A <scp>T</scp>aq<scp>M</scp>an real‐time <scp>PCR</scp> assay for the detection of <i><scp>P</scp>hytophthora</i> ‘taxon <scp>A</scp>gathis’ in soil, pathogen of <scp>K</scp>auri in <scp>N</scp>ew <scp>Z</scp>ealand

Abstract

Summary Kauri A gathis australis, an iconic tree of N ew Z ealand, is under threat from an introduced disease‐causing pathogen provisionally named P hytophthora ‘taxon A gathis’ (referred to as PTA ). This soilborne, P ythiaceous species belongs to the C hromista and causes a collar rot resulting in yellowing of the foliage and thinning of the canopy, which eventually causes death of the infected tree. The management and containment of this pathogen requires rapid and reliable detection in the soil. The current method for soil detection utilizes a soil bioassay involving lupin baits and soil flooding in a process that takes between ten and twenty days. We describe a real‐time PCR assay based on T aq M an chemistry for the specific detection of PTA , which targets the internal transcribed spacer ( ITS ) region of the nuclear ribosomal DNA . This T aq M an real‐time PCR assay could be used with DNA extracted directly from bulk soil samples to enable rapid quantification of PTA within soil. The detection limit was 2 fg of PTA DNA from pure culture, or 20 fg in the presence of DNA extracted from soil. The assay was validated using soil samples taken from a PTA ‐infested site and soil spiked with a known concentration of oospores. We conclude that the T aq M an real‐time PCR assay offers a more time‐efficient method for detection of PTA in soil than existing methods.