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

• Published in: European journal of plant pathology Vol. 170; no. 1; pp. 131 - 156
• Main Authors: Bačová, Aneta, Cooke, David E. L., Milenković, Ivan, Májek, Tomáš, Nagy, Zoltán Á., Corcobado, Tamara, Randall, Eva, Keillor, Beatrix, Cock, Peter J. A., Jung, Marília Horta, Jung, Thomas, Tomšovský, Michal
• Format: Journal Article
• Language: English
• Published: Dordrecht Springer Netherlands 01-09-2024; Springer Nature B.V
• Subjects: Agriculture; Asymptomatic; Baiting; Biomedical and Life Sciences; Deoxyribonucleic acid; DNA; DNA barcoding; Ecology; Ecosystem management; Epidemics; Floating plants; Flowers & plants; Forests; Gene sequencing; Genera; Horticulture; Irrigation; Irrigation water; Leaves; Life Sciences; Nurseries; Pathogens; Phytophthora; Plant diseases; Plant Pathology; Plant Sciences; Rare species; Soil water; Taxa; Water; Water analysis; Water sampling; Czech Republic; Soil microbiome; Oomycetes; Metabarcoding; Infestation; Baiting
• ISSN: 0929-1873; 1573-8469
• DOI: 10.1007/s10658-024-02886-1

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.