Biogeochemical Cycles
14
Jean-Claude Bertrand, Patricia Bonin, Pierre Caumette, Jean-Pierre Gattuso,
Ge ´rald Gre ´gori, Re ´my Guyoneaud, Xavier Le Roux, Robert Matheron,
and Franck Poly
Abstract
All living organisms contribute to the biogeochemical cycles, but microorganisms, due
to their high abundance, their tremendous metabolic capacities and adaptation potential,
play a key role in the functioning and the evolution of biogeochemical cycles. Consequently, they are keyplayers in adaptation, resistance and resilience of ecosystems. The
role of microorganisms in the main biogeochemical cycles (carbon, nitrogen, sulfur,
phosphorus, silicon, metals), in soils, freshwater and marine ecosystems is presented.
Microbial processes involved in the turnover of biogeochemical cycles are discussed
from gene to ecosystem (natural and anthropogenic ecosystems), at global, regional and
local scales, as well as in targeted microenvironments (such as particles or
microniches). The biodiversity of microorganisms is highlighted and their metabolic
pathways on which are based exchanges and biotransformations of organic and mineral
components within ecosystems are described in details. The impacts of human activities
on the microbial actors and processes of biogeochemical cycles, and the cascading
ecological effects (greenhouse gas emissions, acid rains, dystrophic crises, etc.), are also
discussed.
Keywords
Anoxic zones Biogeochemical cycles Carbon cycle Ecosystem functioning Iron cycle
Lake ecosystems Manganese cycle Marine ecosystems Mercury cycle Microbial
functions Nitrogen cycle Oxic zones Phosphate cycle Silicon cycle Soils Sulfur
cycle
J.-C. Bertrand* (*) P. Bonin G. Gre ´gori
Institut Me ´diterrane ´en d’Oce ´anologie (MIO), UM 110, CNRS 7294
IRD 235, Universite ´ de Toulon, Aix-Marseille Universite ´,
Campus de Luminy, 13288 Marseille Cedex 9, France
e-mail: jean-claude.bertrand@univ-amu.fr
P. Caumette R. Guyoneaud
Institut des Sciences Analytiques et de Physico-chimie pour
l’Environnement et les Mate ´riaux (IPREM), UMR CNRS 5254,
Universite ´ de Pau et des Pays de l’Adour, B.P. 1155,
64013 Pau Cedex, France
J.-P. Gattuso
Observatoire Oce ´anologique, Laboratoire d’ Oce ´anographie,
CNRS-UPMC, BP 28, 06234 Villefranche-sur-Mer Cedex, France
* Chapter Coordinator
X. Le Roux F. Poly
Microbial Ecology Center, UMR CNRS 5557 / USC INRA 1364,
Universite ´ Lyon 1, 69622 Villeurbanne, France
R. Matheron
Institut Me ´diterrane ´en de Biodiversite ´ et d’Ecologie marine et
continentale (IMBE), UMR-CNRS-IRD 7263, Aix-Marseille
Universite ´, 13397 Marseille Cedex 20, France
J.-C. Bertrand et al. (eds.), Environmental Microbiology: Fundamentals and Applications: Microbial Ecology,
DOI 10.1007/978-94-017-9118-2_14, # Springer Science+Business Media Dordrecht 2015
511
14
Jean-Claude Bertrand, Patricia Bonin, Pierre Caumette, Jean-Pierre Gattuso,
Ge ´rald Gre ´gori, Re ´my Guyoneaud, Xavier Le Roux, Robert Matheron,
and Franck Poly
Abstract
All living organisms contribute to the biogeochemical cycles, but microorganisms, due
to their high abundance, their tremendous metabolic capacities and adaptation potential,
play a key role in the functioning and the evolution of biogeochemical cycles. Consequently, they are keyplayers in adaptation, resistance and resilience of ecosystems. The
role of microorganisms in the main biogeochemical cycles (carbon, nitrogen, sulfur,
phosphorus, silicon, metals), in soils, freshwater and marine ecosystems is presented.
Microbial processes involved in the turnover of biogeochemical cycles are discussed
from gene to ecosystem (natural and anthropogenic ecosystems), at global, regional and
local scales, as well as in targeted microenvironments (such as particles or
microniches). The biodiversity of microorganisms is highlighted and their metabolic
pathways on which are based exchanges and biotransformations of organic and mineral
components within ecosystems are described in details. The impacts of human activities
on the microbial actors and processes of biogeochemical cycles, and the cascading
ecological effects (greenhouse gas emissions, acid rains, dystrophic crises, etc.), are also
discussed.
Keywords
Anoxic zones Biogeochemical cycles Carbon cycle Ecosystem functioning Iron cycle
Lake ecosystems Manganese cycle Marine ecosystems Mercury cycle Microbial
functions Nitrogen cycle Oxic zones Phosphate cycle Silicon cycle Soils Sulfur
cycle
J.-C. Bertrand* (*) P. Bonin G. Gre ´gori
Institut Me ´diterrane ´en d’Oce ´anologie (MIO), UM 110, CNRS 7294
IRD 235, Universite ´ de Toulon, Aix-Marseille Universite ´,
Campus de Luminy, 13288 Marseille Cedex 9, France
e-mail: jean-claude.bertrand@univ-amu.fr
P. Caumette R. Guyoneaud
Institut des Sciences Analytiques et de Physico-chimie pour
l’Environnement et les Mate ´riaux (IPREM), UMR CNRS 5254,
Universite ´ de Pau et des Pays de l’Adour, B.P. 1155,
64013 Pau Cedex, France
J.-P. Gattuso
Observatoire Oce ´anologique, Laboratoire d’ Oce ´anographie,
CNRS-UPMC, BP 28, 06234 Villefranche-sur-Mer Cedex, France
* Chapter Coordinator
X. Le Roux F. Poly
Microbial Ecology Center, UMR CNRS 5557 / USC INRA 1364,
Universite ´ Lyon 1, 69622 Villeurbanne, France
R. Matheron
Institut Me ´diterrane ´en de Biodiversite ´ et d’Ecologie marine et
continentale (IMBE), UMR-CNRS-IRD 7263, Aix-Marseille
Universite ´, 13397 Marseille Cedex 20, France
J.-C. Bertrand et al. (eds.), Environmental Microbiology: Fundamentals and Applications: Microbial Ecology,
DOI 10.1007/978-94-017-9118-2_14, # Springer Science+Business Media Dordrecht 2015
511