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modeling:no_model

Mechanisms of transient nitric oxide and nitrous oxide production in a complex biofilm

by Frank Schreiber, Birte Loeffler, Lubos Polerecky, Marcel MM Kuypers and Dirk de Beer

The ISME Journal advance online publication 11 June 2009; doi: 10.1038/ismej.2009.55 download

Abstract

Nitric oxide (NO) and nitrous oxide (N2O) are formed during N-cycling in complex microbial communities in response to fluctuating molecular oxygen (O2) and nitrite (NO2-) concentrations. Until now, the formation of NO and N2O in microbial communities has been measured with low spatial and temporal resolution, which hampered elucidation of the turnover pathways and their regulation. In this study, we combined microsensor measurements with metabolic modeling to investigate the functional response of a complex biofilm with nitrifying and denitrifying activity to variations in O2 and NO2-. In steady state, NO and N2O formation was detected if ammonium (NH4+) was present under oxic conditions and if NO2- was present under anoxic conditions. Thus, NO and N2O are produced by ammonia-oxidizing bacteria (AOB) under oxic conditions and by heterotrophic denitrifiers under anoxic conditions. NO and N2O formation by AOB occurred at fully oxic conditions if NO2- concentrations were high. Modeling showed that steady-state NO concentrations are controlled by the affinity of NO-consuming processes to NO. Transient accumulation of NO and N2O occurred upon O2 removal from, or NO2- addition to, the medium only if NH4+ was present under oxic conditions or if NO2- was already present under anoxic conditions. This showed that AOB and heterotrophic denitrifiers need to be metabolically active to respond with instantaneous NO and N2O production upon perturbations. Transiently accumulated NO and N2O decreased rapidly after their formation, indicating a direct effect of NO on the metabolism. By fitting model results to measurements, the kinetic relationships in the model were extended with dynamic parameters to predict transient NO release from perturbed ecosystems.

Model

Matlab codes for the model described in this study, together with the corresponding results, are available here. Each entry in the table describes the prevailing conditions, the type of perturbation and the regulation mechanisms implemented in the model run. It also points to the figure in the paper where the modeled results are plotted. The image shows a more detailed output of the model, displaying the concentrations of O2, NO and NO2 as a function of time at depths of -200 (blue), 0 (green), 200 (red) and 400 (cyan) microns in the biofilm (negative = overlying water, 0 = the biofilm surface, positive = inside the biofilm).

To run the model, you need Matlab (tested for version 6 and higher). Download and unzip the tar.gz files listed in the table, and run model_main.m in the main Matlab window. The parameters used in the model are defined in the load_parameters.m file, the rates and metabolic regulation mechanisms are defined in the fnc/FF.m file.

You can modify the model as you wish. If you want to implement new features or have further questions, we would be happy if you let us know.

Authors: Frank Schreiber (f s c h r e i b @ m p i - b r e m e n . d e) & Lubos Polerecky.

modeling/no_model.txt · Last modified: 2013/09/10 15:33 by lpolerec

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