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Pubudu Handakumbura
Biologist

Dr. Pubudu Handakumbura is a biologist. Handakumbura’s research aims to enhance the resilience of bioenergy crops in challenging environments by combining synthetic biology and systems biology approaches. She is integrating spatially resolved multi-omics, genetics, and advanced phenotyping to investigate the complex interactions between plants, microbes, and the environment. By uncovering these relationships, she seeks to advance our understanding of plant performance and stress resilience under environmental pressures. 

Research Interests

  • Multi-omics approaches in molecular plant phenotyping
  • Lignocellulosic feedstock engineering
  • Plant-microbe-soil interactions

Education

  • PhD in Plant Biology, University of Massachusetts, 2014
  • BS in Plant Biotechnology, University of Colombo, 2007

Awards and Recognition

  • 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)

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 

Patents

Hazen SP, Handakumbura P. 2019. “Plant biomass yield increase by modified SWAM1 gene expression.” US Patent 10,323,252.

Publications

2022

  • 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 https://doi.org/10.1038/s41467-022-28150-w

2021

  • Handakumbura PP, Rivas-Ubach A, Battu AK. (2021) Visualizing the Hidden Half: Plant-Microbe Interactions in the Rhizosphere. mSystems, Vol. 6, No. 5 https://doi.org/10.1128/mSystems.00765-21
  • 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.  https://doi.org/10.1371/journal.pone.0259937
  • 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 https://doi.org/10.1371/journal.pone.0259937
  • 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 https://doi.org/10.1021/acsearthspacechem.0c00299
  • 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

2020

  • 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 https://doi.org/10.3390/ijms21249706
  • 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: https://doi.org/10.1105/tpc.20.00300.
  • 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

2019

  • 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

2018

  • 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. https://doi.org/10.1111/tpj.14047

2017

  • 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

2015

  • 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. https://doi.org/10.1038/nature14099

2014

  • Handakumbura P. 2014. Understanding the transcriptional regulation of secondary cell wall biosynthesis in the model grass Brachypodium distachyon. Doctoral Dissertations, 208. https://doi.org/10.7275/6002117.0

2013

  • 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. https://doi.org/10.1186/1471-2229-13-131

2012

  • Handakumbura PP, Hazen SP. 2012. Transcriptional regulation of grass secondary cell wall biosynthesis: playing catch-up with Arabidopsis thaliana. Frontiers in Plant Science. 3:74. https://doi.org/10.3389/fpls.2012.00074