Faculty | SIU

Research Interests:

Environmental Microbiology 

Microbes, Coal Mining Wastes, and Rare Earth Elements. The sharp decline of the coal mining industry in the Midwest has left the region littered with abandoned mine sites. Areas where pyrite-containing rocks have been brought into contact with the oxygenated surface- or ground-waters yields waters with high levels of acidity, sulfate, ferric iron, and other toxic metals due to the oxidation of pyrite. Passive treatment methods that utilize naturally occurring materials, such as organic matter and limestone to stimulate biological activity are emerging as cost effective and low maintenance options for long-term acid mine drainage (AMD) treatment. Specifically, bioreactors stimulating sulfate-reducing bacteria have been used to generate alkalinity, precipitate metals, and decrease sulfate levels from AMD waters. In conjunction with the negative impacts of AMD, Coal Mining Wastes (CMWs) have recently been proposed as an economical source of critical rare earth elements (REEs). REEs are essential for many industries and can exist in CMW complexed within insoluble phosphate minerals. My lab has been collaborating with Dr. Liliana Lefticariu in the School of Earth and Sustainability at SIU to monitor the performance and effectiveness of AMD treatment technologies as well as to optimize biomining of REEs from CMW. This work involves microbial community analysis using next-generation sequencing and bioinformatics as well as enrichment and characterization of phosphate mineral-solubilizing microbes associated with regional CMWs.

Heliobacteria and Nitrogenase Like Homologs. Heliobacteria are gram-positive anoxygenic phototrophs within the Firmicutes. Because members of the heliobacteria possess the simplest known photosystem, a fermentative lifestyle, and are the only known gram-positive phototrophs, they are hypothesized to be the first phototrophic cells on Earth. Most heliobacteria are also considered diazotrophs and have frequently been isolated from rice paddies, however, previous research has shown that nitrogen fixing activity in Heliophilum fasciatum is much lower than in other heliobacteria. This project focuses on recently identified H. fasciatum genes that are predicted to encode five distinct Nitrogen fixation like (NflDK) proteins. These proteins are divergent from canonical (molybdenum) or alternative (vanadium or iron-only) nitrogenases. These H. fasciatum proteins share homology to NflD type IV group sequences that are not believed to be capable of reducing dinitrogen gas. Interestingly, one of the H. fasciatum NflDK homologs is similar in amino acid identity to MarDK proteins recently characterized as a methylthio-alkane reductase in the gram-negative anoxygenic phototroph Rhodospirillum rubrum. Under sulfur limiting conditions, this enzyme has been shown in R. rubrum to scavenge S from volatile organic sulfur compounds, resulting in ethylene and methane as byproducts (North, J.A. et al. 2020. Science 369: 1094-1098). While methane is a biofuel, ethylene is a valuable precursor to plastic. Our group has recently discovered that H. fasciatum is also able to convert volatile organic sulfur sources to ethylene and methane. Work is ongoing to develop a genetic system in H. fasciatum to confirm our findings as well as to begin characterizing the role of the other four NflDK homologs in nitrogen fixation or other yet to be identified pathways.

Small RNA Analysis and Desulfovibrio. Besides being a model genus for the study of anaerobic sulfate reduction, Desulfovibrio species are microbes of interest based on their ability to immobilize heavy metals and radionuclides, such as iron and uranium, through precipitation. Desulfovibrio are also industrially important because of their ability to corrode metal pipelines and produce toxic sulfides. An understanding of the intrinsic mechanisms by which these anaerobic sulfate reducers regulate their metabolism and adapt to adverse environments is needed for both industrial and environmental remediation purposes. One form of often overlooked regulation in bacteria is that of small regulatory RNAs (sRNAs). sRNAs play a regulatory role in a myriad of bacterial responses including oxidative, iron, cell envelope, carbon usage, quorum sensing, biofilm formation, anaerobic, and stationary phase stresses/conditions. The detection of sRNA molecules in environmental metatranscriptomic data sets also suggests a role for these molecules in microbial assemblages. Thus, analysis of these molecules is essential for uncovering novel regulatory mechanisms involved in microbial processes critical to the metabolism and survival of Desulfovibrio. While sRNAs are frequently identified in many types of bacteria by targeting a chaperone protein known as Hfq, which facilitates binding of sRNAs to their targets, Desulfovibrio species do not possess a recognizable Hfq protein. To identify and characterize novel sRNAs in this model sulfate reducer, my lab is currently employing both RNA sequencing technologies, genetic tool development, and mutant analyses.

Publications:

A list of publications can be found on Google Scholar.