Doty Lab Publications






Aghai, M., Khan, Z., Joseph, M.R., Stoda, A.M., Sher, A.W., Ettl, G.J., and Doty, S.L.
The effect of microbial endophyte consortia on Pseudotsuga menziesii and Thuja plicata survival, growth, and physiology across edaphic gradients Front. Microbiol. 10:1353. doi: 10.3389/fmicb.2019.01353 Endophyte Impact on Conifers
Hyungmin Rho, Sharon L. Doty, and Soo-Hyung Kim
Estimating microbial respiratory CO2 from endophytic bacteria in rice

Plant Signaling & Behavior, DOI:

Endophytic Respiration
Sharon Lafferty Doty
Symbiotic Plant-Bacterial Endospheric Interactions
Microorganisms 2018, 6, 28 doi:10.3390/microorganisms6020028 Editorial
Pierre M. Joubert and Sharon Lafferty Doty
Ch. 1. Endophytic Yeasts: Biology, Ecology, and Applications
in Endophytes of Forest Trees, Ed. Pirttila & Frank, 2nd edition, Springer Endophytic Yeasts
Sharon Lafferty Doty
Successful Field Trial of Endophyte-Assisted Poplar Tree Phytoremediation of TCE
Poplar and Willow News. FAO of the United Nations, Feb 2018 issue, pg 3-4
P&W Newsletter
Hyungmin Rho, Victor Van Epps, Nicholas Wegley, Sharon Lafferty Doty, Soo-Hyung Kim
Salicaceae Endophytes Modulate Stomatal Behavior and Increase Water Use Efficiency in Rice
Front. Plant Sci., 02 March 2018 |
Rice WUE
Levy, A., Gonzalez, I.S., Mittelviefhaus, M., Clingenpeel, S., Paredes, S.H., Miao, J., Wang, K., Devescovi, G., Stillman, K., Monteiro, F., Alvarez, B.R., Lundberg, D., Lu, T-Y., Lebeis, S., Jin, Z., McDonald, M., Klein, A.P., Feltcher, M., Rio, T.G., Grant, S.P., Doty, S.L., Ley, R.E., Zhao, B., Venturi, V., Pelletier, D.A., Vorholt, J.A., Tringe, S.G., Woyke, T., and Dangl, J.L. 2018. Genetic features of bacterial adaptation to plants.  Nature Genetics 50:138-150.
Genomic features of bacterial adaptation to plants
Nature Genetics 50138150 (2018) doi:10.1038/s41588-017-0012-9
Nature Genetics
Kandel, S.L., Joubert, P.M., and Doty, S.L.
Bacterial endophyte colonization and distribution within plants
Microorganisms 2017, 5, 77; doi:10.3390/microorganisms5040077
Colonization Review
Doty, S.L. (editor)
Functional Importance of the Plant Microbiome: Implications for Agriculture, Forestry and Bioenergy
Doty, S.L.
Chapter 1: Functional Importance of the Plant Microbiome
Springer, pgs 1-5
Springer book chapter 1
Doty, S.L.
Chapter 2: Endophytic N-Fixation: Controversy and a Path Forward
Springer, pgs 7-20
Springer book chapter 2
P. Okubara, N. Kumar, L. Hohenwarter, D. Graham, S. Kandel, S.L. Doty, Ute Micknass, Karl-Heinz Kogel, and Jafargholi Imani
Inhibition of fungal and bacterial plant pathogens by VEG’LYS®, an Allium-based antimicrobial formulation.
J Biol. & Nature 8(2)40-51
Rho, H., Hsieh, M., Kandel, S.L., Cantillo, J., Doty, S.L., and Kim, S_H
Do endophytes promote growth of host plants under stress? A meta-analysis on plant stress mitigation by endophytes
Microial Ecology (2017) doi: 10.1007/s00248-017-1054-3
Doty, S.L., Freeman, J. L., Cohu, C. M., Burken, J. G., Firrincieli, A., Simon, A., Khan, Z., Isebrands, J.G., Lukas, J., and Blaylock, M.J.
Enhanced degradation of TCE on a Superfund site using endophyte-assisted poplar tree phytoremediation
Environmental Science and Technology 51 (17): 10050–10058. DOI: 10.1021/acs.est.7b01504
ES&T Endophytes
Legault, E.K., James, C.A., Stewart, K., Muiznieks, I., Doty, S.L., and Strand, S.E.
A field trial of TCE phytoremediation by genetically modified poplars expressing cytochrome P450 2E1
Environmental Science and Technology 6;51(11):6090-6099
ES&T 2E1 Tgnc
Kandel, S. L., Firrincieli, A., Joubert, P.M., Okubara, P.A., Leston, N., McGeorge, K., Mugnozza, G.S., Harfouche, A., Kim, S.-H., and Doty, S.L.
An in vitro study of bio-control and plant growth promotion potential of Salicaceae endophytes
Frontiers in Microbiology vol8, article #386
Biocontrol Endophytes
Khan, Z., Rho, H., Firrincieli, A., Hung, S.H., Luna, V., Masciarelli , O., Kim, S.-H., and Doty, S.L.
Growth enhancement and drought tolerance of hybrid poplar upon inoculation with endophyte consortia
Current Plant Biology 6:38-47
Drought Tolerance
Doty, S.L., Sher, A.W., Fleck, N.D., Khorasani, M., Bumgarner, R.B., Khan, Z., Ko, A.W.K., Kim, S.-H., and DeLuca, T.H.
Variable N-fixation in wild Populus
PLOS ONE 11(5):e0155979
Poplar N-Fixation
Ellen Weir and Sharon L. Doty
Social acceptability of phytoremediation: Role of risk and values
International Journal of Phytoremediation 18(10)1029-1036
Sharon L. Doty
Editorial: Plant microbe symbiotic interactions
Plant Molecular Biology, 90(6):1
Sharon L. Doty
Key roles of the poplar microbiome.
Poplar and Willow News, Issue 6
IPC Newsletter
Khan, Z., Kandel, S., Ramos, D.N., Ettl, G.J., Kim, S.-H., and Doty, S.L. 
Increased biomass of nursery-grown Douglas-fir seedlings upon inoculation with diazotrophic endophytic consortia.
Forests, Vol. 6, 3582-3593
Firrincieli, A., Otillar, R., Salamov, A., Schmutz, J., Khan, Z., Redman, R. S., Fleck, N. D., Lindquist, E., Grigoriev, I. V., and Doty, S.L. 
Genome sequence of the plant growth promoting endophytic yeast Rhodotorula graminis WP1.
Frontiers in Microbiology, Vol. 6, Article 978
Kandel, S., Herschberger, N., Kim, S.-H., and Doty, S.L. 
Diazotrophic endophytes of poplar and willow for growth promotion of rice plants in nitrogen-limited conditions.
Crop Science 55:1765-1772
Khan, Z, Roman, D., Kintz, T., Delas Alas, M., Yap, R., Doty, S.L. 
Degradation, Phytoprotection and Phytoremediation of Phenanthrene by Endophyte PD1
Environmental Science & Technology 48.20: 12221-2228
pdf | summary/erratum | Pubmed
Nagy, L.G., Ohm, R.A., Kovacs, G.M., Floudas, D., Riley, R., Gacser, A., Sipiczki, M., Davis, J.M., Doty, S.L., de Hoog, G.S., Lang, B.F., Spatafora, J.W., Martin, F.M., Grigoriev, I.V., and Hibbett, D.S
Latent Homology and Convergent Regulatory Evolution Underlies the Repeated Emergence of Yeasts
Nature Communications DOI: 10.1038/ncomms5471
Kang, J. W. and Doty, S.L. 
Co-metabolic degradation of trichloroethylene by Burkholderia cepacia G4 with poplar leaf homogenate. 
Canadian Journal of Microbiology DOI 10.1139/cjm-2014-0095
pdf | Pubmed
Knoth, J., Kim, S.H., Ettl, G., and Doty, S. L.
Biological nitrogen fixation and biomass accumulation within poplar clones as a result of inoculations with diazotrophic endophyte consortia
New Phytologist doi 10.1111/nph.12536
Khan, Z., Guelich, G., Phan, H., Redman, R., and Doty, S. L.
Bacterial and yeast endophytes from poplar and willow promote growth in crop plants and grasses
ISRN Agronomy 2012: Article ID 890280; doi:10.5402/2012/890280
Knoth, J., Kim, S.H., Ettl, G., and Doty, S. L.
Effects of cross host species inoculation of nitrogen-fixing endophytes on growth and leaf physiology of maize
GCB Bioenergy 2012: doi:10.1111/gcbb.12006
Vajzovic, A., Bura, R., and Doty, S. L. 
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
Bura, R., Vajzovic, A., and Doty, S. L.
Novel endophytic yeast Rhodotorula mucilaginosa strain PTD3: I. Production of xylitol and ethanol
Journal of Industrial Microbiol. & Biotech. 39(7):1003-1011
Kang, J. W., Khan, Z., and Doty, S. L.
Biodegradation of TCE by an endophyte of hybrid poplar. 
Applied and Environmental Microbiology 78(9):3504-3507
Kang, J. W., J. Song, Doty, S. L., and Lee, D. K.
Diversity of rhizobia associated with leguminous trees in South Korea
Journal of Basic Microbiology 52, 1–8
Lee, K. Y., Strand, S. E., and Doty, S. L.
Phytoremediation of chlorpyrifos by Populus and Salix.
International Journal of Phytoremediation 14(1):48-61
pdf | Pubmed
Miller, R. S., Khan, Z., and Doty, S. L.
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.
Redman, R., Kim, Y., Woodward, C., Greer, C., Espino, L., Doty, S. L., and Rodriguez, R
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 Biology 6(7) e14823.
pdf | Pubmed
Xu, P., Bura, R. and Doty, S. L. 2011.
Genetic analysis of D-xylose metabolism by endophytic yeast strains of Populus.
Genetics and Molecular Biology 34(3):471-478.
pdf | Pubmed
Van Aken, B., Doty, S. L
Transgenic plants and associated bacteria for phytoremediation of chlorinated compounds.
Biotechnol. Genet. Eng. Rev. 26:43-64.
pdf | Pubmed
Kang, J. W., Hui-WenWilkerson ,Federico M. Farin, Theo K.Bammler ,Richard P.Beyer, Stuart E. Strand, and Sharon L. Doty
Mammalian cytochrome CYP2E1 triggered differential gene regulation in response to trichloroethylene (TCE) in a transgenic poplar.
Functional and Integrative Genomics 10(3):417-424.
Xin, G., Glawe, D., and Doty, S.L.
Characterization of three endophytic indole-3- acetic acid-producing yeasts occurring in Populus trees
Mycological Research 113:973-980.
Xin, G., Kang, J. W., Zhang, G., Staley, J. T., and Doty, S. L.
A diazotrophic, indole- 3-acetic acid producing endophyte from wild cottonwood.
Biology and Fertility of Soils 45:669- 674.
James, A., Xin, G., Doty, S. L., Newman, L. A., Strand, S. E.
A mass balance study of the phytoremediation of perchloroethylene-contaminated groundwater
Environmental Pollution. 157(8-9):2564-2569
Khan, Z. and Doty, S. L
Characterization of bacterial endophytes of sweet potato plants
Plant and Soil 322:197-207
Doty, S. L., Oakley, B., Xin, G., Kang, J. W., Singleton, G. L., Khan, Z., Vajzovic, A., Staley, J. T
Diazotrophic endophytes of native black cottonwood and willow
Symbiosis 47: 23-33
James,C.A.; Xin,G., Doty, S. L., Strand, S. E

Degradation of low molecular weight volatile organic compounds by plants genetically modified with mammalian cytochrome P450 2E1
Environ. Sci Technol. 42(1): 289-293
pdf | Pubmed
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
Enhanced phytoremediation of volatile environmental pollutants with transgenic trees.
Proc. Natl. Acad. Sciences 104(43):16816-16821.
pdf | Pubmed
Doty, S. L., Dosher, M. R., Singleton, G. L., Moore, A. L., Van Aken, B., Stettler, R. F., Strand, S. E., Gordon, M. P
Identification of an endophytic Rhizobium in stems of Populus
Symbiosis 39:27-35
Van Aken, B., Peres, C. M., Doty, S. L., Yoon, J. M., and Schnoor, J. L.
Methylobacterium oliveri sp. nov.: A novel aerobic, pink-pigmented, facultatively methylotrophic, methane-utilizing bacterium isolated from poplar trees (Populus deltoides x nigra DN34)
Int J Syst Evol Microbiol 54(4):1191-1196
Doty, S. L., Shang, T., Wilson, A. M., Moore, A. L., Newman, L. A., Strand, S. E., Gordon, M. P
Metabolism of the soil and groundwater pollutants, ethylene dibromide and trichloroethylene, by the tropical leguminous tree, Leuceana leucocephala
Water Research 37: 441-449
Banerjee, S., Shang, T. Q., Wilson, A. M., Moore, A. L., Strand, S. E., Gordon, M. P., and Doty, S. L
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.
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.
Enhanced metabolism of halogenated hydrocarbons in transgenic plants containing mammalian cytochrome P450 2E1
Proc. Natl. Acad. Sciences 97(12):6287- 6291
Newman, L. A., S. L. Doty, K. L. Gery, P. E. Heilman, I. Muiznieks, Q. T. Shang, S. T. Siemieniec, S. E. Strand, X. Wang, A. M. Wilson, and M. P. Gordon.
Phytoremediation of organic contaminants: A review of phytoremediation research at the University of Washington
Journal of Soil Contamination 7(4):531-542
Heath, J. D., M. I. Boulton, D. M. Raineri, S. L. Doty, A. R. Mushegian, T. C. Charles, J. W. Davies, and E. W. Nester.
Discrete regions of the sensor protein VirA determine the strain-specific ability of Agrobacterium to agroinfect maize
Mol. Plant Microbe Interactions 10:221-227
pdf | Pubmed
Charles, T., Doty, S. L., and Nester, E. W
Strain construction in Agrobacterium by electroporation of genomic DNA: Utility in the analysis of chromosomal virulence mutants
Appl. Environ. Microbiol. 60:4192-4194
Doty, S. L., Chang, M., and Nester, E. W.
The chromosomal virulence gene, chvE, of Agrobacterium tumefaciens is regulated by a LysR family member
J. Bacteriol. 175(24):7880- 7886

Book chapters and reviews

1. Doty, S. L., Heath, J. D., Nester, E. W. 1996. Signal detection by VirA. In Crown Gall. S. Gelvin and W. Ream, eds. APS Press.
2. Doty, S. L. 2008. Tansley Review: Enhancing phytoremediation through the use of transgenics and endophytes. New Phytologist 179:318-333. pdf
3. Doty, S. L. and Strand, S. E. 2008. Enhancing Phytoremediation of Volatile Pollutants through Genetic Engineering. ISB (Information Systems for Biotechnology) News Report (January 2008). pdf
4. Dowling, D. N. and Doty, S. L. 2009. (Editorial) Improving phytoremediation through biotechnology. Current Opinion in Biotechnology 20:1-3. Pubmed
5. Bioresource-Based Energy for Sustainable Societies in Handbook of Sustainable Energy; eds WH Lee and VG Cho. 2009.
6. 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.
7. 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
8. 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
9. Khan, Z. and Doty, S. L. 2011. Endophyte Assisted Phytoremediation. Current Topics in Plant Biology 12: 97-105.
10. Khan, Z and Doty, S.L. 2011. Using endophytes to enhance phytoremediation. In Phytotechnologies: Remediation of Environmental Contaminants. Chapter 22, pgs 407-414. Naser A. Anjum Ed. Taylor and Francis.
11. Doty, S. L. 2012. Endophytic yeast: Biology and applications. In Symbiotic Endophytes. R. Aroca, ed. Chapter 17. Springer. Century. A. Altman and P. M. Hasegawa, eds. Elsevier.