Detection of crop pathogens from the air using DNA sequencing technologies

LEGGETT_E21DTP

Airborne pathogens pose a serious threat to food security and are responsible for devastating loss of crop yield. Worryingly, climate change and global trade have contributed to the re-emergence of pathogens and the establishment of existing pathogens in new environments. Early detection can help producers take targeted action to reduce losses but current detection regimes often rely on experts identifying the pathogen from visible plant damage, by which time it is often too late to effectively control disease.

In this project, we are aiming to develop a sequencing-based method to identify crop pathogens from the air before any damage is visible. Using sequencing technology enables an unbiased approach, which means detecting any pathogen – including emergent threats. Sequencing air samples is a new and exciting area of research, with wide-ranging potential applications. This project will build on two different proof-of-concepts run by the supervisory team in which nanopore sequencing was used to characterise aerosol samples.

The project is a collaboration between scientists at the Earlham Institute, John Innes Centre and the Natural History Museum, who are experts in metagenomics, bioinformatics, sequencing technology and crop pathogens. It would suit a student with an interest in food security looking to develop wet lab work and data analysis/bioinformatics. Training will be provided in all areas.

References:
Leggett RM, Alcon-Giner C, Heavens D, Caim S, Brook TC, Kujawska M, Martin S, Hoyles L, Clarke P, Hall LJ, Clark MD (2020). Rapid profiling of the preterm infant gut microbiota using nanopore sequencing aids pathogen diagnostics. Nature Microbiology 5:430–442.

Giolai M, Verweij W, Lister A, Heavens D, Macaulay I, Clark MD(2019). Spatially resolved transcriptomics reveals plant host responses to pathogens. Plant Methods 15:114.

Hales B, Steed A, Giovannelli V, Burt C, Lemmens M, Molnar-Lang M, Nicholson P (2020). Type II Fusarium head blight susceptibility conferred by a region on wheat chromosome 4D. Journal of experimental botany 71:4703-4714.