Next-generation sequencing and waste/wastewater treatment: a comprehensive overview

Microorganisms are responsible for the conversion and breakdown of organic compounds and contaminants in bioreactors designed for the treatment of different types of waste. Organized in highly complex communities, they are the heart of every wastewater treatment plant and solid residue landfill. The detailed characterization of these communities and their taxonomic classification based on phylogenetic data are of great utility in monitoring the responses of the system to changing operational parameters and the development and optimization of favorable conditions within the bioreactors these communities inhabit. Until recently, only a fraction of the microbial diversity could be assessed, limited by the available sequencing technology, which was not suited for a high-throughput implementation. With the introduction of the recent next-generation sequencing (NGS) methods, an enormous advance has taken place allowing researchers in microbial ecology to generate large amounts of phylogenetic data in a short time and at relatively low costs. In this review, we present and discuss how the increase in available information has influenced recent research and the results available phylogenetic data has produced in the field of wastewater treatment. Furthermore, we introduce the data processing of NGS-based experiments, which has become more complex as the millions of sequences that a single sample can yield require the effective use of computational resources and human bioinformatics skills. To address this part of modern microbial ecology, the most popular sequencing techniques, as well as data analysis workflows, are outlined in this review article.