While biofilters are widely used to metabolize ammonia and other wastes in marine recirculating aquaculture systems, the ammonia-oxidizing bacterial and archaeal communities have not been characterized across a diversity of production systems. Using a metagenomics approach, we characterized the ammonia-oxidizing microbiological community of biofilters in a commercial recirculating marine aquaculture system producing hybrid grouper (Epinephelus lanceolatus × E. fuscoguttatus). Cloning and sequencing of the amoA gene showed that nitrifying bacteria included Nitrosomonas europea, N. stercoris, N. cryotolerans, N. eutropha, N. estuarii, eight strains of N. marina, and 15 strains not associated with described species. Nitrifying archaea included eight strains of Nitrosopumilus maritimus, N. koreensis, N. piranensis, N. adriaticus, undescribed congeners, and other undescribed archaea. The species composition of the bacterial and especially the archaeal communities was beyond that yet reported for aquaculture biofilters. While ammonia flux through the respective communities has yet to be estimated, the diverse environmental adaptations of the bacterial and archaeal communities suggest resilience of function under a range of environmental conditions.

The effects of hydraulic retention time (HRT) and influent nitrate-N concentration on nitrogen removal and the microbial community composition of an aerobic denitrification reactor treating recirculating marine aquaculture system effluent were evaluated. Results showed that over 98% of nitrogen was removed and ammonia-N and nitrite-N levels were below 1 mg/L when influent nitrate-N was below 150 mg/L and HRT over 5 h. The maximum nitrogen removal efficiency and nitrogen removal rate were observed at HRT of 6 or 7 h when influent nitrate-N was 150 mg/L. High-throughput DNA sequencing analysis revealed that the microbial phyla Proteobacteria and Bacteroidetes were predominant in the reactor, with an average relative total abundance above 70%. The relative abundance of denitrifying bacteria of genera Halomonas and Denitratisoma within the reactor decreased with increasing influent nitrate-N concentrations. Our results show the presence of an aerobically denitrifying microbial consortium with both expected and unexpected members, many of them relatively new to science. Our findings provide insights into the biological workings and inform the design and operation of denitrifying reactors for marine aquaculture systems.

To develop a system supporting rapid growth of juvenile freshwater mussels, a recirculating aquaculture system was designed and built at the Laboratory for Conservation Aquaculture and Aquatic Ecology, Virginia Polytechnic Institute and State University. The system included a rectangular trough tank, a sump (biofilter), a pump, a microalgae drip feeder, and an air delivery system. An algal turf scrubber (ATS) was evaluated for its potential to maintain and improve water quality within the system. Growth and survival rates of juvenile rainbow mussels Villosa iris after 90 d were compared between system units with and without ATSs. Flow rate through the culture units was approximately 23.3 L/min. Results showed no statistically significant differences between the growth and survival rates of juvenile mussels reared in systems with ATSs and those reared in systems without ATSs. Ammonia and nitrite levels were low and did not differ among treatments. However, systems with ATSs exhibited significantly lower levels of nitrate and phosphate than systems without ATSs. Our results show that freshwater mussel culture systems can be scaled up to increase production and that the use of ATSs may help to maintain water quality in recirculating aquaculture systems during long‐term culture of freshwater mussels.