Agriculture Reference
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from adverse changes in the environment than bacteria in the rhizosphere (Beattie, 2006) and
would be expected to interact closely with their host and face less competition for nutrients.
The rhizosphere region is a microbially diverse, highly competitive, and complex eco-
logical environment for microorganisms. We now know that they exhibit highly regulated
cell-to-cell communication using signaling compounds. The volume of rhizospheric soil is
relatively small compared to the bulk soil of the rooting zone of crops but is nonetheless
extremely important in affecting plant pathogens, plant growth promotion, and biogeo-
chemical processes that together strongly affect the yield and quality of crops (Gregory, 2006).
There has been long-standing recognition of the importance of root exudates as
sources of nutrients and carbon (C) for promoting and sustaining biological organisms.
Roots exude ions, free oxygen and water, extracellular enzymes, mucilage, and a wide
range of primary and secondary metabolites (Bertin et al., 2003; Uren, 2007), which result in
elimination of waste materials of either unknown function or for root lubrication or plant
defense (Uren, 2007). These exudates are an array of low molecular weight compounds,
such as amino acids, sugars, organic acids, phenolics, and other secondary metabolites or
less-diverse high molecular weight exudates of polysaccharides and proteins (Faure et al.,
2009). The latter have a much larger proportion of the exudate mass than the low molecular
weight compounds. Plants expend a considerable amount of energy and C through exuda-
tion, which can include more than 30% of the energy captured by photosynthesis (Morgan
and Whipps, 2001).
These exudates primarily affect microbial communities in two ways. First, they pro-
vide rich and relatively readily available sources of energy and nutrients. Second, there
is growing evidence of a diverse range of chemical signals from plant roots to microor-
ganisms and vice versa that influence community structure and functions. This creates
a functionally complex community with a high level of competition for colonization by
bacteria and fungi that may be beneficial, neutral, or pathogenic toward plants. Although
a general understanding of root exudates and their overall importance relative to plant
nutrition, pathogen responses, and beneficial microbial interactions has been established,
the role and magnitude of chemical signaling of root to root, root to microorganism/inver-
tebrate and microorganism/invertebrate to root are just beginning to be understood. The
mechanisms used by these organisms to select and interpret the signals produced in the
rhizosphere are largely unknown (Uren, 2007).
There is a growing body of evidence that the biology of the rhizosphere could be
exploited by manipulating root and microbial interactions to improve the productivity
and sustainability of agricultural systems. These beneficial rhizospheric organisms have
shown the potential to increase nutrient availability to plants, stimulate growth, and
protect plants from pests and pathogens. This would be particularly valuable toward
the development of sustainable, biologically based agricultural systems because this has
potential for reduced or no external inputs—in effect substituting microbial benefits for
synthetic inputs.
2.1.1 Microbial ecology, genomics, and synergisms
Since 2000, there is increasing evidence for the feasibility of manipulating microorganisms
to substitute for pesticides, significantly reducing the need for off-farm fertilizer inputs,
and stimulating plant growth. In the following sections, the mechanisms, organisms, and
research needs for specific strategies focused on plant protection, disease suppression,
plant growth stimulation, and enhanced plant nutrition are discussed. The goal of this
section is to provide a brief overview of the areas of basic research in microbial ecology
 
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