Characterization of fungi (Fusarium and Rhizoctonia) and oomycetes (Phytophthora and Pythium) associated with apple orchards in South Africa

Several species of fungi and oomycetes including Fusarium, Rhizoctonia, Phytophthora and Pythium have been reported as root pathogens of apple where they contribute to a phenomenon known as apple replant disease. In South Africa, little is known about specific species in these genera and their pathogenicity toward apple. Therefore, these aspects were investigated along with the development and optimization of qPCR tests for detection and quantification of the most virulent oomycete species. In eight investigated orchards, the oomycete Phythophthora cactorum was widely distributed, while nine Pythium species were differentially distributed among the orchards. Pythium irregulare was the most widely distributed and the most virulent species along with P. sylvaticum, P. vexans and Ph. cactorum. Seven binucleate Rhizoctonia anastomosis groups (AGs) were also differentially distributed among the orchards, with the majority appearing to be non-pathogenic while certain AG-I and AG-F isolates exhibited low virulence on apple. In the genus Fusarium, F. oxysporum was widely distributed, but isolates were non-pathogenic. Fusarium solani and F. avenaceum were less frequently encountered, with only some isolates having low virulence. qPCR data obtained from seedling roots inoculated with the most virulent Pythium species (P. irregulare, P. sylvaticum and P. vexans) and the genus Phytophthora were not always reproducible between trials, or isolates of the same species. In general, seedling growth inhibition was associated with the presence of a low amount of pathogen DNA (+/- 40 fg mu l(-1) to 2 pg mu l(-1)) in roots. Pythium irregulare, although having the lowest DNA concentrations in roots, was the only species for which a significant negative correlation was found between seedling weight and pathogen DNA concentration.