Prevalence of the oomycete species on cotton in Alabama and across the cotton belt

Zachary Noel, Auburn University; Morgan Bragg, Auburn University; Oluwakemisola Olofintila, Auburn University; Kathy Lawrence, Auburn University; Tom Allen, Mississippi State University; Melanie B. Bayles, Oklahoma State University; Kaitlyn Bissonnette, Cotton Incorporated; Travis R. Faske, University of Arkansas System Division of Agriculture; Chase A. Floyd, University of Missouri; Heather M. Kelly, University of Tennessee; Robert C. Kemerait, University of Georgia; Cecelia Monclova-Santana, Texas A&M University; Paul Price, Louisiana State University; Alejandro Rojas, Michigan State University; Ian Small, University of Florida; Terry Spurlock, University of Arkansas System Division of Agriculture; Amanda Strayer-Scherer, Auburn University; Terry A. Wheeler, Texas A&M AgriLife Research; Tessie H. Wilkerson, Mississippi State University

Summary

• A two-year survey was conducted to determine which oomycete species were present in Alabama and which can kill cotton seed.

• Globisporangium irregulare (formerly Pythium irregulare) and Phytophthora nicotianae were among the most frequently isolated species and could kill cotton seed in laboratory tests.

• Pathogens were found in different parts of the state, meaning that pathogenic species may differ from one field to the next.

• Across the cotton belt, G. ultimum (formerly Pythium ultimum) was found, especially in western states like Texas and Oklahoma, but less abundant in the southeastern states.

• These results indicate that farmers should tailor seed treatments by region and pathogen to improve seedling disease management.

Seedling diseases of cotton are caused by true fungi and fungal-like organisms called oomycetes. The true fungi include pathogens like Rhizoctonia solani, Fusarium spp., and Berkeleyomyces rouxiae (formerly Thielaviopsis basicola). The oomycetes that can cause seedling diseases of cotton include Pythium spp. (now some species are called Phytopythium and Globisporangium), and Phytophthora. Losses from seedling diseases range from $30 to $200 million annually (Faske et al. 2022).

Seedling disease symptoms often present as skips in the field, resulting in a poor stand, seedlings that collapse and die shortly after emergence, and stunted plants. Knowing which organisms are causing seedling disease is essential because seed treatments do not work equally well on all pathogen species. Marginal planting conditions, such as cool, wet soil, can favor seedling diseases (Rothrock et al. 2012). Practices such as reduced tillage and seed treatments can alter disease incidence.

Historically, the oomycete species associated with cotton seedling diseases was G. ultimum, with limited reports of other species. However, in other crops, such as soybean and corn, additional oomycete species have been reported to cause seedling diseases (Chilvers et al. 2020; Rojas et al. 2020), which likely means that the number of species capable of causing seedling disease in cotton is under reported. In addition to pathogen identification, knowing where these species occur is vital for optimizing seedling disease management.  

Research Goals

• Identify oomycete species present across the cotton belt that can cause seedling diseases.

• Improve disease management by knowing which oomycete species can cause seedling disease.

The Research

Isolation of oomycetes from cotton seedlings

Thirteen fields in 2021 and 12 in 2022 were sampled across three regions in Alabama (North, Central, and Southern Alabama) in the two-year study. Cotton fields were selected based on historical cotton production and different soil textures, representing four of the six soil lineages in the state. Cotton seedlings expressing symptoms of seedling diseases were collected along with the surrounding soil for a more detailed analysis to determine the species of oomycetes present. Oomycetes were isolated from root samples, and oomycete DNA was extracted from the soil and the sampled oomycetes for identification using molecular tools. Black cotton seed (cotton seed with no seed treatment) was placed onto Petri dishes containing agar with the isolated oomycetes to determine if they could colonize and rot the germinating seed.

The study isolated 36 oomycete species from symptomatic cotton seedlings in Alabama. A Pythium species was isolated from every field sampled. However, G. irregulare was isolated from cotton seedlings in each field surveyed, whereas Phytophthora nicotianae was more likely to be isolated in Northern Alabama, with a few exceptions. However, G. ultimum was not isolated.

When tested in the lab, six species were pathogenic to cotton seed including G. irregulare and Phytophthora nicotianae as well as Pythium deliense, Pythium dissotocum, G. spinosum, G. sylvaticum, and Phytopythium helicoides in less abundance. Therefore, it is likely that there are more oomycetes causing seedling diseases in cotton than G. ultimum, which was historically considered the primary seedling disease pathogen of Globisporangium diseases in cotton.

Different groups of oomycete species were detected across soil textures. For example, fewer oomycete species were isolated from soils with greater sand content typical of southern coastal regions of Alabama. More oomycete species were recovered from soils with a greater percentage of silt, clay, soil organic matter (SOM), and cation exchange capacity (CEC) typical of the Northern Alabama Tennessee Valley region. Thus, more species of oomycetes are likely in soils with greater percentages of silt, clay, organic matter, and calcium availability, which may cause an increased risk of seedling diseases when conditions are favorable. However, the relationship between disease outcomes and the number of oomycete species present requires further studies because some are weak pathogens or nonpathogenic.

Identification of oomycetes from cotton soils in Alabama

The survey results were surprising, given that the most frequently reported pathogen (G. ultimum) was not isolated despite our extensive efforts. Therefore, we used an alternative, molecular-based technique on the soils collected near diseased seedlings. We determined that G. ultimum was present in all soil samples but at low abundance, potentially explaining why it was not isolated in our initial survey of diseased seedlings (Bragg et al. 2024). Furthermore, G. irregulare was identified in every soil sampled in high abundance, consistent with our isolation-based survey. Phytophthora nicotianae was also identified, demonstrating the need for more detailed research on these two species and their role as cotton seedling diseases. Due to the historical significance of G. ultimum, we suspect that under different environmental conditions or in other states, G. ultimum may play essential roles in seedling diseases.

Identification of oomycetes across the cotton belt

We expanded our molecular-based survey of soils to include samples collected across the cotton belt (AR, FL, GA, LA, MO, MS, NC, OK, TN, and TX) to determine the oomycete species present. Some of the most abundant oomycete species present in 2023 and 2024 included G. irregulare and Phytopythium vexans, two species capable of causing disease in our initial survey from Alabama (Bragg et al. 2025). Our results spanning the cotton belt agree with our Alabama survey findings that G. irregulare was abundant and detected in all states surveyed, but interestingly, it was less abundant west of the Mississippi River in states like OK and TX, where G. ultimum was more prevalent. This further demonstrates the need for additional research to understand the role of pathogen species in seedling disease, their geographic distribution, and how environmental factors may influence their prevalence. Our molecular survey of the cotton belt is ongoing, and we anticipate providing additional updates as data are analyzed.

Conclusion

Overall, this research demonstrates that oomycete seed and seedling pathogens can vary between fields or states. Therefore, there is an opportunity to tailor seed treatments for specific regions or fields for targeted management. Our results also demonstrate that several species, previously not reported or minimally reported, are abundant and capable of killing cotton seed. Future research will include relating species abundance to soil profile and environmental information and testing which seed treatments may offer protection for specific species.

References

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Acknowledgments

Authors

Zachary Noel, Auburn University; Morgan Bragg, Auburn University; Oluwakemisola Olofintila, Auburn University; Kathy Lawrence, Auburn University; Tom Allen, Mississippi State University; Melanie B. Bayles, Oklahoma State University; Kaitlyn Bissonnette, Cotton Incorporated; Travis R. Faske, University of Arkansas System Division of Agriculture; Chase A. Floyd, University of Missouri; Heather M. Kelly, University of Tennessee; Robert C. Kemerait, University of Georgia; Cecelia Monclova-Santana, Texas A&M University; Paul Price, Louisiana State University; Alejandro Rojas, Michigan State University; Ian Small, University of Florida; Terry Spurlock, University of Arkansas System Division of Agriculture; Amanda Strayer-Scherer, Auburn University; Terry A. Wheeler, Texas A&M AgriLife Research; and Tessie H. Wilkerson, Mississippi State University.