Molecular taxonomy and its application to ecological studies of Pythium species

Abstract

More than 140 Pythium species have been described; 41 of these species have been described since 2000. Many Pythium species cause seed rot and damping off of seedlings. Recent changes in crop culture systems, such as the introduction of hydroponic cultures, have resulted in Pythium diseases of mature plants as well, with symptoms such as root rot, crown rot, and blight. In Japan, newly introduced ornamental and floral plants are vulnerable to high temperatures and humidity, resulting in severe Pythium infections. Once a pathogen invades a greenhouse, it quickly propagates and disperses, resulting in serious yield loss. It is very difficult to identify an isolate at the species level based on morphological characteristics because of overlaps in the size and shape of reproductive structures, heterothallism, and the continuing discovery of new species. New procedures based on DNA sequences have thus been introduced to identify species; in particular, the rDNA ITS region and the coxI gene have been recommended for DNA barcoding. BLAST searches and phylogenic analyses allow for easy and precise identification. PCR techniques are also being used to diagnose plant diseases, and real time PCR can be used for quantifying the pathogen to assess the risk of disease loss. Molecular techniques to analyze population structure help clarify transmission routes of pathogens and the ecology of Pythium flora in natural ecosystems. In this review we discuss recent advances in molecular methods for identifying, detecting, and classifying Pythium species.