eDNA from roots: a robust tool for determining Phytophthora communities in natural ecosystems

Khaliq, Ihsanul and Hardy, Giles E. St. J. and White, Diane and Burgess, Treena I. (2018) eDNA from roots: a robust tool for determining Phytophthora communities in natural ecosystems. FEMS Microbiology Ecology, 94 (5):fiy048. ISSN 0168-6496


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.


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Item Type: Article (Commonwealth Reporting Category C)
Refereed: Yes
Item Status: Live Archive
Additional Information: Permanent restricted access to Published version in accordance with the copyright policy of the publisher.
Faculty/School / Institute/Centre: Current - Institute for Life Sciences and the Environment - Centre for Crop Health (24 Mar 2014 -)
Faculty/School / Institute/Centre: Current - Institute for Life Sciences and the Environment - Centre for Crop Health (24 Mar 2014 -)
Date Deposited: 01 Jun 2020 07:45
Last Modified: 03 Jun 2020 04:45
Uncontrolled Keywords: Phytophthora diversity; high-throughput sequencing; baiting; filters; bait plants; eDNA
Fields of Research : 06 Biological Sciences > 0605 Microbiology > 060504 Microbial Ecology
06 Biological Sciences > 0602 Ecology > 060207 Population Ecology
Socio-Economic Objective: D Environment > 96 Environment > 9604 Control of Pests, Diseases and Exotic Species > 960411 Control of Pests, Diseases and Exotic Species in Urban and Industrial Environments
D Environment > 96 Environment > 9604 Control of Pests, Diseases and Exotic Species > 960404 Control of Animal Pests, Diseases and Exotic Species in Forest and Woodlands Environments
Identification Number or DOI: 10.1093/femsec/fiy048
URI: http://eprints.usq.edu.au/id/eprint/38702

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