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

Several important soil-borne pathogens causing damping-off and root rot of field pea are Oomycetes. Samples of soil from the rhizosphere of pea plants were taken 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. About 4 million high quality sequences were obtained. Clustering took place at 85% coverage and 97% similarity. A representative sequence of each OTU was compared to sequences in the NCBI. Species were identified at (minimum) 90% coverage and 97% similarity, and genera at 80% coverage and similarity. Clusters below 80% coverage or identity were grouped 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 was detected in 71 samples, but at 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 agriculture soil, and that primer optimization for higher resolution for economically important oomycetes such as A. euteiches is warranted.