274
for carbon fixation and their phospholipid fatty acid
(PLFA) composition is generally dominated by saturated
and monosaturated C 16 fatty acids.- Methylocystaceae (known as Type II methanotrophs): the
ICM is parallel to the cell membrane. They use the serine
pathway for carbon fixation and PLFAs are dominated by
C 18 isomers, except for Methylocystis heyeri which also
contains large amounts of C 16 fatty acids (Dedysh et al.
2007 ). - Beijerinckiaceae: this family is metabolically diversified,
with obligate methanotrophs, facultative methanotrophs
and non-methanothrophs (Dunfield et al. 2010 ). - Methylacidiphilaceae: only three acidophilic and ther-
motolerant species are presently affiliated with this family
(Dunfield et al. 2007 ; Islam et al. 2008 ; Op den Camp
et al. 2009 ; Pol et al. 2007 ).
16.4.1.2 Metabolic Pathways and Enzymes
Involved
While several facultative methanotrophs (belonging to the
genera Methylocella (Dedysh et al. 2005 ), Crenothrix
(Stoecker et al. 2006 ), Methylocystis (Belova et al. 2011 ; Im
et al. 2011 ), and Methylocapsa (Dunfield et al. 2010 ) were
recently isolated, most of the aerobic methanotrophs
areobligatory C1-users growing only on CH 4 or methanol.
The aerobic CH 4 oxidation pathway contains four sequential
steps with methanol, formaldehyde and formate as metabolic
intermediates. Formaldehyde plays a central role in the
metabolism of aerobic methanotrophs, since it also consti-
tutes the main carbon source for the anabolic pathway. The
first step of the aerobic oxidation of CH 4 (i.e., conversion to
methanol) is catalyzed by the methane monooxygenase
(MMO) enzymatic complex (See Box 16.1).
16.4.1.3 Examples of Environmental Factors
Affecting Aerobic Methanotrophy
in Freshwater Lakes
- Availability of CH4/O2: The activity of aerobic CH 4 -
oxidizing bacteria depends on the availability and con-
centrations of both CH 4 and O 2. The highest CH 4
consumption rates are located at oxic/anoxic interfaces
where opposite fluxes of CH 4 and O 2 occur. In freshwater
lakes, such interfaces are found in the upper layers of
sediment overlaid by oxic water or in the oxycline of
stratified water columns. Consequently, a large fraction of
CH 4 diffusing from the lacustrine anoxic sediments is oxi-
dized at the sediment interface (66–95 %, Liikanen et al.
2002 ) and at the oxic/anoxic interface of the water col-
umn (45–100 %, Bastviken et al. 2002 ). - Nitrogen: The effect of nitrogen input on methanotrophs
and CH 4 oxidation in freshwater lakes has been investi-
gated in the context of anthropogenic-accelerated eutro-
phication (Liikanen and Martikainen 2003 ; Nold et al.
1999 ). Addition of ammonium generally inhibits CH 4
oxidation (Murase and Sugimoto 2005 ) and incorporation
of CH 4 -derived carbon into lipids of methanotrophs (Nold
et al. 1999 ). This inhibition is attributed to the competi-
tion between ammonium and CH 4 for binding sites on
MMO, because of their similar chemical structure (Bedard
and Knowles 1989 ).- Top-down regulation: Depending on local and seasonal
conditions, methanotrophic bacteria may represent a sub-
stantial fraction of planktonic and/or benthic biomasses in
freshwater lakes (Bastviken et al. 2003 ; Costello et al.
2002 ). A number of observations led to the hypothesis
that a significant fraction of the diet of aquatic consumers
may consist of CH 4 -derived carbon. Accordingly, several
studies based on isotopic labeling (e.g.,^13 C-labeled-CH 4 )
found evidence of CH 4 -derived carbon transfer through
zooplanktons and Chironomidae (Deines et al. 2007 ;
Kankaala et al. 2006 ) or detected lipid biomarkers spe-
cific of methylotrophs (i.e., specific PLFA) in
Chironomidae tissues (Kiyashko et al. 2004 ).
16.4.1.4 Composition of Aerobic
Methanotrophic Communities in Lake
Pavin
The family Methylococcaceae was found to dominate meth-
anotrophic communities inhabiting temperate and boreal
lakes (average annual temperature < 12 °C). Borrel et al.
( 2011 ) demonstrated that the genus Methylobacter is
retrieved in all mid-latitude lakes and that methanotrophs
affiliated to Methylocystaceae dominated the water column
of a tropical dam lake characterized by temperatures com-
prised between 25 and 30 °C.
The methanotrophic communities present in the water
column of Lake Pavin was investigated using the particulate
methane monooxygenase gene (pmoA) (Biderre-Petit et al.
2011 ). The analysis of pmoA transcripts revealed that the
majority of aerobic CH 4 oxidation is carried out by a small
number of phylotypes affiliated to Methylobacter, and par-
ticularly to M. psychrophilus (Fig. 16.5). The temperature
of the water column, ranging between 4 and 5 °C, may
explain the predominance of phylotypes close to psychro-
philic species in the water column of Lake Pavin. Few
sequences of Methylosarcina sp. and Methylocystis sp. were
retrieved but, surprisingly, Methylocystis sp. was recovered
at 20 m depth, a O 2 -rich zone but almost entirely CH 4 -
depleted (Fig. 16.5).
The in-situ analysis of aerobic methanotrophs was com-
pleted by a cultural approach in order to isolate representa-
tives of this metabolic group. Samples for enrichments wereA.-C. Lehours et al.