Epiphytic ecology and nutrition for control of a wheat pathogen

My research concerns a fungus, Zymoseptoria tritici (Zt), which attacks wheat plants, causing a disease known as Septoria tritici blotch (STB). STB costs the UK around £300 Million per year in lost wheat yields and in the cost of the fungicide used on the crops. Worse, the fungus is developing resistance to the fungicides available to treat it. This means that we need new methods to control the infection. To develop new ways to control Zt, it is necessary to gain a full understanding of the ways in which the fungus interacts with the wheat plant, and how that interaction can be affected by environmental conditions.

In previous work, I showed that some isolates of Zt can grow on the leaf surface for around ten days before invading. The amount and duration of leaf surface growth varies between fungal isolates, and also when the same isolate infects different wheat varieties. Most plant pathogenic fungi, by contrast, can't obtain enough nutrients on the leaf surface to survive for more than 24 h. My FLF research programme aimed to determine the importance of this leaf surface growth phase for Zt, whether it is related to disease severity, and how inter-isolate differences in epiphytic growth are encoded in the genome. To understand fungal survival on the leaf surface, my project also aimed to determine what nutrients the fungus is using during this period, and how it interacts with other leaf surface microbes. My team and I are currently describing the epiphytic phenotypes of over 60 GFP-tagged isolates across a panel of wheat cultivars with varying degrees of resistance. We are linking these data to the genotypes and metabolite uptake profiles of the isolates to build a complete picture of the mechanisms underpinning surface survival. We have identified previously undescribed behaviours in Zt, including the ability to form biofilms. We have also carried out extensive field sampling, and are studying the interactions between Zt and other leaf surface microbes.

During the next phase of the project, I will focus on three objectives: First, I will create reporter strains to visualise differences in nutrient uptake between isolates with different epiphytic phenotypes. The genes used to create these reporter strains will be based on the information gathered in the project so far, concerning the genetic and metabolic differences underlying epiphytic phenotypes. The reporters will allow us to visualise, in real time, how different isolates respond to changes in leaf surface nutrient availability due to, for e.g., fertilisation or pollen deposition. I will use this information to propose changes in fungicide/fertiliser application regimes that will optimise disease control. Secondly, I have shown that Zt can form biofilms, which have greater resistance to stresses such as drying, high temperature, and fungicides than do non-biofilm cells. I will determine whether and when biofilm formation occurs under field conditions and whether biofilms alter the outcome of fungicide treatment or survival of the pathogen during, for example, a heatwave. This work will help to develop weather-sensitive fungicide regimes and maximise fungicide efficacy, thus minimising the risk of further fungicide resistance emerging. Thirdly, I will explore options arising from our work to develop biocontrol of Zt. I will search our field-collected epiphyte library for organisms linked to increased/decreased disease in our related field data. I will then conduct experiments to see whether those linked to low disease are viable as biocontrol agents or, conversely, whether those linked to increased disease can be controlled, for example by working with Exeter's Citizen Phage Library to find phages that infect them. These three objectives will provide significant increases in our understanding of Zt infection biology and ecology alongside novel disease control mechanisms, which can then be tested in collaboration with our agricultural partners.