Kinetic Plasticity of Nitrite-Oxidizing Bacteria Containing Cytoplasmic Nitrite Oxidoreductase

Lee, U.-J.; Gwak, J.-H.; Abiola, C.; Lee, S.; Yoo, J.-S.; Si, O.-J.; Cho, H. J.; Quan, Z.-X.; Kitzinger, K.; Daims, H.; Wagner, M.; Jung, M.-Y.; Rhee, S.-K.

doi:10.1101/2025.07.31.663499

bioRxiv · 10.1101/2025.07.31.663499

Kinetic Plasticity of Nitrite-Oxidizing Bacteria Containing Cytoplasmic Nitrite Oxidoreductase

Lee, U.-J.·Gwak, J.-H.·Abiola, C.·Lee, S.·Yoo, J.-S.·Si, O.-J.·Cho, H. J.·Quan, Z.-X.·Kitzinger, K.·Daims, H.·Wagner, M.·Jung, M.-Y.·Rhee, S.-K.

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Abstract

Nitrite oxidation, the second step of nitrification, is essential to the global nitrogen cycle. Nitrite-oxidizing bacteria (NOB) are classified into two groups based on the cellular localization of their key enzyme nitrite oxidoreductase (NXR): periplasmic (pNXR) and cytoplasmic (cNXR). The use of a cNXR by NOB has been reported to be linked to a lower nitrite affinity and energy efficiency of nitrite oxidation, indicating adaptation to nitrogen-rich environments. In this study, cNXR NOB model strains demonstrated nitrite concentration-dependent shifts in optimal growth pH, a behavior not observed in pNXR NOB. Nitrobacter winogradskyi Nb-255 (cNXR NOB), grown at 1 mM nitrite (pH 7.5), exhibited a high nitrite affinity in terms of apparent Km (25.9 M) and a high specific affinity a{degrees} (440.5 l g cells-1 h-1), both comparable to pNXR NOB in microrespirometry-based kinetic assays. Unexpectedly, cells pre-grown at 10 mM nitrite (pH 7.5) achieved a pNXR-like affinity at pH 5.5 without prior adaptation to acidic conditions. In contrast, pNXR NOB exhibited consistent kinetic behavior across different pH conditions. Kinetic inhibition in the presence of nitrate suggested that this plasticity is driven by a regulated interplay between nitrite uniport and nitrite/nitrate antiporter systems. Our findings indicate that Nitrobacter can dynamically modulate nitrite affinity in response to both nitrite concentration and pH, conferring a flexible adaptation strategy that features traits of both r-and K-strategists across a range of environmental conditions. This adaptive plasticity likely extends to other cNXR-containing NOB in response to fluctuating environmental conditions.

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Lee, U.-J., Gwak, J.-H., Abiola, C., Lee, S., Yoo, J.-S., Si, O.-J., Cho, H. J., Quan, Z.-X., Kitzinger, K., Daims, H., Wagner, M., Jung, M.-Y., Rhee, S.-K.. 2025-07-31. Kinetic Plasticity of Nitrite-Oxidizing Bacteria Containing Cytoplasmic Nitrite Oxidoreductase. https://doi.org/10.1101/2025.07.31.663499

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