Junko Munakata Marr

Department Head and Professor, Civil and Environmental Engineering

Junko Munakata Marr

The unifying theme for my research interests is water reclamation and resource recovery, primarily by using microorganisms in engineered systems. Bacteria and other microbes have useful and sometimes surprising metabolic capabilities that we can harness to remove organic pollutants and create valuable products. While microbial communities are inherently dynamic, we can apply molecular biology techniques to assess microbial communities in environmentally relevant systems. Understanding and ultimately controlling these dynamics is important in many applications of environmental engineering microbiology. For example, microbes form the heart of wastewater treatment, degrading organics while also generating methane under specific conditions; any change in microbial activity or populations during treatment 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 treatment effectiveness. I am also interested in assessing the sustainability of new treatment approaches. Current research activities include optimization and microbial characterization of anaerobic primary and secondary treatment, biological nitrogen removal, microbial valorization of methane to more complex organics, and development of a smart irrigation system for reclaimed water.
My teaching interests are diverse; I’ve taught 15 different classes at Mines! I strive to engage every student in each course. I have been actively involved in the Humanitarian Engineering program and teach elective courses (Sustainable Engineering Design, Onsite Water Reclamation and Reuse) that support that program as well as CEE. I continue to deliver core courses as well, such as Environmental Engineering Lab and Contaminant Fate & Transport.


Coolbaugh Hall 206


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

Selected Publications

  • K.L. Lynch, W.A. Jackson, K. Rey, J.R. Spear, F. Rosenzweig and J. Munakata-Marr, “Evidence for biotic perchlorate reduction in naturally perchlorate-rich sediments of Pilot Valley Basin, Utah”, Astrobiology 19(5):629-641 (2019). DOI: 10.1089/ast.2018.1864
  • A. Pfluger, G. Vanzin, J. Munakata-Marr, L. Figueroa, “An anaerobic hybrid bioreactor for biologically enhanced primary treatment of domestic wastewater under low temperatures”, Environmental Science: Water Research & Technology 4:1851-1866 (2018). DOI: 10.1039/C8EW00237A
  • A. PflugerJ. Callahan, J.R. Stokes-Draut, D. RameyS. Gagen, L. Figueroa, J. Munakata-Marr, “Lifecycle comparison of mainstream anaerobic baffled reactor and conventional activated sludge systems for domestic wastewater treatment”, Environmental Science & Technology 52 (18):10500–10510 (2018).DOI: 10.1021/acs.est.7b06684.
  • K. Hickenbottom, L. Miller-Robbie, J. Vanneste, J. Munakata-Marr, M. Heeley and T.Y. Cath, “Comparative Life-Cycle Assessment of a Novel Osmotic Heat Engine and an Organic Rankine Cycle for Energy Production from Low-Grade Heat”, Journal of Cleaner Production 191:490-501 (2018). DOI:10.1016/j.jclepro.2018.04.106
  • A.R. PflugerM.J. Hahn, A.S. Hering, J. Munakata-Marr and L.A. Figueroa, “Statistical exposé of a multiple-compartment anaerobic reactor treating domestic wastewater”, Water Environment Research 90:530-542 (2018). DOI: 10.2175/106143017X15131012153068
  • D. Ramey, J. Munakata-Marr and T. Cath, “Tailored water treatment using enhanced primary clarification for nutrient recovery and production of water for turfgrass irrigation”, Environmental Science: Water Research & Technology 3:671-685 (2017). DOI: 10.1039/C7EW00019G
  • D. Ramey, J. Munakata-Marr and T.Y. Cath, “Hypoaeration of activated sludge to reduce energy requirements at distributed reclaimed water plants: Studies at bench and pilot scales”, Environmental Science: Water Research & Technology 3(2):235-248 (2017). DOI: 10.1039/C6EW00208K
  • S. Phanwilai, C. Wantawin, A. Terada, P. Noophan and J. Munakata-Marr, “Resuscitation of starved suspended-and attached-growth anaerobic ammonium oxidizing bacteria with and without acetate”, Water Science & Technology 75(1):115-127 (2017). DOI: 10.2166/wst.2016.483
  • A.W. GlossnerL.K. Gallagher, L. Landkamer, L. Figueroa, J. Munakata-Marr and K.W. Mandernack, “Factors controlling the co-occurrence of microbial sulfate reduction and methanogenesis in coal bed reservoirs”, International Journal of Coal Geology 165:121-132 (2016). DOI: 10.1016/j.coal.2016.08.012
  • R.W. Holloway, L. Miller-Robbie, M. Patel, J.R. Stokes, J. Munakata-Marr, J. Dadakis and T.Y. Cath, “Life-Cycle Assessment of Two Potable Water Reuse Technologies: MF/RO/UV-AOP Treatment and Hybrid Osmotic Membrane Bioreactors”, Journal of Membrane Science 507:165-178 (2016). DOI:10.1016/j.memsci.2016.01.045
  • D.C. Vuono, J. Munakata-Marr, J.R. Spear and J.E. Drewes, “Disturbance opens recruitment sites for bacterial colonization in activated sludge”,Environmental Microbiology18(1):87-99 (2016). DOI: 10.1111/1462-2920.12824
  • D. Mao, A. Revil, R.D. Hort, J. Munakata-Marr, E.A. Atekwana and B. Kulessa, “Resistivity and self-potential tomography applied to groundwater remediation and contaminant plumes: Sandbox and field experiments”, Journal of Hydrology 530:1-14 (2015). DOI: 10.1016/j.jhydrol.2015.09.031
  • R.D. Hort, D. Mao, A. Revil and J. Munakata-Marr, “Evaluating the Potential for Quantitative Monitoring of In Situ Chemical Oxidation of Aqueous-Phase TCE Using In-Phase and Quadrature Electrical Conductivity”, Water Resources Research51(7):5239-5259 (2015). DOI: 10.1002/2014WR016868
  • B.D. Coday, L. Miller-Robbie, E.G. Beaudry, J. Munakata-Marr and T.Y. Cath, “Life cycle and economic assessments of engineered osmosis and osmotic dilution for desalination of Haynesville shale pit water”, Desalination, 369:188-200 (2015). DOI: 10.1016/j.desal.2015.04.028
  • D.C. Vuono, J. Benecke, J. Henkel, W.C. Navidi, T.Y. Cath, J. Munakata-Marr, J.R. Spear and J.E. Drewes, “Disturbance and temporal partitioning of the activated sludge metacommunity”, International Society for Microbial Ecology Journal9:425-435 (2015). DOI: 10.1038/ismej.2014.139
  • K.G. Dahm, K.L. Guerra, J. Munakata-Marr and J.E. Drewes, “Trends in water quality variability for coalbed methane produced water”, Journal of Cleaner Production80:840-848 (2014). DOI: 10.1016/j.jclepro.2014.04.033