About

Jonathan Jacobs is an Associate Professor in the Department of Plant Pathology at The Ohio State University. His research focuses on emerging infectious diseases, bacteriology, plant-microbe interactions, and international agriculture. He is based in 477B Kottman Hall, Columbus, and can be contacted via jacobs.1080@osu.edu. The information provided highlights his involvement in key areas of plant pathology, particularly in understanding and addressing new and evolving plant diseases through the study of bacterial pathogens and their interactions with plants, as well as his engagement with global agricultural challenges.

Research topics

• Biology
• Genetics
• Botany
• Ecology
• Evolutionary biology
• Immunology
• Computational biology

Selected publications

• The EPS-I exopolysaccharide transforms <i>Ralstonia</i> wilt pathogen biofilms into viscoelastic fluids for rapid dissemination in planta

  Proceedings of the National Academy of Sciences · 2026-01-22 · 2 citations

  articleOpen access

  Ralstonia solanacearum species complex (RSSC) pathogens cause destructive plant wilt diseases of a wide variety of crops, leading to significant agricultural losses worldwide. These bacteria rapidly spread through the water-transporting xylem where they grow prolifically and produce abundant biofilm that clogs xylem vessels. To understand RSSC biofilm behavior in planta, we examined their complex fluid mechanics. Rheological analyses revealed that unlike all previously analyzed microbial biofilms, RSSC biofilms are shear-thinning, viscoelastic fluids at physiologically relevant shear forces. To determine which factors confer these unique mechanics, we analyzed biofilms of bacterial mutants with altered biofilm components. Genetic analysis demonstrated that development of the viscous-dominant biofilms required production of EPS-I, an amphiphilic exopolysaccharide that is a major virulence factor for all RSSC pathogens. We show that EPS-I confers “biofilm mobility”, which allows wild-type RSSC colonies to passively expand when deformed. Despite its high metabolic cost, bioassays demonstrated that EPS-I production conferred a net fitness benefit where biofilm mobility allowed the pathogen to spread and access more nutrients in complex environments like xylem vessels. The RSSC are a monophyletic lineage of aggressive plant wilt pathogens, and our evolutionary hypothesis testing suggests the origin of the eps biosynthetic gene cluster coincides with the emergence of wilt pathogenesis in the RSSC ancestor. Furthermore, comparative physiological assays demonstrated that biofilm mobility is unique to the RSSC within the genus Ralstonia . In summary, EPS-I production is a key evolutionary innovation that enables RSSC dispersal and virulence by conferring unique biofilm mechanics.

  PublisherDOI

• Independent, ongoing clade-specific expansions of IS5 elements in Pseudomonas syringae

  Microbial Genomics · 2026-01-30 · 1 citations

  articleOpen accessSenior author

  Insertion sequence (IS) elements are transposable regions of DNA present in a majority of bacterial genomes. It is hypothesized that differences in distributions of IS elements across bacterial strains and species reflect underlying differences in population biology. Therefore, shifts in IS element distributions between closely related strains may be proxies for and reflective of changes in population dynamics. Here, we investigate the presence and distribution of a subclass of IS 5 elements throughout genomes of Pseudomonas syringae by querying complete genomes for the presence of InsH (the main transposase found within these IS 5 elements). We report that this one subclass of IS 5 elements appears to have recently undergone independent expansions in multiple P. syringae clades and find that a majority of IS 5 insertion sites are not conserved across three closely related P. syringae pv. lachrymans genomes. We present further evidence, as has been shown for other members of the IS 5 family in different taxa, that elements from this IS 5 subclass can drive the expression of downstream genes in P. syringae . Taken together, our results highlight how dynamic IS 5 elements can be within and across P. syringae genomes and point towards the potential for IS 5 elements to rewire expression patterns across the P. syringae genome.

  PublisherDOI

• Metagenomics for bacterial spot pathogen and virulence factor tracking for Ohio fresh market tomato and pepper production

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-05-06

  articleOpen accessSenior authorCorresponding

  Bacterial spot is a consistent threat to global tomato and pepper productions; however, Ohios fresh market production currently lacks the updated surveillance data necessary to provide accurate management solutions. While traditional diagnostics focus on identification of a single causal agent, shotgun metagenomic sequencing (MGS) offers a comprehensive view of the infection court. An assignment-first MGS workflow was developed and validated in this study, utilizing Kraken2 databases to extract Xanthomonas species associated with bacterial spot and to characterize the microbial communities of bacterial spot in Ohio production systems. Through in silico spiking experiments, thresholds were established for bacterial spot identification. Species and pathovar identification via average nucleotide identity (ANI) remained accurate at abundance as low as 0.1%. A minimum of 2% Xanthomonas reads were required for high genome completeness (BUSCO &gt;90%) and 3% for reliable type III secretion system (T3SS) effector profiling. Analysis of 63 samples from fresh-market production fields identified Xanthomonas hortorum pv. gardneri, Xanthomonas euvesicatoria pv. euvesicatoria, and Xanthomonas arboricola residing in symptomatic samples, alongside other taxa including Pseudomonas and Stenotrophomonas. Phylogenetic comparisons of metagenome-assembled genomes (MAGs) were comparable to whole genome sequences (WGS) from the same samples, supporting the reliability of culture-independent diagnostics. These results provide a robust framework for utilizing metagenomics as a diagnostic tool, expanding our knowledge of bacterial spot population structure in Ohio, and uncovering the bacterial communities associated with bacterial spot.

  PublisherDOI

• Identification of Halo Blight Disease on Oat in Idaho and Exploration of Resistant Sources in Oat, Barley and Wheat

  Plant Disease · 2026-01-06

  article

  Pseudomonas coronafaciens pv. coronafaciens (Pcc), the causal agent of Bacterial Halo blight (BHB) on oat, has been infrequently reported in the United States, with historical records limited to the 1920s through the 1960s. In 2023, oat trial fields in Aberdeen, Idaho were severely infected with an unknown disease that formed necrotic lesions on leaves. Preliminary identification based on colony morphology suggested a pathogen belonging to the genus Pseudomonas. Subsequent polymerase chain reaction amplified a 298 bp fragment that is diagnostic to Pcc. Further analysis using whole-genome sequencing confirmed 99.6% average nucleotide identity (ANI) with Pcc. This marks the first detection of Pcc in Idaho, and the first detailed description of the pathogen in the United States after over half a century. Host range and pathogenicity assessments on multiple cereal crops showed that Pcc was pathogenic on oat, barley, and corn. However, wheat, rye and triticale displayed chlorosis and early cell death in response to the pathogen. Evaluation of oat and barley genotypes revealed resistance in the two crop species to be rare with only 2.5, and 4.5% of oat and barley genotypes exhibiting some level of resistance. Notably, the four resistant and moderately resistant barley genotypes identified in this study: DH170472, Celebration, Legacy and Quest are the first to be reported as sources of resistance to BHB. Results of the present study provide a basis for further research toward a better understanding of disease epidemiology, the genetics of host-pathogen interaction and the management of BHB on oat, barley and corn.

  PublisherDOI

• Tissue-Specific Experimental Evolution Reveals Adaptive Trade-Offs in the Plant Vascular Pathogen <i>Clavibacter michiganensis</i>

  The ISME Journal · 2026-05-03

  articleOpen access

  Abstract The plant pathogenic bacterium Clavibacter michiganensis (Cm) is a systemic vascular pathogen that colonizes both xylem vessels and the intracellular apoplast during different stages of infection. To identify traits and loci associated with adaptation to these distinct host microenvironments, we conducted tissue-specific experimental evolution. Twenty independent Cm lineages were repeatedly passaged in either tomato stems or leaves to promote adaptation to vascular or apoplastic lifestyles, respectively. After fifteen passages, adapted clones were characterized for virulence and virulence-related traits. These characterizations demonstrated clear differential associations of virulence-associated traits with the adapted tissue. The majority of vascular-adapted clones displayed enhanced surface attachment, reduced cellulase activity, reduced exopolysaccharide (EPS) production, and attenuated virulence on tomato compared to the parent clone. In contrast, apoplast-adapted clones displayed reduced biofilm formation and enhanced EPS production and retained their virulence on tomato. Whole-genome sequencing of all adapted clones revealed candidate loci linked to tissue adaptation. Six of ten vascular-adapted clones carried two independent mutations in CMM_1284, a putative HipB/XRE-type transcriptional regulator. A CMM_1284 marker exchange mutant displayed phenotypes similar to vascular-adapted clones, suggesting a role for this regulator in vascular colonization. Together, these findings highlight the role of phenotypic plasticity in tissue adaptation of plant pathogens, showing that tissue-specific adaptation involves modulation of surface attachment, EPS production, and cell wall–degrading enzymes and suggest a trade-off between vascular persistence, supported by strong surface attachment, and systemic virulence, which depends on bacterial dispersal and migration.

  PublisherDOI

• The EPS-I exopolysaccharide transforms <i>Ralstonia</i> wilt pathogen biofilms into viscoelastic fluids for rapid dissemination <i>in planta</i>

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-05-22

  preprintOpen access

  Abstract Ralstonia solanacearum species complex (RSSC) pathogens cause destructive plant wilt diseases of a wide variety of crops, leading to significant agricultural losses worldwide. These bacteria rapidly spread through the water-transporting xylem where they grow prolifically and produce abundant biofilm that clogs xylem vessels. To understand RSSC biofilm behavior in planta , we examined their complex fluid mechanics. Rheological analyses revealed that unlike all previously analyzed microbial biofilms, RSSC biofilms are shear-thinning, viscoelastic fluids at physiologically relevant shear forces. To determine which factors confer these unique mechanics, we analyzed biofilms of bacterial mutants with altered biofilm components. Genetic analysis demonstrated that development of the viscous-dominant biofilms required production of EPS-I, an amphiphilic exopolysaccharide that is a major virulence factor for all RSSC pathogens. We show that EPS-I confers “biofilm mobility”, which allows wildtype RSSC colonies to passively expand when deformed. Despite its high metabolic cost, bioassays demonstrated that EPS-I production conferred a net fitness benefit where biofilm mobility allowed the pathogen to spread and access more nutrients in complex environments like xylem vessels. The RSSC are a monophyletic lineage of aggressive plant wilt pathogens, and our evolutionary hypothesis testing suggests the origin of the eps biosynthetic gene cluster coincides with the emergence of wilt pathogenesis in the RSSC ancestor. Furthermore, comparative physiological assays demonstrated that biofilm mobility is unique to the RSSC within the genus Ralstonia . In summary, EPS-I production is a key evolutionary innovation that enables RSSC dispersal and virulence by conferring unique biofilm mechanics. Significance Statement Ralstonia solanacearum species complex (RSSC) pathogens threaten global food security by fatally wilting plants. A soft matter physics lens demystified the cryptic role of a major virulence factor, the EPS-I exopolysaccharide. EPS-I transforms RSSC biofilms into viscoelastic fluids, a mechanical behavior not previously described for other microbial biofilms that are almost always viscoelastic solids. We demonstrate that the development of fluid biofilms was a key evolutionary innovation that enabled pathogenic success of these aggressive pathogens that rapidly wilt plants.

  PublisherOA PDFDOI

• Infecting Micropropagated Potato Plants with the Natural Potato Endophyte <i>Arthrobacter</i> sp. UW852 Increases Seed Tuber Productivity

  Phytobiomes Journal · 2025-07-29 · 1 citations

  articleOpen access

  Plant-associated microbes can reduce dependance on conventional agrochemicals by enhancing plant health and productivity through the production of biomolecules. Potato growers depend on healthy seed tubers, but chemical inputs are currently needed to ensure good yields of pathogen-free seed tubers. Adding beneficial microorganisms to a plant micropropagation system offers a more sustainable way to enhance productivity. We hypothesized that introducing natural potato endophytic bacteria to plantlets in tissue culture could increase seed potato minitubers. Bacterial endophytes were isolated from field-grown potato tubers and stems, selected for ability to harmlessly bacterize (colonize) in vitro plantlets, and screened for effects on plant growth and productivity. One promising candidate, named UW852, significantly increased tuber productivity in greenhouse trials. Phylogenetic analysis of the complete UW852 genome identified it as an actinomycete in the genus Arthrobacter. The genome putatively encodes synthesis of at least one iron-sequestering siderophore and the plant growth substance gibberellic acid. In vitro assays confirmed that the UW852 culture cell-free supernatant contains both siderophore activity and lettuce hypocotyl elongation activity consistent with production of gibberellic acid. UW852 remained detectable in 70% of daughter tubers harvested from plants that had been bacterized in vitro, suggesting that this bacterium can confer beneficial effects over a growing season or longer. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

  PublisherDOI

• A Pilot Study Using Casino Shifts to Improve Sleep for Emergency Medicine Fellows Working Night Shifts

  Pediatric Emergency Care · 2025-09-09

  article

  OBJECTIVES: Casino shifts, which end at 4 AM and allow sleep during the circadian "anchor period," may improve sleep and reduce fatigue for pediatric emergency medicine (PEM) fellows working night shifts. We hypothesized that using a casino shift model would improve perceived fatigue levels and measured sleep metrics. METHODS: In this pilot prospective observational cohort study, fellows worked traditional night shifts for one month (control) followed by casino shifts for one month (intervention). Sleep data were collected using a validated wrist actigraph (ReadiBand), and subjective perceptions of fatigue were collected using surveys. RESULTS: Eight fellows participated in the study. Compared with the control month, the intervention month was associated with increased sleep quantity and sleep efficiency as measured by the actigraph. Fellows also reported reduced perceived fatigue and improved energy levels during the intervention month. CONCLUSIONS: Switching to a casino shift schedule was associated with improvements in measured sleep and perceived fatigue among a cohort of PEM fellows in this pilot study. These preliminary findings warrant further investigation with larger samples and randomized scheduling to further explore the potential benefits and limitations of casino shift models in emergency medicine.

  PublisherDOI

• Application of multiple parallel mineralization method to grow lettuce, Swiss chard, and peppers in a simplified deep flow technique hydroponic system

  MethodsX · 2025-12-06

  articleOpen access

  Organic fertilizers are not widely used in hydroponics due to an absence of mineralizing microbes that process organic inputs into plant available forms. The Multiple Parallel Mineralization (MPM) method enables this microbial processing to occur in hydroponic systems. The objective of this method is to provide an accessible protocol for use of the MPM method in simplified deep flow technique hydroponic systems without a need for laboratory testing of nutrient content. The method described here provides hydroponic growers with an alternative option to mineral fertilizers. We provide information about yields and the affordability of this method that growers can use to determine the economic viability of this method in their respective markets. Swiss chard, lettuce, and bell peppers were grown with this method Aquarium nitrate test kits are used to replace lab testing typically used with the MPM method to validate the presence of nitrate as an indicator of microbial activity.

  PublisherDOI

• Identification of Halo Blight Disease on Oat in Idaho and Exploration of Resistant Sources in Oat, Barley and Wheat

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-03-07

  preprintOpen access

  Abstract Pseudomonas coronafaciens pv. coronafaciens ( Pcc ), the causal agent of Bacterial Halo blight (BHB) on oat, has been infrequently reported in the United States, with historical records limited to the 1920s through the 1960s. In 2023, oat trial fields in Aberdeen, Idaho were severely infected with an unknown disease that formed necrotic lesions on leaves. Preliminary identification based on colony morphology suggested a pathogen belonging to the genus Pseudomonas . Subsequent whole-genome sequencing confirmed 99.6% average nucleotide identity (ANI) with Pseudomonas coronafaciens pv. coronafaciens (Pcc) . This marks the first detection of Pcc in Idaho, and the first detailed description of the pathogen in the United States after over half a century. Host range and pathogenicity assessments on multiple cereal crops showed that Pcc was pathogenic on oat, barley, and corn. However, wheat, rye and triticale displayed chlorosis and early cell death in response to the pathogen. Evaluation of oat and barley genotypes revealed resistance in the two crop species to be rare with only 2.5, and 4.5% of oat and barley genotypes exhibiting some level of resistance. Notably, the four resistant and moderately resistant barley genotypes identified in this study: DH170472, Celebration, Legacy and Quest are the first to be reported as sources of resistance to BHB. Results of the present study provides a basis for further research toward a better understanding of disease epidemiology, the genetics of host-pathogen interaction and the management of BHB on oat, barley and corn.

  PublisherDOI

Recent grants

• NSF Postdoctoral Fellowship in Biology FY 2013

  NSF · $162k · 2013–2015

Frequent coauthors

• Ralf Koebnik

  Plant Health Institute de Montpellier

  185 shared

• Boris Szurek

  130 shared

• Álvaro L. Pérez‐Quintero

  129 shared

• Sébastien Cunnac

  Centre Occitanie-Montpellier

  116 shared

• Emilie Thomas

  Centre Léon Bérard

  98 shared

• Séverine Lacombe

  Université Joseph Ki-Zerbo

  97 shared

• Christophe Brugidou

  Université Joseph Ki-Zerbo

  97 shared

• Aurore Comte

  85 shared

Education

• Ph.D., Plant Pathology

  The Ohio State University

  1992

• M.S., Plant Pathology

  The Ohio State University

  1988

• B.S., Botany

  The Ohio State University

  1986

Awards & honors

• A. J. Hoffmann Award
• CC Allison Award
• 2022 Complete Genome Sequence Resource for Xanthomonas trans…