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A leaf baiting isolation technique and, in two nurseries, also Illumina DNA metabarcoding were used to reveal the diversity of <jats:italic>Phytophthora<\/jats:italic> in soil and irrigation water and compare the efficacy of both approaches. In total, baiting revealed the occurrence of 12 <jats:italic>Phytophthora<\/jats:italic> taxa in 59.4% of soil samples from seven (87.5%) nurseries. Additional baiting of compost was carried out in two nurseries and two <jats:italic>Phytophthora<\/jats:italic> 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 <jats:italic>Phytophthora<\/jats:italic> species were obtained. Illumina sequencing of soil and water samples was done in two and one nurseries, respectively. <jats:italic>Phytophthora<\/jats:italic> reads were identified as 45 <jats:italic>Phytophthora<\/jats:italic> 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 <jats:italic>Globisporangium<\/jats:italic>, <jats:italic>Hyaloperonospora<\/jats:italic>, <jats:italic>Nothophytophthora<\/jats:italic>, <jats:italic>Peronospora<\/jats:italic> and <jats:italic>Plasmopara<\/jats:italic>. Overall, with both techniques 50 <jats:italic>Phytophthora<\/jats:italic> taxa were detected with five taxa (<jats:italic>P.<\/jats:italic> taxon <jats:italic>organica, P. plurivora, P. rosacearum, P. syringae<\/jats:italic> and <jats:italic>P. transitoria<\/jats:italic>) being exclusively detected by baiting and 38 only by DNA metabarcoding. Particularly common records in DNA barcoding were <jats:italic>P. cinnamomi<\/jats:italic> and <jats:italic>P. lateralis<\/jats:italic> 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 <jats:italic>Phytophthora<\/jats:italic> in managed or natural ecosystems and reveal the presence of rare or unknown <jats:italic>Phytophthora<\/jats:italic> taxa.<\/jats:p>","DOI":"10.1007\/s10658-024-02886-1","type":"journal-article","created":{"date-parts":[[2024,6,17]],"date-time":"2024-06-17T16:02:53Z","timestamp":1718640173000},"page":"131-156","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["Hidden Phytophthora diversity unveiled in tree nurseries of the Czech Republic with traditional and metabarcoding techniques"],"prefix":"10.1007","volume":"170","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3663-3670","authenticated-orcid":false,"given":"Aneta","family":"Ba\u010dov\u00e1","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9154-7954","authenticated-orcid":false,"given":"David E. 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