Recent Publications
Sher, A. W., Tournay, R. J., Gomez-Rivas, E., and Doty, S. L. 2024 (in press). Bacterial synergies amplify nitrogenase activity in diverse systems. ISME Communications (in press) DOI: 10.1093/ismeco/ycae158
Oyedoh, O.P., Compant, S., Doty, S.L., Santoyo, G., Glick, B.R., and Babalola, O. O. 2024 (in press). Root colonizing microbes associated with notable abiotic stress of global food and cash crops. Plant Stress. doi: https://doi.org/10.1016/j.stress.2024.100714
Sher, A. W., Aufrecht, J. A., Herrera, D., Zimmerman, A. E., Kim, Y-M, Munoz, N., Trejo, J. B., Paurus, V. L., Cliff, J. B., Hu, D., Chrisler, W. B., Tournay, R. J., Gomez-Rivas, E., Orr, G., Ahkami, A.H., and Doty, S.L. 2024. Dynamic nitrogen fixation in an aerobic endophyte of Populus. The ISME Journal 2024, 18(1), 1-14. https://doi.org/10.1093/ismejo/wrad012
Freeman, J., Firrincieli, A., Baker, D., and Doty, S. 2024. Curtobacterium salicis sp. nov, isolated from willow tree stems in Washington State. Antonie van Leeuwenhoek 2024, 117-62. https://doi.org/10.1007/s10482-024-01956-y
Tournay, R. J., Firrincieli, A., Parikh, S. S., Sivitilli, D. M., and Doty, S. L. 2023. Effect of arsenic on EPS synthesis, biofilm formation, and plant growth-promoting abilities of the endophytes Pseudomonas PD9R and Rahnella laticis PD12R. Environ. Sci. Tecnol. 57: 8728-8738.
Doty, S. L., Joubert, P. M., Firrincieli, A., Sher, A. W., Tournay, R., Kill, C., Parikh, S. S. and Okubara, P. 2023. Potential biocontrol activities of Populus endophytes against several plant pathogens using different inhibitory mechanisms. Pathogens 12(1), 13. https://doi.org/10.3390/pathogens12010013
Tamas Varga, Kim K Hixson, Amir H Ahkami, Andrew W Sher, Morgan E Barnes, Rosalie K Chu, Anil Krishna Battu, Carrie D Nicora, Tanya E Winkler, Loren R Reno, Sirine Fakra, Olga Antipova, Dilworth Y Parkinson, Jackson R Hall, Sharon Lafferty Doty. 2020. Endophyte-Promoted Phosphorus Solubilization in Populus. Frontiers in Plant Science 21Oct2020
Firrincieli, A., Khorasani, M., Frank, A.C., and Doty, S. L. 2020. Influence of climate on phyllosphere endophytic bacterial communities of wild poplar. Frontiers in Plant Science. doi: 10.3389/fpls.2020.00203
Rho, H., Doty, S. L., and Kim, S.H. 2020. Endophytes Alleviate the Elevated CO2-dependent Decrease in Photosynthesis in Rice, Particularly under Nitrogen Limitation. Journal of Experimental Botany 71(2)707-718
Rho, H., van Epps, V., Kim, S. H., and Doty, S. L. 2020. Endophytes increased fruit quality with higher soluble sugar production in Honeycrisp apple (Malus pumila). Microorganisms 8:699. doi:10.3390/microorganisms8050699
Outreach publications:
Hall, J.R., Sher, A. W., Varga, T., and Doty, S.L. 2022. Bacteria can unlock an essential nutrient for plants. Frontiers for Young Minds.
Ordukhani, L., Firrincieli, A., Freeman, J. L., and Doty, S. L. 2022. How plants and bacteria can clean the Earth. Frontiers for Young Minds 10:722958. doi: 10.3389/frym.2022.722958
Tournay, R. J. and Doty, S. L. 2022. Chapter 29. Microbial Endophytes for Clean-Up of Pollution in The Good Microbes in Medicine, Food Production, Biotechnology, Bioremediation and Agriculture. 1st edition. Eds Debruijn, F., Smidt, H., Cocolin, L., Sauer, M., Dowling, D., and Thomashow, L. John Wiley & Sons, UK.
All our earlier journal articles
Year |
Authors |
Title |
Reference |
Availability |
| 2019 |
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 |
| 2018 |
Hyungmin Rho, Sharon L. Doty, and Soo-Hyung Kim
|
Estimating microbial respiratory CO2 from endophytic bacteria in rice
|
Plant Signaling & Behavior, DOI: |
Endophytic Respiration |
| 2018 |
Sharon Lafferty Doty
|
Symbiotic Plant-Bacterial Endospheric Interactions
|
Microorganisms 2018, 6, 28 doi:10.3390/microorganisms6020028 | Editorial |
| 2018 |
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 |
| 2018 |
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 |
| 2018 |
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 | doi.org/10.3389/fpls.2018.00188
|
Rice WUE |
| 2017 |
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 50, 138–150 (2018) doi:10.1038/s41588-017-0012-9
|
Nature Genetics |
| 2017 |
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 |
| 2017 |
Doty, S.L. (editor)
|
Functional Importance of the Plant Microbiome: Implications for Agriculture, Forestry and Bioenergy
|
Springer
|
Springer |
| 2017 |
Doty, S.L.
|
Chapter 1: Functional Importance of the Plant Microbiome
|
Springer, pgs 1-5
|
Springer book chapter 1 |
| 2017 |
Doty, S.L.
|
Chapter 2: Endophytic N-Fixation: Controversy and a Path Forward
|
Springer, pgs 7-20
|
Springer book chapter 2 |
| 2017 |
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
|
Veglys |
| 2017 |
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
|
Meta-Analysis |
| 2017 |
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 |
| 2017 |
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 |
| 2017 |
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 |
| 2016 |
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 |
| 2016 |
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 |
| 2016 |
Ellen Weir and Sharon L. Doty
|
Social acceptability of phytoremediation: Role of risk and values
|
International Journal of Phytoremediation 18(10)1029-1036
|
Weir&Doty |
| 2016 |
Sharon L. Doty
|
Editorial: Plant microbe symbiotic interactions
|
Plant Molecular Biology, 90(6):1
|
Editorial |
| 2016 |
Sharon L. Doty
|
Key roles of the poplar microbiome.
|
Poplar and Willow News, Issue 6
|
IPC Newsletter |
| 2015 |
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
|
Forests |
| 2015 |
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
|
WP1 |
| 2015 |
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
|
Rice |
| 2014 |
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 |
| 2014 |
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
|
Nature |
| 2013 |
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 |
| 2013 |
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
|
|
| 2012 |
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
|
|
| 2012 |
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
|
|
| 2012 |
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
|
Pubmed |
| 2012 |
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
|
Pubmed |
| 2012 |
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
|
PDN3 |
| 2012 |
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
|
Rhizobia |
| 2012 |
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 |
| 2011 |
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.
|
|
| 2011 |
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 | |
| 2010 |
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 |
| 2010 |
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.
|
Pubmed |
| 2009 |
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.
|
Pubmed |
| 2009 |
Xin, G., Kang, J. W., Zhang, G., Staley, J. T., and Doty, S. L.
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A diazotrophic, indole- 3-acetic acid producing endophyte from wild cottonwood.
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Biology and Fertility of Soils 45:669- 674.
|
|
| 2009 |
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
|
pdf | Pubmed |
| 2009 |
Khan, Z. and Doty, S. L
|
Characterization of bacterial endophytes of sweet potato plants
|
Plant and Soil 322:197-207
|
|
| 2009 |
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
|
|
| 2008 |
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 |
| 2007 |
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.
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pdf | Pubmed |
| 2005 |
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
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Symbiosis 39:27-35
|
|
| 2004 |
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
|
|
| 2003 |
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
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Water Research 37: 441-449
|
|
| 2002 |
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
|
Pubmed |
| 2001 |
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
|
Pubmed |
| 2000 |
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
|
|
| 1998 |
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
|
TandFonline |
| 1997 |
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 |
| 1994 |
Charles, T., Doty, S. L., and Nester, E. W
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Strain construction in Agrobacterium by electroporation of genomic DNA: Utility in the analysis of chromosomal virulence mutants
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Appl. Environ. Microbiol. 60:4192-4194
|
|
| 1993 |
Doty, S. L., Chang, M., and Nester, E. W.
|
The chromosomal virulence gene, chvE, of Agrobacterium tumefaciens is regulated by a LysR family member
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J. Bacteriol. 175(24):7880- 7886
|
Pubmed |
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.