of valence. The phosphorus atom, for example, does not
change valence unlike carbon, oxygen, nitrogen, sulfur,
iron or manganese.
Moreover, the use of an element will not always depend
on its concentration in the environment but its chemical
status. For example, molecular nitrogen which is the most
abundant gas in the atmosphere (80 %) is not used by plants
which are able to assimilate nitrogen only in the form of
nitrate or ammonia.
14.1.2 The Qualitative and Quantitative
Evolution of Biological Elements
Depends on the Spatial and Temporal
Scales of Interest
At the spatial scale, the evolution of an element can be
studied from a global point of view (at global, regional, or
local scales) to that of a targeted microenvironment (of a
particle or a microniche).
The global cycle of an element can be expressed as the
speed of movement of an element from a compartment to
another, each of which is considered a “black box” or a
reservoir wherein the elements are stored for a period of time
(residence time). The term reservoir can be applied to different
compartments of the biosphere (e.g., hydrosphere, lithosphere,
atmosphere) or to the different trophic levels of a food chain
(primary producers ! primary consumers ! secondary
consumers ! tertiary consumers ! decomposers). The
speed of transfer from one compartment to another, so-called
“flow”, provides quantitative information on the intensity of a
biogeochemical cycle.
In contrast, the study of biogeochemical cycles may be
addressed at a micro-scale. For example, particles
sedimenting in the water column can form anaerobic
microhabitats within an environment that is globally well
oxygenated (Fig. 14.3).
Aerobic bacteria will develop on the surface of the sinking particles, primarily nitrifying bacteria which extensively
use the available oxygen at the periphery of the particles.
Below this aerobic zone, the oxygen concentration will
quickly decrease, setting the conditions for certain steps
of the denitrification process (NO 3
À
! NO 2
À
! N 2 O)
(cf. Sect. 14.3.5). Anoxic conditions will then be established
in the center area of the particles and favor the development
of
fermentative
denitrifying
(NO 3
À
! N 2 )
and
methanogenic bacteria, recruited primarily from the digestive tract of zooplankton (Karl and Tilbrook 1994). In the
absence of oxygen, a detrital anaerobic food chain becomes
prevalent. Different aerobic and anaerobic bacterial
communities can thus coexist in a microenvironment.
Particles as aggregates are sites of intense microbial
activity often called “hotspots”. Such heterogeneous distribution of microbial activity which is associated with a heterogeneous distribution of the organic matter is found in
sediments and soils.
In addition, some elements are produced, used, and
regenerated on a limited geographical area. This may be
the case of nitrogen in soils. In contrast, for other
elements, the production site may be quite distant from
the site where the elements are used. This is the case for
gas products (oxygen, molecular nitrogen, nitrogen
oxides, carbon dioxide, etc.) which can be transported
via atmospheric circulation (winds, vertical circulation)
around the Earth, far away from their source of production. An autotrophic organism can use the CO 2 released
into the atmosphere by another organism living in a far
different geographical province.
The processes to which an element is subjected during
its biogeochemical cycle can occur in time scales that can
be very long, concerning events that took place in geologic times (millions of years in the cases of oil or coal
formation), or extremely brief (the duration of an enzymatic reaction). It is therefore important to know the
lifetime of an element which is defined by the time
elapsed between its fixation in the organic material by
autotrophic organisms, and its regeneration in the form
of minerals. Thus, in the ocean, the carbon fixed in bacterial biomass is recycled in a few hours, while the carbon
of macroorganisms such as fishes and mammals is
sequestered for several years.
14.1.3 Role of Microorganisms
in Biogeochemical Cycles
Because of their high numbers everywhere on Earth, coupled
to tremendous metabolic capacities and the related adaptation potentials, microorganisms will have a key role in the
functioning and transformation of biogeochemical cycles
and, consequently, of ecosystems (Madsen 2011).
In the biosphere, microorganisms include producers,
consumers, and decomposers. During three billion years,
all stages of biogeochemical cycles were performed only
by microorganisms. Currently, they are involved in almost
all steps of the cycles and they are the sole organisms
capable of performing some of these steps.
For example, processes such as sulfate-reduction, denitrification, nitrogen fixation, and the production and consumption of methane are specifically related to the activity of
microorganisms. In their absence, all essential elements for
life would remain trapped in organic molecules of cadavers
and wastes. The maintenance of life for plants, animals and
514
J.-C. Bertrand et al.
change valence unlike carbon, oxygen, nitrogen, sulfur,
iron or manganese.
Moreover, the use of an element will not always depend
on its concentration in the environment but its chemical
status. For example, molecular nitrogen which is the most
abundant gas in the atmosphere (80 %) is not used by plants
which are able to assimilate nitrogen only in the form of
nitrate or ammonia.
14.1.2 The Qualitative and Quantitative
Evolution of Biological Elements
Depends on the Spatial and Temporal
Scales of Interest
At the spatial scale, the evolution of an element can be
studied from a global point of view (at global, regional, or
local scales) to that of a targeted microenvironment (of a
particle or a microniche).
The global cycle of an element can be expressed as the
speed of movement of an element from a compartment to
another, each of which is considered a “black box” or a
reservoir wherein the elements are stored for a period of time
(residence time). The term reservoir can be applied to different
compartments of the biosphere (e.g., hydrosphere, lithosphere,
atmosphere) or to the different trophic levels of a food chain
(primary producers ! primary consumers ! secondary
consumers ! tertiary consumers ! decomposers). The
speed of transfer from one compartment to another, so-called
“flow”, provides quantitative information on the intensity of a
biogeochemical cycle.
In contrast, the study of biogeochemical cycles may be
addressed at a micro-scale. For example, particles
sedimenting in the water column can form anaerobic
microhabitats within an environment that is globally well
oxygenated (Fig. 14.3).
Aerobic bacteria will develop on the surface of the sinking particles, primarily nitrifying bacteria which extensively
use the available oxygen at the periphery of the particles.
Below this aerobic zone, the oxygen concentration will
quickly decrease, setting the conditions for certain steps
of the denitrification process (NO 3
À
! NO 2
À
! N 2 O)
(cf. Sect. 14.3.5). Anoxic conditions will then be established
in the center area of the particles and favor the development
of
fermentative
denitrifying
(NO 3
À
! N 2 )
and
methanogenic bacteria, recruited primarily from the digestive tract of zooplankton (Karl and Tilbrook 1994). In the
absence of oxygen, a detrital anaerobic food chain becomes
prevalent. Different aerobic and anaerobic bacterial
communities can thus coexist in a microenvironment.
Particles as aggregates are sites of intense microbial
activity often called “hotspots”. Such heterogeneous distribution of microbial activity which is associated with a heterogeneous distribution of the organic matter is found in
sediments and soils.
In addition, some elements are produced, used, and
regenerated on a limited geographical area. This may be
the case of nitrogen in soils. In contrast, for other
elements, the production site may be quite distant from
the site where the elements are used. This is the case for
gas products (oxygen, molecular nitrogen, nitrogen
oxides, carbon dioxide, etc.) which can be transported
via atmospheric circulation (winds, vertical circulation)
around the Earth, far away from their source of production. An autotrophic organism can use the CO 2 released
into the atmosphere by another organism living in a far
different geographical province.
The processes to which an element is subjected during
its biogeochemical cycle can occur in time scales that can
be very long, concerning events that took place in geologic times (millions of years in the cases of oil or coal
formation), or extremely brief (the duration of an enzymatic reaction). It is therefore important to know the
lifetime of an element which is defined by the time
elapsed between its fixation in the organic material by
autotrophic organisms, and its regeneration in the form
of minerals. Thus, in the ocean, the carbon fixed in bacterial biomass is recycled in a few hours, while the carbon
of macroorganisms such as fishes and mammals is
sequestered for several years.
14.1.3 Role of Microorganisms
in Biogeochemical Cycles
Because of their high numbers everywhere on Earth, coupled
to tremendous metabolic capacities and the related adaptation potentials, microorganisms will have a key role in the
functioning and transformation of biogeochemical cycles
and, consequently, of ecosystems (Madsen 2011).
In the biosphere, microorganisms include producers,
consumers, and decomposers. During three billion years,
all stages of biogeochemical cycles were performed only
by microorganisms. Currently, they are involved in almost
all steps of the cycles and they are the sole organisms
capable of performing some of these steps.
For example, processes such as sulfate-reduction, denitrification, nitrogen fixation, and the production and consumption of methane are specifically related to the activity of
microorganisms. In their absence, all essential elements for
life would remain trapped in organic molecules of cadavers
and wastes. The maintenance of life for plants, animals and
514
J.-C. Bertrand et al.