Applied and Environmental Science

100 Years of Fighting Pollution with Microbiomes 

An Introduction to Wastewater Treatment 

For over 100 years, people have depended on microbiomes to protect public health by using them to purify wastewater and keep natural aquatic environments clean.  In 1914, Arden and Lockett demonstrated that, by aerating sewage, organic matter was gradually oxidized and a deposit of “humus” was formed.1  They also observed that ammonia in wastewater was converted to nitrate and, under some conditions, nitrogen escaped the wastewater as nitrogen gas.

The heterotrophic oxidation of reduced organic matter, autotrophic ammonium oxidation, and heterotrophic denitrification observed by Arden and Lockett remain central to biological wastewater treatment.  These microbiomic processes collectively produce “activated sludge,” which grows in mass until it settles out of the liquid that surrounds it.  Another microbiome anaerobically digests the sludge mass, and starts the methane production process by reducing the mass to simple substrates that are fermented to acetate and hydrogen.  Ultimately, methanogenic archaea are brought in to convert these two products to methane gas.2

Reinventing Wastewater Treatment with Specialized Microbiomes

We can recover water, energy, and nutrients economically from wastewater using both aerobic and anaerobic microbiomes.  Phosphorous removal relies on an anaerobic community of polyphosphate-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 PAOs take up more phosphate than they released during anaerobic digestion, resulting in the removal of most of the phosphate in the wastewater stream.4  After the phosphate is removed, the PAO biomass settles and becomes part of the sludge.  The phosphorous  released during anaerobic digestion can be recovered as a fertilizer through chemical precipitation.5

Nitrogen removal has historically been accomplished by aerobically oxidizing ammonium to nitrite and nitrate (nitrification), then reducing the nitrate that is produced to nitrogen gas (denitrification).  Recently, environmental engineers have begun using anaerobic ammonium oxidizing (anammox) bacteria in the second part of the process because anaerobic bacteria require less oxygen to do the job.6, 7  Half the ammonium is aerobically converted to nitrate, and then anammox bacteria are added to release nitrogen gas from the remaining ammonium and nitrite without using additional oxygen.  This process relies on a community of ammonium oxidizing and annamox bacteria, and heterotrophic bacteria which seem to be important to making the system work as well.8

Rather than producing methane from sludge, researchers are trying to produce other more valuable fermentation products, including medium-chain fatty acids, from high-strength industrial wastewaters.9  If we can shape anaerobic microbiomes to produce valuable chemicals or liquid transportation fuels from all types of wastewater streams, we can not only reduce the costs of treating wastewater, 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, but until now we lacked the molecular tools necessary to fully understand the microbial communities in our wastewater treatment plants.  With the development of meta-omics, environmental engineers can now explore the microbiomes they use and develop strategies to not only reduce treatment costs, but recover additional useful products from wastewater.

Practical challenges abound.  Can we maintain tailored communities in an open environment based on sewage, which is a complex, varying substrate?  As we gain the tools necessary to develop and maintain robust microbiomes in complex environments, we will be able to revolutionize the way we 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.



2017-06-04 11:04:52

What an amazing article!


2017-06-04 10:40:30

Looking for new products through bioremediation may help us to find some useful substances like fertilizer etc so it important to understand these processes


2017-06-04 10:34:30

Great look to the future. Interested to see where this research will take us!


2017-06-04 08:13:53

Amajor concern whixh is still unsolved.but bioremediation is the answer


2017-06-01 20:06:19

Microbes has great potential to be used for many useful purposes other than bioremediation


    2017-06-02 22:37:27

    I absolutely agree, it is amazing to see all of the many different paths that microbes take and the use of them in different situations!


      2017-06-03 11:21:15

      Actually we need to explore the potential of microbes, there are many more left yet to be characterized