Exploring hidden Phytophthora via amplicon Pyrosequencing using eDNA from soil and water

Autores UPV
CONGRESO Exploring hidden Phytophthora via amplicon Pyrosequencing using eDNA from soil and water


Phytophthora is one of the most important and aggressive plant pathogens in agriculture and forestry. Early detection and identification of its pathways are of high importance to minimize the threat that they pose to natural ecosystems. Therefore, a new improved method for its detection in environmental samples is proposed. eDNA was extracted from soil and water from rivers and streams from Fagus sylvatica and Abies alba forests, and Chamaecyparis lawsoniana and Pseudotsuga menziesii plantations in the north of Spain (Irati Forest and Villanua). A Phytophthora-specific amplicon pyrosequening based on the barcoding target ITS1 was applied. Different score coverage threshold values were tested for optimal Phytophthora species separation. Clustering at 99 % was the best criteria to separate most of the Phytophthora species. Of the total of 37 Phytophthora species detected in the environmental samples, 24 were known to science (P. lacustris, P. gonapodyides, P. syringae, P. hedraiandra, P. cambivora, P. taxon PgChlamydo, P. alni subsp. uniformis, P. cactorum, P. pseudosyringae, P. porri, P. gallica, P. asparagi, P. megasperma, P. cryptogea, P. gregata/gibbosa, P. europaea, P. lactucae, P. niederhauserii, P. drechsleri, P. inundata, P. psychrophila, P. plurivora, P. trifolii and P. quercina) and 14 were unknown to science. Thirteen of the unknown species were detected in rivers and streams revealing that water environments could represent important pathways and a potential source for pathogen discovery. Pyrosequencing of soil samples revealed low Phytophthora diversity (14 species) in comparison with the 35 species detected in water samples, representing the 95 % of the total Phytophthora community. Water eDNA pyrosequencing proved to be a valuable method for the detection of Phytophthora species in natural ecosystems.