Denitrification versus respiratory ammonification: environmental controls of two competing dissimilatory NO3-/NO2- reduction pathways in Shewanella loihica strain PV-4

Denitrification and respiratory ammonification are two competing, energy-conserving NO3-/NO2- reduction pathways that have major biogeochemical consequences for N retention, plant growth and climate. Batch and continuous culture experiments using Shewanella loihica strain PV-4, a bacterium possessing both the denitrification and respiratory ammonification pathways, revealed factors that determine NO3-/NO2- fate. Denitrification dominated at low carbon-to-nitrogen (C/N) ratios (that is, electron donor-limiting growth conditions), whereas ammonium was the predominant product at high C/N ratios (that is, electron acceptor-limiting growth conditions). pH and temperature also affected NO3-/NO2- fate, and incubation above pH 7.0 and temperatures of 30 degrees C favored ammonium formation. Reverse-transcriptase real-time quantitative PCR analyses correlated the phenotypic observations with nirK and nosZ transcript abundances that decreased up to 1600-fold and 27-fold, respectively, under conditions favoring respiratory ammonification. Of the two nrfA genes encoded on the strain PV-4 genome, nrfA(0844) transcription decreased only when the chemostat reactor received medium with the lowest C/N ratio of 1.5, whereas nrfA(0505) transcription occurred at low levels (<= 3.4 x 10(-2) transcripts per cell) under all growth conditions. At intermediate C/N ratios, denitrification and respiratory ammonification occurred concomitantly, and both nrfA(0844) (5.5 transcripts per cell) and nirK (0.88 transcripts per cell) were transcribed. Recent findings suggest that organisms with both the denitrification and respiratory ammonification pathways are not uncommon in soil and sediment ecosystems, and strain PV-4 offers a tractable experimental system to explore regulation of dissimilatory NO3-/NO2- reduction pathways.