Research Article: Low Probability of Initiating nirS Transcription Explains Observed Gas Kinetics and Growth of Bacteria Switching from Aerobic Respiration to Denitrification

Date Published: November 6, 2014

Publisher: Public Library of Science

Author(s): Junaid Hassan, Linda L. Bergaust, I. David Wheat, Lars R. Bakken, Robinson Fulweiler

Abstract: In response to impending anoxic conditions, denitrifying bacteria sustain respiratory metabolism by producing enzymes for reducing nitrogen oxyanions/-oxides (NOx) to N2 (denitrification). Since denitrifying bacteria are non-fermentative, the initial production of denitrification proteome depends on energy from aerobic respiration. Thus, if a cell fails to synthesise a minimum of denitrification proteome before O2 is completely exhausted, it will be unable to produce it later due to energy-limitation. Such entrapment in anoxia is recently claimed to be a major phenomenon in batch cultures of the model organism Paracoccus denitrificans on the basis of measured e−-flow rates to O2 and NOx. Here we constructed a dynamic model and explicitly simulated actual kinetics of recruitment of the cells to denitrification to directly and more accurately estimate the recruited fraction (). Transcription of nirS is pivotal for denitrification, for it triggers a cascade of events leading to the synthesis of a full-fledged denitrification proteome. The model is based on the hypothesis that nirS has a low probability (, h−1) of initial transcription, but once initiated, the transcription is greatly enhanced through positive feedback by NO, resulting in the recruitment of the transcribing cell to denitrification. We assume that the recruitment is initiated as [O2] falls below a critical threshold and terminates (assuming energy-limitation) as [O2] exhausts. With  = 0.005 h−1, the model robustly simulates observed denitrification kinetics for a range of culture conditions. The resulting (fraction of the cells recruited to denitrification) falls within 0.038–0.161. In contrast, if the recruitment of the entire population is assumed, the simulated denitrification kinetics deviate grossly from those observed. The phenomenon can be understood as a ‘bet-hedging strategy’: switching to denitrification is a gain if anoxic spell lasts long but is a waste of energy if anoxia turns out to be a ‘false alarm’.

Partial Text: A complete denitrification pathway includes the dissimilatory reduction of nitrate () through nitrite (), nitric oxide (NO), and nitrous oxide (N2O) to di-nitrogen (N2). Typically, the genes encoding reductases for these nitrogen oxyanions/-oxides (NOx) are not expressed constitutively but only in response to O2 depletion, making denitrification a facultative trait [1]. Hence, during anoxic spells, the process enables denitrifying bacteria to sustain respiratory metabolism, replacing O2 by NOx as the terminal electron (e−) acceptors. Since permanently anoxic environments lack available NOx, denitrification is confined to sites where O2 concentration fluctuates, such as biofilms, surface layers of sediments, and drained soil (which turns anoxic in response to flooding).