For a while, some of us have had a hangup on the “atmospheric footprint” (N2O) of prokaryotes’ oxidation and reduction of NOx. The following text is a brief narrative of some of our findings, opinions and speculations (cited papers can be found in the publication list)
Ammonia- and nitrite oxidizing prokaryotes were previously thought to be potent sources of N2O emission to the atmosphere, but mounting evidences suggest otherwise. Our studies of cultured ammonia oxidizing bacteria (Jiang and Bakken 1999) demonstrated that only traces (1 per mil) of the oxidized ammonium is released as N2O. Our stable isotope investigations of N2O produced by soil microbial communities (Mørkved et al 2007) confirmed the minor contribution of nitrification for N2O emission, even under oxygen limiting conditions. We acknowledge that N2O flux data in various investigations have suggested a significant role of nitrification to N2O emissions, but only in periods when total fluxes are low. Of course, nitrifying bacteria play an indirect role for the N2O flux by producing NO3- and not the least NO2-. In two recent studies in our group (Bergaust et al 2008, Morley et al 2008), we have found that NO2- is a strong inducer of denitrification under micro-aerobic conditions, and that denitrification in the presence of oxygen is a potent source of N2O due to inhibition of the enzyme N2O reductase (Morley et al 2008, Mao et al 2008).
Thus, we believe that nitrifying bacteria play a key role for N2O production, not by their own production of N2O but by providing NO2- and NO3- for denitrification to take place. To understand the regulation of N2O production at the cellular level, we need to focus on the ecology and regulatory biology of denitrifying prokaryotes!
Denitrifying prokaryotes, their regulatory biology and ecophysiology are the targets of our basic research. Phenotype characteristics are as important for us as the genotype or the phylogeny of the organism. We are convinced that great progress in microbial ecology can be achieved by combining “genomics” with “phenomics”, and that our investigations of denitrifying communities can illustrate this:
We have previously compared denitrifying communities of contrasting soils regarding their kinetics of denitification and N2O reduction under various incubation conditions. We found consistent differences between the communities, and a general congruence with annual N2O fluxes (Holtan Harwig et al. 2000, 2002; Dörsch and Bakken, 2004, Dörsch et al. manuscript in prep). In other words, the N2O fluxes were significantly affected by the phenotypic characteristics of the denitrifying communities. Recently, we have done a complementary genomic investigation of the contrasting communities (PCR-cloning and sequencing of functional denitrification genes nir, nor and nos), which demonstrated profoundly different species composition between the communities (Braker et al, manuscript in prep).
The combination of phenomic and genomic approaches thus provides a sound basis for concluding that species composition of the denitrifying community soils has implications for N2O emission to the atmosphere. Further, the genomic analysis is a basis for hypotheses generation regarding the relative role of different phylogenetic groups.
In theory, this combination of phenotyping and genotyping of denitrifying communities could provide a basis for predictive genomic analyses: the propensity of a soil to emit N2O could be predicted by its genetic fingerprint (TRFLP or DGGE of functional genes). It would be premature, and possibly futile, to deliberately pursue this goal, however. One reason for this is the complicated causal chain from genetic makeup to N2O emission, as revealed in our comparative studies of denitrifying bacteria regarding their translational and post-translational regulation of different steps in denitrification. We do find some congruence between phylogeny and the ability to control the accumulation of NO during oxic/anoxic conditions, but the same is not true for N2O. It appears that N2O reductase activity is not a necessity for being a relatively successful denitrifying prokaryote! Implications for future emissions of N2O form a nitrate-enriched biosphere can be apocalyptic...
