ORCID Profile
0000-0002-1553-2013
Current Organisation
The Ohio State University
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Publisher: Scientific Societies
Date: 02-2021
Publisher: Scientific Societies
Date: 26-08-2023
DOI: 10.1094/PHYTO-10-22-0373-SC
Abstract: Evolutionarily, early-branching xanthomonads, also referred to as clade-1 xanthomonads, include major plant pathogens, most of which colonize monocotyledonous plants. Seven species have been validly described, among them the two sugarcane pathogens Xanthomonas albilineans and Xanthomonas sacchari, as well as Xanthomonas translucens, which infects small-grain cereals and erse grasses but also asparagus and pistachio trees. Single-gene sequencing and genomic approaches have indicated that this clade likely contains more, yet-undescribed species. In this study, we sequenced representative strains of three novel species using long-read sequencing technology. Xanthomonas c estris pv. phormiicola strain CFBP 8444 causes bacterial streak on New Zealand flax, another monocotyledonous plant. Xanthomonas sp. strain CFBP 8443 has been isolated from common bean, and Xanthomonas sp. strain CFBP 8445 originated from banana. Complete assemblies of the chromosomes confirmed their unique phylogenetic position within clade 1 of Xanthomonas. Genome mining revealed novel genetic features, hitherto undescribed in other members of the Xanthomonas genus. In strain CFBP 8444, we identified genes related to the synthesis of coronatine-like compounds, a phytotoxin produced by several pseudomonads, which raises interesting questions about the evolution and pathogenicity of this pathogen. Furthermore, strain CFBP 8444 was found to contain a second, atypical flagellar gene cluster in addition to the canonical flagellar gene cluster. Overall, this research represents an important step toward better understanding the evolutionary history and biology of early-branching xanthomonads.
Publisher: American Society for Microbiology
Date: 16-12-2021
DOI: 10.1128/MRA.00893-21
Abstract: Erwinia amylovora is the causative agent of fire blight, a devastating disease of apples and pears worldwide. Here, we report draft genome sequences of four streptomycin-sensitive strains of E. amylovora that were isolated from diseased apple trees in Ohio.
Publisher: Scientific Societies
Date: 20-04-2023
DOI: 10.1094/PHYTO-12-22-0477-SC
Abstract: Strains of Xanthomonas citri pv. malvacearum cause bacterial blight of cotton, a potentially serious threat to cotton production worldwide, including in sub-Saharan countries. Development of disease symptoms, such as water soaking, has been linked to the activity of a class of type 3 effectors, called TAL (transcription activator-like) effectors, which induce susceptibility genes in the host’s cells. To gain further insight into the global ersity of the pathogen, to elucidate their repertoires of TAL effector genes and to better understand the evolution of these genes in the cotton-pathogenic xanthomonads, we sequenced the genomes of three African strains of X. citri pv. malvacearum using nanopore technology. We show that the cotton-pathogenic pathovar of X. citri is a monophyletic lineage containing at least three distinct genetic subclades, which appear to be mirrored by their repertoires of TAL effectors. We observed an atypical level of TAL effector gene pseudogenization, which might be related to resistance genes that are deployed to control the disease. Our work thus contributes to a better understanding of the conservation and importance of TAL effectors in the interaction with the host plant, which can inform strategies for improving resistance against bacterial blight in cotton.
Publisher: Cold Spring Harbor Laboratory
Date: 07-04-2022
DOI: 10.1101/2022.04.05.487151
Abstract: Xanthomonas translucens pv. translucens (Xtt) is a global barley pathogen and a concern for resistance breeding and regulation. Long-read whole genome sequences allow in-depth understanding of pathogen ersity. We have completed long-read PacBio sequencing of two Minnesotan Xtt strains and an in-depth analysis of available Xtt genomes. We found that average nucleotide identity(ANI)-based approaches organize Xtt strains differently than the previously standard MLSA approach. According to ANI, Xtt forms a separate clade from Xanthomonas translucens pv. undulosa and consists of three main groups which are represented on multiple continents. The global distribution of Xtt groups suggests that regulation of seed is not important for prevention of Xtt spread. Some virulence factors, such as 17 Type III-secreted effectors, are highly conserved and offer potential targets for the elicitation of broad resistance. However, there is a high degree of variation in virulence factors meaning that germplasm should be screened for resistance with a erse panel of Xtt.
Publisher: Scientific Societies
Date: 11-2019
Publisher: Scientific Societies
Date: 04-05-2023
DOI: 10.1094/PHYTO-04-22-0113-SC
Abstract: Xanthomonas translucens pv. translucens (Xtt) is a global barley patho-gen and a concern for resistance breeding and regulation. Long-read whole genome sequences allow in-depth understanding of pathogen ersity. We have completed long-read PacBio sequencing of two Minnesotan Xtt strains and an in-depth analysis of available Xtt genomes. We found that average nucleotide identity (ANI)-based approaches organize Xtt strains different from the previous standard multilocus sequencing analysis approach. According to ANI, Xtt forms a separate clade from X. translucens pv. undulosa and consists of three main groups which are represented on multiple continents. Some virulence factors, such as 17 Type III-secreted effectors, are highly conserved and offer potential targets for the elicitation of broad resistance. However, there is a high degree of variation in virulence factors, meaning that germplasm should be screened for resistance with a erse panel of Xtt.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 13-11-2020
Abstract: A single gene with a dynamic evolutionary history allows plant pathogenic bacteria to spread systemically through their hosts.
Publisher: Cold Spring Harbor Laboratory
Date: 10-07-2022
DOI: 10.1101/2022.07.09.499425
Abstract: Bacterial leaf streak, blight and black chaff caused by Xanthomonas translucens pathovars are major diseases affecting small grains. Xanthomonas translucens pv. translucens and X. translucens pv. undulosa are seedborne pathogens that cause similar symptoms on barley, but only X. translucens pv. undulosa causes bacterial leaf streak of wheat. Recent outbreaks of X. translucens have been a concern for wheat and barley growers in the Northern Great Plains and Upper Midwest however, there are limited diagnostic tools for pathovar differentiation. We developed a multiplex PCR based on whole-genome differences to distinguish X. translucens pv. translucens and X. translucens pv. undulosa . We validated the primers across different Xanthomonas and non- Xanthomonas strains. To our knowledge, these are the first multiplex PCR to distinguish X. translucens pv. translucens and X. translucens pv. undulosa . These molecular tools will support disease management strategies enabling detection and pathovar incidence analysis of X. translucens .
Publisher: Cold Spring Harbor Laboratory
Date: 15-05-2021
DOI: 10.1101/2021.05.12.443947
Abstract: Xylella fastidiosa ( Xf ) is a globally distributed plant pathogenic bacterium. The primary control strategy for Xf diseases is eradicating infected plants therefore, timely and accurate detection is necessary to prevent crop losses and further pathogen dispersal. Conventional Xf diagnostics primarily relies on quantitative PCR (qPCR) assays. However, these methods do not consider new or emerging variants due to pathogen genetic recombination and sensitivity limitations. We developed and tested a metagenomics pipeline using in-house short-read sequencing as a complementary approach for affordable, fast, and highly accurate Xf detection. We used metagenomics to identify Xf to strain level in single and mixed infected plant s les at concentrations as low as one picogram of bacterial DNA per gram of tissue. We also tested naturally infected s les from various plant species originating from Europe and the United States. We identified Xf subspecies in s les previously considered inconclusive with real-time PCR (Cq 35). Overall, we showed the versatility of the pipeline by using different plant hosts and DNA extraction methods. Our pipeline provides taxonomic and functional information for Xf diagnostics without extensive knowledge of the disease. We hope this pipeline can be used for early detection of Xf and incorporated as a tool to inform disease management strategies. Xylella fastidiosa (Xf) destructive outbreaks in Europe highlight this pathogen’s capacity to expand its host range and geographical distribution. The current disease diagnostic approaches are limited by a multiple-step process, biases to known sequences, and detection limits. We developed a low-cost, user-friendly metagenomic sequencing tool for Xf detection. In less than three days, we were able to identify Xf subspecies and strains in field-collected s les. Overall, our pipeline is a diagnostics tool that could be easily extended to other plant-pathogen interactions and implemented for emerging plant threat surveillance.
Publisher: Scientific Societies
Date: 06-2023
DOI: 10.1094/PHYTOFR-04-22-0037-FI
Abstract: Disease-free planting stocks and formal certification systems are critical for the profitable production of vegetatively propagated crops. Propagation through seed tubers is the standard and preferred process for potato production. Seed tuber certification systems are used in the United States and throughout the world to mitigate degeneration and promote the use of high-quality planting stocks. Seed certification uses molecular and serological diagnostic methods for stock testing. While the molecular assays available are well-validated and offer high sensitivity, the rapidly evolving pathogens they target routinely develop mutations that allow them to evade detection. Ex les of these limitations are the potato diseases soft rot and blackleg, caused by Pectobacterium and Dickeya species. These diseases are challenging for current diagnostics tools because of high pathogen genomic variability, identical symptom development, and co-infections. Given the rapidly changing genetics of soft rot and blackleg bacteria, metagenomic sequencing should be adopted as a tool for routine validation of currently accepted diagnostic methods, and for the development of new diagnostic assays. We propose metagenome sequencing usage to enhance the diagnostic capabilities and complement molecular epidemiology approaches. We envision that metagenomics will accelerate diagnosis, shorten response time to outbreaks caused by unknown microorganisms, and provide more accurate and sustainable management strategies for seed certification programs. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Publisher: Scientific Societies
Date: 2021
DOI: 10.1094/PBIOMES-12-20-0092-SC
Abstract: Root-associated bacteria play critical roles in shaping plant health for abiotic and biotic stress tolerance. The Leifsonia genus includes pathogenic and beneficial bacteria but limited research is available comparatively across species regarding their association with plants. We recently identified the plant growth-promoting Leifsonia sp. C5G2 isolated from the rhizosphere of Plectranthus scutellarioides (coleus) that increased stress tolerance and quality of water-stressed greenhouse ornamentals. Using this beneficial strain as a model, we performed comparative genomics with beneficial, commensal, and pathogenic Leifsonia spp. to better understand plant association and growth promotion under abiotic stress. Comparative phylogenetic analyses showed that beneficial and commensal Leifsonia spp. clustered separately from pathogenic Leifsonia xyli subsp. xyli. In addition, the beneficial or commensal strains share biosynthetic gene and orthologous protein clusters that are not shared with known phytopathogens in our analysis. The phytopathogenic Leifsonia strains also share noticeably higher percent homology with plant-associated virulence factors in closely related Clavibacter spp. than the beneficial or commensal strains. Genome analysis supplemented with in vitro assays validated the findings that our model growth-promoting Leifsonia sp. strain C5G2 was highly prolific on erse carbon sources. This is unlike known fastidious growth behaviors of phytopathogenic Leifsonia spp. Beneficial Leifsonia sp. C5G2 imparts water stress tolerance in plants, and multiple genes were identified in the genomes of beneficial Leifsonia strains that are potentially involved in bacterial osmotic stress and the production of osmoprotectants and vitamin B9. This work sheds light on the ersity of the genus Leifsonia, with a better understanding of potential mechanisms employed by poorly understood beneficial bacteria.
Publisher: Scientific Societies
Date: 2021
DOI: 10.1094/PDIS-06-20-1269-A
Abstract: Ralstonia solanacearum phylotype II sequevar 1 (RsII-1, formerly race 3 biovar 2) causes tomato bacterial wilt, potato brown rot, and Southern wilt of geranium. Strains in RsII-1 cause wilting in potato and tomato at cooler temperatures than tropical lowland R. solanacearum strains. Although periodically introduced, RsII-1 has not established in the United States. This pathogen is of quarantine concern and listed as a Federal Select Agent. We report a rapidly sequenced ( days) draft genome of UW848, a RsII-1 isolate introduced to the United States in geranium cuttings in spring 2020. UW848 belongs to the near-clonal cluster of RsII-1 global pandemic strains.
Publisher: Scientific Societies
Date: 2020
DOI: 10.1094/PDIS-05-19-1103-A
Abstract: Xanthomonas translucens pv. translucens causes bacterial leaf streak and bacterial blight diseases of barley. This pathogen limits barley production globally but remains understudied, with limited genomic resources. To better understand the biology of this X. translucens subgroup, we sequenced the complete genome of the X. translucens pv. translucens strain UPB886.
Publisher: Scientific Societies
Date: 07-2023
Publisher: Cold Spring Harbor Laboratory
Date: 23-05-2023
DOI: 10.1101/2023.05.23.541994
Abstract: Quickly understanding the genomic changes that lead to pathogen emergence is necessary to launch mitigation efforts and reduce harm. Often the evolutionary events that result in an epidemic typically remain elusive long after an outbreak, which is particularly true for plant pathogens. To rapidly define the consequential evolutionary events result in pathogen emergence, we tracked in real-time a 2022 bacterial plant disease outbreak in US geranium ( Pelargonium x hortorum ) caused by Xhp2022, a novel lineage of Xanthomonas hortorum . Genomes from 31 Xhp2022 isolates from seven states showed limited chromosomal variation, and all contained a single plasmid (p93). Time tree and SNP whole genome analysis estimated that Xhp2022 emerged in the early 2020s. Phylogenomic analysis determined that p93 resulted from cointegration of three plasmids (p31, p45, and p66) present in a 2012 outbreak. p31, p45 and p66 were in idually found in varying abundance across X. hortorum isolates from historical outbreaks dating to 1974 suggesting these plasmids were maintained in the broader metapopulation. p93 specifically arose from two co-integration events from homologous and Tn 3 and XerC-mediated site-specific recombination. Although p93 suffered a 49kb nucleotide reduction, it maintained critical fitness gene functions encoding, for ex le, metal resistance and virulence factors, which were likely selected by the ornamental production system. Overall we demonstrate how rapid sequencing of current and historical isolates track the evolutionary history of an emerging, ongoing threat. We show a recent, tractable event of genome reduction for niche adaptation typically observed over millenia in obligate and fastidious pathogens. Genome-resolved epidemiology is rapidly changing how we track pathogens in real-time to support stakeholders and health. This research highlights how we responded to a current disease outbreak of geranium. Our work revealed that a new group of the bacterial plant pathogen Xanthomonas horotrum emerged in 2022 as a result of a recent genome reduction. We determined that three distinct plasmids were present in the broader X. hortorum metapopulation since 1974. In 2012, the three plasmids were altogether present in in idual isolates then in 2022, all three plasmids co-integrated while maintaining critical fitness genes but losing extraneous genomic material. This parallels genome efficiency and reduction that we see across millenia or even millions of years with obligate parasites with increased niche-specificity.
Publisher: Scientific Societies
Date: 06-2023
Publisher: Scientific Societies
Date: 07-2023
Publisher: Scientific Societies
Date: 09-2022
Publisher: Cold Spring Harbor Laboratory
Date: 10-10-2022
DOI: 10.1101/2022.10.10.511549
Abstract: Evolutionary early-branching xanthomonads, also referred to as clade-1 xanthomonads, include major plant pathogens, most of which colonize monocotyledonous plants. Seven species have been validly described, among them the two sugarcane pathogens Xanthomonas albilineans and Xanthomonas sacchari , and Xanthomonas translucens , which infects small grain cereals, erse grasses, but also asparagus and pistachio trees. Single-gene sequencing and genomic approaches indicated that this clade likely contains more, yet undescribed species. In this study, we sequenced representative strains of three novel species using long-read sequencing technology. Xanthomonas sp. pv. phormiicola strain CFBP 8444 causes bacterial streak on New Zealand flax, another monocotyledonous plant. Xanthomonas sp. strain CFBP 8443 has been isolated from common bean and Xanthomonas sp. strain CFBP 8445 originated from banana. Complete assemblies of the chromosomes confirmed their unique taxonomic position within clade 1 of Xanthomonas . Genome mining revealed novel genetic traits, hitherto undescribed in other members of the Xanthomonas genus. In strain CFBP 8444, we identified genes related to the synthesis of coronatine-like compounds, a phytotoxin produced by several pseudomonads, which raises interesting questions about the evolution and pathogenicity of this pathogen. In addition, strain CFBP 8444 was found to encode a second, atypical flagellar gene cluster in addition to the canonical flagellar gene cluster. Overall, this research represents an important step toward better understanding the evolutionary history and biology of early-branching xanthomonads.
Publisher: Cold Spring Harbor Laboratory
Date: 22-07-2023
DOI: 10.1101/2023.07.22.549466
Abstract: Plant pathogenic bacteria often have a narrow host range, which can vary among different isolates within a population. Here we investigated the host range of the tomato pathogen Clavibacter michiganensis (Cm). We determined the genome sequences of 40 tomato Cm isolates and screened them for pathogenicity on tomato and eggplant. Our screen revealed that out of the tested isolates, five were unable to cause disease on any of the hosts, 33 were exclusively pathogenic on tomato, and two were capable of infecting both tomato and eggplant. Through comparative genomic analyses, we identified that the five non-pathogenic isolates lacked the chp/tomA pathogenicity island, which has previously been associated with virulence in tomato. In addition, we found that the two eggplant-pathogenic isolates encode a unique allelic variant of the serine protease chpG ( chpG C ), an effector that is recognized in eggplant. Introduction of chpG C into a chpG inactivation mutant in the eggplant-non-pathogenic strain Cm101, failed to complement the mutant, which retained its ability to cause disease in eggplant and failed to elicit hypersensitive response (HR). Conversely, introduction of the chpG variant from Cm101 into an eggplant pathogenic isolate (CmC48), eliminated its pathogenicity on eggplant, and enabled CmC48 to elicit HR. Our study demonstrates that allelic variation in the chpG effector gene is a key determinant of host range plasticity within Cm populations.
Publisher: American Society for Microbiology
Date: 26-10-2021
DOI: 10.1128/MSYSTEMS.00591-21
Abstract: Destructive Xylella fastidiosa ( Xf ) outbreaks in Europe highlight this pathogen’s capacity to expand its host range and geographical distribution. The current disease diagnostic approaches are limited by a multiple-step process, biases to known sequences, and detection limits.
Location: France
No related grants have been discovered for Jonathan Michael Jacobs.