even limited to some phyla (nitrifiers, methanogens,
methanotrophs, sulfate-reducers, iron-, and manganese bacteria). It must be underlined that prokaryotes are the greatest
source of biodiversity still unknown on Earth. Regularly new
microorganisms are discovered. This knowledge leads to
complete the array of microbial actors involved in some
functions, for example, the 2005 discovery of archaea able
to oxidize ammonium.
The metabolic plasticity of prokaryotes is probably far
from being completely understood, since new functions and
physiological characteristics are part of the most recent
discoveries in the functioning of biogeochemical cycles
and, more generally, in microbial ecology. By the intrinsic
characteristics of microorganisms (metabolic plasticity,
short generation time, exchange of genetic materials), new
metabolic functions appear under the influence of human
activities on relatively short time scales (few decades),
such as the metabolism of xenobiotics. This metabolic plasticity confers to prokaryotes this large ecological valence.
The discovery of new metabolic pathways broadens the
concepts related to biogeochemical cycle functioning, and
many microbial functions were recently discovered. For
example, the anaerobic methane or ammonium oxidation,
the thiosulfate disproportionation, the hydrocarbon anaerobic mineralization, or the iron oxidation by phototrophic
anoxygenic bacteria, are known prokaryotic activities that
remain to be explored. Similarly, some well-characterized
functional groups have shown new metabolic capabilities;
for example, some sulfate-reducing bacteria, identified as
anaerobic microorganisms, are able to process sulfatereduction and grow under oxic conditions. Similarly, some
nitrifying bacteria are able to achieve denitrification. These
findings tend to demonstrate that our knowledge of the role
and capabilities of microorganisms in biogeochemical
cycles, even if already large, is not exhaustive and new
discoveries are still expected in that domain.
14.6.3 Evolutive Cycles
For millions of years, the global cycles of elements were
stable and only environmental changes, often global
changes, affected them. In contrast, since two centuries and
especially during the past 50 years, demographic pressure
and human activity development have trigerred important
imbalances in biogeochemical cycles. Hence, disturbances
in carbon and nitrogen cycles led to the acceleration of
greenhouse effects from emissions of CO 2 , CH 4 , and nitrogen oxides resulting from excessive use of fossil fuels, waste
disposal, and intense fertilisation of agricultural soils. Similarly, disturbances in the sulfur cycle appear in some
environments to be subject to anthropogenic sulfur-oxide
emissions that generate acid rains.
References
Aller RC (1994) Bioturbation and remineralisation of sedimentary
organic matter: effects of redox oscillation. Chem Geol 114:331–345
Amblard C, Boisson J-C, Fontvielle D, Gayte X, Sime-Ngando T
(1998) Microbial ecology in aquatic systems: a review from viruses
to protozoa. Rev Sci Eau N
Special: 145–162
An SM, Gardner WS, Kana T (2001) Simultaneous measurement of
denitrification and nitrogen fixation using isotope pairing with
membrane inlet mass spectrometry analysis. Appl Environ
Microbiol 67:1171–1178
Arumugam M et al (2011) Enterotypes of the human gut microbiome.
Nature 473:174–180
Azam F, Fenchel T, Gray JG, Meyer-Reil LA, Thingstad TF (1983) The
ecological role of water-column microbes in the sea. Mar Ecol Prog
Ser 10:257–263
Bak F, Cypionka H (1987) A novel type of energy metabolism involving
fermentation of inorganic sulphur compounds. Nature 326:891–892
Barkay T, Miller SM, Summers AO (2003) Bacterial mercury resistance from atoms to ecosystems. FEMS Microbiol Rev 27:355–384
Barnes RO, Goldberg ED (1976) Methane production and consumption
in anoxic marine sediments. Geology 4:297–300
Bazylinski DA, Frankel RB (2004) Magnetosome formation in
prokaryotes. Nat Rev 2:217–230
Beal EJ, House CH, Orphan VJ (2009) Manganese- and iron-dependent
marine methane oxidation. Science 325:184–187
Beatty JT et al (2005) An obligately photosynthetic bacterial anaerobe
from a deep-sea hydrothermal vent. Proc Natl Acad Sci USA
102:9306–9310
Beauchamp B (2004) Natural gas hydrates: myths, facts and issues. C R
Geosci 336:751–765
Benitez-Nelson CR (2000) The biogeochemical cycling of phosphorus
in marine systems. Earth Sci Rev 51:109–135
Berelson WM, Balch WM, Najjar R, Feely RA, Sabine C, Lee K (2007)
Relating estimates of CaCO3 production, export, and dissolution in
the water column to measurements of CaCO3 rain into sediment
traps and dissolution on the sea floor: a revised global carbonate
budget. Glob Biogeochem Cycles 21, GB1024
Bernalier A, Rochet V, Leclerc M, Dore ´ J, Pochart P (1996) Diversity
of H 2 /CO 2 -utilizing acetogenic bacteria from feces of non-methaneproducing humans. Curr Microbiol 33:94–99
Berner RA (2004) The Phanerozoic carbon cycle: CO 2 and O 2 . Oxford
University Press, Oxford
Blain S et al (2007) Effect of natural iron fertilization on carbon
sequestration in the Southern Ocean. Nature 446:1070–1075
Blumenberg M, Seifert R, Reitner J, Pape T, Michaelis W (2004)
Membrane lipid patterns typify distinct anaerobic methanotrophic
consortia. Proc Natl Acad Sci USA 101:11111–11116
Boetius A et al (2000) A marine microbial consortium apparently
mediating anaerobic oxidation of methane. Nature 407:623–626
Bond JH, Engel RR, Levitt MD (1971) Factors influencing pulmonary
methane excretion in man. An indirect method of studying the in
situ metabolism of the methane-producing colonic bacteria. J Exp
Med 133:572–588
Bonin P, Gilewicz M (1992) A direct demonstration of “co-respiration”
of oxygen and nitrogen oxides by Pseudomonas nautica. FEMS
Microbiol Lett 80:183–188
Bonin P, Omnes P, Chamalet A (1998) Simultaneous occurence of
denitrification and nitrate ammonification in sediments of French
Mediterranean Coast. Hydrobiologia 389:169–182
Boyd PW et al (2007) Synthesis and future directions. Science
315:612–617
Brauman A, Fonty G, Roger P (2008) La Me ´thanisation. E ´ ditions Tech
& Doc-Lavoisier, Paris
612
J.-C. Bertrand et al.
methanotrophs, sulfate-reducers, iron-, and manganese bacteria). It must be underlined that prokaryotes are the greatest
source of biodiversity still unknown on Earth. Regularly new
microorganisms are discovered. This knowledge leads to
complete the array of microbial actors involved in some
functions, for example, the 2005 discovery of archaea able
to oxidize ammonium.
The metabolic plasticity of prokaryotes is probably far
from being completely understood, since new functions and
physiological characteristics are part of the most recent
discoveries in the functioning of biogeochemical cycles
and, more generally, in microbial ecology. By the intrinsic
characteristics of microorganisms (metabolic plasticity,
short generation time, exchange of genetic materials), new
metabolic functions appear under the influence of human
activities on relatively short time scales (few decades),
such as the metabolism of xenobiotics. This metabolic plasticity confers to prokaryotes this large ecological valence.
The discovery of new metabolic pathways broadens the
concepts related to biogeochemical cycle functioning, and
many microbial functions were recently discovered. For
example, the anaerobic methane or ammonium oxidation,
the thiosulfate disproportionation, the hydrocarbon anaerobic mineralization, or the iron oxidation by phototrophic
anoxygenic bacteria, are known prokaryotic activities that
remain to be explored. Similarly, some well-characterized
functional groups have shown new metabolic capabilities;
for example, some sulfate-reducing bacteria, identified as
anaerobic microorganisms, are able to process sulfatereduction and grow under oxic conditions. Similarly, some
nitrifying bacteria are able to achieve denitrification. These
findings tend to demonstrate that our knowledge of the role
and capabilities of microorganisms in biogeochemical
cycles, even if already large, is not exhaustive and new
discoveries are still expected in that domain.
14.6.3 Evolutive Cycles
For millions of years, the global cycles of elements were
stable and only environmental changes, often global
changes, affected them. In contrast, since two centuries and
especially during the past 50 years, demographic pressure
and human activity development have trigerred important
imbalances in biogeochemical cycles. Hence, disturbances
in carbon and nitrogen cycles led to the acceleration of
greenhouse effects from emissions of CO 2 , CH 4 , and nitrogen oxides resulting from excessive use of fossil fuels, waste
disposal, and intense fertilisation of agricultural soils. Similarly, disturbances in the sulfur cycle appear in some
environments to be subject to anthropogenic sulfur-oxide
emissions that generate acid rains.
References
Aller RC (1994) Bioturbation and remineralisation of sedimentary
organic matter: effects of redox oscillation. Chem Geol 114:331–345
Amblard C, Boisson J-C, Fontvielle D, Gayte X, Sime-Ngando T
(1998) Microbial ecology in aquatic systems: a review from viruses
to protozoa. Rev Sci Eau N
Special: 145–162
An SM, Gardner WS, Kana T (2001) Simultaneous measurement of
denitrification and nitrogen fixation using isotope pairing with
membrane inlet mass spectrometry analysis. Appl Environ
Microbiol 67:1171–1178
Arumugam M et al (2011) Enterotypes of the human gut microbiome.
Nature 473:174–180
Azam F, Fenchel T, Gray JG, Meyer-Reil LA, Thingstad TF (1983) The
ecological role of water-column microbes in the sea. Mar Ecol Prog
Ser 10:257–263
Bak F, Cypionka H (1987) A novel type of energy metabolism involving
fermentation of inorganic sulphur compounds. Nature 326:891–892
Barkay T, Miller SM, Summers AO (2003) Bacterial mercury resistance from atoms to ecosystems. FEMS Microbiol Rev 27:355–384
Barnes RO, Goldberg ED (1976) Methane production and consumption
in anoxic marine sediments. Geology 4:297–300
Bazylinski DA, Frankel RB (2004) Magnetosome formation in
prokaryotes. Nat Rev 2:217–230
Beal EJ, House CH, Orphan VJ (2009) Manganese- and iron-dependent
marine methane oxidation. Science 325:184–187
Beatty JT et al (2005) An obligately photosynthetic bacterial anaerobe
from a deep-sea hydrothermal vent. Proc Natl Acad Sci USA
102:9306–9310
Beauchamp B (2004) Natural gas hydrates: myths, facts and issues. C R
Geosci 336:751–765
Benitez-Nelson CR (2000) The biogeochemical cycling of phosphorus
in marine systems. Earth Sci Rev 51:109–135
Berelson WM, Balch WM, Najjar R, Feely RA, Sabine C, Lee K (2007)
Relating estimates of CaCO3 production, export, and dissolution in
the water column to measurements of CaCO3 rain into sediment
traps and dissolution on the sea floor: a revised global carbonate
budget. Glob Biogeochem Cycles 21, GB1024
Bernalier A, Rochet V, Leclerc M, Dore ´ J, Pochart P (1996) Diversity
of H 2 /CO 2 -utilizing acetogenic bacteria from feces of non-methaneproducing humans. Curr Microbiol 33:94–99
Berner RA (2004) The Phanerozoic carbon cycle: CO 2 and O 2 . Oxford
University Press, Oxford
Blain S et al (2007) Effect of natural iron fertilization on carbon
sequestration in the Southern Ocean. Nature 446:1070–1075
Blumenberg M, Seifert R, Reitner J, Pape T, Michaelis W (2004)
Membrane lipid patterns typify distinct anaerobic methanotrophic
consortia. Proc Natl Acad Sci USA 101:11111–11116
Boetius A et al (2000) A marine microbial consortium apparently
mediating anaerobic oxidation of methane. Nature 407:623–626
Bond JH, Engel RR, Levitt MD (1971) Factors influencing pulmonary
methane excretion in man. An indirect method of studying the in
situ metabolism of the methane-producing colonic bacteria. J Exp
Med 133:572–588
Bonin P, Gilewicz M (1992) A direct demonstration of “co-respiration”
of oxygen and nitrogen oxides by Pseudomonas nautica. FEMS
Microbiol Lett 80:183–188
Bonin P, Omnes P, Chamalet A (1998) Simultaneous occurence of
denitrification and nitrate ammonification in sediments of French
Mediterranean Coast. Hydrobiologia 389:169–182
Boyd PW et al (2007) Synthesis and future directions. Science
315:612–617
Brauman A, Fonty G, Roger P (2008) La Me ´thanisation. E ´ ditions Tech
& Doc-Lavoisier, Paris
612
J.-C. Bertrand et al.