Hidden Phytophthora diversity unveiled in tree nurseries of the Czech Republic with traditional and metabarcoding techniques

Phytophthora diversity was examined in eight forest and ornamental nurseries in the Czech Republic. A leaf baiting isolation technique and, in two nurseries, also Illumina DNA metabarcoding were used to reveal the diversity of Phytophthora in soil and irrigation water and compare the efficacy of both approaches. In total, baiting revealed the occurrence of 12 Phytophthora taxa in 59.4% of soil samples from seven (87.5%) nurseries. Additional baiting of compost was carried out in two nurseries and two Phytophthora species were recovered. Irrigation water was examined in three nurseries by baiting or by direct isolation from partially decomposed floating leaves collected from the water source, and two Phytophthora species were obtained. Illumina sequencing of soil and water samples was done in two and one nurseries, respectively. Phytophthora reads were identified as 45 Phytophthora taxa, 15 of them previously unknown taxa from Clades 6, 7, 8 and 9. Another 11 taxa belonged to known or undescribed species of the oomycete genera Globisporangium, Hyaloperonospora, Nothophytophthora, Peronospora and Plasmopara. Overall, with both techniques 50 Phytophthora taxa were detected with five taxa (P. taxon organica, P. plurivora, P. rosacearum, P. syringae and P. transitoria) being exclusively detected by baiting and 38 only by DNA metabarcoding. Particularly common records in DNA barcoding were P. cinnamomi and P. lateralis which were not isolated by baiting. Only seven species were detected by both techniques. It is recommended to use the combination of both techniques to determine true diversity of Phytophthora in managed or natural ecosystems and reveal the presence of rare or unknown Phytophthora taxa.