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

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.

Application of NGS for studying the antibiotic resistant microbiome in Wrocław tap water

“…Similar observations were reported in the literature [23]. However, Proteobacteria are among the most abundant phyla of tap water microbiome in many studies [21][22][23][24].…”

“…were observed to occur in less than 10% of chlorinated systems but at least in 75% of chloraminated systems, suggesting the possible influence of disinfectant on their prevalence in water distribution systems [22]. Similar observations were reported in the literature [23]. However, Proteobacteria are among the most abundant phyla of tap water microbiome in many studies [21][22][23][24].…”

Assessment of the microbiological quality of recreational waters: indicators and methods

“…In general, most new methods are still under study, and require standardization and validation before becoming widely available. An overview of the future directions on the evaluation technology of microbiological quality of recreational water, in particular regarding the next-generation sequencing approaches can be found at Gomi et al (2014) and Tan et al (2015).…”

The occurrence of antibiotic resistance genes in tap water – a review

“…This hindrance may be overcome with the application of newly designed technologies for high-throughput sequencing and bioinformatics investigations of obtained sequences. The increasingly used in environmental microbiology studies Next Generation Sequencing (NGS) approach becomes more available and allows to gain seemingly more information of tested sample [66][67][68]. However, as indicated in this study, the successful implementation of NGS in tap water samples research requires proven, reliable and reproductive procedures of highefficiency DNA extraction from this medium.…”