Vertical distribution of Phytophthora agathidicida oospore DNA in kauri forest soils: implications for optimized sampling and disease monitoring.

UNLABELLED: Phytophthora species are globally significant soilborne oomycetes responsible for widespread ecosystem decline. Standard soil sampling protocols, originally developed for qualitative baiting assays, typically require collecting substantial soil volumes to capture viable propagules. While effective for culture-based detection, these protocols are labor-intensive and can damage the shallow root systems of sensitive host species such as New Zealand kauri (Agathis australis). Phytophthora agathidicida (PA), the causal agent of kauri dieback, is routinely surveyed using these methods. However, quantitative data describing the vertical distribution of PA in natural forest soils are lacking. Consequently, it remains unclear where in the soil profile PA is most concentrated and, therefore, the depth that should be sampled to ensure optimal detection. In this study, we applied a quantitative oospore DNA (oDNA) qPCR assay to characterize the fine-scale vertical distribution of PA at four soil depth increments (0-5, 6-10, 11-15, and 16-20 cm) from 12 kauri trees representing a range of disease stages. Results revealed distinct vertical stratification, with PA DNA concentrations peaking within the upper 0-10 cm of soil in non-symptomatic and possibly symptomatic trees. In symptomatic trees, the absolute peak occasionally reached 11-15 cm, while pathogen signals remained consistently detectable within the top 10 cm. Field validation from an additional eight trees confirmed that targeted 0-10 cm "shallow" sampling yielded higher PA concentrations than deeper sampling. Together, these findings provide a quantitative basis for refining soil sampling strategies, which will enable more sensitive molecular detection while minimizing disturbance and logistical effort in fragile ecosystems.

IMPORTANCE: Phytophthora species are among the most destructive soilborne pathogens globally, requiring robust diagnostic tools for both agricultural and conservation settings. Traditional sampling methods were designed around the biological requirements of baiting bioassays, which often necessitate collecting large soil volumes over broad depth profiles to maximize the likelihood of recovering viable propagules. However, this high-volume collection is labor-intensive and can cause significant soil and root disturbance in sensitive forest ecosystems. This study provides a quantitative assessment of how Phytophthora agathidicida (PA) DNA is distributed vertically in the soil profile around kauri trees at different stages of disease severity. We demonstrated that while peak absolute abundance shifts within the 0-15 cm range as infection progresses, the pathogen signal remains consistently detectable within the top 10 cm. Our findings indicate that targeted, shallow sampling enhances sensitivity by reducing signal dilution, thereby offering a lower-impact pathway for kauri dieback surveillance.