Description Details Author(s) References
Estimating microbial parameters
x0: initial microbial biomass
r0: initial microbial activity
mumax: maximum growth rate of microbial community
by fitting kinetic models to microbial respiration data.
Microbial parameters are inferred by comparing the predictions of a microbial growth model to observations. Observations are time series of measured increasing respiration after a soil sample has been amended with substrate for microbial growth.
The microbial model is Equation 5 in Wutzler et al. 2012. It has parameters
x0: initial biomass
r0: initial activity
mumax: maximum growth rate
of the microbial community responding to the applied growth substrate.
When fitting the model in his form, the uncertainty of the model coefficients are meaningful for the inferred microbial parameters.
The model, however, can be simplified to the following equation, here called beta-form:
beta0 + beta1*exp(beta2*x)
Fitting the beta-form is usually faster and sometimes more robust. Hence it is used to compare models to constrain respiration time series to the period of unlimited growth.
Getting the respiration data into correct format: setFactorKinrespData
Confining the time series to the unlimited growth phase: kinrespGrowthphaseExperiment
Fitting the beta parameter form of the kinetic model to respiration data: fitKinrespBetaReplicate
Fitting the microbial paramter form of the kinetic model to respiration data: fitKinrespExperiment
Access the coefficients and confidence intervals of fitted models: coefKinresp.default
respWutzler10
: Example respiration dataset of used in Wutzler et al. 2012
fitKinrespExperiment
: Includes a worked example
Thomas Wutzler
Wutzler, T.; Blagodatsky, S.; Blagodatskaya, E. & Kuzyakov, Y. (2012) Soil microbial biomass and its activity estimated by kinetic respiration analysis - Statistical guidelines. Soil Biology and Biochemistry, 45, 102-112
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