Nitrogen pollution

Nitrogen (N) pollution is a globally important environmental problem influencing human and environmental health, ozone layer destruction, and global warming. One of the major sources of N pollution is agricultural activity, such as manure and fertilizer application to fields. To control and mitigate N pollution, we need to clarify the mechanisms of N cycle in the environment. 

Microorganisms play key roles in the N cycle. For example, a group of microbes 
called nitrifiers can convert ammonium (NH4+) to nitrite (NO2-) and then nitrate (NO3-). 

Nitrification is the major cause of N loss (e.g., nitrate leaching) from agricultural fields because NO2- and NO3- are not well-retained in soils. Groundwater contamination with NO2- and NO3- is a priority health concern because ground water is frequently used for drinking, and the uptake of NO2-/NO3- can cause severe human diseases (e.g., blue baby syndrome). Nitrate leaching can also cause eutrophication and harm aquatic ecosystems in rivers, lakes, and oceans. N leaching from the upper Midwest States, including Minnesota, is considered a major cause of the dead zone in the Gulf of Mexico.

Denitrification can remove NO2- and NO3- from soil and water environments. However, denitrification requires organic substrates and oxygen-free (anoxic) conditions to proceed, conditions that do not frequently occur in drained agricultural fields. In addition, N2O, a strong greenhouse gas and a major contributor to ozone layer destruction, can be produced via nitrification and denitrification. To mitigate these globally-important environmental problems, we need to identify when, where, and under what conditions these N cycle processes actively occur, and which microbes are responsible for these reactions.

My lab uses state-of-the-art techniques (e.g., stable-isotope analysis, single-cell isolation technique, high-throughput sequencing analysis, genomic approach) to advance the science on these critical issues. We are also working to develop novel bioreactors to remove NO2-/NO3- from agricultural runoff water. By using these bioreactors, we aim to mitigate N pollution at low cost and low-maintenance requirement, thereby greatly contributing to the ecosystem stabilization and public health.

Related publications:

  • Segawa, T., S. Ishii, N. Ohte, A. Akiyoshi, A. Yamada, F. Maruyama, Z. Li, Y. Hongoh, and N. Takeuchi. 2014. The nitrogen cycle in cryoconites: naturally occurring nitrification-denitrification granules on a glacier. Environ. Microbiol. 16:3250-3262.
  • Ishii, S., Y. Song, L. Rathnayake, H. Satoh, A. Tumendelger, S. Toyoda, N. Yoshida, and S. Okabe. 2014. Identification of key N2O production pathways in aerobic partial nitrifying granules. Environ. Microbiol. 16:3168-3180.
  • Ishii, S., H. Ohno, M. Tsuboi, S. Otsuka, and K. Senoo. 2011. Identification and isolation of active N2O reducers in rice paddy soil. ISME J. 5:1936-1945.


  • MnDRIVE field-scale bioreactor for the bioremediation of agricultural runoff video link