In a study published online in Applied and Environmental Microbiology, a team led by Prof. QIU Dongru from Institute of Hydrobiology of the Chinese Academy of Sciences, based on ambient carbon/nitrogen (C/N) ratios, revealed that cyclic AMP receptor protein (CRP)1, which is widely encoded in bacteria, is required for dissimilatory nitrate reduction to ammonium (DNRA) in Shewanella loihica PV-4 strain, while the CRP2 paralogue is required for transcription of the nitrite reductase gene nirK for denitrification. 

Some microbes utilize different dissimilatory nitrate reduction (DNR) pathways, including DNRA and denitrification pathways, for anaerobic respiration in response to ambient C/N ratio changes. However, little is known about the molecular mechanism underlying the choice of two competing DNR pathways.    

Through a series of molecular genetics and analytical chemistry experiments, the researchers found that deletion of crp1 could accelerate the reduction of nitrite to nitric oxide (NO) under both low and high C/N ratios. CRP1 is not required for denitrification and actually suppresses production of NO and nitrous oxide (N₂O) gases. Deletion of either of the NO-forming nitrite reductase genes nirK or crp2 blocked production of NO gas.    

Furthermore, real-time PCR and electrophoretic mobility shift assays (EMSAs) demonstrated that the transcription levels of DNRA-relevant genes such as nap-β (napDABGH), nrfA, and cymA were upregulated by CRP1, while nirK transcription was dependent on CRP2.   

It is clear that both CRP paralogues are involved in the bacterial choice of two competing dissimilatory nitrate reduction pathways, DNRA and denitrification. Sufficient C source leads to the predominance of DNRA for more energy per mol nitrate as electron acceptor and ammonia available for amino acid synthesis, while denitrification is favored for more energy per mol lactate as electron donor and saving C sources for bacterial growth under low C/N ratios.    

Nevertheless, C source/electron donor deficiency may result in an incomplete denitrification process, raising the concern of high levels of N₂O emission from nitrate-rich and C source-poor waters and soils.   

This study sheds light on the understanding of microbe-driven biogeochemistry cycles of N, and provides implications for efficient control of emission of N₂O to the atmosphere from both the hydrosphere and the soil sphere.