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The Use of Diazotrophic Endophytes as a Means for Climate Change Mitigation and
Adaptation In Agroecosystems
Project Director: Sharon L. Doty, ProfessorCo-PD: Soo-Hyung Kim, Assoc. Professor
University of Washington, Seattle
NIFA Agroclimatology Project Directors MeetingDecember 16-18, 2016
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The Plant Microbiome: Microbial communities within a plant
Benefits from endophytes
Stress toleranceDrought
TemperatureSalt
Elevated CO2
Reduced phytotoxicity of
pollutantsOrganic pollutants
Inorganic pollutants
Growth PromotionHormones
Nutrients (N, P, Fe)
Pathogen resistanceAnti-microbial compounds
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Hypothesis: Pioneer tree species use symbiosis with N-fixing (diazotrophic) endophytes to thrive
in low-nutrient conditions
Rivers in the Pacific Northwest (USA) are fed by snow-melt from the mountains.
Total N is only 0.05 to 0.3 mg/L
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N2 fixation in wild poplar was demonstrated using the direct 15N2 incorporation assay and
the indirect acetylene reduction assay
Doty, S.L., Sher, A.W., Fleck, N.D., Khorasani, M., Bumgarner, R., Ko, A., Khan, Z., Kim, S.H., and DeLuca, T. H. 2016 PLOS ONE 11(5):e0155979
• NifH sequences included Burkholderia, Sphingomonas, Azospirillum, Bradyrhizobium,
Rhodospirillum, Methanococcus, and more
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Poplar & willow endophytes isolated from surface-sterilized branches
• Rhizobium tropici• Burkholderia sp.• Herbaspirillum sp.• Pseudomonas graminis• Rhanella sp.• Sphingomonas sp.• Acinetobacter sp.• Enterobacter sp.• Rhodotorula graminis
Doty, S. L., et al. (2005) Symbiosis 39: 27-35Doty, S. L., et al. (2009) Symbiosis 47: 23-33Xin, G., et al. (2009) Biology and Fertility of Soils 45:669-674Firrincieli, et al. (2015) Frontiers in Microbiology 6: 978
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15N dilution assay indicated that hybrid poplar inoculated with strains from wild poplar received 65%
of the foliar N from biological nitrogen fixation
Inoculated with wild poplar
endophytes
Un‐inoculated controls
Knoth, et al (2014) New Phytologist 201:599-609
USDA AFRI grant # 2010-05080
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Implications for this research:Helps Explain the Biology of Populus
NOTE: Poplar and willow are not nodulating species
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Can we use the N-fixing endophytes of wild poplar and willow to promote growth of non-
legume crop plants and forest trees?
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Increased growth and yields of inoculated plants grown in low-nutrient soil
Khan, Z, Guelich, G., Phan, H., Redman, R., and Doty, S. L. 2012. ISRN Agronomy
Dr. Zareen Khan
Controls without added endophytes
With endophyte added
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Colonization and growth enhancement of rice with diazotrophic endophytes
S. Kandel, N. Herschberger, S.H. Kim, and S.L. Doty (2015) Crop Science 55:1765-1772
ShyamKandel
0
0.5
1
1.5
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2.5
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Total Root Shoot
Wei
ght (
g)
Inoculated (NIF) vs Non-Inoculated (NS) Dry Weight
NIFNS
NIF n=24NS n=12
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Increased growth of Douglas-fir in nutrient-poor soil
No added microbes
With added endophytes
Zareen Khan
Khan, Z., Ramos, D. Ettl, G., Kim, S.H., and Doty, S.L. 2015 Forests 6:3582-3593
N=12
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The Plant Microbiome: Microbial communities within a plant
Benefits from endophytes
Stress toleranceDrought
TemperatureSalt
Reduced phytotoxicity of
pollutants
Growth PromotionHormones
Nutrients (N, P, Fe)
Pathogen resistanceAntimicrobial compounds
Solubilize phosphate Produce siderophores
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Poplar inoculated with endophytes from wild poplar have increased growth and survive drought stress longer
Poplar inoculated with endophytes one month without watering
Uninoculated controls
0
5
10
15
20
25
avg control avg innoc
mass (g)
Total mass (dry)
* p << 0.01
Khan, Z., Rho, H., Firrincieli, A., Hung, S.H., Luna, V., Masciarelli, O., Kim, S.H., and Doty, S.L. 2016. Current Plant Biology 6:38-47
USDA AFRI grant # 2010-05080
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Several possible mechanisms for the endophyte-conferred drought tolerance
• Phytohormone production– IAA, ABA,
• Increased nutrients • Reduction of ROS• Genetic evidence for:
– Osmolyte trehalose– VOCs Acetoin and 2,3-
butanediol
Inoculated Control
Khan, Z., Rho, H., Firrincieli, A., Hung, S.H., Luna, V., Masciarelli, O., Kim, S.H., and Doty, S.L. 2016. Current Plant Biology 6:38-47.
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Endophyte consortium increased water use efficiency (WUE) in rice
and in maize
Tony Rho
Hyungmin Rho, Sharon Doty, and Soo-Hyung Kim (unpublished)
Unpublished data was removed for posting
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Reduced mortality of conifers under
drought conditions• Western redcedar (Thuja plicata)• After two seasons of simulating
seasonal moisture fluctuations• No mortality in wet treatment
conditions• 50% mortality reduction in normal
conditions• 90% mortality reduction in drought
conditions
Matthew Aghai
Matthew Aghai, Sharon Doty, and Gregory Ettl (unpublished)
Unpublished data was removed for posting
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Reduced mortality of conifers under drought conditions
• Douglas-fir (Pseudotsuga menzeisii)
• 10-40% mortality reduction across all moisture conditions
• Endophyte treatments were significant (P<0.05)
• Black pineleaf scale outbreak – inoculated seedlings still had improved survival
Matthew Aghai
Matthew Aghai, Sharon Doty, and Gregory Ettl (unpublished)
Unpublished data was removed for posting
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Improved salt tolerance using an estuary plant endophyte Andrew Sher
Andrew Sher, Sharon Doty, and Alisa Huffaker (unpublished)
Arabidopsis Maize
Unpublished data was removed for posting
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The Plant Microbiome: Microbial communities within a plant
Benefits from endophytes
Stress toleranceDrought
TemperatureSalt
* Elevated CO2
Reduced phytotoxicity of pollutants
Organic pollutants (ie. TCE, PAHs)Inorganic pollutants (ie. As)
Growth PromotionHormones
Nutrients (N, P, Fe)
Pathogen resistanceAntimicrobial compounds
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ELE (800 ppm)ELE (800 ppm)AMB (400 ppm)AMB (400 ppm)
Douglas Research Conservatory, Seattle, WA
Co-Director: Assoc. Prof. Soo-Hyung Kim
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Alleviation of photosynthetic down-regulation in rice under elevated CO2
Hyungmin Rho, Sharon Doty, and Soo-Hyung Kim (unpublished)
Unpublished data was removed for posting
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Implications for this research:Endophytes For Sustainable Agriculture, Forestry, and
Biomass Production
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Elizabeth Pennisi 2015 Sciencemag.org 348:6237
Joe Funk, editor Seed Today 3rd Quarter 2015
Samples of press in response to our research
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Outreach
Created a Plant Microbiology Lab class–students characterized new isolates
Licensed strains to IntrinsyxTechnologies; sublicensed to Verdesian Life Sciences, Performance Ag, Indigo, BioConsortia, ICL, etc.- Testing on strawberries, broccoli, maize, tomatoes, grapes, jalapenos, lettuce, beets, bell pepper, stone fruit trees, etc.
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Implications for this Research:Climate Change Mitigation
Uninoculated controls
• Plants can increase C sequestration only if nutrients and water are not limiting
• Using more chemical fertilizers is inconsistent with mitigation
Endophytes can promote plant growth naturally through improved nutrient acquisition,
phytohormone production, & stress tolerance
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Funding and technology provided by:
NIFA climate change mitigation program
Grant # 2012-68002-19824
Byron and Alice Lockwood Foundation Professorship
Conifer studies additionally funded by:Corkery Endowed Chair (University of Washington)McIntire Stennis Cooperative Forestry Research Funding
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http://depts.washington.edu/envaplab
Dr. Zareen Khan(Research Scientist)
Students and research staff involved in the presented research
Undergraduate researchers especially Grant Guelich, Jack Emery, Beverly Hung, Daniela Ramos, Nick Wegley, and Pierre Joubert
Special thanks to Dr. John Freeman (Intrinsyx) and Dr. Mike Blaylock
(Edenspace) for their partnerships in moving the research from lab to field
Previous grad students and research staff: Jenny Knoth, Mahsa Khorasani, Neil Fleck,
and Andrea Firrincieli
Shyam Kandel(grad student)
Special thanks to Assoc. Prof. Greg Ettl for collaboration on the conifer research
Andrew Sher(grad student)
Matthew Agai(grad student)
Hyungmin Rho(grad student)