Team Leader/Biologist
Team Leader/Biologist


Dr. Pubudu Handakumbura is the lead on the Plant and Ecosystem Phenotyping team in PNNL’s Environmental Molecular Sciences Division and the Environmental Molecular Sciences Laboratory (EMSL) user program. She has extensive experience in advanced molecular biology techniques, genetic engineering, plant tissue culture, and plant multi-omics techniques.  

The focus areas of Handakumbura’s current research are to develop biomarkers to engineer and improve crop resilience under changing climates to improve photosynthetic performance and carbon partition in plants and enhancing feed stock attributes in lignocellulosic biomass for bioenergy production. She is using systems and synthetic biology approaches to study plant-microbe-soil interactions under abiotic stress. 

Research Interest

  • Multi-omics approaches in molecular plant phenotyping 

  • Lignocellulosic feedstock engineering 

  • Plant-microbe-soil interactions


  • PhD in Plant Biology, University of Massachusetts, 2014 

  • BS in Plant Biotechnology, University of Colombo, 2007 

Affiliations and Professional Service

  • American Association for the Advancement of Science  

  • American Society for Plant Biologists 

  • Key contributor of EPICON (U.S. Department of Energy project)  

  • STEM Ambassador, PNNL

Awards and Recognitions

  • Best Poster Presentation, Postdoctoral Category, Northeast Regional American Society of Plant Biologists Conference (2015) 

  • Gilgut Fellowship, University of Massachusetts Amherst (2012 – 2013) 

  • National Travel Awards, American Society of Plant Biologists (2012, 2013) 

  • Best Oral Presentation, Life Sciences Graduate Research Symposium, University of Massachusetts (2012) 

  • Professor BLT de Silva Memorial Prize for Botany, University of Colombo (2007) 

  • Sir Nigel Ball Award for Botany, University of Colombo (2007) 

  • Gold Medalist, Outstanding Science Student of the Year, University of Colombo (2007) 




  • Cho SH, Tóth, K, Kim D, Vo, PH, Lin CH, Handakumbura PP, Rivas Ubach A, Evans S, Pasa-Tolic L, Stacey G. (2022) Activation of the plant mevalonate pathway by extracellular ATP. Nature Communications, 13, 450


  • Handakumbura PP, Rivas-Ubach A, Battu AK. (2021) Visualizing the Hidden Half: Plant-Microbe Interactions in the Rhizosphere. mSystems, Vol. 6, No. 5
  • Peterson MJ, Handakumbura PP, Thompson AM, Russell ZR, Kim Y, Fansler SJ, Smith ML, Toyoda JG, Chu RK, Stanfill BA, Fransen SC, Bailey VL, Jansson C, Hixson KK, and Callister SJ (2021) Deciphering the microbial and molecular responses of geographically diverse Setaria accessions grown in a nutrient-poor soil, PLOS ONE, 16(12): e0259937.
  • Jansson C, China S, Handakumbura PP, Ahkami A. (2021) Chemical interactions in the Plant-Atmosphere-Soil system, ACS Earth and Space Chemistry, 5 (12), 3279-3280
  • Dewhirst RA, Handakumbura PP, Clendinen CS, Arm E, Tate K, Wang W, Washton NM, Young RP, Mortimer JC, McDowell NG, Jardine KJ. (2021) High Temperature Acclimation of Leaf Gas Exchange, Photochemistry, and Metabolomic Profiles in Populus trichocarpa, ACS Earth and Space Chemistry, 5 (8), 1813-1828
  • 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. 
  • Jansson C, Faiola C, Wingler A, Zhu X-G, Kravchenko A, de Graaff M-A, Ogden AJ, Handakumbura PP, Werner C and Beckles DM (2021) Crops for Carbon Farming. Frontiers in Plant Sciences, 12:636709. doi: 10.3389/fpls.2021.636709


  • Ogden A, Abdhali S, Engbrecht K, Zhou M, Handakumbura PP. 2020. Novel drought adaptation strategies identified by comparing organelle- and cytoplasmic-enriched protein profiles of two Sorghum bicolor genotypes (RTx430 and BTx642) with differing pre-flowering drought tolerance. International Journal of Molecular Sciences. 21 (24), 9706
  • Abraham-Juarez MJ, Schrager-Lavelle A, Man J, Whipple CJ, Handakumbura PP, Babbitt CC, Bartlett M. 2020. Evolutionary variation in MADS-box dimerization affects floral development and protein degradation dynamics in maize, Plant Cell, DOI:
  • Liu W, Huang L, Komorek RE, Handakumbura P, Zhou Y, Hu D, Engelhard MH, Jiang H, Yu X-Y, Jansson C, Zhu Z. 2020. Correlative Surface Imaging Reveals Chemical Signatures for Bacterial Hotspots on Plant Roots. Analyst 145, no. 2:393-401. doi:10.1039/C9AN01954E


  • Handakumbura P, Stanfill BA, Rivas-Ubach A, Fortin DC, Vogel JP, Jansson GC. 2019. Metabotyping as a Stopover in Genome-to-Phenome Mapping.Scientific Reports 9, no. 1:Article Number 1858.. doi:10.1038/s41598-019-38483-0


  • Handakumbura PP., Brow K, Whitney I, Zhao K, Sanguinet K, Lee S, Olins J, Romero-Gamboa S, Harrington M, Bascom C, Veling M, Bezanilla M, Bartley L, Hazen S. 2018. Brachypodium distachyon SWAM1 is a positive regulator of secondary cell wall synthesis and biofuel feedstock attributes and is not found in the Brassicaceae. The Plant Journal, 96 (3), 532-545.


  • Ahkami A, White RA, Handakumbura PP, Jansson GC. 2017. Rhizosphere Engineering: Enhancing Sustainable Plant Ecosystem Productivity in a Challenging Climate. Rhizosphere 3, no. 2:233-243. PNNL-SA-124740. doi:10.1016/j.rhisph.2017.04.012
  • Handakumbura P, Hixson K, Purvine SO, Jansson GC, Pasa Tolic L. 2017. Plant iTRAQ-based proteomics. Current Protocols in Plant Biology 2, no. 2:158-172. doi:10.1002/cppb.20052


  • Taylor-Teeples M, Lin L, de Lucas M, Turco G, Toal TW, Gaudinier A, Young NF, Trabucco GM, Veling MT, Lamothe R, Handakumbura PP, Xiong G, Corwin, Tsoukalas N, Pauly M, Kliebenstein DJ, Tagkopoulos I, Breton G, Pruneda-Paz JL, Ahnert S, Kay SA, Brady SM, Hazen SP. 2015. An Arabidopsis Gene Regulatory Network for Secondary Wall Synthesis. Nature, 571–575.


  • Handakumbura P. 2014. Understanding the transcriptional regulation of secondary cell wall biosynthesis in the model grass Brachypodium distachyon. Doctoral Dissertations, 208.


  • Handakumbura PP, Matos DA, Osmont KS, Harrington MJ, Heo K, Kafle K, Kim SH, Baskin TI, Hazen SP. 2013. Perturbation of Brachypodium distachyon CELLULOSE SYNTHASE A4 or 7 results in abnormal cell walls. BMC Plant Biology, 13(1):131.


  • Handakumbura PP, Hazen SP. 2012. Transcriptional regulation of grass secondary cell wall biosynthesis: playing catch-up with Arabidopsis thalianaFrontiers in Plant Science. 3:74.