Millions of years of co-evolution between bacteria, fungi and plants has resulted in a vast microbial biodiversity which is as yet mostly unknown to science. My research aims to use ecological approaches to bioprospect for beneficial microbes throughout terrestrial biomes and sift through this immense biological resource using high throughput plate screening, plant bioassays and studies of plant microbiomes. Similar methods can also be used to discover the causes of emerging plant diseases.
Beneficial microbes and biochemicals are discovered in the laboratory, but need to be scaled up, formulated and field tested before becoming products with an impact in agriculture. I have developed formulations for seed and seedling inoculation and conducted numerous field trials on maize, strawberries, wheat, soybeans, and tomatoes in Canada, USA, Argentina and Austria. I hope to continue developing and testing methods to successfully install probiotics into agricultural plants.
Microbial ecology is the study of the interactions of microorganisms with their environment, each other, and other species with which they associate. I have been particularly interested in how bacteria and fungi colonize and live inside plants, how these microbes make up plant microbiomes and how these microbes affect plant productivity and health. Traditionally plant microbiomes were believed to derive from the soil, however I have shown that seeds transmit many bacterial species to the next generation.
Chemicals are the main way that microbes interact/communicate with other organisms and possess great potential to help us improve agriculture. By studying endophytic microbes, I hope to discover novel biochemicals that alter plant growth or combat pathogens. In order to help characterize microbes, I also use known traits such as plant hormone production as biomarkers to screen microbial libraries as shown above. These screens are often based on colour change in response to biochemical production in 96 well plates, allowing quick and economical screening of thousands of isolates for dozens of traits.
Functional genomics attempts to make use of the vast wealth of data produced by genomic and transcriptomic projects to understand gene function and discover useful new DNA. Application of these techniques to the study of plant-microbe interactions can lead to novel targets for high throughput microbial screening or molecular and classical breeding of plants. For example, the Arabidopis CTL1 mutant pictured above was first predicted bioinformatically, then confirmed by microscopy to have defects in cell wall formation. Transgenically inserting homologous genes from poplar and spruce trees "cures" this mutation suggesting these genes could be targets for breeding trees with different qualities of wood.
The study of plant form and function is critical for understanding how microbes affect plant health. Pathogens can promote disease by secreting hormones to overstimulate leaf formation, while symbionts can improve plant health by enhancing root growth, but how is this is happening? A powerful technique for studying these physiological changes fuses "reporters" such as the blue GUS protein seen above to gene regulators such as those involved in hormone production. I am interested in developing biosensor plants to aid in the discovery of beneficial microbes and biochemicals they use to change plant growth.