Research

I have a wide range of interests in environmental microbiology and the application of biotechnologies in engineering systems. Basically, I am fascinated by the questions of “why” and “how” of the amazing microbial world. Why are microbial communities so diversified while amazing patterns can still emerge? Why some microbes can withstand the attacks of antibiotics while others can not? More important, how can we inhibit the growth of pathogens and preserve beneficial bacteria? How can we develop cost-effective wastewater treatment systems and generate renewable biofuels to meet human needs in a sustainable way? All these questions are of great interest to me and I believe that they can only be answered through a combination of scientific disciplines. Some of my recent research projects are listed as follows:

Water Quality
  • Bioaccumulation and biosorption of PFAS and their precursors in the environment
    U.S. Geological Survey, 2024 – 2027
    Per- and polyfluoroalkyl substances (PFAS) are a large group of chemicals that have been widely used in industry and consumer products for over 80 years. PFAS are often called “forever chemicals” as they are extremely persistent and can be detected in drinking water, air, soil, wildlife, and in almost all Americans’ blood. Exposure to PFAS may lead to multiple adverse health problems, but limited information is available on how PFAS are absorbed, accumulated, and transformed in various processes in the environment. In this study, we will investigate the adsorption and accumulation of PFAS and their potential biotransformation in biofilms and benthic macroinvertebrates. The results will contribute improved understanding of the fate and transport of PFAS in the natural environment. The new knowledge will also help professionals and the general public to understand biological processes related to PFAS and better manage PFAS to protect human health.
  • Retention of PFAS on spent POU/POE Filters
    Water Quality Research Foundation, 2023 – 2025
    Point-of-use (POU) and point-of-entry (POE) water filtration systems are effective in removing PFAS, a.k.a., “forever chemicals”. However, limited knowledge is available on PFAS retention by spent POU and POE filters after disposal. The overall research goal of this project is to evaluate the retention of PFAS on spent filters. PFAS retention from spent activated carbon (AC) filters and reverse osmosis (RO) membranes will be determined. Breakthrough curves from anion exchange (AX) resins will be determined using small-scale laboratory columns. PFAS retention from spent AC filters, AX resins, and RO membranes will be evaluated using batch end-over-end mixing at a fixed speed. Factors contributing to PFAS retention will be evaluated. The anticipated outcomes include new knowledge on PFAS leaching from spent filters, PFAS breakthrough from AX resin materials, and the effects of pH and anions on PFAS retention. The knowledge generated from this study is expected to help the POU and POE industry to better understand and select the adsorbents with high adsorption and retention capacity to remove and retain PFAS in POU and POE systems to reduce their long-term environmental risk. Results will also help the solid waste industry to effectively design and manage landfills to reduce the public health risks of PFAS.
  • Advancing remote sensing of the biogeochemical state of midwestern inland waters
    National Aeronautics and Space Administration, 2022 – 2025
    As water quality experiences pressures from both environmental and anthropogenic events, it is critical that we can effectively identify current potential threats in multiple waterways to reduce impact on both human and ecosystem health. To do so, remote sensing technologies must be capable of providing useful information across a range of inland waterways from small ponds and rivers to reservoirs. The primary goal of this project is to improve the rapid quantification of the biogeochemical state of both river and lake water by remote analysis of optical and thermal properties so that preconditions leading to harmful algal blooms can be identified and timely prediction of harmful algal bloom occurrences in Midwestern U.S. lakes and rivers can be improved. An improved prediction model for regional harmful algal blooms based on remote sensing imagery will be developed. Significantly, this approach will enable time and resource efficient analysis and predictive capacities that will allow for the implementation of active strategies for HABs management in real time as well as across field seasons.
  • Microbial source tracking for Gunpowder Creek watershed in Kentucky
    Sanitation District No. 1 of Northern Kentucky and Boone County Conservation District, 2015 – 2016
    Microbial source tracking (MST) is a technique to detect dominant sources of fecal contamination in environmental waters. Fecal pollution poses a health risk to humans via pathogens and MST has been developed during the last two decades to monitor fecal pollution. As it is unrealistic to monitor all pathogens in surface waters, cultivable fecal indicator bacteria (FIB), such as E. coli, have been traditionally used to evaluate fecal pollution. However, FIB are not always correlated well with pathogens, and cultivable microorganisms typical only represent less than 1% of microorganisms in the total microbial community, which could result in an inaccurate estimation of fecal pollution of surface waters. Instead, molecular culture-independent and library-independent method, such as real-time PCR, can be used to trace host-specific gene markers in humans and animals in the total microbial community. The objective of this project is to identify the origin of potential fecal pollution for NKY watersheds to improve environmental quality and protect public health.
  • Rapid and accurate quantification of antibiotic resistant bacteria and quantitative risk assessment for water security
    Singapore National Research Foundation, 2013 – 2016
    Antibiotics have been widely used in humans and animals and bacterial resistance to antibiotics may pose a health risk to humans and animals. The levels of antibiotic resistance in environmental samples will be measured. Molecular microbiology techniques will be further optimized for environmental samples, such as surface water, sediments, and soils. Prevalence of antibiotic resistance, antibiotic resistance genes, and biosynthetic genes will be quantified. Various factors on the development and persistence of antibiotic resistance will be evaluated. Quantitative risk assessment will be conducted to evaluate the risks of antibiotic resistance and to optimize strategies of minimizing antibiotic resistance in water bodies to improve water security.
  • Evaluation of macrolide-lincosamide-streptogramin B antimicrobial resistance at environmental samples
    Singapore Ministry of Education, 2010 – 2013

    Macrolide-lincosamide-streptogramin B (MLSB) antimicrobials are a group of three classes of chemically distinct but functionally similar inhibitors of bacterial protein synthesis. MLSB antimicrobials have been widely used in humans and animals to treat and prevent infections. Antimicrobials used in humans and agriculture are transferred to feces and animal wastes and finally transferred into the environment. The extensive use of antimicrobials correlates with the development of antimicrobial resistant bacteria in the environment and threatens human health. The information on MLSB antimicrobials and MLSB antimicrobial resistance is important to evaluate the linkage between antimicrobial use and resistance levels and potential health risks posed to humans. Hence, quantification of antimicrobials, antimicrobial resistance, and persistence of antimicrobial resistant microorganisms and their resistance genes in environmental samples will provide important information for environmental risk assessment.
  • Monitoring microconstituents in an advanced wastewater treatment (AWT) facility and modeling discharge of reclaimed water to surface canals for indirect potable use
    U.S. WateReuse Research Foundation, 2007 – 2010

    The detection of various trace level organic pollutants in U.S. drinking water supplies recently has created substantial concern in the public and regulatory communities. Current research suggests that the trace organics, a.k.a., endocrine disrupting compounds (EDCs) and pharmaceuticals and personal care products (PPCPs), found in reverse osmosis permeate pose no human health risk, though public concern over these compounds remains a substantial hurdle. However, existing literature does indicate that some trace organic compounds at or above 1 ng/L will induce hormonal changes in aquatic life. This project was designed to demonstrate the removal of trace organics through various membrane processes (membrane bioreactors, ultrafiltration, and reverse osmosis); correlate trace organic concentration to toxicological response using tissue culture and live fish bioassays; and track the fate and transport of trace organics from a surface water injection point to groundwater supply wells.
  • MLSB antimicrobial resistance in soil amended with swine wastes
    National Pork Board, 2005 – 2007

    Antimicrobials are poorly absorbed by animals and it is estimated that between 30% and 90% of the administered antimicrobials is excreted into feces. Therefore, animal manure could be a substantial reservoir of antimicrobials and antimicrobial resistant microorganisms through land application of swine manure in agriculture. If the antimicrobial resistant bacteria are pathogens, they can directly threaten human health. Even if the antimicrobial resistant bacteria are not pathogens, they can serve as reservoirs of resistance genes and these genes may spread through horizontal gene transfer to pathogenic organisms. Traditional culture-based methods focus on monitoring resistance in enteric bacteria or specific pathogens because of their direct impact on public health, but these bacteria are often present in low abundance (< 1%) and may not reflect the overall resistance level in the microbial community. PCR-based methods can be used to measure the prevalence of antibiotic resistance genes in total microbial communities, but still requires the choice of specific genes and cannot identify the resistant organisms. To overcome the shortcomings of culture-based methods and PCR, I have developed a variation of fluorescence in situ hybridization (FISH) probe to measure the methylation site of 23S rRNAs that encodes MLSB antimicrobial resistance. Combined with phylogenetic probes, the levels of antimicrobial resistance in particular microorganism were determined.
  • Development of image analysis and statistical tools for microbial ecology studies
    U
    niversity of Illinois at Urbana-Champaign, 2002 – 2007
    Image analysis is the basis for many molecular microbiology techniques, such as fluorescence in situ hybridization and microarray. However, the quantification of fluorescence signals is difficult because of the large variability of all microbial communities. Commonly used quantification techniques such as fixed value thresholds or signal-to-noise ratio thresholds have intrinsic problems because these thresholds often vary between experiments. Accurate quantification needs both precise normalization and extraction of biological signals and robust post-processing of extracted information. I have developed a macro package for automated and quantitative analysis (AQUAN) of fluorescence in situ hybridization images, which can automatically separate and extract more than thirty features of each cell while keeping the interference of other cells and background at a minimal level. Statistical tools are necessary for the classification of signals. Fuzzy c-means (FCM) clustering was used to analyze the intrinsic data structure of extracted signals and the classification was much more robust than threshold-based techniques. As a result, I significantly increased the accuracy of fluorescence in situ hybridization image analysis through the combination of computational and statistical methods with molecular techniques and cut the analysis time by more than 80%.
Water Treatment
  • When blue is green: Sustainable blue food systems driven by integrated aquaponics
    U.S. Department of Agriculture, 2023 – 2028
    While current global food systems produce sufficient calories to keep pace with US population growth, many Americans consume nutrient-poor diets that contribute to increased incidence of diet-related obesity and chronic diseases. “Blue foods”, i.e., foods derived from aquatic animals, plants or algae (used interchangeably with seafood), can provide more nutritional benefits and be produced more sustainably than land-based foods. Aquaponics is an integrated food production system that integrates aquaculture and plant production systems (often as hydroponics) into a single closed/semi-closed loop system. These systems intensively produce diverse, high-quality seafood and specialty crops in controlled environments, contributing to climate-smart agriculture. The goal of this project is to increase local and regional production of adequate, nutritious, and affordable blue foods with a minimal environmental footprint to ultimately diversify US agricultural systems and dietary patterns.
  • Technology for water defluoridation pumping systems
    Shah Lab Seed Grant, 2021 – 2023
    Dungarpur, Rajasthan is a tribal district and many of the villages have fluoride rich and highly saline/ TDS rich natural water sources e.g. ground water and pond water resources. Fluoride in the water effects the health, lives and livelihoods of the poor women members from informal economy. In the absence of solutions, farmers cannot optimize their farm yields and incomes, leading to them being trapped in the vicious cycle of poverty. The solution needs co-creating support and designing the effective technology keeping in mind the end users who are poor women members / small and marginal farmers from the informal economy. The goal of our proposed project is to develop cost-effective and affordable defluoridation treatment and monitoring systems for local communities in Dungarpur, Rajasthan.
  • Emerging contaminant removal and microbial growth in membrane filtration and activated carbon point-of-use systems
    Water Quality Research Foundation, 2018 – 2021
    Point-of-use (POU) water treatment systems provide many benefits to remove trace-level contaminants that remain in treated drinking water. Membrane filtration systems and activated carbon systems are two highly efficient POU systems, but their potentials to remove emerging contaminants, including per- and Polyfluoroalkyl Substances (PFAS), uranium, and manganese, have not been fully explored. Our overall research objective is to systematically evaluate emerging contaminant removal with POU systems. Upon the successful completion of this project, it is anticipated that this study will yield performance data on removal efficiencies of representative emerging contaminants, new knowledge on the effects of water quality on the performance of POU systems, and mechanisms of microbial growth. These outcomes are expected to have significant potential to positively improve the efficiency of POU water treatment devices. Information collected in this study will be valuable in developing cost-effective treatment devices to improve water quality and mitigate risks of emerging contaminants in drinking water. The new knowledge generated from this study is expected to provide important information for developing cost-effective POU systems to remove emerging contaminants.
  • Removal of off-flavor compounds by electrochemical carbon nanotube filters
    Singapore National Research Foundation, 2013 – 2015
    Development of cost-effective water treatment techniques is critical to tackle global water quality challenges. The proliferation of cyanobacteria in surface water during algal blooms is a global issue that leads to the production of off-flavor compounds, which usually cause taste and odor issues. Conventional water treatment technologies can remove some of these contaminants but usually result in high energy consumption. It is therefore important to develop cost-effective advanced water treatment technologies to remove contaminants and odors to improve water quality. Electrochemical carbon nanotube filters proposed in this study have great potential to remove chemical contaminants with minimal energy consumption. The efficiency of CNT filters was evaluated for the removal of off-flavor compounds for point-of-use water quality improvement. We also developed a novel graphene-based electrochemical filter to utilize both the high specific surface area and high conductivity of graphene to physically adsorb and electrochemically oxidize chemical contaminants.
  • Guidelines for engineered storage for direct potable reuse systems
    U.S. WateReuse Research Foundation, 2013 – 2015
    As communities move towards more direct potable reuse (incorporation of highly purified recycled water into a drinking water source without an environmental buffer), it will be imperative to provide utilities with guidance on sizing, design, and response procedures for potential changes in water quality in engineered storage systems as they will become increasingly important in overall water management. The availability of an engineered storage buffer is a key element in direct potable reuse using current treatment and monitoring techniques. The engineered storage buffer must be of a sufficient capacity to allow for the protection of public health from inadequate treatment and for the measurement of specific constituents to be assured that the quality of the water provided meets all applicable public health standards. The project will develop recommendations for optimizing engineered storage systems for direct potable reuse through examining current practices and existing research to generate a guidance document and report.
  • Low-cost technologies for small-scale water reclamation plants
    U.S. WateReuse Research Foundation, 2008 – 2010
    The shortage of fresh water is a severe problem for many areas of the world. Water reclamation and reuse provide promising opportunities to ease fresh water shortage problems. However, data and technical information for low-cost treatment technologies for small-scale water reuse projects are often unavailable, especially to communities with limited financial and technical resources in rural areas and in developing countries. In response to this need, the U.S. WateReuse Research Foundation funded this study to identify and evaluate established and innovative technologies that provide treatment of flows of less than one million gallons per day (mgd). A total of 26 treatment processes in 284 utilities were evaluated as part of this project. The primary value of this work is the extensive cost database, where the cost and operations data from existing small-scale wastewater treatment and water reuse facilities have been gathered and synthesized. From these data, the costs and maintenance issues for the various types of treatment technologies are compared and contrasted.
  • Ultraviolet (UV) disinfection bioassay tests and system performance evaluations
    Carollo Engineers, 2007 – 2010
    As a consulting engineer at Carollo Engineers, which dominates the US UV validation market, I have conducted more than 30 UV disinfection system validations and performance evaluations for five major UV equipment manufacturers in the world. The performance of UV disinfection systems can be affected by many factors, such as reactor configuration, end-of-lamp life, fouling factor, flow rate, power, UVT, and turbidity. The comparison of the performance of UV reactors with multiple variables between different sites and tests is a challenge and statistical tools have to be used. Various statistical tools, such as multivariate linear regression, analysis of variance, and factorial design, can significantly improve the accuracy and cut the costs of engineering testing.
Bioenergy
  • Nature-inspired cost-effective production of biofuels with algal viruses
    Purdue Research Foundation, 2018
    Algal biofuel has been advocated as a sustainable and environmentally friendly renewable energy source. However, intensive chemical usage, high energy consumption, and high operation and maintenance costs associated with current cell disruption methods have been identified as main challenges to cost-effective production of algal biofuel. Viral infection of algae is a natural process that can lyse algal cells under ambient conditions without using chemicals or energy-intensive equipment. This study, for the first time, provides a comprehensive and in-depth evaluation of the feasibility of using viruses to assist algal lipid extraction. Detailed mechanistic studies were conducted to evaluate the impact on mechanical strength of algal cell walls, lipid yield, and lipid distribution when Chlorella sp. were infected by Paramecium bursaria Chlorella virus 1 (PBCV-1). Our results indicated that viral disruption significantly reduced the mechanical strength of algal cells. Lipid yield with viral disruption increased more than three times compared to no disruption controls and was similar to that of ultrasonic disruption. Moreover, lipid composition analysis showed that the quality of extracted lipids was not affected by viral infection. The results showed that viral infection is a highly cost-effective technique to promote lipid extraction without extensive energy input and chemicals required by existing disruption methods. The results of this study provided new insights in the development of nature-inspired lipid extraction methods for cost-efficient biofuel production.
  • A new type of photosynthesis through electrodedriven anaerobic respiration
    Singapore Ministry of Education, 2012 – 2014
    A new type of photosynthesis through electrode-driven anaerobic respiration will be tested to convert carbon dioxide and water to biofuels. Compared to oxygenic photosynthesis, this new type of photosynthesis utilizes carbon dioxide and water to produce extracellular compounds instead of biomass. Therefore all the energy and efforts for processing biomass can be saved and the overall efficiency of biofuel production will be greatly enhanced. As a carbon-neutral and high-efficiency process, the technique proposed in this project could greatly enhance the production efficiency of biofuel.
  • Photoelectrochemical water splitting for the production of value-added chemicals
    Singapore, Peking and Oxford Research Enterprise, 2010 – 2013
    Solar energy will be used to split up water into hydrogen and oxygen. Then hydrogen or protons will be used to reduce carbon dioxide to produce value-added products, such as biofuels.  Anaerobic microorganisms will be used for carbon dioxide fixation and conversion. Molecular microbiology techniques will be utilized for microbial community characterization and performance enhancement.