261directly assimilated by different microbial respiratory
processes (sulfate-reduction, methanogenesis, denitrifi-
cation, dissimilatory metal reduction).
(3) The more complex metabolites (e.g., alcohols and fatty
acids with more than two carbon atoms, aromatic and
branched fatty acids) are secondarily converted by oxi-
dative bacteria into substrates consumed through differ-
ent anaerobic metabolic pathways.
(4) The terminal step of the anaerobic degradation of organic
matter leads to the production of CO 2 , CH 4 and other
reduced compounds (H 2 S, Fe(II), etc.). This step depends
mainly on the availability of various electron acceptors
(see following sections).
In sulfate-poor freshwater environments where methano-
genesis is a dominant process, biomass is converted mainly
to CH 4 and CO 2 by a complex community of fermentative
bacteria in cooperation with methanogens and homoaceto-
gens which keep the hydrogen partial pressure in the range of
10 −4–10−5 atm. (Schink 1997 ; Schink and Stams 2001 ).
Under such conditions, the fermentation of sugars by fer-
mentative bacteria is shifted from the production of reduced
sideproducts such as butyrate or ethanol to nearly exclusive
formation of acetate, CO 2 and H 2 (Ianotti et al. 1973 ; Zeikus
1977 , 1983 ; Tewes and Thauer 1980 ). Alternatively, formate
could be formed instead of H 2 with a similar energy yield
(−202 kJ mol−1, Müller et al. 2008 ).
16.3.1.2 Energetic Considerations
In anoxic environments, the use of a variety of electron
acceptors by microorganisms affects the biogeochemical
cycles of numerous inorganic elements (e.g., hydrogen,
nitrogen, sulfur, iron, manganese). Equilibrium constants
and free energy diagram can be used to predict which reac-
tions are thermodynamically possible. These thermodynamic
considerations allow suggesting that the most energetically
favorable process is realized first and condition the subse-
quent redox sequences. For example, a reducer such as
organic carbon (e.g., CH 2 O) can be first degraded through
oxidation with O 2 , followed by the successive use of NO 3 −,
Mn4+, Fe3+, SO 4 2− and CO 2 as final electron acceptors.
Methanogenesis, by reducing CO 2 , is therefore the least
energetically favorable process among anaerobic metabo-
lisms. These sequences are, within certain limits, a realistic
description of what happens in stable ecosystems (e.g., sedi-
ment) and add a spatial dimension to thermodynamic consid-
erations. However, many other conditions such as kinetic
factors and syntrophic couplings are also required for the
occurrence of some reactions (see following sections).
16.3.2 Methanogens and MethanogenesisAs aforementioned, methanogens act in the terminal step of
the anaerobic food chain, converting methanogenic sub-
strates to CH 4 through methanogenesis. To date, none metha-
nogen has been identified that can grow without producing
CH 4. These Archaea are all obligate CH 4 -producers that are
uniquely specialized for this lifestyle (Hedderich and
Whitman 2006 ).16.3.2.1 Evolutionary Aspects
of Methanogenesis
Methanogens constitute the largest described group within
the domain Archaea and are among the most ancient of
extant forms of life. Growing evidences suggest that
methanogenic microbes evolved close to the time of the
origin of life providing a window on the early evolution of
Earth’s biosphere (Battistuzzi et al. 2004 ). Studies on the
origin of methanogenesis [estimated between −4.11 Ga
and −3.78 Ga, Battistuzzi et al. 2004 ] suggest that metha-
nogens were present on Earth during the Archean period
which is consistent with the CH 4 greenhouse theory
(Pavlov et al. 2000 ).16.3.2.2 Taxonomic Diversity of Methanogens^3
Methanogens are exclusive to the Euryarchaeota kingdom of
the Archaea domain. They are currently classified into 5
classes (Methanopyri, Methanococci, Methanobacteria,
Methanomicrobia, and Thermoplasmata) and 7 orders
(Methanobacteriales, Methanococcales, Methanomicrobiales,
Methanosarcinales, Methanopyrales, Methanocellales,
Methanomassiliicoccales (Paul et al. 2012 ; Iino et al. 2013 ).16.3.2.3 Metabolic Diversity of Methanogens^4
Methanogens derive their metabolic energy from the con-
version of a restricted number of substrates to CH 4. The
three main methanogenic substrates are H 2 , acetate and
methylated compounds (such as methanol, methylated
amines and methylated sulfides). Therefore, several distinct
pathways for CH 4 production exist and none of these meth-
anogenic metabolisms have been currently found in
Bacteria or eukaryotes. The different pathways for CH 4
production are:(^3) For detailed informations, see Nazaries et al. 2013.
(^4) For more informations, see Hedderich and Whitman 2006 ; Borrel et al.
2011 ; Nazaries et al. 2013.
16 Methanogens and Methanotrophs in Lake Pavin
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