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

Article


Khaliq, Ihsanul, Hardy, Giles E. St. J., 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). https://doi.org/10.1093/femsec/fiy048
Article Title

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

ERA Journal ID15100
Article CategoryArticle
AuthorsKhaliq, Ihsanul (Author), Hardy, Giles E. St. J. (Author), White, Diane (Author) and Burgess, Treena I. (Author)
Journal TitleFEMS Microbiology Ecology
Journal Citation94 (5)
Article Numberfiy048
Number of Pages11
Year2018
Place of PublicationOxford, United Kingdom
ISSN0168-6496
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.

KeywordsPhytophthora diversity; high-throughput sequencing; baiting; filters; bait plants; eDNA
ANZSRC Field of Research 2020310703. Microbial ecology
310307. Population ecology
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Byline AffiliationsMurdoch University
Institution of OriginUniversity of Southern Queensland
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