Exploring the Oomycete Microbiome Associated with Soybean Seedling Diseases in the U.S

Oomycete pathogens of soybean (Glycine max) can result in low stand establishment and root rot often reducing yield. There is limited information regarding abundance and diversity of oomycetes species across most soybean producing states.   A two-year culture based survey was conducted across 11 states to determine diversity of oomycetes associated with soybean seedling diseases, a total of 3500 isolates were collected. Isolates were identified using the ITS region of rDNA and GIS data was used to find association between species and environmental data.  In 2011, sequence results distinguished a total of 52 Pythium, 2 Phytopythium and 3 Phytophthora spp., with Py. sylvaticum (16%) and Py. oopapillum (12%) being the most frequently recovered.  In 2012, a total of 57 Pythium spp., 7 Phytophthora spp., and 4 Phytopythium were found, with Py. sylvaticum (15%) and Py. heterothallicum (13%) species being most abundant.  Oomycete species composition frequency was noted to fluctuate greatly, and the resulting species diversity was correlated with latitude and temperature gradients. Seed and seedling rot assays were conducted to determine the pathogenicity and aggressiveness of the 83 oomycete species identified in the survey. To further investigate and characterize oomycete communities associated with agricultural systems we are developing markers for amplicon-based community analysis. Amplicon-based community analysis together with our oomycete culture phenotype data (i.e. pathogenicity and aggressiveness) will be a powerful tool to not only understand diversity, but to address questions related to the effects of management decisions such as crop rotation, tillage practices and seed treatments. Improved understanding of the phytobiome and the factors that influence the phytobiome will enable improved disease management and will assist with maximizing yield.