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The indoor recirculating aquaculture system (RAS) is a sustainable alternative to traditional aquaculture systems, and a biofilter is a crucial component for the stable operation of this system. In this study, the bacterial communities within different sections of the biofilter in a full‐scale RAS for the culture of Tongue Sole Cynoglossus semilaevis were investigated using polymerase chain reaction–based 454 pyrosequencing. A total of 67,368 effective sequences of the 16S rRNA gene with V1–V3 regions were obtained from samples collected from the front section, rear section, and sludge of the biofilter. Using a 3% cut‐off level and sufficient sequencing depth, a total of 5,185 operational taxonomic units (OTUs) were identified in these sequences across all samples. However, a low shared richness of 570 OTUs (11.0% of the reads) was found in all samples, indicating a high diversity of bacterial profiles even in a single biofilter. Based on the SILVA database classifier of phylogenetic taxa, Proteobacteria (average, 35.6%) and Bacteroidetes (average, 30.7%) were found to be the predominant species in all samples, followed by Nitrospirae (6.0%) in the front section, Acidobacteria (7.9%) in the rear section, and Planctomycetes (9.7%) in the sludge. Overall, 404 genera were assigned to all samples. But among the 10 most common genera, only Nitrospira, Owenweeksia, and Marinicella were found in all samples. The results of the phylogenetic analysis suggest that the nitrifying groups of ammonia‐oxidizing bacteria belong to Nitrosomonas clusters, and the nitrite‐oxidizing bacteria are related to Nitrospira and Nitrospina clusters. In summary, our results indicate that the RAS fixed‐film biofilter is a highly species‐rich ecosystem. For this reason, a potential precision‐operated strategy to manage the microbial resources in the biological treatment section in an RAS should be adopted, with consideration being given to the peculiarities and requirements of the species being cultured.

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The anaerobic ammonium oxidation (anammox) process, which can simultaneously remove ammonium and nitrite, both toxic to aquatic animals, can be very important to the aquaculture industry. Here, the presence and activity of anammox bacteria in the sediments of four different freshwater aquaculture ponds were investigated by using Illumina-based 16S rRNA gene sequencing, quantitative PCR assays and (15)N stable isotope measurements. Different genera of anammox bacteria were detected in the examined pond sediments, including Candidatus Brocadia, Candidatus Kuenenia and Candidatus Anammoxoglobus, with Candidatus Brocadia being the dominant anammox genus. Quantitative PCR of hydrazine synthase genes showed that the abundance of anammox bacteria ranged from 5.6 × 10(4) to 2.1 × 10(5) copies g(-1) sediment in the examined ponds. The potential anammox rates ranged between 3.7 and 19.4 nmol N2 g(-1) sediment day(-1), and the potential denitrification rates varied from 107.1 to 300.3 nmol N2 g(-1) sediment day(-1). The anammox process contributed 1.2-15.3% to sediment dinitrogen gas production, while the remainder would be due to denitrification. It is estimated that a total loss of 2.1-10.9 g N m(-2) per year could be attributed to the anammox process in the examined ponds, suggesting that this process could contribute to nitrogen removal in freshwater aquaculture ponds.

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