Pathogen detection and beyond: Development and application of new sequence-based methods for characterisation of real-world microbial communities [Poster Presentation]

Fungal diseases of plants are responsible for major losses in agriculture, highlighting the need for rapid and accurate identification of fungal plant pathogens. Disease outcomes are defined not only by main pathogens but are influenced by diverse microbial communities known as microbiomes at sites of infection. We conducted the first use of whole community DNA sequencing with a portable sequencer as a method for detecting fungal pathogens from wheat (Triticum aestivum) in a standard molecular biology laboratory. The data revealed that our method is robust and capable of diagnosing stripe rust (caused by Puccinia striiformis f. sp. tritici), septoria blotch (caused by Zymoseptoria tritici) and yellow spot (caused by Pyrenophora tritici repentis). We also identified the bacterial genus Pseudomonas co-present with Puccinia and Zymoseptoria but not Pyrenophora infections. One limitation of the method is the over-representation of redundant wheat genome sequences from samples. This could be addressed by long-range amplicon-based meta-barcode sequencing approaches and host DNA depletion during or after DNA extraction. Here we will present recent progress in our method development and the biological insight gained during this process. Our work outlines a new approach for detection of a broad range of plant pathogens and associated microbes using a portable sequencer, providing the basis for the development of a high-throughput, large scale and on-site disease monitoring system