Research Project: Mitigation of Domestic, Exotic, and Emerging Diseases of Subtropical and Temperate Horticultural Crops

Location: Subtropical Plant Pathology Research

2024 Annual Report

Objectives
Objective 1: Characterize ecology, biology, and epidemiology of domestic, exotic, newly emerging, and re-emerging pathogens of horticultural crops. (NP303, C1, PS1A; C2, PS2A, PS2B, PS2C, PS2D) 1.A: Characterize the basic biology of ‘Candidatus Liberibacter asiaticus (Las),’ the bacterium associated with citrus huanglongbing (HLB) by in vitro culture, and characterize new seed-transmissible diseases of citrus. 1.B: Characterize the basic biology, molecular biology, vector interactions and/or epidemiology of orthotospoviruses, Xanthomonas fragariae [cause of angular leaf spot (ALS) on strawberry] and other pathogens of vegetables, citrus, ornamentals, and weeds. Objective 2: Develop and improve reliable detection and sampling methods for pathogens of subtropical and temperate horticultural crops. (NP303, C1, PS1A, PS1B) 2.A: Develop and/or improve detection and sampling methods for orthotospoviruses, Las and Xanthomonas fragariae on strawberry. 2.B: Train canines to detect thrips-transmitted TCSV and whitefly-transmitted SqVYV. Objective 3: Develop or improve comprehensive integrated disease management strategies to mitigate existing or emerging diseases of horticultural crops. (NP303, C3, PS3A, PS3B) 3.A: Develop and implement the most efficacious strategies for disease management of HLB, Xanthomonas fragariae on strawberry, fungal foliar diseases on cucurbits, and viruses of vegetables and ornamentals. 3.B: Develop new and/or augment existing surveillance methods and protocols for HLB and other new citrus diseases, and areawide management of insect-vectored viral diseases of vegetables.

Approach
The overall approach is to thoroughly characterize plant pathogens causing domestic, exotic and emerging diseases at multiple levels: cellular, molecular and/or biochemical levels of host-pathogen-vector interaction and traditional and newer stochastic epidemiological analysis at field and regional levels. New pathogens will be identified and characterized by biological and traditional cultural methods. Recombinant DNA and genomics technologies will be applied to study host-pathogen interactions. Resulting knowledge will be used to develop new detection and sampling methods, and management strategies, for these pathogens.

Progress Report
Research continues in the third year of the project on characterizing the ecology, biology, and epidemiology, and the detection, diagnosis, sampling, surveillance, and management of domestic, exotic, newly emerging, and re-emerging pathogens of horticultural crops. Field experiments monitoring whitefly populations and virus infections in sequentially planted vegetable crops were maintained throughout the year by ARS researchers at Fort Pierce, Florida to better understand the effects of environmental conditions and crop types for inclusion in, and eventual refinement of models used to manage whitefly populations and whitefly-transmitted viruses. Research continues to refine methods to identify vegetable crops from satellite imagery using an algorithm in collaboration with commercial partners to identify and map distribution with the goal of developing landscape-level risk maps of whitefly and whitefly-transmitted viruses. Continued testing in southwest Florida shows that improvements to the algorithm have resulted in greater accuracy and it can predict crop types in most cases although very young crops remain challenging to identify in satellite images. Very young crops may still be misidentified as fallow ground. Further refining of the algorithm is underway, and we anticipate the landscape-level risk maps will be incorporated into an areawide pest management (AWPM) program for management of whitefly-transmitted viral epidemics. Key findings indicate spatial associations for whitefly populations up to 1500 m and virus incidence up to 750 m, emphasizing the importance of spatially focused management practices. Temporal analysis revealed that both whitefly populations and virus incidence are strongly influenced by temperature, particularly during the February to May period. The presence of surrounding vegetable fields significantly influenced whitefly dispersal, with correlations extending up to 9000 m during peak months. These insights underscore the need for targeted monitoring and management strategies, focusing on temperature fluctuations and spatial crop distributions, to effectively control whitefly and virus outbreaks. Continuing to work with local crop consultants and agricultural technology companies, we have refined the tools for real-time mapping of pest and diseases, and a system for information delivery to foster development of AWPM as a new strategy for managing whitefly-transmitted virus epidemics in Florida and elsewhere in the southeastern U.S. Off-season scouting continues to be actively pursued to identify areas that serve as sources of whitefly or virus for the following production season. Having the ability to fully characterize the landscape in real time is a necessary component for AWPM. Researchers at Fort Pierce, Florida have developed a new detection technology for early and low titer infection and relative cell activities of the HLB bacterium, Candidatus Liberibacter asiatics (CLas). By combining qPCR and RT-qPCR, not only is the detection sensitivity for Las significantly increased when using the new diagnostic test, but also the live and dead cells of CLas can be easily identified. After multiple years’ selection and evaluation, scientists at Fort Pierce FL have obtained several commercial potential new citrus lines that have significantly improved HLB resistance/tolerance. These new citrus lines have gone through a clean-up process by Florida Division of Plant industry, and they have been moved into the next phase of field trials before being released to the public. Using the Las co-culture system, new antimicrobials have been isolated. Since the assay directly target Las cells in vitro, the mode of action of these antimicrobials can be revealed, and therefore be used to develop more effective antimicrobial products. Scientists at Fort Pierce, Florida have rehabilitated a wind tunnel/rain facility for use to study aspects of the epidemiology various pathogens including citrus black spot (Phyllosticta citricarpa) and citrus canker (Xanthomonas citri) of citrus. Unusual samples of viruses on vegetable crops were collected from various stakeholder fields and tested to determine the identities of the causal agents. Research scientists at Fort Pierce, Florida have compared methods to detect X. fragariae (cause of angular leaf spot) of strawberry. The seven tests for detection of X. fragariae have been completed. The tests to detect X. fragariae include standard PCR, recombinase polymerase amplification (RPA), LAMP (HNB), PCR, ELISA, and LAMP (SYTO 9) and simple dilution plating. Latent class analysis will be used to estimate the test characteristics of the seven diagnostic tests. Improved approaches to survey and surveil the devastating disease of citrus, citrus HLB continue. A spatially explicit stochastic agent-based model to investigate the spread of ACP/HLB in California was previously developed and focuses on providing comprehensive scenario-based simulations to identify effective management strategies tailored to diverse citrus compositions and climatological conditions. The goal is to support regulatory agencies and citrus growers in formulating sustainable and cost-effective control measures to mitigate the impact of ACP/HLB on commercial citrus production. Over the past year, sixteen new landscapes have been included for simulation, integrating comprehensive climate data from 276 weather stations to assess their influence on ACP/HLB dynamics. Early detection models and enhanced interactive simulation tools to support tailored management strategies are being developed. The simulation tool will aid regulatory agencies and growers in effectively mitigating the spread of ACP/HLB. The risk-based survey (RBS) method for California to detect HLB and ACP continues to be implemented in cooperation with USDA APHIS and the California Department of Food and Agriculture (CDFA). By refining and validating the data-driven risk model, Estimation methods continue to be improved using land parcel data to significantly enhance the identification of residential citrus hosts. HLB prevalence and positivity rates at the county level and within specific grid areas have been estimated, revealing significant trends that inform future sampling efforts. Extensive analyses have been conducted to evaluate and optimize the weighting of various risk factors in the predictive model, thereby improving its accuracy in forecasting HLB spread. The development and refinement of RBS protocols have ensured efficient and effective resource allocation to high-risk areas, providing valuable support to CDFA for enhancing early detection efforts. Additionally, the project has explored cost-effective methods for delimitation by reducing the radius to 250 meters, optimizing resource use, and freeing up significant manpower and resources for other program needs. A predictive model that builds upon previously established methodologies to estimate the dispersal of plant pests and diseases driven by major weather events continues to be refined. By integrating the model with existing mapping and surveillance efforts, enhances rapid response capabilities. The ultimate goal is to provide a robust decision support tool that can accurately forecast the spread of pests and diseases post-weather events, thereby guiding effective mitigation strategies and optimizing resource allocation for regulatory agencies and stakeholders in the agricultural sector. Comprehensive data on three exotic citrus diseases and pests, including Citrus Canker and Citrus Black Spot, has been cleaned and processed to fit a GIS framework. Additionally, extensive meteorological data, including daily, hourly, and 15-minute interval measurements, from NOAA's National Centers for Environmental Information and the Florida Automated Weather Network (FAWN) has been obtained. An integrated predictive model with existing mapping and surveillance efforts, significantly enhancing our ability to manage the spread of diseases like Citrus Black Spot following hurricanes such as Irma, Ian, and Nicole. Furthermore, we have developed and refined an online application that enables users to predict and visualize disease spread within the context of a hurricane event, supporting user-defined input data and providing detailed risk assessments.

Accomplishments
1. HLB surveillance model for huanglongbing in California. ARS researchers in Fort Pierce, Florida in collaboration with scientists at the University of California, Davis, and stakeholders in California, developed a refined survey protocol – a risk-based survey (RBS) to aid survey of the disease in the complex urban and peri-urban landscapes of southern California. Using the model, resource use can be optimized, and resource allocation determined depending on climate, ACP/HLB incidence, and other factors affecting ACP/HLB spread. The RBS is updated with new detection data and further refined continuously to guide surveillance. An online interface allows the newest RBS to be available to stakeholders.

2. Ca. Liberibacter asiaticus in vitro culture and completion of Koch’s postulates. ARS researchers in Fort Pierce, Florida in collaboration with scientists at the University of Florida and Clemson University developed a semi-selective medium and protocol for successful culture of Las in vitro and the completion of Koch’s postulates for Las bacteria. The in vitro Las culturing system provides enormous opportunities for accelerating HLB research and therefore better solutions for HLB control.

Review Publications
Zheng, D., Armstrong, C.M., Yao, W., Wu, B., Luo, W., Powell, C., Hunter, W.B., Luo, F., Gabriel, D., Duan, Y. Towards the completion of Koch’s postulates for the citrus huanglongbing bacterium, Candidatus Liberibacter asiaticus. Horticulture Research. 2024. https://doi.org/10.1093/hr/uhae011.
Adkins, S.T., Brown, K., De La Torre, J.C., Digiaro, M., Hughes, H.R., Junglen, S., Lambert, A.J., Maes, P., Marklewitz, M., Palacios, G., Sasaya, T., Zhang, Y., Turina, M., Kuhn, J.H. ICTV Virus Taxonomy Profile: Leishbuviridae 2023. Journal of General Virology. 104:12. 2023. https://doi.org/10.1099/jgv.0.001934.
Kuhn, J.H., Adkins, S.T., Brown, K., De La Torre, J.C., Digiaro, M., Hughes, H.R., Junglen, S., Lambert, A.J., Maes, P., Marklewitz, M., Palacios, G., Sasaya, T., Turina, M., Zhang, Y. ICTV Virus Taxonomy Profile: Cruliviridae 2023. Journal of General Virology. 104:12. 2023. https://doi.org/10.1099/jgv.0.001930.
Kuhn, J.H., Adkins, S.T., Brown, K., De La Torre, J.C., Digiaro, M., Hughes, H.R., Junglen, S., Lambert, A.J., Maes, P., Marklewitz, M., Palacios, G., Sasaya, T., Zhang, Y., Turina, M. ICTV Virus Taxonomy Profile: Discoviridae 2023. Journal of General Virology. 104:12. 2023. https://doi.org/10.1099/jgv.0.001926.
Kuhn, J.H., Adkins, S.T., Brown, K., De La Torre, J.C., Digiaro, M., Hughes, H.R., Junglen, S., Lambert, A.J., Maes, P., Marklewitz, M., Palacios, G., Sasaya, T., Turina, M., Zhang, Y. ICTV Virus Taxonomy Profile: Mypoviridae 2023. Journal of General Virology. 104:12. 2023. https://doi.org/10.1099/jgv.0.001931.
Kuhn, J.H., Adkins, S.T., Brown, K., De La Torre, J.C., Digiaro, M., Hughes, H.R., Junglen, S., Lambert, A.J., Maes, P., Marklewitz, M., Palacios, G., Sasaya, T., Zhang, Y., Turina, M. ICTV Virus Taxonomy Profile: Tulasviridae 2023. Journal of General Virology. 104:12. 2023. https://doi.org/10.1099/jgv.0.001933.
Kuhn, J.H., Adkins, S.T., Brown, K., De La Torre, J.C., Digiaro, M., Hughes, H.R., Junglen, S., Lambert, A.J., Maes, P., Marklewitz, M., Palacios, G., Sasaya, T., Turina, M., Zhang, Y. ICTV Virus Taxonomy Profile: Wupedeviridae 2023. Journal of General Virology. 104:12. 2023. https://doi.org/10.1099/jgv.0.001932.
Maneechoat, P., Chiemsombat, P., Lopez Jr, S., Adkins, S.T. The complete genome sequence of tomato necrotic ringspot virus in chilli in Thailand derived from next-generation sequencing. Archives of Virology. 169:64. 2024. https://doi.org/10.1007/s00705-024-05981-0.
Dey, K., Vilez-Climent, M., Soria, P., Mcvay, J.M., Adkins, S.T. First report of mixed infection of jasmine mosaic-associated virus (JMaV) and jasmine virus H (JaVH) in jasmine species in Florida, United States. New Disease Reports. 25(2):210–211. 2024. https://doi.org/10.1094/PHP-08-23-0073-BR.
Gautam, S.; Gadhave, K.R.; Buck, J.W.; Dutta, B.; Coolong, T.;Adkins, S.; Simmons, A.M.; Srinivasan, R. Effects of Host Plants and Their Infection Status on Acquisition and Inoculation of A Plant Virus by Its Hemipteran Vector. Pathogens 2023, 12, 1119. https://doi.org/10.3390/pathogens12091119
Oliver, J.E., Rotenberg, D., Agosto-Shaw, K., Mcinnes, H.A., Lahre, K.A., Mulot, M., Adkins, S.T., Whitfield, A.E. Multigenic hairpin transgenes in tomato confer resistance to multiple orthotospoviruses including Sw5 resistance-breaking tomato spotted wilt virus. Phytopathology. 114:1137-1149. 2024. https://doi.org/10.1094/PHYTO-07-23-0256-KC.
Ivey, C., Rossitto De Marchi, B., Beuzelin, J., Soto-Adames, F., Hochmuth, R., Turechek, W., Smith, H. Susceptibility to insecticides of Megalurothrips usitatus (Bagnall) and Frankliniella insularis (Franklin) (Thysanoptera: Thripidae) infesting Lablab purpureus in Florida. Crop Protection. 175:106448. 2023. https://doi.org/10.1016/j.cropro.2023.106448.
Grunwald, N.J., Bock, C.H., Chang, J.H., Alves De Souza, A., Del Ponte, E.M., du Toit, L.J., Dorrance, A.E., Dung, J., Gent, D.H., Goss, E.M., Lowe-Power, T., Madden, L.V., Martin, F.N., McDowell, J., Naegele, R.P., Potnis, N., Quesada-Ocampo, L.M., Sundin, G.W., Thiessen, L., Vinatzer, B.A., Zeng, Q. 2024. Open access and reproducibility in plant pathology research: Guidelines and best practices. Phytopathology. 114(5):910-916. https://doi.org/10.1094/PHYTO-12-23-0483-IA.
Wang, N., Sundin, G.W., De La Fuente, L., Cubero, J., Tatineni, S., Brewer, M.T., Zeng, Q., Bock, C.H., Cunniffe, N.J., Wang, C., Candresse, T., Chappell, T., Coleman, J.J., Munkvold, G. 2024. Key challenges in plant pathology in the next decade. Phytopathology. 114(5):837-842.
Vosburg, C., Sinn, J., Orbovic, V., Ferrarezi, R., Zapién Macías, J., Taylor, E.L., Hilf, M.E., Mccollum, G., Gottwald, T.R., Stover, E.W., Mcnellis, T.W. 2024. Assessment of grapefruit expressing anti-NodT antibody for huanglongbing resistance. PhytoFrontiers. 4:172-182. https://doi.org/10.1094/PHYTOFR-06-23-0078-R.