Yuri Gorby

Marine Environmental Biology University of Southern California Los Angeles, CA 90089 ygorby@usc.edu 858-232-9688

SUMMARY OF QUALIFICATIONS Over 20 years as a laboratory researcher and bioprocess engineer. Developed controlled cultivation laboratories at The Pacific Northwest National Laboratory and the J. Craig Venter Institute in San Diego, CA. Pioneered the emerging field of electromicrobiology with research targeting components and mechanisms of extracellular electron transfer in diverse microbial systems. Organized numerous workshops and symposia dedicated to controlled cultivation as an important component of systems microbiology research. 5 years adjunct professor, Washington State University, graduate student advisor, team-teaching courses in environmental microbiology and microbial physiology. Guest lecturer in Geobiology and Microbial Physiology at the University of Southern California. Currently directing a team of graduate students and post-doctoral fellows from USC, CalTech and the University of Aarhus to apply controlled cultivation approaches for investigating the components and mechanisms of extracellular electron transfer in a variety of microbes, including oxygenic and anoxygenic phototrophic cyanobacteria. EXPERIENCE Associate Research Professor, Marine Environmental Biology Department, University of Southern California, Los Angeles, CA (2011-present) Established a multidisciplinary research program to investigate the molecular and electronic properties of conductive protein filaments called bacterial nanowires in diverse microbial systems. Mentored undergraduate, graduate and post-doctoral researchers in fundamental and advanced principals in controlled cultivation technologies, including continuously stirred tank reactors, fixed-film bioreactors, and biofilm reactors containing poised-potential electrodes as electron donors and acceptors. Developed international collaborations with scientists in Russia, Denmark, Canada and South America to investigate the prominence of bacterial nanowires in diverse microbial systems ranging from redox transition zones in marine sediments to opportunistic, pathogenic biofilms. Assistant Professor, J. Craig Venter Institute, San Diego CA (2006-2011) Established and directed the Electromicrobiology Group to develop and apply controlled cultivation techniques for investigating microbial physiology and ecology of a broad spectrum of microorganisms. Developed collaborations with physicists to establish a mechanistic understanding of electron transfer through and along conductive bacterial nanowires. Supervised post doctoral research and hosted international visiting scientists to integrate concepts of extracellular electron transfer into microbial fuel cells research, wastewater treatment, and biogeochemical processes of redox transition zones in marine and freshwater environments.

Organized a collaborative research team with professors of physics, dentistry and microbiology to investigate the role of bacterial nanowires in a variety of opportunistic pathogenic bacteria, including oral biofilms that promote osteonecrosis of the jaw and pseudomonas cultures associated with wound infections and cystic fibrosis lung tissues. Senior staff Scientist, Environmental Microbiology Group, Pacific Northwest National Laboratory, Richland, WA (1993-2006) Designed and directed the Microbial Cell Dynamics Laboratory, which is still considered one of the top controlled cultivation facilities within the DOE National Lab system. Maintained a programmatic funding stream to support research principally targeting enzymatic reduction of heavy metals, radionuclides and chlorinated hydrocarbons. Integrated controlled cultivation with advanced analytical technologies (MS-based proteomics, transcriptomics and metabolomics) as part of a systems biology approach for investigating gene regulation and protein expression by a variety of bacteria of environmental relevance. Organized and participated in workshops and principal investigators meetings targeting the bioremediation, environmental sustainability and alternative energy. Adjunct Faculty, Washington State University, Richland, WA (2000-2006). Team-taught courses in microbial physiology and ecology. Mentored undergraduate and graduate students and served as research advisor. Post Doctoral Research Fellow, Pacific Northwest National Lab, Richland WA (1991-1993). Developed facilities and approaches needed for investigating heavy metal and radionuclide reduction at DOE National Labs. Attended DOE program planning workshops that lead to the development of the Natural and Accelerated Bioremediation Research Program (NABIR). Developed bioprocess for removing uranium from contained waste streams. Incorporated anaerobic techniques for investigating the role of metal reducing bacteria in reduction of iron in clay minerals and the reduction of chelated forms of cobalt. National Research Council Post Doctoral Research Fellow, US Geological Survey, Reston VA (1989-1991) Discovered enzymatic reduction and precipitation of uranium by dissimilatory iron reducing bacteria. Developed approaches for quantifying uranium reduction by bacteria. This research lead to the development of multiple DOE programs to investigate biogeochemical processes influencing the fate and transport of heavy metals and radionuclides in contaminated subsurface systems. EDUCATION

University of New Hampshire, Durham, NH Ph.D, Microbiology, 1989 Bethany College, Bethany, WV B.S., Biology, 1983. University of Guam, Marine Biology, 1980-1981.

INVITED PRESENTATIONS (recent)

Montana State University Center for Biofilm Engineering Seminar Series, Bozeman, MT. Bacterial Nanowires and Extracellular Electron Transfer in Diverse Microbial Biofilm Communities. November 4, 2011. 6th Annual Nobel Prize Forum for Medicine and Physiology, St. Petersburg, Russia, Bacterial Nanowires: Potential Targets for Innovative Treatment of Opportunistic Pathogenic Biofilms September 19-23, 2011 Science at the Edge (SATE) Seminar Series, Michigan State University, East Lansing, Michigan. Approaches and Tools for Investigating the Molecular and Electronic Properties of Bacterial Nanowires. September 15, 2011.
PUBLICATIONS K.M. Leung, G. Wanger, Q. Guo, Y.A. Gorby, G. Southam, W.M. Lau and J. Yang. Bacterial nanowires: conductive as silicon, soft as polymer, Soft Matter, 7, 6617, 2011. Kan, J., Clingenpeel, S., Macur, R. E., Inskeep, W. P., Lovalvo, D., Varley, J., Gorby, Y., McDermott, T. R., & Nealson, K. 2011. Archaea in yellowstone lake. ISME Journal, 5(11): 1784-1795. Clingenpeel, S., Macur, R. E., Kan, J., Inskeep, W. P., Lovalvo, D., Varley, J., Mathur, E., Nealson, K., Gorby, Y., Jiang, H., Lafracois, T., & McDermott, T. R. 2011. Yellowstone Lake: high-energy geochemistry and rich bacterial diversity. Environ. Microbiol. M.Y. El-Naggar, G. Wanger, K.M. Leung, T.D. Yuzvinsky, G. Southam, J. Yang, W.M. Lau, K.H. Nealson, and Y.A. Gorby. Electrical Transport Along Bacterial Nanowires from Shewanella oneidensis MR-1, Proceedings of the National Academy of Sciences of the United States of America, 107, 18127-18131, 2010. McLean, J. S., Wanger, G., Gorby, Y. A., Wainstein, M., McQuaid, J., Ishii, S. I., Bretschger, O., Beyenal, H., & Nealson, K. H. 2010. Quantification of electron transfer rates to a solid phase electron acceptor through the stages of biofilm formation from single cells to multicellular communities. Environ. Sci. Technol., 44(7): 2721-2727. Torres, C. I., Krajmalnik-Brown, R., Parameswaran, P., Marcus, A. K., Wanger, G., Gorby, Y. A., & Rittmann, B. E. 2009. Selecting anode-respiring bacteria based on anode potential: phylogenetic, electrochemical, and microscopic characterization. Environ. Sci. Technol., 43(24): 9519-9524.

Gorby, Y., J. McLean, A. Korenevsky, K. Rosso, M. Y. El-Naggar, and T. J. Beveridge. 2008. Redox-reactive membrane vesicles produced by Shewanella. Geobiology 6:232-41. El-Naggar, M. Y., Y. A. Gorby, W. Xia, and K. H. Nealson. 2008. The molecular density of states in bacterial nanowires. Biophys J 95:L10-2. Elias, D. A., S. L. Tollaksen, D. W. Kennedy, H. M. Mottaz, C. S. Giometti, J. S. McLean, E. A. Hill, G. E. Pinchuk, M. S. Lipton, J. K. Fredrickson, and Y. A. Gorby. 2008. The influence of cultivation methods on Shewanella oneidensis physiology and proteome expression. Arch Microbiol 189:313-24 McLean, J. S., G. E. Pinchuk, O. V. Geydebrekht, C. L. Bilskis, B. A. Zakrajsek, E. A. Hill, D. A. Saffarini, M. F. Romine, Y. A. Gorby, J. K. Fredrickson, and A. S. Beliaev. 2008. Oxygen-dependent autoaggregation in Shewanella oneidensis MR-1. Environ Microbiol 10:1861-76. Biju, V., D. Pan, Y. A. Gorby, J. Fredrickson, J. McLean, D. Saffarini, and H. P. Lu. 2007. Combined spectroscopic and topographic characterization of nanoscale domains and their distributions of a redox protein on bacterial cell surfaces. Langmuir 23:1333-8. Bretschger, O., A. Obraztsova, C. A. Sturm, I. S. Chang, Y. A. Gorby, S. B. Reed, D. E. Culley, C. L. Reardon, S. Barua, M. F. Romine, J. Zhou, A. S. Beliaev, R. Bouhenni, D. Saffarini, F. Mansfeld, B. H. Kim, J. K. Fredrickson, and K. H. Nealson. 2007. Current production and metal oxide reduction by Shewanella oneidensis MR-1 wild type and mutants. Appl Environ Microbiol 73:7003-12. Fang, R., D. A. Elias, M. E. Monroe, Y. Shen, M. McIntosh, P. Wang, C. D. Goddard, S. J. Callister, R. J. Moore, Y. A. Gorby, J. N. Adkins, J. K. Fredrickson, M. S. Lipton, and R. D. Smith. 2006. Differential label-free quantitative proteomic analysis of Shewanella oneidensis cultured under aerobic and suboxic conditions by accurate mass and time tag approach. Mol Cell Proteomics 5:714-25. Kolker, E., A. F. Picone, M. Y. Galperin, M. F. Romine, R. Higdon, K. S. Makarova, N. Kolker, G. A. Anderson, X. Qiu, K. J. Auberry, G. Babnigg, A. S. Beliaev, P. Edlefsen, D. A. Elias, Y. A. Gorby, T. Holzman, J. A. Klappenbach, K. T. Konstantinidis, M. L. Land, M. S. Lipton, L.-A. McCue, M. Monroe, L. Pasa-Tolic, G. Pinchuk, S. Purvine, M. H. Serres, S. Tsapin, B. A. Zakrajsek, W. Zhu, J. Zhou, F. W. Larimer, C. E. Lawrence, M. Riley, F. R. Collart, J. R. Yates, III, R. D. Smith, C. S. Giometti, K. H. Nealson, J. K. Fredrickson, and J. M. Tiedje. 2005. Global profiling of Shewanella oneidensis MR-1: Expression of hypothetical genes and improved functional annotations. PNAS 102:2099-2104. Phoenix, V. R., A. A. Korenevsky, F. G. Ferris, Y. A. Gorby, and T. J. Beveridge. 2007. Influence of lipopolysaccharide on the surface proton-binding behavior of Shewanella spp. Curr Microbiol 55:152-7. Shi, L., B. Chen, Z. Wang, D. A. Elias, M. U. Mayer, Y. A. Gorby, S. Ni, B. H. Lower, D. W. Kennedy, D. S. Wunschel, H. M. Mottaz, M. J. Marshall, E. A. Hill, A. S. Beliaev, J. M. Zachara, J. K. Fredrickson, and T. C. Squier. 2006. Isolation of a highaffinity functional protein complex between OmcA and MtrC: Two outer membrane

decaheme c-type cytochromes of Shewanella oneidensis MR-1. J Bacteriol 188:470514. Shi, L., S. Deng, M. J. Marshall, Z. Wang, D. W. Kennedy, A. C. Dohnalkova, H. M. Mottaz, E. A. Hill, Y. A. Gorby, A. S. Beliaev, D. J. Richardson, J. M. Zachara, and J. K. Fredrickson. 2008. Direct involvement of type II secretion system in extracellular translocation of Shewanella oneidensis outer membrane cytochromes MtrC and OmcA. J Bacteriol 190:5512-6. Gorby YA, S Yanina, JS Mclean, KM Rosso, DM Moyles, A Dohnalkova, TJ Beveridge, IS Chang, BH Kim, KS Kim, DE Culley, SB Reed, MF Romine, D Saffarini, EA Hill, L Shi, DA Elias DA, DW Kennedy, GE Pinchuk, K Watanabe, S Ishii, B Logan, KH Nealson and JK Fredrickson. 2006. Electrically conductive bacterial nanowires produced by Shewanella oneidensis strain MR-1 and other microorganisms. Proceedings of the National Academy of Sciences of the United States of America 103(30):11358-11363. doi:10.1073/pnas.0604517103 Majors PD, JS McLean, GE Pinchuk, JK Fredrickson, YA Gorby, KR Minard and RA Wind. 2005. NMR methods for in-situ biofilm metabolism studies. Journal of Microbiological Methods 62(3): 377-344. Liu, C., J. M. Zachara, Y. A. Gorby, J. E. Szecsody, and C. F. Brown. 2002. Microbial Reduction of Fe(III) and Sorption/Precipitation of Fe(II) on Shewanella putrefaciens, strain CN32. Environ. Sci. Technol. 37:1385-1393. Parmar N., Y. A. Gorby, T. J. Beveridge, F. G. Ferris. 2001. Formation of green rust and immobilization of nickel in response to bacterial reduction of hydrous ferric oxide. Geomicrobiol. J. 18:703-712. Wildung, R. E., Y. A. Gorby, K. M. Krupka, N. J. Hess, A. E. Plymale, J. P. McKinley, and J. K. Fredrickson. 2000. Effect of Electron Donor and Solution Chemistry on the Products of Dissimilatory Reduction of Technetium by Shewanella putrefaciens. Appl. Environ. Microbiol. 66:2451-2460. Fredrickson J. K., J. M. Zachara, R. K. Kukkadapu, Y. A. Gorby, S. C. Smith, and C. F. Brown CF. 2001. Biotransformation of Ni-Substituted Hydrous Ferric Oxide by an Fe(III)-Reducing Bacterium. Environ. Sci. Tech. 35:703-712. Amonette J. E., D. J., Workman, D. W. Kennedy, Y.A. Gorby and J. S. Fruchter 2000. Dechlorination of carbon tetrachloride by Fe(II) associated with goethite Environ. Sci. Technol. 34: 4606-4613. Sokolov, I., D. S. Smith, G. S. Henderson, Y. Gorby, and F. G. Ferris. 2000. Cell Surface Electrochemical Heterogeneity of the Fe(III)-reducing Bacteria Shewanella putrefaciens. Environ. Sci. Tech. 35:341-347. Fredrickson, J. K., J. M. Zachara, D. W. Kennedy, M. C. Duff, Y. A. Gorby, S. W. Li, and K. M. Krupka. 2000. Reduction of U(VI) in Goethite (a-FeOOH) Suspensions by a Dissimilatory Metal-reducing Bacterium. Geochim. Cosmochim. Acta 64:30853098. Kieft, T. L., J. K. Fredrickson, T. C. Onstott, Y. A. Gorby, H. M. Kostandarithes, T. J. Bailey, D. W. Kennedy, S. W. Li, A. E. Plymale, C. M. Spadoni, and M. S. Gray.

1999. Dissimilatory Reduction of Fe(III) and Other Electron Acceptors by a Thermus Isolate. Appl. Environ. Microbiol. 65(3):1214-21 Gorby, Y. A., F. Caccavo, Jr., and H. Bolton, Jr. 1998. Microbial Reduction of Co(III)-EDTA in the Presence and Absence of Manganese(IV) Oxide. Environ. Sci. Technol. 32:244-247. Workman, D., M. Truex, Y. Gorby, and J. Fredrickson. 1997. Microbial Reduction of Vitamin B12 by Shewanella alga Strain BrY with Subsequent Transformation of Carbon Tetrachloride. Environ. Sci. Technol. 31:2292-2297. Truex, M. J., B. M. Peyton, N. B. Valentine, and Y. A. Gorby. 1997. Kinetics of U(VI) Reduction by a Dissimilatory Fe(III)-reducing Bacterium under Non-growth Conditions. Biotechnol. Bioengin. 55:490-496. Fredrickson, J. K., and Y. A. Gorby. 1996. Environmental Processes Mediated by Iron-reducing Bacteria. Curr. Opin. Biotech. 7:287-294. Bolton, Jr., H., and Y. A. Gorby. 1995. An Overview of the Bioremediation of Inorganic Contaminants. In Bioremediation of Inorganics, eds. R. E. Hinchee, J. L. Means, and D. R. Burris, pp. 1-16. Battelle Press, Columbus. Lovley, D. R., S. J. Giavanoni, D. R. White, J. E. Champine, E. J. P. Phillips, Y. A. Gorby, and S. Goodwin. 1993. Geobacter metallireducens gen. nov. sp. nov., A Microorganism Capable of Coupling the Complete Oxidation of Organic Compounds to the Reduction of Iron and Other Metals. Arch. Microbiol. 159:336-344. Lovley, D. R., E. J. Phillips, Y. A. Gorby, and E. Landa. 1991. Microbial Uranium Reduction. Nature 350:413-416. Gorby, Y. A., and D. R. Lovley. 1992. Enzymatic Uranium Precipitation. Environ. Sci. Technol. 26:205-207. Gorby, Y. A., and D. R. Lovley. 1991. Electron Transport in the Dissimilatory IronReducer, GS-15. Appl. Environ. Microbiol. 57:867-870.