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16.3.2.6 Diversity, Distribution and Abundance
of Methanogens in Lake Pavin
In freshwater lakes, analyses of clone libraries and/or quan-
tification of methanogenic communities by fluorescent in
situ hybridization (FISH) revealed that the
Methanomicrobiales and the Methanosarcinales dominate
the methanogenic communities (e.g., Auguet et al. 2010 ;
Briee et al. 2007 ; Chan et al. 2005 ) and that the
Methanobacteriales occur scarcely (e.g., Conrad et al. 2010 ;
Ye et al. 2009 ). These patterns are consistent with observa-
tions done from samples collected in the anoxic water col-
umn and sediments of Lake Pavin.
- Anoxic water column
Both clone libraries and fluorescent in situ hybridization
(FISH) approaches based on 16S rDNA sequences revealed
similar distribution patterns of archaeal communities in the
anoxic water column of Lake Pavin (− 60 to −92 m) (Lehours
et al. 2005 , 2007 ). Archaeal communities exhibit a homoge-
neous distribution along the water column and are dominated
by sequences related to the Methanosarcinales and to the
Methanomicrobiales with a ratio of 2:3 and 1:3, respectively
(Fig. 16.1a). The abundance of Methanosarcinales (includ-
ing Methanosaeta and Methanosarcina) increased with
depth in the monimolimnion and the Methanomicrobiales
peaked below the chemocline (Fig. 16.1a). Methanobacteriales
were only quantifiable at the interface of the oxic and anoxic
zones of the water column (Fig. 16.1a).
CH 4 concentrations in the anoxic water layer of Lake
Pavin are significantly correlated (r = 0.8, P < 0.01) with the
abundance of Methanosarcinales, which are mainly
represented (71 %) by sequences related to Methanosaeta
concilii, a strictly acetotrophic methanogen. Acetotrophic
methanogenesis is therefore probably a major process in the
anoxic zone of the water column of Lake Pavin. The carbon
and hydrogen stable isotopic compositions of CH 4
[δ^13 C-CH 4 = −60 ‰, δD CH 4 = −276 ‰, Agrinier P. Personal
communication] support this hypothesis because such isoto-
pic signatures are similar to that of the methyl group of
acetate.
- Sediment
The composition of archaeal communities within the
anoxic sediments of Lake Pavin was investigated along a
40-cm sediment core collected at the vertical of the 92 m
isobath (Borrel et al. 2012a). The composition of the metha-
nogenic communities within the sediments was similar to
that detected in the anoxic water column (Fig. 16.1a).
However, differences in distribution of the methanogenic
communities are observed within both compartments. Unlike
the water column the distribution of methanogens is not
homogeneous down core. Methanogenic lineages are the
dominant Archaea in the uppermost sediment layer (66 % of
acetoclastic Methanosaetaceae and 25 % of hydrogenotro-
phic Methanomicrobiales) while below 5 cm sediment depth,
clone libraries were mainly composed of uncultured archaeal
lineages (Marine Benthic group B (MBG-D) and
Miscelleanous Group G (MCG), Borrel et al. 2012a).
The main archaeal function in the superficial layer of the
sediment of Lake Pavin monimolimnion is CH 4 production.
Methanogens occurrence in the surface sediment layer is
consistent with Lake Pavin meromicticity, as the reduction of
the main inorganic electron acceptors (e.g., sulfate, ferric
iron, nitrate) occurs in the anoxic water column (Lopes et al.
2011 ). These observations, based on the relative proportions
of sequences in clone libraries, were confirmed by quantifi-
cation of these archaeal groups by quantitative PCR per-
formed on genomic DNA and complementary DNA (Borrel
et al. 2012a).16.3.3 Factors Influencing Methanogens
and Methanogenesis (Fig. 16.3)Many factors impact the CH 4 production rates (MPRs) by
affecting methanogenic populations either directly or indi-
rectly by structuring the surrounding microbial community
which contains suppliers of methanogenic substrates and
competitors for these substrates. Environmental factors can
also act on the dominant methanogenic pathways in freshwa-
ter lakes (Schulz and Conrad 1996 ; Nüsslein et al. 2003 ;
Glissmann et al. 2004 ; Chan et al. 2005 ; Nozhevnikova et al.
2007 ).16.3.3.1 Brief Overview of Physiological
Factors- Bottom-Up Regulations
The intrinsic characteristics of each microorganism deter-
mine its survival, its growth and its abundance but also the
interactions that it establishes with other life forms and with
the abiotic environment. This section on the factors related to
the physiology of microorganisms is not exhaustive; a simple
enumeration of potentially important factors is proposed
with some examples related to methanogenic populations.
These bottom-up regulations impact methanogens directly or
indirectly by structuring the surrounding microbial
community.- The growth rate is highly variable from a microbial spe-
cies to another and depends besides intrinsic character-
istics, on various parameters such as the energy source,
the pH, the temperature, the concentration of nitrogen
source, the transfer through membranes, etc. For exam-
ple, oxygen concentrations above 10 p.p.m. completely
inhibit most methanogens because several cofactors and
enzymes involved in their metabolism (e.g., CO dehy-
drogenase acetyl-CoA synthase, F420) are oxygen-sen-
sitive (Schonheit et al. 1981 ; Ragsdale and Kumar
1996 ). Temperature may affect composition patterns of
A.-C. Lehours et al.