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 effect of temperature and organic loading change on anaerobic digesters, the effect of electrode materials on the performance microbial fuel cells, and microbial odour production in recirculating aquaculture systems. The goal is to clarify how these environmental and operational factors affects the microbial communities that carry out important functions in the systems. Illumina shotgun sequencing and assembly of metagenome-assembled genomes is used to get information about the identity and potential functions of the microbes in the systems.