The Different Spatial Distribution Patterns of Nitrifying and Denitrifying Microbiome in the Biofilters of the Recirculating Aquaculture System

In this study, the distribution patterns of the nitrifying and denitrifying microbiome in a large-scale biofilter (587.24 m³) in a cold freshwater recirculating aquaculture system (RAS) was investigated. Previous studies have revealed that the water quality, nitrification, and denitrification rates in the front (BFF), middle (BFM), and back (BFB) of this biofilter are different. The results showed the highest diversity of the denitrifying microbiome in the BFB, followed by BFF and BFM, whereas nitrifying microbiome diversity remained consistent across different positions. Two genera, <i>Nitrosomonas</i> and <i>Nitrosospira</i>, dominated the nitrifying microbiome, while <i>Pseudomonas</i>, <i>Thauera</i>, <i>Cupriavidus</i>, <i>Dechloromonas</i>, <i>Azoarcus</i>, and <i>Paracoccus</i> comprised the top six denitrifying genera. Principal coordinate analysis indicated a distinct spatial distribution pattern of the denitrifying microbiome but not the nitrifying microbiome. The genera <i>Pseudomonas</i> and <i>Dechloromonas</i> were the biomarkers of the BFF and BFB, respectively. Redundancy analysis showed that nitrite, nitrate, dissolved oxygen, and soluble reactive phosphorus influenced the functional microbiome distribution pattern. Network correlation analysis identified one nitrifying hub (<i>Nitrosospira</i>) in the BFF, five denitrifying hubs (<i>Aromatoleum</i>, <i>Dechloromonas</i>, <i>Paracoccus</i>, <i>Ruegeria</i>, and <i>Thauera</i>) in the BFM, and three denitrifying hubs (<i>Azoarcus</i>, <i>Magnetospirillum</i>, and <i>Thauera</i>) in the BFB. Exclusively negative correlations were found between hubs and its adjacent nodes in the BFF and BFB. This study demonstrates that habitat can shape the distribution patterns of the nitrifying and denitrifying microbiome in the biofilter of the RAS, with the BFF exhibiting greater benefits for the nitrification process.