Existing models and understanding of denitrification and N2O emissions from soils and sediments are based on ancient experiments with intact soils and “paradigm strains” such as Paracoccus denitrificans and Pseudomomonas stutzeri. Paradigms persist only as long as their “predictive capacity” or causal structure is not seriously challenged by new new information.
There is mounting evidence that current models are based on assumptions that are bluntly wrong, and that they lack representation of essential regulators. Why has so little of the novel findings in biochemistry and ecology of denitrification emanated into new concepts and models of denitrification?
One reason for this lack of conceptualization is that phenotype studies lag behind the great progress in biochemistry and molecular biology of denitrification. As biochemists have continued to improve their understanding of a few paradigm strains, molecular ecologists have demonstrated that nature is dominated by anything but these paradigm strains. We believe that it is about time to launch “phenomics” in denitrification research. We need rigorous testing of a variety of organisms, preferably organisms that dominate in the environment (rather than those dominating text books).
Phenotype studies of denitrifying bacteria may be rewarding for other reasons as well. Bioinformatic analyses of the functional and regulatory genes have provided a number of hypotheses which need to be tested experimentally with varieties of genotypes.
We are convinced that denitrifying bacteria represents an ideal model system for systems biology approaches in microbiology: there are a limited number of functional genes involved whose coordinated expression during transition from oxic to anoxic conditions must be strictly controlled to avoid toxicity of intermediates. Thus, tight and efficient regulation is necessary for survival. At present, the functional genes and enzymes have been characterized, most regulatory mechanisms are known at least for type strains, but no one has put the nuts and bolts together in a mathematical model to explore the coordinated action in silico.
