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Keywords
Methane cycle • Methanogens • Methanotrophs • Ferric iron reduction • Fermentation •
Anaerobic food chain • Biogeochemistry • Anoxic freshwater layersList of Abbreviations
ANME Anaerobic Methanotrophs
AOM Anaerobic Oxidation of Methane
CARD Catalyzed Reporter Deposition
CLSM Confocal Laser Scanning Microscopy
DAPI Diamidino-2-phenylindole
FISH Fluorescent in situ hybridization
FRB Ferric Iron Reducing Bacteria
HRP Horseradish Peroxidase
MBGD Marine Benthic Group D
MMO Methane Mono-Oxygenase
MPR Methane Production Rate
NRB Nitrate Reducing Bacteria
pMMO Particulate Methane Mono-Oxygenase
p.p.m. Parts Per Millions
PLFA Phospholipids Fatty Acids
rRNA Ribosomal RNA
sMMO Soluble Methane Mono-Oxygenase
SRB Sulfate Reducing Bacteria
TEM Transmission Electron Microscopy
16.1 Introduction
“A bacterium, an amoeba...what destiny can they dream
of other than forming two bacteria, two amoebae...?”
This rhetorical question of François Jacob illustrates the
“leitmotiv” of microorganisms: optimizing their growth
and, achieving this objective implies a remarkable effi-
ciency and adaptability to environmental conditions and
fluctuations. Their adaptive strategies determine the effec-
tiveness and the nature of their regulatory processes. The
optimization of the prokaryotic cellular machinery is vis-
ible on the scale of ecosystems, in which microorganisms
are involved in the biogeochemical cycles of many ele-
ments. The influence of the prokaryotic component on the
biotope is probably exacerbated in anoxic ecosystems in
which microorganisms are almost hegemonic. In these
environments, the use of a variety of electron acceptors
confers to the anaerobic prokaryotes a key role in the dis-
tribution of a large number of minerals (e.g., iron, sulfur,
manganese) and implies the establishment by these com-
munities of metabolic processes and functional specializa-
tions as well as numerous cooperative and competitive
interactions.
The microbial ecological studies in marine or freshwater
environments have focused primarily on the aerobic layers,
in which the roles of heterotrophic microorganisms in the
aquatic food web were particularly analyzed. In these eco-
systems, the processes occurring in the anoxic zones, often
reduced to sediment and, in some cases, to deep pelagic lay-
ers, may appear "decoupled" from processes of the microbial
loop. However, anaerobic prokaryotes are likely to play
important roles in aquatic systems allowing the regeneration
of bioactive elements, deriving some of the carbon and
energy, and providing access through the sedimentation pro-
cess to a complete mineralization of the organic material.
These anaerobic microbial processes are therefore critical to
maintain the homeostasis of aquatic systems and are impor-
tant drivers of biogeochemical cycles.
The present article focuses on the microorganisms and
processes involved in the biogeochemical cycle of methane
(CH 4 ) in freshwater systems with a focus on Lake Pavin.
CH 4 is a key metabolite in freshwater lakes where methano-
genesis (i.e., biogenic CH 4 production) accounts for 10 to
50 % of organic matter mineralization (Bastviken et al.
2008 ). The diversity and the physiology of the microorgan-
isms involved in the biogeochemical cycle of CH 4 and the
environmental factors that regulate their activities are
detailed in the following sections. As all anaerobic microbial
metabolic groups build competitive and cooperative rela-
tionships, some bacterial processes tightly linked to CH 4
cycle are also addressed. These elements are presented in a
conceptual context, that of freshwater lakes and in particular
that of Lake Pavin for which past and current researches
aspire to (1) identify microbial agents involved in CH 4 bio-
geochemical cycle, (2) identify novel microbial processes
responsible of CH 4 production and/or consumption, (3) link
in situ observations with the ecophysiology of the targeted
microorganisms, (4) develop complementary cognitive and
methodological approaches to access to these informations.16.2 Brief Overview of Methane Cycle
16.2.1 Methane16.2.1.1 Ecological Importance of CH 4
in the Context of Climate Change
CH 4 has played an important role since the beginning of life
on Earth, helping the planet to remain warm and habitable. It
still plays a key role in ecosystems, mainly in the biogeo-A.-C. Lehours et al.