Bayesian simulation of ammonium oxidation in microcosm experiments: Modeling code and data

This repository contains source code and data to simulate microcosm experiments with a nitrifying community from streambed sediments. The publication accompanies the manuscript Linking abundance and activity of ammonia-oxidizing bacteria and archaea in an agriculturally impacted first-order stream.

The reaction model describes the conversion of ammonium to nitrate, and the growth of ammonia-oxidizing archaea and bacteria in incubations of streambed sediments. It simulates different experimental conditions with or without the amendment of ammonium as substrate and two nitrification inhibitors (acetylene and 1-octyne). Model parameters are inferred with a Bayesian modeling framework that accounts for uncertainty of parameters and data, using experimental data from microcosm incubations.

The source code is written in Python, using the library PyMC for parameter estimation. Experimental data (ammonium and nitrate concentrations, qPCR data of amoA and 16S rRNA genes) are included in the upload, as well as the simulation results and posterior parameter samples.