Taxonomic and functional profiling of nitrifying biofilms in freshwater, brackish and marine RAS biofilters

Abstract

In recirculating aquaculture systems (RAS), the crucial step of eliminating toxic N compounds like ammonia and nitrite is mediated via nitrifying microorganisms and takes place in biofilters. In this study, analyses of microorganisms colonizing biocarriers of nine moving-bed biofilters of three different RAS operated with freshwater, brackish or marine process water uncovered site specific communities. Illumina-based amplicon sequencing of the V4-region of the 16S rRNA gene revealed a high microbial diversity with 1000–2500 species-level operational taxonomic units (OTUs) in all biofilters with the highest diversity in the brackish RAS. Proteobacteria, Bacteriodetes, Plantomycetes, Chloroflexi and Nitrospirae represented the most abundant phyla. 76 out of 674 known genera occurred in all nine biofilters and were defined as core-taxa, including nitrifying bacteria (Nitrosomonas and Nitrospira) as well as members of the (heterotrophic) genera Planctomyces, Blastopirellula, Nannocystis and Lewinella. Nitrifying communities composed of different, closely related and so far uncultured members of Nitrosomonas and Nitrospira were identified, strongly indicating that several potentially novel ammonia and nitrite oxidizing species are present in RAS biofilters. Relatives of known comammox Nitrospira were detected in the brackish biofilters, revealing 94–99 % identity of the 16S rRNA gene sequence to Ns. inopinata. Salinity tolerance tests with biocarriers derived from biofilters of the three distinct RAS showed an unexpected broad physiological flexibility with regard to salinity. Nitrification performance of freshwater nitrifiers was drastically reduced with increasing salinity and nearly completely inhibited at 15 PSU, while the brackish and marine nitrifiers showed a high resistance and maintained nitrification activity in a broad range of salt concentrations. This data can help to improve the nitrification process in RAS with changing salinity of the process water.