Deregulation of Ribosome Biogenesis in Nitrite-Oxidizing Bacteria Leads to Nitrite Accumulation

Nitrite (NO₂^-) accumulation caused by nitrite-oxidizing bacteria (NOB) inhibition in nitrification is a double-edged sword, i.e., a disaster in aquatic environments but a hope for innovating nitrogen removal technology in wastewater treatment. However, little information is available regarding the molecular mechanism of NOB inhibition at the cellular level. Herein, we investigate the response of NOB inhibition on NO₂^- accumulation established by a side-stream free ammonia treatment unit in a nitrifying reactor using integrated metagenomics and metaproteomics. Results showed that compared with the baseline, the relative abundance and activity of NOB in the experimental stage decreased by 91.64 and 68.66%, respectively, directly resulting in a NO₂^- accumulation rate of 88%. Moreover, RNA polymerase, translation factors, and aa-tRNA ligase were significantly downregulated, indicating that protein synthesis in NOB was interfered during NO₂^- accumulation. Further investigations showed that ribosomal proteins and GTPases, responsible for bindings between either ribosomal proteins and rRNA or ribosome subunits, were remarkably downregulated. This suggests that ribosome biogenesis was severely disrupted, which might be the key reason for the inhibited protein synthesis. Our findings fill a knowledge gap regarding the underlying mechanisms of NO₂^- accumulation, which would be beneficial for regulating the accumulation of NO₂^- in aquatic environments and engineered systems.