A central small RNA regulatory circuit controlling bacterial denitrification and N₂O emissions

Global atmospheric loading of the climate active gas nitrous oxide (N₂O) continues to increase. A significant proportion of anthropogenic N₂O emissions arise from microbial transformation of nitrogen-based fertilisers during denitrification, making microbial N₂O emissions a key target for greenhouse gas reduction strategies. The genetic, physiological and environmental regulation of microbial mediated N₂O flux is poorly  understood and is therefore a critical knowledge gap in development of successful  mitigation approaches. We have previously mapped the transcriptional landscape of 1 the model soil denitrifying bacterium, Paracoccus denitrificans. Here, we show that a 32 single bacterial sRNA can control the denitrification rate of P. denitrificans by stalling denitrification at nitrite reduction to limit production of downstream pathway intermediates and N₂O emissions. Overexpression of sRNA-29 downregulates nitrite reductase and limits NO and N₂O production by cells. RNA-seq analysis revealed 53 genes are controlled by sRNA-29, one of which is a previously uncharacterised GntR- type transcriptional regulator. Overexpression of this regulator phenocopies sRNA-29 overexpression and allows us propose a model whereby sRNA-29 enhances levels of  the regulator to repress denitrification in appropriate conditions. Our identification of a new regulatory pathway controlling the core denitrification pathway in bacteria highlights the current chasm in knowledge regarding genetic regulation of this pivotal biogeochemical process, which needs to close to support future biological and chemical N₂O mitigation strategies.