S1083: Ecological and genetic diversity of soilborne pathogens and indigenous microflora

(Multistate Research Project)

Status: Active

Project Menu

SAES-422 Reports

Annual/Termination Reports:

[01/23/2024]

Date of Annual Report: 01/23/2024

Report Information

Annual Meeting Dates: 11/15/2023 - 11/15/2023
Period the Report Covers: 10/01/2022 - 09/30/2023

Participants

In attendance:
• Nathan Slaton – Advisor – University of Arkansas
• Sean Toporek – South Dakota State
• Sydney Everhart - U Connecticut
• Sara Thomas-Sharma – Louisiana State U
• Soledad Benitez – Ohio State U
• Mia Maltz - U Connecticut
• Sharifa Crandall – Pennsylvania State U
• Terry Spurlock – University of Arkansas
• Alejandro Rojas – Michigan State University

Participants Attachment:

S1083_Agenda_BusinessMeeting_2023_minutes.docx

Brief Summary of Minutes

In attendance:

Nathan Slaton – Advisor – University of Arkansas

Sean Toporek – South Dakota State

Sydney Everhart - U Connecticut

Sara Thomas-Sharma – Louisiana State U

Soledad Benitez – Ohio State U

Mia Maltz - U Connecticut

Sharifa Crandall – Pennsylvania State U

Terry Spurlock – University of Arkansas

Alejandro Rojas – Michigan State University

Election of officer/secretary for 2024

The chair and vice chair were nominated by Sydney Everhart. Sharifa was nominated as chair and Sara was nominated as vice-chair. Both accepted the nomination and were selected.

Chair: Sharifa Crandall

Vice-chair: Sara Thomas-Sharma

Planning for the meeting either online or in conjunction with a professional society meeting is ok, but participation should be encouraged, to strengthen collaboration between participants. The goal is to enhance collaboration and support members, especially those who are new members and assistant professors.

Opportunities to collaborate:

Review paper: “Soilborne plant disease across time and space: the next frontier in integrative research”. The paper's final draft should be shared with the full group in the next month.

Minutes Attachment:

S1083_Agenda_BusinessMeeting_2023_minutes.docx

Accomplishments

1. ACCOMPLISHMENTS Dr. Sharifa Crandall – Penn State  Soil Ecology and Desinfestation (Crandall Lab)  In 2023, we initiated research on a project that is line with both multi-state hatch objectives, namely to (1) evaluate the biology and diversity of soilborne pathogens in Pennsylvania and Ohio, (2) to conduct efficacy trials to assess which combination of steaming disinfection and ASD methods effectively suppress a suite of soilborne pathogens that devastate tomato crops in high tunnel systems.  Briefly, pathogens that disperse through the soil are a significant problem for organic farmers, especially when they infect vegetables during high tunnel production in the Northeastern and Midwestern United States. Steaming the soil to high temperatures and Anaerobic Soil Disinfestation (ASD) are two disease management methods that are chemical-free and have the potential to kill problematic soilborne pathogens without using synthetic fungicides or fertilizers. In 2023, my Soilborne Disease Ecology lab group at Penn State in collaboration with the USDA-ARS station in Wooster, OH (Testen Lab), prepared for and set into motion planning for efficacy trials. These trials will compare how well soil steaming and ASD suppresses soilborne diseases of vegetables with a focus on high tunnel tomatoes. Because this research started in 2023, we have limited accomplishments to report thus far. In subsequent years, we will: determine soil microbial community recovery (composition/diversity) after steaming and/or ASD and impacts on plant health, and try to understand the factors that affect farmers' willingness to adopt sustainable soilborne disease management practices. We aim to share best practices with organic growers from these two promising, innovative organic farming practices. We will eventually disseminate results at farmer conferences and meetings, through peer-reviewed publications, extension materials, factsheets, and webinars. The target audiences will include partnering organically certified farmers, those who are interested in or who are in transition to organic production, industry partners, federal and academic scientists, and the public at large.   Short-term Outcomes: This research will inform management practices for farmers with high tunnels in Ohio and Pennsylvania, especially those that are in transition to organic or those that are currently certified. A cost-benefit analysis will be made available for the adoption of technological practices such as soil steaming disinfection and ASD. Moreover, another short-term outcome will be an increased awareness among growers of phytosanitary methods and their utility for high tunnel agricultural systems. Finally, growers will receive extension educational support and networking opportunities to share best practices at workshops and conferences.   Outputs: In 2023, we hired a post-doc and graduate student for this project. In the future, at least 1 more graduate student will be hired and mentored jointly by the PD and Co-PD. In years 2 onward, we expect an output of at least 2 peer-reviewed research articles and at least 2 extension factsheets or other form of outreach materials. At least 1-2 exhibits per year will be presented at Agricultural Progress Days held in August at Penn State to showcase ongoing projects to vegetable growers. Finally, at least 3-4 stakeholder workshops will be given over the duration of the project and/or webinars on suppressing soilborne pathogens through soil steaming and ASD.   Activities: In 2023, we planned obj. 1 (see milestones below) which involved initial on-station experimental set-up and we obtained large equipment for the trials (e.g., field steaming engine). Personnel were trained on how to use this equipment. The graduate student started their Master’s degree program, began a literature search and began creating inoculum for the soilborne pathogens in the lab for the trials.   Milestones: Milestones broadly for this project are to 1) set up and conduct on-station efficacy trials at the USDA-ARS in year 1-2 (obj.1); 2) measure the diversity of soil fungi post-soilborne pathogen suppression (steaming/ASD) on-station and on partnering organic farms in years 1-4 (obj.2), and 3) assess the willingness of vegetable high tunnel growers to adopt these innovations and the barriers to do so in years 2-5 (obj. 3). In 2023, we planned obj.1 which involved initial on-station experimental set-up and obtained and trained personnel on large equipment for the trials (e.g., field steaming engine). The graduate student started their program and began researching information about suppression of soilborne pathogens on tomato and worked in the lab to start to create inoculum for the soilborne pathogens on-station trials. Target pathogens were: Pseudopyrenochaeta lycopersici, C. coccodes, V. dahliae, Fusarium oxysporium f. sp. lycopersici, Phytophthora spp. and the nematode M. hapla.   Dr. Soledad Benitez – Ohio State University   Research in the Benitez Ponce Laboratory at OSU is focused on understanding the relationships between agricultural production practices, crop health, and the agricultural microbiome. For this project, the emphasis is on corn and soybean production systems, practices that promote soil health through crop diversification, and understanding interactions between microorganisms in agricultural systems. Accomplishments are presented below by Objective.   Objective 1:   Short-term outcomes: - Characterization of fungal communities in soils across the state of Ohio - Description of relationships between fungal communities’ distribution, soil properties, and abundance of soybean cyst nematodes on farms.   Outputs: - A graduate student-led manuscript ready for submission - One graduate student grant (USD 5,000) - Two faculty grants (USD 116,000) - Additional training of one undergraduate student - One international talk, two national oral presentations, three conference presentations - One extension presentation   Activities: In 2022-2023, we completed the data analysis and manuscript draft on the relationships between communities of fungi in soils across the state of Ohio and the abundance of soybean cyst nematodes (SCN). The manuscripts present three data types: fungal communities, as studied from long-read amplicon metabarcoding of the ribosomal region; edaphic properties, and SCN abundance, as estimated from the number of eggs recovered from 100 cm3 of soil. SCN is the most economically damaging disease of soybean in the continental USA. Being soilborne, its early detection is challenging, and often its presence is confirmed once yields have been compromised. Current management of SCN relies on crop rotations, resistance varieties and limited use of nematicides. From other work, SCN is known to interact with fungi in the soil, for example, synergism has been observed with the fungus Fusarium virguliforme (causal agent of sudden death syndrome of soybean); as well as be parasitized by certain groups of soil fungi. From this work, we learned that, soil properties in Ohio differ by region (previously described by other authors); that the communities of fungi recovered from samples of the same region are more similar to each other. That, regardless of influence by region (and soil properties), the communities of fungi, and the interactions thereof, are influenced by the abundance of SCN in the soil. Lastly, we hypothesize, that in the presence of SCN, the communities of fungi adapt to either the nematode, or the effects that the nematode causes to the plant, and hence selects for a subset of fungi. This work sets the foundation for developing mechanistic hypotheses related to fungi:SCN interactions in soybean production systems.   Milestones: To generate hypotheses and develop a mechanistic understanding of the plant and soil drivers that result in the selection of fungi when SCN is at higher abundance. To search for potential fungi as targets of biological control agents against SCN.   Objective 2: Short-term outcomes: - Analysis of arbuscular mycorrhizal fungal (AMF) communities in Ohio soils, and their response to rotation and cover crop management - Adapt bioinformatic pipelines for the analysis of long-read amplicon metabarcoding for the study of AMF in soils Outputs: - 1 Peer reviewed manuscript - Sequence data and taxonomic description of AMF recovered from Ohio soils - Training in multivariate statistical analysis of a post-doctoral research associate Activities: The successful application of biological control products and other microbial inoculants is often dependent on environmental variables and management practices, as complex interactions often occur in the plant-soil interface. The Benitez Lab is continuing research on beneficial fungi, with emphasis on the arbuscular mycorrhizal fungi (AM). During the 2022-2023 period our team worked on the analysis of AMF sequences recovered from soils across Ohio. Specifically, we worked with two sets of samples. First, AMF were recovered from soils of a rotation/cover crop experiment. This experiment was established in 2012 to contrast corn-soybean with corn-soybean-wheat rotations at two OSU research stations. Further, in 2020, cover crop treatments, including a corn-rye-soybean sequence were added as a split plot. We analyzed the effect of cover crop, rotation and location on the communities of AMF from soils collected in 2021 and 2022. From this we learned that the communities of AMF showed different responses than the communities of total fungi (as analyzed by metabarcoding of the ITS region). Specifically, for data from 2021, AMF were less influenced by sampling location, and had greater response to the rye cover crop. Further, the networks of cooccurrence of AMF fungi across rotations were slightly more connected, with individual AMF taxa showing differential associations between rotations, and different hubs recovered from the plots under the rye treatment than those with no rye history. No significant effects were observed for the 2022 data.  Second, a subset of 28 soil samples (from Objective 1) were used to characterize AMF communities in Ohio soils. The samples used in this experiment correspond to samples that cover the different soil regions in the state, spread through 13 counties. The sequencing and sequence processing for these samples have been completed. Further analysis of this data will include characterization of which soil properties, as well as other fungal community data, are influencing the structure of AMF. In addition we will determine the most common groups of AMF in Ohio and could potentially use this information to differentiate between natural inoculum colonizing soybean and commercial inoculants applied in a production setting.   Milestones: - To describe relationships between communities of AMF in Ohio soils, both in production settings (on-farm research) and experimental research stations.   Dr. Terry Spurlock – University of Arkansas   <ul> <li>Short-term Outcomes: My laboratory identified varieties susceptible to soybean taproot decline, caused by the fungus Xylaria necrophora, and a few that may have some tolerance. We also established an in-furrow fungicide recommendation for soybean taproot decline that will help to management the seedling disease caused by necrophora.</li> <li>Outputs: Disease management recommendations were presented at county and regional production and scientific meetings throughout the year. The regional (county-level) distribution of soybean taproot decline was updated to include observations of severe and yield limiting disease in the northeastern part of Arkansas, an area where this disease had not been seen before.</li> <li>Activities: My laboratory had over 60 individual field trials in crop year 2023. Many of these dealt with economically important soil-borne disease issues impacting soybean, cotton, corn, and rice. In 2023, I had 27 publications (2 peer reviewed journal articles and 25 research and technical reports, extension publications, conference proceedings, and blog articles), some of which dealt with management of soil-borne disease issues.</li> <li>Milestones: A multi-state project was submitted and funded by the United Soybean Board to continue important work on best management practices for taproot decline. The funding for this project was discontinued after one field season, so a similar proposal was submitted to the Mid-south Soybean Promotion Board.</li> </ul>   Dr. Alejandro Rojas – University of Arkansas   The Soilborne Pathology and Ecology lab at University of Arkansas has been focused on addressing challenges in three main areas: (1) Evaluation of chemical and biological agents for control of soilborne pathogens, (2) soybean seed quality issues and their management, and (3) ecology of soilborne pathogens in horticultural and field crops. Within this framework the lab has contributed with the following activities and outputs: Objective 1 <ul> <li>Short-term Outcomes: <ul> <li>Developed a qPCR diagnostic to evaluate soil and plant samples infested with Xylaria necrophora, and currently we are processing three year’s worth of samples that represent field trails looking cover crop practices and disease development within a season.</li> <li>Conducted a field trial to monitor the epidemiology and biology of Xylaria necrophora adopting new technologies such as remote and short-distance sensing to study disease progression</li> <li>145 isolates of Rhizoctonia solani AG1-1A from rice (Sheath blight) and soybean (Aerial blight) were sequenced for genetic diversity analysis</li> </ul> </li> </ul>   <ul> <li>Outputs: <ul> <li>One oral and one poster presentation at an international scientific conference</li> <li>One student poster presentations at national conference (Plant Health 2023)</li> <li>One student poster presentation at regional conference</li> <li>Two invited talks at extension meetings</li> </ul> </li> </ul>   <ul> <li>Activities:</li> </ul> In 2022-2023, In we have conducted field trial focused on understanding the epidemiology of Taproot decline caused by X. necrophora.  We have used a combined approach to monitor the disease non-destructively and destructively collecting data using remote and short-distance sensing approaches.  Soil and plant samples were collected for four physiological stages.  We are currently processing samples and using the qPCR developed for quantifying and evaluating the progression of X. necrophora under the three cultivars with high susceptibility to tolerant responses. <ul> <li>Isolates of Rhizoctonia solani have been collected in Arkansas and received from collaborators in the Southern US for genotyping and population genomics analyses. As part of the development, we are phenotypically characterizing those isolates for growth rates and tolerance to fungicide.</li> </ul>   <ul> <li>Milestones:</li> <li>Understand the biology and epidemiology of necrophora for the development of better management practices</li> <li>Characterize the genetic diversity of soilborne pathogens, especially Rhizoctonia solani AG1-1A, and the implications on the selection of plant-resistant material</li> <li>Implement non-destructive technologies to monitor the effect of soilborne diseases on hosts physiology and performance</li> </ul>     Objective 2 <ul> <li>Short-term Outcomes: <ul> <li>Generated two years of fungal and bacterial diversity data for a corn-soybean and cover crop rotation system, a total of 160 samples were processed for amplicon data</li> <li>A long-term field trial was established to monitor the effect of cover crop on the production of strawberries under plasticulture</li> </ul> </li> </ul>   <ul> <li>Outputs: <ul> <li>An invited presentation to an international conference: International Congress of Plant Pathology 2023</li> <li>One student poster presentation at regional conference</li> <li>Train and mentored an REU student from minority serving institution</li> </ul> </li> </ul>   <ul> <li>Activities: <ul> <li>In 2023, we established a collection of bacteria and fungi associated with corn under a cover crop rotation system and we are currently analyzing data for microbiome to determine key players in plant responses. The study will be continued focusing on sampling during the cover crop and at the seedling stage.</li> <li>In collaboration with Horticulture dept. at University of Arkansas, we concluded a funded grant through USDA CARE program focused on the management of pathogens in hydroponic systems.</li> <li>In collaboration with Horticulture dept. at University of Arkansas, we finished a study focused on effect of chemigation for the management of soilborne pathogens in strawberry grown in plasticulture. A new study was established to determine the role of cover crops on soil microbial diversity and disease management.</li> </ul> </li> </ul>   <ul> <li>Milestones: <ul> <li>In collaboration with Horticulture dept. at University of Arkansas, we will continue the monitoring of soilborne pathogens and evaluating the effects on management practices on the soil microbial diversity</li> <li>We will continue in lab assays and field trials to monitor the efficacy of chemical products to control soilborne plant pathogens</li> </ul> </li> </ul> 2. IMPACTS (No character limit) Activities: <ul> <li>(Benitez lab) Training of one PhD student, one undergraduate researcher and two research associates.</li> <li>(Benitez lab) Results have been presented through multiple venues, including scientific conferences, extension presentations, and meetings with growers.</li> <li>(Spurlock lab) - a new product brought to market by FMC was evaluated in on-farm trials as well as traditional replicated small plot research on experiment stations in 2021, 2022 and 2023. The product was determined to cause phytotoxicity in fields where corn was planted relatively early by AR standards.  Efficacy against both soilborne and foliar diseases were inconclusive in all years. Due to the phytotoxicity issue, the label was re-written, and growers were advised to discontinue placing the product in the seed furrow but rather at least 0.5 inches away from the seed in a 2x2 application.  This information was repeatedly extended by FMC and Extension.  As a result, I do not have any reports of phytotoxicity where this product was applied in 2023.  Our project evaluating the impacts of this product was funded by the Arkansas Corn and Grain sorghum Promotion Board. </li> <li>(Rojas lab) Training of three PhD students, two Masters students and four undergraduate students. One PhD student defended and graduated.</li> </ul>   Milestones: <ul> <li>To characterize variability in fungal communities in corn and soybean production systems</li> <li>To identify groups of fungi that could potentially be beneficial to soybean growth and soil health</li> <li>To explain relationships between different groups of microorganisms in the soil environment</li> <li>Develop diagnostic assays and markers to monitor pathogen specific populations during the crop growth season and monitor their effect on plant health</li> <li></li> </ul>   Indicators: <ul> <li> Adoption of crop diversification practices that promote soil and plant health</li> <li>Development of microbial markers as indicators of soil health</li> <li>Description of parameters that enrich for specific fungal populations in soils</li> <li>Development of diagnostic tools to monitor soilborne pathogens</li> </ul>

Publications

Peer-reviewed manuscripts: Crandall, S.G. (Primary Author), Miles, A., Chung, T. Cloutier, M., Garcia-Rodriguez, R., Schweigkofler, W., & Couradeau, E. (2023). Temporal and spatial dynamics of bacterial and fungal microbiomes in nursery soils post-steam sterilization. PhytoFrontiers. https://doi.org/10.1094/PHYTOFR-07-22-0071-R.  Frey T, Huo D, Medina Lopez M, Ritter BC, Lindsey L, Benitez Ponce MS. Fungal communities associated with corn in a diverse long-term crop rotation in Ohio. PhytoFrontiersTM 2023. Hamilton R, Jacobs JL, McCoy AG, Kelly HM, Bradley C, Malvick D, Rojas JA, Chilvers MI. Multistate sensitivity monitoring of Fusarium virguliforme to the SDHI fungicides fluopyram and pydiflumetofen in the United States. Plant Disease. 2023 Dec 21(ja). Helms KM, Dickson RW, Bertucci MB, Rojas AA, Gibson KE. Metal Micronutrient and Silicon Concentration Effects on Growth and Susceptibility to Pythium Root Rot for Hydroponic Lettuce (Lactuca sativa). Horticulturae. 2023; 9(6):670. https://doi.org/10.3390/horticulturae9060670 Larson, E. (Post-doctoral Scholar) & Crandall, S.G. (Corresponding Author). (2023). Recovery of the soil fungal microbiome after steam disinfection to manage the plant pathogen Fusarium solani. Frontiers in Plant Science. Sec. Plant Pathogen Interactions. 14: 1-14. https://doi.org/10.3389/fpls.2023.1128518. Shrestha, B., Ward, B., Allen, T., Da Silva, E., Zulli, H., Dunford, W., Doyle, V., Bradley, C., Buckley, B., Chen, P., Clubb, M., Kelly, H., Koebernick, J., Padgett, G., Rupe, J., Sikora, E., Spurlock, T. N., Thomas-Sharma, S., Tolbert, A., Gen Zhou, X., Price, P. (2023). Characterization of QoI-fungicide resistance in Cercospora isolates associated with Cercospora leaf blight of soybean from the southern United States. Plant Disease. <a href="https://doi.org/10.1094/pdis-03-23-0588-re">https://doi.org/10.1094/pdis-03-23-0588-re</a> Mohan, K., Kontz, B., Allen, T., Bergstrom, G., Bissonette, K., Bonkowski, J., Bradley, C., Buck, J., Chilvers, M., Dorrance, A., Giesler, L., Kelly, H., Koehler, A., Lopez-Nicora, H., Mangel, D., Markell, S., Mueller, D., Price, P., Rojas, A., Shires, M., Smith, D., Spurlock, T. N., Webster, R., Wise, K., Yabwalo, D., Mathew, F. (2023). Variation in Isolate Virulence and Accession Resistance Associated with Diaporthe aspalathi, D. caulivora, and D. longicolla in Soybean. Plant Health Progress. <a href="https://doi.org/10.1094/PHP-04-23-0041-RS">https://doi.org/10.1094/PHP-04-23-0041-RS</a> Swenie RA, Looney BP, Ke YH, Alejandro Rojas J, Cubeta MA, Langer GJ, Vilgalys R, Brandon Matheny P. PacBio high‐throughput multi‐locus sequencing reveals high genetic diversity in mushroom‐forming fungi. Molecular Ecology Resources. 2024 Jan;24(1):e13885.   Conference presentations: Melanie Medina López, Timothy I. Ralston, Horacio D. Lopez-Nicora, and Soledad Benitez Ponce. Soybean cyst nematode (SCN) is associated with changes in fungal community composition in the agricultural soils of Ohio. ASM Microbe 2023. Houston, TX. June 2023. Melanie Medina López. Soil dwelling nematodes as plant allies and adversaries. PPGSA Spring Symposium. Wooster, OH. May 2023. Frey, T.S., D. Shah, L. Taylor, L. Lindsey, C. Sprunger, M.S. Benitez Ponce. Soybean yield, soil health and their relationships to microbial communities in rotations and a rye cover crop. American Phytopathological Society. August 2023, Denver, CO.    Oral presentations: Benitez Ponce MS, Medina Lopez M, Huo D, Lindsey L, Guevara F, Frey T. Interacciones microbianas en ecosistemas agrícolas. Latinamerican Congress of Microbiology. August 2023. Melanie Medina López, Timothy Ralston, Horacio D. López-Nicora and Soledad Benitez Ponce. Heterodera glycines is associated with shifts in fungal community composition in Ohio agricultural soils. Society of Nematologists annual meeting. Columbus, OH. July 2023. Melanie Medina López, Timothy Ralston, Horacio D. López-Nicora and Soledad Benitez Ponce. Soybean cyst nematode infestation is associated with changes in fungal community composition in agricultural soils of Ohio. Midwest Microbiome Symposium. Columbus, OH. May 2023.   Extension and outreach presentations: Melanie Medina López, Edwin D. Navarro. La microbiología en la producción agrícola. UPRM Microbiology Student Association webinar series. Online. February 2023.   Related grants: Medina-Lopez, M. OSU, CFAES Internal Grant Graduate Program | $5,000 April 2023- October 2024 Title: Examining the Taxonomic Resolution of Long-Read Amplicon Sequencing of Fungal Barcoding Genes Benitez Ponce, MS. Ohio Soybean Council. $26,000. August 2023 – July 2024. Title: Undergraduate Training through Characterization of Fungal Isolates from Soybean Fields in Ohio and their Interactions with the Soybean Cyst Nematodes. Frey T, Benitez Ponce MS, Lopez Nicora H, Roth M. Ohio Soybean Council. $90,000. Soybean Root Sugars in Soybean Cyst Nematode (SCN)-Fungal Interactions.

Impact Statements

new product brought to market by FMC was evaluated in on-farm trials as well as traditional replicated small plot research on experiment stations in 2021, 2022 and 2023.