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Next-generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities.

Tan B, Ng C, Nshimyimana JP, Loh LL, Gin KY, Thompson JR - Front Microbiol (2015)

Bottom Line: This review discusses the challenges and benefits of applying NGS-based methods to water quality research and assessment.Secondly, we will examine case studies from recent literature where NGS based methods have been applied to topics in water quality assessment, including development of bioindicators for sewage pollution and microbial source tracking, characterizing the distribution of toxin and antibiotic resistance genes in water samples, and investigating mechanisms of biodegradation of harmful pollutants that threaten water quality.Finally, we provide a short review of emerging NGS platforms and their potential applications to the next generation of water quality assessment tools.

View Article: PubMed Central - PubMed

Affiliation: Center for Environmental Sensing and Modelling, Singapore-MIT Alliance for Research and Technology Centre Singapore, Singapore.

ABSTRACT
Water quality is an emergent property of a complex system comprised of interacting microbial populations and introduced microbial and chemical contaminants. Studies leveraging next-generation sequencing (NGS) technologies are providing new insights into the ecology of microbially mediated processes that influence fresh water quality such as algal blooms, contaminant biodegradation, and pathogen dissemination. In addition, sequencing methods targeting small subunit (SSU) rRNA hypervariable regions have allowed identification of signature microbial species that serve as bioindicators for sewage contamination in these environments. Beyond amplicon sequencing, metagenomic and metatranscriptomic analyses of microbial communities in fresh water environments reveal the genetic capabilities and interplay of waterborne microorganisms, shedding light on the mechanisms for production and biodegradation of toxins and other contaminants. This review discusses the challenges and benefits of applying NGS-based methods to water quality research and assessment. We will consider the suitability and biases inherent in the application of NGS as a screening tool for assessment of biological risks and discuss the potential and limitations for direct quantitative interpretation of NGS data. Secondly, we will examine case studies from recent literature where NGS based methods have been applied to topics in water quality assessment, including development of bioindicators for sewage pollution and microbial source tracking, characterizing the distribution of toxin and antibiotic resistance genes in water samples, and investigating mechanisms of biodegradation of harmful pollutants that threaten water quality. Finally, we provide a short review of emerging NGS platforms and their potential applications to the next generation of water quality assessment tools.

No MeSH data available.


Environments where studies of water quality have been advanced by NGS. (A) Fluorescence microscopy showing biofilm grown on a stainless steel surface in a laboratory potable water biofilm reactor for 14 days (image from Donlan, 2002). Drinking water is thought to contain a mixture of both planktonic and dissociated biofilm bacteria. Using NGS methods, a repertoire of microbial species including potential pathogens have been detected in water distribution systems, raising the concern of the effectiveness of water treatment on microbial water safety. (B) A water reservoir in Singapore impacted by a cyanobacterial bloom characterized by Penn et al. (2014). With global warming, cHAB is predicted to occur more regularly with likely severe consequences (e.g., toxin loading) that can diminish water quality. (C) An oil sands tailings pond in Alberta, Canada characterized by Tan et al. (2015). Inset (D) shows microcosms established to study degradation of unrecovered hydrocarbons deposited in oil sands tailings pond. NGS has been used to characterize the microbial communities in oil sands tailings ponds (http://www.hydrocarbonmetagenomics.com/) in order to better understand mechanisms of pollutant degradation.
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Figure 1: Environments where studies of water quality have been advanced by NGS. (A) Fluorescence microscopy showing biofilm grown on a stainless steel surface in a laboratory potable water biofilm reactor for 14 days (image from Donlan, 2002). Drinking water is thought to contain a mixture of both planktonic and dissociated biofilm bacteria. Using NGS methods, a repertoire of microbial species including potential pathogens have been detected in water distribution systems, raising the concern of the effectiveness of water treatment on microbial water safety. (B) A water reservoir in Singapore impacted by a cyanobacterial bloom characterized by Penn et al. (2014). With global warming, cHAB is predicted to occur more regularly with likely severe consequences (e.g., toxin loading) that can diminish water quality. (C) An oil sands tailings pond in Alberta, Canada characterized by Tan et al. (2015). Inset (D) shows microcosms established to study degradation of unrecovered hydrocarbons deposited in oil sands tailings pond. NGS has been used to characterize the microbial communities in oil sands tailings ponds (http://www.hydrocarbonmetagenomics.com/) in order to better understand mechanisms of pollutant degradation.

Mentions: Next-generation sequencing has been used to survey the microbial composition in drinking water distribution systems including source waters (Chao et al., 2013), end-point taps (Chao et al., 2013; Shi et al., 2013; Huang et al., 2014), and various stages of the drinking water treatment and distribution process (Gomez-Alvarez et al., 2012; Chao et al., 2013; Shi et al., 2013; Huang et al., 2014), as well as biofilm matrices associated with distribution pipelines (Figure 1A; Hong et al., 2010). While most microorganisms in treated drinking water are harmless, outbreaks of diseases linked to pathogens in drinking water may be due to compromised water treatment and contaminated source waters (MacKenzie et al., 1994; Howe et al., 2002). Pathogens that have evaded treatment and disinfection processes may persist in water distribution pipelines as biofilms, leading to dissemination to end users through the process of sloughing (Figueras and Borrego, 2010). A recent study noted an increase in microbial diversity in end-point drinking water relative to source water which was linked to dispersal of biofilm-associated microbes during passage through the water distribution pipeline (Huang et al., 2014). Consumption of untreated well-water poses an additional risk, where waterborne pathogens such as Legionella and Campylobacter are among some of the main well-waterborne disease agents in the USA (CDC, 2013). Other causative agents of waterborne diseases in both developed and developing countries include parasites such as Cryptosporidium parvum, Toxoplasma gondii, Cyclospora cayetanesis, Giardia lamblia and viruses such as norovirus (Ashbolt, 2015). Metagenomic surveys of water within distribution systems and end-point drinking waters have detected DNA indicative of several of these potential opportunistic pathogens (e.g., Legionella, Mycobacterium, Pseudomonas, and Leptospira) and virulence factors (e.g., AR and pathogenicity islands, Gomez-Alvarez et al., 2012; Shi et al., 2013; Huang et al., 2014). Several recent studies have used NGS to shed light on the fate of microbial populations, including pathogens, during various stages of the water treatment process.


Next-generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities.

Tan B, Ng C, Nshimyimana JP, Loh LL, Gin KY, Thompson JR - Front Microbiol (2015)

Environments where studies of water quality have been advanced by NGS. (A) Fluorescence microscopy showing biofilm grown on a stainless steel surface in a laboratory potable water biofilm reactor for 14 days (image from Donlan, 2002). Drinking water is thought to contain a mixture of both planktonic and dissociated biofilm bacteria. Using NGS methods, a repertoire of microbial species including potential pathogens have been detected in water distribution systems, raising the concern of the effectiveness of water treatment on microbial water safety. (B) A water reservoir in Singapore impacted by a cyanobacterial bloom characterized by Penn et al. (2014). With global warming, cHAB is predicted to occur more regularly with likely severe consequences (e.g., toxin loading) that can diminish water quality. (C) An oil sands tailings pond in Alberta, Canada characterized by Tan et al. (2015). Inset (D) shows microcosms established to study degradation of unrecovered hydrocarbons deposited in oil sands tailings pond. NGS has been used to characterize the microbial communities in oil sands tailings ponds (http://www.hydrocarbonmetagenomics.com/) in order to better understand mechanisms of pollutant degradation.
© Copyright Policy
Related In: Results  -  Collection

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Figure 1: Environments where studies of water quality have been advanced by NGS. (A) Fluorescence microscopy showing biofilm grown on a stainless steel surface in a laboratory potable water biofilm reactor for 14 days (image from Donlan, 2002). Drinking water is thought to contain a mixture of both planktonic and dissociated biofilm bacteria. Using NGS methods, a repertoire of microbial species including potential pathogens have been detected in water distribution systems, raising the concern of the effectiveness of water treatment on microbial water safety. (B) A water reservoir in Singapore impacted by a cyanobacterial bloom characterized by Penn et al. (2014). With global warming, cHAB is predicted to occur more regularly with likely severe consequences (e.g., toxin loading) that can diminish water quality. (C) An oil sands tailings pond in Alberta, Canada characterized by Tan et al. (2015). Inset (D) shows microcosms established to study degradation of unrecovered hydrocarbons deposited in oil sands tailings pond. NGS has been used to characterize the microbial communities in oil sands tailings ponds (http://www.hydrocarbonmetagenomics.com/) in order to better understand mechanisms of pollutant degradation.
Mentions: Next-generation sequencing has been used to survey the microbial composition in drinking water distribution systems including source waters (Chao et al., 2013), end-point taps (Chao et al., 2013; Shi et al., 2013; Huang et al., 2014), and various stages of the drinking water treatment and distribution process (Gomez-Alvarez et al., 2012; Chao et al., 2013; Shi et al., 2013; Huang et al., 2014), as well as biofilm matrices associated with distribution pipelines (Figure 1A; Hong et al., 2010). While most microorganisms in treated drinking water are harmless, outbreaks of diseases linked to pathogens in drinking water may be due to compromised water treatment and contaminated source waters (MacKenzie et al., 1994; Howe et al., 2002). Pathogens that have evaded treatment and disinfection processes may persist in water distribution pipelines as biofilms, leading to dissemination to end users through the process of sloughing (Figueras and Borrego, 2010). A recent study noted an increase in microbial diversity in end-point drinking water relative to source water which was linked to dispersal of biofilm-associated microbes during passage through the water distribution pipeline (Huang et al., 2014). Consumption of untreated well-water poses an additional risk, where waterborne pathogens such as Legionella and Campylobacter are among some of the main well-waterborne disease agents in the USA (CDC, 2013). Other causative agents of waterborne diseases in both developed and developing countries include parasites such as Cryptosporidium parvum, Toxoplasma gondii, Cyclospora cayetanesis, Giardia lamblia and viruses such as norovirus (Ashbolt, 2015). Metagenomic surveys of water within distribution systems and end-point drinking waters have detected DNA indicative of several of these potential opportunistic pathogens (e.g., Legionella, Mycobacterium, Pseudomonas, and Leptospira) and virulence factors (e.g., AR and pathogenicity islands, Gomez-Alvarez et al., 2012; Shi et al., 2013; Huang et al., 2014). Several recent studies have used NGS to shed light on the fate of microbial populations, including pathogens, during various stages of the water treatment process.

Bottom Line: This review discusses the challenges and benefits of applying NGS-based methods to water quality research and assessment.Secondly, we will examine case studies from recent literature where NGS based methods have been applied to topics in water quality assessment, including development of bioindicators for sewage pollution and microbial source tracking, characterizing the distribution of toxin and antibiotic resistance genes in water samples, and investigating mechanisms of biodegradation of harmful pollutants that threaten water quality.Finally, we provide a short review of emerging NGS platforms and their potential applications to the next generation of water quality assessment tools.

View Article: PubMed Central - PubMed

Affiliation: Center for Environmental Sensing and Modelling, Singapore-MIT Alliance for Research and Technology Centre Singapore, Singapore.

ABSTRACT
Water quality is an emergent property of a complex system comprised of interacting microbial populations and introduced microbial and chemical contaminants. Studies leveraging next-generation sequencing (NGS) technologies are providing new insights into the ecology of microbially mediated processes that influence fresh water quality such as algal blooms, contaminant biodegradation, and pathogen dissemination. In addition, sequencing methods targeting small subunit (SSU) rRNA hypervariable regions have allowed identification of signature microbial species that serve as bioindicators for sewage contamination in these environments. Beyond amplicon sequencing, metagenomic and metatranscriptomic analyses of microbial communities in fresh water environments reveal the genetic capabilities and interplay of waterborne microorganisms, shedding light on the mechanisms for production and biodegradation of toxins and other contaminants. This review discusses the challenges and benefits of applying NGS-based methods to water quality research and assessment. We will consider the suitability and biases inherent in the application of NGS as a screening tool for assessment of biological risks and discuss the potential and limitations for direct quantitative interpretation of NGS data. Secondly, we will examine case studies from recent literature where NGS based methods have been applied to topics in water quality assessment, including development of bioindicators for sewage pollution and microbial source tracking, characterizing the distribution of toxin and antibiotic resistance genes in water samples, and investigating mechanisms of biodegradation of harmful pollutants that threaten water quality. Finally, we provide a short review of emerging NGS platforms and their potential applications to the next generation of water quality assessment tools.

No MeSH data available.