Incorporation of Dynamic pH into an Integrative Model of a Nitrification Microcosm Co-Culture of Nitrosomonas Europaea and Nitrobacter Winogradskyi

Understanding coupled biogeochemical systems is important for elucidating anthropogenic environmental impacts. Nitrifying bacteria are fundamental elements of the nitrogen (N) Cycle. N gases production by soils through microbial action can be a significant source of atmospheric NO_x and N₂O. Multi-level genome-scale modeling of N. europaea and N. winogradskyi in a microcosm suggests a key role for NO in the abiotic and biotic chemistry of nitifying systems[1]. Further refinement of the integrative model to incorporate dynamic pH profiling resulted in additional insights into the physiology of N. europaea. Matching the dynamic pH profile of the microcosm required the use of the Euclidean norm for flux distribution minimization during optimization of the genome-scale model component of the integrative model. The requirement for the Euclidean norm suggested that N. europaea in the microcosm operates in a manner that optimizes metabolite channeling[2]. Modeling with the enhanced integrative model also suggested that N. europaea facilitates conversion of ammonium ion to ammonia. A possible mechanism for ammonium conversion is uptake by ammonium transporter (amtB; NE0448) or active membrane-potential-driven mechanisms into a more basic cytoplasm[3].

[1] Mellbye, B.L., Giguere, A., Murthy, G.S., Bottomley, P.J. Sayavedra-Soto, L.A. and Chaplen F. (2018) Genome-scale, constraints-based modeling of nitrogen oxide fluxes during co-culture of Nitrosomonas europaea and Nitrobacter winogradskyi. mSystems 3(3): e00170-17. (Editor’s Pick) Retrieved from http://dx.doi.org/10.1128/mSystems.00170-17

[2] Wu, H.-Q., Cheng, M.-L., Lai, J.-M., Wu, H.-H., Chen, M.-C., Liu, W.-H., Wu, W.-H., Chang, P., M.-H., Huang, C.-Y. H., Tsou, A.-P., Shaio, M.-S., and Wang, F.-S. (2017) Flux balance analysis predicts Warburg-like effects of mouse hepatocyte deficient in miR-122a. PLOS Comput. Biol. 13(7):e1005618. Https://doi.org/10.1371/journal.pcbi.1005618.

[3] Cherif-Zahar, B., Durand, A., Schmidt, I., Hamdaoui, N., Matic, I., Merrick, M, and Matassi, G. (2007) Evolution and functional characterization of the RH50 gene from ammonia-oxidizing bacterium Nitrosomonas europaea. J. Bacteriol. 189(24):9090-2100. Doi:10.1128/JB.01089-07