eDNA from roots: a robust tool for determining Phytophthora communities in natural ecosystems
Article
Article Title | eDNA from roots: a robust tool for determining Phytophthora communities in natural ecosystems |
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ERA Journal ID | 15100 |
Article Category | Article |
Authors | Khaliq, Ihsanul (Author), Hardy, Giles E. St. J. (Author), White, Diane (Author) and Burgess, Treena I. (Author) |
Journal Title | FEMS Microbiology Ecology |
Journal Citation | 94 (5) |
Article Number | fiy048 |
Number of Pages | 11 |
Year | 2018 |
Place of Publication | Oxford, United Kingdom |
ISSN | 0168-6496 |
1574-6941 | |
Digital Object Identifier (DOI) | https://doi.org/10.1093/femsec/fiy048 |
Web Address (URL) | https://academic.oup.com/femsec/article/94/5/fiy048/4944903 |
Abstract | Proper isolation and identification of Phytophthora species is critical due to their broad distribution and huge impact on natural ecosystems throughout the world. In this study, five different sites were sampled and seven methods were compared to determine the Phytophthora community. Three traditional isolation methods were conducted (i) soil baiting, (ii) filtering of the bait water and (iii) isolation from field roots using Granny Smith apples. These were compared to four sources of eDNA used for metabarcoding using Phytophthora-specific primers on (i) sieved field soil, (ii) roots from field, (iii) filtered baiting water and (iv) roots from bait plants grown in the glasshouse in soil collected from these sites. Six Phytophthora species each were recovered by soil baiting using bait leaves and from the filtered bait water. No Phytophthora species were recovered from Granny Smith apples. eDNA extracted from field roots detected the highest number of Phytophthora species (25). These were followed by direct DNA isolation from filters (24), isolation from roots from bait plants grown in the glasshouse (19), and DNA extraction from field soil (13). Therefore, roots were determined to be the best substrate for detecting Phytophthora communities using eDNA. |
Keywords | Phytophthora diversity; high-throughput sequencing; baiting; filters; bait plants; eDNA |
ANZSRC Field of Research 2020 | 310703. Microbial ecology |
310307. Population ecology | |
Public Notes | Files associated with this item cannot be displayed due to copyright restrictions. |
Byline Affiliations | Murdoch University |
Institution of Origin | University of Southern Queensland |
https://research.usq.edu.au/item/q5v7z/edna-from-roots-a-robust-tool-for-determining-phytophthora-communities-in-natural-ecosystems
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