Diversity of peronosporomycete (oomycete) communities associated with the rhizosphere of different plant species

Abstract

Peronosporomycete (oomycete) communities inhabiting the rhizospheres of three plant species were characterized and compared to determine whether communities obtained by direct soil DNA extractions (soil communities) differ from those obtained using baiting techniques (bait communities). Using two sets of Peronosporomycete-specific primers, a portion of the 5' region of the large subunit (28S) rRNA gene was amplified from DNA extracted either directly from rhizosphere soil or from hempseed baits floated for 48 h over rhizosphere soil. Amplicons were cloned, sequenced, and then subjected to phylogenetic and diversity analyses. Both soil and bait communities arising from DNA amplified with a Peronosporomycetidae-biased primer set (Oom1) were dominated by Pythium species. In contrast, communities arising from DNA amplified with a Saprolegniomycetidae-biased primer set (Sap2) were dominated by Aphanomyces species. Neighbor-joining analyses revealed the presence of additional taxa that could not be identified with known Peronosporomycete species represented in GenBank. Sequence diversity and mean sequence divergence (Theta pi) within bait communities were lower than the diversity within soil communities. Furthermore, the composition of Peronosporomycete communities differed among the three fields sampled and between bait and soil communities based on F(st) and parsimony tests. The results of our study represent a significant advance in the study of Peronosporomycetes in terrestrial habitats. Our work has shown the utility of culture-independent approaches using 28S rRNA genes to assess the diversity of Peronosporomycete communities in association with plants. It also reveals the presence of potentially new species of Peronosporomycetes in soils and plant rhizospheres.