Ammonia-oxidizing bacteria and archaea within biofilters of a commercial recirculating marine aquaculture system

Zhitao Huang,Teng Ma,Lei Peng,Yuli Jiang,Wensheng Li,Jieming Zhai,Dengpan Dong,Xiefa Song,Eric Hallerman

doi:10.1186/s13568-018-0551-1

Abstract

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.

Highlights

Effective biological filtration is critical to fish production in a recirculating aquaculture system (RAS)
Since nitrification was well established in the series of biofilters before culture commenced, neither total ammonia nitrogen (TAN) nor nitrite accumulated during fish production
DNA barcoding using the ammonia monooxygenase (amoA) gene showed the ammoniaoxidizing bacteria (AOB) community to be dominated by numerous Nitrosomonas species and strains and the ammonia-oxidizing archaea (AOA) community by Nitrosopumilus species and strains

Summary

Introduction

Effective biological filtration is critical to fish production in a recirculating aquaculture system (RAS). Classical characterization of biological filtration involves measurement of chemical parameters (e.g., ammonia, nitrite, and nitrate concentrations, biochemical oxygen demand), and culture-based identification of key species within the microbial consortium. Production is carried out in flow-through systems (Wang et al 2004), highly intensive culture ponds (Li et al 2013), and more recently in recirculating aquaculture systems (Yang et al 2016)

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Conclusion