A multidisciplinary approach to the surveillance of microorganisms on grain
Microbiology and Grain Genomics Program
Dr. Sean Walkowiak
Research scientist/program manager
Microbiology and Grain Genomics
sean.walkowiak@grainscanada.gc.ca
Team members
Research scientist/program manager
- Dr. Sean Walkowiak
Biologists
- Niradha Withana Gamage
- Janice Bamforth
- Dr. Sung-Jong Lee
- Dr. Tiffany Chin
Technicians
- Tehreem Ashfaq
Student
- Mayantha Shimosh Kurera
The Microbiology and Grain Genomics program uses the latest technologies to investigate the bacteria and fungi found on grain. We identify which species are present and explore how they are affected by environmental factors, such as geography and climate. This helps the grain sector understand the trends and risks associated with both the microorganisms that are beneficial and those that are harmful to plants, humans or livestock. We also identify crop varieties in grain shipments using DNA testing and currently have a database that contains the DNA information for more than 800 varieties. By monitoring microorganisms and grain varieties, we help ensure the safety, integrity and marketability of Canadian grain.
Monitoring microbial communities using DNA
Bacteria and fungi often exist in diverse communities and have complex interactions with each other and their environment. As they adapt to different conditions, changes occur in microbial communities that could have implications for the production, quality and safety of grain. One tool that we use to study microorganisms is targeted DNA testing. This type of testing allows us to determine if a microorganism is present or absent, the species it belongs to and the toxins it may produce. For example, we grow bacteria from grain samples in our laboratory and test the DNA to find out if the bacterial community contains plant pathogens, such as bacterial leaf streak (Xanthamonas sp.), or bacteria that cause foodborne illnesses, such as E. coli (Figure 1). We also perform high-throughput DNA tests on grain affected by fungi, such as Fusarium damaged kernels or ergot bodies (Figure 2). These types of fungal infections can reduce the production and quality of cereal grains and contaminate grain with toxins. Our tests can identify the fungal species that are present and also determine if they have the genes that are responsible for producing the toxins that may be a concern for food safety.
Biochemical profiles of fungi
Another part of our work is developing new methods that improve the efficiency of testing and enhance the quality of the information we collect. In partnership with the Western Grains Research Foundation, Saskatchewan Wheat Development Commission and Manitoba Crop Alliance, we developed a method to identify and characterize Fusarium and rust fungi using Matrix Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry (Figure 3). This technique ionizes the contents of a fungal sample, allowing each chemical within the sample to be separated based on its mass and charge. The pattern of biochemicals, referred to as a profile, is unique for each fungal species and acts like a fingerprint for identification. Compared to traditional methods, this technique gives results more rapidly and is more cost effective.
Forecasting the risk of microbial disease
To better understand the potential for diseases of grain to change over time, we combine the DNA and biochemical data we collect with information on the pathogen, the host plant, farming practices and environmental factors. Using advanced statistics, analytics and predictive modelling, we are developing models that can forecast the risk of microbial diseases. We have applied this approach to fungal diseases of cereals, such as Fusarium and ergot, and blackleg of canola. This information helps the grains sector to stay informed on how the microorganisms on grain may respond to changes in climate.
Recent publications
- Gamage, N.W., Ashfaq, T., Chin, T., Bamforth, J. and S. Walkowiak. 20232024. Draft genome sequence of Enterobacter sp. from wheat grain. Microbiol. Resour. Announc. 13e00576-23. https://doi.org/10.1128/mra.00576-23
- Chin, T., Pleskach, K., Tittlemier, S.A., Henriquez, M.A., Bamforth, J., Gamage, N.W., Ashfaq, T., Lee, S.-J., Kurera, M.S., Patel, B. and S. Walkowiak. 2023. A status update on fusarium head blight on Western Canadian wheat. Can. J. Plant Path. 45 (3): 277-289. https://doi.org/10.1080/07060661.2023.2177352
- Kannangara, S.K., Bullock, P., Walkowiak, S. and W.G.D. Fernando. 2023. Species diversity of Fusarium head blight and deoxynivalenol (DON) levels in Western Canadian wheat fields. Can. J. Plant Path. 46(2): 128-141. https://doi.org/10.1080/07060661.2023.2290034
- Zhao, L., Harding, M.W., Peng, G., Lange, R., Walkowiak, S. and W.G.D. Fernando. 2023. Artificial intelligence analysis of contributive factors in determining blackleg disease severity in canola farmlands. Can. J. Plant Path. 46(2): 114-127. https://doi.org/10.1080/07060661.2023.2290039
- Rowland, B.E., Henriquez, M.A., Nilsen, K.T., Subramaniam, R. and S. Walkowiak. 2023. Unraveling plant-pathogen Interactions in cereals using RNA-seq. In: Foroud, N.A., Neilson, J.A.D. (eds) Plant-Pathogen Interactions. Methods Mol. Biol. 2659: 103-118. https://doi.org/10.1007/978-1-0716-3159-1_9