Skip to main content

Amir Ahkami
Rhizosphere Function IRP Leader

Dr. Amir Ahkami is a biologist and the leader of the Rhizosphere Function Integrated Research Platform. Ahkami joined EMSL in 2015 to support the development of the plant science research program. He also holds the position of adjunct assistant professor at Washington State University in Pullman, WA. He is currently leading research projects as a principal investigator focusing on poplar (Populus spp.) and model grasses’ (Brachypodium and Setaria) responses to abiotic stresses, molecular physiology of root formation, and physiological phenotyping to narrow the genotype-to-phenotype knowledge gap for crop improvement. He employs state-of-the-art technologies, including single cell-type specific molecular profiling coupled with high-resolution cellular imaging to address plant biology research gaps on molecular and physiological mechanisms that control bioenergy crop productivity and fitness in relationship to microbial communities in the rhizosphere. He is also assisting EMSL collaborators and users in the development of creative new applications for plant sciences.  

Research Interests

  • Analysis of root system architecture and rhizosphere engineering for improved plant productivity  

  • Plant molecular physiology (primary carbohydrate metabolism and source-sink relationships) 

  • Regulation of gene expression in response to individual and combined abiotic stresses in plants 

  • Systems and synthetic biology for biofuel applications (in higher plants) 

  • Metabolic engineering of natural products in plants 


  • Postdoctoral Research Associate in Plant Specialized Metabolism and Molecular Biology, Washington State University, 2014  

  • PhD in Life Sciences (Plant Biology), Martin-Luther-Universität of Halle-Wittenberg, 2010 

  • Research Assistant, Institute of Plant Genetics and Crop Plant Research, 2010 

  • MS in Plant Biotechnology, Tehran University, 2005 

  • BS in Plant Breeding, Shiraz University, 2002 



Mehta D., A. Ahkami, J. Walley, S. Xu, and R.G. Uhrig. 2022. "The Incongruity of Validating Quantitative Proteomics using Western Blots." Nature Plants. PNNL-SA-179445. doi:10.1038/s41477-022-01314-8.

Yang Y., T.A. Chaffin, A. Ahkami, E. Blumwald, and C. Stewart. 2022. "Plant synthetic biology innovations for biofuels and bioproducts." Trends in Biotechnology. PNNL-SA-174610. doi:10.1016/j.tibtech.2022.09.007.

Yang Y., Y. Shao, T.A. Chaffin, J. Lee, M.R. Poindexter, A. Ahkami, and E. Blumwald, et al. 2022. "Performance of abiotic stress-inducible synthetic promoters in genetically engineered hybrid poplar (Populus tremula x Populus alba)." Frontiers in Plant Science 13. PNNL-SA-174829. doi:10.3389/fpls.2022.1011939.

Christer Jansson, Swarup China, Pubudu Handakumbura, and Amir H. Ahkami. 2022. "Chemical Interactions in the Plant-Atmosphere-Soil System." ACS Earth and Space Chemistry 2021 5 (12), 3279-3280 DOI: 10.1021/acsearthspacechem.1c00380.


Jha S.G., P. Agarwal, A. Ahkami, C.R. Anderton, A.T. Borowsky, S. Briggs, and J.A. Brophy, et al. 2021. A Roadmap for the Plant Cell Atlas. eLife. eLife 2021;10:e66877 DOI: 10.7554/eLife.66877.

Balasubramanian, V. K., Purvine, S. O., Liang, Y., Kelly, R. T., Pasa-Tolic, L., Chrisler, W. B., Blumwald, E., Stewart, C. N., Zhu, Y., & Ahkami, A. H*. 2021. "Cell-type-specific Proteomics Analysis of Small Number of Plant Cells by Integrating Laser Capture Microdissection with a Nanodroplet Sample Processing Platform." Current Protocols in Plant Biology 1, no. e153. doi:10.1002/cpz1.153.

Yongil Yang, Jun Hyung Lee, Magen R. Poindexter, Yuanhua Shao, Wusheng Liu, Scott C. Lenaghan, Amir H. Ahkami, et al. 2021. Rational design and testing of abiotic stress inducible synthetic promoters from poplar cis-regulatory elements. Plant Biotechnology Journal. doi:10.1111/pbi.13550.

Zhou M., S.H. Abdali, D. Dilworth, L. Liu, B. Cole, N. Malhan, and A. Ahkami, et al. 2021. Isolation of Histone from Sorghum Leaf Tissue for Top Down Mass Spectrometry Profiling of Potential Epigenetic Markers. JoVE. doi:10.3791/61707.

Balasubramanian V.K., Jansson C., Baker S.E., Ahkami A.H. (2021) Molecular Mechanisms of Plant–Microbe Interactions in the Rhizosphere as Targets for Improving Plant Productivity. In: Gupta V.V.S.R., Sharma A.K. (eds) Rhizosphere Biology: Interactions Between Microbes and Plants. Rhizosphere Biology. Springer, Singapore.  


Rice, S, Fryer, E, Jha, SG, et al; The Plant Cell Atlas Consortium. First plant cell atlas workshop report. Plant Direct. 2020; 00: 1– 10.

Varga T, Hixson KK, Ahkami AH, Sher AW, Barnes ME, Chu RK, Battu AK, Nicora CD, Winkler TE, Reno LR, Fakra SC, Antipova O, Parkinson DY, Hall JR and Doty SL (2020) Endophyte-Promoted Phosphorus Solubilization in Populus. Front. Plant Sci. 11:567918. doi: 10.3389/fpls.2020.567918.  

China, S., D. Veghte, A. H. Ahkami, J. Weis, C. Jansson, A. B. Guenther, M. K. Gilles, and A. Laskin. 2020. "Microanalysis of Primary Biological Particles from Model Grass over Its Life Cycle." ACS Earth and Space Chemistry 4 (10): 1895-1905.

Ogden, A. J., T. W. Wietsma, T. Winkler, Y. Farris, G. L. Myers, and A. H. Ahkami. 2020. "Dynamics of Global Gene Expression and Regulatory Elements in Growing Brachypodium Root System." Scientific Reports 10 (1).

Veličković, D., R. K. Chu, G. L. Myers, A. H. Ahkami, and C. R. Anderton. 2020. "An approach for visualizing the spatial metabolome of an entire plant root system inspired by the Swiss-rolling technique." Journal of Mass Spectrometry 55 (4).  


Ahkami, A. H., W. Wang, T. W. Wietsma, T. Winkler, I. Lange, C. Jansson, B. M. Lange, and N. G. McDowell. 2019. "Metabolic shifts associated with drought-induced senescence in Brachypodium." Plant Science 289.  

Fang, Y., S. B. Yabusaki, A. H. Ahkami, X. Chen, and T. D. Scheibe. 2019. "An efficient three-dimensional rhizosphere modeling capability to study the effect of root system architecture on soil water and reactive transport." Plant and Soil 441 (1-2): 33-48.  

Zhou, M., N. Malhan, A. H. Ahkami, K. Engbrecht, G. Myers, J. Dahlberg, J. Hollingsworth, J. A. Sievert, R. Hutmacher, M. Madera, P. G. Lemaux, K. K. Hixson, C. Jansson, and L. Paša-Tolić. 2019. "Top-down mass spectrometry of histone modifications in sorghum reveals potential epigenetic markers for drought acclimation." Methods.  


Ahkami, A. H., R. Allen White, III, P. P. Handakumbura, and C. Jansson. 2017. "Rhizosphere engineering: Enhancing sustainable plant ecosystem productivity." Rhizosphere 3: 233-243.  

Vining, K. J., S. R. Johnson, A. Ahkami, I. Lange, A. N. Parrish, S. C. Trapp, R. B. Croteau, S. C. K. Straub, I. Pandelova, and B. M. Lange. 2017. "Draft Genome Sequence of Mentha longifolia and Development of Resources for Mint Cultivar Improvement." Molecular Plant 10 (2): 323-339.  


Ahkami, A., S. R. Johnson, N. Srividya, and B. M. Lange. 2015. "Multiple levels of regulation determine monoterpenoid essential oil compositional variation in the mint family." Molecular Plant 8 (1): 188-191.  


Ahkami, A., U. Scholz, B. Steuernagel, M. Strickert, K. T. Haensch, U. Druege, D. Reinhardt, E. Nouri, N. Von Wirén, P. Franken, and M. R. Hajirezaei. 2014. "Comprehensive transcriptome analysis unravels the existence of crucial genes regulating primary metabolism during adventitious root formation in Petunia hybrida." PLoS ONE 9 (6).  

Druege, U., P. Franken, S. Lischewski, A. H. Ahkami, S. Zerche, B. Hause, and M. R. Hajirezaei. 2014. "Transcriptomic analysis reveals ethylene as stimulator and auxin as regulator of adventitious root formation in petunia cuttings." Frontiers in Plant Science 5 (SEP).


Ahkami, A. H., M. Melzer, M. R. Ghaffari, S. Pollmann, M. Ghorbani Javid, F. Shahinnia, M. R. Hajirezaei, and U. Druege. 2013. "Distribution of indole-3-acetic acid in Petunia hybrida shoot tip cuttings and relationship between auxin transport, carbohydrate metabolism and adventitious root formation." Planta 238 (3): 499-517.  

Markus Lange, B., and A. Ahkami. 2013. "Metabolic engineering of plant monoterpenes, sesquiterpenes and diterpenes-current status and future opportunities." Plant Biotechnology Journal 11 (2): 169-196.


Breuillin, F., J. Schramm, M. Hajirezaei, A. Ahkami, P. Favre, U. Druege, B. Hause, M. Bucher, T. Kretzschmar, E. Bossolini, C. Kuhlemeier, E. Martinoia, P. Franken, U. Scholz, and D. Reinhardt. 2010. "Phosphate systemically inhibits development of arbuscular mycorrhiza in Petunia hybrida and represses genes involved in mycorrhizal functioning." Plant Journal 64 (6): 1002-1017.  


Ahkami, A. H., S. Lischewski, K. T. Haensch, S. Porfirova, J. Hofmann, H. Rolletschek, M. Melzer, P. Franken, B. Hause, U. Druege, and M. R. Hajirezaei. 2009. "Molecular physiology of adventitious root formation in Petunia hybrida cuttings: Involvement of wound response and primary metabolism." New Phytologist 181 (3): 613-625.