Our lab seeks to unravel complex microbial community composition and function in environmental and engineered systems, and understand how they can be harnessed to help society develop in a sustainable manner. Research involves components of the urban water cycle in the context of nutrient and carbon removal from wastewater treatment systems, understanding factors driving community and functional assembly in urban waterways, and studying the effects of microbial and chemical pollution in freshwater and marine systems.
Microbial source tracking, pathogen detection, QMRA
A key question in public health and recreational water quality is how pathogens reach the urban environment (their transport routes) and what determines their survival in the waterways (their fate). The following projects investigate the role of biofilms as repositories of pathogens and the effect of shear force to ascertain potential ramifications that might need consideration in restructured waterways.
We are using hydrodynamic modeling and metagenomic sequencing to study the fate and transport of common waterborne pathogens in freshwater systems, and their effect on mature biofilm communities. Four surrogates are used to represent pathogens: Pseudomonas aeruginosa, Enterococcus faecalis and the bacteriophages P22 and GA. Varying flow regimes representing conditions in urban canals during dry weather and rainfall periods are assessed. Replicated (n = 4) experiments use laminar flow flumes (n = 4), two of which are spiked once with the surrogates, and surrogate populations, with nucleic acids and viable cells or phages in water and sediment biofilms being tracked. Additionally, microbial community assembly is monitored through metagenomic sequencing of the biofilms collected from flumes with and without surrogates.
Currently, we are extending our approach to study the fate and effects of human and fish pathogens in coastal waters, specifically, when they reach the sediment-water interface. The main hypothesis is based on the a priori assumption that any one biological agent does not exist in isolation but rather tends to adhere to or form aggregates.
Microbial source tracking
The occurrence of waterborne diseases among recreational water users in developed countries and high annual deaths associated with faecal pollution of water sources in developing countries underscore the need for comprehensive microbial water quality assessment to protect public health. We validated host-associated Bacteroidales genetic markers for microbial source tracking in Singapore and determined sediment-associated decay rates of the best-performing human-associated markers, B. theta and BacHum (previously developed by our group at UC Davis), and those of faecal indicator bacteria (FIB) in the presence and absence of grazing protozoa. Two human- (B. theta and BacHum) and one canine-associated (BacCan) Bacteroidales markers, and one universal Bacteroidales marker (BacUni) were validated for microbial source tracking (MST) in Southeast Asia using 295 faecal samples from animals. These findings provided insights into the utility of widely used genetic markers for microbial water quality assessment in the urban tropical environments of Singapore and Southeast Asia. The validated markers are now ready for use in urban freshwater environments.
Drinking water biofilms
Singapore has a tropical rainforest climate with no distinct seasons and high uniform temperature and humidity. These environmental conditions expedite the decay of monochloramine by auto-decomposition producing free ammonia. Thus, the ammonia is available as an energy source for ammonia oxidising bacteria and archaea by oxidation to nitrite. Nitrite can react with chloramine, reinforcing its decay, and/or be oxidised to nitrate by nitrite oxidising bacteria, promoting the development of biofilms and leading to nitrification in the pipeline network. Consequently, drinking water stability is compromised and problems arise such as microbially influenced corrosion and unpleasant odour and taste, and there is a potential risk that biofilms act as a refuge for waterborne pathogens.
A comprehensive and in-depth study of biofilms from full-scale monochloraminated DWDS was performed using next generation sequencing techniques and a multiparametric approach to characterise the microbial community. Emphasis was placed on nitrifiers and bacteria of hygienic relevance to understand their effect on drinking water safety in a tropical country. Information of this type is extremely scarce because of the cost, inconvenience and limited access to water mains.
Fundamentals of EBPR and N removal
Nitrogen (N)- and phosphorus (P)-containing inorganic ions are the key nutrients present in wastewater that need to be transformed and removed before treated water is discharged into receiving waters or reclaimed for beneficial uses. In Singapore, N removal is part of the planned design of water reclamation plants. Our research aims to improve the efficiency of N removal by understanding and implementing the forces that select for specific biochemical pathways in a treatment plant. Until recently, there was no planned biological P removal at any of the full-scale treatment plants. SCELSE’s research has led to the discovery of unplanned enhanced biological P removal (EBPR) at one full-scale plant in Singapore and unraveled the mechanism behind it. We are now monitoring the performance of other full-scale plants to understand the relationship between communal carbon utilization patterns and specific microbial communities that are involved in EBPR.
Anaerobic digestion microbiome
Bacterial community properties are critical to the operation of anaerobic digestion of sewage in Singapore and, therefore, understanding the relationship of the bacterial community and the plant parameters is essential for optimising process performance in different full-scale sewage sludge digesters in Singapore.
Anaerobic digestion (AD) is a complex biological system that is heavily influenced by different parameters such as solids retention time (SRT), temperature, and substrate characteristics. It is therefore important to understand how these parameters influence the microbial community of a digester because its community is the core of any biological system. This is a long-term study of the microbial community and functional gene dynamics associated with process performance in different full-scale sewage sludge digesters in Singapore. Metagenomic and transcriptomic studies targeting taxonomic and functional indicators are periodically conducted and combined with process operation data in a systems biology approach. Laboratory-scale experiments explore the relationship between SRT, microbial functions and AD process performance.
Microbial communities and ecological theory
We employ laboratory-scale bioreactors of varying sizes and dimensions to investigate how microbial community structure and function are affected by varying experimental conditions, and to evaluate and apply ecological theory derived from higher organisms in the context of microbial biofilm communities. The highly complex biofilm communities present in activated sludge bioreactors provide a tractable system in which to study the interactions of microorganisms from a community ecology perspective, with the dual advantage of elucidating the hidden ‘universe’ of microbes performing such intricate functions.
Improved sensing and monitoring is needed for effective environmental applications such as microbial water quality monitoring. The presence and abundance of indicator organisms such as Escherichia coli or Enterococcus faecalis are monitored to infer the probable extent of faecal contamination. Traditional approaches to biosensor optimisation focus on specific physical aspects of the system (such as electrode material), without applying a more holistic perspective. We have developed a small-volume E. coli detector based on a screen-printed electrode (SPE) bioelectrochemical system that can be used in a small volume set up, which lowers detection time after volume reduction. We applied a statistical assessment method targeting improved detection of a simulated sample from a concentration device. Our aim is to more completely understand device performance limitations and develop system improvements based on such insights.