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

Authors: LARSEN, LETA - University Of Minnesota; Schlatter, Daniel; NIMPOENO, JASON - University Of Minnesota; HINES-SNIDER, CARLA - Land O'Lakes, Inc; Samac, Deborah - Debby

Submitted to: Phytobiomes Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/4/2023
Publication Date: 12/15/2023
Citation: Larsen, L., Schlatter, D.C., Nimpoeno, J., Hines-Snider, C., Samac, D.A. 2023. Rhizosphere and root community analysis of oomycetes associated with poor alfalfa (Medicago sativa) seedling establishment. Phytobiomes Journal. 7(4):526-537. https://doi.org/10.1094/PBIOMES-02-23-0005-R.
DOI: https://doi.org/10.1094/PBIOMES-02-23-0005-R

Interpretive Summary: Alfalfa stand health and persistence is dependent on rapid and uniform seedling emergence. There are several pathogens that infect alfalfa seedlings and cause a seedling diseases in poorly drained soils. Poor establishment of disease resistant cultivars protected by seed treatments in these soils suggests the presence of additional previously unrecognized pathogens. The entire community of water molds in soil near roots and within roots was cataloged from eight locations with poor seedling establishment. Two well known pathogens causing Aphanomyces root rot and Phytophthora root rot dominated the root and soil communities and several organisms were identified in roots that were not previously known to infect alfalfa but infect crops in rotation with alfalfa. Assays to quantify the Aphanomyces root rot and Phytophthora root rot in field soil samples found that the pathogens were unevenly distributed in the plots but 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 pathogens to help farmers establish productive and long lasting alfalfa stands.

Technical Abstract: 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 is dependent 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 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.