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Denitrifying bacteria accumulateNO  2  −, NO, and N 2 O, the amounts depending on transcriptional regulation of core denitrification genes in response to O 2 -limiting conditions. The genes include  nar ,  nir ,  nor  and  nosZ , encodingNO  3  −-,NO  2  −-, NO- and N 2 O reductase, respectively. We previously constructed a dynamic model to simulate growth and respiration in batch cultures of  Paracoccus denitrificans . The observed denitrification kinetics were adequately simulated by assuming a stochastic initiation of  nir -transcription in each cell with an extremely low probability (0.5% h -1 ), leading to product- and substrate-induced transcription of  nir  and  nor , respectively, via NO. Thus, the model predicted cell diversification: after O 2  depletion, only a small fraction was able to grow by reducingNO  2  −. Here we have extended the model to simulate batch cultivation withNO  3  −, i.e.,NO  2  −, NO, N 2 O, and N 2  kinetics, measured in a novel experiment including frequent measurements ofNO  2  −.  Pa .  denitrificans  reduced practically allNO  3  −toNO  2  −before initiating gas production. TheNO  2  −production is adequately simulated by assuming stochastic  nar -transcription, as that for  nirS , but with a higher probability (0.035 h -1 ) and initiating at a higher O 2  concentration. Our model assumes that all cells express  nosZ , thus predicting that a majority of cells have only N 2 O-reductase (A), while a minority (B) hasNO  2  −-, NO- and N 2 O-reductase. Population B has a higher cell-specific respiration rate than A because the latter can only use N 2 O produced by B. Thus, the ratioB  Ais low immediately after O 2  depletion, but increases throughout the anoxic phase because B grows faster than A. As a result, the model predicts initially low but gradually increasing N 2 O concentration throughout the anoxic phase, as observed. The modelled cell diversification neatly explains the observed denitrification kinetics and transient intermediate accumulations. The result has major implications for understanding the relationship between genotype and phenotype in denitrification research.

plos computational biology/plos computational biology

Transient Accumulation of NO2- and N2O during Denitrification Explained by Assuming Cell Diversification by Stochastic Transcription of Denitrification Genes