Exploring the ecological niche of comammox Nitrospira by in-situ enrichment within mainstream nitrification systems

Complete-ammonia-oxidization bacteria (Comammox Nitrospira) hold promising potential for reducing carbon footprint in mainstream wastewater treatment. However, the inadequate understanding of comammox Nitrospira within wastewater systems has greatly hindered the utilization of these novel microbial resources. This study explored the ecological niche of comammox Nitrospira within mainstream nitrification systems by enriching them under varied operational conditions. The joint analysis of multiple linear regression and random forest model have identified in-situ ammonium concentration and pH as the two most important parameters influencing the growth of comammox Nitrospira, followed by nitrogen loading rate, nitrogen source type, and dissolved oxygen (DO). Meanwhile, the ecological niche preference of comammox Nitrospira was revealed. The optimal ranges of in-situ ammonium concentration and pH for comammox Nitrospira was found below 0.5 mg NH₄⁺-N/L and 6.5-7.5, respectively, indicating that low free ammonia conditions favor their growth. Furthermore, comammox Nitrospira exhibited a competitive advantage over Nitrosomonas under weakly acidic pH (6.0-6.5), and adapted to DO fluctuations by interspecies shifts, whereas Nitrosomonas preferred relatively high DO (1.5-2 mg O₂/L). Comparative genomics further confirmed the above niche differentiation of two groups from reconstructed comammox Nitrospira and Nitrosomonas genomes. Overall, these findings provide guidance for the application of comammox process in wastewater treatment, thereby supporting the transition of mainstream nitrification process toward a more sustainable and energy-efficient pathway.