DNA Metabarcoding and Isolation by Baiting Complement Each Other in Revealing <i>Phytophthora</i> Diversity in Anthropized and Natural Ecosystems
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 &l...
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MDPI AG
2022-03-01
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| Series: | Journal of Fungi |
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| Online Access: | https://www.mdpi.com/2309-608X/8/4/330 |
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| author | Federico La Spada Peter J. A. Cock Eva Randall Antonella Pane David E. L. Cooke Santa Olga Cacciola |
| author_facet | Federico La Spada Peter J. A. Cock Eva Randall Antonella Pane David E. L. Cooke Santa Olga Cacciola |
| author_sort | Federico La Spada |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-09T13:27:56Z |
| format | Article |
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| institution | Directory Open Access Journal |
| issn | 2309-608X |
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| last_indexed | 2024-03-09T13:27:56Z |
| publishDate | 2022-03-01 |
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| spelling | doaj.art-1f3d8af130534d37af16aac9d050509a2023-11-30T21:21:44ZengMDPI AGJournal of Fungi2309-608X2022-03-018433010.3390/jof8040330DNA Metabarcoding and Isolation by Baiting Complement Each Other in Revealing <i>Phytophthora</i> Diversity in Anthropized and Natural EcosystemsFederico La Spada0Peter J. A. Cock1Eva Randall2Antonella Pane3David E. L. Cooke4Santa Olga Cacciola5Department of Agriculture, Food and Environment, University of Catania, 95123 Catania, ItalyThe James Hutton Institute, Invergowrie, Dundee DD2 5DA, UKThe James Hutton Institute, Invergowrie, Dundee DD2 5DA, UKDepartment of Agriculture, Food and Environment, University of Catania, 95123 Catania, ItalyThe James Hutton Institute, Invergowrie, Dundee DD2 5DA, UKDepartment of Agriculture, Food and Environment, University of Catania, 95123 Catania, ItalyIsolation 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.https://www.mdpi.com/2309-608X/8/4/330leaf baitingDNA sequencingeDNAmetabarcodingIlluminaASVs |
| spellingShingle | Federico La Spada Peter J. A. Cock Eva Randall Antonella Pane David E. L. Cooke Santa Olga Cacciola DNA Metabarcoding and Isolation by Baiting Complement Each Other in Revealing <i>Phytophthora</i> Diversity in Anthropized and Natural Ecosystems Journal of Fungi leaf baiting DNA sequencing eDNA metabarcoding Illumina ASVs |
| title | DNA Metabarcoding and Isolation by Baiting Complement Each Other in Revealing <i>Phytophthora</i> Diversity in Anthropized and Natural Ecosystems |
| title_full | DNA Metabarcoding and Isolation by Baiting Complement Each Other in Revealing <i>Phytophthora</i> Diversity in Anthropized and Natural Ecosystems |
| title_fullStr | DNA Metabarcoding and Isolation by Baiting Complement Each Other in Revealing <i>Phytophthora</i> Diversity in Anthropized and Natural Ecosystems |
| title_full_unstemmed | DNA Metabarcoding and Isolation by Baiting Complement Each Other in Revealing <i>Phytophthora</i> Diversity in Anthropized and Natural Ecosystems |
| title_short | DNA Metabarcoding and Isolation by Baiting Complement Each Other in Revealing <i>Phytophthora</i> Diversity in Anthropized and Natural Ecosystems |
| title_sort | dna metabarcoding and isolation by baiting complement each other in revealing i phytophthora i diversity in anthropized and natural ecosystems |
| topic | leaf baiting DNA sequencing eDNA metabarcoding Illumina ASVs |
| url | https://www.mdpi.com/2309-608X/8/4/330 |
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