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Metagenomic analysis of oomycete communities in rhizosphere soil from field pea on the Canadian prairies using Illumina Miseq

A. Esmaeili Taheri, S. Chatterton, N.A. Foroud, B.D. Gossen and D.L. McLaren. Metagenomic analysis of oomycete communities in rhizosphere soil from field pea on the Canadian prairies using Illumina Miseq. Annual Meeting of the American Phytopathology Society, Tampa FL, USA, July 30 – August 3, 2016. (poster presentation)

Abstract

Oomycetes include several important soil-borne pathogens that cause damping-off and root rot in many crops including pea. Samples of soil from the rhizosphere of pea plants were collected from patches of healthy or diseased plants (127 samples from 26 commercial fields) on the Canadian prairies in 2013 and 2014. Oomycete communities were characterized using metagenomic analysis of the ITS1 region on Illumina Miseq. Roughly 4 million high quality sequences were obtained. Clustering took place at 85% coverage and 97% similarity. A representative sequence of each operational taxonomic unit (OTU) was compared to NCBI sequences. Species were identified at (minimum) 90% coverage and 97% similarity, and genera at 80% coverage and similarity. Clusters below 80% coverage or identity were labelled as unidentified. From 102 identified OTUs, 43 species and 16 oomycete genera were identified. Pythium was the dominant genus and P. heterothalicum was the most prevalent species. Aphanomyces euteiches, a very important pea root rot pathogen, was detected in 71 sites, but in very low abundance (≈ 0.2%). Multivariate analysis revealed difference in oomycete communities of healthy and diseased sites, and among years and provinces. This study shows that deep amplicon sequencing on Miseq can reveal unknown diversity of oomycete communities in agricultural soil, and that primer optimization for higher detection power of economically important oomycetes such as A. euteiches is warranted.

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