Diversity and Characterization of Oomycetes Associated with Corn Seedlings in Michigan

Abstract

Corn is a staple feed and biofuel crop with a value close to $3.7 billion dollars for Michigan’s economy. Knowledge about distribution and abundance of seedling pathogens in Michigan corn fields is limited. Here we used a combination of culture-based and next-generation sequencing of soil samples to determine the extent of species associated with diseased corn seedlings and those present in soil. Over 2 years, symptomatic seedlings and associated soil samples were collected from 11 Michigan fields. A total of 170 oomycete cultures were obtained from seedlings using a semiselective medium (CMA-PARPB) and identified using the internal transcribed spacer region. Thirty-three species were isolated, with Pythium inflatum (25%; clade B) and P. sylvaticum (12%; clade F) being the most abundant species. For the amplicon-based approach, the cytochrome oxidase subunit I marker (COI) mitochondrial region was amplified from soil samples and sequenced using Illumina MiSeq. The dominant Pythium clades present in the soil were F, I, D, and B and accounted for at least 75% of the abundance in all locations. Pythium clades F, I, and D were recovered with similar trends with the culture and amplicon approach; however, clade B was highly abundant in plant isolation, but not in soil. The 20 most abundant species were characterized for pathogenicity and fungicide sensitivity. P. irregulare and P. ultimum var. ultimum were the most virulent at both 15 and 20°C. Isolates were tested for their sensitivity to mefenoxam and ethaboxam. Most isolates were sensitive to both chemistries, but P. rostratifingens and P. aff. torulosum were less sensitive to ethaboxam and P. ultimum var. ultimum less sensitive to mefenoxam. The survey and isolate characterization provides a better understanding of seedling and root rot disease of corn and opportunities to improve management of this disease complex.