During these various reactions and transformations,
the molecular weight of humic compounds continuously
increases due to the enrichment by compounds from
microbial activity: bacterial polysaccharides, fungal
pigments, etc. Humic substances obtained this way have a
molecular weight which may range from 700 to 300,000 Da,
and are often classified into three main types: fulvic acids
(rich in lateral chains and relatively soluble in water), humic
acids (rich in aromatic nuclei and poor in lateral chains,
relatively poorly soluble), and humins (moderately rich in
lateral chains, slightly soluble). These compounds have a
“sponge” structure and offer a large surface for exchanges,
with hydrophilic and hydrophobic zones. They are often
associated with inorganic particles, forming threedimensional structures which are poorly accessible to any
enzymatic attack. Their properties are very important to
explain the physico-chemical characteristics of soils, such
as cation exchange capacity, adsorption of solutes, etc. Note
that direct humification (i.e., without any role of biological
activity) may occur in areas where pedoclimatic conditions
hinder the development of microorganisms. In this case,
humic compounds result from slow oxidations and
physico-chemical condensation, and have a lower molecular
weight.
The turnover time of humus is typically 2–5 % per year
and varies depending on soil and climatic conditions. For
comparison, about 50 % of the lignin supplied in a soil
typically disappears within a year (Maier et al. 2000).
When protected in microsites which are hardly accessible
to microorganisms or when the availability of labile energetic substrates is low, humic components are protected
from biodegradation and contribute to carbon sequestration
in soils. Conversely, if accessible to microorganisms and if
the availability labile energetic substrates is sufficient, a
“priming effect” may occur (Box 14.4) (Fontaine et al.
2004): Humus is then a source of carbon, nitrogen (humus
is rich in nitrogen), and energy for microbial populations
(secondary mineralization). This explains why soil cultivation from forest or grassland greatly accelerates the mineralization of organic matter already present through a priming
effect-like process: without organic matter amendment, the
quantity of humus decreases after land conversion to cropping systems, slowly but steadily.
14.2.6 Carbon Cycle in Lakes
The physical, chemical, and biological processes that govern
the major biogeochemical cycles in general, and that of
carbon in particular, are globally similar in marine and
lacustrian ecosystems (Box 14.6). This is particularly the
case for pelagic areas, highly original and characterized by
microbial communities ensuring almost all of the primary
Box 14.6: The Carbon Cycle in Freshwater Ecosystems
Gerard Fonty
Lakes are closed and spatially well-delimited
ecosystems and represent stagnant water surfaces that
occupy natural or arranged depressions on the earth.
Although it is possible to describe a general dynamics
of carbon cycle in these aquatic biotopes, each lake
possesses its own characteristics which can only be
understood in regards to its morphometrical, physicochemical, and biological features. These characteristics
depend on the geographical localization of the lake and
on its mode of alimentation. Lakes are very diverse by
their size, shape, depth, and also genesis.
Morphometrical features of lakes and stratification
of physico-chemical parameters. Morphometrical
characteristics condition the physical, chemical, and
biological functioning of the lakes. Depth of light
penetration in the water column, wind action, temperature, and oxygen concentration of water are major
factors determining the ecological function of lakes.
The vertical stratification of light determines a euphotic upper layer in photosynthesis takes place, and an
aphotic zone where the intensity of light is too weak to
authorize this process. Due to the variation of water
density with temperature, the water column stratifies
vertically in the absence of turbulences according to a
vertical gradient of temperature. This stratification
depends on the lake depth. In summer time, in deep
lakes, three zones can be distinguished: the upper
warm zone called epilimnion, an intermediate compartment where temperature rapidly decreases with
depth named metamolimnion, and finally a deep zone
where temperature remains low, the hypolimnion. In
deep lakes, hypolimnion temperature is near to 4
C.
The sharp variation of temperature in hypolimnion
determines a thermocline that plays a fundamental
role in the functioning of the lakes because it
constitutes a barrier for the transfers between the
hypo- and the epilimnion. The vertical thermocline
position changes with the seasons according to the
warming and the water turbulence in the epilimnion.
Seasonal variations of water density lead to a more or
less pronounced mixing of the water column.
According to the frequency of water mixing lakes are
classified into: (1) meromictic lakes (one annual
period of destratification); (2) dimictic lakes (water
G. Fonty (*)
Laboratoire des Microorganismes: Ge ´nome et Environnement
(LMGE), UMR CNRS 6023, Universite ´ Blaise Pascal, Clermont
Universite ´, B.P. 80026, 63171 Aube `re Cedex, France
(continued)
14 Biogeochemical Cycles
551
the molecular weight of humic compounds continuously
increases due to the enrichment by compounds from
microbial activity: bacterial polysaccharides, fungal
pigments, etc. Humic substances obtained this way have a
molecular weight which may range from 700 to 300,000 Da,
and are often classified into three main types: fulvic acids
(rich in lateral chains and relatively soluble in water), humic
acids (rich in aromatic nuclei and poor in lateral chains,
relatively poorly soluble), and humins (moderately rich in
lateral chains, slightly soluble). These compounds have a
“sponge” structure and offer a large surface for exchanges,
with hydrophilic and hydrophobic zones. They are often
associated with inorganic particles, forming threedimensional structures which are poorly accessible to any
enzymatic attack. Their properties are very important to
explain the physico-chemical characteristics of soils, such
as cation exchange capacity, adsorption of solutes, etc. Note
that direct humification (i.e., without any role of biological
activity) may occur in areas where pedoclimatic conditions
hinder the development of microorganisms. In this case,
humic compounds result from slow oxidations and
physico-chemical condensation, and have a lower molecular
weight.
The turnover time of humus is typically 2–5 % per year
and varies depending on soil and climatic conditions. For
comparison, about 50 % of the lignin supplied in a soil
typically disappears within a year (Maier et al. 2000).
When protected in microsites which are hardly accessible
to microorganisms or when the availability of labile energetic substrates is low, humic components are protected
from biodegradation and contribute to carbon sequestration
in soils. Conversely, if accessible to microorganisms and if
the availability labile energetic substrates is sufficient, a
“priming effect” may occur (Box 14.4) (Fontaine et al.
2004): Humus is then a source of carbon, nitrogen (humus
is rich in nitrogen), and energy for microbial populations
(secondary mineralization). This explains why soil cultivation from forest or grassland greatly accelerates the mineralization of organic matter already present through a priming
effect-like process: without organic matter amendment, the
quantity of humus decreases after land conversion to cropping systems, slowly but steadily.
14.2.6 Carbon Cycle in Lakes
The physical, chemical, and biological processes that govern
the major biogeochemical cycles in general, and that of
carbon in particular, are globally similar in marine and
lacustrian ecosystems (Box 14.6). This is particularly the
case for pelagic areas, highly original and characterized by
microbial communities ensuring almost all of the primary
Box 14.6: The Carbon Cycle in Freshwater Ecosystems
Gerard Fonty
Lakes are closed and spatially well-delimited
ecosystems and represent stagnant water surfaces that
occupy natural or arranged depressions on the earth.
Although it is possible to describe a general dynamics
of carbon cycle in these aquatic biotopes, each lake
possesses its own characteristics which can only be
understood in regards to its morphometrical, physicochemical, and biological features. These characteristics
depend on the geographical localization of the lake and
on its mode of alimentation. Lakes are very diverse by
their size, shape, depth, and also genesis.
Morphometrical features of lakes and stratification
of physico-chemical parameters. Morphometrical
characteristics condition the physical, chemical, and
biological functioning of the lakes. Depth of light
penetration in the water column, wind action, temperature, and oxygen concentration of water are major
factors determining the ecological function of lakes.
The vertical stratification of light determines a euphotic upper layer in photosynthesis takes place, and an
aphotic zone where the intensity of light is too weak to
authorize this process. Due to the variation of water
density with temperature, the water column stratifies
vertically in the absence of turbulences according to a
vertical gradient of temperature. This stratification
depends on the lake depth. In summer time, in deep
lakes, three zones can be distinguished: the upper
warm zone called epilimnion, an intermediate compartment where temperature rapidly decreases with
depth named metamolimnion, and finally a deep zone
where temperature remains low, the hypolimnion. In
deep lakes, hypolimnion temperature is near to 4
C.
The sharp variation of temperature in hypolimnion
determines a thermocline that plays a fundamental
role in the functioning of the lakes because it
constitutes a barrier for the transfers between the
hypo- and the epilimnion. The vertical thermocline
position changes with the seasons according to the
warming and the water turbulence in the epilimnion.
Seasonal variations of water density lead to a more or
less pronounced mixing of the water column.
According to the frequency of water mixing lakes are
classified into: (1) meromictic lakes (one annual
period of destratification); (2) dimictic lakes (water
G. Fonty (*)
Laboratoire des Microorganismes: Ge ´nome et Environnement
(LMGE), UMR CNRS 6023, Universite ´ Blaise Pascal, Clermont
Universite ´, B.P. 80026, 63171 Aube `re Cedex, France
(continued)
14 Biogeochemical Cycles
551