3. Evaluation of Next-Generation Sequencing Technologies for Environmental Monitoring in Wastewater Abatement

The waste generation and disposal into natural water bodies become a serious topic to be concerned by researchers today. Consequently, there is a demand for new strategies and technologies to address wastewater treatment and subsequent recycle and reuse especially in arid/semiarid areas. The harmful microbial load in raw sewage, toxic chemicals, and nutrients may cause pollution and can render water utilities unfit for human consumption or recreational activities. Biological treatment process is advantageous and constitutes tools to biodegrade organic matter, transfer toxic compounds into harmless products, and remove nutrient in wastewater microbiology. Bio-monitoring employs sentinel or indicator species in water bodies to infer water quality, ecosystem health status, and to protect public health from waterborne risks. Next-Generation Sequencing is one of the most leveraging studies focus on the ecology of microbial-mediated processes that influence freshwater quality such as algal blooms, contaminant biodegradation, and pathogen dissemination. Sequencing methods targeting small subunit (SSU) rRNA hypervariable regions have allowed for identification of microbial species which serve as bioindicators for sewage contamination in raw, treated, semi-treated water utilities. In addition, hidden diversity of unknown or uncultured microorganisms reveals the genetic capabilities for biodegradation of toxins and other contaminants. This chapter aims to provide brief knowledge about the development of bioindicators for sewage pollution and microbial source tracking, characterizing the distribution of toxin and antibiotic resistance genes in water samples. The assessment of biological risk, suitability, and unfairness inherent in the application of Next-Generation Sequencing may be a prior concern.