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Research Project Description

Use of Molecular Techniques to Study Nitrification Inhibition
Research Participation Program
Office of Research and Development
National Risk Management Laboratory
U.S. Environmental Protection Agency
Cincinnati, OH


Project Description:

A postdoctoral research project training opportunity is currently available at the U.S. Environmental Protection Agency’s (EPA) National Risk Management Research Laboratory (NRMRL) in Cincinnati, Ohio. This project will be served in EPA’s Water Supply and Water Resources Division (WSWRD).

WSWRD’s research within EPA assists in the development and evaluation of methods used to better manage wastewater systems in the United States. Currently, research involves detecting microbial populations involved in nitrogen removal in wastewater systems and providing scientific information to the EPA for policy and regulatory development related to implementing the federal Safe Drinking Water and Clean Water Act. As nitrification is a key process to nitrogen removal, conditions that diminish nitrification rates can result in poor removal of ammonia and nitrous oxide emissions that are above regulatory standards. Some of the research areas that WSWRD is currently addressing are:

  • the effect of metals, nanoparticles, and toxic organic compounds on nitrification rates
  • the use of molecular techniques to determine the presence of nitrifying bacteria and to measure nitrification rates
  • the effect of low dissolve oxygen on the rate and efficacy of nitrogen removal
  • development of approaches and molecular tools to better characterize and manipulate engineered systems

Staff within WSWRD’s Water Quality Management Branch (WQMB) is conducting wastewater research by using bioreactor systems and collecting samples from nitrifying wastewater treatment plants. WQMB provides technical support to EPA's Office of Water, EPA regional offices, state governments, communities, and homeowners. Staff members also engage in collaborative research with water utilities, consultants, and academic institutions.

Joining WQMB, the research participant will be involved in developing, evaluating, optimizing and applying multiple molecular techniques to assess the levels of nitrification inhibition in wastewater systems exposed to different contaminants. Specific activities may include:

  • Developing and maintaining nitrifying bioreactors
  • Preparing water and wastewater samples for nucleic acids (RNA and DNA) analyses
  • Using methods, such as PCR and qPCR, to detect the presence of active nitrifying populations
  • Determining: the effect of metals, such as copper, zinc, chromium and organic compounds, on nitrification rates targeting different gene targets; the diversity of nitrifying bacteria at the phylogenetic and functional level in wastewater systems; the population kinetics of nitrifying archaeal and bacterial populations in reactors and wastewater treatment plants exposed to different dissolve oxygen concentrations; and the level of structure and functional variability within nitrifying wastewater treatment plants using bioinformatics and microbial diversity indices.

Additionally, s/he will be involved in developing and evaluating molecular methods to assess chemical and physical stressors in order to determine the inhibition effect of metals and toxic organics on nitrification within wastewater systems and nitrifying reactors. 

The research participant will learn and apply several modern molecular techniques for detecting and quantifying a diversity of nitrifying microorganisms, including bacteria and archaea. S/he will learn to use PCR and qPCR assays, cloning, sequencing of phylogenetic genes as well as metagenomes of nitrifying populations using next generation sequencing techniques, and bioinformatics. S/he will be involved in application of microbial ecology concepts on engineering systems and to summarize the findings in peer-reviewed publications.


Applicants must have received a doctoral degree in microbiology, molecular microbiology, environmental or a closely related field within five years of the desired starting date, or completion of all requirements for the degree should be expected prior to the starting date.

The program is open to all qualified individuals without regard to race, sex, religion, color, age, physical or mental disability, national origin, or status as a Vietnam era or disabled veteran. U.S. citizenship or lawful permanent resident status is preferred (but can also hold an appropriate visa status, however, an H1B visa is not appropriate).

The appointment is full-time for one year and may be renewed for up to three additional years upon recommendation of EPA contingent on the availability of funds. The participant will receive a monthly stipend. The participant must show proof of health and medical insurance. The participant does not become an EPA employee.

Funding may be made available to reimburse a research participant's travel expenses to present the results of his/her research at scientific conferences. No funding will be made available to cover travel costs for pre-appointment visits, relocation costs, tuition or fees, or a participant's health insurance.

Technical Questions:

The contact for this project is Jorge W. Santo Domingo (

How to Apply:

An application can be found at Please reference Project # EPA-ORD/NRMRL-WSWRD-2014-05 when calling or writing for information.