265methanogenic communities as well as MPRs (Borrel
et al. 2011 ). Accordingly, cold adapted methanogens
dominate in the hypolimnion and the profound sediment
of mid-latitude lakes and are different from methano-
gens identified in tropical and equatorial lakes or in shal-
low sediments of temperate lakes (Conrad et al. 2010 ).
Moreover, the growth rate of methanogens may be
directly limited by in situ temperature (Yvon-Durocher
et al. 2014 ), which is generally below the growth opti-
mum of methanogens (Borrel et al. 2011 ) and/or indi-
rectly by limiting the production rate of methanogenic
substrates (Schulz and Conrad 1996 ).- The preferential substrate utilization by microbial spe-
cies allows them to select the most efficient growth sub-
strate while limiting the enzymatic synthesis (catabolic
repression). This phenomenon allows understanding the
diversity of ecosystems; it explains why several species
occupying apparently similar ecological niches can coex-
ist in an ecosystem.- Affinity for the substrate: when nutrient availability is
limited, microorganisms cannot grow at their maximum
growth rate and the affinity for the substrate becomes a
major determinant of growth and competition between
species. For example, the concentrations of H 2 and acetate
in the methanogenic zone of freshwater lakes, close to the
minimal threshold for substrate uptake by Methanosaeta
(Jetten et al. 1992 ) and hydrogenotrophic methanogens
(Zinder 1993 ) reflect the limitation of MPRs by substrate
availability. - Energy requirements: microorganisms need energy for
growth and to ensure their cellular integrity (maintenance
energy) but a decoupling of energy (i.e., a fermentation
without growth) may be observed. When the growth rate
is high, the proportion of the energy required for mainte-
nance is low, but when the growth rate decreases (e.g.,
nutritional deficiency), all the energy may be used for cell
maintenance. The maintenance energy varies greatly
between microbial species. When substrate is limiting,
species with low maintenance energy needs are favored
and can become predominant in the ecosystem. - Others factors: in complex ecosystems, the growth,
development and eventually the survival of microorgan-
isms depend on many other factors such as: energy yields
(the effectiveness of ATP use varies from species to spe-
cies), resistance to various environmental factors (e.g.,
pH, heavy metals, antibiotics, xenobiotics), adherence to
substratum and ability to form biofilms, mobility, response
to concentration gradients of physico-chemical parame-
ters, distance between cells, resistance to fast regenera-
tion systems or storage energy, mutations in the stationary
phase and quorum sensing.
16.3.3.2 Example of Bottom-Up Factors
Affecting the Composition
of Methanogenic Communities
in the Sediment of Lake Pavin- Substrate availability: in Lake Pavin sediment, the
abundance of Methanosaetaceae significantly
decreased with depth along the sediment core (Fig.
16.1a) whereas the content in organic matter and
organic carbon did not decrease significantly with
depth (Fig. 16.1d). This trend is attributed to the
decrease in content and lability of organic matter which
becomes more and more depleted and recalcitrant with
depth due to its longer exposure to degradation pro-
cesses (Borrel et al. 2012a). This hypothesis of a gradi-
ent of microbial activities along the sediment core is
sustained by the decrease of the 16S rRNA to 16S
rDNA ratio and by thermograms of sediment samples
(Fig. 16.1e, Box 16.2).
Fig. 16.3 Schematic representation of some factors (abiotic and biotic)
influencing methanogens and consequently methane production rates
(MPRs). To summarize, environmental conditions such as temperature
and oxygen levels affect the methanogenic communities according to
their physiology. But these factors also affect the syntrophic (e.g., fer-
mentative bacteria) and competitive communities of methanogens and
consequently the availability of substrates. The affinity for the available
substrates of different methanogenic communities determines the struc-
ture and the diversity of methanogenic assemblages. Thus methanogens
are subjected to bottom-up regulation, and depend on cooperative and
competitive interactions. More works remain to be done to get the
methane cycle right, notably a big missing in methanogens ecology is
our ignorance of top-down regulation (impact of viruses)
16 Methanogens and Methanotrophs in Lake Pavin