PhD Defense by Yael Toporek

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In partial fulfillment of the requirements for the degree of


Doctor of Philosophy in Biology

In the

School of Biological Sciences


Yael Toporek


Will defend her dissertation


Molecular mechanisms of microbial pathways

for environmental contaminant remediation


January 9th, 2023

3:00 pm




 Thesis Advisor:

Thomas DiChristina, Ph.D.

School of Biological Sciences

Georgia Institute of Technology


Committee Members:

Brian Hammer, Ph.D.

School of Biological Sciences

Georgia Institute of Technology


Frank Stewart, Ph.D.

Department of Microbiology and Cell Biology

Montana State University


Amit Reddi, Ph.D.

School of Chemistry and Biochemistry

Georgia Institute of Technology


Martial Taillefert, Ph.D.

School of Earth and Atmospheric Sciences

Georgia Institute of Technology



This thesis examines the molecular mechanism of alternate strategies for remediation of contaminated environments. Radioiodine, perfluoroalkyl substances (PFAS), and 1,4-dioxane represent emerging contaminants of national concern. For example, microbially-catalyzed reductive methylation of 129IO3- has received recent attention as an alternate strategy for remediation of radioiodine-contaminated environments. This thesis identified enzymes required for IO3- reduction coupled to organic acid oxidation in the facultative anaerobe Shewanella oneidensis: cytoplasmic electron donors are oxidized, and the electrons are transferred through the periplasm via cytochromes of the metal-reducing pathway to extracellular dimethylsulfoxide (DMSO) reductase, which directly reduces IO3- to iodide (I-) as an alternate substrate. Future work aims to investigate the apparent import of I- back to the cytoplasm, where it is putatively methylated and volatilized by a promiscuous thiopurine methyltransferase, presenting a potential strategy for bioremediation of radioiodine.  

In the case of PFAS, the industrial surfactant and flame retardant perfluorooctanoic acid (PFOA) has been designated as an emerging contaminant. In the present study, the microbially driven Fenton reaction (MFR) was employed to attempt degradation of PFOA by cycling between aerobic and anaerobic ferric iron (Fe(III))-reducing conditions. Under aerobic conditions, S. oneidensis reduced molecular oxygen (O2) to hydrogen peroxide (H2O2), while under anaerobic conditions, S. oneidensis reduced Fe(III) to Fe(II). During aerobic-to-anaerobic transition periods, Fe(II) and H2O2 interacted chemically via the Fenton reaction to produce contaminant-degrading hydroxyl (HO•) radicals, which in turn interacted with PFOA. PFOA concentrations, however, remained unchanged, which most likely reflects the stability of carbon-fluorine bonds and consequent inability of HO• radicals to oxidatively degrade PFOA. 

Finally, the present study aimed to describe the contribution of several genes related to oxidative stress response in S. oneidensis during aerobic respiration and H2O2 stress. In contrast to S. oneidensis anaerobic respiration, aerobic respiration is understudied, and a key contributor to the success of MFR in degrading organic and chlorinated environmental contaminants like 1,4-dioxane. This work describes the contribution of individual genes, particularly catalases and peroxidases, to intracellular H2O2 scavenging rates using the genetically-encoded ratiometric fluorescent sensor HyPer-3 as a reporter.



  • Workflow Status:Published
  • Created By:Tatianna Richardson
  • Created:12/16/2022
  • Modified By:Tatianna Richardson
  • Modified:12/16/2022