The Diversity of Oomycetes from Alabama Cotton Soils Using Culture-Independent Methods

Seedling disease management recommendations rely on comprehensive identification of the pathogens. A recent article isolated oomycetes from diseased cotton (Gossypium hirsutum L.) roots to identify the species associated. However, culture-dependent surveys may miss species because of the microbiological medium and work required to isolate and maintain all cultured organisms. Alternatively, culture-independent methods using PCR amplification and high-throughput sequencing can identify species' presence and relative abundance, including obligate pathogens and rare members of communities. We used culture-independent sequencing from the same cotton soils in the culture-based survey to determine the oomycete species in oomycete-containing soils. The results of the two methods were generally similar regarding the species identified. Similar to the culture-based method, Globisporangium irregulare accounted for 24% of the relative abundance and was encountered in all fields sequenced. In contrast, we identified three operational taxonomic units matching Globisporangium ultimum, but they accounted for less than 0.06% of total relative abundance, potentially explaining why it was not isolated from cotton roots in the original survey. Phytophthora nicotianae was identified in soils but not at the concentrations recorded in the culture-based study. The results of this study, combined with the results of the culture-based survey, demonstrate the most comprehensive identification of oomycetes associated with cotton in the cotton belt and the oomycetes related to seedling disease. The combined results will be essential for future research into the specific pathogen species mentioned and stimulate similar research in other states.