Faculty | SIU

Research Interests:

My research laboratory focuses on microbial diversity in oligotrophic, geothermal, and ancient environments. Microorganisms from these environments possess characteristics valuable to applied research. The underlying fundamental principles are analyzed using biochemistry and bioinformatics, where we examine extant/extinct microbial biomes, characterize novel pathways to produce value added molecules/biofuels, determine critical species involved in remediation/recovery processes, and piecing together the mechanisms that support the origins of life.

While my research interests cover many areas of microbial biochemistry, the three research themes pursued currently are to: 1) isolate/characterize deep subsurface microorganisms to determine how life is sustained in oligotrophic environments; 2) design/develop anaerobic consolidated bioprocessing using microorganisms from geothermal/subsurface environments to convert bio-waste to value added molecules/biofuels; 3) design/develop algorithms based on next generation sequencing data that can evaluate the severity and recovery of damage to ecosystems from pollution.

Subsurface microorganisms. Subsurface prokaryotic microorganisms likely constitute more biomass than all life on the surface of the Earth. Although very little is known about the vast subsurface microbial ecosystems, diverse populations of microorganisms have been detected around the world. How do these microorganisms metabolically sustain themselves without exposure to the sun? Which rock types influence microbial diversity? What are the microbial and viral dynamics in the subsurface? And are the subsurface ecosystems analogues to life on other planets/moons?

Consolidated bioprocessing microbial driven conversion of bio-waste to value added molecules/biofuels. Reliance upon extraction of hydrocarbon molecules to support our global infrastructure is neither economically nor environmentally viable. Investment in alternate technologies based on renewable resources has become economically practical as well as necessary for preserving our natural resources. Microorganisms found in every ecological niche on this planet have adapted/developed enzymatic means to covert molecules from one redox state to another. Some microorganisms live optimally in extreme environments, favoring their use in applied industrial methods to produce chemicals and fuels. My laboratory is exploring novel methods and microorganisms that can be used in conversion of toxic recalcitrant biomass into value added products.

Design/develop algorithms for molecular tools/metrics to evaluate ecological recovery. Next generation sequencing has made it possible to sequence a single biological organism or whole microbial communities from any environment. While genomes and environmental sequencing is reshaping how microbiology is conducted, new algorithms must be developed to keep pace with the development of novel sequencing technology and to be able use the ‘big data’ to answer questions. This laboratory is examining how benthic and soil microbial communities adapt/react to environmental events as a metric to understanding the magnitude and length of time to recovery from disturbances.

Undergraduates and high school students who want to learn laboratory research techniques and are interested in contributing to ongoing projects are encourage discuss ideas/opportunities with me.

Publications:

• Hamilton-Brehm SD, Onstott T, Sherwood-Lollar B, Zavarin M, Grzymski J, Russel C, Caldwell M, Lawson PA, Neveux I, Moser DP, Stewart L. Thermoanaerosceptrum fracticalcis gen. nov. sp. nov., a novel fumarate-fermenting microorganism from a deep fractured carbonate aquifer of the US Great Basin. Frontiers in Microbiology. 2019;10:2224. Link
• Sackett JD, Huerta DC, Kruger BR, Hamilton-Brehm SD, Moser DP. 2018. A comparative study of prokaryotic diversity and physicochemical characteristics of Devils Hole and the Ash Meadows Fish Conservation Facility, a constructed analog. PLoS ONE 13(3): e0194404. Link
• Hamilton-Brehm SD, Hristova LT, Edwards SR, Wedding JR, Snow M, Kruger BR, Moser DP. Ancient human mitochondrial DNA and radiocarbon analysis of archived quids from the Mule Spring Rockshelter, Nevada, USA. PloS one. 2018;13(3):e0194223. Link
• Clarkson SM, Hamilton-Brehm SD, Giannone RJ, Engle NL, Tschaplinski TJ, Hettich RL, Elkins JG. A comparative multidimensional LC-MS proteomic analysis reveals mechanisms for furan aldehyde detoxification in Thermoanaerobacter pseudethanolicus 39E. Biotechnology for biofuels. 2014 Dec;7(1):165.
• Vishnivetskaya TA, Hamilton-Brehm SD, Podar M, Mosher JJ, Palumbo AV, Phelps TJ, Keller M, Elkins JG. Community analysis of plant biomass-degrading microorganisms from Obsidian Pool, Yellowstone National Park. Microbial ecology. 2015 Feb 1;69(2):333-45.
• Wan, Q., Kovalevsky, A., Zhang, Q., Hamilton-Brehm, S., Upton, R., Weiss, K.L., Mustyakimov, M., Graham, D., Coates, L. and Langan, P. 2014. Heterologous expression, purification, crystallization and preliminary X-ray analysis of Trichoderma reesei xylanase II and four variants. Acta. Crystallogr. Sect. F. Struct. Biol. Cryst. Commun. Mar 1; 69(Pt 3):320-3.
• Elkins, J.G., Hamilton-Brehm, S.D., Lucas S., Han J., Lapidus A., Cheng J.F., Goodwin L.A., Pitluck, S., Peters, L., Mikhailova, N., Davenport, K.W., Detter, J.C., Han, C.S., Tapia, R., Land, M.L., Hauser, L., Kyrpides, N.C., Ivanova, N.N., Pagani, I., Bruce, D., Woyke, T. and Cottingham, R.W. 2013. Complete Genome Sequence of the Hyperthermophilic Sulfate-Reducing Bacterium Thermodesulfobacterium geofontis OPF15T. Genome. Announc. Apr 11; 1(2).
• Wan, Q., Zhang, Q., Hamilton-Brehm, S.D., Weiss, K., Mustyakimov, M., Coates, L., Langan, P., Graham, D.E., Kovalevsky, A. 2013. X-ray Crystallographic Studies of Family 11 Xylanase Michaelis and Product Complexes: Implications for the Catalytic Mechanism of Retaining Glycoside Hydrolases. Acta. Crystallogr. D. Biol. Crystallogr. 2014 Jan; 70(Pt 1):11-23.
• Wang, Z.W., Lee, S.H., Elkins, J.G., Li, Y., Hamilton-Brehm, S. and Morrell-Falvey, J.L. 2013. Continuous live cell imaging of cellulose attachment by microbes under anaerobic and thermophilic conditions using confocal microscopy. J. Environ. Sci. (China). 2013 May 1;25(5):849-56.
• Hamilton-Brehm, S.D., Gibson, R.A., Green, S.J., Hopmans, E.C., Shields, J.P. and Elkins, J.G. 2013. Thermodesulfobacterium geofontis sp. nov., a hyperthermophilic, sulfate-reducing bacterium isolated from Obsidian Pool, Yellowstone National Park. Extremophiles. Mar; 17(2):251-63. Link
• Yee, K.L., Rodriguez, M. Jr, Tschaplinski, T.J., Engle, N.L., Martin, M.Z., Fu C., Wang, Z.Y., Hamilton-Brehm, S.D. and Mielenz J.R. 2012. Evaluation of the bioconversion of genetically modified switchgrass using simultaneous saccharification and fermentation and a consolidated bioprocessing approach. Biotechnol. Biofuels. Nov 12; 5(1):81.
• Blumer-Schuette, S.E., Giannone, R.J., Zurawski, J.V., Ozdemir, I., Ma, Q., Yin, Y., Xu, Y., Kataeva, I., Poole, F.L. 2nd, Adams, M.W., Hamilton-Brehm, S.D., Elkins, J. G., Larimer, F. W., Land, M.L., Hauser, L.J., Cottingham, R.W., Hettich, R.L. and Kelly R.M. 2012. Caldicellulosiruptor core and pangenomes reveal determinants for noncellulosomal thermophilic deconstruction of plant biomass. J. Bacteriol. Aug; 194(15):4015-28. Link
• Hamilton-Brehm, S.D., Vishnivetskaya, T.A., Allman, S.L., Mielenz, J.R. and Elkins J.G. 2012. Anaerobic high-throughput cultivation method for isolation of thermophiles using biomass derived substrates. Methods. Mol. Biol. 908:153-68.
• Elkins, J. G., Lochner, A., Hamilton-Brehm, S.D., Davenport, K.W., Podar, M., Brown, S.D., Land, M.L., Hauser, L.J., Klingeman, D.M., Raman, B., Goodwin, L.A., Tapia, R., Meincke, L.J., Detter, C.J., Bruce, D.C., Han, C.S., Palumbo, A.V., Cottingham, R.W., Keller, M. and Graham, D.E. 2010. Complete Genome Sequence of the Cellulolytic Thermophile Caldicellulosiruptor obsidiansis OB47. J. Bacteriol. 192(22): 6099-100.
• Wang, Z.W., Hamilton-Brehm S.D., Lochnerm A., Elkinsm J.G. and Morrell-Falvey, J.L. 2010. Hydrolysate diffusion and utilization in cellulolytic biofilms of the extreme thermophile Caldicellulosiruptor obsidiansis. Bioresour. Technol. 102(2011): 3155-3162. Link
• Hamilton-Brehm, S.D., Mosher, J.J., Vishnivetskaya, T., Podar, M., Carroll, S., Allman, S., Phelps, T. J., Keller, M. and Elkins, J. G. 2010. Caldicellulosiruptor obsidiansis sp. nov., an anaerobic, extremely thermophilic, cellulolytic bacterium isolated from Obsidian Pool, Yellowstone National Park. Appl. Environ. Microbiol. 76(4):1014-20.
• Yang, S.J., Kataeva, I., Hamilton-Brehm, S.D., Engle, N.L., Tschaplinski, T.J., Doeppke, C., Davis, M., Westpheling, J. and Adams, M.W.W. 2009. Efficient degradation of lignocellulosic plant biomass, without pretreatment, by the thermophilic anaerobe "Anaerocellum thermophilum" DSM 6725. Appl. Environ. Microbiol. 75(14):4762-9.
• Hamilton-Brehm, S.D., Schut, G.J. and Adams, M.W. 2009. Antimicrobial Activity of the Iron Sulfur Nitroso Compound Roussin’s Black Salt (Fe4S3(NO)7) on the Hyperthermophilic Archaeon Pyrococcus furiosus. Appl. Environ. Microbiol. 75(7):1820-5.
• Adams, M.W.W., Jenney, F.E. Jr., Chou, C.J., Hamilton-Brehm, S., Poole, F.L., Shockley, K.R., Tachdjian, S. and Kelly R.M. 2007. Transcriptomics, Proteomics and Structural Genomics of Pyrococcus furiosus. Archaea: Evolution, Physiology, and Molecular Biology (Garrett, R. and Klenk, H. P., eds.), Blackwell, 239-246.
• Lee, H.S., Shockley, K.R., Schut, G.J., Conners, S.B., Montero, C.I., Johnson, M.R., Chou, C.J., Bridger, S.L., Wigner, N., Brehm, S.D., Jenney, F.E. Jr., Comfort, D.A., Kelly, R.M. and Adams, M.W. 2006. Transcriptional and biochemical analysis of starch metabolism in the hyperthermophilic archaeon Pyrococcus furiosus. J. Bacteriol 188:2115-25.
• Hamilton-Brehm, S.D., Schut, G.J. and Adams, M.W. 2005. Metabolic and evolutionary relationships among Pyrococcus Species: genetic exchange within a hydrothermal vent environment. J. Bacteriol 187:7492-9.
• Weinberg, M.V., Schut, G.J., Brehm, S., Datta, S. and Adams M.W. 2005. Cold shock of a hyperthermophilic archaeon: Pyrococcus furiosus exhibits multiple responses to a suboptimal growth temperature with a key role for membrane-bound glycoproteins. J. Bacteriol 187:336-48.
• Schut, G.J., Brehm, S.D., Datta, S. and Adams M. W. 2003. Whole-genome DNA microarray analysis of a hyperthermophile and an archaeon: Pyrococcus furiosus grown on carbohydrates or peptides. J. Bacteriol 185:3935-47.