Fungal and oomycete pathogen detection in the rhizosphere of organic tomatoes grown in cover crop-treated soils

Soil management practices, including the use of cover crops, affect soil and plant health through varied mechanisms. Impacts on microbial communities are known to be important, but are not well understood. Various techniques are used to measure the effect of treatments on microbial communities, but rarely are the results of more than one technique compared. This field study examined the impacts of a single-season application of cover crops on detection of pathogen species in the tomato crop rhizosphere. The study took place in Maryland, New York and Ohio (MD, NY and OH) in the summers of 2010 and 2011, with a total of 260 plots tested using both macroarray and T-RFLP analyses. The macroarray used in this study was specifically designed to detect thirty-one pathogens of solanaceous crops and had not previously been used for such a field study. The results of T-RFLP analysis, which is a common tool for examining microbial communities, were compared to the macroarray results and the limitations and benefits of each are presented. While not a quantitative measure, the macroarray was able to detect certain fungi with much greater sensitivity than T-RFLP. Our findings suggest that the results of PCR-based techniques used for microbial community studies should be compared to other methods to verify sensitivity.