| Summary: | Isolation techniques supplemented by sequencing of DNA from axenic cultures have provided a robust methodology for the study of <i>Phytophthora</i> communities in agricultural and natural ecosystems. Recently, metabarcoding approaches have emerged as new paradigms for the detection of <i>Phytophthora</i> species in environmental samples. In this study, Illumina DNA metabarcoding and a conventional leaf baiting isolation technique were compared to unravel the variability of <i>Phytophthora</i> communities in different environments. Overall, 39 rhizosphere soil samples from a natural, a semi-natural and a horticultural small-scale ecosystem, respectively, were processed by both baiting and metabarcoding. Using both detection techniques, 28 out of 39 samples tested positive for <i>Phytophthora</i>. Overall, 1,406,613 <i>Phytophthora</i> internal transcribed spacer 1 (ITS1) sequences and 155 <i>Phytophthora</i> isolates were obtained, which grouped into 21 taxa, five retrieved exclusively by baiting (<i>P. bilorbang; P. cryptogea; P. gonapodyides; P. parvispora</i> and <i>P. pseudocryptogea</i>), 12 exclusively by metabarcoding (<i>P. asparagi; P. occultans; P. psycrophila; P. syringae; P. aleatoria</i>/<i>P. cactorum; P. castanetorum</i>/<i>P. quercina; P. iranica</i>-like; <i>P.</i> unknown sp. 1; <i>P.</i> unknown sp. 2; <i>P.</i> unknown sp. 3; <i>P.</i> unknown sp. 4; <i>P.</i> unknown sp. 5) and four with both techniques (<i>P. citrophthora</i>, <i>P. multivora</i>, <i>P. nicotianae</i> and <i>P. plurivora</i>). Both techniques complemented each other in describing the variability of <i>Phytophthora</i> communities from natural and managed ecosystems and revealing the presence of rare or undescribed <i>Phytophthora</i> taxa.
|
|---|