Our environmental rationale is that we need to improve our understanding of the biological and ecological control of the emissions of NO and N2O from biosphere to atmosphere. The ultimate scientific goal is to “bridge” from genotype to phenotype, both for single strains and microbial communities.
Denitrification Regulatory Phenotype
We study the phenotypes of denitrifying prokaryotes with special emphasis on their transcriptional and post transcriptional regulation of the various enzymes involved in nitrogen redox reactions. We define Denitrification Regulatory Phenotype (DRP) as the characteristic "programmed" response to oxygen depletion. These studies include paradigm strains (such as Paracoccus denitrificans) and suitable mutants, as well as prokaryotes isolated from environmental samples.
Genotype-phenotype / phylogeny / function
The relationship between phylogeny and phenotypic traits within functional groups of prokaryotes is studied, primarily for denitrifying and nitrogen fixing organisms. We find a a variaty of DRP among closely related organisms, with no apparent congruence with phylogeny. Which may be depressing news for molecular ecologist who believe that ecological functions can be predicted by community DNA analyses.
We also work along the same lines with microbial assemblages (communities) from environmental samples, identifying their patterns of response to environmental parameters (i.e. community phenotyping) as well as their genetic makeup (genotyping). This study of communities is also used to test the ecological relevance of phenomena observed in model/paradigm strains. For instance,we found compelling evidence for a post transcriptional inhibitory effect of low pH on the expression of N2O reductase in Paracoccus denitrificans, and recent experiments with bacteria extracted from soils have demonstrated that soil bacteria are line P. denitrficans.
Enzyme kinetics in vivo, and modellingModelling is routinely integrated with our experimental studies of the regulation and kinetics of oxic and anoxic respiration. This has helped us to generate hypotheses and design experiment to test them. Enzyme kinetics determined in vitro are useless, and this forced us to design experiments to determine enzyme kinetic parameters in vivo.