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Sharon Lafferty Doty, Ph.D.
Associate Professor
School of Environmental and Forest Sciences; College of the Environment
University of Washington
Seattle, WA 98195-2100

The website that is kept up to date is:


B.S. in Genetics, University of California (1989)

Ph.D. in Microbiology, University of Washington (1995)

Postdoctoral research in plant biochemistry, University of Washington

Faculty since 2003


Current Roles

Chair of the working party on Environmental Applications for the International Poplar Commission (IPC) of the Food and Agriculture Organization of the United Nations:

Chair of the SEFS Curriculum Committee; Curriculum Coordinator for Environmental Science and Resource Management (ESRM) of the School of Environmental and Forest Sciences; Member of the UW Astrobiology Program (Astrobiology Group); Associate faculty of the UW Molecular and Cellular Biology Program (MCB)


Current Research Interests:  Bioresource sciences with an emphasis on plant-microbe interactions using the tools of molecular biology, biochemistry, and microbiology.  The main areas of research in my lab are in phytoremediation, nitrogen fixation, and bioenergy.

1.  Phytoremediation
With funding from the National Institute of Environmental Health Sciences Superfund Research Program, we are studying the effectiveness of using poplar and willow plants to remove and degrade the common insecticide, chlorpyrifos (NIEHS).

In addition, with funding from the NSF Environmental Engineering program, USDA, NIH SBIR, and McIntire-Stennis, my lab has studied the impact of endophytes (beneficial microbes that live within plants) for improving phytoremediation of TCE and PAHs.  We have isolated novel TCE-degrading and PAH-degrading endophytes with the potential to improve removal of these important environmental pollutants.

2.  Symbiotic Plant-Microbe Interactions
I isolated a variety of microorganisms from the stems of our poplar hybrids. One of the isolates was a close match to
Rhizobium tropici. Native poplar and willow grow in low-nitrogen settings including the rocky habitat alongside the Snoqualmie River in Western Washington.  Many of the endophytes of poplar and willow at this site are able to grow under nitrogen-limitation.  I am studying how endophytic microorganisms may help poplar and willow to grow under nitrogen-limitation.  We recently received funding from the American Recovery and Reinvestment Act (ARRA) through the NSF Energy for Sustainability Program.  This project is to research the use of nitrogen-fixing endophytes for improved growth of bioenergy crops without the use of environmentally-harmful chemical fertilizers. A news summary on this project is linked here.  With funding from the UW Center for Commercialization, we demonstrated that these microbes can also profoundly benefit crop plants and grasses.  We recently received funding from AFRI for testing the use of the N-fixing poplar endophytes on plantation poplar for biofuel production.

3.  Bioenergy Research

I have several research projects aimed at increasing the efficiency of bioethanol production.  By lowering the cost of bioethanol production, this locally-made fuel can be made more attractive as an alternative to foreign oil.  In collaboration with Professor Renata Bura, we studied yeasts isolated from plants with several advantages over traditional baker's yeast for the production of bioethanol.  One of these strains was sequenced by the DOE Joint Genome Initiative.  As part of the UW IGERT program on bioenergy, Prof. Dan Schwartz and I have a project to screen additional environmental samples for superior yeast strains.  Our IGERT program is focused on training graduate students for research into environmentally sustainable bioenergy production.  The School of Environmental and Forest Sciences Bioenergy Team is dedicated to research on biofuel production from non-food crops. 


Currently, there are 5 Ph.D. graduate students in my lab.  Undergraduate research is also an important aspect of my laboratory.  For example, currently (autumn 2013), there are over twenty undergraduates conducting research in my lab. 

Recent Publications



Knoth, J., Kim, S.H., Ettl, G., and Doty, S. L.  2013.  Biological nitrogen fixation and biomass accumulation within poplar clones as a result of inoculations with diazotrophic endophyte consortia.  New Phytologist.  In press.



1.  Doty, S. L.  2011.  Nitrogen-fixing endophytic bacteria for improved plant growth.  In Bacteria in Agrobiology: Plant Growth Responses.  DK Maheshwari, ed.  Chapter 9, pgs 183-199.  Springer.


2.  Xu, P., Bura, R. and Doty, S. L.  2011.  Genetic analysis of D-xylose metabolism by endophytic yeast strains of PopulusGenetics and Molecular Biology 34(3):471-478.


3.  Redman, R., Kim, Y., Woodward, C., Greer, C., Espino, L., Doty, S. L., and Rodriguez, R.

2011.  Increased Fitness and Adaptation of Rice Plants to Cold, Drought and Salt Stress Via Habitat Adapted Symbiosis: A Strategy for Mitigating Impacts of Climate Change.  PloS ONE 6(7) e14823.


4.  Doty, S. L.  2011.  Growth-promoting endophytic fungi of forest trees.  In Endophytes of Forest Trees:  Biology and Applications.  AM Pirttila and AC Carolin, eds.  Springer. doi: 10.1007/978-94-007-1599-8.


5.  Dhankher, O., Pilon-Smits, E., Meagher, R. B., and Doty, S. L.  2011.  Chapter 20:  Biotechnological approaches for phytoremediation. In Plant Biotechnology and Agriculture:  Prospects for the 21st Century.  A. Altman and P. M. Hasegawa, eds.  Elsevier.


6.  Lee, K. Y., Strand, S. E., and Doty, S. L.  2012. Phytoremediation of chlorpyrifos by Populus and SalixInternational Journal of Phytoremediation 14(1):48-61. 


7.  Khan, Z and Doty, S.L. 2011. Endophyte-assisted phytoremediation, Current Topics in Plant Biology, Vol. 12, 97-105.


8.  Kang, J. W., Khan, Z., and Doty, S. L. 2012. Biodegradation of TCE by an endophyte of hybrid poplar.  Applied and Environmental Microbiology 78(9):3504-3507


9.  Khan, Z and Doty, S.L. 2011. Using endophytes to enhance phytoremediation. In Phytotechnologies: Remediation of Environmental Contaminants. Naser A. Anjum Ed. Taylor and Francis.


10.  Miller, R. S., Khan, Z., and Doty, S. L.  2011.  Comparison of trichloroethylene toxicity, removal, and degradation by varieties of Populus and Salix for improved phytoremediation applications.  Journal of Bioremediation and Biodegradation S7:001. DOI: 10.4172/2155-6199.S7-001 (open access).


11. Kang, J. W., Song, J., Doty, S. L., and Lee, D. K. 2012.  Diversity of rhizobia associated with leguminous trees growing in South Korea.  J. Basic Microbiology 52:1-8.

12. Bura, R., Vajzovic, A., and Doty, S. L.  2012.  Novel endophytic yeast Rhodotorula mucilaginosa strain PTD3:  I. Production of xylitol and ethanol.  Journal of Industrial Microbiology & Biotechnology 39(7):1003-1011.

13. Vajzovic, A., Bura, R., and Doty, S. L.  2012.  Novel endophytic yeast Rhodotorula mucilaginosa strain PTD3:  II. Production of xylitol and ethanol in the presence of inhibitors.  Journal of Industrial Microbiology & Biotechnology 39(10):1453-1463.

14. Knoth, J., Kim, S.H., Ettl, G., and Doty, S. L.  2012.  Effects of cross host species inoculation of nitrogen-fixing endophytes on growth and leaf physiology of maize.  GCB Bioenergy doi: 10.1111/gcbb.12006

15. Khan, Z., Guelich, G., Phan, H., Redman, R., and Doty, S. L.  2012.  Bacterial and yeast endophytes from poplar and willow promote growth in crop plants and grasses.  Agronomy doi: 10.5402/2012/890280. Open Access



Kang, J. W., Wilkerson, H-W, Farin, F. M., Bammler, T. K., Beyer, R. P., Strand, S. E., and Doty, S. L.  2010.  Mammalian cytochrome CYP2E1 triggered differential gene regulation in response to trichloroethylene (TCE) in a transgenic poplar.  Functional and Integrative Genomics 10(3):417-424.


Doty, S. L., Oakley, B., Xin, G., Kang, J. W., Singleton, G., Khan, Z., Vajzovic, A., and Staley, J. T.  2009.  Diazotrophic endophytes of native black cottonwood and willow.  Symbiosis 47:27-33.

Xin, G., Zhang, G., Kang, J. W., Staley, J. T., and Doty, S. L.  2009.  A diazotrophic, indole-3-acetic acid-producing endophyte from wild cottonwoodBiology and Fertility of Soils 45:669-674.


Xin, G., Glawe, D., and Doty, S. L.  2009.  Characterization of three endophytic indole-3-acetic acid-producing yeasts occurring in Populus trees.  Mycological Research 113: 973-980.

Khan, Z. and Doty, S. L.  2009.  Characterization of bacterial endophytes of sweet potato plants.  Plant and Soil322:197-207.

Dowling, D. N. and Doty, S. L. 2009.  Improving phytoremediation through biotechnology.  Current Opinion in Biotechnology 20:1-3.

James, C. A., Xin, G., Doty, S. L., Muiznieks, I., Newman, L., and Strand, S. E. 2009.  A mass balance study of the phytoremediation of perchloroethylene-contaminated groundwater.  Environmental Pollution 157(8-9)2564-2569.

Van Aken, B. and Doty, S. L. 2009.  Transgenic plants and associated bacteria for phytoremediation of chlorinated compounds.  Biotechnology and Genetic Engineering Reviews 26:43-64.

Doty, S. L.  2008.  Tansley Review:  Enhancing phytoremediation through the use of transgenics and endophytes.  New Phytologist 179:  318-333.

Doty, S. L. and Strand, S. E.  2008.  Phytoremediation of volatile pollutants through genetic engineering.  ISB News Report.  January issue (pgs 1-3).

James,C.A.; Xin,G., Doty, S. L., Strand, S. E. 2008. Degradation of low molecular weight volatile organic compounds by plants genetically modified with mammalian cytochrome P450 2E1. Environ. Sci Technol. 42:289-293.

Doty,S.L.; James,C.A.; Moore,A.L.; Vajzovic,A.; Singleton,G.L.; Ma,C.; Khan,Z.; Xin,G.; Kang,J.W.; Park,J.Y.; Meilan,R.; Strauss,S.H; Wilkerson, J., Farin, F., and Strand,S.E. 2007. Enhanced phytoremediation of volatile environmental pollutants with transgenic trees. Proc. Natl. Acad. Sciences 104(43):16816-16821.

Doty, S. L., Dosher, M. R., Singleton, G. L., Moore, A. L., Van Aken, B., Stettler, R. F., Strand, S. E., Gordon, M. P.  2005.  Identification of an endophytic Rhizobium in stems of PopulusSymbiosis 39(1):27-36.

Van Aken, B., Peres, C. M., Doty, S. L., Yoon, J. M., and Schnoor, J. L.  2004.   Methylobacterium oliveri sp. nov.: A novel aerobic, pink-pigmented, facultatively methylotrophic, methane-utilizing bacterium isolated from poplar trees (Populus deltoides x nigra DN34). International Journal of Systematic and Evolutionary Microbiology 54: 1191-1196.

Doty, S. L., Shang, T. Q., Wilson, A. M., Moore, A. L., Strand, S. E., Oda, C. and Gordon, M. P. Metabolism of the halogenated hydrocarbons, TCE and EDB, by the tropical leguminous tree, Leuceana leucocephala. 2003. Water Research 37(2):441-449.

Banerjee, S., Shang, T. Q., Wilson, A. M., Moore, A. L., Strand, S. E., Gordon, M. P., and Doty, S. L. 2002. Expression of functional mammalian P450 2E1 in hairy root cultures. Biotechnology and Bioengineering, 77(4):463-466.

Shang, T. Q., Doty, S. L., Wilson, A. M., Howald, W. N., and Gordon, M. P. 2001. Trichloroethylene oxidative metabolism in plants: the trichloroethanol pathway. Phytochemistry 58:1055-1065.

Doty, S. L., Q. T. Shang, Wilson, A. M., Westergreen, A. D., Newman, L. A., Strand, S. E. and Gordon, M. P. 2000. Enhanced metabolism of halogenated hydrocarbons in transgenic plants containing mammalian cytochrome P450 2E1. Proc. Natl. Acad. Sciences 97(12):6287-6291.