targeting certain families of key molecules (lignin,
sugar, etc.).
The chemical heterogeneity of soil organic matter partly
reflects its spatial location: The characteristics of the fresh
organic matter brought to the soil as litter and other debris
differ from those of the more labile organic matter
associated with macro-aggregates, and from those of the
stable organic matter associated with micro-aggregates or
clay-organic matter complexes (Fig. 14.16).
This biochemical and spatial heterogeneity of soil
organic matter has led very often to drastically simplify the
characterization of its properties in the analysis of soil
carbon cycle.
14.2.5.2 The Soil Biota
Numerous organisms, with size ranging from few
centimeters to a micrometer, are involved in soil carbon
cycle. These ecosystems contain macrofauna (earthworms,
termites, ants, etc.), mesofauna (insects, mites, microarthropods, etc.), microfauna (nematodes, etc.), and eukaryotic and prokaryotic microorganisms which are abundant
and extremely diverse. All these organisms coexist and can
interact. Their actions are complementary or redundant (i.e.,
functional redundancy) and ultimately contribute to the main
functions in soils, including the recycling of organic material
whose degradation can lead to its mineralization and to
the release of essential inorganic compounds (nitrogen,
phosphorus, etc.) for plant growth.
The smallest organisms are also the most abundant and
the most diversified ones. In particular, the diversity of soil
micro-organisms is huge, the estimated number of bacterial
taxa ranging from 2000 to several millions per gram of soil
(Gans et al. 2005; Schloss and Handelsman 2006; Roesch
et al. 2007).
With prokaryotes, fungi, symbiotic or not, have a particularly important role in carbon cycle in soils compared with
aquatic environments (cf. Sect. 13.3.4). Indeed, saprophytic
Fungi play a key role in the decomposition of organic matter
(Koide et al. 2005); Mycorrhizal Fungi play the role of
interface between the plant roots and soil in many ecosystems.
Few studies have so far focused on soil Archaea that generally
are considered to play a minor role, excepted in carbon-rich
and anoxic soils such as rice crop fields where methanogens
(Goevert and Conrad 2009) and ammonia-oxidizing chemolithotrophs (Schauss et al. 2009) are numerous.
Within a soil, the activity of the diverse organisms varies
in time and space. Indeed, because the availability of carbon
depends on plants, all physiological changes in plant activity
alter the amount and the nature of exudates and litters and
ultimately micro-organisms over time. Moreover, carbon
inputs and transformations are not uniform throughout the
soil, but instead are localized in locations of intense activity
known as “hot spots” (Box 14.4), in particular the rhizosphere (area under the influence of roots), the surroundings
of organic detritus, or the physical structures produced by
soil fauna (earthworm or termite burrows, etc.). As in the
sediments, microbial activity is often higher in these “hot
spots” (Ruiz-Rueda et al. 2009; Hernesmaa et al. 2005), due
to favorable conditions and increased availability of organic
compounds. “Hot spots” generally are associated with
intense biochemical transformations, and are considered as
“oases” that are important for the functioning of soil
ecosystems as a whole, seen as a very heterogeneous environment. Given the size and the generation time of
microorganisms, microbial communities react quickly to
the favorable conditions provided by “hot spots”, even at
small spatial scale (<1 mm). This leads to strong variations
in the activity of microorganisms that can also be
accompanied by changes in the composition of soil microbial communities over time and space (Hernesmaa et al.
2005; Weisskopf et al. 2005).
If fungi and bacteria are the main actors in the chemical
alteration of organic material, the macrofauna (earthworms,
termites, ants, snails, crustaceans, etc.) is also significantly
involved in several degradation processes of organic matter
(OM), such as:
1. Fragmentation of OM that increases the surface offered
for colonization by micro-organisms;
2. Redistribution of OM by soil bioturbation;
3. Oxygenation and, more generally, promotion of gas and
water movements through the creation of a network of
burrows within the soil;
4. Changes in the physical properties of soils. For example,
a compact and impermeable soil may become soft and
porous under the action of burrowing macrofauna;
5. Neutralization of the soil pH, for example, after the transit
of organic material in the digestive tract of earthworms;
6. Grazing pressure and selective grazing that can shape the
microbial community structure and influence microbial
turnover (cf. Sect. 13.3.4).
Some data highlight the importance of bioturbation by
macrofauna. A soil may contain 100–500 earthworms
per m
2 , and up to 2,000 individuals per m
2 in some soils
(Lavelle and Spain 2001). Given that a worm ingests
three times its own mass of soil per day, for a soil containing
100 worms per m
2 , the latter can incorporate 5 t of dry leaves
per year and 50 t (dry mass) of soil (Frontier and PichodViale 1998).
544
J.-C. Bertrand et al.
sugar, etc.).
The chemical heterogeneity of soil organic matter partly
reflects its spatial location: The characteristics of the fresh
organic matter brought to the soil as litter and other debris
differ from those of the more labile organic matter
associated with macro-aggregates, and from those of the
stable organic matter associated with micro-aggregates or
clay-organic matter complexes (Fig. 14.16).
This biochemical and spatial heterogeneity of soil
organic matter has led very often to drastically simplify the
characterization of its properties in the analysis of soil
carbon cycle.
14.2.5.2 The Soil Biota
Numerous organisms, with size ranging from few
centimeters to a micrometer, are involved in soil carbon
cycle. These ecosystems contain macrofauna (earthworms,
termites, ants, etc.), mesofauna (insects, mites, microarthropods, etc.), microfauna (nematodes, etc.), and eukaryotic and prokaryotic microorganisms which are abundant
and extremely diverse. All these organisms coexist and can
interact. Their actions are complementary or redundant (i.e.,
functional redundancy) and ultimately contribute to the main
functions in soils, including the recycling of organic material
whose degradation can lead to its mineralization and to
the release of essential inorganic compounds (nitrogen,
phosphorus, etc.) for plant growth.
The smallest organisms are also the most abundant and
the most diversified ones. In particular, the diversity of soil
micro-organisms is huge, the estimated number of bacterial
taxa ranging from 2000 to several millions per gram of soil
(Gans et al. 2005; Schloss and Handelsman 2006; Roesch
et al. 2007).
With prokaryotes, fungi, symbiotic or not, have a particularly important role in carbon cycle in soils compared with
aquatic environments (cf. Sect. 13.3.4). Indeed, saprophytic
Fungi play a key role in the decomposition of organic matter
(Koide et al. 2005); Mycorrhizal Fungi play the role of
interface between the plant roots and soil in many ecosystems.
Few studies have so far focused on soil Archaea that generally
are considered to play a minor role, excepted in carbon-rich
and anoxic soils such as rice crop fields where methanogens
(Goevert and Conrad 2009) and ammonia-oxidizing chemolithotrophs (Schauss et al. 2009) are numerous.
Within a soil, the activity of the diverse organisms varies
in time and space. Indeed, because the availability of carbon
depends on plants, all physiological changes in plant activity
alter the amount and the nature of exudates and litters and
ultimately micro-organisms over time. Moreover, carbon
inputs and transformations are not uniform throughout the
soil, but instead are localized in locations of intense activity
known as “hot spots” (Box 14.4), in particular the rhizosphere (area under the influence of roots), the surroundings
of organic detritus, or the physical structures produced by
soil fauna (earthworm or termite burrows, etc.). As in the
sediments, microbial activity is often higher in these “hot
spots” (Ruiz-Rueda et al. 2009; Hernesmaa et al. 2005), due
to favorable conditions and increased availability of organic
compounds. “Hot spots” generally are associated with
intense biochemical transformations, and are considered as
“oases” that are important for the functioning of soil
ecosystems as a whole, seen as a very heterogeneous environment. Given the size and the generation time of
microorganisms, microbial communities react quickly to
the favorable conditions provided by “hot spots”, even at
small spatial scale (<1 mm). This leads to strong variations
in the activity of microorganisms that can also be
accompanied by changes in the composition of soil microbial communities over time and space (Hernesmaa et al.
2005; Weisskopf et al. 2005).
If fungi and bacteria are the main actors in the chemical
alteration of organic material, the macrofauna (earthworms,
termites, ants, snails, crustaceans, etc.) is also significantly
involved in several degradation processes of organic matter
(OM), such as:
1. Fragmentation of OM that increases the surface offered
for colonization by micro-organisms;
2. Redistribution of OM by soil bioturbation;
3. Oxygenation and, more generally, promotion of gas and
water movements through the creation of a network of
burrows within the soil;
4. Changes in the physical properties of soils. For example,
a compact and impermeable soil may become soft and
porous under the action of burrowing macrofauna;
5. Neutralization of the soil pH, for example, after the transit
of organic material in the digestive tract of earthworms;
6. Grazing pressure and selective grazing that can shape the
microbial community structure and influence microbial
turnover (cf. Sect. 13.3.4).
Some data highlight the importance of bioturbation by
macrofauna. A soil may contain 100–500 earthworms
per m
2 , and up to 2,000 individuals per m
2 in some soils
(Lavelle and Spain 2001). Given that a worm ingests
three times its own mass of soil per day, for a soil containing
100 worms per m
2 , the latter can incorporate 5 t of dry leaves
per year and 50 t (dry mass) of soil (Frontier and PichodViale 1998).
544
J.-C. Bertrand et al.