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Berlin Brandenburg

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  • 1
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 13 November 2018, Vol.115(46), pp.11820-11825
    Description: When oxygen becomes limiting, denitrifying bacteria must prepare for anaerobic respiration by synthesizing the reductases NAR (NO → NO ), NIR (NO → NO), NOR (2NO → NO), and NOS (NO → N), either or sequentially, to avoid entrapment in anoxia without energy. Minimizing the metabolic burden of this precaution is a plausible fitness trait, and we show that the model denitrifier achieves this by synthesizing NOS in all cells, while only a minority synthesize NIR. Phenotypic diversification with regards to NIR is ascribed to stochastic initiation of gene transcription, which becomes autocatalytic via NO production. Observed gas kinetics suggest that such bet hedging is widespread among denitrifying bacteria. Moreover, in response to oxygenation, preserves NIR in the poles of nongrowing persister cells, ready to switch to anaerobic respiration in response to sudden anoxia. Our findings add dimensions to the regulatory biology of denitrification and identify regulatory traits that decrease NO emissions.
    Keywords: Bet Hedging ; Denitrification ; Ecophysiology ; Nitrous Oxide
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 2
    Language: English
    In: Journal of Bacteriology, June, 2014, Vol.196(11-12), p.2190(21)
    Description: Many denitrifying organisms contain the norEF gene cluster, which codes for two proteins that are thought to be involved in denitrification because they are expressed during the reduction of nitrite and nitric oxide. The products of both genes are predicted to be membrane associated, and the norE product is a member of the cytochrome c oxidase subunit III family. However, the specific role of norEF is unknown. The denitrification phenotypes of Rhodobacter sphaeroides strains with and without norEF genes were studied, and it was found that loss of norEF lowered the rate of denitrification from nitrate and resulted in accumulation of micromolar concentrations of nitric oxide during denitrification from nitrite. norEF appears to have no direct role in the reduction of nitric oxide; however, since deletion of norEF in the wild-type 2.4.3 strain had essentially no influence on the kinetics of potential nitric oxide reduction (Vmax and Ks), as measured by monitoring the depletion of a bolus of nitric oxide injected into anoxic cultures without any other electron acceptors. However, norEF-deficient cells that had undergone a more chronic exposure to micromolar concentrations of nitric oxide showed an ?50% reduction in Vmax but no change in apparent Ks. These results can explain the occurrence of norEF in the 2.4.3 strain of R. sphaeroides, which can reduce nitrate to nitrous oxide, and their absence from strains such as 2.4.1, which likely use nitric oxide reductase to mitigate stress due to episodic exposure to nitric oxide from exogenous sources.
    Keywords: Nitrification -- Research ; Proteobacteria -- Physiological Aspects ; Proteobacteria -- Research
    ISSN: 0021-9193
    Source: Cengage Learning, Inc.
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  • 3
    Language: English
    In: Applied and Environmental Microbiology, 2010, Vol.76(19), p.6387(10)
    Description: The regulation of denitrification is examined in the model organism Paracoccus denitrificans during transition to anoxia both at pH 7 and when challenged with pHs ranging from 6 0t 7.5. The studies have shown that the inhibition has occurred during protein synthesis/assembly rather than transcription and have helped in understanding the regulation of the [N.sub.2]O redustase and the important role of pH in [N.sub.2]O emission.
    Keywords: Denitrification – Analysis ; Ph – Analysis ; Protein Synthesis – Analysis
    ISSN: 0099-2240
    E-ISSN: 10985336
    Source: Cengage Learning, Inc.
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  • 4
    Language: English
    In: Soil Biology and Biochemistry, September 2016, Vol.100, pp.1-8
    Description: Human activities have greatly increased the input of nitrate to natural and managed ecosystems, but the fate of excess soil nitrate is still unclear. Many studies assume that dissimilatory reduction of nitrate to nitrite is an anaerobic process, but this first step of denitrification can occur in some bacteria at oxygen concentrations that are high enough to repress downstream reduction of nitrite to gaseous products. Here, we examine whether dissimilatory reduction of nitrate under aerobic conditions is an additional, underappreciated fate of nitrate in soil. Aerobic nitrate reduction occurred in soils when provided with both nitrate and a carbon source, with the greatest nitrite accumulation in the wetland sites. The addition of a nitrification inhibitor did not significantly reduce aerobic nitrate reduction activity, nor did an assimilation repressor. Average nitrite production in soils with added carbon, nitrate, and nitrification inhibitor ranged from 7.5 to 50% of added N-nitrate in a five-hour incubation. Bacteria capable of aerobic nitrate reduction were readily isolated from these soils, comprising approximately 35% of the isolates retrieved. Sequencing16S rDNA of these isolates revealed both gram-negative and gram-positive bacteria, with the majority being gram-negative proteobacteria. In six of the isolates, onset of nitrate reduction occurred at 45–86% of atmospheric oxygen concentrations. Reduction of nitrate under aerobic and semi-aerobic conditions did not result in significant enhancements in carbon dioxide production or total electron flow rate to electron acceptors. The genomes of these six isolates were sequenced and targeted RT-qPCR revealed a wide diversity of regulatory controls on the nitrate reductase(s). The results suggest that aerobic nitrate reduction can occur in diverse bacteria, have multiple types of physiological controls, and can occur independently of the gas-forming reactions of denitrification. Thus, it is an unappreciated fate of nitrate in soil.
    Keywords: Aerobic Nitrate Reduction ; Bacterial Genome ; Dissimilatory Nitrate Reductase ; Nitrite Production ; Agriculture ; Chemistry
    ISSN: 0038-0717
    E-ISSN: 1879-3428
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  • 5
    In: Philosophical Transactions of the Royal Society B, 2012, Vol.367(1593), pp.1226-1234
    Description: Denitrifying prokaryotes use NO x as terminal electron acceptors in response to oxygen depletion. The process emits a mixture of NO, N 2 O and N 2 , depending on the relative activity of the enzymes catalysing the stepwise reduction of NO 3 − to N 2 O and finally to N 2 . Cultured denitrifying prokaryotes show characteristic transient accumulation of NO 2 − , NO and N 2 O during transition from oxic to anoxic respiration, when tested under standardized conditions, but this character appears unrelated to phylogeny. Thus, although the denitrifying community of soils may differ in their propensity to emit N 2 O, it may be difficult to predict such characteristics by analysis of the community composition. A common feature of strains tested in our laboratory is that the relative amounts of N 2 O produced (N 2 O/(N 2 +N 2 O) product ratio) is correlated with acidity, apparently owing to interference with the assembly of the enzyme N 2 O reductase. The same phenomenon was demonstrated for soils and microbial communities extracted from soils. Liming could be a way to reduce N 2 O emissions, but needs verification by field experiments. More sophisticated ways to reduce emissions may emerge in the future as we learn more about the regulation of denitrification at the cellular level.
    Keywords: Articles
    ISSN: 0962-8436
    E-ISSN: 1471-2970
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  • 6
    Language: English
    In: Applied and Environmental Microbiology, 2010, Vol. 76(24), p.8285
    ISSN: 0099-2240
    ISSN: 00992240
    Source: American Society of Microbiology
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  • 7
    Language: English
    In: Applied and Environmental Microbiology, 2010, Vol. 76(19), p.6387
    ISSN: 0099-2240
    ISSN: 00992240
    Source: American Society of Microbiology
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  • 8
    Language: English
    In: Applied and environmental microbiology, October 2010, Vol.76(19), pp.6387-96
    Description: 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.
    Keywords: Denitrification ; Gene Expression Regulation, Bacterial ; Oxidoreductases -- Biosynthesis ; Paracoccus Denitrificans -- Enzymology
    ISSN: 00992240
    E-ISSN: 1098-5336
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  • 9
    Language: English
    In: Microbiology, March, 2012, Vol.158(3), p.826(9)
    Description: The reductases performing the four steps of denitrification are controlled by a network of transcriptional regulators and ancillary factors responding to intra- and extracellular signals, amongst which are oxygen and N oxides (NO and NO2). Although many components of the regulatory network have been identified, there are gaps in our understanding of their role(s) in controlling the expression of the various reductases, in particular the environmentally important N2O reductase (N2OR). We investigated denitrification phenotypes of Paracoccus denitrificans mutants deficient in: (i) regulatory proteins (three FNR-type transcriptional regulators, NarR, NNR and FnrP, and NirI, which is involved in transcription activation of the structural nir cluster); (ii) functional enzymes (NO reductase and N2OR); or (iii) ancillary factors involved in N2O reduction (NirX and NosX). A robotized incubation system allowed us to closely monitor changes in concentrations of oxygen and all gaseous products during the transition from oxic to anoxic respiration. Strains deficient in NO reductase were able to grow during denitrification, despite reaching micromolar concentrations of NO, but were unable to return to oxic respiration. The FnrP mutant showed linear anoxic growth in a medium with nitrate as the sole NOx, but exponential growth was restored by replacing nitrate with nitrite. We interpret this as nitrite limitation, suggesting dual transcriptional control of respiratory nitrate reductase (NAR) by FnrP and NarR. Mutations in either NirX or NosX did not affect the phenotype, but the double mutant lacked the potential to reduce N2O. Finally, we found that FnrP and NNR are alternative and equally effective inducers of N2OR.
    Keywords: Proteobacteria -- Genetic Aspects ; Proteobacteria -- Research ; Denitrification -- Research ; Oxidoreductases -- Research ; Nitric Oxide -- Research ; Transcription (Genetics) -- Research
    ISSN: 1350-0872
    Source: Cengage Learning, Inc.
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  • 10
    In: Environmental Microbiology, October 2013, Vol.15(10), pp.2816-2828
    Description: Denitrifiers differ in how they handle the transition from oxic to anoxic respiration, with consequences for and emissions. To enable stringent comparisons we defined parameters to describe denitrification regulatory phenotype () based on accumulation of and , oxic/anoxic growth and transcription of functional genes. Eight strains were divided into two distinct types. Four strains were characterized by a rapid, complete onset () of all denitrification genes and no detectable nitrite accumulation. The others showed progressive onset () of the different denitrification genes. The group accumulated nitrite, and no transcription of (encoding nitrite reductase) was detected until all available nitrate (2 mM) was consumed. Addition of a new portion of nitrate to an actively denitrifying culture of a strain () resulted in a transient halt in nitrite reduction, indicating that the electron flow was redirected to nitrate reductase. All eight strains controlled at nano‐molar concentrations, possibly reflecting the importance of strict control for survival. Transient accumulation differed by two orders of magnitude between strains, indicating that control of is less essential. No correlation was seen between phylogeny (based on 16 and functional genes) and .
    Keywords: Denitrification;
    ISSN: 1462-2912
    E-ISSN: 1462-2920
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