Kelly Bender | Microbiology | SIU

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Kelly Bender

Associate Professor and Director, Molecular Biology, Microbiology and Biochemistry Graduate Program

Kelly Bender

Life Science II 106
Phone: 618-453-2868
Fax: 618-453-8036
E‑mail: bender@micro.siu.edu

Research Specialties: Environmental Microbiology; Sulfate-reducing bacteria; Small RNA Analysis; Community Analysis of Acid Mine Drainage Impacted Sites.                                     

Education:

PhD, 2003, Southern Illinois University

Courses Taught:

MICR 301: Principles of Microbiology
MICR/MBMB 470: Prokaryotic Diversity
MICR/MBMB 481: Diagnostic and Applied Microbiology Laboratory

Research Interests:

Environmental Microbiology 

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 regulation that has recently come to the forefront in bacteria is that of small regulatory RNAs (sRNAs). sRNAs are molecules ranging in size from 20-200 nucleotides that predominantly affect gene regulation by binding to complementary mRNA in an anti-sense fashion. Thus induction of sRNAs under specific conditions provides both an immediate response independent of protein modification and an additional layer of regulation for genes that must be tightly controlled or are critical to multiple cellular responses. As such, sRNAs are now known to 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 recent 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.

Community Analysis of Sites Affected by Coal-Generated Acid Mine Drainage (AMD). 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 treatment. Specifically, bioreactors stimulating sulfate-reducing bacteria have been used to generate alkalinity, precipitate metals, and decrease sulfate levels from AMD waters. In Carbondale IL, a passive bioreactor system has been constructed at an abandoned mine site to stimulate sulfate-reducing bacteria to remove sulfate, precipitate metals, and raise the pH of the system. My lab has been collaborating with Dr. Liliana Lefticariu in the Department of Geology at SIU to monitor the performance and effectiveness of this full-scale bioreactor and that of engineered smaller field-scale bioreactors. To characterize the microbial community present throughout different regions of the site and reactors we are using next-generation sequencing of the 16S rRNA gene and bioinformatics. We are also using traditional cloning and Sanger sequencing of the dsrAB (encoding the dissimilatory (bi)sulfite reductase genes involved in biological sulfate reduction) to profile the diversity of sulfate-reducing bacteria present. Based on our community profiling data, we are also focused on isolating sulfur- and iron-cycling microorganisms unique to this site.

Publications:

Articles in Professional Journals

  • Lefticariu L., Sutton, S.R., Bender, K.S., Lefticariu, M., Pentrak, M., and Stucki. J.W. 2016. Impacts of detrital nano- and micro-scale particles (dNP) on contaminant dynamics in a coal mine AMD treatment system. Sci. Total Environ. S0048-9697(16): 32084-32088. PubMed link
  • Bender, K.S. 2016. Environmental (per)chlorate reduction: a collaborative effort in syntrophy? Environ. Microbiol. 18: 3205-3206 PubMed link
  • Lefticariu, L., Walters, E.R., Pugh, C.W., and Bender, K.S. 2015. Sulfate reducing bioreactor dependence on organic substrates for remediation of coal-generated acid mine drainage: Field experiments. Appl. Geochem. 63: 70-82. Link
  • Burns, A.S., Pugh, C.W., Segid, Y.T., Behum, P.T., Lefticariu, L. and Bender, K.S. 2012. Performance and microbial community dynamics of a sulfate-reducing bioreactor treating coal generated acid mine drainage. Biodegradation 23(3):415-29. PubMed link
  • Chambers, J.R. and Bender, K.S. 2011. The RNA chaperone Hfq is important for growth and stress tolerance in Francisella novicida. PLoS One 6: e19797. PubMed link
  • Behum, P.T., Lefticariu, L., Bender, K.S., Segid, Y.T., Burns, A.S. and Pugh, C.W. 2011. Remediation of coal-mine drainage by a sulfate-reducing bioreactor: A case study from the Illinois coal basin, USA. Appl. Geochem. 26: S162-S166. Link
  • Zhou, A., He, Z., Redding-Johanson, A.M., Mukhopadhyay, A., Hemme, C.L., Joachimiak, M.P., Luo, F., Deng, Y., Bender, K.S., He, Q., Keasling, J.D., Stahl, D.A., Fields, M.W., Hazen, T.C., Arkin, A.P., Wall, J.D. and Zhou, J. 2010. Hydrogen peroxide-induced oxidative stress response in Desulfovibrio vulgaris Hildenborough. Environ. Microbiol. 12:2645-2657. PubMed link
  • Keller, K.L., Bender, K. and Wall, J.D. 2009. Development of a markerless genetic exchange system in Desulfovibrio vulgaris Hildenborough and its use in generating a strain with increased transformation efficiency. Appl. Environ. Microbiol. 75:7682-7691. PubMed link
  • Liang, Y., Yesuf, J. Schmitt, S., Bender, K. and Bozzola, J. 2009. Study of cellulases from a newly isolated thermophilic and cellulolytic Brevibacillus sp. strain JXL. J. Ind. Microbiol. Biotechnol. 36:961-970. Link
  • Morrone, D., Chambers, J., Lowry, L., Kim, G., Anterola, A., Bender, K. and Peters, R.J. 2009. Gibberellin biosynthesis in bacteria: separate ent-copalyl diphosphate and ent-kaurene synthases in Bradyrhizobium japonicum. FEBS Lett. 583:475-480.
  • Bender, K.S., Yen, H.C., Hemme, C.L., Yang, Z., He, Z., He, Q., Zhou, J., Huang, K.H., Alm, E.J., Hazen, T.C., Arkin, A.P., Wall, J.D. 2007 Analysis of a ferric uptake regulator (Fur) mutant of Desulfovibrio vulgaris Hildenborough. Appl Environ Microbiol. 73:5389-5400. PubMed link
  • Bender, K.S., Yen, H.-C. and Wall, J.D. 2006. Analysing the metabolic capabilities of Desulfovibrio species through genetic manipulation. Biotechnol. Genet. Eng. Rev. 23:157-174.
  • Achenbach, L.A., Bender, K.S., Sun, Y. and Coates, J.D. 2006. The biochemistry and genetics of microbial perchlorate reduction. In B. Gu and J.D. Coates (Eds). Perchlorate, Environmental Occurrence, Interactions, and Treatment. Springer: New York, NY. pp. 297-310.
  • Bender, K.S., Chang, C., Chakraborty, R., Belchik, S.M., Coates, J.D. and Achenbach, L.A. 2005. Identification, characterization, and classification of genes encoding perchlorate reductase. J. Bacteriol. 187: 5090-5096. PubMed link
  • Bender, K.S., Rice, M.R., Fugate, W.H., Coates, J.D. and Achenbach, L.A. 2004. Metabolic primers for detection of (per)chlorate-reducing bacteria in the environment and phylogenetic analysis of cld gene sequences. Appl. Environ. Microbiol. 70: 5651-5658. PubMed link
  • Bender, K.S., O'Connor, S.M., Chakraborty, R., Coates, J.D. and Achenbach, L.A. 2002. Sequencing and transcriptional analysis of the chlorite dismutase gene of Dechloromonas agitata and its use as a metabolic probe. Appl. Environ. Microbiol. 68: 4820-4826. PubMed link
  • Coates, J.D., Chakraborty, R., Lack, J.G., O'Connor, S.M.,Cole, K.A., Bender, K.S. and Achenbach, L.A. 2001. Anaerobic benzene oxidation coupled to nitrate reduction in pure culture by two strains of Dechloromonas. Nature 411: 1039-1043. PubMed link