Biology subjects

Goss, E.

Publications and source records attributed to Goss, E..

8 recordsLinked to original sources

bioRxiv2026

Seed Microbiome Transfer Mitigates Intergenerational Dysbiosis, Modulates Plant Defenses and Suppresses Foliar Disease

Antibiotic-induced disruption of plant-associated microbiomes has the potential to alter host health beyond the directly exposed generation, yet whether the effects of dysbiosis are transmitted through the seed microbiome remains unknown. Here, we investigated the intergenerational impacts of streptomycin-induced dysbiosis in tomato (Solanum lycopersicum), demonstrated that seed microbiome transfer (SMT) restores progeny microbiome function and disease resistance, and characterized the underlying physiological and genetic mechanisms. Parental streptomycin exposure altered the composition of progeny rhizosphere bacterial communities, reduced expression of defense-associated genes, and increased susceptibility to Xanthomonas perforans. Suppression of immune gene expression was strongly associated with increased disease severity, indicating that parental dysbiosis impaired progeny plants ability to mount effective immune responses. Transfer of the seed microbiome from healthy plant donors partially restored rhizosphere community composition, reduced disease severity and recovered defense gene expression of three genes. Together, our findings demonstrated that antibiotic exposure microbiome disturbance generates intergenerational legacy effects that influence plant immunity and disease susceptibility and seed microbiome transfer can counteract this dysbiosis across generations.

plant biology↗

bioRxiv2026

Allelic Diversity and Core Conservation of Type III Effectors Across Xanthomonads Causing Bacterial Spot of Pepper and Tomato

Bacterial spot of tomato and pepper (BST/P) is an economically devastating disease caused by four distinct Xanthomonas pathogens: X. euvesicatoria pv. euvesicatoria (Xe), X. euvesicatoria pv. perforans (Xp), X. hortorum pv. gardneri (Xg), and X. vesicatoria (Xv). A key component of virulence in these pathogens is the type III secretion system (T3SS), which delivers type III effector (T3E) proteins into host plant cells. To comprehensively characterize T3E repertoires and assess the stability of core effectors at a population scale, we evaluated a global dataset comprising 1,037 quality-filtered genomes, including 585 Xp, 350 Xe, 69 Xg, and 33 Xv strains. Across this collection, genes for six effectors were present in 100% of the examined genomes (XopK, XopL, XopM, XopN, XopX, and XopZ1) and an additional four effectors in [≥]95% of genomes (XopK, XopL, XopM, XopN, XopX, and XopZ1). Xp and Xe populations maintained large total effector repertoires with extensive allelic variation, displaying exceptional polymorphism within XopD and XopAD. In contrast, Xg and Xv exhibited highly stable effector profiles with markedly reduced allelic diversification across geographic regions and decades. Disruptive mutations, including early stop codons and frameshifts mutations, in genes for XopAZ, XopAF, and XopAR were prevalent across specific pathogens pointing to ongoing pseudogenization and targeted gene loss. These findings provide a high-resolution characterization of the conserved and variable components of the BST/P pathogen effector arsenal and serve as a foundation for monitoring population evolution and breeding durable disease resistance to multiple pathogens.

genomics↗

bioRxiv2026

Antibiotics and copper drive compartment-specific dysbiosis and functional reprogramming in tomato microbiomes

Plant-associated microbiomes help sustain plant immunity and productivity, yet the degree to which agricultural antimicrobials reshape these microbial networks and alter disease outcomes remains poorly characterized. Here, we quantified how chemical inputs such as copper and streptomycin trigger distinct, compartment-specific dysbiosis in tomato (Solanum lycopersicum), fundamentally decoupling microbiome-mediated immunity from pathogen defense. We demonstrated that chemical disturbance correlates with increased susceptibility to bacterial spot caused by Xanthomonas perforans. Notably, streptomycin-induced dysbiosis increased epidemic intensity, characterized by physiological and growth trade-offs, including reduced fruit number, mass, and seed weight, alongside a decline in photosynthetic gas exchange; while copper-induced dysbiosis had intermediate effects. Chemical perturbation restructured microbiomes in a niche-dependent manner based on amplicon profiling: seeds and the phyllosphere showed the greatest instability, including higher dispersion, taxon turnover, and network reorganization under streptomycin, whereas rhizosphere communities remained more deterministic but were structurally reshaped by copper. Rhizosphere metagenomics further revealed enrichment of antibiotic-resistance functions under streptomycin treatment and of metal-tolerance and oxidative-stress functions under copper treatment, along with shifts in genes linked to cell-envelope remodeling and redox metabolism. These findings identify microbiome dysbiosis as a mechanistic bridge between chemical stress and plant disease, and support crop protection strategies that preserve microbiome integrity.

plant biology↗

bioRxiv2026

Patching the Leak or Rebuilding the Boat? Evaluating Targeted Probiotic Cyanobacteria and Microbiome Transplants to Counteract Rhizosphere Dysbiosis

Antibiotic use in agricultural systems can unintentionally disrupt beneficial rhizosphere microorganisms, yet the consequences of this dysbiosis for plant fitness remain insufficiently understood. Building on previous findings that application of streptomycin to the roots decreases cyanobacteria and increases tomato plant susceptibility to foliar Xanthomonas infection, this study aimed to determine whether this relationship reflects causation or correlation. We evaluated whether targeted inoculation with the filamentous nitrogen-fixing cyanobacterium Cylindrospermum sp. (CI) or a complex rhizosphere microbiome transplant (RMT) could mitigate antibiotic-induced dysbiosis. As expected, streptomycin treatment significantly increased bacterial spot disease severity and reduced microbial richness in the rhizosphere, marked by a pronounced decline in cyanobacterial and Cylindrospermum operational taxonomic units. Co-occurrence network analysis revealed that this dysbiotic state was defined by reduced community connectivity and increased negative associations, indicating a breakdown in cooperative microbial relationships. Notably, both CI and RMT reduced plant disease severity, though they caused distinct rhizosphere community reassembly outcomes. While RMT relied on microbial functional redundancy, the targeted CI approach achieved more robust colonization and effectively "patched" the functional gap left by dysbiosis. Microbiome restoration directly influenced host physiology, significantly reducing the overactivation of ethylene-mediated defense genes, such as ERF1, and partially reinstating auxin-responsive signaling pathways (IAA21) that were disrupted under dysbiosis. These findings suggest that targeted microbial inoculation could reverse dysbiosis and enhance plant resilience under pathogen pressure as effectively as complex microbial transplants. This work highlights a shift in microbiome management: from the complex rebuilding of communities to the strategic repair of specific functional gaps.

microbiology↗

bioRxiv2025

Rapid population flux in bacterial spot xanthomonads during a transition in dominance between two genotypes in consecutive tomato production seasons and identification of a new species Xanthomonas oklahomensis sp. nov.

In the bacterial spot of tomato disease complex, Xanthomonas euvesicatoria pv. perforans (Xep) is known to outcompete X. euvesicatoria pv. euvesicatoria (Xee). The result, over time in tomato production systems where both pathogens are present, is the anticipated displacement of Xee by Xep. In this study, we characterized the population of recovered strains from grower fields in response to a bacterial spot of tomato outbreak in east and central Oklahoma in 2018 and 2019. Tomato and pepper strains sampled in earlier years were included to provide additional context. Phenotypic and genome-based analyses showed marked differences in race and species composition in recovered strains. All pre-2018 (2001-2014) tomato bacterial spot strains were Xep race T3, except one T4 strain. Tomato bacterial spot strains in 2018 consisted of Xee race T1 and Xep T3, while strains recovered in 2019 from the same locations were exclusively Xep T4 strains. The 2019 Xep T4 strains form the same cluster with the 2014 Xep T4 strain on the phylogenetic tree, suggesting the same population. Only the Xep race T4 strains showed an expanded host range to pepper. The recovered strains were also variable in copper sensitivity and effector content. We additionally recovered non-bacterial spot xanthomonads, one of which belongs to the new species, Xanthomonas oklahomensis sp. nov. These results contributes to novel insights in understanding genomic heterogeneity and seasonal population flux between competing bacterial genotypes during disease outbreaks and can be considered when developing disease management strategies.

plant biology↗

bioRxiv2024

The Underground World of Plant Disease: How Does Rhizosphere Dysbiosis Affect Plant Health Above-ground?

Similar to the human gut microbiome, diverse microbes colonize the plant rhizosphere, and an imbalance of this microbial community, known as dysbiosis, may negatively impact plant health. This study aimed to investigate the influence of rhizosphere dysbiosis on above-ground plant health using tomato plants (Solanum lycopersicum L.) and the foliar bacterial spot pathogen Xanthomonas perforans as model organisms. Four-week-old tomato plants rhizospheres were treated with streptomycin (0.6 g x L-1), or water (negative control) and spray-inoculated with X. perforans (105 cells x mL-1) after 24 h. Half of the plants treated with streptomycin and X. perforans received soil microbiome transplants (SMT) from uninfected plant donors 48 h after streptomycin application. Streptomycin-treated plants showed a 26% increase in disease severity compared to plants that received no antibiotic, while plants that received the SMT had an intermediate level of disease severity. Antibiotic-treated plants showed a reduced abundance of rhizobacterial taxa like Cyanobacteria from the genus Cylindrospermum as well as down-regulation of genes related to plant primary and secondary metabolism and up-regulation of plant defense genes associated with induced systemic resistance (ISR). This study highlights the crucial role of beneficial rhizosphere microbes in disease resistance, even to foliar pathogens.

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↗

bioRxiv2021

Invasive grass litter suppresses native species and promotes disease

Plant litter can alter ecosystems and promote plant invasions by changing resource acquisition, depositing toxins, and transmitting microorganisms to living plants. Transmission of microorganisms from invasive litter to live plants may gain importance as invasive plants accumulate pathogens over time since introduction. It is unclear, however, if invasive plant litter affects native plant communities by promoting disease. Microstegium vimineum is an invasive grass that suppresses native populations, in part through litter production, and has accumulated leaf spot diseases since its introduction to the U.S. In a greenhouse experiment, we evaluated how M. vimineum litter and accumulated pathogens mediated resource competition with the native grass Elymus virginicus. Resource competition reduced biomass of both species and live M. vimineum increased disease incidence on the native species. Microstegium vimineum litter also promoted disease on the native species, suppressed establishment of both species, and reduced biomass of M. vimineum. Nonetheless, interference competition from litter had a stronger negative effect on the native species, increasing the relative abundance of M. vimineum. Altogether, invasive grass litter suppressed both species, ultimately favoring the invasive species in competition, and increased disease incidence on the native species.

ecology↗