Visiting Professor

Phone: 608-262-9578
E-mail: jonathan.jacobs@wisc.edu

885D Russell Laboratories
1630 Linden Dr
Madison, WI 53706

Learn More:

Education

• Ph.D. Plant Pathology (Minor: Microbiology), University of Wisconsin-Madison
• B.S. Bacteriology, Genetics and Spanish, University of Wisconsin-Madison

Research

Bacteria emerge to cause infectious diseases of plants, animals and people. These diseases especially those that limit plant health have important consequences for food security. Our team investigates the biological and evolutionary basis for microbial colonization of plants and how it relates to disease emergence.

The long-term goal of Dr. Jacobs’ lab is to improve global food security through research, education and mentorship by developing and communicating useful scientific knowledge of important plant disease problems in agriculture. Often the models his team studies are related to agricultural biosecurity or current problems faced by producers. His team has advanced agricultural science by defining the genomic events that drive microbial evolution, niche-specificity and pathogen emergence.

Jacobs is also a motivated educator dedicated to advancing science through training the next generation. He leads a thriving lab of undergraduate and graduate students, postdocs, staff and visiting scholars. He has given international workshops and coursework on multiple themes in biological science including: 1) microscopy imaging for live visualization of plant and microbial biology; 2) high throughput sequencing for plant pathogen detection and microbiome taxa and function identification; 3) using Generative Artificial Intelligence to teach students how to advance their research and data visualization with cutting-edge computational and biological science tools.

Bacterial wilt of tomato – Time lapse imaging of wilt disease 

About Jonathan:

He graduated with a B.S. (triple major in Bacteriology, Genetics and Spanish) and Ph.D. (Major: Plant Pathology, Minor: Microbiology) from the University of Wisconsin—Madison. For his postdoctoral research, Dr. Jacobs was a NSF Postdoctoral Fellow in Biology at the Institut de Recherche pour le Développement in Montpellier, France and a USDA NIFA Postdoctoral Fellow at Colorado State University. He is a two-time Fulbright Scholar where he carried out plant-microbial imaging research at Université Catholique de Louvain in Belgium and disease management and detection research on emerging threats to cereal production at la Universidad de la República in Montevideo and el Instituto Nacional de Investigación Agropecuaria. Before joining UW–Madison, he was previously faculty at The Ohio State University and led the Emerging Infectious Disease Ecology laboratory in the Department of Plant Pathology and Infectious Diseases Institute.

His team overall investigates the biological and evolutionary basis for microbial colonization of plants. The factors that contribute to pathogen evolution for niche-specific behavior remain unclear. His team is focused on understanding how pathogenic bacteria evolve and adapt to colonize different plant tissues. Their research uses novel, high-throughput technologies to determine the basis of tissue-specific behaviors in and host colonization by plant pathogenic bacteria.

Courses Taught

• Plant Pathology 875: Tropical & Midwest Agriculture & Conservation

Publications

Beutler J, Li T, Roman-Reyna V, Fleitas MC, Bamrah R, Jacobs JM, Kutcher HR, Tambong JT, Brar GS. First Report of Bacterial Leaf Streak of Barley (Hordeum vulgare) Caused by Xanthomonas translucens pv. translucens in British Columbia, Canada. Plant Dis. 2023 Feb 1. doi: 10.1094/PDIS-09-22-2112-PDN.

Heiden N, Roman-Reyna V, Curland RD, Dill-Macky R, Jacobs JM. Comparative Genomics of Barley-Infecting Xanthomonas translucens Shows Overall Genetic Similarity but Globally Distributed Virulence Factor Diversity. Phytopathology. 2023 Nov;113(11):2056-2061. doi: 10.1094/PHYTO-04-22-0113-SC. Epub 2023 May 4.

Ledman KE, Roman-Reyna V, Curland RD, Heiden N, Jacobs JM, Dill-Macky R. Comparative Genomics of Xanthomonas translucens pv. undulosa Strains Isolated from Weedy Grasses and Cultivated Wild Rice. Phytopathology. 2023 Nov;113(11):2083-2090. doi: 10.1094/PHYTO-09-22-0352-SA. Epub 2023 Nov 20.

Liu Z, Friskop A, Jacobs JM, Dill-Macky R. Bacterial Leaf Streak: A Persistent and Increasingly Important Disease Problem for Cereal Crops. Phytopathology. 2023 Nov;113(11):2020-2023. doi: 10.1094/PHYTO-11-23-0423-SA. Epub 2023 Nov 28

Peduzzi C, Sagia A, Burokienė D, Nagy IK, Fischer-Le Saux M, Portier P, Dereeper A, Cunnac S, Roman-Reyna V, Jacobs JM, Bragard C, Koebnik R. Complete Genome Sequencing of Three Clade-1 Xanthomonads Reveals Genetic Determinants for a Lateral Flagellin and the Biosynthesis of Coronatine-Like Molecules in Xanthomonas. Phytopathology. 2023 Jul;113(7):1185-1191. doi: 10.1094/PHYTO-10-22-0373-SC. Epub 2023 Aug 26.

Pérez-Quintero AL, Rodriguez-R LM, Cuesta-Morrondo S, Hakalová E, Betancurt-Anzola D, Valera LCC, Cardenas LAC, Matiz-Céron L, Jacobs JM, Roman-Reyna V, Muñoz AR, Giraldo AJB, Koebnik R. Comparative Genomics Identifies Conserved and Variable TAL Effectors in African Strains of the Cotton Pathogen Xanthomonas citri pv. malvacearum. Phytopathology. 2023 Aug;113(8):1387-1393. doi: 10.1094/PHYTO-12-22-0477-SC. Epub 2023 Sep 24.

Román-Reyna V, Curland RD, Velez-Negron Y, Ledman KE, Gutierrez-Castillo DE, Beutler J, Butchacas J, Brar GS, Roberts R, Dill-Macky R, Jacobs JM. Development of Genome-Driven, Lifestyle-Informed Markers for Identification of the Cereal-Infecting Pathogens Xanthomonas tran

Zárate-Chaves CA, Audran C, Medina Culma CA, Escalon A, Javegny S, Gagnevin L, Thomas E, Pimparé LL, López CE, Jacobs JM, Noël LD, Koebnik R, Bernal AJ, Szurek B. CRISPRi in Xanthomonas demonstrates functional convergence of transcription activator-like effectors in two divergent pathogens. New Phytol. 2023 May;238(4):1593-1604. doi: 10.1111/nph.18808. Epub 2023 Mar 14. PMID: 36764921 slucens Pathovars undulosa and translucens. Phytopathology. 2023 Nov;113(11):2110-2118. doi: 10.1094/PHYTO-07-22-0262-SA. Epub 2023 Nov 20.

Clavijo, Felipe; Barrera, Claudia; Benćić, Aleksander; Croce, Valentina; Jacobs, Jonathan M.; Bernal, Adriana J.; Koebnik, Ralf; Roman-Reyna, Veronica.  2022.  Complete Genome Sequence Resource for Xanthomonas translucens pv. undulosa MAI5034, a Wheat Pathogen from Uruguay.  Phytopathology Vol. 112 Issue 9, p2036-2039. 4p. DOI: 10.1094/PHYTO-01-22-0025-A.

Dia, Nay C.; Morinière, Lucas; Cottyn, Bart; Bernal, Eduardo; Jacobs, Jonathan M.; Koebnik, Ralf; Osdaghi, Ebrahim; Potnis, Neha; Pothier, Joël F.  2022.  Xanthomonas hortorum – beyond gardens: Current taxonomy, genomics, and virulence repertoires. Molecular Plant Pathology Vol. 23 Issue 5, p 597-621  DOI: 10.1111/mpp.13185.

Reshetnyak, Ganna; Jacobs, Jonathan M.; Auguy, Florence; Sciallano, Coline; Claude, Lisa; Medina, Clemence; Perez-Quintero, Alvaro L.; Comte, Aurore; Thomas, Emilie; Bogdanove, Adam; Koebnik, Ralf; Szurek, Boris; Dievart, Anne; Brugidou, Christophe; Lacombe, Severine; Cunnac, Sebastien. 2021. An atypical class of non-coding small RNAs is produced in rice leaves upon bacterial infection.  Scientific Reports. Vol. 11 Issue 1, p1-20. DOI: 10.1038/s41598-021-03391-9.

Jacobs, Jonathan M.; Wang, Guo-Liang.  2021.  Next-Generation Rice Disease Research. Rice (19398425). 9/27/2021, Vol. 14 Issue 1, p1-2. 2p. DOI: 10.1186/s12284-021-00523-7.

Khadka, R. B., Cardina, J. and Miller, S. A. 2021. Perspectives on anaerobic soil disinfestation for weed management. J. Integr. Pest Manag. 12:1-11.

Roman-Reyna, V., Dupas, E., Cesbron, S., Marchi, G., Campigli, S., Hansen, M. A., Bush, E., Praret, M., Shiplett, K., Lewis Ivey, M. L., Pierzynski, J., Miller, S. A., Hand, F. P., Jacques, M.-A. and Jacobs, J. M. 2021. Metagenomic sequencing for rapid identification of Xylella fastidiosa from leaf samples. BioRxiv doi: https://doi.org/10.1101/2021.05.12.443947. Posted 15 May 2021.

Deblais, L., Miller, S. A. and Rajashekara, G. 2021. Impact of plant pathogens infection on   Salmonella   enterica subsp. enterica serotype Typhimurium persistence in tomato plants. J. Food Protection 84:563-571. https://doi.org/10.4315/JFP-20-291.

Testen, A. L., Rotondo, F., Mills, M. P. Horvat, M. M. and Miller, S. A. 2021. Evaluation of agricultural byproducts and cover crops as anaerobic soil disinfestation carbon sources for managing a soilborne disease complex in high tunnel tomatoes. Frontiers in Sustainable Food Systems 5:645197. doi: 10.3389/fsufs.2021.645197.

Testen, A. L., Bosquez Martínez, M., Jiménez Madrid, A., Deblais, L., Taylor, C. G., Paul, P. A. and Miller, S. A. 2021. On-farm evaluations of anaerobic soil disinfestation and grafting for management of a widespread soilborne disease complex in protected culture tomato production. Phytopathology 111:954-965.

Srivastava, V., Deblais, L., Kathayat, D., Rotondo, F., Helmy, Y. A., Miller, S. A., and Rajashekara. G. 2021. Novel small molecule growth inhibitors of Xanthomonas spp. causing bacterial spot of tomato Phytopathology 111:940-953.

Rizzo, D., Lichtveld, M., Mazet, J., Togami, E. and Miller, S. A. 2021. Plant health and its effects on food safety and security in a One health framework: four case studies. One Health Outlook 3:6. https://doi.org/10.1186/s42522-021-00038-7.

Khadka, R. B. and Miller, S. A. 2021. Synergy of anaerobic soil disinfestation and Trichoderma spp. in Rhizoctonia root rot suppression. Frontiers in Sustainable Food Systems 5:645736. doi: 10.3389/fsufs.2021.645736.

Rotondo, F., Testen, A. L., Horvat, M. M., Roman-Reyna, V., Klass, T. L., Jacobs, J. M., and Miller, S. A. 2021. First report of Xanthomonas hortorum causing bacterial leaf spot of lavender (Lavandula x intermedia) in Ohio. Plant Dis. 105:484.

Gluck-Thaler E*, Cerutti A*, Perez-Quintero A*, Butchacas J, Roman-Reyna V, Madhaven VN, Shantharaj  D, Merfa MV, Pesce C, Jauneau A, Vancheva T, Lang JM, Allen C, Verdier V, Gagnevin L, Szurek B, Cunnac S, Beckham G, De La Fuente L, Patel HK, Sonti RV, Bragard C, Leach JE, Noël LD, Slot  JC, Koebnik R**, Jacobs JM**. Repeated gain and loss of a single gene modulates the evolution of vascular plant pathogen lifestyles. Science Advances. 2020. doi: 10.1126/sciadv.abc4516 *co-first authors, **co-corresponding authors

Koebnik R, Burokiene D, Bragard C, Chang C, Fischer-Le Saux M, Kölliker R, Lang JM, Leach JE, Luna E, Portier P, Sagia A, Ziegle J, Cohen S, Jacobs JM. The complete genome sequence of Xanthomonas theicola, the causal agent of canker on tea plants, reveals novel secretion systems in clade-1 xanthomonads. Phytopathology. 2020. doi: 10.1094/PHYTO-07-20-0273-SC

Rotondo F, Testen AL, Horvat MM, Roman-Reyna V, Klass TL, Jacobs JM, Miller SA. First report of Xanthomonas hortorum causing bacterial leaf spot of lavender (Lavandula intermedia) in Ohio. Plant Dis. 2020 Sep 18. doi: 10.1094/PDIS-08-20-1684-PDN.

Cohen SP, Luna EK, Lang JM, Ziegle J, Chang C, Leach JE, Le-Saux MF, Portier P, Koebnik R, Jacobs JM. High-Quality Genome Resource of Xanthomonas hyacinthi Generated via Long-Read Sequencing. Plant Dis. 2020 Apr;104(4):1011-1012. doi: 10.1094/PDIS-11-19-2393-A. Epub 2020 Feb 17.

Klass TL, Hayes M, Seng KH, Shoaf W, An C, Rotondo F, Tho KE, Ong S, Allen C, Miller SA, Jacobs JM. First report of bacterial wilt of tomato caused by Ralstonia pseudosolanacearum (Ralstonia solanacearum phylotype I) in Cambodia. 2019. Plant Disease. https://doi.org/10.1094/PDIS-09-19-1823-PDN

Roman-Reyna V, Pesce C, Luna E, Vancheva T, Chang C, Ziegle J, Bragard C, Koebnik R, Lang JM, Leach JE, Jacobs JM. Genome resource of barley bacterial blight and leaf streak pathogen Xanthomonas transluscens pv. translucens strain UPB886. 12 Aug 2019 https://doi.org/10.1094/PDIS-05-19-1103-A

Klass TL, Long JJ, Summer JL, Roman-Reyna V, Koebnik R, Jacobs JM*, and Hand F*. First report of bacterial blight of peony caused by Xanthomonas hortorum in Ohio. Plant Disease. 2019. https://doi.org/10.1094/PDIS-05-19-1123-PDN *co-corresponding authors

Lang JM, Pérez-Quintero AL, Koebnik R, DuCharme E, Sarra S, Doucoure H, Keita I, Ziegle J, Jacobs JM, Oliva R, Koita O, Szurek B, Verdier V, Leach JE. A Pathovar of Xanthomonas oryzae Infecting Wild Grasses Provides Insight Into the Evolution of Pathogenicity in Rice Agroecosystems. Front Plant Sci. 2019 doi: 10.3389/fpls.2019.00507

Cohen SP, Jacobs JM, Leach JE. In Planta Bacterial Transcriptomics Predict Plant Disease Outcomes. Trends Plant Sci. 2018 Sep;23(9):751-753. doi:10.1016/j.tplants.2018.06.008. Epub 2018 Jun 28. PubMed PMID: 30149853.

Schandry N, Jacobs JM, Szurek B, Perez-Quintero AL. A cautionary TALE: how plant breeding may have favoured expanded TALE repertoires in Xanthomonas. Mol Plant Pathol. 2018 Jun;19(6):1297-1301. doi: 10.1111/mpp.12670. PubMed PMID:
29723447.

Pesce C, Jacobs JM, Berthelot E, Perret M, Vancheva T, Bragard C, Koebnik R. Comparative Genomics Identifies a Novel Conserved Protein, HpaT, in Proteobacterial Type III Secretion Systems that Do Not Possess the Putative
Translocon Protein HrpF. Front Microbiol. 2017 Jun 26;8:1177. doi:10.3389/fmicb.2017.01177. eCollection 2017. PubMed PMID: 28694803; PubMed Central
PMCID: PMC5483457.

Tollenaere C, Lacombe S, Wonni I, Barro M, Ndougonna C, Gnacko F, Sérémé D, Jacobs JM, Hebrard E, Cunnac S, Brugidou C. Virus-Bacteria Rice Co-Infection in Africa: Field Estimation, Reciprocal Effects, Molecular Mechanisms, and Evolutionary Implications. Front Plant Sci. 2017 May 1;8:645. doi:10.3389/fpls.2017.00645. eCollection 2017. PubMed PMID: 28507553; PubMed Central PMCID: PMC5410622.

Medina CA, Reyes PA, Trujillo CA, Gonzalez JL, Bejarano DA, Montenegro NA, Jacobs JM, Joe A, Restrepo S, Alfano JR, Bernal A. The role of type III effectorsfrom Xanthomonas axonopodis pv. manihotis in virulence and suppression of plant immunity. Mol Plant Pathol. 2018 Mar;19(3):593-606. doi: 10.1111/mpp.12545. Epub 2017 Apr 5. PubMed PMID: 28218447.

Lowe-Power TM, Jacobs JM, Ailloud F, Fochs B, Prior P, Allen C. Degradation of the Plant Defense Signal Salicylic Acid Protects Ralstonia solanacearum from Toxicity and Enhances Virulence on Tobacco. MBio. 2016 Jun 21;7(3). pii: e00656-16. doi: 10.1128/mBio.00656-16. PubMed PMID: 27329752; PubMed Central PMCID: PMC4916378.

Meng F, Babujee L, Jacobs JM, Allen C. Comparative Transcriptome Analysis Reveals Cool Virulence Factors of Ralstonia solanacearum Race 3 Biovar 2. PLoS One. 2015 Oct 7;10(10):e0139090. doi: 10.1371/journal.pone.0139090. eCollection 2015. PubMed PMID: 26445498; PubMed Central PMCID: PMC4596706.

Jacobs JM, Pesce C, Lefeuvre P, Koebnik R. Comparative genomics of a cannabis  pathogen reveals insight into the evolution of pathogenicity in Xanthomonas. Front Plant Sci. 2015 Jun 16;6:431. doi: 10.3389/fpls.2015.00431. eCollection 2015. PubMed PMID: 26136759; PubMed Central PMCID: PMC4468381.

Jacobs JM, Milling A, Mitra RM, Hogan CS, Ailloud F, Prior P, Allen C. Ralstonia solanacearum requires PopS, an ancient AvrE-family effector, for virulence and To overcome salicylic acid-mediated defenses during tomato pathogenesis. MBio. 2013 Nov 26;4(6):e00875-13. doi: 10.1128/mBio.00875-13. PubMed PMID: 24281716; PubMed Central PMCID: PMC3870264.

Jacobs JM, Babujee L, Meng F, Milling A, Allen C. The in planta transcriptome of Ralstonia solanacearum: conserved physiological and virulence strategies during bacterial wilt of tomato. MBio. 2012 Aug 31;3(4). pii: e00114-12. doi: 10.1128/mBio.00114-12. Print 2012. PubMed PMID: 22807564; PubMed Central PMCID: PMC3413399.

commented in: Vinatzer BA. “Listening in” on how a bacterium takes over the plant vascular
system. MBio. 2012 Sep 11;3(5):e00269-12. doi: 10.1128/mBio.00269-12. Print 2012.
PubMed PMID: 22967979; PubMed Central PMCID: PMC3445969.

Remenant B, de Cambiaire JC, Cellier G, Jacobs JM, Mangenot S, Barbe V, Lajus A, Vallenet D, Medigue C, Fegan M, Allen C, Prior P. Ralstonia syzygii, the Blood Disease Bacterium and some Asian R. solanacearum strains form a single genomic species despite divergent lifestyles. PLoS One. 2011;6(9):e24356. doi: 10.1371/journal.pone.0024356. Epub 2011 Sep 8. PubMed PMID: 21931687; PubMed Central PMCID: PMC3169583.

Wackler B, Schneider P, Jacobs JM, Pauly J, Allen C, Nett M, Hoffmeister D. Ralfuranone biosynthesis in Ralstonia solanacearum suggests functional divergence in the quinone synthetase family of enzymes. Chem Biol. 2011 Mar 25;18(3):354-60. doi: 10.1016/j.chembiol.2011.01.010. PubMed PMID: 21439480.

Schneider P, Jacobs JM, Neres J, Aldrich CC, Allen C, Nett M, Hoffmeister D.  The global virulence regulators VsrAD and PhcA control secondary metabolism in the plant pathogen Ralstonia solanacearum. Chembiochem. 2009 Nov
23;10(17):2730-2. doi: 10.1002/cbic.200900510. PubMed PMID: 19830761.