Monitoring soil-borne protist pathogens is essential for sustainable crop production, yet choosing the right molecular marker remains a critical challenge. This project benchmarks three ribosomal markers of increasing length — a short V4 fragment (~450bp), a medium full-length 18S rRNA (~1,800bp), and a long ribosomal operon (~4,500bp) — for their ability to detect protist pathogens in agricultural soils.

Markers were validated against reference protist cultures before being applied to field samples from two agricultural sites, including one with confirmed Plasmodiophora brassicae infection. Both Illumina and Oxford Nanopore sequencing platforms were used, allowing a direct comparison across technologies.

Our results reveal clear trade-offs : shorter markers offer broader pathogen detection but limited species-level resolution, while longer markers improve taxonomic interpretability at the cost of amplification efficiency. These findings support multi-marker strategies for routine soil pathogen surveillance and provide a practical framework for marker selection under constrained sampling conditions.

A collaboration between HES-SO Changins and Sion. Manuscript in preparation.