Date of Award

Summer 8-2023

Degree Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

School

Biological, Environmental, and Earth Sciences

Committee Chair

Dmitri V. Mavrodi

Committee Chair School

Biological, Environmental, and Earth Sciences

Committee Member 2

Alex S. Flynt

Committee Member 2 School

Biological, Environmental, and Earth Sciences

Committee Member 3

Micheal A. Davis

Committee Member 3 School

Biological, Environmental, and Earth Sciences

Committee Member 4

Kevin A. Kuehn

Committee Member 4 School

Biological, Environmental, and Earth Sciences

Committee Member 5

Fengwei Bai

Committee Member 5 School

Biological, Environmental, and Earth Sciences

Abstract

The term “rhizosphere” describes the dynamic interface between plant roots and soil influenced by root exudates. It is a hotspot of microbial activity, plant-microbe, and microbe-microbe interactions. Distinct variations in bacterial diversity are thought to be driven by plant root exudates. However, the molecular details of these processes still remain unclear.

I addressed this gap by focusing on two strains, Pseudomonas synxantha 2-79 and Burkholderia lata 383, representing diverse groups of Gammaproteobacteria comprised of species with environmental, agricultural, and medical significance. In the first part of this project, we used a combination of metabolomics and RNA-seq to characterize transcriptome responses of P. synxantha 2-79 to the root exudates of barley. Our results revealed that root exudates perturb bacterial genes that function in the uptake and catabolism of C and N sources, synthesis of antimicrobials, and biofilm formation. The second part of my project explored exudate-mediated interactions between 2-79 and wheat under water stress. Metabolomic profiling of root exudates from wheat showed that the water-stressed plants exude significantly higher amounts of osmoprotectants called quaternary ammonium compounds (QACs). Transcriptome profiling of 2-79 grown in the presence of these exudates revealed changes in the expression of genes for the catabolism of QACs. These results portray the effects of drought on the rhizosphere microbiome and demonstrate that plant root exudates play a significant role in the survival of root-associated microorganisms in water-deprived conditions.

My final aim dealt with redox-active secondary phenazine metabolites produced by B. lata 383. Using a combination of transposon mutagenesis and RNA-seq, we identified multiple genes that function in the phenazine biosynthesis, its cell density-dependent regulation, and inherent tolerance to these redox-active metabolites. This is the first study to demonstrate that phenazine production in Burkholderia is regulated in response to quorum sensing. Finally, we analyzed transcriptome responses to phenazine methosulfate in B. lata 383 and two closely related phenazine-non-producing Burkholderia strains. Our results revealed that Burkholderia spp. cope with phenazine toxicity by upregulating pathways involved in oxidative stress response, iron-sulfur cluster biogenesis, and multidrug efflux. Collectively, these results will provide new insight into interspecies interactions with rhizosphere communities and molecular processes underpinning the adaptation of plants and their associated microbes to abiotic stress.

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