Fourth, importing seeds, seedlings, and plants from
remote areas brings microorganisms that interact with
plants. Unintentional deliveries can also occur through the
use of agricultural tools or machinery (farming practices),
while some phytobeneficial microorganisms are deliberately
introduced to inoculate crops (Agrios 1997; Dobbelaere
et al. 2001; Alabouvette et al. 2006).
Fifth, the plant itself can be a source of microorganisms.
Indeed, the microorganisms present on living plants or plant
remnants (litter, crop residues) are a source of inoculum for
plants that will later develop in the same place. For example,
mycotoxin-producing Fusarium can survive in overwintered
corn stalk residues and may colonize wheat in the following
growing season (Leplat et al. 2013). In addition, certain
microorganisms are present in the seed, whether as internal
or external contamination. These microorganisms are in a
favorable position to colonize plant seedlings emerging from
these seed. Finally, endophytic microorganisms can be
found in plants of the next generation if these plants are
propagated vegetatively, as with sugarcane cuttings.
In the end, microorganisms associated with plants have
contrasting sources, and they have undergone dissemination
phenomena at different spatial scales. In terms of biogeography, even though many of them have an endemic distribution, some microorganisms appear to be transported over
long distances (Ramette and Tiedje 2007). This is particularly the case of microorganisms associated with cultivated
plants, which colonize plant shoots and/or are easily spread
by wind, and some of them are plant pathogens.
11.3.4 Diversity and Activity of Microorganisms
Associated with Plants
11.3.4.1 Ecological Factors
Due to high microbial numbers and the importance of microbial interactions in the rhizosphere, the ecological
specificities of this microbial habitat are summarized
below. In comparison with non-rhizosphere soil, the rhizosphere has specific physical and (bio) chemical features.
From a physical point of view, the root surface is not homogeneous in terms of topography and rhizodeposit flux,
noticeably with the occurrence of a groove and the preferential release of exudates at the junction of epidermal cells
(Beattie and Lindow 1999). The level of hydrophobicity of
the root surface (and thus its contact properties) may vary
depending on the plant considered. Root growth results in
the creation of a root-based soil macroporosity, which leads
to compaction of the rhizospheric soil. It is also in the
rhizosphere that diffusion of soluble rhizodeposits occurs,
resulting in stimulation of microbial populations. Insoluble
rhizodeposits render the mucigel gelatinous, which
facilitates adhesion between root and soil particles. The
mucigel also affects water movement in the rhizosphere,
thereby modulating the availability of water to roots.
From a chemical point of view, the properties of the
rhizosphere are largely related to the presence of
rhizodeposits (formerly referred to as root exudates).
Depending on the mode of release of rhizodeposits in the
soil (Fig. 11.8), we distinguish exudates (in the modern
sense of the term) or diffusates (soluble or gaseous lowmolecular-weight compounds released by passive transport),
secretions (compounds actively transported out of the root
cells), cell lysates (compounds released during the lysis of
epidermal cells, cortical cells, or senescent sloughed-off
cells detached from the root cap), and the mucigel (plant
polysaccharides, to which microbial exopolysaccharides can
be added) (Nguyen 2003). Quantitatively, the rhizodeposits
represent 15–20 % of the net organic carbon from photosynthesis, i.e., about half the organic carbon translocated to
roots (Nguyen 2003). The organic rhizodeposits have a
high functional and chemical diversity. They include the
following:
1. Simple substrates, namely, a very large number of amino
acids, organic acids, sugars, fatty acids, sterols, nucleic
acid derivatives, etc.
2. Insoluble polymers (cellulose and other carbohydrates)
3. Vitamins and other growth factors (biotin, inositol, thiamine, etc.)
4. Phytohormones (auxins, cytokinins, etc.)
5. Enzymatic proteins (amylases, phosphatases, proteases,
etc.)
6. Toxins (e.g., calystegines) and defense compounds (such
as phytoalexins and glucosinolates)
7. Signals acting on microorganisms as chemoattractants
(sugars, organic acids, etc.) and/or transcription inducers
(e.g., flavonoids), etc. (Bais et al. 2006).
The rhizosphere exhibits other chemical particularities,
which are also related to root functioning. Plant nutrition
requires selective uptake of mineral nutrients by roots,
which leads to accumulation and sometimes also precipitation (e.g., calcium carbonate or iron oxide) of excess
constituents and especially depletion for metabolized
nutrients (to a larger extent for soluble anions such as nitrate
than for poorly soluble anions such as phosphate or for
cations) in the rhizosphere. Cations and anions uptake
involves parallel excretion of proton or hydroxide anion,
respectively, which can lead to local pH change in the
rhizosphere (Hinsinger et al. 2003). Finally, root (and microbial) respiration may lead to a decrease in oxygen concentration, with a parallel increase in carbon dioxide content, in
particular, when soil is very wet. However, these processes
can be offset by the ease of gas exchange in the root
macroporosity. This is particularly the case in soils
containing swelling clays, which retract during drying. It
can be noted that certain plants that thrive in submerged
11 Microorganisms and Biotic Interactions
409
remote areas brings microorganisms that interact with
plants. Unintentional deliveries can also occur through the
use of agricultural tools or machinery (farming practices),
while some phytobeneficial microorganisms are deliberately
introduced to inoculate crops (Agrios 1997; Dobbelaere
et al. 2001; Alabouvette et al. 2006).
Fifth, the plant itself can be a source of microorganisms.
Indeed, the microorganisms present on living plants or plant
remnants (litter, crop residues) are a source of inoculum for
plants that will later develop in the same place. For example,
mycotoxin-producing Fusarium can survive in overwintered
corn stalk residues and may colonize wheat in the following
growing season (Leplat et al. 2013). In addition, certain
microorganisms are present in the seed, whether as internal
or external contamination. These microorganisms are in a
favorable position to colonize plant seedlings emerging from
these seed. Finally, endophytic microorganisms can be
found in plants of the next generation if these plants are
propagated vegetatively, as with sugarcane cuttings.
In the end, microorganisms associated with plants have
contrasting sources, and they have undergone dissemination
phenomena at different spatial scales. In terms of biogeography, even though many of them have an endemic distribution, some microorganisms appear to be transported over
long distances (Ramette and Tiedje 2007). This is particularly the case of microorganisms associated with cultivated
plants, which colonize plant shoots and/or are easily spread
by wind, and some of them are plant pathogens.
11.3.4 Diversity and Activity of Microorganisms
Associated with Plants
11.3.4.1 Ecological Factors
Due to high microbial numbers and the importance of microbial interactions in the rhizosphere, the ecological
specificities of this microbial habitat are summarized
below. In comparison with non-rhizosphere soil, the rhizosphere has specific physical and (bio) chemical features.
From a physical point of view, the root surface is not homogeneous in terms of topography and rhizodeposit flux,
noticeably with the occurrence of a groove and the preferential release of exudates at the junction of epidermal cells
(Beattie and Lindow 1999). The level of hydrophobicity of
the root surface (and thus its contact properties) may vary
depending on the plant considered. Root growth results in
the creation of a root-based soil macroporosity, which leads
to compaction of the rhizospheric soil. It is also in the
rhizosphere that diffusion of soluble rhizodeposits occurs,
resulting in stimulation of microbial populations. Insoluble
rhizodeposits render the mucigel gelatinous, which
facilitates adhesion between root and soil particles. The
mucigel also affects water movement in the rhizosphere,
thereby modulating the availability of water to roots.
From a chemical point of view, the properties of the
rhizosphere are largely related to the presence of
rhizodeposits (formerly referred to as root exudates).
Depending on the mode of release of rhizodeposits in the
soil (Fig. 11.8), we distinguish exudates (in the modern
sense of the term) or diffusates (soluble or gaseous lowmolecular-weight compounds released by passive transport),
secretions (compounds actively transported out of the root
cells), cell lysates (compounds released during the lysis of
epidermal cells, cortical cells, or senescent sloughed-off
cells detached from the root cap), and the mucigel (plant
polysaccharides, to which microbial exopolysaccharides can
be added) (Nguyen 2003). Quantitatively, the rhizodeposits
represent 15–20 % of the net organic carbon from photosynthesis, i.e., about half the organic carbon translocated to
roots (Nguyen 2003). The organic rhizodeposits have a
high functional and chemical diversity. They include the
following:
1. Simple substrates, namely, a very large number of amino
acids, organic acids, sugars, fatty acids, sterols, nucleic
acid derivatives, etc.
2. Insoluble polymers (cellulose and other carbohydrates)
3. Vitamins and other growth factors (biotin, inositol, thiamine, etc.)
4. Phytohormones (auxins, cytokinins, etc.)
5. Enzymatic proteins (amylases, phosphatases, proteases,
etc.)
6. Toxins (e.g., calystegines) and defense compounds (such
as phytoalexins and glucosinolates)
7. Signals acting on microorganisms as chemoattractants
(sugars, organic acids, etc.) and/or transcription inducers
(e.g., flavonoids), etc. (Bais et al. 2006).
The rhizosphere exhibits other chemical particularities,
which are also related to root functioning. Plant nutrition
requires selective uptake of mineral nutrients by roots,
which leads to accumulation and sometimes also precipitation (e.g., calcium carbonate or iron oxide) of excess
constituents and especially depletion for metabolized
nutrients (to a larger extent for soluble anions such as nitrate
than for poorly soluble anions such as phosphate or for
cations) in the rhizosphere. Cations and anions uptake
involves parallel excretion of proton or hydroxide anion,
respectively, which can lead to local pH change in the
rhizosphere (Hinsinger et al. 2003). Finally, root (and microbial) respiration may lead to a decrease in oxygen concentration, with a parallel increase in carbon dioxide content, in
particular, when soil is very wet. However, these processes
can be offset by the ease of gas exchange in the root
macroporosity. This is particularly the case in soils
containing swelling clays, which retract during drying. It
can be noted that certain plants that thrive in submerged
11 Microorganisms and Biotic Interactions
409