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.
Highlights
Specialty section: This article was submitted to Aquatic Microbiology, a section of the journal Frontiers in Microbiology
We will examine case studies from recent literature where next-generation sequencing (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
Water quality for drinking and recreational purposes has been largely assessed based on culture-based enumeration and detection of fecal indicator bacteria (FIB), e.g., total coliforms, Escherichia coli, or Enterococci: a practice that has been regarded as the “gold standard” in the assessment of microbial safety of water (Figueras and Borrego, 2010)
Summary
Rivers and streams, are important aquatic ecosystems and are a source of drinking water in many countries. Advances in molecular methods and next-generation sequencing (NGS) have ushered in new opportunities for water quality assessment through analysis of waterborne microbial communities for the development of indicators and sentinels, new markers for microbial source tracking, and observation of microbially mediated processes As these new tools are developed, biases and uncertainties associated with nucleic-acid based methods and NGS must be considered. To circumvent problems associated with quantification of VBNC and otherwise difficult to culture bacteria, cultivationindependent molecular methods were developed for detection and quantification of specific bacteria (recently reviewed by Ramamurthy et al, 2014) Such methods target DNA extracted from environmental and clinical samples which is subsequently subjected to analysis for the presence or abundance of genes from indicator species or pathogens of interest. Risk assessment frameworks to define thresholds of “acceptable risk” will be necessary before incorporating quantification of microbial risk agents by DNA-based approaches into decision-making for water quality management
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