Assessing populations of a disease suppressive microorganism and a plant pathogen using DNA arrays

Understanding the relationships between disease suppressive microbial populations and plant pathogens is essential to develop procedures for effective and consistent disease control. Currently, DNA array technology is the most suitable technique to simultaneously detect multiple microorganisms. Although this technology has been successfully applied for diagnostic purposes, its utility to assess different microbial populations, as a basis for further study of population dynamics and their potential interactions, has not yet been investigated. In this study, a DNA macroarray with multiple levels of phylogenetic specificity was developed to measure population densities of a specific disease suppressive microorganism, Trichoderma hamatum isolate 382, and the plant pathogen Rhizoctonia solani. Amongst others, the DNA array contained genus-, species- and isolate-specific detector oligonucleotides and was optimized for sensitive detection and reliable quantification of the target organisms in potting mix samples. Furthermore, this DNA array was used to quantify disease severity as well as incidence of severe disease based on pathogen population densities in the growing medium. Taking into account the unlimited expanding possibilities of DNA arrays to include detector oligonucleotides for other and more microorganisms, this technique has the potential for studying the population dynamics and ecology of several target populations in a single assa