Brief Summary of Minutes of Annual Meeting

The four objectives of the S1083 project were reiterated. The primary discussion of this annual meeting was how to re-focus the efforts of the S1083 technical committee on collaborative activities and away from reporting on individual research programs. Two structural changes were made to facilitate overall continuity: (1) starting this year, all leadership roles will be for a two-year period, and (2) instead of meeting once a year, the group will meet twice a year and explore if one of the meetings can be in-person. The group also identified some short- and medium-term collaborative activities and identified committees responsible for these activities. Yet another concern that was discussed was the size of the technical committee and recruitment of new members. It was decided that once we have outcomes of collaborative activities, we could use the success of these activities to recruit members. Detailed minutes are attached.

The current technical committee has eight members that contribute to the project objectives with each member focusing on 2-3 of the objectives. The research spans several pathogen genera (Verticillium, Fusarium, Meloidogyne, Phytophthora, Rhizoctonia, Colletotrichum fiorinae, Neopestalotiopsis, Xylaria, and Diaporthe), crops (soybean, corn, sweet potato, tomato, strawberry, potato, dry bean), and agricultural systems (conventional production, organic productions, high-tunnel systems).

Short-term outcomes:

Stakeholder-focused outcomes for 2025 included outreach and participatory research. Dr. Benitez Ponce’s team conducted two soil health outreach events delivered to six groups of middle school students in Ohio. Dr. Crandall reached five farms in OH and 18 high tunnel growers in PA, involving 23 farmers on research projects. The outcomes were directly in line with the project milestones defined in the proposal to assess the effect of management practices, and development of outreach material.

Outputs

The outputs of 2025 were directly in line with the project milestones to develop new collection, detection and diagnostic protocols, assess the effect of management practices, update the management of Taproot decline in soybean, conduct data analyses, publish scientific reports and outreach materials, and participate at the APS national and regional meetings,

• Dr. Benitez Ponce’s team developed a manuscript draft on arbuscular mycorrhizal fungi (AMF) in Ohio soils and published a manuscript on crop rotation, cover crops and microbial communities.
• Dr. Thomas-Sharma’s team conducted greenhouse screening of core block varieties for resistance to aerial blight and submitted the data for publication in the 2026 Soybean Variety Yields & Production Practices.
• Dr. Crandall collaborated with the One Health Microbiome Center to represent research on soilborne plant diseases. They also submitted three publications and had two publications accepted.
• Dr. Shanmugam’s team presented two posters at the 89th Annual Mississippi Academy of Sciences Meeting in Biloxi, MS on ‘The role of nitrogen and sulfur fertilization in shaping soybean root associated microbial diversity in soybeans’. Additionally oral and poster presentations were made at the American Society of Microbiology Annual Meeting, Los Angeles, CA on ‘Enhancing soil microbial diversity and nitrogen cycling in Mississippi corn production system’.
• Dr. Rojas’s team presented at Honolulu, HI in Plant Health 2025 on topics of fungicide resistance, development of detection assay for tap root decline, and the impact of temperature on the interaction of cotton seedling disease and root-associated fungal communities. Their team also developed an extension publication on the prevalence of an oomycete species on cotton in Alabama and the cotton belt.

Activities

In 2025 the individual members of the technical committee contributed directly to the project objectives by conducting the following activities:

• For Objective 1, Dr. Rojas’s team characterized the biology, population structure, and functional diversity of soil and seed-borne fungal pathogens. They also evaluated pathogen interactions with beneficial or antagonistic microorganisms under varying environmental conditions, contextualizing disease emergence within whole-system phytobiome dynamics.
• For Objective 2, Dr. Benitez Ponce’s team analyzed datasets of arbuscular mycorrhizal fungi (AMF) recovered from Ohio soils. Dr. Crandall’s team tested how AMF fungi and other biocontrol agents suppress disease in potato. They used amplicon-based sequencing to follow the succession of the microbiome, assess the health and yield of soybean in a high microbiome and low microbiome environments, and to detect and model potential soilborne pathogens that are aerially dispersed during dust storms. They studied microbial activity in the rhizosphere of roots to understand their movement from soil into roots. Dr. Ownley’s team conducted shotgun metagenomic analyses to resolve the microbial mechanisms underlying differences between sorghum–sudangrass–based and wheat-based anaerobic soil disinfestation (ASD) to improve plant health. Dr. Rojas’s team applied integrated culturing, targeted amplicon sequencing, and shotgun metagenomic approaches to assess spatial and temporal variation in soil and root associated microbial communities across soybean and dry bean production systems. These analyses were focused on seedling health, and fungicide or seed treatment responses.  
• For Objective 3, Dr. Thomas-Sharma’s team screened commercial soybean varieties grown in Louisiana for resistance to the soil borne pathogen Rhizoctonia solani AG 1-IA that causes aerial blight on soybean. Dr. Crandall’s team and collaborators tested the efficacy of soil steaming disinfection and ASD, to suppress soilborne pathogens of tomato in high tunnels in PA and OH. Dr. Ownley’s group assessed the effects of microbial biostimulants, compared with an untreated control, on plant growth parameters of tomato seedlings grown under low-nutrient conditions.
• For Objective 4, Dr. Benitez Ponce’s team continued training undergraduate students and visiting scholars in soil fungi and microbial antagonisms and delivered outreach events on soil health. Dr. Thomas-Sharma’s team trained a research associate and undergraduate students and made information from the aerial blight screening available to growers prior to planting. Dr. Crandall trained a post-doctoral fellow to conduct studies on soilborne disease and publish results. Dr. Ownley’s team trained graduate students in soilborne plant pathology and disease ecology through hands-on diagnostic investigations of diseased strawberry plants collected from grower fields. The first reports and associated findings from this training are being developed into peer-reviewed publications that will support improved strawberry disease management in Tennessee and the surrounding region.

Since this group includes members working on diverse crops, pathogens, and agricultural systems, they have had a direct impact on stakeholders through their research and extension. In the long-term, the goal of S1083 is to develop collaborative activities that will have multi-state impact. Here we list the intended potential short, mid, and long-term outcomes and impacts that are built on previous members’ grant / funding successes, and current collaborative efforts. Foremost are the intended stakeholder's impacts which are a long-term extension of the activities for this past period through four member-driven initiatives. Here we list our intended activities and milestones, which were discussed and developed as a collaborative group in 2025 and will be the focus moving forward.

1. Biostimulants whitepaper development. Project members (Drs. Ownley, Shanmugam) will synthesize and consolidate current knowledge on biostimulant science and management into a publicly available whitepaper. The document will integrate research findings and practical resources/best practices to support decision-making by both researchers and growers and will be designed to reach a broad audience.
2. Extension article on aerial blight of soybean. Project members (Drs. Thomas-Sharma, Rojas, Crandall) will collaborate to develop an Extension article documenting regional challenges and management practices for soybean aerial blight across the southern (Louisiana), Midwestern (Michigan), and Mid-Atlantic (Pennsylvania) U.S. The article will compare best management practices by production region and will be disseminated through Extension outlets at Louisiana State University, Michigan State University, and The Pennsylvania State University, and common stakeholder websites such as Crop Protection Network.
3. Soilborne disease review article. Project members (Drs. Benitez Ponce, Ownley, Shanmugam, Thomas-Sharma, Crandall, Rojas) will prepare a comprehensive review examining soilborne disease epidemiology across spatial scales, from plant roots to regional cropping systems. The review will highlight case studies spanning major pathogen groups, including fungi, bacteria, oomycetes, nematodes, and viruses, to inform integrated disease management strategies.
4. Soilborne disease curriculum and educational content development. Project members (Drs. Ownley, Benitez Ponce, Shanmugam, Thomas-Sharma, Rojas) will develop educational materials on soilborne diseases, including case studies, pathogen biology, diversity, and disease cycles. The content will incorporate active-learning approaches and will be designed for adoption at multiple educational levels (pre-college and undergraduate), benefiting educators and students.

Milestones

Milestone 1: Completion and dissemination of science-based written outputs (short-term): Completion, submission, and publication of the biostimulants whitepaper, soilborne disease review article, and soybean aerial blight Extension article, with materials made publicly available to researchers, Extension personnel, and growers.

Milestone 2: Cross-institutional extension and outreach nationwide (mid-term): Distribution of growing regionally relevant Extension content on soybean aerial blight through Extension platforms at three land-grant universities representing distinct U.S. soy production regions.

Milestone 3: Development of adoptable educational resources on soilborne diseases (long-term): Creation of active-learning soilborne disease curriculum materials suitable for use across multiple institutions, educational levels and have the potential to be adapted for workshops, classrooms, or for agricultural field days.

Dr. Rojas

Integrated soybean seed health management – a Diaporthe Complex, USDA–NIFA–AFRI, 05/2026 – 04/2029, Principal Investigator (Total Costs: $889,222)

Strengthening regional plant pathogen biosurveillance through improved diagnostics and sample processing for environmental matrices, USDA–NIFA–AFRI, 06/2026 – 05/2029,  Principal Investigator (Total Costs: $670,000)

CAREER: Fungal lifestyle transitions - understanding the endophyte–pathogen continuum, National Science Foundation (NSF), 03/2026 – 02/2031, Principal Investigator (Total Costs: $978,202)

Dr. Thomas-Sharma

When there are three to tango: Characterizing the interplay of Rhizoctonia solani AG1-IA on two rotational hosts (soybean, rice) to improve disease management’, USDA-NIFA-AFRI, Principle Investigator.

Screening of Soybean Core block varieties for resistance to aerial blight to the Louisiana Soybean and Grain Research and Promotion Board, Principle Investigator.

Dr. Ownley

Delivering Integrated Solutions for Soilborne Pests and Pathogens in High Tunnel Systems, USDA-NIFA-SCRI

Dr. Shanmugam

Integrating double legume cover cropping with sunn hemp and biostimulants to enhance nitrogen cycling, Rhizobium activity, and soybean productivity. Principal Investigator. Mississippi Soybean Promotion Board.

Harnessing regenerative practices for soil microbial resilience and weed suppression. USDA-NIFA, Principal Investigator.

Biochar–herbicide–microbe interactions to enhance soil health and weed management in soybean systems. Co–Principal Investigator. USDA-NIFA.

Accelerating Palmer amaranth seed decay: Roles of soil microbiome and physicochemical factors. Co–Principal Investigator. USDA-NIFA.

Dr. Crandall

These grants were submitted and awarded to students in my soilborne disease lab group:

Larson, E. (2025). Watts Endowment for Potato Research, Department of Plant Pathology and Environmental Microbiology. “Managing Verticillium dahliae in potato fields, testing the efficacy of steam disinfestation and a biocontrol fungus.” Pennsylvania State University, University Park, PA, USA. 

Weikel, J. (2025). College of Agricultural Sciences (CAS), Summer Undergraduate Student Research Grant, Post-doctoral Mentor. “An investigation into Verticillium nonalfalfae’s impact on Pennsylvania trees and forest soil.” Pennsylvania State University, University Park, PA, USA. 

Dr. Benitez Ponce

Frey, T; Shah D; Lindsey L, Sprunger C, Lopez Nicora H, Benitez Ponce MS. 2025.Crop rotation and a rye cover crop have minor impacts on soil health, microbial communities, and soybean yield in Ohio. Frontiers of Soil Science. 5: https://doi.org/10.3389/fsoil.2025.1535734.

Dr. Shanmugam

Chinthalapudi, D. P., Narayana, N. K., Poudel, S., Brooks, J. P., Shanmugam, S. G., and Bheemanahalli, R. 2025. Drought-induced shifts in cowpea rhizoplane bacterial communities across different vegetative and reproductive stages. Plant Stress https://doi.org/10.1016/j.stress.2025.100915

Chinthalapudi, D. P., Kingery, W., and Shanmugam, S. G. 2025. A review of plant-mediated and fertilization-induced shifts in ammonia oxidizers: Implications for nitrogen cycling in agroecosystems. Land 14(6):1182. https://doi.org/10.3390/land14061182

Chinthalapudi, D. P., Narayana, N. K., Nekkalapudi, L., Sinha, N., and Shanmugam, S. G. 2026. Soil microbial diversity, stability, and function are enhanced by cover cropping: A machine learning-based pooled analysis of Mississippi agroecosystems. Sci. Total Environ. 1014:181365. https://doi.org/10.1016/j.scitotenv.2026.181365

Ginnan, N., Crandall, S.G. (Co-Author, 40%), Imchen, M., Dini Andreote, F., Miyashiro, T., Singh, V., Ganda, E., & Bordenstein, S. (2025). Ecologically expanding the One Health framework to unify the microbiome sciences. mBio 16(6). DOI: 10.1128/mbio.03147-24.

Dr. Crandall

Harris, J. E., Bledsoe, R. B., Guha, S., Omari, H., Crandall, S. G., Burghardt, L. T., et al. (2025). The activity of soil microbial taxa in the rhizosphere predicts the success of root colonization. mSystems, 10(9), e00458‑25. https://doi.org/10.1128/msystems.00458-25

Ali, M. U. (Primary Author, Visiting Scholar), Muhammad, A., Ahmad, H., Crandall, S.G. (Co-Author, 5%), & Rajput, N. A. The effect of desert plant extracts for managing Phytophthora capsici, the cause of root rot disease in chili pepper. Plant Disease. (pp. 1-24). [Submitted 2025].  Peer Reviewed.

Calderón, R., Pavilck, R., Crandall, S.G. (Co-Author, 20%), Mahowald, N., & Gold, K. M. Global risk of Fusarium wilt in crops increases under climate change. Nature Climate Change. (pp. 1-32). [Submitted 2025].  Peer Reviewed.

May, S. R., Luisa, P. M., Laura, M. A., Crandall, S.G. (Co-Author, 20%), & Woodhall, J. W. Verticillium wilt of potato: a diagnostic guide. Plant Health Progress. (pp. 1-42). [Submitted 2025].  Peer Reviewed.

Dr. Rojas

Hatlen, R. J., Gil, J., Rojas, J. A., & Miles, T. D. (2025). A draft genome assembly for Diaporthe humulicola, the causal agent of halo blight of hop. PhytoFrontiers. Advance online publication.

Hatlen, R. J., Rojas, J. A., & Miles, T. D. (2025). Diversity and structure of Diaporthe humulicola populations from eastern North America. Phytopathology. Advance online publication.

Hatlen, R. J., Szymanski, S., Adair, N., Fan, Q., Panwar, P., Sysak, R., Miles, L. A., Higgins, D., Rojas, J. A., Gent, D. H., et al. (2025). Development of a translation elongation factor 1 alpha (TEF)–based TaqMan qPCR assay for Diaporthe humulicola, the causal agent of halo blight of hop. Plant Disease. Advance online publication.

Alnasrawi, A., Li, J., Sanadhya, P., Rojas, J. A., & Goggin, F. L. (2025). Optimizing conditions for Bacillus subtilis ectopic gene expression and delivery via seed treatment. Plants, 14(20), 3184. https://doi.org/10.3390/plants14203184

Rupe, J. C., da Silva, M. P., Rojas, J. A., Holland, R., & Zaia, R. (2025). Estimating the potential for soybean seed infection by Diaporthe spp. and Cercospora spp. at physiological maturity. PhytoFrontiers. Advance online publication.

Segalin, S. R., Holland, R. T., Spurlock, T. N., Rojas, J. A., & Rupe, J. C. (2025). Response of the soybean seed borne pathogens Diaporthe spp. and Cercospora spp. to foliar fungicides in Arkansas. PhytoFrontiers. Advance online publication.

Noel, Z., Bragg, M., Olofintila, O., Lawrence, K., Allen, T., Bayles, M. B., Bissonnette, K., Faske, T. R., Floyd, C. A., Kelly, H. M., Kemerait, R. C., Monclova-Santana, C., Price, P., Rojas, A., Small, I., Spurlock, T., Strayer-Scherer, A., Wheeler, T. A., & Wilkerson, T. H. (2025, March 13). Prevalence of the oomycete species on cotton in Alabama and across the cotton belt (CPN-5017). Crop Protection Network. https://doi.org/10.31274/cpn-20250317-0.