Associate Professor
Water Quality and Extremophile Biotechnology

Office Location: N2-01c-68



  • PhD (Joint Program in Biological Oceanography), Massachusetts Institute of Technology (Civil and Environmental Engineering), and Woods Hole Oceanographic Institution (Biology), USA (2005)
  • M.Sc. (Environmental Engineering and Science), Stanford University (1999)
  • B.Sc. (Biological Sciences), Stanford University (1998).


I am an environmental microbiologist and engineer in the Asian School of the Environment at the Nanyang Technological University, Singapore. I am also a principal investigator at the Singapore Centre for Environmental Life Sciences Engineering (SCELSE). My lab works on topics in water quality and extremophile biotechnology. My research and teaching are driven by a desire to achieve a sustainable future through careful stewardship of energy and water resources. I have previously served as a principal investigator and associate director at the Singapore-MIT Alliance for Research and Technology and have taught in the Environmental Engineering program at MIT. My research is carried out through multidisciplinary collaborations, including undergraduate and graduate students.

Research Experience:

  • Nov 2019 - Present: Associate Professor, Asian School of the Environment, NTU
  • Sep 2016 – Mar. 2019: Associate Director for Outreach, Singapore-MIT Alliance for Research and Technology
  • July 2015 – Aug 2018: Resident Principal Investigator, Centre for Environmental Sensing and Modelling (CENSAM)
  • July 2007 – June 2015: Assistant Professor Civil and Environmental Engineering, Massachusetts Institute of Technology
  • 2006-2007: Visiting Scientist, Prince of Songkla University, Hat Yai, Thailand
  • Nov. 2005-June 2007: Postdoctoral Fellow, Harvard Medical School

Research Interests:

My research uses tools of modern molecular ecology, environmental genomics, and systems biology to investigate the roles and applications of microorganisms in natural and engineered contexts. I am currently leading a newly funded NRF IntraCREATE project on wastewater epidemiology, co-lead out of MIT, and including collaborators at  SMART, NUS, Duke-NUS and the NEA Environmental Health Institute. We are looking at wastewater to understand when and where outbreaks of diseases like COVID-19 occur and how widespread they are in the population.

Other ongoing and recent projects focus on exploring biological mediators of water quality and marine health in the tropics, investigating geologic carbon dioxide sequestration's impacts on subsurface microbial communities, and developing new approaches for bioproduction of sustainable chemicals and fuels leveraging extremophilic microbes. I am currently building up an environmental microbiology research team based at the Asian School of the Environment and the Singapore Center for Environmental Life Sciences Engineering (SCELSE), working on topics in water quality and extremophile biology.

For a full list of publications please click here


ES9002 Emergent Life - Introduction to Astrobiology

I have previously taught courses on environmental health engineering and microbiology as part of a core curriculum for MIT’s Environmental Engineering students. At NTU I am developing a new intro-level course on Astrobiology and Abiogenesis.

Selected Publications:

1) Nshimyimana, J. P., Cruz, M. C., and Wuertz, S. and Thompson J. R. (2019) Variably improved microbial source tracking with digital droplet PCR. Water Research. 159:192-202.

2) Boock, J. T.#, Freedman, A.J.E.#, Tompsett, G. A., Timko, M. T., Prather, K. L. J.*, Thompson, J. R. (2019) Engineered microbial biofuel production and recovery under supercritical carbon dioxide. (#equal contribution). Nature Communications 10: 587. DOI=10.1038/s41467-019-08486-6

3) Nshimiymana, J.P., Freedman, A.J.E., Shanahan, P., Chua, L.C.H. and Thompson, J.R.  (2017) Variation of bacterial communities with water quality in an urban tropical catchment. Environmental Science and Technology 51 (10), pp 5591–5601

4) Freedman, A.J.E, Tan, B. F., and Thompson, J. R. (2017) Microbial potential for carbon and nutrient cycling in a geogenic supercritical CO2 reservoir. Environmental Microbiology 19(6):2228-2245.

5) Tan, B.F., Ng, C., Nshimiymana, J.P., Loh, L.L., Gin, K. and Thompson, J.R.* (2015) Next-generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities. Frontiers in Microbiology 6:1027-.

6) Thompson, J. R., Rivera, H., Closek, C., Medina, M. (2015) Microbes in the coral holobiont: partners through evolution, development and ecological interactions.  Frontiers in Cellular and Infection Microbiology. 4:176-.

7) Peet, K.C., Freedman, A., Hernandez, H.H., Britto, V., Boreham, C., Ajo-Franklin, J. and Thompson, J.R. (2015) Microbial growth under supercritical CO2. Applied and Environmental Microbiology 81(8):2881-92.