Streptomyces bacteria: Antibiotic production in the wheat endosphere

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Plants use photosynthesis to fix carbon dioxide from the air into glucose which they use as food. However, up to 40% of the carbon they fix is released into the soil from their roots and this appears to be a mechanism to attract beneficial bacteria from the surrounding soil. The bacteria use the root exudates as food and this helps the plants assemble a healthy microbiome. Some of these microbes protect the plants against disease and others help them get important nutrients from the soil. The root microbiome is therefore essential for plant health, but crop breeding over hundreds of years has selected traits such as bigger plants with more grain while perhaps neglecting the (unknown) effects on the microbiome. There is now growing interest in manipulating the microbiomes of crop plants such as wheat to make them more resistant to disease and to abiotic stresses like drought and salinity. Wheat is a staple crop for about 4 billion people and one of the most important crops in the world so increasing yields is essential if we are to support a growing world population. Our project focuses on a genus of soil bacteria called Streptomyces. The ~600 known species of Streptomyces make numerous secondary metabolites, and these account for half of all the known antibiotics. They are easy to isolate from soil but also form stable interactions with plant roots and can colonise the rhizosphere and endosphere of a wide range of different plants. We have found they are abundant inside wheat roots and that some strains can protect wheat against fungal diseases such as Take-all which can cause devastating crop losses. For one of these strains we have identified the molecules and genes responsible for this antifungal activity and shown it is increased two-fold when we add indole 3 acetic acid, a plant hormone present in wheat root exudates, to the growth medium. In this proposal we aim to look in more detail at the colonisation of wheat roots by soil dwelling, antibiotic-producing Streptomyces bacteria. We will sequence the genomes of 10 strains we have isolated from wheat plants which inhibit the take-all fungus on agar plates, identify the antifungals made by these strains and determine if they can protect wheat plants against take-all disease. We will also try to discover which molecules in wheat root exudates can feed these bacteria and switch on their production of secondary metabolites. Since Streptomyces bacteria form spores which can be dried and stored for long periods, we are interested in developing wheat seed coatings containing these spores so the bacteria grow into the roots of germinating wheat plants and protect them against disease. We will also test the role of the type VII secretion system in root colonisation by these strains since we have preliminary evidence that this system helps them outcompete other bacteria for wheat root colonisation. Our ultimate aim is to develop streptomycetes as seed coatings to protect wheat plants against fungal disease and to discover molecules from wheat root exudates that we can use to switch on secondary metabolite production in vitro because we know that 90% of the secondary metabolites they encode are not made under laboratory conditions. This could help us discover new and useful molecules from these bacteria.