Copper availability controls niche differentiation between comammox Nitrospira and ammonia-oxidizing bacteria

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Abstract The biological oxidation of ammonia, the first step of nitrification, is central to biological water purification processes for nitrogen removal. For drinking water treatment, particularly sourced from groundwater, low concentrations of available copper often limit the efficiency of nitrification. Copper dosing both enhances nitrification and affects the composition of the nitrifying microbial community. The mechanisms underlying the effect of copper on nitrifying community composition, ammonia oxidation, and subsequent nitrogen removal processes remain unknown. The objective of this study was to confirm the effects of copper availability on the relative abundance of complete (comammox) and canonical ammonia-oxidizing bacteria (AOB) in nitrifying communities within the drinking water treatment plant and to determine differences in their copper transport mechanisms. Comparative metagenomic analysis revealed that, unlike most AOB, many comammox Nitrospira encode PcoB/CopB-type high-affinity copper uptake systems, indicating that they are more competitive in low-copper environments. This niche adaptation was confirmed in laboratory-scale bioreactors, which showed that comammox Nitrospira became dominant under copper-limited conditions, while AOB dominated at high copper concentrations. Furthermore, specific detection of comammox amoA mRNA by catalyzed reporter deposition-fluorescent in situ hybridization confirmed that the transcriptional activity of comammox Nitrospira was higher compared to AOB under copper limitation. Thus, these results suggest that copper availability may play an important role in shaping the dominant ammonia-oxidizing bacterial guild, with potential implications for engineered water treatment processes.

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