The physiological genetics of denitrifying bacteria

The genetics of denitrification is a relatively unexplored area that has great promise. Species of Pseudomonas are probably best suited for study because they are widely found among natural denitrifying populations and are quite readily amenable to genetic analysis. The techniques for mutagenesis and for the exchange of chromosomal genes to characterize mutant strains have been well-developed in P. aeruginosa and are being developed in P. stutzeri. Mutants defective in the denitrification of nitrate, nitrite, and nitrous oxide are now available and will aid in describing the catalytic and regulatory elements of the denitrification pathway.     

Monitoring microaerobic denitrification of Pseudomonas aeruginosa by online NAD(P)H fluorescence

Defined as the transition conditions in which the organism(s) performs simultaneous aerobic and anaerobic respiration or fermentation, microaerobic conditions are commonly present in the nature. Microaerobic metabolism of microorganisms is however poorly characterized. Being extremely sensitive to the change in cellular electron-accepting mechanisms, NAD(P)H fluorescence provides a useful ways for online monitoring of microaerobic metabolism. Its application to studies of microbial nitrate respiration and particularly, denitrification of Pseudomonas aeruginosa is reviewed here, centering on four topics: (1) online monitoring of anaerobic nitrate respiration by NAD(P)H fluorescence, (2) effects of denitrification on P. aeruginosa phenotypes, (3) microaerobic denitrification of P. aeruginosa in continuous culture, and (4) correlation between NAD(P)H fluorescence and denitrification-to-respiration ratio. Online NAD(P)H fluorescence is shown to sensitively detect the changes of cellular metabolism. For example, it revealed the intermediate nitrite accumulation in C-limited Escherichia coli performing anaerobic nitrate respiration via dissimilative ammonification, by exhibiting two-stage profiles with intriguing fluorescence oscillation. When applied to continuous culture studies of P. aeruginosa (ATCC 9027), the online fluorescence helped to identify that the bacterium conducted denitrification even at DO > 1 mg/l. In addition, the fluorescence profile showed a unique correlation with the fraction of electrons accepted by denitrification (out of all the electrons accepted by aerobic and anaerobic respiration). The applicability of online NAD(P)H fluorescence in monitoring and quantitatively describing the sensitive microaerobic state of microorganisms is clearly demonstrated.     

Comparison of dentrification by Paracoccus denitrificans, Pseudomonas stutzeri and Pseudomonas aeruginosa.

The course of denitrification of nitrate, nitrite and both compounds together by static cultures of Paracoccus denitrificans, Pseudomonas stutzeri and Pseudomonas aeruginosa was studied. These strains represent three different types of denitrification: 1. reduction of nitrate to gaseous nitrogen without accumulation of nitrite (P. denitrificans); 2. partial accumulation of nitrite in growing cultures during reduction of nitrate to gaseous nitrogen (P. aeruginosa) and 3. two-phase denitrification that includes reduction of nitrates at the very beginning of the process, and then, after depletion of the former, the reduction of nitrates to gaseous nitrogen (P. stutzeri). These observations differ from the results reported in the literature and possible reasons are discussed.     

Monitoring microaerobic denitrification of Pseudomonas aeruginosa by online NAD(P)H fluorescence

Defined as the transition conditions in which the organism(s) performs simultaneous aerobic and anaerobic respiration or fermentation, microaerobic conditions are commonly present in the nature. Microaerobic metabolism of microorganisms is however poorly characterized. Being extremely sensitive to the change in cellular electron-accepting mechanisms, NAD(P)H fluorescence provides a useful ways for online monitoring of microaerobic metabolism. Its application to studies of microbial nitrate respiration and particularly, denitrification of Pseudomonas aeruginosa is reviewed here, centering on four topics: (1) online monitoring of anaerobic nitrate respiration by NAD(P)H fluorescence, (2) effects of denitrification on P. aeruginosa phenotypes, (3) microaerobic denitrification of P. aeruginosa in continuous culture, and (4) correlation between NAD(P)H fluorescence and denitrification-to-respiration ratio. Online NAD(P)H fluorescence is shown to sensitively detect the changes of cellular metabolism. For example, it revealed the intermediate nitrite accumulation in C-limited Escherichia coli performing anaerobic nitrate respiration via dissimilative ammonification, by exhibiting two-stage profiles with intriguing fluorescence oscillation. When applied to continuous culture studies of P. aeruginosa (ATCC 9027), the online fluorescence helped to identify that the bacterium conducted denitrification even at DO > 1 mg/l. In addition, the fluorescence profile showed a unique correlation with the fraction of electrons accepted by denitrification (out of all the electrons accepted by aerobic and anaerobic respiration). The applicability of online NAD(P)H fluorescence in monitoring and quantitatively describing the sensitive microaerobic state of microorganisms is clearly demonstrated.

     

好氧反硝化微生物学机理与应用研究进展

近年来,关于好氧反硝化过程的研究主要集中在三个方面:分别是好氧反硝化菌株的分离和脱氮性能表征,好氧反硝化微生物的应用潜力分析,以及好氧反硝化过程的机理研究。好氧反硝化菌株分布范围广泛,可从多种环境中分离得到,种属以Pseudomonas sp.、Alcaligenes sp.和Paracoccus sp.为主。好氧反硝化菌株及菌群在实验室条件下表现出优良的耐冷、耐盐特性,并具有可降解毒性有机物及N_2O减排的潜力。关于好氧反硝化过程的机理研究表明,虽然硝酸盐作为电子受体的竞争力比氧气弱,但反硝化作为辅助电子传递途径,可提高产能效率,防止NAD(P)H的过量积累。因此,硝酸盐可与氧气同时参与微生物的新陈代谢,即发生好氧反硝化现象。未来除了继续分离更新更好的好氧反硝化菌株外,应加强对好氧反硝化机理及实际生物强化方面的研究。     

Influence of the Pseudomonas quinolone signal on denitrification in Pseudomonas aeruginosa

Denitrification is a well-studied respiratory system that is also important in the biogeochemical nitrogen cycle. Environmental signals such as oxygen and N-oxides have been demonstrated to regulate denitrification, though how denitrification is regulated in a bacterial community remains obscure. Pseudomonas aeruginosa is a ubiquitous bacterium that controls numerous genes through cell-to-cell signals. The bacterium possesses at least two N-acyl-L-homoserine lactone (AHL) signals. In our previous study, these quorum-sensing signals controlled denitrification in P. aeruginosa. In addition to the AHL signals, a third cell-to-cell communication signal, 2-heptyl-3-hydroxy-4-quinolone, referred to as the Pseudomonas quinolone signal (PQS), has been characterized. In this study, we examined the effect of PQS on denitrification to obtain more insight into the respiratory regulation in a bacterial community. Denitrification in P. aeruginosa was repressed by PQS, which was partially mediated by PqsR and PqsE. Measuring the denitrifying enzyme activities indicated that nitrite reductase activity was increased by PQS, whereas PQS inhibited nitric oxide reductase and the nitrate-respiratory chain activities. This is the first report to demonstrate that PQS influences enzyme activities, suggesting this effect is not specific to P. aeruginosa. Furthermore, when iron was supplied to the PQS-added medium, denitrifying activity was almost restored, indicating that the iron chelating property of PQS affected denitrification. Thus, our data indicate that PQS regulates denitrification primarily through iron chelation. The PQS effect on denitrification was relevant in a condition where oxygen was limited and denitrification was induced, suggesting its role in controlling denitrification where oxygen is present.     

Emerging principles of inorganic nitrogen metabolism in Paracoccus denitrificans and related bacteria

The taxonomy of Paracoccus denitrificans and related bacteria is discussed. Evidence is given which shows that the physiological differences between P. denitrificans and Thiosphaera pantotropha are less fundamental than previously thought. A proposal to consider a species P. pantotropha is mentioned. The properties of the denitrifying enzymes and the genes involved in their formation in P. denitrificans is discussed. The synthesis of the membrane-bound nitrate reductase is regulated by FNR, that of the nitrite- and nitric oxide reductase by NNR. Evidence is given that FNR acts as a redox sensor rather than an oxygen sensor. The occurrence of aerobic denitrification and coupled heterotrophic nitrification-denitrification in the original strain of Thiosphaera pantotropha are explained by a limiting respiratory activity which activates FNR. Aerobic denitrification leads to a lower growth yield and an increase in µmax in batch culture when a limiting respiratory activity is assume d and when excess substrate is present. Coupled heterotrophic nitrification-denitrification gives a smaller increase in µmax and a more drastic reduction in yield. Both processes are thus advantageous to the organism. In a chemostat with limiting substrate these processes are disadvantageous. T. pantotropha has lost the ability for aerobic denitrification during extended cultivation. Possibly the substrate concentration was limiting during extended cultivation giving a selective advantage to variants which have lost these properties. The calculations predict that P. denitrificans should be able to grow chemolithotrophically with hydroxylamine.     

Inhibition of denitrification activity but not of mRNA induction in Paracoccus denitrificans by nitrite at a suboptimal pH

The influence of pH on the denitrification activity of a continuous culture of Paracoccus denitrificans was studied in relation to the presence of nitrite. After a transition from aerobic to anaerobic conditions at the suboptimal pH of 6.8, P. denitrificans was not able to build up a functional denitrification pathway. Nitrite accumulated in the medium as the predominant denitrification product. Although the nitrite reductase gene was induced properly, the enzyme could not be detected at sufficient amounts in the culture. These observations indicate that either translation was somehow inhibited, or once synthesized nitrite reductase was inactivated, possibly by the high concentrations of nitrous acid (HNO₂. Interestingly, when a P. denitrificans culture which was grown to steady-state under anaerobic conditions was then exposed to suboptimal pHs, cells exhibited a reduced overall denitrification activity, but neither nitrite nor any other denitrification intermediate accumulated.     

Comparison between the nitric oxide reductase family and its aerobic relatives,the cytochrome oxidases

The denitrification pathway has been studied in the hyperthermophilic archaeon Pyrobaculum aerophilum. In contrast with Gram-negative bacteria, all four denitrification enzymes are membrane-bound. P. aerophilum is also the only denitrifyer identified so far in which menaquinol is the electron donor to all four denitrification reductases. The NO reductase (NOR) of P. aerophilum belongs to the superfamily of haem-copper oxidases and is of the qNOR (quinol-dependent) type. Three types of NOR have been purified so far: cNOR (cytochrome c/pseudoazurin-dependent), qNOR and qCu(A)NOR (qNOR that contains Cu(A) at the electron entry site). It is proposed that the NORs and the various cytochrome oxidases have evolved by modular evolution, in view of the structure of their electron donor sites. qNOR is further proposed to be the ancestor of all NORs and cytochrome oxidases belonging to the superfamily of haem-copper oxidases.     

Importance of sediment deposition and denitrification for nutrient retention in floodplain wetlands

Questions: Various floodplain communities may differ in their relative abilities to influence water quality through nutrient retention and denitrification. Our main questions were: (1) what is the importance of sediment deposition and denitrification for plant productivity and nutrient retention in floodplains; (2) will rehabilitation of natural floodplain communities (semi‐natural grassland, reedbed, woodland, pond) from agricultural grassland affect nutrient retention? Location: Floodplains of two Rhine distributaries (rivers Ussel and Waal), The Netherlands. Methods: Net sedimentation was measured using mats, denitrification in soil cores by acetylene inhibition and bio‐mass production by clipping above‐ground vegetation in winter and summer. Results: Sediment deposition was a major source of N and P in all floodplain communities. Highest deposition rates were found where water velocity was reduced by vegetation structure (reedbeds) or by a drop in surface elevation (pond). Sediment deposition was not higher in woodlands than in grassland types. Denitrification rates were low in winter but significantly higher in summer. Highest denitrification rates were found in an agricultural grassland (winter and summer) and in the ponds (summer). Plant productivity and nutrient uptake were high in reedbeds, intermediate in agricultural grasslands, ponds and semi‐natural grasslands and very low in woodlands (only understorey). All wetlands were N‐limited, which could be explained by low N:P ratios in sediment. Conclusions: Considering Rhine water quality: only substantial P‐retention is expected because, relative to the annual nutrient loads in the river, the floodplains are important sinks for P, but much less for N. Rehabilitation of agricultural grasslands into ponds or reedbeds will probably be more beneficial for downstream water quality (lower P‐concentrations) than into woodlands or semi‐natural grasslands.     

Nitric oxide and nitrous oxide production and cycling during dissimilatory nitrite reduction by Pseudomonas perfectomarina

The denitrifier Pseudomonas perfectomarina reduced nitrite under conditions of kinetic competition between cells and gas sparging for extracellular dissolved nitric and nitrous oxides, NOaq and N2Oaq, in a chemically defined marine medium. Time courses of nitrite reduction and NOg and N2Og alpha removal were integrated to give NOg and N2Og yields. At high sparging rates, the NOg yield was greater than 50% of nitrite-N reduced, and the yield of NOg + N2Og was approximately 75%. Hence interrupted denitrification yields NOaq and N2Oaq as major products. The yields varied with sparging rates in agreement with a quantitative model of denitrification (Betlach, M. P., and Tiedje, J.M. (1981) Appl. Environ. Microbiol. 42, 1074-1084) that applies simplified Michaelis-Menten kinetics to NO2-----NOaq----N2Oaq----N2. The fit gave an estimate of the maximum scavengeable NOaq yield of 73 +/- 8% of nitrite-N. Thus a minor path independent of NOaq is also required. The fit of the model to data at lower sparging rates, where normal denitrification products predominate, implies that the extracellular NOaq pool yield is independent of gas sparging rate. Thus in P. perfectomarina NOaq and N2Oaq are intermediates, or facilely equilibrate with true intermediates, during complete denitrification. The recovery of most nitrite-N as NO and/or N2O under perturbed conditions is not an artifact of irreversible product removal, but an attribute of denitrification in this species, and most probably it is characteristic of denitrification in other species as well.     

cbb3-Type Cytochrome c Oxidases,Aerobic Respiratory Enzymes,Impact the Anaerobic Life of Pseudomonas aeruginosa PAO1

For bacteria, many studies have focused on the role of respiratory enzymes in energy conservation; however, their effect on cell behavior is poorly understood. Pseudomonas aeruginosa can perform both aerobic respiration and denitrification. Previous studies demonstrated that cbb₃-type cytochrome c oxidases that support aerobic respiration are more highly expressed in P. aeruginosa under anoxic conditions than are other aerobic respiratory enzymes. However, little is known about their role under such conditions. In this study, it was shown that cbb₃ oxidases of P. aeruginosa PAO1 alter anaerobic growth, the denitrification process, and cell morphology under anoxic conditions. Furthermore, biofilm formation was promoted by the cbb₃ oxidases under anoxic conditions. cbb₃ oxidases led to the accumulation of nitric oxide (NO), which is produced during denitrification. Cell elongation induced by NO accumulation was reported to be required for robust biofilm formation of P. aeruginosa PAO1 under anoxic conditions. Our data show that cbb₃ oxidases promote cell elongation by inducing NO accumulation during the denitrification process, which further leads to robust biofilms. Our findings show that cbb₃ oxidases, which have been well studied as aerobic respiratory enzymes, are also involved in denitrification and influence the lifestyle of P. aeruginosa PAO1 under anoxic conditions.     

The influence of an invasive plant on denitrification in an urban wetland

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Impact of drying and re-wetting on N,P and K dynamics in a wetland soil

As increased nutrient availability due to drainage is considered a major cause of eutrophication in wetlands rewetting of drained wetlands is recommended as a restoration measure. The effect of soil drying and rewetting on the contribution of various nutrient release or transformation processes to changed nutrient availability for plants is however weakly understood. We measured effects of soil drying and re-wetting on N mineralization, and denitrification, as well as on release of dissolved organic nitrogen (DON), phosphorus, and potassium in incubated soil cores from a wet meadow in southern Sweden. Additionally, the impact of re-wetting with sulphate-enriched water was studied. Soil drying stimulated N mineralization (3 times higher) and reduced denitrification (5 times lower) compared to continuously wet soil. In the wet cores, denitrification increased to 20 mg N m^–2 d^–1, which was much higher than denitrification measured in the field. In the field, increased inorganic-N availability for plants due to drainage seemed primarily to be caused by increased N mineralization, and less by decreased denitrification. Soil drying also stimulated the release of DON and K, but P release was not affected. Re-wetting of dried soil cores strongly stimulated denitrification (up to 160 mg N m^–2 d^–1), but N mineralization was not significantly decreased, neither were DON or K release. In contrast, the extractable P pool increased upon soil wetting. Re-wetting with sulphate-enriched water had no effect on any of the nutrient release or transformation rates. We conclude that caution is required in re-wetting of drained wetlands, because it may unintendently cause internal eutrophication through an increased P availability for plants.     

The complex effects of the invasive polychaetes Marenzelleria spp. on benthic nutrient dynamics

The effects of the polychaetes Marenzelleria sp. (Polychaeta, Spionidae), nonindigenous, rapidly increasing species in the Baltic Sea, on benthic nutrient fluxes, denitrification and sediment pore water nutrient concentration were studied in laboratory experiments using a flow-through setup with muddy sediment from coastal regions of the Gulf of Finland. In addition, different forms of sediment phosphorus (P), separated by chemical fractionation, were studied in three sediment layers. At a population density corresponding to about half the highest measured in the northern Baltic Sea, Marenzelleria sp. increased the fluxes of P and ammonium to the water column. No effect could be recorded for denitrification. Since the previously dominant species of the area, Monoporeia affinis, can enhance denitrification and lower the amount of dissolved P in the pore water, the replacement of M. affinis with Marenzelleria spp. may lead to increased P flux to the water column and decreased denitrification, further increasing the ammonium flux to the water column. However, sediment reworking by Marenzelleria spp. also oxidizes the surface sediment in the long run, improving its ability to retain P and support nitrification. Therefore, the impact of Marenzelleria spp. on sediment nutrient release may not be as drastic as the initial reactions seen in our experiments suggest.     

Effects of photoperiod on growth of and denitrification by Pseudomonas chlororaphis in the root zone of Glyceria maxima,studied in a gnotobiotic microcosm

The emergent macrophyte Glyceria maxima was subjected to different photoperiods and grown with ammonium or nitrate as nitrogen source in presterilized microcosms with spatially separated root and non-root compartments. The microcosms were inoculated with the denitrifying bacterium Pseudomonas chlororaphis. The effect of the plant and the photoperiod on growth and denitrification by P. chlororaphis was assessed. The plant had a strong positive effect on the growth of the bacteria. The bacterial numbers in the root compartment of the planted microcosms were 19-32 times higher than found in the non-root sediment of the unplanted systems. Lengthening the photoperiod resulted in elevated bacterial numbers due to the higher carbon exudation of the plant. This effect was greater still with the nitrate-fed plants, where additional P. chlororaphis growth could proceed via denitrification, indicating oxygen-limiting conditions in the microcosms. Higher porewater N₂O concentrations in the root compartments as compared to the non-root compartments, which were highest for the long photoperiod, were also indicative of a plant-induced stimulation of denitrification. An effect of a diurnal oxygen release pattern of G. maxima on denitrification could not be detected. The gnotobiotic microcosm used in this study represents a potential system for the study of the behaviour and interactions of important bacterial groups, such as nitrifying and denitrifying bacteria where plant roots drive bacterial activity.     

A Network Biology Approach to Denitrification in Pseudomonas aeruginosa

Pseudomonas aeruginosa is a metabolically flexible member of the Gammaproteobacteria. Under anaerobic conditions and the presence of nitrate, P. aeruginosa can perform (complete) denitrification, a respiratory process of dissimilatory nitrate reduction to nitrogen gas via nitrite (NO₂), nitric oxide (NO) and nitrous oxide (N₂O). This study focuses on understanding the influence of environmental conditions on bacterial denitrification performance, using a mathematical model of a metabolic network in P. aeruginosa. To our knowledge, this is the first mathematical model of denitrification for this bacterium. Analysis of the long-term behavior of the network under changing concentration levels of oxygen (O₂), nitrate (NO₃), and phosphate (PO₄) suggests that PO₄ concentration strongly affects denitrification performance. The model provides three predictions on denitrification activity of P. aeruginosa under various environmental conditions, and these predictions are either experimentally validated or supported by pertinent biological literature. One motivation for this study is to capture the effect of PO₄ on a denitrification metabolic network of P. aeruginosa in order to shed light on mechanisms for greenhouse gas N₂O accumulation during seasonal oxygen depletion in aquatic environments such as Lake Erie (Laurentian Great Lakes, USA). Simulating the microbial production of greenhouse gases in anaerobic aquatic systems such as Lake Erie allows a deeper understanding of the contributing environmental effects that will inform studies on, and remediation strategies for, other hypoxic sites worldwide.     

三江平原典型小叶章湿地土壤硝化反硝化作用与氧化亚氮排放

应用C₂H₂抑制原状土柱培育法研究了三江平原典型小叶章湿地土壤N₂O排放速率及反硝化速率的变化,分析了它们与环境因子的关系,并估算了N₂O排放量及反硝化损失量.结果表明：草甸沼泽土和腐殖质沼泽土N₂O排放速率的变化基本一致,其范围分别为0.020～0.089 kg N·hm^-2·d^-1和0.012～0.033 kg N·hm^-2·d^-1,前者的N₂O排放速率均明显高于后者(平均为1.79±1.07倍),且其差异达到显著水平(P＜0.05);二者反硝化速率的变化并不一致,其范围分别为0.024～0.127 kg N·hm^-2·d^-1和0.021～0.043 kg N·hm^-2·d^-1,前者的反硝化速率一般也要高于后者(平均为1.67±1.56倍),但其差异并未达到显著水平(P＞0.05);硝化作用在前者N₂O排放和氮素损失过程中发挥了重要作用,而反硝化作用则是导致后者N₂O排放和氮素损失的重要过程;氮素物质基础不是影响二者硝化-反硝化作用的重要因素;温度对前者硝化 反硝化作用的影响比后者更为明显,其反硝化速率与5、10和15 cm地温均呈显著正相关(P＜0.05);二者所处湿地水分条件的差异是导致其N₂O排放速率及反硝化速率差异的重要原因.生长季内,前者的N₂O排放量和反硝化损失量分别为5.216 kg N·hm^-2和6.166 kg N·hm^-2,而后者分别为3.196 kg N·hm^-2和4.407 kg N·hm^-2;在二者的反硝化产物中,N₂O/N₂的比率最高,分别为5.49和3.76,表明N₂在后者反硝化产物中所占的比例明显高于前者,说明季节积水条件会导致N₂O/N₂比例降低.     

Denitrification and nitrite reduction: Pseudomonas aeruginosa nitrite-reductase

Present knowledge of the different enzymatic steps of the denitrification chains in various bacteria, particularly Paracoccus denitrificans and Pseudomonas aeruginosa has been briefly reviewed. The question whether nitric oxide (NO), nitrous oxide (N2O) and other nitrogen derivatives are obligatory intermediates has been discussed. The second part is an extensive review of the structure and the function of a key enzyme in denitrification, cytochrome c551-nitrite-oxidoreductase from P. aeruginosa. Recent results on the stoichiometry of nitrite reduction have been discussed.