Rhizosphere and root community analysis of oomycetes associated with poor alfalfa (Medicago sativa) seedling establishment

Alfalfa (Medicago sativa) seeds planted in cold, wet soil are prone to seed rot, pre- and post-emergence damping-off, and seedling root rot. These diseases reduce initial stand density and impact forage yields and winter survival when root systems are stunted by infection. Successful management depends on identifying the causal agents, but isolation in pure culture is time consuming and may fail to recover slow growing organisms or those requiring special growth conditions. Here, the oomycetes in rhizosphere soil and root endospheres from eight locations with a history of poor alfalfa establishment were identified by amplicon sequence analysis. Seedling bioassays were done with bulk soil and quantitative PCR assays were done using DNA from bulk soil, rhizosphere soil, and the root endosphere for Aphanomyces euteiches, Phytophthora medicaginis, Pythium irregulare, P. sylvaticum, and P. ultimum var. ultimum. In the endosphere and rhizosphere, A. euteiches was the dominant taxon, followed by Phytophthora medicaginis and P. sansomeana, a broad host range pathogen not previously known to infect alfalfa. Pythium inflatum and Globisporangium perplexum were also significantly over-represented in roots at five of the eight locations, indicating that these taxa are commonly enriched in alfalfa roots, but had not previously been identified as alfalfa pathogens. The qPCR assays of bulk soil showed that A. euteiches and P. medicaginis were unevenly distributed in the plots and low concentrations of the pathogens led to high levels of root rot disease. These results support development of cultivars with high levels of resistance to the most common oomycete pathogens.