.
iv. Ecological and evolutionary aspects of heterotrophic
methanotrophs. Why are most of the known methan-
otrophs obligately methylotrophic?
v. Ecological and evolutionary aspects of gut symbio-
ses with methanogens, reasons for existence and
non-existence.
Acknowledgments
I thank A. Brune and W. Liesack for helpful discussion and the
Fonds der Chemischen Industrie for financial support.
References
Baani, M., and Liesack, W. (2008) Two isozymes of par-
ticulate methane monooxygenase with different methane
290 R. Conrad
oxidation kinetics are found in Methylocystis sp. strain
SC2. Proc Natl Acad Sci USA 105: 10203–10208.
Bastviken, D., Ejlertsson, J., and Tranvik, L. (2002) Measure-
ment of methane oxidation in lakes: a comparison of
methods. Environ Sci Technol 36: 3354–3361.
Beerling, D.J., Gardiner, T., Leggett, G., McLeod, A., and
Quick, W.P. (2008) Missing methane emissions from
leaves of terrestrial plants. Global Change Biol 14: 1821–
1826.
Bender, M., and Conrad, R. (1992) Kinetics of CH4 oxidation
in oxic soils exposed to ambient air or high CH4 mixing
ratios. FEMS Microbiol Ecol 101: 261–270.
Boetius, A., Ravenschlag, K., Schubert, C.J., Rickert, D.,
Widdel, F., Gieseke, A., et al. (2000) A marine microbial
consortium apparently mediating anaerobic oxidation of
methane. Nature 407: 623–626.
Bousquet, P., Ciais, P., Miller, J.B., Dlugokencky, E.J.,
Hauglustaine, D.A., Prigent, C., et al. (2006) Contribution
of anthropogenic and natural sources to atmospheric
methane variability. Nature 443: 439–443.
Brune, A. (2009) Methanogenesis in the digestive tracts of
insects. In Microbiology of Hydrocarbons. Timmis, K. (ed.).
Heidelberg, Germany: Springer (in press).
Cavanaugh, C.M. (1993) Methanotroph-invertebrate symbio-
ses in marine environment: ultrastructural, biochemical and
molecular studies. In Microbial Growth on C1 Compounds.
Murrell, J.C., and Kelly, D.P. (eds). Andover, MA, USA:
Intercept, pp. 315–328.
Conrad, R. (1984) Capacity of aerobic microorganisms to
utilize and grow on atmospheric trace gases. In Current
Perspectives in Microbial Ecology. Klug, M.G., and Reddy,
C.A. (eds). Washington, DC, USA: American Society for
Microbiology, pp. 461–467.
Conrad, R. (2007) Microbial ecology of methanogens and
methanotrophs. Adv Agron 96: 1–63.
Conrad, R., Klose, M., Noll, M., Kemnitz, D., and Bodelier,
P.L.E. (2008) Soil type links microbial colonization of rice
roots to methane emission. Global Change Biol 14: 657–
669.
Damm, E., Kiene, R.P., Schwarz, J., Falck, E., and Dieck-
mann, G. (2008) Methane cycling in Arctic shelf water and
its relationship with phytoplankton biomass and DMSP.
Mar Chem 109: 45–59.
DeAngelis, M.A., and Lee, C. (1994) Methane production
during zooplankton grazing on marine phytoplankton.
Limnol Oceanogr 39: 1298–1308.
Dedysh, S.N., Knief, C., and Dunfield, P.F. (2005) Methylo-
cella species are facultatively methanotrophic. J Bacteriol
187: 4665–4670.
Deines, P., Bodelier, P.L.E., and Eller, G. (2007) Methane-
derived carbon flows through methane-oxidizing bacteria
to higher trophic levels in aquatic systems. Environ Micro-
biol 9: 1126–1134.
Dueck, T.A., DeVisser, R., Poorter, H., Persijn, S., Gorissen,
A., DeVisser, W., et al. (2007) No evidence for substantial
aerobic methane emission by terrestrial plants: a 13C-
labelling approach. New Phytol 175: 29–35.
Dunfield, P.F. (2007) The soil methane sink. In Greenhouse
Gas Sinks. Reay, D.S., Hewitt, N., Smith, K.A., and Grace,
J. (eds). Wallingford, UK: CABI Publishing, pp. 152–
170.
© 2009 Society for Applied Microbiology and Blackwell Publishing Ltd, Environmental Microbiology Reports, 1, 285–292
Dunfield, P.F., and Conrad, R. (2000) Starvation alters the
apparent half-saturation constant for methane in the type
II methanotroph Methylocystis strain LR1. Appl Environ
Microbiol 66: 4136–4138.
Dunfield, P.F., Liesack, W., Henckel, T., Knowles, R., and
Conrad, R. (1999) High-affinity methane oxidation by a soil
enrichment culture containing a type II methanotroph. Appl
Environ Microbiol 65: 1009–1014.
Dunfield, P.F., Yuryev, A., Senin, P., Smirnova, A.V., Stott,
M.B., Hou, S.B., et al. (2007) Methane oxidation by an
extremely acidophilic bacterium of the phylum Verrucomi-
crobia. Nature 450: 879–882.
Erkel, C., Kube, M., Reinhardt, R., and Liesack, W. (2006)
Genome of Rice Cluster I archaea – the key methane
producers in the rice rhizosphere. Science 313: 370–372.
Ettwig, K.F., Shima, S., VandePas-Schoonen, K.T., Kahnt, J.,
Medema, M.H., OpdenCamp, H.J.M., et al. (2008) Deni-
trifying bacteria anaerobically oxidize methane in the
absence of Archaea. Environ Microbiol 10: 3164–3173.
Fallon, R.D., Harrits, S., Hanson, R.S., and Brock, T.D.
(1980) The role of methane in internal carbon cycling
in Lake Mendota during summer stratification. Limnol
Oceanogr 25: 357–360.
Frankenberg, C., Meirink, J.F., VanWeele, M., Platt, U., and
Wagner, T. (2005) Assessing methane emissions from
global space-borne observations. Science 308: 1010–
1014.
Frenzel, P. (2000) Plant-associated methane oxidation in rice
fields and wetlands [Review]. Adv Microb Ecol 16: 85–114.
Girguis, P.R., Cozen, A.E., and DeLong, E.F. (2005) Growth
and population dynamics of anaerobic methane-oxidizing
archaea and sulfate-reducing bacteria in a continuous-flow
bioreactor. Appl Environ Microbiol 71: 3725–3733.
Groot, T.T., VanBodegom, P.M., Harren, F.J.M., and Meijer,
H.A.J. (2003) Quantification of methane oxidation in the
rice rhizosphere using 13C-labelled methane. Biogeochem
64: 355–372.
Grosskopf, R., Stubner, S., and Liesack, W. (1998) Novel
euryarchaeotal lineages detected on rice roots and in the
anoxic bulk soil of flooded rice microcosms. Appl Environ
Microbiol 64: 4983–4989.
Hackstein, J.H.P., Langer, P., and Rosenberg, J. (1996)
Genetic and evolutionary constraints for the symbiosis
between animals and methanogenic bacteria. Environ
Monit Assess 42: 39–56.
Hallam, S.J., Putnam, N., Preston, C.M., Detter, J.C.,
Rokhsar, D., Richardson, P.M., and DeLong, E.F. (2004)
Reverse methanogenesis: testing the hypothesis with
environmental genomics. Science 305: 1457–1462.
Henckel, T., Jäckel, U., Schnell, S., and Conrad, R. (2000)
Molecular analyses of novel methanotrophic communi-
ties in forest soil that oxidize atmospheric methane. Appl
Environ Microbiol 66: 1801–1808.
Hoehler, T.M., Alperin, M.J., Albert, D.B., and Martens, C.S.
(1994) Field and laboratory studies of methane oxidation in
an anoxic marine sediment: evidence for a methanogen–
sulfate reducer consortium. Global Biogeochem Cycles
8: 451–463.
Holmes, A.J., Roslev, P., McDonald, I.R., Iversen, N.,
Henriksen, K., and Murrell, J.C. (1999) Characterization
of methanotrophic bacterial populations in soils showing

atmospheric methane uptake. Appl Environ Microbiol 65:
3312–3318.
Holmes, M.E., Sansone, F.J., Rust, T.M., and Popp, B.N.
(2000) Methane production, consumption, and air–sea
exchange in the open ocean: an evaluation based on
carbon isotopic ratios. Global Biogeochem Cycles 14:
1–10.
Islam, T., Jensen, S., Reigstad, L.J., Larsen, O., and Birke-
land, N.K. (2008). Methane oxidation at 55°C and pH 2 by
a thermoacidophilic bacterium belonging to the Verrucomi-
crobia phylum. Proc Natl Acad Sci USA 105: 300–304.
Janssen, P.H., and Kirs, M. (2008) Structure of the archaeal
community of the rumen [Review]. Appl Environ Microbiol
74: 3619–3625.
Jones, R.I., Carter, C.E., Kelly, A., Ward, S., Kelly, D.J., and
Grey, J. (2008) Widespread contribution of methane-cycle
bacteria to the diets of lake profundal chironomid larvae.
Ecology 89: 857–864.
Karl, D.M., and Tilbrook, B.D. (1994) Production and trans-
port of methane in oceanic particulate organic matter.
Nature 368: 732–734.
Keppler, F., Hamilton, J.T.G., Brass, M., and Röckmann, T.
(2006) Methane emissions from terrestrial plants under
aerobic conditions. Nature 439: 187–191.
Knief, C., Lipski, A., and Dunfield, P.F. (2003) Diversity and
activity of methanotrophic bacteria in different upland soils.
Appl Environ Microbiol 69: 6703–6714.
Knief, C., Kolb, S., Bodelier, P.L.E., Lipski, A., and Dunfield,
P.F. (2006) The active methanotrophic community in hydro-
morphic soils changes in response to changing methane
concentration. Environ Microbiol 8: 321–333.
Knittel, K., Losekann, T., Boetius, A., Kort, R., and Amann, R.
(2005) Diversity and distribution of methanotrophic
archaea at cold seeps. Appl Environ Microbiol 71: 467–
479.
Krüger, M., Meyerdierks, A., Glöckner, F.O., Amann, R.,
Widdel, F., Kube, M., et al. (2003) A conspicuous nickel
protein in microbial mats that oxidize methane anaerobi-
cally. Nature 426: 878–881.
Lelieveld, J., Crutzen, P.J., and Dentener, F.J. (1998)
Changing concentrations, lifetime and climate forcing of
atmospheric methane. Tellus 50B 128–150.
Liu, Y., and Whitman, W.B. (2008) Metabolic, phylogenetic,
and ecological diversity of the methanogenic archaea. Ann
N Y Acad Sci 1125: 171–189.
Lu, Y.H., and Conrad, R. (2005) In situ stable isotope probing
of methanogenic archaea in the rice rhizosphere. Science
309: 1088–1090.
Lösekann, T., Knittel, K., Nadalig, T., Fuchs, B., Niemann, H.,
Boetius, A., and Amann, R. (2007) Diversity and abun-
dance of aerobic and anaerobic methane oxidizers at the
Haakon Mosby mud volcano, Barents Sea. Appl Environ
Microbiol 73: 3348–3362.
McDonald, I.R., Bodrossy, L., Chen, Y., and Murrell, J.C.
(2008) Molecular ecology techniques for the study of
aerobic methanotrophs [Review]. Appl Environ Microbiol
74: 1305–1315.
McLeod, A.R., Fry, S.C., Loake, G.J., Messenger, D.J.,
Reay, D.S., Smith, K.A., and Yun, B.W. (2008) Ultraviolet
radiation drives methane emissions from terrestrial plant
pectins. New Phytol 180: 124–132.
© 2009 Society for Applied Microbiology and Blackwell Publishing Ltd, Environmental Microbiology Reports, 1, 285–292
Global methane cycle 291
Marty, D., Nival, P., and Yoon, W.D. (1997) Methanoarchaea
associated with sinking particles and zooplankton collected
in the northeastern tropical Atlantic. Oceanol Acta 20:
863–869.
Murase, J., and Frenzel, P. (2007) A methane-driven micro-
bial food web in a wetland rice soil. Environ Microbiol
9: 3025–3034.
Nauhaus, K., Albrecht, M., Elvert, M., Boetius, A., and
Widdel, F. (2007) In vitro cell growth of marine archaeal–
bacterial consortia during anaerobic oxidation of methane
with sulfate. Environ Microbiol 9: 187–196.
Nouchi, I., Mariko, S., and Aoki, K. (1990) Mechanisms of
methane transport from the rhizosphere to the atmosphere
through rice plants. Plant Physiol 94: 59–66.
OpdenCamp, H.J.M., Islam, T., Stott, M.B., Harhangi, H.R.,
Hynes, A., Schouten, S., et al. (2009) Environmental,
genomic and taxonomic perspectives on methanotrophic
Verrucomicrobia. Environ Microbiol Rep (in press).
doi:10.1111/j.1758-2229.2009.00022.x.
Oremland, R.S. (1979) Methanogenic activity in plankton
samples and fish intestines: a mechanism for in situ metha-
nogenesis in oceanic surface waters. Limnol Oceanogr
24: 1136–1141.
Orphan, V.J., House, C.H., Hinrichs, K.U., McKeegan, K.D.,
and DeLong, E.F. (2001) Methane-consuming archaea
revealed by directly coupled isotopic and phylogenetic
analysis. Science 293: 484–487.
Orphan, V.J., House, C.H., Hinrichs, K.U., McKeegan, K.D.,
and DeLong, E.F. (2002) Multiple archaeal groups mediate
methane oxidation in anoxic cold seep sediments. Proc
Natl Acad Sci USA 99: 7663–7668.
Ploug, H., Kuehl, M., Buchholz-Cleven, B., and Joergensen,
B.B. (1997) Anoxic aggregates – an ephemeral phenom-
enon in the pelagic environment? Aquat Microb Ecol 13:
285–294.
Pol, A., Heijmans, K., Harhangi, H.R., Tedesco, D., Jetten,
M.S.M., and OpdenCamp, H.J.M. (2007) Methanotrophy
below pH 1 by a new Verrucomicrobia species. Nature 450:
874-878.
Purdy, K.J. (2007) The distribution and diversity of euryar-
chaeota in termite guts. Adv Appl Microbiol 62: 63–80.
Radajewski, S., Ineson, P., Parekh, N.R., and Murrell, J.C.
(2000) Stable-isotope probing as a tool in microbial
ecology. Nature 403: 646–649.
Raghoebarsing, A.A., Smolders, A.J.P., Schmid, M.C.,
Rijpstra, W.I.C., Wolters-Arts, M., Derksen, J., et al. (2005)
Methanotrophic symbionts provide carbon for photosyn-
thesis in peat bogs. Nature 436: 1153–1156.
Raghoebarsing, A.A., Pol, A., van de Pas-Schoonen, K.T.,
Smolders, A.J.P., Ettwig, K.F., Rijpstra, W.I.C., et al. (2006)
A microbial consortium couples anaerobic methane oxida-
tion to denitrification. Nature 440: 918–921.
Reeburgh, W.S. (2003) Global methane biogeochemistry.
In Treatise on Geochemistry, Vol. 4: The Atmosphere.
Keeling, R.F., Holland, H.D., and Turekian, K.K. (eds).
Oxford, UK: Elsevier-Pergamon, pp. 65–89.
Reeburgh, W.S. (2007) Oceanic methane biogeochemistry
[Review]. Chem Rev 107: 486–513.
Ricke, P., Erkel, C., Kube, M., Reinhardt, R., and Liesack, W.
(2004) Comparative analysis of the conventional and novel
pmo (particulate methane monooxygenase) operons from
292 R. Conrad
Methylocystis strain SC2. Appl Environ Microbiol 70:
3055–3063.
Ricke, P., Kube, M., Nakagawa, S., Erkel, C., Reinhardt, R.,
and Liesack, W. (2005) First genome data from uncultured
upland soil cluster alpha methanotrophs provide further
evidence for a close phylogenetic relationship to Methylo-
capsa acidiphila B2 and for high-affinity methanotrophy
involving particulate methane monooxygenase. Appl
Environ Microbiol 71: 7472–7482.
Rudd, J.W.M., and Taylor, C.D. (1980) Methane cycling in
aquatic environments. Adv Aquat Microbiol 2: 77–150.
Rusch, H., and Rennenberg, H. (1998) Black alder [Alnus
glutinosa (L.) Gaertn.] trees mediate methane and nitrous
oxide emission from the soil to the atmosphere. Plant Soil
201: 1–7.
Sakai, S., Imachi, H., Sekiguchi, Y., Ohashi, A., Harada, H.,
and Kamagata, Y. (2007) Isolation of key methanogens for
global methane emission from rice paddy fields: a novel
isolate affiliated with the clone cluster rice cluster I. Appl
Environ Microbiol 73: 4326–4331.
Sakai, S., Imachi, H., Hanada, S., Ohashi, A., Harada, H.,
and Kamagata, Y. (2008) Methanocella paludicola gen.
nov., sp. nov., a methane-producing archaeon, the first
isolate of the lineage ‘Rice Cluster I’, and proposal of the
new archaeal order Methanocellales ord. nov. Int J Syst
Evol Microbiol 58: 929–936.
Schink, B., Ward, J.C., and Zeikus, J.G. (1981) Microbiology
of wetwood: importance of pectin degradation and
Clostridium species in living trees. Appl Environ Microbiol
42: 526–532.
Schmidt, I., and Bock, E. (1997) Anaerobic ammonia oxida-
tion with nitrogen dioxide by Nitrosomonas eutropha. Arch
Microbiol 167: 106–111.
Schmidt, I., VanSpanning, R.J.M., and Jetten, M.S.M. (2004)
Denitrification and ammonia oxidation by Nitrosomonas
europaea wild-type, and NirK- and NorB-deficient mutants.
Microbiology – UK 150: 4107–4114.
Schmidt, U., and Conrad, R. (1993) Hydrogen, carbon mon-
oxide, and methane dynamics in Lake Constance. Limnol
Oceanogr 38: 1214–1226.
Schütz, H., Seiler, W., and Conrad, R. (1989) Processes
involved in formation and emission of methane in rice
paddies. Biogeochem 7: 33–53.
Sieburth, J.M., Johnson, P.W., Macario, A.J.L., and Conway-
DeMacario, E. (1993) C1 bacteria in the water column of
Chesapeake Bay, USA. 2. The dominant O2-tolerant and
H2S-tolerant methylotrophic methanogens, coenriched with
their oxidative and sulphate reducing bacterial consorts,
© 2009 Society for Applied Microbiology and Blackwell Publishing Ltd, Environmental Microbiology Reports, 1, 285–292
are all new immunotypes and probably include new taxa.
Mar Ecol Prog Ser 95: 81–89.
Stoecker, K., Bendinger, B., Schöning, B., Nielsen, P.H.,
Nielsen, J.L., Baranyi, C., et al. (2006) Cohn’s Crenothrix is
a filamentous methane oxidizer with an unusual methane
monooxygenase. Proc Natl Acad Sci USA 103: 2363–
2367.
Terazawa, K., Ishizuka, S., Sakatac, T., Yamada, K., and
Takahashi, M. (2007) Methane emissions from stems of
Fraxinus mandshurica var. japonica trees in a floodplain
forest. Soil Biol Biochem 39: 2689–2692.
Thauer, R.K., and Shima, S. (2008) Methane as fuel for
anaerobic microorganisms [Review]. Ann N Y Acad Sci
1125: 158–170.
Theisen, A.R., Ali, M.H., Radajewski, S., Dumont, M.G.,
Dunfield, P.F., McDonald, I.R., et al. (2005) Regulation
of methane oxidation in the facultative methanotroph
Methylocella silvestris BL2. Mol Microbiol 58: 682–692.
Trotsenko, Y.A., and Murrell, J.C. (2008) Methabolic aspects
of aerobic obligate methanotrophy. Adv Appl Microbiol 63:
183–229.
Valentine, D.L., and Reeburgh, W.S. (2000) New perspec-
tives on anaerobic methane oxidation [Review]. Environ
Microbiol 2: 477–484.
Vigano, I., VanWeelden, H., Holzinger, R., Keppler, F.,
McLeod, A., and Röckmann, T. (2008) Effect of UV radia-
tion and temperature on the emission of methane from
plant biomass and structural components. Biogeosciences
5: 937–947.
Vigliotta, G., Nutricati, E., Carata, E., Tredici, S.M.,
DeStefano, M., Pontieri, P., et al. (2007) Clonothrix fusca
Roze 1896, a filamentous, sheathed, methanotrophic
gamma-proteobacterium. Appl Environ Microbiol 73:
3556–3565.
Wang, J.S., Logan, J.A., McElroy, M.B., Duncan, B.N.,
Megretskaia, I.A., and Yantosca, R.M. (2004) A 3-D model
analysis of the slowdown and interannual variability in
the methane growth rate from 1988 to 1997 [Review].
Global Biogeochem Cycles 18: B3011. doi:10.1029/
2003GB002180.
Watanabe, A., Takeda, T., and Kimura, M. (1999) Evaluation
of origins of CH4 carbon emitted from rice paddies.
J Geophys Res 104: 23623–23629.
West, A.E., and Schmidt, S.K. (1999) Acetate stimulates
atmospheric CH4 oxidation by an alpine tundra soil. Soil
Biol Biochem 31: 1649–1655.
Zeikus, J.G., and Ward, J.C. (1974) Methane formation in
living trees: a microbial origin. Science 184: 1181–1183.