Genetic basis for denitrification in Ensifer meliloti
© Torres et al.; licensee BioMed Central Ltd. 2014
Received: 19 February 2014
Accepted: 28 May 2014
Published: 2 June 2014
Denitrification is defined as the dissimilatory reduction of nitrate or nitrite to nitric oxide (NO), nitrous oxide (N2O), or dinitrogen gas (N2). N2O is a powerful atmospheric greenhouse gas and cause of ozone layer depletion. Legume crops might contribute to N2O production by providing nitrogen-rich residues for decomposition or by associating with rhizobia that are able to denitrify under free-living and symbiotic conditions. However, there are limited direct empirical data concerning N2O production by endosymbiotic bacteria associated with legume crops. Analysis of the Ensifer meliloti 1021 genome sequence revealed the presence of the napEFDABC, nirK, norECBQD and nosRZDFYLX denitrification genes. It was recently reported that this bacterium is able to grow using nitrate respiration when cells are incubated with an initial O2 concentration of 2%; however, these cells were unable to use nitrate respiration when initially incubated anoxically. The involvement of the nap, nirK, nor and nos genes in E. meliloti denitrification has not been reported.
E. meliloti nap, nirK and norC mutant strains exhibited defects in their ability to grow using nitrate as a respiratory substrate. However, E meliloti nosZ was not essential for growth under these conditions. The E. meliloti napA, nirK, norC and nosZ genes encode corresponding nitrate, nitrite, nitric oxide and nitrous oxide reductases, respectively. The NorC component of the E. meliloti nitric oxide reductase has been identified as a c-type cytochrome that is 16 kDa in size. Herein, we also show that maximal expression of the E. meliloti napA, nirK, norC and nosZ genes occurred when cells were initially incubated anoxically with nitrate.
The E. meliloti napA, nirK, norC and nosZ genes are involved in nitrate respiration and in the expression of denitrification enzymes in this bacterium. Our findings expand the short list of rhizobia for which denitrification gene function has been demonstrated. The inability of E. meliloti to grow when cells are initially subjected to anoxic conditions is not attributable to defects in the expression of the napA, nirK, norC and nosZ denitrification genes.
Denitrification is the respiratory reduction of nitrate or nitrite to the gaseous products nitric oxide (NO), nitrous oxide (N2O), or dinitrogen (N2). N2O is a powerful greenhouse gas (GHG) that has a 300-fold greater global warming potential than CO2 based on its radiative capacity and could persist for up to 150 years in the atmosphere [IPCC 2007, ]. In bacteria, the denitrification process requires four separate enzymatically catalysed reactions. The first reaction in denitrification is the reduction of nitrate to nitrite, which is catalysed by a membrane-bound nitrate reductase (Nar) or a periplasmic nitrate reductase (Nap) (reviewed in [2–6]). In denitrifying bacteria, the reduction of nitrite to nitric oxide is catalysed by two types of respiratory Nir: the NirS cd 1 nitrite reductase, a homodimeric enzyme with haems c and d 1, and NirK, a copper-containing Nir [7–11]. Then, nitric oxide is reduced to nitrous oxide by three types of nitric oxide reductase (Nor), which are classified based on the nature of their electron donor as cNor, qNor or qCuANor (reviewed in [4, 9, 10, 12]). The final step in denitrification consists of the two-electron reduction of nitrous oxide to dinitrogen gas. This reaction is performed by nitrous oxide reductase (Nos), a copper-containing homodimeric soluble protein located in the periplasmic space (reviewed in [9–11, 13–15]). Bacteria of the order Rhizobiales, collectively referred to as rhizobia, are best known for their ability to establish N2-fixing symbiosis on legume roots and on the stems of some aquatic leguminous plants. In addition to fixing N2, many rhizobia species have enzyme-encoding genes for some or all of the four reductase reactions in denitrification. Several studies have reported that legume crops contribute to N2O production by providing N-rich residues for decomposition  and by associating with some rhizobia that are able to denitrify under free-living and under symbiotic conditions, producing N2O [17–19]. However, soybean endosymbiont Bradyrhizobium japonicum is the only rhizobia species for which it has been demonstrated that the napEDABC, nirK, norCBQD and nosRZDYFLX genes are involved in complete denitrification [17, 19, 20].
Ensifer (formerly Sinorhizobium) meliloti is a rhizobial species that establishes symbiotic N2-fixing associations with plants of the genera Medicago, Melilotus and Trigonella. Genes for the complete denitrification pathway are present in the E. meliloti pSymA megaplasmid [21, 22]. Transcriptomic analyses have shown that the E. meliloti nap, nir, nor and nos genes are induced in response to O2 limitation . Under these conditions, the expression of denitrification genes is coordinated via a two-component regulatory system, FixLJ, and via a transcriptional regulator, FixK . Recent transcriptomic studies demonstrated that denitrification genes (nirK and norC) and other genes related to denitrification (azu1, hemN, nnrU and nnrS) are also induced in response to NO and that the regulatory protein NnrR is involved in the control of this process . In symbiotic association with M. truncatula plants, recent findings have demonstrated that the E. meliloti napA and nirK denitrification genes contribute to nitric oxide production in root nodules . Although the regulation and symbiotic characterisation of E. meliloti denitrification genes is well understood, the roles of these genes in nitrate reduction through denitrification and in the emission of N2O are not known.
Recent results from our group  reported the capability of E. meliloti to use nitrate or nitrite as respiratory substrates when cells were incubated with an initial oxygen concentration of 2%; however, nitrate and nitrite could not be used as respiratory substrates when the cells were initially incubated anoxically. In the present work, functional analyses of the E. meliloti napA, nirK, norC and nosZ genes reveal their involvement in the ability of E. meliloti to grow using nitrate as a respiratory substrate and in the expression of denitrification enzymes.
Nitrate-dependent growth of E. meliloti napA, nirK, norC and nosZ mutants
Wild type; Smr
Meade et al., 1982 
Casse et al., 1979 
napA::mini-Tn5 Smr, Kmr
Pobigaylo et al., 2006 
napC::mini-Tn5; Smr, Kmr
Pobigaylo et al.,
nirK::mini-Tn5; Smr, Kmr
Pobigaylo et al.,
norC::Pl.G1PELR32E8; Smr, Kmr
Becker et al., 2009 
nosZ::mini-Tn5; Smr, Kmr
Pobigaylo et al., 
E. meliloti napA, nirK, norC and nosZ genes encode functional reductases
The methyl viologen-dependent (MV + ) nitrate reductase (MV + -NR), nitrite reductase (MV + -Nir) and nitric oxide reductase (Nor) activities of E. meliloti 1021 (WT) and the napA, nirK , and norC mutant strains incubated in MMN under 2% initial O 2 or anoxic conditions
We also investigated the ability of the E. meliloti nirK and norC mutants to produce nitric oxide. After incubation for 18 h with an initial O2 concentration of 2%, NO production rates were determined in an NO-electrode chamber after adding nitrite to the reaction mixture. A significant decrease in NO production was observed in the nirK mutant compared with the WT strain (0.57 ± 0.19 vs. 202 ± 15 nmol NO · mg protein-1 · min-1, respectively), whereas the norC mutant produced 4.6-fold more NO than the WT cells (943 ± 4.52 vs. 202 ± 15 nmol NO · mg protein-1 · min-1, respectively). The high levels of NO produced by the norC mutant are most likely due to its defect in NO consumption activity. After 18 h of incubation in MMN under an initial O2 concentration of 2%, the norC mutant cells demonstrated NO consumption activity that was practically abolished compared with the activity of WT cells (Table 2); the same results were observed when the norC mutant cells were incubated under initially anoxic conditions.
Identification of E. meliloti NorC
Expression of E. meliloti denitrification genes
We analysed the expression of the E. meliloti napA, nirK, norC and nosZ genes using qRT-PCR analyses. With the exception of nirK expression, which was induced 36-fold by nitrate, the presence of nitrate in the growth medium of cells incubated under an initial O2 concentration of 2% provoked the induction of napA, norC and nosZ expression by 1.5-, 3.6- and 4.2-fold, respectively, compared with the expression observed in the absence of nitrate (Figure 4). When the cells were incubated anoxically from the beginning of culture, the napA, nirK, norC and nosZ genes were induced approximately 4-, 48-, 84- and 32-fold by nitrate compared with the expression levels observed after a 12 h incubation in MM at an initial O2 concentration of 2% (Figure 4). These results indicate that the maximal expression of the E. meliloti napA, nirK, norC and nosZ denitrification genes occurs when the cells are initially incubated anoxically and when nitrate is present in the growth medium.
E. meliloti has been considered a partial denitrifier because of its traditionally reported inability to use nitrate as an electron acceptor for ATP generation and growth under anoxic conditions [18, 33]. Recent results from our group confirmed the inability of E. meliloti to grow via nitrate respiration when cells were initially incubated under anoxic conditions ; however, E. meliloti 1021 was able to use nitrate as a respiratory substrate when cells were initially incubated with 2% O2 in the headspace . Under these conditions, O2 was consumed after 6 h of incubation, as we demonstrated in the present manuscript. In this work, we demonstrated that E. meliloti nap genes are involved in E. meliloti nitrate-dependent growth and that nitrite derived from nitrate reduction is produced by Nap. The low levels of NR activity observed in the napA mutant explain the growth defect and the inability of this strain to produce nitrite in cells incubated in MMN with 2% initial O2. The majority of the most well-characterised denitrifying bacteria use the membrane-bound nitrate reductase (Nar) to catalyse the first step of denitrification. In contrast to Nar, which has a respiratory function, Nap systems demonstrate a range of physiological functions, including the disposal of reducing equivalents during aerobic growth on reduced carbon substrates or anaerobic nitrate respiration [2–6]. Our results support the proposed role of Nap in nitrate respiration. Some rhizobial species, such as Pseudomonas sp. G179 (Rhizobium galegae) and Bradyrhizobium japonicum, could express nap genes under anaerobic conditions, and the disruption of these genes is lethal for growth under denitrifying conditions [32, 34].
Whereas the deletion of nosZ did not have a significant effect on the ability of E. meliloti to respire nitrate and increase growth yield, the nirK and norC mutants exhibited clear defects in nitrate-dependent growth, most likely because of the toxicity of the intermediates nitrite and nitric oxide, respectively. Nitrite or NO were accumulated by the nirK and norC mutants, respectively, because of the strong defects in Nir and Nor activities observed in these mutants compared with WT levels. Similar phenotypes for nirK and norC mutants were reported for B. japonicum[35, 36] and Rhizobium etli. The increased levels of N2O accumulated by the nosZ mutant relative to the WT cells indicated that this gene is involved in nitrous oxide reduction in E. meliloti. Similar observations were noted with a B. japonicum nosZ mutant . In addition to demonstrate the involvement of the E. meliloti napA, nirK, norC and nosZ genes in nitrate, nitrite, nitric oxide and nitrous oxide reduction, respectively, we have identified the NorC subunit of nitric oxide reductase as a cytochrome c that is approximately 16 kDa in size.
Growth experiments in this study and in previous studies  clearly demonstrated that E. meliloti utilises nitrate-dependent growth when transitioning to anoxic conditions occurs when cells are incubated under an initial O2 concentration of 2%; however, nitrate-dependent growth does not occur when cells are subjected to anoxic conditions starting at the beginning of the incubation period. To understand the differential responses of E. meliloti denitrification capability to these different anoxically induced conditions, we investigated the ability of E. meliloti to express the denitrification genes in cells incubated under 2% initial O2 compared with cells initially subjected to anoxic conditions. Despite the inability of E. meliloti to grow, we demonstrated that the napA, nirK, norC and nosZ denitrification genes were fully induced in cells initially subjected to anoxia and in the presence of nitrate. Furthermore, denitrification enzymes are active in cells initially incubated under anoxic conditions; we were able to detect significant MV+-NR, MV+-NiR and Nor activity levels and N2O production under these conditions. In contrast, the protein levels corresponding to NorC and the FixP and FixO components of the high affinity cbb 3 oxidase were very weak after incubation of the cells under anoxic conditions starting at the beginning of the incubation period. The latter observations might explain the limited nitrate-dependent growth capacity of E. meliloti when anoxic conditions are induced starting at the beginning of the growth period. Under these conditions, cells would be trapped, without energy, and they would be unable to produce the proteins required to cope with the oxygen-limiting conditions, most likely because of the lack of energy. Supporting this hypothesis, it was reported in Pseudomonas sp. G59 that the formation of nitrate reductase and nitrous oxide reductase did not occur under aerobic or anaerobic conditions; however, nitrate reductase and nitrous oxide reductase were produced under microaerobic incubation . The latter study suggests that dependence on microaerobiosis for the formation of these reductases was attributable to an inability to produce energy anaerobically until these anaerobic respiratory enzymes formed . Recent studies have shown that the soil bacterium Agrobacterium tumefaciens is unable to maintain balanced expression of denitrification genes if oxygen depletion occurs too quickly [40, 41]. Similarly, the soil bacterium P. denitrificans appears unable to effectively switch from oxic to anoxic respiration, leaving a large fraction of the cell population in anoxia without a chance to express the denitrification proteome . As suggested by Nadeem and co-workers , “microaerobic” denitrification is an essential trait for securing an efficient transition to anaerobic denitrification. Considering that B. japonicum, which is able to grow under anoxic nitrate-respiring conditions, is a slow-growth bacterium and E. meliloti is a fast-growth bacterium, the transition from oxic to anoxic metabolism might be different in these species. Supporting this suggestion, we observed that B. japonicum cells are able to express the FixO and FixP subunits of the cbb 3 oxidase under anoxic conditions (E. Bueno, personal communication). However, as shown in this work, E. meliloti does not express the FixO and FixP proteins under anoxic conditions. A lack of the energy necessary for protein synthesis might contribute to the inability of E. meliloti to grow via nitrate respiration when cells are initially incubated anoxically.
The potential impact of denitrification by plant endosymbiotic bacteria on the emission of the greenhouse gas N2O has been poorly investigated. The results of this work demonstrate the involvement of the napA, nirK, norC and nosZ genes in the previously reported ability of E. meliloti to grow via nitrate respiration when cells are subjected initially to 2% O2. Furthermore, the roles of the reductases encoded by napA, nirK, norC and nosZ in nitrite, nitric oxide, N2O production and N2O reduction, respectively, were demonstrated. Thus, our results contribute to the investigation of the unexplored genetic basis for denitrification in the alfalfa endosymbiont E. meliloti. This knowledge will be instrumental in the development of agricultural strategies and management practices for mitigating the release of N2O from legume crops.
Bacterial strains and growth conditions
The bacterial strains used in this study are listed in Table 1. E. meliloti strains were routinely grown aerobically at 30°C in tryptone yeast (TY) complete medium . These cultures were then used as the inocula for subsequent incubation experiments, which were performed in minimal medium (MM)  or in MM medium supplemented with 10 mM KNO3 (MMN); the cells were subjected to two experimental oxygen-limiting conditions. In the first set of experiments, 17-ml serum tubes or 500-ml flasks containing 5 or 200 ml medium, respectively, were sealed with rubber septa, and the headspace atmospheres were replaced with a gas mixture (2% oxygen, 98% argon) at the starting point of the incubation. In the second experiment, the cells were incubated in completely filled 200-ml bottles or 17-ml tubes without added oxygen; these conditions are referred to throughout the manuscript as “anoxic conditions”. Antibiotics were added to the cultures at the following concentrations (μg · ml-1): streptomycin, 200; and kanamycin, 200.
Headspace O2 measurements
After inoculation at an OD600 of 0.2, 1 ml of each culture was placed in a 3-ml thermostatted and magnetically stirred reaction chamber with an O2 electrode (Hansatech, Norkfolk, England). The headspace atmosphere in the chamber was replaced with a gas mixture (2% oxygen, 98% argon) at the starting point of the incubation. The kinetics of oxygen depletion in the chamber were monitored.
Determination of nitrate reductase and nitrite reductase activity
E. meliloti cells were incubated (initial OD600 of approximately 0.15-0.2) under 2% initial oxygen or under anoxic conditions for 18 h in MMN medium. The cells were harvested by centrifugation at 8000 g for 10 min at 4°C, washed with 50 mM Tris/HCl buffer (pH 7.5) until no nitrite was detected and then resuspended in 0.5 ml of the same buffer. The methyl viologen-dependent nitrate reductase (MV+-NR) activity was analysed essentially as described by Delgado and colleagues (2003) . To determine the methyl viologen-dependent nitrite reductase (MV+-Nir) activity, the reaction mixture contained 50 mM Tris/HCl buffer (pH 7.5), 200 μM NaNO2, 400 μM methyl viologen (MV) and 100 μl of cell suspension (0.02–0.04 mg of protein). The reaction was started by the addition of 50 μl of freshly prepared sodium dithionite solution (30 mg · ml-1 in 300 mM NaHCO3). After incubation for 20 min at 30°C, the reaction was stopped by vigorous shaking until the samples lost their blue colour.
E. meliloti cells grown aerobically in 150 ml of TY medium were harvested by centrifugation at 8000 g for 5 min, washed twice with MM, resuspended in 200 ml of MM or MMN at an OD600 of 0.15-0.2 and incubated under 2% initial O2 or anoxic (filled bottles) conditions for 24 h. The cell pellets were resuspended in 3 ml of 50 mM potassium phosphate buffer (pH 7) containing 100 μM 4-(2-aminoethyl) benzene-sulfonyl fluoride hydrochloride (ABSF), RNAse (20 μg · ml-1) and DNAse I (20 μg · ml-1). The cells were disrupted using a French pressure cell at a constant pressure of approximately 1000 psi (SLM Aminco, Jessup, MD, USA). The cell extract was centrifuged at 10,000 g for 20 min to remove the unbroken cells, and the supernatant was centrifuged at 140,000 g for 1 h. The membrane pellet was resuspended in 100 μl of the same buffer. The membrane protein aliquots were diluted in sample buffer [124 mM Tris–HCl, pH 7.0, 20% glycerol, 4.6% sodium dodecyl sulphate (SDS) and 50 mM 2-mercaptoethanol] and incubated at room temperature for 10 min. The membrane proteins were separated at 4°C using 12% SDS-polyacrylamide gel electrophoresis, transferred to a nitrocellulose membrane and stained for haem-dependent peroxidase activity, as described previously , using the SuperSignal chemiluminescence detection kit (Pierce, Thermo Fisher Scientific, IL, USA).
The nitrite concentration was estimated after diazotisation by adding the sulphanilamide/naphthylethylene diamine dihydrochloride reagent . The protein concentration was estimated using the Bradford method (Bio-Rad Laboratories, Richmond, CA) with a standard curve constructed with varying bovine serum albumin concentrations.
Nitric oxide determination
E. meliloti cells were incubated at an OD600 of 0.15-0.2 in MMN under 2% initial O2 or anoxic conditions, harvested and washed similar to the NR or Nir activity assays. Nitric oxide was measured amperometrically with a 2-mm ISONOP electrode APOLO 4000® (World Precision Inst., Sarasota, FL, USA) in a 3-ml thermostatted and magnetically stirred reaction chamber . The membrane-covered electrode was situated at the bottom of the chamber above the stirrer, and the reactants were injected using a Hamilton syringe through a port in the glass stopper. To determine the net production of NO, the 3-ml cuvette was filled with 1.410 ml of 25 mM phosphate buffer (pH 7.4), 250 μl (0.1-0.2 mg protein) of a cellular solution, 100 μl of an enzymatic mix containing glucose oxidase (Aspergillus niger) (80 units/2 ml) and catalase (bovine liver) (500 units/2 ml), 90 μl of 1 M sodium succinate and 100 μl of 320 mM glucose. When oxygen was consumed and a steady base line was observed, 50 μl of 1 M NaNO2 was added to the cuvette to begin the reaction. Each assay was continued until NO was detected. To determine the NO consumption rates, the electrode chamber was filled with 1.655 ml of 25 mM phosphate buffer (pH 7.4), 5 μl (0.02-0.04 mg protein) of a cellular solution, 100 μl of an enzymatic mix containing glucose oxidase (Aspergillus niger) (80 units/2 ml) and catalase (bovine liver) (500 units/2 ml), 90 μl of 1 M sodium succinate and 100 μl of 320 mM glucose. Once a steady base line was observed, 50 μl of a saturated NO solution (1.91 mM at 20°C) was added to the cuvette to start the reaction. Each assay was continued until NO detection dropped to zero (when all of the NO was consumed).
Nitrous oxide determination
E. meliloti cells were incubated in MMN with an initial O2 concentration of 2% in the headspace or anoxically. After 18 or 36 h of incubation, 500-μl gaseous aliquots were taken from the culture headspaces to determine the N2O level. In anoxic cultures (filled tubes), headspace was created by transferring 10 ml of liquid culture into a 20-ml headspace vial (Supelco®). Gas–liquid phase equilibration was performed by incubating the vials for 2 h at 30°C and at 185 rpm. To stop cell growth, 200 μl of 1 mg · ml-1 HgCl2 was added to each vial. The N2O production in liquid cultures was corrected using the dissolved N2O Bunsen solubility coefficient (47.2% at 30°C). Then, N2O was measured with a gas chromatograph type HP 4890D equipped with an electron capture detector (ECD). The column was packed with Porapak Q 80/100 MESH (6 ft), and the carrier gas was N2 at a flow rate of 23 ml/min. The injector, column and detector temperatures were 125, 60 and 375°C, respectively. The N2O peaks were integrated using GC ChemStation Software (Agilent Technologies© 1990–2003). The samples were injected manually through a Hamilton® Gastight syringe. The concentrations of N2O in each sample were calculated from pure nitrous oxide standards (Air Liquid, France).
Quantitative real-time PCR analysis
For immediate stabilisation of the bacterial RNA, the RNAprotect Bacteria Reagent (Qiagen Valencia, CA, USA) was added directly to cells incubated for 12 h in MM or MMN with an initial headspace O2 concentration of 2% or anoxically. Bacterial lysis was performed by resuspension and incubation of the cell pellet in 1 mg/ml lysozyme from chicken egg whites (Sigma-Aldrich) in Tris-EDTA buffer, pH 8.0. The total RNA was isolated using the RNeasy Mini kit (Qiagen). The isolated RNA was subjected to DNase (Qiagen) treatment. The RNA was quantified using a NanoDrop 1000 Spectrophotometer (Thermo Scientific, USA), and intactness was verified by the visual inspection of rRNA bands in electrophoretically separated total RNA . Reverse transcription reactions were performed with 0.8 μg of total RNA per reaction using the First Strand cDNA Synthesis kit for RT-PCR (Roche) with random hexamers. The cDNA synthesis reaction mixture was diluted 50 times with distilled water before use in real-time PCR analysis.
The primers for the PCR reactions were designed using Primer Express v3.0 software (PE Applied Biosystems, Foster City, CA, USA) to have a melting temperature of approximately 57°C to 62°C and to produce a PCR product of approximately 50 to 100 bp. The primer sequences were as follows: napA (forward, 5′-CCGGCTATCGTGGCAAGA-3′; reverse, 5′-CGGGAAGCTGTCGACATTG-3′); nirK (forward, 5′-CCGCGCGACGCAAA-3′; reverse, 5′-TCGAGCGTATCGGCATAGG-3′); norC (forward, 5′-AGCTCACAGAGCAGGAACTGAAC-3′; reverse, 5′-TGATGCGGCTCGTCCATT-3′); and nosZ (forward, 5′-CGAGGATCTCACGCATGGAT-3′; reverse, 5′-GCGGTGCAACCTCCATGT-3′). sMC00128 was used as an internal standard [49, 50] (forward, 5′-ACGAGATCGAGATCGCCATT-3′; reverse, 5′-CGAACGAGGTCTTCAGCATGA-3′).
Each PCR reaction contained 7.5 μl of SYBR Green PCR master mix (PE Applied Biosystems), 5 μl of cDNA and various final concentrations of each primer depending on the studied gene. This concentration was 0.2 μM for norC and sMC00128 and 0.4 μM for napA, nosZ and nirK. The final volume of the PCR reactions was 15 μl. The real-time PCR reactions were performed on a 7300 Real Time PCR System (PE Applied Biosystems). The initial denaturing time of 10 min was followed by 40 PCR cycles consisting of 95°C for 15 s and 60°C for 60 s. A melting curve was run after the PCR cycles. During real-time PCR, the efficiency of nirK gene amplification was approximately equal to that of the housekeeping (internal standard) gene; in this case, the comparative CT method (also called ∆∆CT method) was applied for relative quantification. For the other genes, the amplification efficiencies were different from that of the housekeeping gene; the comparative CT method could not be applied, and it was necessary to use the standard curve method. The data were analysed using the 7300 System Software (PE Applied Biosystems). The gene expression values under different conditions were expressed relative to the values of cells incubated under an initial O2 concentration of 2% in the absence of nitrate.
This work was supported by a Fondo Europeo de Desarrollo Regional (FEDER)-co-financed grant (AGL2010-18607) and grant AGL2009-10371 from the Ministerio de Economía y Competitividad (Spain). Grant S2009/AMB-1511 from the Comunidad de Madrid and support from the Junta de Andalucía to Group BIO-275 are also acknowledged. We thank G. Tortosa for technical support and A. Becker for providing the E. meliloti mutants. MJT was supported by a fellowship from the Consejo Superior de Investigaciones Cientificas I3P Programme.
- Bates BC, Kundzewicz ZW, Wu S, Palutikof JP: Climate Change and Water.Technical Paper of the Intergovernmental Panel on Climate Change. 2008, Geneva, Switzerland: IPCC Secretariat, 210-Google Scholar
- Gonzalez PJ, Correia C, Moura I, Brondino CD, Moura JJ: Bacterial nitrate reductases: molecular and biological aspects of nitrate reduction. J Inorg Biochem. 2006, 100 (5–6): 1015-1023.View ArticlePubMedGoogle Scholar
- Kraft B, Strous M, Tegetmeyer HE: Microbial nitrate respiration–genes, enzymes and environmental distribution. J Biotechnol. 2011, 155 (1): 104-117. 10.1016/j.jbiotec.2010.12.025.View ArticlePubMedGoogle Scholar
- Richardson DJ: Redox complexes of the nitrogen cycle. Nitrogen Cycling in Bacteria. Edited by: Moir JWB. 2011, Norkfolk, UK: Caister Academic Press, 23-39.Google Scholar
- Richardson DJ, Berks BC, Russell DA, Spiro S, Taylor CJ: Functional, biochemical and genetic diversity of prokaryotic nitrate reductases. Cell Mol Life Sci. 2001, 58 (2): 165-178. 10.1007/PL00000845.View ArticlePubMedGoogle Scholar
- Richardson DJ, van Spanning RJ, Ferguson SJ: The prokaryotic nitrate reductases. Biology of the Nitrogen Cycle. Edited by: Bothe H, Ferguson SJ, Newton WE. 2007, The Nerthelands: Elservier, 21-35.View ArticleGoogle Scholar
- Rinaldo S, Arcovito A, Giardina G, Castiglione N, Brunori M, Cutruzzola F: New insights into the activity of Pseudomonas aeruginosa cd1 nitrite reductase. Biochem Soc Trans. 2008, 36 (Pt 6): 1155-1159.View ArticlePubMedGoogle Scholar
- Rinaldo S, Cutruzzola F: Nitrite reductases in denitrification. Biology of the Nitrogen Cycle. Edited by: Bothe H, Ferguson SJ, Newton WE. 2007, The Netherlands: Elservier, 37-56.View ArticleGoogle Scholar
- van Spanning RJ, Delgado MJ, Richardson DJ: The nitrogen cycle: denitrification and its relationship to N2 fixation. Nitrogen Fixation in Agriculture, Forestry, Ecology and the Environment. Edited by: Werner D, Newton WE. 2005, Netherlands: Springer, 277-342.View ArticleGoogle Scholar
- van Spanning RJ, Richardson DJ, Ferguson SJ: Introduction to the biochemistry and molecular biology of denitrification. Biology of the Nitrogen Cycle.3-20. Edited by: Bothe H, Ferguson SJ, Newton WE. 2007, Amsterdam: Elsevier ScienceGoogle Scholar
- van Spanning RJ: Structure, function, regulation and evolution of the nitrite and nitrous oxide reductase: denitrification enzymes with a b-propeller fold. Nitrogen Cycling in Bacteria. Edited by: Moir JWB. 2011, Norkfolk, UK: Caister Academic Press, 135-161.Google Scholar
- de Vries R, Suharti R, Pouvreau LAM: Nitric oxide reductase: structural variations and catalytic mechanism. Biology of the Nitrogen Cycle. Edited by: Bothe H, Ferguson SJ, Newton WE. 2007, The Netherlands: Elsevier, 57-66.View ArticleGoogle Scholar
- Zumft WG, Kroneck PM: Respiratory transformation of nitrous oxide (N2O) to dinitrogen by Bacteria and Archaea. Adv Microb Physiol. 2007, 52: 107-227.View ArticlePubMedGoogle Scholar
- Thomson AJ, Giannopoulos G, Pretty J, Baggs EM, Richardson DJ: Biological sources and sinks of nitrous oxide and strategies to mitigate emissions. Philos Trans R Soc Lond B Biol Sci. 2012, 367 (1593): 1157-1168. 10.1098/rstb.2011.0415.PubMed CentralView ArticlePubMedGoogle Scholar
- Hartsock A, Shapleigh JP: Identification, functional studies, and genomic comparisons of new members of the NnrR regulon in Rhodobacter sphaeroides. J Bacteriol. 2010, 192 (4): 903-911. 10.1128/JB.01026-09.PubMed CentralView ArticlePubMedGoogle Scholar
- Baggs EM, Rees RM, Smith KA, Vinten AJA: Nitrous oxide emission from soils after incorporating crop residues. Soil Use Manag. 2000, 16 (2): 82-87.View ArticleGoogle Scholar
- Bedmar EJ, Robles EF, Delgado MJ: The complete denitrification pathway of the symbiotic, nitrogen-fixing bacterium Bradyrhizobium japonicum. Biochem Soc Trans. 2005, 33 (Pt 1): 141-144.View ArticlePubMedGoogle Scholar
- Garcia-Plazaola JI, Becerril JM, Arrese-Igor C, Hernandez A, Gonzalez-Murua C, Aparicio-Tejo PM: Denitrifying ability of thirteen Rhizobium meliloti strains. Plant Soil. 1993, 149: 43-50. 10.1007/BF00010761.View ArticleGoogle Scholar
- Sánchez C, Bedmar EJ Delgado MJ: Denitrification in Legume-associated endosymbiotic Bacteria. Nitrogen cycling in Bacteria. Edited by: Moir JWB. 2011, Norfolk, UK: Caister Academic Press, 197-210.Google Scholar
- Delgado MJ, Casella S, Bedmar EJ: Denitrification in rhizobia-legume symbiosis. Biology of the Nitrogen Cycle. Edited by: Bothe H, Ferguson SJ, Newton WE. 2007, Amsterdam: Elsevier Science, 83-93.View ArticleGoogle Scholar
- Torres MJ, Rubia MI, Bedmar EJ, Delgado MJ: Denitrification in Sinorhizobium meliloti. Biochem Soc Trans. 2011, 39 (6): 1886-1889. 10.1042/BST20110733.View ArticlePubMedGoogle Scholar
- Barnett MJ, Fisher RF, Jones T, Komp C, Abola AP, Barloy-Hubler F, Bowser L, Capela D, Galibert F, Gouzy J, Gurjal M, Hong A, Huizar L, Hyman RW, Kahn D, Kahn ML, Kalman S, Keating DH, Palm C, Peck MC, Surzycki R, Wells DH, Yeh KC, Davis RW, Federspiel NA, Long SR: Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid. Proc Natl Acad Sci U S A. 2001, 98 (17): 9883-9888. 10.1073/pnas.161294798.PubMed CentralView ArticlePubMedGoogle Scholar
- Becker A, Berges H, Krol E, Bruand C, Ruberg S, Capela D, Lauber E, Meilhoc E, Ampe F, de Bruijn FJ, Fourment J, Francez-Charlot A, Kahn D, Kuster H, Liebe C, Puhler A, Weidner S, Batut J: Global changes in gene expression in Sinorhizobium meliloti 1021 under microoxic and symbiotic conditions. Mol Plant Microbe Interact. 2004, 17 (3): 292-303. 10.1094/MPMI.2004.17.3.292.View ArticlePubMedGoogle Scholar
- Bobik C, Meilhoc E, Batut J: FixJ: a major regulator of the oxygen limitation response and late symbiotic functions of Sinorhizobium meliloti. J Bacteriol. 2006, 188 (13): 4890-4902. 10.1128/JB.00251-06.PubMed CentralView ArticlePubMedGoogle Scholar
- Meilhoc E, Cam Y, Skapski A, Bruand C: The response to nitric oxide of the nitrogen-fixing symbiont Sinorhizobium meliloti. Mol Plant Microbe Interact. 2010, 23 (6): 748-759. 10.1094/MPMI-23-6-0748.View ArticlePubMedGoogle Scholar
- Horchani F, Prevot M, Boscari A, Evangelisti E, Meilhoc E, Bruand C, Raymond P, Boncompagni E, Aschi-Smiti S, Puppo A, Brouquisse R: Both plant and bacterial nitrate reductases contribute to nitric oxide production in Medicago truncatula nitrogen-fixing nodules. Plant Physiol. 2011, 155 (2): 1023-1036. 10.1104/pp.110.166140.PubMed CentralView ArticlePubMedGoogle Scholar
- Meade HM, Long SR, Ruvkun GB, Brown SE, Ausubel FM: Physical and genetic characterization of symbiotic and auxotrophic mutants of Rhizobium meliloti induced by transposon Tn5 mutagenesis. J Bacteriol. 1982, 149 (1): 114-122.PubMed CentralPubMedGoogle Scholar
- Casse F, Boucher C, Julliot JS, Michel M, Dénarié J: Identification and Characterization of Large Plasmids in Rhizobium meliloti using Agarose Gel Electrophoresis. J Gen Microbiol. 1979, 113 (2): 229-242. 10.1099/00221287-113-2-229.View ArticleGoogle Scholar
- Pobigaylo N, Wetter D, Szymczak S, Schiller U, Kurtz S, Meyer F, Nattkemper TW, Becker A: Construction of a large signature-tagged mini-Tn5 transposon library and its application to mutagenesis of Sinorhizobium meliloti. Appl Environ Microbiol. 2006, 72 (6): 4329-4337. 10.1128/AEM.03072-05.PubMed CentralView ArticlePubMedGoogle Scholar
- Becker A, Barnett MJ, Capela D, Dondrup M, Kamp PB, Krol E, Linke B, Ruberg S, Runte K, Schroeder BK, Weidner S, Yurgel SN, Batut J, Long SR, Puhler A, Goesmann A: A portal for rhizobial genomes: RhizoGATE integrates a Sinorhizobium meliloti genome annotation update with postgenome data. J Biotechnol. 2009, 140 (1–2): 45-50.PubMed CentralView ArticlePubMedGoogle Scholar
- Torres MJ, Hidalgo-Garcia A, Bedmar EJ, Delgado MJ: Functional analysis of the copy 1 of the fixNOQP operon of Ensifer meliloti under free-living micro-oxic and symbiotic conditions. J Appl Microbiol. 2013, 114 (6): 1772-1781. 10.1111/jam.12168.View ArticlePubMedGoogle Scholar
- Delgado MJ, Bonnard N, Tresierra-Ayala A, Bedmar EJ, Muller P: The Bradyrhizobium japonicum napEDABC genes encoding the periplasmic nitrate reductase are essential for nitrate respiration. Microbiology. 2003, 149 (Pt 12): 3395-3403.View ArticlePubMedGoogle Scholar
- García-Plazaola JI: Denitrification in lucerne nodules is not involved in nitrite detoxification. Plant Soil. 1996, 182: 149-155. 10.1007/BF00011003.View ArticleGoogle Scholar
- Bedzyk L, Wang T, Ye RW: The periplasmic nitrate reductase in Pseudomonas sp. strain G-179 catalyzes the first step of denitrification. J Bacteriol. 1999, 181 (9): 2802-2806.PubMed CentralPubMedGoogle Scholar
- Velasco L, Mesa S, Delgado MJ, Bedmar EJ: Characterization of the nirK gene encoding the respiratory, Cu-containing nitrite reductase of Bradyrhizobium japonicum. Biochim Biophys Acta. 2001, 1521 (1–3): 130-134.View ArticlePubMedGoogle Scholar
- Mesa S, Velasco L, Manzanera ME, Delgado MJ, Bedmar EJ: Characterization of the norCBQD genes, encoding nitric oxide reductase, in the nitrogen fixing bacterium Bradyrhizobium japonicum. Microbiology. 2002, 148 (Pt 11): 3553-3560.View ArticlePubMedGoogle Scholar
- Gomez-Hernandez N, Reyes-Gonzalez A, Sanchez C, Mora Y, Delgado MJ, Girard L: Regulation and symbiotic role of nirK and norC expression in Rhizobium etli. Mol Plant Microbe Interact. 2011, 24 (2): 233-245. 10.1094/MPMI-07-10-0173.View ArticlePubMedGoogle Scholar
- Velasco L, Mesa S, Xu CA, Delgado MJ, Bedmar EJ: Molecular characterization of nosRZDFYLX genes coding for denitrifying nitrous oxide reductase of Bradyrhizobium japonicum. Antonie Van Leeuwenhoek. 2004, 85 (3): 229-235.View ArticlePubMedGoogle Scholar
- Aida T, Hata S, Kusunoki H: Temporary low oxygen conditions for the formation of nitrate reductase and nitrous oxide reductase by denitrifying Pseudomonas sp. G59. Can J Microbiol. 1986, 32 (7): 543-547. 10.1139/m86-101.View ArticlePubMedGoogle Scholar
- Bergaust L, Shapleigh J, Frostegard A, Bakken L: Transcription and activities of NOx reductases in Agrobacterium tumefaciens: the influence of nitrate, nitrite and oxygen availability. Environ Microbiol. 2008, 10 (11): 3070-3081. 10.1111/j.1462-2920.2007.01557.x.View ArticlePubMedGoogle Scholar
- Bergaust L, Mao Y, Bakken LR, Frostegard A: Denitrification response patterns during the transition to anoxic respiration and posttranscriptional effects of suboptimal pH on nitrous oxide reductase in Paracoccus denitrificans. Appl Environ Microbiol. 2010, 76 (19): 6387-6396. 10.1128/AEM.00608-10.PubMed CentralView ArticlePubMedGoogle Scholar
- Nadeem S, Dorsch P, Bakken LR: The significance of early accumulation of nanomolar concentrations of NO as an inducer of denitrification. FEMS Microbiol Ecol. 2013, 83 (3): 672-684. 10.1111/1574-6941.12024.View ArticlePubMedGoogle Scholar
- Beringer JE: R factor transfer in Rhizobium leguminosarum. J Gen Microbiol. 1974, 84 (1): 188-198. 10.1099/00221287-84-1-188.PubMedGoogle Scholar
- Robertsen BK, Aman P, Darvill AG, McNeil M, Albersheim P: The structure of acidic extracellular polysaccharides secreted by Rhizobium leguminosarum and Rhizobium trifolii. Plant Physiol. 1981, 67 (3): 389-400. 10.1104/pp.67.3.389.PubMed CentralView ArticlePubMedGoogle Scholar
- Vargas C, McEwan AG, Downie JA: Detection of c-type cytochromes using enhanced chemiluminescence. Anal Biochem. 1993, 209 (2): 323-326. 10.1006/abio.1993.1127.View ArticlePubMedGoogle Scholar
- Nicholas DJD, Nason A: Determination of nitrate and nitrite. Methods in Enzymology, VOlume III. Edited by: Colowick SP, Kaplan NO. 1957, London: Academic Press, 974-977.Google Scholar
- Zhang X, Broderick M: Amperometric detection of nitric oxide. Mod Asp Immunobiol. 2000, 1 (4): 160-165.Google Scholar
- Sambrook J, Fritsch EF, Maniatics T: Molecular cloning: a laboratory manual. 1989, New York: Cold Spring Harbor Laboratory PressGoogle Scholar
- Glenn SA, Gurich N, Feeney MA, Gonzalez JE: The ExpR/Sin quorum-sensing system controls succinoglycan production in Sinorhizobium meliloti. J Bacteriol. 2007, 189 (19): 7077-7088. 10.1128/JB.00906-07.PubMed CentralView ArticlePubMedGoogle Scholar
- Krol E, Becker A: Global transcriptional analysis of the phosphate starvation response in Sinorhizobium meliloti strains 1021 and 2011. Mol Genet Genomics. 2004, 272 (1): 1-17.View ArticlePubMedGoogle Scholar
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