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Antibiotic resistance has emerged as a critical global health threat in the 21st century, leading to untreatable infectious diseases and significantly increasing human morbidity and mortality. Rapid, portable, and user-friendly detection of antibiotics, microbial pathogens, and antibiotic-resistant organisms in aquatic environment plays a key role in controlling the spread of diseases and combating the emergence of antibiotic resistance. Unfortunately, current environmental monitoring practices are tedious, expensive and slow. These limitations impede timely detection and response to emerging threats, allowing the spread of diseases and antibiotic-resistant pathogens to human populations. This dissertation research aims to develop environmental monitoring strategies that streamline the current monitoring timeline and make it accessible to a wider range of users. This effort will contribute to more frequent and efficient monitoring of antibiotics, microbial pathogens, and antibiotic-resistant organisms in water matrices. Through this research, I first investigated the application of Surface Enhanced Raman Scattering (SERS) for label-free monitoring of antibiotics in wastewater. By utilizing carefully designed SERS substrates and artificial intelligence (AI) algorithms, I successfully quantified the target antibiotics even in the presence of other organic and inorganic molecules in wastewater. Next, I developed a portable and semi-automatic virus detection centrifugal microfluidic disc (CD) that integrates sample concentration, purification, amplification, and quantification steps for environmental water monitoring. The on-CD assay is completed in less than 1.5 hours, and its performance is comparable to that of the benchtop in-tube assay. Lastly, building upon the foundation of the virus detection CD system, I further designed a microfluidic CD that integrates the phenotypic bacterial culture with genotypic pathogen identification for monitoring of antibiotic resista

The effects of climate change, population growth, and future hydrologic uncertainties necessitate increased water conservation, new water resources, and a shift towards sustainable urban water supply portfolios. Diversifying water portfolios with non-traditional water sources can play a key role. Rooftop harvested rainwater, stormwater, recycled wastewater and greywater, desalinated seawater and brackish water, and atmospheric and condensate harvesting are all currently utilized and rapidly emerging non-traditional water sources. Given the unique challenges and various pros and cons of each individual source, quantitative models and process analyses highlight the strength of comparative assessments across scenarios and water supply options to ultimately aid in decision making efforts. Larger frameworks including technoeconomic assessment (TEA) and quantitative microbial risk assessment (QMRA) paired with new, scenario specific efforts can quantify priority metrics to highlight areas of both improvement and concern. Through this research, three different non-traditional water sources were approached individually to demonstrate three aims: 1) assessment of processes, layouts, and local factors for specific facilities to identify opportunities for capital cost reduction and conditions required to adopt seawater reverse osmosis desalination as a water source; 2) locally conducted surveys and water sample collection used to both quantify health risks and local perception of water use and quality for harvested rainwater after major tropical hurricanes; and 3) implementation of a dose-response model accounting for antibiotic resistance to produce a new outcome of quantified health risks to augment our understanding of risk-based regulations for non-potable reclaimed wastewater. The outcomes of this research will provide better understanding of cost origins, health risks, and where critical efforts are needed to improve design and use of these water sources.

Skin is the body’s first line of defense against the external environment and exposure to recreational water can compromise the skin’s protective functions. Recreational water often contains harmful algal blooms and cyanotoxins, pathogenic bacteria, antibiotics and antibiotic resistance genes. This research investigated the following effects of recreational water exposure on human skin: cyanotoxin skin penetration potential, changes in the human skin microbiome and acquisition of exogenous antibiotic resistance genes (ARGs), antibiotic biosynthesis genes (ABSGs) and virulence factor genes (VFGs).Cyanotoxin penetration potential was investigated in an in-depth examination of the state of knowledge on cyanotoxins and their potential to cause negative health effects through dermal permeation. Epidemiological and toxicological studies of the health effects from algal toxin exposure are summarized to highlight the importance of better understanding of the effects on human skin. This research identified a disparity between the human health effects described in epidemiology case studies and toxicological dermal exposure data indicating potential dermal penetration. The penetrative abilities of specific cyanotoxins were predicted by their physiochemical properties indicating the potential for skin penetration. These predictions and the known comprehensive algal toxin data can be used to better evaluate human health risks.Another component of the skin’s protective role is the microbiome, which has been shown to provide immunity against exogenous bacterial colonization. This study explored the link between ocean water exposure and the human skin microbiome demonstrating that there are post-exposure alterations. Skin microbiome samples were collected from human participants’ calves before and after they swam in the ocean, and at 6 hours and 24 hours post-swim and were analyzed using 16s rRNA gene and metagenomic sequencing. Beta diversity analysis revealed that the skin microb

Skin is the body’s first line of defense against the external environment and exposure to recreational water can compromise the skin’s protective functions. Recreational water often contains harmful algal blooms and cyanotoxins, pathogenic bacteria, antibiotics and antibiotic resistance genes. This research investigated the following effects of recreational water exposure on human skin: cyanotoxin skin penetration potential, changes in the human skin microbiome and acquisition of exogenous antibiotic resistance genes (ARGs), antibiotic biosynthesis genes (ABSGs) and virulence factor genes (VFGs).Cyanotoxin penetration potential was investigated in an in-depth examination of the state of knowledge on cyanotoxins and their potential to cause negative health effects through dermal permeation. Epidemiological and toxicological studies of the health effects from algal toxin exposure are summarized to highlight the importance of better understanding of the effects on human skin. This research identified a disparity between the human health effects described in epidemiology case studies and toxicological dermal exposure data indicating potential dermal penetration. The penetrative abilities of specific cyanotoxins were predicted by their physiochemical properties indicating the potential for skin penetration. These predictions and the known comprehensive algal toxin data can be used to better evaluate human health risks.Another component of the skin’s protective role is the microbiome, which has been shown to provide immunity against exogenous bacterial colonization. This study explored the link between ocean water exposure and the human skin microbiome demonstrating that there are post-exposure alterations. Skin microbiome samples were collected from human participants’ calves before and after they swam in the ocean, and at 6 hours and 24 hours post-swim and were analyzed using 16s rRNA gene and metagenomic sequencing. Beta diversity analysis revealed that the skin microb

Coastal seawater desalination using reverse osmosis (RO) membranes has the potential to alleviate water stress in arid regions. However, membrane biofouling, caused by bacterial biofilm formation, is a significant challenge for seawater desalination plants. Biofilm formation is regulated by quorum sensing (QS) pathways where bacteria secrete auto-inducer molecules to communicate with neighboring bacteria to activate biofilm formation. This research investigated the role of the QS system and the effect of QS inhibiting (QSIs) compounds on marine biofilm production and membrane biofouling. This study revealed that four different marine bacteria isolated from fouled RO membranes in a desalination plant produced two low molecular weight auto-inducer 1 (AI-1) QS molecules. Vanillin and cinnamaldehyde were then identified as the most effective QSI compounds with reduction of marine biofilm formed by RO membrane biofouling isolates and native uncultured seawater bacterial communities by more than 79% and 70%, respectively in a microtiter plate assay. Further investigation into the anti-biofouling capabilities of vanillin and cinnamaldehyde in a cross-flow membrane bio-monitoring system indicated that vanillin in the bulk fluid (1200 mg/L) significantly reduced extracellular polysaccharides (>40%) and dead cells (>20%) on the RO membrane surface. In order to improve the membrane in-situ anti-biofouling potential, vanillin and cinnamaldehyde were physically adsorbed onto various RO membrane surfaces. The addition of the QSI layer on the RO membrane surface significantly altered the membrane surface contact angle along with a less than 16% reduction in pure water permeability, but there was no significant change in salt rejection compared to unmodified membranes. Under biofouling conditions consisting of four mixed marine bacterial species in a high pressure RO system, QSI modified membranes experienced a minimal loss in permeate flux compared to unmodified membranes. E

Coastal seawater desalination using reverse osmosis (RO) membranes has the potential to alleviate water stress in arid regions. However, membrane biofouling, caused by bacterial biofilm formation, is a significant challenge for seawater desalination plants. Biofilm formation is regulated by quorum sensing (QS) pathways where bacteria secrete auto-inducer molecules to communicate with neighboring bacteria to activate biofilm formation. This research investigated the role of the QS system and the effect of QS inhibiting (QSIs) compounds on marine biofilm production and membrane biofouling. This study revealed that four different marine bacteria isolated from fouled RO membranes in a desalination plant produced two low molecular weight auto-inducer 1 (AI-1) QS molecules. Vanillin and cinnamaldehyde were then identified as the most effective QSI compounds with reduction of marine biofilm formed by RO membrane biofouling isolates and native uncultured seawater bacterial communities by more than 79% and 70%, respectively in a microtiter plate assay. Further investigation into the anti-biofouling capabilities of vanillin and cinnamaldehyde in a cross-flow membrane bio-monitoring system indicated that vanillin in the bulk fluid (1200 mg/L) significantly reduced extracellular polysaccharides (>40%) and dead cells (>20%) on the RO membrane surface. In order to improve the membrane in-situ anti-biofouling potential, vanillin and cinnamaldehyde were physically adsorbed onto various RO membrane surfaces. The addition of the QSI layer on the RO membrane surface significantly altered the membrane surface contact angle along with a less than 16% reduction in pure water permeability, but there was no significant change in salt rejection compared to unmodified membranes. Under biofouling conditions consisting of four mixed marine bacterial species in a high pressure RO system, QSI modified membranes experienced a minimal loss in permeate flux compared to unmodified membranes. E

The primary concern associated with water reuse practices is the public health risk caused by the potential exposure to microbial contaminants, such as pathogenic protozoa, bacteria and viruses. The detection and removal of microbial pathogens is therefore of great importance to ensure the reclaimed water is “safe” for the intended end uses. This research studied the microbial pathogen removal in three different water reuse schemes. In the first study, a rapid direct virus detection method based on Accuri C6 flow cytometry (FCM) was developed to quantify the virus removal rate in a water reclamation plant using microfiltration-reverse osmosis (MF-RO) process for indirect potable reuse water production. This new method, in combination with online total organic carbon and nanoparticle analysis, has shown to be a viable way for online monitoring of high-pressure RO membrane integrity and the potential breakthrough of viral particles. In the second study, the effectiveness of microbial pathogen removal by constructed stormwater wetlands (CSW) in the U.S. and Australia was investigated using digital droplet PCR (ddPCR) and 454-pyrosequcing techniques. The results showed that the two US CSW and one of the three Australian CSW had good performance in terms of indicator bacteria removal during dry weather flow. The treated stormwater can meet the recreational water quality criteria/guidelines. No Cryptosporidium was detected in any of the CSW, while Adenovirus were present at all sites. Human specific HF183 Bacteroides were only found in Australian sites indicating the potential contamination from sewage ingression. The microbial community analysis showed a clear increase of Cyanobacteria in the outflow of CSW with better performance. The water residence time was determined as a critical factor affecting the efficacy of microbial pathogen removal or inactivation. In the last study, pathogen removal efficiency was investigated in a solar-powered mobile toilet system for dece

Increases in frequency and intensity of freshwater cyanobacterial blooms (cyanoHABs) place significant challenges to drinking water plants for human health protection from exposure to algal toxins. Specifically, microcystins (MC), the hepatotoxin produced by cyanobacteria, is not effectively removed by the current water treatment processes. The goal of this study is to isolate and characterize bacteria that are capable of degrading MC in order to develop biofilters that can effectively remove the toxin. Water and sediment samples from a drinking water reservoir and a freshwater pond were collected and enriched for MC degrading bacteria. Among nearly 100 fast growing bacterial isolates were obtained from the enrichment culture and identified by gene sequencing, none were MC degraders due to the carryover of the trace amount of ethanol in the MC stock that were used by fast growing non-degraders. On the contrary, the bacterial consortia obtained from enrichment cultures can efficiently degrade MC. Although both consortia enriched in the presence or absence of ethanol can perform MC degradation, the degradation rates were improved for most of the consortia when the ethanol was removed from the enrichment culture in spite of lower cell growth rate. This indicates that the fast growing bacteria in the enrichment culture are not the key players in the degradation of MC. Bacterial community analysis also confirmed the higher diversity in consortia associated with ethanol. However, there is not a clear separation of bacterial diversity between the MC degrading and non-degrading consortia, indicating the complexity of consortia in MC degradation.

The primary concern associated with water reuse practices is the public health risk caused by the potential exposure to microbial contaminants, such as pathogenic protozoa, bacteria and viruses. The detection and removal of microbial pathogens is therefore of great importance to ensure the reclaimed water is “safe” for the intended end uses. This research studied the microbial pathogen removal in three different water reuse schemes. In the first study, a rapid direct virus detection method based on Accuri C6 flow cytometry (FCM) was developed to quantify the virus removal rate in a water reclamation plant using microfiltration-reverse osmosis (MF-RO) process for indirect potable reuse water production. This new method, in combination with online total organic carbon and nanoparticle analysis, has shown to be a viable way for online monitoring of high-pressure RO membrane integrity and the potential breakthrough of viral particles. In the second study, the effectiveness of microbial pathogen removal by constructed stormwater wetlands (CSW) in the U.S. and Australia was investigated using digital droplet PCR (ddPCR) and 454-pyrosequcing techniques. The results showed that the two US CSW and one of the three Australian CSW had good performance in terms of indicator bacteria removal during dry weather flow. The treated stormwater can meet the recreational water quality criteria/guidelines. No Cryptosporidium was detected in any of the CSW, while Adenovirus were present at all sites. Human specific HF183 Bacteroides were only found in Australian sites indicating the potential contamination from sewage ingression. The microbial community analysis showed a clear increase of Cyanobacteria in the outflow of CSW with better performance. The water residence time was determined as a critical factor affecting the efficacy of microbial pathogen removal or inactivation. In the last study, pathogen removal efficiency was investigated in a solar-powered mobile toilet system for dece

Increases in frequency and intensity of freshwater cyanobacterial blooms (cyanoHABs) place significant challenges to drinking water plants for human health protection from exposure to algal toxins. Specifically, microcystins (MC), the hepatotoxin produced by cyanobacteria, is not effectively removed by the current water treatment processes. The goal of this study is to isolate and characterize bacteria that are capable of degrading MC in order to develop biofilters that can effectively remove the toxin. Water and sediment samples from a drinking water reservoir and a freshwater pond were collected and enriched for MC degrading bacteria. Among nearly 100 fast growing bacterial isolates were obtained from the enrichment culture and identified by gene sequencing, none were MC degraders due to the carryover of the trace amount of ethanol in the MC stock that were used by fast growing non-degraders. On the contrary, the bacterial consortia obtained from enrichment cultures can efficiently degrade MC. Although both consortia enriched in the presence or absence of ethanol can perform MC degradation, the degradation rates were improved for most of the consortia when the ethanol was removed from the enrichment culture in spite of lower cell growth rate. This indicates that the fast growing bacteria in the enrichment culture are not the key players in the degradation of MC. Bacterial community analysis also confirmed the higher diversity in consortia associated with ethanol. However, there is not a clear separation of bacterial diversity between the MC degrading and non-degrading consortia, indicating the complexity of consortia in MC degradation.