We use metagenomics to study microbial communities in several environmental engineering processes including microbial fuel cells, anaerobic digesters, activated sludge, and the water treatment in recirculating aquaculture systems. The microbial fuel cell is a new technology for converting organic compounds into electricity, the anaerobic digester is an established technology for converting organics into biogas, and the activated sludge technology is widely used for removing organics and nutrients during wastewater treatment. In recirculating aquaculture systems, microbial biofilms are used to remove nutrients from the water. Currently, we are investigating the role of bacteriophages on the anaerobic digestions process. Illumina shotgun sequencing and assembly of metagenome-assembled genomes will be used to get information about the identity and potential functions of phages and prokaryotes in the system.