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Integrated plant health management in the (meta)genomics era

Klass, Taylor Lauren
http://orcid.org/0009-0004-2693-145X
http://rave.ohiolink.edu/etdc/view?acc_num=osu1713501760054294

Abstract Details

2024, Doctor of Philosophy, Ohio State University, Plant Pathology.
Often overshadowed by staple crops, vegetables contain many essential vitamins and minerals and play a key role in global food and nutritional security. However, vegetable production is threatened by a variety of diseases, including bacterial wilt and bacterial spot. My dissertation research utilizes genomic surveys to elucidate the diversity of the bacteria causing these diseases, both globally and locally. Bacterial wilt disease is endemic within the country of Cambodia, causing significant yield losses for Cambodian growers. However, the diversity of the Ralstonia solanacearum Species Complex (RSSC), the causal agent responsible for bacterial wilt disease, has not been defined in Cambodia. Therefore, we conducted a bacterial wilt survey within Cambodia, collecting RSSC isolates from four distinct host plants (tomato, hot pepper, long bean, and bitter gourd) over three locations, for a total of 24 RSSC isolates. We found that all 24 of the Cambodian RSSC isolates belong to phylotype I and are classified as Ralstonia pseudosolanacearum. Through disease progress assays on susceptible hosts, we observed that variation in the Cambodian isolate’s ability to cause consistent wilt was dependent on the method of inoculation. Additionally, the Cambodian R. pseudosolanacearum isolates exhibited a wide range of phylogenomic diversity. When comparing the core and accessory genome and the Type III effector profile of the Cambodian isolates, we found that the R. pseudosolanacearum accessory genome better reflected the host of isolation and host range of the isolates compared to the core genome. Altogether, this research provides a glimpse into the RSSC diversity present within Cambodia and insight into R. pseudosolanacearum host range. Bacterial spot disease affects tomato and pepper production worldwide and is caused by a species complex of Xanthomonas bacteria: X. hortorum pv. gardneri, X. euvesicatoria pv. euvesicatoria, X. euvesicatoria pv. perforans, and X. vesicatoria. We set out to elucidate the current species diversity in Ohio fresh market tomato and pepper production and field test the integration of genomics into bacterial spot diagnostics/surveillance. During the 2022 field season, we collected symptomatic plant tissue and assessed Ohio growers’ perceptions of using genomic technologies in bacterial spot diagnostics/surveillance. After conducting whole genome sequencing on 34 Xanthomonas isolates from our survey, we determined that Ohio contains a wide diversity of bacterial spot causing Xanthomonads in fresh market tomato and pepper production systems, including X. arboricola, which had not been associated with tomato or pepper in Ohio before this survey. The diversity present within these Xanthomonas isolates became further evident after defining the Type III effector profile and the presence/absence of copper resistance genes in each isolate. We also created and validated a metagenomic pipeline for bacterial spot diagnostics/surveillance, finding comparable results from metagenomic and whole genome analysis from the same samples. Ohio growers’ perceptions of integrating genomic technologies into diagnostics/surveillance were favorable, with a difference in the perceptions of Amish/Mennonite growers (more neutral) compared to non-Amish/Mennonite growers (more agreeable). Through this research, we defined the current diversity of bacterial spot in Ohio fresh market tomato and pepper production, discovered the presence of an emerging species of Xanthomonas on tomato and pepper, field tested the use of metagenomics in bacterial spot diagnostics/surveillance, and analyzed the perceptions of Ohio growers towards using genomic technologies in diagnostics.
Jonathan Jacobs (Advisor)
Mary Rodriguez (Committee Member)
Francesca Hand (Committee Member)
Sally Miller (Advisor)
173 p.
Plant Pathology
Ralstonia pseudosolanacearum; bacterial wilt; bacterial spot; Xanthomonas; metagenomics; whole genome sequencing; plant pathogen genomic survey; diagnostics; surveillance; integrated plant health management; perception research; diffusion of innovations; X. arboricola; phylotype I; Cambodia; Ohio; vegetables; plant pathology

Recommended Citations

Citations

  • Klass, T. L. (2024). Integrated plant health management in the (meta)genomics era [Doctoral dissertation, Ohio State University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=osu1713501760054294

    APA Style (7th edition)

  • Klass, Taylor. Integrated plant health management in the (meta)genomics era. 2024. Ohio State University, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=osu1713501760054294.

    MLA Style (8th edition)

  • Klass, Taylor. "Integrated plant health management in the (meta)genomics era." Doctoral dissertation, Ohio State University, 2024. http://rave.ohiolink.edu/etdc/view?acc_num=osu1713501760054294

    Chicago Manual of Style (17th edition)

osu1713501760054294
110
© 2024, all rights reserved.
This open access ETD is published by The Ohio State University and OhioLINK.