Brief Summary of Minutes of Annual Meeting

Rhizoctonia zeae (Everhart) – Project focused on fungicide resistance lead by two PhD student Nikita Gambhir and Srikanth Kodati.  In vitro testing of three chemistries using isolates from corn and soybean.  No difference by host but most isolates were sensitive.  Among the chemistries, azoxystrobin was investigated further, since SHAM was not effective on controlling alternative oxidation, a greenhouse assay was conducted.  Stand counts and disease index showed that azoxystrobin did not reduce disease severity. Further analysis included population genetics using markers derived from genome sequencing.  With a set of markers there was enough resolution to divide the population and the population is mixed, which could mean a higher risk for fungicide resistance.

Verticillium dahlia (Crandall) – VCG to identify populations moving from weeds and other hosts to economically important crops.  V. dahliae could serve as an endophyte in other hosts that could increase the potential for reservoir populations that increase genetic diversity.  There are two main groups VCG4A and 4B, both causing disease on potato.  Currently, Sharifa’s group is working on developing and optimizing the primers for detection of the two VCG groups.  There is also ongoing field work with different gradients of inoculation using potato and oats to determine pathogen movement and looking at microbiome component to determine the role of rotation and beneficial communities.

Fusarium oxysporum (Crandall) – Another project is focused on continental movement of soilborne pathogens through a NASA grant in collaboration with Katie Gold from Cornell.  Using F. oxysporum to understand movement of spores in dust plumes and contributing to spread of major diseases.  The questions are could we model pathogen movement in air currents and proof of concept of detection of F. oxysporum with spore trapping in key areas in the Caribbean.

Xylaria necrophora (Rojas) --  Etiology and epidemiology of taproot decline. Continue work on taproot decline combining remote sensing, disease severity and molecular diagnostics to understand disease progression and epidemiology of the pathogen.  Yield and plant stand were used as parameters, showing an effect of cover crop without pathogen, but the effect increases with pathogen present.  In 2021-2022, 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. Milestones for this project include developing an understanding of the biology and epidemiology of X. necrophora for improved disease management practices. There were multiple short-term outcomes achieved, such as development of a qPCR diagnostic tool to evaluate soil and plant samples infested with Xylaria necrophora, conducting a field trial to monitor epidemiology and biology of Xylaria necrophora adapting new technologies such as remote and short-distance sensing to study disease progression.

Rhizoctonia solani (Rojas) – Also looking at the population genetics of Rhizoctonia solani AG 1-1A using existing collections at Arkansas but increasing sampling effort in current populations in Arkansas and nearby states. Working on cover crop rotations within a corn-soybean rotation system, data analysis.  Isolates of Rhizoctonia solani have been collected in Arkansas and received from collaborators in the Southern US for genotyping and population genomics analyses. A short term outcome was sequencing of 108 isolates of Rhizoctonia solani AG1-1A from rice (Sheath blight) and soybean (Aerial blight) for genetic diversity analysis. Additionally, we are phenotypically characterizing those isolates for growth rates and tolerance to fungicide.  Milestones for this project include Characterize the genetic diversity of soilborne pathogens, especially Rhizoctonia solani AG1-1A, and the implications on selection of plant resistant material. Implement non-destructive technologies to monitor the effect of soilborne diseases on hosts physiology and performance. We will continue in lab assays and field trials to monitor the efficacy of chemical products to control soilborne plant pathogens.

Phytobacteriology and agricultural microbiomes lab (Benitez) – Obj. 1 – Soil management history, fungal communities and SCN infestation.  Soil samples from SCN coalition were stored for microbiome analysis and SCN data.  Using full length ITS region using a third-party lab.  The idea is to fully classify the fungal species present in the soil.  There is no significant difference in diversity across SCN pressure levels.  There are key species already identified that could be associated with healthy areas, such as Trichoderma and Clonostachys.  Also using grid sampling to understand field scale variation in collaboration with Horacio Lopez-Nicora.

Phytobacteriology and agricultural microbiomes lab (Benitez) Obj. 2 – cover crop rotation and soybean interaction.  Different rotation systems including corn-soy rotation, corn-rye-soybean, corn-fallow-soybean-wheat-corn.  Most of the analysis is focused corn-rye-soybean rotation to develop an understanding of beneficial nematodes, carbon pools, and the interactions.  Generated were 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.

Applied disease management (Spurlock) – On corn, 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 and 2022.  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 2022 as well.  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.

Impacts and upcoming activities within the S1083 group include:

Research impacts include the adoption of cover practices by growers in Arkansas, development of diagnostic tools to monitor multiple different soilborne pathogens, adoption of molecular assays by plant health clinics, and revision of chemical fungicide labels due to phytotoxic effects discovered.  New collaborations also resulted, including one with scientists in the Department of Horticulture at the University of Arkansas in order to monitor soilborne pathogens and evaluating the effects on management practices on the soil microbial diversity.

The Soil Microbiology and Root Diseases (SMRD) and Diagnostics Committees have joined forces to propose a new activity for the American Phytopathological Society (APS) Councilor's Challenge for 2023, "Developing & Delivering Diagnostics Online Resources (D³OR)." There is an urgent need to create and disseminate new plant pathogen diagnostics tools, especially for soilborne pathogens, that are accurate, up-to-date, and accessible for a wide audience.

We proposed to develop and deliver new diagnostic online resources that will open the door for current members to engage in this topic as well as attract new, diverse members to consider careers in plant diagnostics.  There are two major outputs of this program. (1) We will develop digital diagnostics online tools that are short videos created by practicing diagnosticians who work across a spectrum of organizations and who are in different career stages. (2) By leveraging the new call from the APS journal Plant Health Progress, we will write and publish new Diagnostic Guides with a focus on soilborne diseases

Publications:

1. Crandall, S.G., Spychalla, J., Crouch, U., Acevedo, F., Naegele, R., Miles, T.D. 2022. Rotting grapes don’t improve with age: cluster rot disease complexes, management, and future prospects. Feature Article, Plant Disease. https://doi.org/10.1094/PDIS-04-21-0695-FE.
2. Gambhir, N., Kodati, S., Huff, M., Silva, F., Ajayi-Oyetunde, O., Staton, M., Bradley, C., Adesemoye, A.O. and Everhart, S.E., 2021. Prevention and detection of fungicide resistance development in Rhizoctonia zeae from soybean and corn in Nebraska. Plant Health Progress, pp.PHP-11.
3. Gambhir, N., Kodati, S., Huff, M., Silva, F., Ajayi-Oyetunde, O., Staton, M., Bradley, C., Adesemoye, A.O. and Everhart, S.E., 2021. Prevention and detection of fungicide resistance development in Rhizoctonia zeae from soybean and corn in Nebraska. Plant Health Progress, pp.PHP-11.
4. Gil, J., Ortega, L., Rojas, J.A. and Rojas, C.M., 2022. Genome Sequence Resource of Burkholderia glumae PhytoFrontiers™, 2(2), pp.140-142.
5. Kodati, S., Adesemoye, A.O., Yuen, G.Y., Volesky, J.D. and Everhart, S.E., 2021. Origin of agricultural plant pathogens: Diversity and pathogenicity of Rhizoctonia fungi associated with native prairie grasses in the Sandhills of Nebraska. PLoS ONE, 16(4), p.e0249335.
6. Kodati, S., N. Gambhir, G. Yuen, A.O. Adesemoye, S.E. Everhart. 2022. Diversity and aggressiveness of Rhizoctonia spp. From Nebraska on soybean and cross-pathogenicity to corn and wheat. Plant Disease. 106:2689-2700.
7. Larson, E.R. and Crandall, S.G. (In-Review). Recovery of the soil fungal microbiome using steam disinfection and biocontrol to manage the plant pathogen Fusarium solani.Special Issue: “Detection, characterization, and management of plant pathogens.” Frontiers in Plant Science. 
8. Lin, F., Chhapekar, S.S., Vieira, C.C., Da Silva, M.P., Rojas, A., Lee, D., Liu, N., Pardo, E.M., Lee, Y.C., Dong, Z. and Pinheiro, J.B., 2022. Breeding for disease resistance in soybean: a global perspective. Theoretical and Applied Genetics, pp.1-100.
9. Matczyszyn, J.N., Harris, T., Powers, K., Everhart, S.E. and Powers, T.O., 2022. Ecological and morphological differentiation among COI haplotype groups in the plant parasitic nematode species. Journal of Nematology, 54(1), pp.1-24.
10. Spurlock, T. N. (2022). Evaluation of In-furrow Fungicides on Corn, 2021. Arkansas Corn and Grain Sorghum Research Studies, 2021.
11. Spurlock, T. N., Tolbert, A.C., Hoyle, R.C. (2022). Evaluation of cotton seed treatments against Rhizoctonia solani AG-4 in southeast AR, 2021. (ST009 ed., vol. 16).
12. Spurlock, T. N., Tolbert, A.C., Hoyle, R.C. (2022). Evaluation of cotton seed treatments against Rhizoctonia solani AG-4 on DP1646 B2XF and DP2141B3XF in southeast AR, 2021. (CF119 ed., vol. 16) https://www.plantmanagementnetwork.org/pub/trial/pdmr/reports/2022/CF119.pdf
13. Spurlock, T. N., Tolbert, A.C., Hoyle, R.C. (2022). Evaluation of experimental cotton seed treatments against Pythium ultimum in southeast AR, 2020. (ST008 ed., vol. 16). https://www.plantmanagementnetwork.org/pub/trial/pdmr/reports/2022/ST008.pdf
14. Spurlock, T. N., Tolbert, A.C., Hoyle, R.C. (2022). Impact of biological in-furrow applications on corn in Southeast AR, 2021. (CF097 ed., vol. 16). https://www.plantmanagementnetwork.org/pub/trial/pdmr/reports/2022/CF097.pdf https://doi.org/10.1094/PDMR16
15. Spurlock, T. N., Tolbert, A.C., Hoyle, R.C. (2022). Impact of foliar and in-furrow fungicide applications on soybean in Southeast AR, 2021. (CF121 ed., vol. 16). https://www.plantmanagementnetwork.org/pub/trial/pdmr/reports/2022/CF121.pdf https://doi.org/10.1094/PDMR16
16. Spurlock, T. N., Tolbert, A.C., Hoyle, R.C. (2022). Impact of in-furrow fungicide applications on corn in Southeast AR, 2021. (CF098 ed., vol. 16). https://www.plantmanagementnetwork.org/pub/trial/pdmr/reports/2022/CF098.pdf https://doi.org/10.1094/PDMR16
17. Spurlock, T. N., Tolbert, A.C., Hoyle, R.C. (2022). Impacts of products applied in-furrow on corn in Southeast AR, 2021. (CF099 ed., vol. 16). https://www.plantmanagementnetwork.org/pub/trial/pdmr/reports/2022/CF099.pdf https://doi.org/10.1094/PDMR16