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.
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 MR1: 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 high-affinity
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, and J. S. Fruchter Gorby, Y. A.
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.
CURRENT AND PENDING SUPPORT
Support: _X_ Current __ Pending __ Submission Planned in Near Future __ *Transfer of Support
PI: Y.Gorby
Project/Proposal Title: Bacterial Nanowires and Extracellular Electron Transfer to Heavy Metals and
Radionuclides by Bacterial Isolates from DOE Field Research Centers
Source of Support: Department of Energy
Total Award Amount: $ 1,071,217.00 Total Award Period Covered: 06/01/2010 – 05/31/2013
Location of Project: Yr 1: J Craig Venter Institute, Inc., Years 2 – 3 at University of Southern California
Person-Months Per Year Committed to the Project: Cal: 3 months
Support: _X_ Current __ Pending __ Submission Planned in Near Future __ *Transfer of Support
PI: Kenneth Nealson, USC PI, Gorby PI of Sub when sub was at J Craig Venter Institute
Project/Proposal Title: Bioengineered Fuel Cell: Optimizing Via Genetic Approaches And Multi-Scale
Modeling
Source of Support: USC prime, transferring to USC, original support from Dept of Defense (AFOSR)
Total Award Amount: $ 419,374 Total Award Period Covered: 01/01/2010 – 12/31/2012
Location of Project: USC
Person-Months Per Year Committed to the Project: Cal months 6
Support: __ Current _X_ Pending __ Submission Planned in Near Future __ *Transfer of Support
PI: Yuri Gorby
Project/Proposal Title: Collaborative Research: Mechanisms, Modeling and Geochemical
Consequences of Electron Flow in Acid Mine Drainage-Induced Sediments (this proposal)
Source of Support: NSF
Total Award Amount: $ 253,233 Total Award Period Covered: 03/01/2012 – 02/28/2015
Location of Project: USC
Person-Months Per Year Committed to the Project: Cal: 1 month
Support: __ Current _X_ Pending __ Submission Planned in Near Future __ *Transfer of Support
PI: Kenneth H. Nealson
Project/Proposal Title: Microbial Network Models: Predicting Physiological Responses and Genetic
Adaptations
Source of Support: Department of Defense, Office of Naval Research
Total Award Amount: $ 6,686,788 Total Award Period Covered: 06/01/2012 – 05/31/2017
Location of Project: USC
Person-Months Per Year Committed to the Project: Cal: 2 months
Support: __ Current _X_ Pending __ Submission Planned in Near Future __ *Transfer of Support
PI: Yuri Gorby, co-PI: Roy Price, Edmond Leung
Project/Proposal Title: Conductive Nanowires in Marine Hydrothermal Vent Communities
Source of Support: NSF Center for Dark Energy Biosphere Investigators
Total Award Amount: $ 50,000 Total Award Period Covered: 06/01/2012 – 05/31/2013
Location of Project: USC
Person-Months Per Year Committed to the Project: Cal: 0.5 months