Microbial communities in agroecosystems change with management history. In continuous cropping systems, cycling of pathogens and antagonists of pathogens and changes in crop yields can often be seen due to alteration in the disease pressure over time. An example of this is the decline of a disease of wheat called take-all decline that is the result of a change in the soil microbial community. The microbial community shifts to favor growth of antagonists of the pathogen Gaeumannomyces graminis var. tritici which results in decline of the disease (Cook, 1981). An example of the use of soil microbial diversity is the emerging area of biological control of plant pathogens (Cook and Baker, 1983). Microbes have the potential to be used in biological control, which is the suppression of one pest by using its natural predator or antagonist. Biocontrol can be used to control insects, pathogens, and weeds by either lowering the populations of the pest or by reducing the impact of the pest (DeBach, 1964). Microbes function as a direct delivery system for the natural pesticide they produce. Bacteria and fungi that produce different types of antibiotics can be used to control many plant pathogens (Cook and Baker, 1983).
Crop rotation is a key component in sustainable systems because it enhances beneficial microbes, interrupts the cycle of pathogens, and reduces weed populations. Legumes in rotation supply symbiotically fixed nitrogen to the system, aid in maintaining proper water status, and reduce pathogen load. Studies have shown the positive effects of crop rotation on crop growth, attributing this to changes in the microbial community composition (Shipton, 1977; Cook, 1981; Johnson et al., 1992a). Continuous monocropping led to changes in the soil community which increased the pathogen load and reduced barley growth when compared with grains in multiple-crop rotation (Olsson and Gerhardson, 1992). The populations and aggressiveness of pathogens can be altered with crop rotation, illustrating the changes in microbial diversity and function due to management (El Nashaar and Stack, 1989). In a long-term study, Cochliobolus sativus, a pathogen of spring wheat, was found in higher numbers and individual isolates exhibited greater aggressiveness or ability to cause severe disease in continuous wheat rotation, when compared with wheat in a 3-year rotation.
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