Biology subjects

Schurr, U.

Publications and source records attributed to Schurr, U..

6 recordsLinked to original sources

bioRxiv2025

Phage biocontrol reduces the burden on plant immunity through suppression of bacterial virulence

Bacteriophages are increasingly recognized as key players in modulating plant-microbe interactions, including their potential in the biocontrol of plant pathogenic bacteria. In this study, we investigated the tripartite interaction between Arabidopsis thaliana, the bacterial plant pathogen Xanthomonas campestris pv. campestris (Xcc), and the lytic phage Seregon. Using parallel transcriptomic profiling, we characterized host and pathogen responses during infection and phage treatment. While treatment with phage Seregon did not lead to the eradication of Xcc, it significantly mitigated Xcc-induced disease symptoms, restoring leaf area to levels comparable to the uninfected control within 14 days post-inoculation. Our data revealed that phage-mediated protection is associated with early bacterial recognition, and suppression of Jasmonate (JA)-related responses in the host. Analysis of nuclear localized reporter plant lines further confirmed a significant reduction in ROS levels and JA biosynthesis in phage-treated plants. Concurrently, Xcc exhibited significant transcriptional downregulation of key virulence factors in the presence of the phage, including the genes encoding the type III secretion system, its associated effectors, and components involved in flagella biosynthesis. Remarkably, phage treatment did not lead to a significant increase in bacterial resistance to phage infection, which is in stark contrast to in vitro conditions. Taken together, this study provides first mechanistic insight into how phages can be harnessed to shape plant-pathogen interactions and highlights their potential role in enhancing plant resilience through targeted modulation of both host immunity and pathogen behavior.

microbiology↗

bioRxiv2024

Seed coating with phages for sustainable plant biocontrol of plant pathogens and influence of the seed coat mucilage

Pathogens resistant to classical control strategies are on the rise and cause significant damage in crop yield production with seeds as one major transmission route. Bacteriophages are specialized viruses of bacteria and their interaction with seeds holds great potential as targeted and sustainable solution to this problem. In this study, we isolated and characterized two novel phages, Athelas and Alfirin, infecting Pseudomonas syringae and Agrobacterium tumefaciens, respectively, and included the recently published phage Pfeifenkraut infecting Xanthomonas translucens. The three phages were tested for their interaction with the seed coat mucilage. Phage binding on Arabidopsis seeds, which exude the mucilage as a polysaccharide-polymer-matrix, was assessed by comparison to seeds with removed mucilage. Two of the three phages were dependant on mucilage for seed binding, and podophage Athelas showed the highest dependency. Further podoviruses of the Autographiviridae obtained from the systematic E. coli (BASEL) phage collection were tested and showed a similar dependency on the mucilage for seed adhesion. Comparative analysis using a set of Arabidopsis seed coat mutants revealed the diffusible cellulose fraction as important component for phage binding. Long-term activity tests revealed a high stability of phages on seed surfaces and phage coating effectively increased the survival rate of plant seedling in the presence of the pathogen. Utilization of non-virulent host strains was further successfully applied to boost the presence of infectious phage particles on seed surfaces. Altogether, our study highlights the high potential of phage-based applications as sustainable biocontrol strategy on the seed level.

microbiology↗

bioRxiv2023

Nitrogen availability during domestication shaped the divergence of tetraploid wheat

The domestication of crops, with the development of the agroecosystems, is associated with major environmental changes and represent a model to test the role of phenotypic plasticity. Here we investigated 32 genotypes representing key stages of tetraploid wheat domestication. We developed a dedicated pipeline combining RNA-Seq data, estimates of evolvability and QST to characterize the plasticity of gene expression and identify signatures of selection under different nitrogen conditions. The analysis of gene expression diversity showed contrasting results between primary and secondary domestication in relation to nitrogen availability. Indeed, nitrogen triggered the expression of twice the number of genes in durum wheat compared to emmer and wild emmer. QST distributions and QST-FST comparisons revealed distinct selection signatures at each domestication stage. While primary domestication affected the expression of genes involved in biotic interactions, secondary domestication was associated with changes in expression of genes involved in metabolism of amino acids, particularly lysine. Selection signatures were found also in differentially expressed genes, specifically involved in nitrogen metabolism, such as glutamate dehydrogenase. Overall, our findings show that nitrogen availability had a pivotal role during the domestication and adaptive responses of a major food crop, with varying effects across different traits and growth conditions.

genetics↗

bioRxiv2021

In vivo imaging and quantification of carbon tracer dynamics in nodulated root systems of pea plants

Legumes associate with root colonizing rhizobia that provide fixed nitrogen to its plant host in exchange for recently fixed carbon. There is a lack in understanding how individual plants modulate carbon allocation to a nodulated root system as a dynamic response to abiotic stimuli. One reason is that most approaches are based on destructive sampling, making quantification of localized carbon allocation dynamics in the root system difficult. We established an experimental workflow for routinely using non-invasive Positron Emission Tomography (PET) to follow the allocation of leaf-supplied 11C tracer towards individual nodules in a three-dimensional (3D) root system of pea (Pisum sativum). Nitrate was used for triggering the shutdown of biological nitrogen fixation (BNF) expected to rapidly affect carbon allocation dynamics in the root-nodule system. This nitrate treatment lead to a reduction of 11C tracer allocation to nodules by 40% - 47% in 5 treated plants while the variation in control plants was less than 11%. The established experimental pipeline enabled for the first time that several plants could consistently be labelled and measured using 11C tracer in a PET approach to quantify C-allocation to individual nodules following a BNF shutdown. This demonstrates the strength of using 11C tracers in a PET approach for non-invasive quantification of dynamic carbon allocation in several growing plants over several days. A major advantage of the approach is the possibility to investigate carbon dynamics in small regions of interest in a 3D system such as nodules in comparison to whole plant development. One sentence summaryPositron Emission Tomography for quantification of carbon allocation dynamics in individual nodules within a 3D root system revealed strong effect of nitrate on carbon allocation.

plant biology↗

bioRxiv2020

Comparative analysis based on transcriptomics and metabolomics data reveal differences between emmer and durum wheat in response to nitrogen starvation

Mounting evidence indicates the key role of Nitrogen (N) on diverse processes in plant, including not only yield but also development and defense. Using a combined transcriptomics and metabolomics approach, we studied the response of seedlings to N starvation of two different tetraploid wheat genotypes from the two main domesticated subspecies, emmer (Triticum turgidum ssp. dicoccum) and durum wheat (Triticum turgidum ssp. durum). We found that durum wheat exhibits broader and stronger response in comparison to emmer as evidenced by the analysis of the differential expression pattern of both genes and metabolites and gene enrichment analysis. Emmer and durum wheat showed major differences in the responses to N starvation for transcription factor families. While emmer showed differential reduction in the levels of primary metabolites to N starvation, durum wheat exhibited increased levels of most metabolites, including GABA as an indicator of metabolic imbalance. The correlation-based networks including the differentially expressed genes and metabolites revealed tighter regulation of metabolism in durum wheat in comparison to emmer, as evidenced by the larger number of significant correlations. We also found that glutamate and GABA had highest values of centrality in the metabolic correlation network, suggesting their critical role in the genotype-specific response to N starvation of emmer and durum wheat, respectively. Moreover, this finding indicates that there might be contrasting strategies associated to GABA and Glutamate signaling modulating shoot vs root growth in the two different wheat subspecies.

plant biology↗

bioRxiv2017

Reconstructing The Gigabase Plant Genome Of Solanum pennellii Using Nanopore Sequencing

Recent updates in sequencing technology have made it possible to obtain Gigabases of sequence data from one single flowcell. Prior to this update, the nanopore sequencing technology was mainly used to analyze and assemble microbial samples1-3. Here, we describe the generation of a comprehensive nanopore sequencing dataset with a median fragment size of 11,979 bp for the wild tomato species Solanum pennellii featuring an estimated genome size of ca 1.0 to 1.1 Gbases. We describe its genome assembly to a contig N50 of 2.5 MB using a pipeline comprising a Canu4 pre-processing and a subsequent assembly using SMARTdenovo. We show that the obtained nanopore based de novo genome reconstruction is structurally highly similar to that of the reference S. pennellii LA7165 genome but has a high error rate caused mostly by deletions in homopolymers. After polishing the assembly with Illumina short read data we obtained an error rate of <0.02 % when assessed versus the same Illumina data. More importantly however we obtained a gene completeness of 96.53% which even slightly surpasses that of the reference S. pennellii genome5. Taken together our data indicate such long read sequencing data can be used to affordably sequence and assemble Gbase sized diploid plant genomes.\n\nRaw data is available at http://www.plabipd.de/portal/solanum-pennellii and has been deposited as PRJEB19787.

genomics↗