Agriculture Reference
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compounds to activate beneficial microbial responses as needed at critical growth stages
or to withstand pathogenic and environmental stress.
The communication networking of microorganisms is closely related to spatial distri-
butions and interactions of microbial communities. In soils, there is recognition of the
potential role of hyphal organisms such as fungi and actinomycetes versus unicellular
organisms (mostly bacteria) relative to exploitation-specific niches. For example, fungi
dominate on the surface of larger aggregates (>250 μ) of soils compared to microaggregates
and pores where bacteria dominate (Gupta and Germida, 1988). At the same time, cells of
singular or multiple species can adhere to each other to form biofilms, which are defined
as interphase boundaries (solid/gas, solid/liquid, and liquid/gas).
A biofilm consists of an assemblage of heterogeneous microcolonies (e.g., protozo-
ans, fungi, nematodes, and prokaryotes) that are encapsulated in extracellular polymeric
substances (EPSs). Microorganisms embedded in biofilms often have altered phenotypic
expression in comparison to the same cells in a planktonic state (Watnick and Kolter, 2000).
Each component of biofilms has a unique function: The liquid interface is the source of
nutrients and energy; the EPSs provide physical structure, protection from environmen-
tal extremes, spatial distribution of organisms, and a medium for diffusion of nutrients
and signaling chemicals. The organisms can work in consortia to perform biogeochemical
processes or cooperatively to aid individual microorganisms. Interestingly, there is now
speculation that biofilms have complex cell-cell signaling and physical structures such
as water channels to disperse nutrients, metabolites, and waste products (Sauer et al.,
2007) and “nanowires” that transfer energy (Schaudinn et al., 2007). Early biofilm research
focused on aquatic systems because they were easily observed. Recently, preliminary
research suggests biofilms do exist in soils, but this remains largely unexplored. Biofilms
on rhizoplanes have been established and related to rhizodeposits of roots that result in
discontinuous nonuniform colonies (Rovira and Campbell, 1974; Hansel et al., 2001).
Clearly, recent advances in molecular biology and microscopy have provided informa-
tion on the importance of biofilms on roots in performing certain tasks (e.g., plant protec-
tion, transforming nutrients to plant-available forms) and hint that biofilms do exist in
bulk soil. However, the complexity and intricacies of organismal relationships and biogeo-
chemical processes are largely unknown in these biofilm communities. Indeed, scientists
are debating the existence of biofilms in bulk soil and how to define biofilms in terms of
cell number or species complexity.
and sustainable rhizospheres
2.2.1 Phytostimulators
A diverse array of bacteria and some fungi has been identified that can produce PGP
substances and increase crop yields (Chen et al., 1994; Amara and Dahdoh, 1997; Biswas
et al., 2000a, 2000b; Hilali et al., 2001; Asghar et al., 2002; Khalid et al., 2004; Larkin,
2008). Phytohormones that are known to be produced by PGP microorganisms are auxin,
cytokinins, indole-3-acetic acid (IAA), and gibberellin, with auxin of primary interest
(Garcia de Salamone et al., 2001; Steenhoudt and Vanderleyden, 2000; Cleland, 1990;
Hagen, 1990).
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