Characterizing the diversity of oomycetes associated with diseased cotton seedlings in Alabama

Abstract

Many oomycete species are associated with the seedlings of crops, including upland cotton (Gossypium hirsutum L.), leading to annual threats. The diversity of oomycete species in Alabama needs to be better understood since the last survey of oomycetes associated with cotton in Alabama was twenty years ago, before significant updates to taxonomy and improvements in identification of oomycetes using molecular tools. Our current study aimed to identify oomycetes associated with Alabama cotton seedlings, correlate diversity with soil edaphic factors, and assess virulence toward cotton seed. Thirty symptomatic cotton seedlings were collected independently from 25 fields in 2021 and 2022 two to four weeks after planting. Oomycetes were isolated by plating root sections onto a semi-selective medium. The internal transcribed spacer region was sequenced to identify the resulting isolates. A seed virulence assay was conducted in vitro to verify pathogenicity. Three hundred and forty-seven oomycete isolates were obtained representing 36 species. Northern Alabama soils had the richest oomycete communities and a greater silt and clay concentration than sandier soils in the central and southern coastal plains. Globisporangium irregulare and Phytophthora nicotianae were consistently recovered from cotton roots in both years. Globisporangium irregulare was pathogenic and recovered from all Alabama regions, whereas P. nicotianae was pathogenic but recovered primarily in areas with lower sand content in northern Alabama. Many oomycete species have not been previously reported in Alabama or the southeastern United States. Altogether, this knowledge will help facilitate effective management strategies for cotton seedling diseases caused by oomycetes in Alabama and the U.S.