This project explored the efficacy of metabarcoding and metagenomics for the detection of high-risk pathogens in soil associated with traded products. Using example bacterial, fungal and nematode pests, metabarcoding was found to be the more sensitive method when equivalent levels of sequencing were carried out (approximately same overall cost). When tested on unknown samples metabarcoding struggled to identify potential pathogens down to an appropriate level (species). Metabarcoding did however identify genera with potential high-risk members. If used as part of an overall threat analysis including looking at the genera of the potential pathogen, host plant and geographical origins of the suspect sample this could form part of a useful targeting workflow informing the need for further specific analysis.
This project was commissioned via FPPH. Future Proofing Plant Health (FPPH) was established in 2014 as a collaboration between Defra, Fera Science Ltd, Forest Research, Royal Botanic Gardens Kew, Joint Nature Conservation Committee and Natural England, to consolidate plant health research and development requirements delivered by Defra network organisations and encourage greater collaboration across the department’s core science providers
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For more information about our wider research view our Plant health research and development plan