Prokaryotic and Eukaryotic Diversity in Wastewater Treatment: Phenotypic Characterization, Molecular Techniques, and Bioprospecting

Abstract Microbiota structure changes throughout the treatment of wastewater according to the prevailing physicochemical characteristics. Under optimal conditions, prokaryotic and eukaryotic assemblages participate in the coordinated sequential elimination of contaminants. The relevance of the identification and quantification of the prevailing microorganisms in treatment plants is based on the fact that they play key roles as biological indicators of plant performance and wastewater quality. In this chapter, we focus on molecular and phenotypic methods as complementary strategies to understand the microbial composition and metabolic activities in wastewater. To identify and quantify prokaryotic and eukaryotic groups of organisms, very useful are molecular methods such as sequencing and phylogenetic analysis with molecular markers (i.e., 16 or 18S rRNA genes), fluorescent in situ hybridization, and metagenomics. Phenotypic methods complement the data obtained by the mentioned techniques. Among them, are the micromorphological analysis and grouping the identified organisms into prokaryotic metabolic groups. In this work, examples of the application of these techniques in urban solid waste leachates are discussed. Additionally, we propose out both approaches as useful tools for providing information for the bioprospecting of microorganisms with potential for biotechnological applications such as bioremediation and production of valuable commercial products, for example, bioplastics and biofuels.