Agriculture Reference
In-Depth Information
microorganisms but also to determine the underlying mode of action at the physiologi-
cal and genetic levels. This will require improvements in the ability to culture microor-
ganisms from soil in addition to the novel culture-independent methods described in
this chapter.
Theories on the role of species diversity are largely based on the ecology of above-
ground terrestrial organisms with little understanding of the significance for soil and
rhizospheres (Wardle and Giller, 1996; Ohtonen et al., 1997; Griffiths et al., 2000). This is
further complicated for soil microbial ecology by the aforementioned limitations of how
to define species and implications of gene flow for identifying species. Thus, the links
between biodiversity and soil functioning are poorly understood, yet fundamental to
exploit microorganisms and their interactions with plants to improve the productivity of
crops. Consequently, as research proceeds, there will be a need for in-depth studies of
functional genes and gene flow, as well as determining an appropriate definition of micro-
bial species (or discarding the importance of species diversity per se in favor of other, as-
yet-unknown means of describing microbial community structure).
2.1.3 Signaling
Besides species diversity and gene flow, another important and poorly understood phe-
nomenon is cell-cell communication
by chemical signaling among microorganisms and
between microorganisms and plants. There are likely a large number of chemicals that
allow microorganisms to coordinate gene expression on a population-wide scale. One
such system is quorum sensing (QS), which involves production, secretion, and subse-
quent detection of small hormone-like signaling molecules known as autoinducers, first
discovered over 25 years ago in marine bacteria (Nealson and Hastings, 1979). Signal com-
pounds are produced by bacteria, which on reaching a critical level, induce gene expression
encoding for a variety of phenotypical and physiological responses, such as biolumines-
cence, pathogenicity and pigment induction, cell conjugation, growth regulation, nodula-
tion (e.g., rhizobial-legume symbiosis), biofilm formation, and cell motility (Lithgow et al.,
2000; Fray, 2002). The most widely studied QS compounds are N-acylhomoserine lactones
(AHLs), which vary in length, oxidation state, and degree of saturation of their acyl side
chains to provide a degree of species specificity (Badri et al., 2009). A range of gram-neg-
ative bacterial species employs AHLs, whereas gram-positive bacteria typically use pep-
tides as the QS molecule. Signaling can also occur by volatile compounds.
There has been great progress in understanding plant QS compounds that target bac-
terial receptors for favorable biocontrol responses. In particular, AHLs produced by rhi-
zobacteria have been shown to promote biocontrol agents or interfere with pathogens of
biocontrol or affect other rhizosphere processes (Lugtenberg and Leveau, 2007). There is
evidence that plants can produce and secrete substances that mimic AHL activity and
could therefore influence the density-dependent behavior of biocontrol and other benefi-
cial rhizobacteria (Teplitski et al., 2000). This offers an opportunity through plant breeding
or transgenic gene insertion to develop crops with roots that can produce QS AHL-
mimicking compounds that stimulate or optimize the application of biocontrol strains
(Chin-A-Woeng et al., 2001; Castang et al., 2004) by inducing regulated genes via specific
AHL receptors on biocontrol bacteria. This has great potential for engineered crops to deal
with both pathogens and symbionts.
To utilize beneficial microorganisms fully, a fundamental understanding of signaling
mechanisms and the array of signaling compounds is required.
The impacts of signal-
ing are multifaceted, with microorganisms communicating with each other to carry out
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