well-defined concentrations. The synthesis of cellular
materials associates carbon, as cell carbon and/or energy
source, to the incorporation of a wide variety of mineral
elements (oxygen, hydrogen, nitrogen, phosphorus, sulfur,
iron, etc.). Some of them also act as electron acceptors or
donors during redox reactions that are at the root of the
various biogeochemical cycles. Organic matter mineralization returns mineral elements back to the natural environment under many chemical forms, enabling their recycling.
In this chapter, the cycles of iron, manganese, nitrogen,
and sulfur were described as if they operated independently.
But all these cycles are intimately linked by oxido-reduction
reactions, even if all the involved actors are not yet known.
For example, in some cases, there is an anaerobic oxidation
of sulfur or ammonium in the presence of manganese (IV) or
iron oxide as electrons acceptor. In some ecosystems, CH 4
can be oxidized in the anoxic zone by one or several
syntrophic mechanisms that associate methanogenic archaea
with other bacterial functional groups such as sulfatereducing bacteria or denitrifying bacteria.
14.6.1 The Critical Role of Microorganisms
All living beings participate into the functioning of biogeochemical cycles as known these days. However, higher
organisms are not essential to these cycle functioning. Prokaryotic microorganisms express all the functions that
are necessary to biogeochemical cycles, enabling them to
ensure all biotransformations of chemical elements. They
have acquired and achieve these functions over geological
times. For 3 billion years, life was strictly prokaryotic and the
functioning of biogeochemical cycles was totally ensured by
prokaryotic microorganisms (cf. Chap. 4). From their biogeochemical functions, prokaryotes have created environmental
conditions in terrestrial habitats in which eukaryotic life forms
could appear, grow, and diversify.
14.6.2 Microorganism Plasticity
An important property of prokaryotes is their metabolic
plasticity that enables them to use different sources of carbon, energy, and electron acceptors, thereby contributing
directly to the functioning of several biogeochemical cycles.
For example:
1. autotrophic
and
chemolithotrophic
Thiobacillus
denitrificans uses sulfide as electron donor and nitrate as
electron acceptor to produce its energy, and CO 2 as
carbon source. These bacteria are thus directly involved
in the biogeochemical cycles of sulfur, nitrogen and
carbon;
2. several bacteria within the genus Shewanella can live
under chemolithotrophic conditions using hydrogen, or
under chemo-organotrophic conditions with simple
organic compounds. Under both conditions, they grow
either aerobically with oxygen as electron acceptor, or
anaerobically with various electron acceptors such as
iron, manganese, vanadium, arsenic, fumarate, the
TMAO (trimethylamine oxide) and DMSO (dimethylsulfoxide). These very bacteria are also involved in the
biogeochemical cycles of many pollutants (aromatic
compounds, metals) and contribute to contaminated ecosystem bioremediation;
3. some photosynthetic bacteria are able to grow under
very different environmental conditions. For example,
the sulfur-oxidizing Thiocapsa roseopersicina uses
light as energy source under anaerobic conditions and
oxide sulfur compounds (sulfides, thiosulfate). In the
dark and in the presence of dioxygen, this bacterium
is able to achieve aerobic respiration using the same
sulfur compounds or simple organic compounds
(pyruvate, lactate, acetate, etc.) as energy sources. In
addition, this species can use CO 2 (autotrophy) or the
same simple organic compounds (heterotrophy) as carbon
sources.
The prokaryote plasticity is confirmed by findings related
to the strain “Candidatus Desulforudis audaxviator.” This
bacterium alone makes 99.9 % of the microbial community
observed in a fault of the earth’crust located at 2.8 km depth
(Chivan et al. 2008). The metagenomic investigation
established that this organism has all the metabolic
capacities necessary for an autonomous life and was perfectly adapted to its environment. Thus, this anaerobic, thermophilic, sporulated, and mobile bacterium uses sulfate as
the main electron acceptor, contains dehydrogenases, and
makes all its cell syntheses with organic or mineral carbon
as carbon source and ammoniacal nitrogen or dinitrogen as
nitrogen source. The absence of a complete protection system with respect to dioxygen suggests an ancient isolation
from the Earth surface.
All functions performed by microorganisms (functional
diversity) are variously distributed among the different
known microorganisms (taxonomic diversity). Hence, if
some steps in biogeochemical cycles are carried out by
very diverse microorganisms present in almost all phyla
(denitrifying, organic carbon users), others are conducted
by more specialized groups (CO 2 users, nitrogen fixers)
14 Biogeochemical Cycles
611
materials associates carbon, as cell carbon and/or energy
source, to the incorporation of a wide variety of mineral
elements (oxygen, hydrogen, nitrogen, phosphorus, sulfur,
iron, etc.). Some of them also act as electron acceptors or
donors during redox reactions that are at the root of the
various biogeochemical cycles. Organic matter mineralization returns mineral elements back to the natural environment under many chemical forms, enabling their recycling.
In this chapter, the cycles of iron, manganese, nitrogen,
and sulfur were described as if they operated independently.
But all these cycles are intimately linked by oxido-reduction
reactions, even if all the involved actors are not yet known.
For example, in some cases, there is an anaerobic oxidation
of sulfur or ammonium in the presence of manganese (IV) or
iron oxide as electrons acceptor. In some ecosystems, CH 4
can be oxidized in the anoxic zone by one or several
syntrophic mechanisms that associate methanogenic archaea
with other bacterial functional groups such as sulfatereducing bacteria or denitrifying bacteria.
14.6.1 The Critical Role of Microorganisms
All living beings participate into the functioning of biogeochemical cycles as known these days. However, higher
organisms are not essential to these cycle functioning. Prokaryotic microorganisms express all the functions that
are necessary to biogeochemical cycles, enabling them to
ensure all biotransformations of chemical elements. They
have acquired and achieve these functions over geological
times. For 3 billion years, life was strictly prokaryotic and the
functioning of biogeochemical cycles was totally ensured by
prokaryotic microorganisms (cf. Chap. 4). From their biogeochemical functions, prokaryotes have created environmental
conditions in terrestrial habitats in which eukaryotic life forms
could appear, grow, and diversify.
14.6.2 Microorganism Plasticity
An important property of prokaryotes is their metabolic
plasticity that enables them to use different sources of carbon, energy, and electron acceptors, thereby contributing
directly to the functioning of several biogeochemical cycles.
For example:
1. autotrophic
and
chemolithotrophic
Thiobacillus
denitrificans uses sulfide as electron donor and nitrate as
electron acceptor to produce its energy, and CO 2 as
carbon source. These bacteria are thus directly involved
in the biogeochemical cycles of sulfur, nitrogen and
carbon;
2. several bacteria within the genus Shewanella can live
under chemolithotrophic conditions using hydrogen, or
under chemo-organotrophic conditions with simple
organic compounds. Under both conditions, they grow
either aerobically with oxygen as electron acceptor, or
anaerobically with various electron acceptors such as
iron, manganese, vanadium, arsenic, fumarate, the
TMAO (trimethylamine oxide) and DMSO (dimethylsulfoxide). These very bacteria are also involved in the
biogeochemical cycles of many pollutants (aromatic
compounds, metals) and contribute to contaminated ecosystem bioremediation;
3. some photosynthetic bacteria are able to grow under
very different environmental conditions. For example,
the sulfur-oxidizing Thiocapsa roseopersicina uses
light as energy source under anaerobic conditions and
oxide sulfur compounds (sulfides, thiosulfate). In the
dark and in the presence of dioxygen, this bacterium
is able to achieve aerobic respiration using the same
sulfur compounds or simple organic compounds
(pyruvate, lactate, acetate, etc.) as energy sources. In
addition, this species can use CO 2 (autotrophy) or the
same simple organic compounds (heterotrophy) as carbon
sources.
The prokaryote plasticity is confirmed by findings related
to the strain “Candidatus Desulforudis audaxviator.” This
bacterium alone makes 99.9 % of the microbial community
observed in a fault of the earth’crust located at 2.8 km depth
(Chivan et al. 2008). The metagenomic investigation
established that this organism has all the metabolic
capacities necessary for an autonomous life and was perfectly adapted to its environment. Thus, this anaerobic, thermophilic, sporulated, and mobile bacterium uses sulfate as
the main electron acceptor, contains dehydrogenases, and
makes all its cell syntheses with organic or mineral carbon
as carbon source and ammoniacal nitrogen or dinitrogen as
nitrogen source. The absence of a complete protection system with respect to dioxygen suggests an ancient isolation
from the Earth surface.
All functions performed by microorganisms (functional
diversity) are variously distributed among the different
known microorganisms (taxonomic diversity). Hence, if
some steps in biogeochemical cycles are carried out by
very diverse microorganisms present in almost all phyla
(denitrifying, organic carbon users), others are conducted
by more specialized groups (CO 2 users, nitrogen fixers)
14 Biogeochemical Cycles
611