Research Topics

Through my research career, I am very fortunate to have the opportunity to extend my research interests into four major areas in environmental engineering and science. They are wastewater biotechnology, advanced molecular technology, water quality microbiology, and environmental monitoring.

Wastewater Biotechnology

I have conducted long-term research in enhanced biological phosphorus removal (EBPR) processes (my PhD research), membrane bioreactor and biofouling, and anaerobic methanogenic processes. The ultimate research goal is to achieve excellent reduction in carbon and nutrients (i.e., N and P), to recover bioenergy (i.e., methane), and to reclaim and reuse wasted water (a concept known as ‘zero-liquid discharge'). In addition to achieve the engineering goals, we study the microbial ecology of the biological processes, and try to understand how microbes interact with each other and perform their functions in the biological processes. Collectively, we use “wastewater microbiome” to represent all microbes found in biological treatment processes. Recently, we are focusing on a very intriguing microbial interaction known as syntrophy in anaerobic methanogenic processes (see more information below).

Water Quality Microbiology

In water quality microbiology, we focus on the biological aspect of water quality from source water to tap. We try to understand the roles of microbes during the water treatment processes, and study how biological filters can be used to remove high ammonia concentration (>1 mg-N/L) in source water. We further study the diversity of microbes present in the entire drinking water distribution system or so called “drinking water microbiome”. The microbes include those present in the drinking water and in the suspended particles after leaving the water treatment plant and before the water leaving the tap in a household, as well as the biofilms growing on the surface of pipes in the entire distribution system. For example, we would like to know how different disinfection treatments can affect the stability of the drinking water microbiome, and suppress the growth of opportunistic pathogens. An extension of the drinking water study is the characterization of ‘biosand’ filters that my colleague Professor Helen Nguyen has widely used to provide safe water in developing countries in Africa and Southeast Asia.

Advanced Molecular Technology

Various traditional microbiological, physical and chemical tools, and advanced molecular tools have been applied or developed in my research group to address important microbial ecology questions in wastewater microbiome, drinking water microbiome, and infant gut microbiome. Some of these methods include 16S rRNA gene sequencing using the ‘next-gen’ sequencing platform, meta-omics for studying function, expression, and metabolites, CLSM-FISH (confocal laser scanning microscopy and fluorescence in-situ hybridization), lab-on-a-chip for rapid virus and bacterial cells detection, single cell genomics and microbial fingerprinting technology (e.g., T-RFLP [terminal restriction fragment length polymorphism). In particular, singel cell genomics is a very power tool to open our view about the microbial diversity and function in the natural and engineered environment as demonstrated in a recent joint publication we had with Joint Genome Institute (see here for more information).  Also, the T-RFLP technology that I have developed with my formal colleagues at Michgan State University has been an effective tool to monitor the microbial population dynamics in a given microbial ecosystem since 1997. Until recently, it has been gradually replaced by the next-gen sequencing technologies. (a figure below shown how it works)

T-RFLP fingerprinting patterns of amplified 16S rRNA genes were used to compare the bacterial community structures in the biofilms and sludge samples taken from a methanogenic hybrid bioreactor degrading terephthalate. Different dominant T-RFs (terminal restriction fragments) or bacterial populations that involve in the syntrophic degradation of terephthalate with methanogens were observed in the biofilms and sludge samples. This difference is likely due to a difference in the growth temperature and growth format (attached vs. suspended) between these two samples. The two most dominant T-RFs (93-bp and 123-bp) were further identified to correspond to the 16S rRNA gene clones from the Desulfotomaculum subcluster Ih.

Environmental Monitoring

In this area, we primarily focus on the monitoring of microbial contamination in river, lake and ocean by human activities and animal waste. An approach so called “microbial source tracking” that relies on the use of 16S rRNA gene as specific biomarkers for different sourcse of contamination is used. Recently, we have applied this concept for monitoring the presence of Asian carp in the Mississippi water basin and Chicago area waterways. An interesting article can be found here.


In methanogenic environments, only poor electron acceptors (i.e., H+, CO2, and organic metabolites) are available and degradation of various compounds becomes thermodynamically restricted. Degradation of specific compounds (e.g., fatty acids and aromatic compounds) actually becomes endergonic (dG>0) as metabolic byproducts (e.g., acetate and H2) accumulate! In order to circumvent this thermodynamic hurdle, "syntrophic metabolizers" form unique interactions with partner methanogens, which maintain the byproducts at low concentrations and increase the thermodynamic favorability of syntrophic substrate degradation.

However, there are still many mysteries about how these syntrophic metabolizers accomplish life at the thermodynamic limit. One of our missions is to elucidate the biochemical reactions and organism-organism interactions that these organisms employ to perform energy-limited syntrophic metabolism. We previously investigated the microbial community degrading terephthalate (TA) and found that two syntrophic metabolizers may also syntrophically interact with each other to improve the thermodynamic favorability of substrate degradation. We termed this phenomenon "secondary syntrophy." This is an on-going investigation/theme in our lab, so keep your eyes out for upcoming publications!

Ongoing projects

1. Association of Pathogens with Biofilms in Drinking Water Distribution Systems (2011-2015)
2. Development of a Rapid nd Quantitative Genetic-Based Asian Carp Detection Method (2011-2014)
3. Primary Colonizers Eco-physiology in Submerged UF Membranes for Wastewater Treatment and Reuse: Effect of Cleaning and Composition of Membrane (2012-2014)
4. Understanding Bio-Augmentation for UASB Treating PTA (Purified Terephthalate Acid) Wastewater through Ecogenomics Tools (2014-2016)
5. Development, Optimization and Enhancement of Near Zero Liquid-Discharge Wastewater Treatment Technology. (2013-2016)