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Article

DNA Metabarcoding and Isolation by Baiting Complement Each Other in Revealing Phytophthora Diversity in Anthropized and Natural Ecosystems

1
Department of Agriculture, Food and Environment, University of Catania, 95123 Catania, Italy
2
The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
*
Authors to whom correspondence should be addressed.
Academic Editor: Lei Cai
J. Fungi 2022, 8(4), 330; https://doi.org/10.3390/jof8040330
Received: 7 March 2022 / Revised: 19 March 2022 / Accepted: 21 March 2022 / Published: 22 March 2022
Isolation techniques supplemented by sequencing of DNA from axenic cultures have provided a robust methodology for the study of Phytophthora communities in agricultural and natural ecosystems. Recently, metabarcoding approaches have emerged as new paradigms for the detection of Phytophthora species in environmental samples. In this study, Illumina DNA metabarcoding and a conventional leaf baiting isolation technique were compared to unravel the variability of Phytophthora 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 Phytophthora. Overall, 1,406,613 Phytophthora internal transcribed spacer 1 (ITS1) sequences and 155 Phytophthora isolates were obtained, which grouped into 21 taxa, five retrieved exclusively by baiting (P. bilorbang; P. cryptogea; P. gonapodyides; P. parvispora and P. pseudocryptogea), 12 exclusively by metabarcoding (P. asparagi; P. occultans; P. psycrophila; P. syringae; P. aleatoria/P. cactorum; P. castanetorum/P. quercina; P. iranica-like; P. unknown sp. 1; P. unknown sp. 2; P. unknown sp. 3; P. unknown sp. 4; P. unknown sp. 5) and four with both techniques (P. citrophthora, P. multivora, P. nicotianae and P. plurivora). Both techniques complemented each other in describing the variability of Phytophthora communities from natural and managed ecosystems and revealing the presence of rare or undescribed Phytophthora taxa. View Full-Text
Keywords: leaf baiting; DNA sequencing; eDNA; metabarcoding; Illumina; ASVs; rhizosphere soil; new species; detection; nature reserve; botanical garden; citrus orchards leaf baiting; DNA sequencing; eDNA; metabarcoding; Illumina; ASVs; rhizosphere soil; new species; detection; nature reserve; botanical garden; citrus orchards
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MDPI and ACS Style

La Spada, F.; Cock, P.J.A.; Randall, E.; Pane, A.; Cooke, D.E.L.; Cacciola, S.O. DNA Metabarcoding and Isolation by Baiting Complement Each Other in Revealing Phytophthora Diversity in Anthropized and Natural Ecosystems. J. Fungi 2022, 8, 330. https://doi.org/10.3390/jof8040330

AMA Style

La Spada F, Cock PJA, Randall E, Pane A, Cooke DEL, Cacciola SO. DNA Metabarcoding and Isolation by Baiting Complement Each Other in Revealing Phytophthora Diversity in Anthropized and Natural Ecosystems. Journal of Fungi. 2022; 8(4):330. https://doi.org/10.3390/jof8040330

Chicago/Turabian Style

La Spada, Federico, Peter J. A. Cock, Eva Randall, Antonella Pane, David E. L. Cooke, and Santa Olga Cacciola. 2022. "DNA Metabarcoding and Isolation by Baiting Complement Each Other in Revealing Phytophthora Diversity in Anthropized and Natural Ecosystems" Journal of Fungi 8, no. 4: 330. https://doi.org/10.3390/jof8040330

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