From Protocol to Practice: Airborne Pathogen Surveillance in Agricultural Settings

Berelson, Mia Fay Gee (2025) From Protocol to Practice: Airborne Pathogen Surveillance in Agricultural Settings. Doctoral thesis, University of East Anglia.

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Abstract

Crop pathogens present a persistent threat to yields and global food security, and the current heavy reliance on fungicides is unsustainable. Improved monitoring strategies are therefore essential. This thesis describes experiments aimed to test, refine, and validate AirSeq, a sequencing-based approach for the detection of airborne pathogens. AirSeq was first applied in a commercial greenhouse to monitor strawberry pathogens, where detections correlated with manual disease scores, demonstrating its potential as a surveillance tool. Field and laboratory experiments were then conducted to refine the protocol, identifying the most effective sampler and extraction methods, and highlighting the importance of experimental controls. Using the optimised method, seasonal monitoring in wheat fields revealed community-level dynamics of fungi and oomycetes, with pathogen detections often coinciding with favourable environmental conditions and, in some cases, preceding visible symptoms. Short-term sampling further showed that airborne microbial communities fluctuate substantially over diurnal and seasonal timescales. To enhance interpretation of these datasets, a custom bioinformatic pipeline, MARMoT (Metagenomic Alignment and Reporting for Monitoring of Threats), was developed, enabling detection of high-risk pathogens from airborne samples. While some detections, were robust others may have represented false positives, emphasising the need for caution in species-level assignments.

Overall, the work in this thesis demonstrates that AirSeq can capture airborne microbial diversity and track pathogen dynamics across multiple temporal and spatial scales. The method shows clear promise as an early-warning system for crop pathogens and could be integrated into future disease surveillance frameworks. However, further validation and refinements are required before outputs can be routinely translated into actionable crop protection strategies.

Item Type:	Thesis (Doctoral)
Faculty \ School:	Faculty of Science > School of Biological Sciences
Depositing User:	Chris White
Date Deposited:	31 Mar 2026 13:20
Last Modified:	31 Mar 2026 13:20
URI:	https://ueaeprints.uea.ac.uk/id/eprint/102672
DOI:

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