Microbial Ecology

, Volume 51, Issue 1, pp 36–50 | Cite as

Diversity of Peronosporomycete (Oomycete) Communities Associated with the Rhizosphere of Different Plant Species

  • Jessica M. Arcate
  • Mary Ann Karp
  • Eric B. Nelson
Article
First Online:
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Accepted:

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.

Keywords

Sorghum Rhizosphere Soil Soil Community Pythium Species Rhizosphere Soil Sample 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
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Notes

Acknowledgments

Special thanks are due to Dr. André Levesque for providing 28S rDNA sequences of a wide range of Peronosporomycete species, especially those of Pythium spp., many of which represented the type or neotype strain. We also thank Kathie Hodge for her helpful discussions and review of the manuscript and Michael Milgroom, Fernando Ponce, Angelika Rumberger, and Sofia Windstam for their helpful comments on the manuscript. The work was supported by grants to JMAfrom the CALS Charitable Trust, The Fredric N. Gabler Memorial Research Honors Endowment, and Hatch/Multistate Funds for Undergraduate Student Research.

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Copyright information

© Springer Science+Business Media, Inc. 2006

Authors and Affiliations

  • Jessica M. Arcate
    • 1
  • Mary Ann Karp
    • 1
  • Eric B. Nelson
    • 1
  1. 1.Department of Plant PathologyCornell UniversityIthacaUSA

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