Biology subjects

Toth, H.

Publications and source records attributed to Toth, H..

5 recordsLinked to original sources

bioRxiv2026

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

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 >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.

genomics↗

bioRxiv2025

Effector loss and gain drives pathogen host range at a fitness cost

Epidemic preparedness depends on tracking microbial evolution that drives shifts in ecological behaviors such as disease emergence. However, the genetic constraints for microbial host adaptation to emerge for generalist and specialist behaviors remain poorly described. Here, we show that generalist cereal pathogen Xanthomonas translucens arose from a specialist ancestor via the loss of a single effector gene, xopAL1. Deleting barley-specialist X. translucens xopAL1 recapitulated the host jump to wheat and demonstrates risk across each globally distributed genetic lineage. However, this niche expansion via XopAL1 loss incurs a significant pathogenic fitness cost to colonize barley. Moreover, the specialist lineage gained an additional effector gene, xopAJ, which enhanced virulence on barley while restricting oat infection, thereby reinforcing niche specialization. We further identified key host pathways mediating resistance to the specialist lineage of X. translucens, opening avenues for potentially identifying targets for crop improvement. Our work provides an experimentally validated evolutionary framework to understand mechanisms of intergenera host jump. Overall, we demonstrate that single events of gene loss and gain shape ecological behaviors of pathogens by creating a dynamic trade-off between niche breadth and specialization.

microbiology↗

bioRxiv2025

Uncovering the transcriptional hallmarks of endothelial cell aging via integrated single-cell analysis

Endothelial cells (ECs) are critical regulators of vascular function and exhibit specialized, organ-specific roles across tissues. During aging, these cells become dysfunctional, resulting in increased susceptibility to cardiovascular disease and its associated mortality. While single-cell transcriptomics studies have revealed extensive endothelial heterogeneity across tissues and conditions, a comprehensive atlas of human EC transcriptomes over the course of the adult human lifespan is still lacking. Here, we present the Human Aging Endothelial Cell Atlas (HAECA), a harmonized single-cell transcriptomic compendium of over 375,000 ECs from 12 human tissues throughout adulthood. Using HAECA, we identified age-associated transcriptional shifts, including a decline in angiogenic gene expression in venous ECs and widespread alterations in extracellular matrix (ECM)- and mechanotransduction-associated pathways. We validated these findings in aging human skin and further uncovered a p21-linked transcriptional program in ECs, confirmed in both in vitro and in vivo models and linked to cellular senescence. Together, our study provides a high-resolution transcriptome reference across spatial as well as temporal axes of the human endothelium.

cell biology↗

bioRxiv2025

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

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.

plant biology↗

bioRxiv2023

Live tracking of a plant pathogen outbreak reveals rapid and successive, multidecade episome reduction

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 individually 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 Tn3 and XerC-mediated site-specific recombination. Although p93 suffered a 49kb nucleotide reduction, it maintained critical fitness gene functions encoding, for example, 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. SignificanceGenome-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 individual 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.

microbiology↗