This Auxiliary Material includes five supplementary tables (Table S1-S5), fifteen supplementary figures (Figs. S1-S15) and ten supplementary texts(Text S1-S10). Detailed methods and mathematical techniques are described in the supplementary texts; all the simulated model results in the form of tables and figures are presented in the auxiliary figures and tables. This material presents how the nitrogen biochemical system runs and is regulated over time and how it is responded to external ammonium supply.