Epiphytic ecology and nutrition for control of a wheat pathogen

My research concerns a fungus, Zymoseptoria tritici, 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 beginning to develop resistance to the fungicides that are available to treat it. This means that we need new methods to control the infection. To develop new ways to control Z. tritici, 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 Z. tritici 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. If the particular wheat variety is resistant to a particular Z. tritici isolate, then that isolate will never invade the leaf. However, it appears that such 'avirulent' isolates can persist on the leaf surface instead, and even reproduce there, making new spores for dispersal to more susceptible wheat plants. Most plant pathogenic fungi, by contrast, can't obtain enough nutrients on the leaf surface to survive for more than 24 hours. I therefore want to determine, firstly, how important this leaf surface growth phase is for Z. tritici, and whether it is related to how effective the fungus is at causing disease. I also want to find out whether some isolates are more likely than others to spend a prolonged period of time on the leaf surface, and whether such differences in behaviour can be attributed to differences in the genomes of the fungal isolates. Secondly, I aim to determine what nutrients the fungus is using when it is on the leaf surface. For example, the fungus might be relying on internal lipid stores, or taking advantage of nutrients that are exuded from the leaf, or of agricultural inputs like fertilisers. Alternatively, it might be able to secrete enzymes which digest structural components of the leaf such as waxes, to obtain nutrients from those. The fungus might also be able to take advantage of the activities of other microbes on the leaf surface which secrete such enzymes, or which cause nutrients to leak from the leaf by damaging the leaf surface. Thirdly, therefore, I intend to sample wheat leaves in the field and use metagenomics to study which microbes are present on the leaf surface. I will then compare these microbial communities, taking note of how severely affected the wheat in each field was by Z. tritici, to look for correlations between the presence of particular microbes and the promotion of fungal infection.

Having obtained these data about leaf surface growth in Z. tritici, I intend to use them to build a detailed picture of what the fungus needs to survive throughout this first period of infection, before it enters the leaf; or to persist and reproduce on the leaf surface if the wheat is resistant and it cannot enter. This will allow me to identify any vulnerabilities the fungus has that we might be able to exploit in order to control the disease. For instance, if leaf surface growth is boosted by the presence of fertiliser, then it may be possible to increase the usefulness of fungicides by inter-relating the timings of fertiliser and fungicide application. Alternatively, if the fungus relies on a particular metabolic pathway to obtain nutrients, then that pathway could be targeted for new forms of chemical or other control. Or, if the fungus gains a large advantage sharing the leaf surface with a particular bacterium, then controlling that bacterium, perhaps via bio-control with a competing bacterium that is not able to promote fungal growth, might indirectly control the fungus.

Outside of academia, the main beneficiaries of this research will be:

1. The global population:

Wheat is the second most important crop (after rice) worldwide in terms of calories consumed by humans. Thus, the protection of wheat crops against increasingly fungicide-resistant pathogens is fundamentally important for global food security. Where elite resistant varieties are not grown and fungicides are not used, yield losses from Septoria tritici blotch (STB; caused by Zymoseptoria tritici) can reach as high as > 40 % of harvest. A cheap and reliable control method is therefore of particular importance in developing countries. This project will provide a basis for the development of such control methods.

2. The UK economy / UK public:

Wheat is grown in the UK for domestic consumption, and is also the UK's main food export. It has a value of around £2 Billion to the UK economy every year. This value could be increased if yield losses due to STB were mitigated; losses currently stand at around 5-10%, even when fungicides are used in combination with the most resistant wheat varieties.

3. Governmental bodies e.g. the Agriculture and Horticulture Development Board (AHDB) and Department for the Environment, Food and Rural Affairs (DEFRA)

These bodies must currently expend a great deal of resource in the attempt to reduce losses from diseases such as STB. AHBD tests wheat cultivars' susceptibility to several diseases in order to produce recommended lists for growers, while DEFRA, inter alia, monitor the development of fungicide resistance and regulation of fungicide use. Reliable control methods for STB, such as those expected to emerge from this work, are therefore of interest to these bodies.

4. Wheat growers and agronomists:

To protect wheat from STB growers rely on elite varieties and the use of fungicides, at considerable cost (fungicide use to control STB in the UK is estimated to cost around £150M per year). Moreover, fungicide resistance has emerged in many Z. tritici populations and is expected to become an increasingly severe problem. This project aims to develop or allow the development of i) novel agronomic solutions to STB; ii) novel methods of control e.g. biocontrol agents and iii) novel avenues to explore for the development of new fungicides. Each of these will help the control of STB, while i) and ii) will also help to reduce reliance upon fungicides. Together, these solutions should minimise costs and increase yields in wheat production.

5. Agri-tech or biotech companies with an interest in developing and producing biocontrols or fungicides against Z. tritici.

The proposed research will provide novel insights into the nutrient acquisition pathways and microbial partners which are important to Z. tritici for colonisation of wheat, virulence on wheat, and dispersal to new wheat plants. These will in turn suggest targets for manipulation or interruption as part of novel control methods against Z. tritici. These targets can be used in the development of new products by these companies.