Please use this identifier to cite or link to this item: https://hdl.handle.net/10356/80959
Title: Next-generation sequencing (NGS) for assessment of microbial water quality : current progress, challenges, and future opportunities
Authors: Tan, BoonFei
Ng, Charmaine
Nshimyimana, Jean Pierre
Loh, Lay Leng
Gin, Karina Y.-H.
Thompson, Janelle R.
Keywords: Next-generationsequencing
Waterquality
Fecalindicator
Antibioticresistance
Harmfulalgalbloom
Biodegradation
Sewage
Issue Date: 2015
Source: Tan, B., Ng, C., Nshimyimana, J. P., Loh, L. L., Gin, K. Y. -H., & Thompson, J. R. (2015). Next-generation sequencing (NGS) for assessment of microbial water quality : current progress, challenges, and future opportunities. Frontiers in Microbiology, 6, 1027-.
Series/Report no.: Frontiers in Microbiology
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.
URI: https://hdl.handle.net/10356/80959
http://hdl.handle.net/10220/39025
ISSN: 1664-302X
DOI: 10.3389/fmicb.2015.01027
Schools: School of Civil and Environmental Engineering 
Research Centres: Singapore Centre for Environmental Life Sciences Engineering 
Rights: © 2015 Tan, Ng, Nshimyimana, Loh, Gin and Thompson. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
Fulltext Permission: open
Fulltext Availability: With Fulltext
Appears in Collections:CEE Journal Articles
SCELSE Journal Articles

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