Denitrification Response Patterns during the Transition to Anoxic Respiration and Posttranscriptional Effects of Suboptimal pH on Nitrogen Oxide Reductase in Paracoccus denitrificans

Abstract

ABSTRACT Denitrification in soil is a major source of atmospheric N 2 O. Soil pH appears to exert a strong control on the N 2 O/N 2 product ratio (high ratios at low pH), but the reasons for this are not well understood. To explore the possible mechanisms involved, we conducted an in-depth investigation of the regulation of denitrification in the model organism Paracoccus denitrificans during transition to anoxia both at pH 7 and when challenged with pHs ranging from 6 to 7.5. The kinetics of gas transformations (O 2 , NO, N 2 O, and N 2 ) were monitored using a robotic incubation system. Combined with quantification of gene transcription, this yields high-resolution data for direct response patterns to single factors. P. denitrificans demonstrated robustly balanced transitions from O 2 to nitric oxide-based respiration, with NO concentrations in the low nanomolar range and marginal N 2 O production at an optimal pH of 7. Transcription of nosZ (encoding N 2 O reductase) preceded that of nirS and norB (encoding nitrite and NO reductase, respectively) by 5 to 7 h, which was confirmed by observed reduction of externally supplied N 2 O. Reduction of N 2 O was severely inhibited by suboptimal pH. The relative transcription rates of nosZ versus nirS and norB were unaffected by pH, and low pH had a moderate effect on the N 2 O reductase activity in cells with a denitrification proteome assembled at pH 7. We thus concluded that the inhibition occurred during protein synthesis/assembly rather than transcription. The study shed new light on the regulation of the environmentally essential N 2 O reductase and the important role of pH in N 2 O emission.