Journal article
eDNA from roots: a robust tool for determining Phytophthora communities in natural ecosystems
FEMS Microbiology Ecology, Vol.94(5), Article fiy048
2018
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.
Details
- Title
- eDNA from roots: a robust tool for determining Phytophthora communities in natural ecosystems
- Authors/Creators
- I. Khaliq (Author/Creator) - Murdoch UniversityG.E.St.J. Hardy (Author/Creator) - Murdoch UniversityD. White (Author/Creator) - Murdoch UniversityT.I. Burgess (Author/Creator) - Murdoch University
- Publication Details
- FEMS Microbiology Ecology, Vol.94(5), Article fiy048
- Publisher
- Oxford University Press
- Identifiers
- 991005542822207891
- Copyright
- © FEMS 2018
- Murdoch Affiliation
- Centre for Phytophthora Science and Management
- Language
- English
- Resource Type
- Journal article
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- Citation topics
- 3 Agriculture, Environment & Ecology
- 3.97 Plant Pathology
- 3.97.1439 Phytophthora Management
- Web Of Science research areas
- Microbiology
- ESI research areas
- Microbiology