Metabarcoding reveals a high diversity of woody host-associated<i>Phytophthora</i>spp. in soils at public gardens and amenity woodlands in Britain

Abstract

Forests and woodlands worldwide are being severely impacted by invasive <i>Phytophthora</i> species, with initial outbreaks in some cases occurring on host trees located in public parks and gardens. These highly disturbed sites with diverse planting practices may indeed act as harbours for invasive <i>Phytophthora</i> pathogens which are particularly well adapted to surviving in soil. High throughput Illumina sequencing was used to analyse <i>Phytophthora</i> species diversity in soil samples collected from 14 public garden/amenity woodland sites in northern Britain. Bioinformatic analyses revealed some limitations to using internal transcribed spacer as the barcode region; namely reporting of false positives and ambiguous species matches. Taking this into account, 35 distinct sequences were amplified across the sites, corresponding to 23 known <i>Phytophthora</i> species as well as twelve oomycete sequences with no match to any known <i>Phytophthora</i> species. <i>Phytophthora pseudosyringae</i> and <i>P. austrocedri</i>, both of which cause serious damage to trees and are regarded as fairly recent introductions to Britain, were the two most abundant <i>Phytophthora</i> species detected. There was no evidence that any of the detected <i>Phytophthora</i> species were more associated with any one type of host, healthy or otherwise. This study has demonstrated the ubiquity and diversity of <i>Phytophthora</i> species endemic in highly managed, extensively planted soil environments in Britain. Suggested improvements to the methodology and the practical implications of the findings in terms of mitigating <i>Phytophthora</i> spread and impact are discussed.