The big picture


For over a hundred years, environmental engineers have used microbiomes to clean wastes and protect public health. In these engineered processes, microbiomes transform organic matter and nutrients in anthropogenic wastes to less harmful products. Using molecular techniques, we aim to further dissect the roles within these microbiomes so that we can direct communities of microbes to produce more valuable end products, including pipeline quality natural gas and industrial chemicals. We employ multi-omics techniques to understand the full genomic potential of microbiomes (metagenomics) and the expression of genes within microbiomes (metatranscriptomics). Future work aims to elucidate roles within microbiomes using protein sequencing (metaproteomics) and the flow of substrates within and between organisms (metafluxomics). In total, our work aims to model and predict microbiome behavior so that we can employ microbiomes to reduce costs associated with waste management and achieve a circular carbon and nutrient economy.

Our Mission

The EMERG lab will develop sustainable microbiome-based technologies to protect public health, reduce anthropogenic impacts on the environment, and offset demands for fossil fuels.

Microbiomes protecting the environment

An Introduction to Wastewater Treatment

For over 100 years, humans have been putting microbiomes to work to protect public health and natural aquatic environments. In 1914, Arden and Lockett demonstrated that by aerating sewage, organic matter was gradually oxidized and a deposit of “humus” formed1. They also observed that ammonia was converted to nitrate, and, under some conditions, nitrogen escaped the wastewater as nitrogen gas.

The processes observed by Arden and Lockett remain central to biological wastewater treatment: heterotrophic oxidation of reduced organic matter, autotrophic ammonium oxidation, and heterotrophic denitrification. Collectively, these mcirobiome processes are termed “activated sludge”. After bacterial biomass is grown from the nutrients in wastewater, it is settled out of the liquid stream. This settled cellular biomass can undergo anaerobic digestion to produce biogas. In this process, a microbiome hydrolizes the cell biomass and other organic material to simple substrates, the simple substrates are fermented to acetate and hydrogen, and, ultimately, methane is produced by methanogenic archaea2.

Reinventing Wastewater Treatment with Specialized Microbiomes

Utilizing both aerobic and anaerobic microbiomes, we can recover water, energy, and nutrients from wastewater and reduce overall treatment costs. Phosphorous removal relies on an anaerobic community of poly-phosphate accumulating organisms (PAOs)3. In the anaerobic stage of an activated sludge process, complex organic waste is fermented to acetate and other simple organics, and these simple organics are consumed by PAOs as they release their poly-phosphate stores. Then, in the presence of a terminal electron acceptor (nitrite, nitrate, or oxygen), the PAO’s uptake more phosphate than they released in the anaerobic environment, resulting in removal of most of the phosphate in the wastewater stream4. The PAO biomass is then settled to become part of the sludge. The phosphorous is released during anaerobic digestion, and can ultimately be recovered as a fertilizer through chemical precipitation5.

Nitrogen removal has historically been performed by oxidizing ammonium to nitrite and nitrate aerobically (nitrification), then reducing the produced nitrate to nitrogen gas (denitrification). Recently, environmental engineers have utilized anaerobic ammonimum oxidizing (anammox) bacteria to remove nitrogen with less oxygen inputs6, 7. By aerobically converting half of the ammonium to nitrite, anammox bacteria can utilize the remaining ammonium and nitrite to produce nitrogen gas without additional oxygen. This process relies on a community of ammonium oxidizing bacteria and annamox. Heterotrophic bacteria also seem to be important for these systems8.

Rather than producing methane from sludge, research is being performed to produce other more valuable fermentation products, including medium-chain fatty acids9. Currently, this has only been investigated for high-strength industrial wastewaters. If we can shape anaerobic microbiomes to produce valuable chemicals or liquid transportation fuels, we can not only reduce the costs to treat wastewater, but we can incentivize wastewater treatment in areas of the world currently lacking adequate sanitation.

The Next 100 Years

Wastewater treatment has successfully relied on microbiomes for over 100 years without the molecular tools necessary to fully understand the microbial communities present in our wastewater treatment plants. With the development of meta-omics, environmental engineers can now gain insights into these robust microbiomes and develop strategies to not only reduce treatment costs, but also recover additional useful products from wastewater; however, practical challenges abound:

  • Can we maintain tailored communities in an open environment fed the complex, varying substrate that is municipal sewage?
  • Can we leverage specialized microbiomes to convert agricultural wastes to beneficial products at centralized or de-centralized facilities in rural areas?
  • Can we steer biogas producing microbial communities towards production of higher-quality, pipeline-ready natural gas?
  • Can we use microbiomes to recover nutrients from wastes for use as fertilizers?

As we gain the tools necessary to develop and maintain robust microbiomes in complex environments, we stand to revolutionize the way humans recover and protect our most valuable resource: water.


1. E. Ardern and W. T. Lockett, Journal of the Society of the Chemical Industry, 1914, 33, 523-529.

2. I. Vanwonterghem, P. D. Jensen, K. Rabaey and G. W. Tyson, Environ. Microbiol., 2016, 18, 3144-3158.

3. H. Garcia Martin, N. Ivanova, V. Kunin, F. Warnecke, K. W. Barry, A. C. McHardy, C. Yeates, S. He, A. A. Salamov, E. Szeto, E. Dalin, N. H. Putnam, H. J. Shapiro, J. L. Pangilinan, I. Rigoutsos, N. C. Kyrpides, L. L. Blackall, K. D. McMahon and P. Hugenholtz, Nat. Biotechnol., 2006, 24, 1263-1269.

4. P. Y. Camejo, B. R. Owen, J. Martirano, J. Ma, V. Kapoor, J. S. Domingo, K. D. McMahon and D. R. Noguera, Water Res., 2016, 102, 125-137.

5. J. D. Doyle and S. A. Parsons, Water Res., 2002, 36, 3925-3940.

6. B. Wett, Water Sci. Technol., 2007, 56, 81-88.

7. U. van Dongen, M. S. Jetten and M. C. van Loosdrecht, Water Sci. Technol., 2001, 44, 153-160.

8. D. R. Speth, M. H. In 't Zandt, S. Guerrero-Cruz, B. E. Dutilh and M. S. Jetten, Nat Commun, 2016, 7, 11172.

9. L. T. Angenent, H. Richter, W. Buckel, C. M. Spirito, K. J. J. Steinbusch, C. M. Plugge, D. Strik, T. I. M. Grootscholten, C. J. N. Buisman and H. V. M. Hamelers, Environ. Sci. Technol., 2016, 50, 2796-2810.