Research Spotlight

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Dec 18
Research Highlight: Evolution of the ToxB gene in Pyrenophora tritici-repentis and related species
​Reem Aboukhaddour, Cereal Pathology Lab, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada​

Overall Background

Across the expansive Canadian prairies, wheat can stretch as far as the eye can see, and during the growing season, its green leaves are a food source to several foliar-infecting pathogens. Among these pathogens is the fungus Pyrenophora tritici-repentis, which causes tan spot of wheat, a destructive foliar disease that emerged as a specialized necrotroph about 50 years ago. Since its emergence as a wheat pathogen, it has caused significant losses in North America, Australia, and other parts of the world. Today, tan spot is still one of the most destructive foliar diseases of wheat, and it is mainly managed by fungicides applications.

Why This Work and How It Came to Be

The question of how this fungus became a pathogen has been a pivotal inquiry among the research community, including my team, and aligns well with the ongoing exploration of the emergence of necrotrophic diseases. Since 2016, my lab has concentrated on wheat diseases, resulting in this paper as part of our overall studies. I have actively engaged with inquiries from students and scientists globally, providing guidance on accurately identifying the tan spot fungus and troubleshooting various aspects of working with the system. Some interactions were driven by my interest in tracing the pathogen's identification as a wheat pathogen in Japan in 1928, seeking old isolates, well characterized at the University of Manitoba and collected by my late Ph.D. supervisor, Dr. Lamari, who dedicated his research to establishing the tan spot-wheat interaction as a model system. These isolates, collected along the silk road, hold significant value for comparative genomic studies to trace the pathogen's evolution. Chance encounters with collaborators at conferences and meetings have further contributed to the establishment of a collaborative network spanning North and South America, North Africa, Europe, Japan, and Australia.

What began as a simple quest to single-spore the pathogen and conduct its proper characterization, though laborious and time-consuming, resulted in a substantial collection of isolates from diverse global locations and hosts and covering an interesting time scale. The increasing affordability of full genome sequencing, coupled with COVID-19 restrictions, prompted a shift in focus. Collaborating with experts, including Dr. Megan McDonald from the University of Birmingham in the United Kingdom, we released the pathogen's pangenome, chromosomal structural organization, and the reorganization of its effector-encoding genes and surrounding regions (Gourlie et al., 2022). Simultaneously, we explored the allelic diversity of effector-encoding genes in a broader collection of wheat leaf-spotting pathogens, with a specific emphasis on the ToxA gene, a key virulence determinant in North America and Australia (Aboukhaddour et al., 2023). Our research extended beyond the tan spot pathogen to encompass related species.

Simultaneously, our investigation of P. tritici-repentis virulence in North Africa (Kamel et al., 2019) revealed a prevalent ToxB effector in the pathogen populations. The ToxB gene, relatively understudied due to limited access in North American and Australian labs, presented an intriguing aspect for exploring virulence evolution in the fungal genome given its multicopy nature. Tan spot, increasingly concerning in North Africa and neighboring regions where ToxB is widespread, contrasts with North America, where ToxB is nearly absent; instead, a nonfunctional homolog prevails in certain pathogen races infecting durum wheat or recovered from grasses. A few years ago, we accidentally discovered that ToxB-producing isolates induce mild chlorosis in specific barley genotypes. Identifying a dominant single locus responsible for conferring sensitivity to ToxB-producing isolates in barley, a secondary host for the pathogen, added an interest to explore further the ToxB evolution (Aboukhaddour and Strelkov, 2016; Wei et al, 2020).

Considering these findings, the research highlighted here by Hafez et al. delves into the diversity and evolution of ToxB in tan spot pathogens and related species. This work complements our broader investigation into the evolutionary puzzle of tan spot virulence, shedding light on the sudden emergence of this wheat pathogen. The paper provides the research community with a more comprehensive understanding of the diversity of the ToxB gene and its homologs and access to valuable information from a large global collection that would otherwise be challenging to obtain. Ongoing research, in collaboration with Dr. McDonald, aims to decipher the mechanism of virulence gene duplications in the fungal genome. Armed with a wealth of well-studied isolates and continually expanding resources, this endeavor feels like a generational effort booming into an international collaboration to decode the emergence of this wheat pathogen.

Learn more about Mohamed Hafez in his InterConnections article​​.

Jun 28
Review Highlight: Molecular Mechanisms of Pseudomonas Assisted Plant Nitrogen Uptake—Opportunities for Modern Agriculture

Borjana Arsova, Root Dynamics group, IBG 2- Plant sciences, Research center Julich, Julich, Germany

​Full disclosure: when as plant scientists our group started using microbes as a means to improve plan​​t performance, I thought of them as a "means to an end." Now I know this is naïve.

The Root Dynamics group in the Plant Sciences Institute in the Research Center in Jülich (IBG-2), Germany, mostly focuses on the plant response to beneficial microbes, and how plants adjust their metabolic pathways under suboptimal (nutrient) conditions, with and without these beneficial organisms. We observe that the nature of the interaction changes depending on the complex environment in which plants and microbes interact. We showed this, for example, in Kuang et al. (2022, Journal of Experimental Botany) and brought it into focus during the work presented here.

Conceptual figure of shared nitrogen biochemistry and transport across root and bacterial cells in the rhizosphere (Sanow e​t al., 2023; Fig. 3). ​Bacterial processes that impact plant N content. The left side represents plants growing with limited N, resulting in a decreased aerial biomass and increased root growth, whereas the right side represents potential plant growth-promoting mechanisms by Pseudomonas species that increase the aerial biomass under the same limited N conditions. Ammonium (NH4+) and nitrate (NO3) are taken up by the plant via dedicated transporters of the AMT and NRT families, respectively (left side, Bock and Wagner, 2001; Daims et al., 2015). PGPB increase availability of inorganic N to plants through the following mechanisms: (i) ammonification of organic N by P. psychrotolerans (Kang et al., 2020); (ii) P. stutzeri upregul​ating nif genes in A. brasilense via DAPG, resulting in the conversion of N2 into NH4+ (BNF) (Day et al., 2001; Combes-Meynet et al., 2011); and (iii) production and release of NH4+ by P. fluorescens (Zhang et al., 2012). Dashed lines indicate reactions from or to the bacterium that occur based on the concentration of each reaction product in the respective space and the pH of the environment.

The use of a particular Pseudomonas strain in our lab happened by chance. A colleague sent us a sample, which was supposed to be a Sinorhizobium sp. Their lab had indications of growth promotion, but the project had stopped for various reasons. We also found plant growth-promotion ability, but the phenotype of our plants differed from the preliminary results of our colleagues. The sequencing results showed this to be a Pseudomonas strain. However, the phenotype was interesting, and our Ph.D. student Stefan Sanow was getting promising results in plants grown under low-nitrogen conditions, so he kept working with the new bacterium. This led to the initial question: Are the known molecular mechanisms in plant–bacteria interactions general for all bacteria, or can they be subdivided for specific phylogenetic groups?

Thus, Sanow started compiling evidence about known processes relevant to the Pseudomonadaceae. We found that there are many indications of horizontal gene transfer, which can clearly be linked between different bacterial groups. At the same time there are some differences that seem to be genera specific. The review by Sanow et al. (2023) published in MPMI is the result of this work. We think that this is a novel perspective on this complex genus that could set an example for understanding other genera as well.

The team behind this review comes from three continents—Europe, Australia, and Asia—and, in addition to the research center in Jülich, includes the University of Bonn (Germany), the University of Melbourne (Australia), Australian National University (Australia), and Hunan University of Arts and Science (China).

Learn more about Stefan Sanow in his InterConnections article. 

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