Submitted to: Annual Review of Phytopathology
Publication Type: Review Article
Publication Acceptance Date: January 10, 2004
Publication Date: March 5, 2004
Citation: Mazzola, M. 2004. Assessment and management of soil microbial community structure for disease suppression. Annual Review of Phytopathology. 42:35-39. Interpretive Summary: Identification of the biological properties contributing to the function of suppressive soils is a necessary first step to the management of such systems for use in the control of soilborne diseases. The development and application of molecular methods for the characterization and monitoring of soil microbial properties will enable a more rapid and detailed assessment of the biological nature of soil suppressiveness. Though suppressive soils have provided a wealth of microbial resources that have subsequently been applied for the biological control of soilborne plant pathogens, the full functional capabilities of the phenomena have not been realized in production agricultural ecosystems. Cultural practices such as the application of soil amendments have the capacity to enhance suppression, though the biolgical modes of action may vary from that intially resident to the soil. Plants have a distinct impact on characteristics and activity of resident soil microbial communities, and therefore play an important role in determining the develoment of the disease suppressive state. Likewise, plant genotype will modulate these same communities, and should be considered when developing systems to exploit the potential of such a natural disease control phenomenon. Implementation of effective strategies to manage this resource in an economically and environmentally feasible manner will require more detailed investigaiton of these biologically complex systems and refinement of currently available methods.
Technical Abstract: Soil microorganisms play an important role in a number of processes important to soil quality and plant health. Optimum use of microbial resources requires a broad understanding of the composition and diversity of microorganisms resident to soil habitats. Traditional culture-based methods used in describing these populations has only allowed for examination of a fraction of the soil microbial community. There has been an extensive effort to develop methods with the capacity to elucidate the composition and diversity of microorganism in soil environments without need or cultivation during the process of examination. Certain physiological-based and molelcular-based methods have been developed which partially fulfill this goal. Substrate utilization profiling allows for description of changes in the functional composition of microbial communities, but is hindered by the continued need for cultivation. Phospholipid fatty acid analysis circumvents some of the problems inherent with culture-based methods and is suitable for description of whole communities but is of little value for the identification of individual species. The primary advantage of nucleic acid-based methods is that individuals and microbial communities can be analyzed without need for culturing of the microorganism. Most methods currently employed are based on the polymerase chain reaction, with the small subunit rRNA as the target gene. Methods have been developed for analysis of the amplicons including sequence analysis, TGGE, DGGE and microarrays.