Document Type

Dissertation - Open Access

Award Date


Degree Name

Doctor of Philosophy (PhD)


Biology and Microbiology

First Advisor

Senthil Subramanian

Second Advisor

Volker Brözel


Rhizodeposits play a key role in shaping rhizosphere microbial communities. In soybean, isoflavonoids are a key rhizodeposit component that aid in plant defense and enable symbiotic associations with rhizobia. However, it is uncertain if and how they influence rhizosphere microbial communities. Isoflavonoid biosynthesis was silenced via RNA interference of isoflavone synthase in soybean hairy root composite plants. Successive sonication was implemented to isolate soil fractions from 3 different rhizosphere zones at 1 and 3 weeks post planting. PCR amplicons from 16S rRNA gene variable regions V1- V3 and V3-V5 from these soil fractions were analyzed via denaturing gradient gel electrophoresis and/or Roche 454 sequencing profiles. Extensive diversity analysis of the denaturing gradient gel electrophoresis patterns indicated that, indeed, isoflavonoids significantly influenced soybean rhizosphere bacterial diversity. These results also suggested a temporal gradient effect of rhizodeposit isoflavonoids on the rhizosphere. Roche 454 sequencing data was resolved using MOTHUR and vegan to identify bacterial taxa and evaluate changes in rhizosphere bacterial communities. The soybean rhizosphere was enriched in Proteobacteria and Bacteroidetes, and had relatively lower levels of Actinobacteria and Acidobacteria compared to bulk soil. Isoflavonoids had a small effect on bacterial community structure, and in particular on the abundance of Xanthomonads and Comamonads. Additionally, isoflavonoids appeared to have a temporal gradient effect on the rhizosphere. The effect of hairy root transformation on rhizosphere bacterial communities was largely similar to untransformed plant roots with ~74% of the bacterial families displaying similar colonization underscoring the suitability of this technique to evaluate the influence of plant roots on rhizosphere bacterial communities. However, hairy root transformation had notable influence on Sphingomonads and Acidobacteria.

Library of Congress Subject Headings

Soybean -- Roots.
Plant-microbe relationships.
Soil microbial ecology.


Includes bibliographical references



Number of Pages



South Dakota State University


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