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.