This book discusses the key problems and solutions with various applicable approaches to combat antibiotic-resistant genes in industrial waste water. Several genes are selected within the chapters to illustrate the past and future roles of molecular ecophysiology and genomics in the development of wastewater microbiology as an important subdiscipline of microbial ecology. As we have very limited knowledge of composition, dynamics and stability of microbial communities, various processes in wastewater treatment have been generally considered to be "black box." In recent years, with the development of several new high throughput sequencing platforms, metagenome sequencing strategies and bioinformatics toolboxes, the analysis of the genome of complex communities has become much more accessible and means easier. The opening of the biological wastewater treatment “black box” is not the unpleasant experience it was before. The viable, but not cultural, ceases tobe the inconsequential, uncharacterizable enigma that existed today. Metagenomics leads the way for more specific studies in related fields. Finally, genomic studies of wastewater treatment microbes, in addition to their biotechnological applications, are also an excellent testing ground for variety of other ecological and environmental burns questions. Wastewater treatment plants are considered hotspots for the environmental dissemination of antimicrobial-resistant determinants. Comparative genomics of antibiotic resistant genes isolated from conventional activated sludge and biological aerated filter wastewater treatment plants is discussed.