Junko Munakata Marr

Associate Department Head, Professor, Civil and Environmental Engineering

Junko Munakata MarrThe unifying theme for my research interests is microorganisms. Natural systems contain a plethora of bacteria and other microbes that have useful and sometimes surprising metabolic capabilities. For example, microorganisms can transform a multitude of organic compounds. By harnessing such metabolic activity, we can engineer systems to remove organic pollutants microbially. For example, stimulation of indigenous microorganisms can lead to biodegradation of such groundwater contaminants as petroleum hydrocarbons, aromatic compounds, and chlorinated solvents. In addition, microorganisms can produce useful metabolic products. Microbes may, for instance, generate methane from coal under specific conditions.

Microbial communities are inherently dynamic. Understanding and ultimately controlling these dynamics is important in many applications of environmental engineering microbiology. For example, in situ remediation may require years for sufficient biodegradation to occur; any change in microbial activity or populations during such extended contaminant exposure may have significant implications for the treatment effectiveness. By understanding the community dynamics during the treatment process, we may be better able to control the biodegradation achieved. We can apply molecular biology techniques to assess microbial communities in environmentally relevant systems ranging from groundwater bioremediation, centralized and on-site wastewater treatment systems, and to identify sources of microbial contamination.
Current research activities include evaluation of the compatibility of reductive dechlorination activity with polymers used for flow control, microbial communities associated with methane generation from coal, and the coordinated use of molecular biology and chemical analyses for microbial source tracking. I am also involved in educational research projects to develop new curricula related to humanitarian engineering and to broaden participation in engineering disciplines.


Coolbaugh Hall 254


  • PhD, Civil Engineering, Stanford University
  • MS, Civil Engineering, Stanford University
  • BS (with honor), Chemical Engineering, Caltech (California Institute of Technology)

Selected Publications

  • S. Panwivia, S. Sirvithayapakorn , C. Wantawin , P. Noophan and J. Munakata-Marr, “Comparison of nitrogen removal rates and nitrous oxide production from enriched anaerobic ammonium oxidizing bacteria in suspended and attached growth reactors”, Journal of Environmental Science and Health, Part A: Toxic/ Hazardous Substances and Environmental Engineering, 49(7):851-856 (2014). DOI: 10.1080/10934529.2014.882674
  • L.K. Gallagher, A.W. Glossner, L.L. Landkamer, L.A. Figueroa, K.W. Mandernack and J. Munakata-Marr, “The effect of coal oxidation on methane production and microbial community structure in Powder River Basin coal”, International Journal of Coal Geology 115:71-78 (2013). DOI: 10.1016/j.coal.2013.03.005
  • K.G. Dahm, C.M. Van Straaten, J. Munakata-Marr and J.E. Drewes, “Identifying Well Contamination through the use of 3-D Fluorescence Spectroscopy to Classify Coalbed Methane Produced Water”, Environmental Science & Technology, 47(1):649-656 (2013). DOI: 10.1021/es303866k
  • J. Schneider and J. Munakata-Marr (2013). “Connecting the ‘Forgotten’:  Transportation Engineering, Poverty, and Social Justice in Sun Valley, Colorado”. In J. Lucena, ed., Engineering Education for Social Justice: Critical Explorations and Opportunities, Springer. http://link.springer.com/chapter/10.1007/978-94-007-6350-0_8
  • J.A.K. Silva, M.M. Smith, J. Munakata-Marr and J.E. McCray, “The Effect of System Variables on In situ Sweep-Efficiency Improvement via Viscosity Modification”, Journal of Contaminant Hydrology, 136-137:117-130 (2012). DOI: 10.1016/j.jconhyd.2012.05.006
  • N. Sinbuathong, P. Sirirote, B. Sillapacharoenkul, J. Munakata-Marr and S. Chulalaksananukul, “Biogas production from two-stage anaerobic digestion of Jatropha curcas seed cake”, Energy Sources Part A, 34(22):2048-2056 (2012). DOI: 10.1080/15567036.2012.664947
  • J. Munakata-Marr, K.S. Sorensen Jr., B.G. Petri and J. Cummings (2011). “Principles of Combining ISCO with Other In situ Remedial Approaches”. In R.L. Siegrist, M.L. Crimi and T. Simpkin, eds., In situ Chemical Oxidation for Remediation of Contaminated Groundwater, Springer Science+Business Media, New York. http://link.springer.com/chapter/10.1007%2F978-1-4419-7826-4_7
  • P. Noophan, S. Sripiboon, M. Damrongsri and J. Munakata-Marr, “Ammonium and Nitrite Removal by Ammonium Oxidizing Bacteria under Anaerobic Conditions “, Journal of Environmental Management, 90:967-972 (2009).
  • M.M. Smith, J.A.K. Silva, J. Munakata-Marr and J.E. McCray, “Compatibility of Polymers and Chemical Oxidants for Enhanced Groundwater Remediation”, Environmental Science & Technology, 42(24): 9296-9301 (2008).
  • C. Wantawin, J. Juateea, P.L. Noophan and J. Munakata-Marr, “Autotrophic Nitrogen Removal in Sequencing Batch Biofilm Reactors at Different Oxygen Supply Modes”, Water Science and Technology: Water Supply, 58(10):1889-1894 (2008).
  • A. Kaplan, J. Munakata-Marr and T.H. Illangasekare, “Biodegradation of Residual Tetrachloroethene in DNAPL Source Zones: Effects on Mass Transfer”, Bioremediation Journal, 12(1):23-33 (2008).
  • K.C. Glover, J. Munakata-Marr, and T.H. Illangasekare, “Biologically Enhanced Mass Transfer of Tetrachloroethene from DNAPL in Source Zones: Experimental Evaluation and Influence of Pool Morphology”, Environmental Science & Technology, 41(4):1384-1389 (2007).
  • J.W. Sahl, J. Munakata-Marr, M.L. Crimi, R.L. Siegrist, “Coupling Permanganate Oxidation with Microbial Dechlorination of Tetrachloroethene”, Water Environment Research, 79(1):5-12 (2007).