Energy conservation in Nitrobacter

Abstract The generation of ATP and NADH in total cells of Nitrobacter was measured under aerobic and anaerobic conditions. NADH synthesis was driven by an ATP independent reaction with nitrite or nitric oxide as electron donors. The rate of NADH formation was about 200 times higher, if nitric oxide instead of nitrite served as electron donor. Approximately 2 mol nitric oxide were needed for reduction of 1 mol NAD⁺. Nitrite caused an end-product inhibition of the nitric oxide induced NADH synthesis. ATP was synthesized by NADH oxidation with oxygen and nitrate as terminal electron acceptors.     

Selenate reduction by a Pseudomonas species: a new mode of anaerobic respiration

The high levels of selenium (selenate, selenite) in agricultural drainage water in the San Joaquin Valley of California, which have led to environmental problems, might be lowered if the selenate/selenite could be reduced to elemental insoluble selenium. Two organisms have been newly isolated which do this in anaerobic coculture. One, a strictly anaerobic, Gram-positive rod, reduces selenite to elemental selenium. The other, a Pseudomonas species, was shown to respire selenate to selenite. Cells grown anaerobically in Minimal Medium on acetate plus selenate oxidized 14C-acetate to 14CO2 with concomitant reduction of selenate to selenite and small amounts of elemental selenium.     

Membrane-bound nitrite oxidoreductase of Nitrobacter: evidence for a nitrate reductase system

Nitrite oxidoreductase, the essential enzyme complex of nitrite oxidizing membranes, was isolated from cells of the nitrifying bacterium Nitrobacter hamburgensis. The enzyme system was solubilized and purified in the presence of 0.25% sodium deoxycholate. Nitrite oxidoreductase oxidized nitrite to nitrate in the presence of ferricyanide. The pH optimum was 8.0, and the apparent K_m value for nitrite amounted to 3.6 mM. With reduced methyl-and benzylviologen nitrite oxidoreductase exhibited nitrate reductase activity with an apparent K_m value of 0.9 mM for nitrate. NADH was also a suitable electron donor for nitrate reduction. The pH optimum was 7.0.Treatment with SDS resulted in the dissociation into 3 subunits of 116,000, 65,000 and 32,000. The enzyme complex contained iron, molydbenum, sulfur and copper. A c-type cytochrome was present. Isolated nitrite oxidoreductase is a particle of 95±30 Å in diameter.Abbreviation DOC sodium deoxycholate     

Cleavage of dimethylsulfoniopropionate and reduction of acrylate by Desulfovibrio acrylicus sp. nov.

From anoxic intertidal sediment, a dimethylsulfoniopropionate (DMSP)-cleaving anaerobe (strain W218) was isolated that reduced the acrylate formed to propionate. The bacterium was vibrio- to rod-shaped and motile by means of multiple polar flagella. It reduced sulfate, thiosulfate, and acrylate, and used lactate, fumarate, succinate, malate, pyruvate, ethanol, propanol, glycerol, glycine, serine, alanine, cysteine, hydrogen, and formate as electron donors. Sulfate and acrylate were reduced simultaneously; growth with sulfate was faster than with acrylate. Extracts of cells grown in the presence of DMSP contained high DMSP lyase activities (9.8 U/mg protein). The DNA mol% G+C was 45.1. On the basis of its characteristics and the 16S rRNA gene sequence, strain W218 was assigned to a new Desulfovibrio species for which the name Desulfovibrio acrylicus is proposed. A variety of other sulfate-reducing bacteria (eight of them originating from a marine or saline environment and five from other environments) did not reduce acrylate. Received: 22 March 1996 / Accepted: 8 May 1996     

Detection of genes for membrane-bound nitrate reductase in nitrate-respiring bacteria and in community DNA

A nested PCR primed by four degenerate oligonucleotides was developed for the specific amplification of sequences from the narG gene encoding the membrane-bound nitrate reductase. This approach was used to amplify fragments of the narG gene from five Pseudomonas species previously shown to be able to express the membrane-bound nitrate reductase and from community DNA extracted from a freshwater sediment. Amino acid sequences encoded by the narG fragments were compared to one another, and to the corresponding regions of related enzymes. This comparison indicates that the amplification protocols are specific for their intended targets. Sequences amplified from community DNA were tightly clustered, which may indicate a degree of homogeneity in the sediment community. The PCR primers and amplification protocols described will be useful in future studies of nitrate respiring populations.     

Growth and substrate consumption of Nitrobacter agilis cells immobilized in carrageenan: part 2. Model evaluation

A dynamic model that predicts substrate and biomass concentration profiles across gel beads and from that the overall substrate consumption rate by the gel beads containing growing cells was evaluated with immobilized Nitrobacter agilis cells in an airlift loop reactor with oxygen as the limiting substrate. The model predictions agreed well with the observed oxygen consumption rates at three different liquid phase oxygen concentrations. Image analysis showed that 90% of the immobilized cells after 42 days of cultivation was situated in the outer shells in a film of 140 mum, while the bead radius was about 1 mm. The maximum biomass concentration in the outmost film of 56 mum was 11 kg . m(-3) gel.     

Oxygen uptake activity by Nitrobacter spp. in the presence of metal ions and sulfooxyanions

Abstract Several metal ions inhibited the oxygen uptake activity of Nitrobacter agilis , but their effects on the kinetic parameters of nitrite oxidation were mixed. Growth of Nitrobacter winogradskyi was inhibited by persulfate (>0.1 mM), tetrathionate (>0.5 mM), and trithionate (>5 mM). Oxygen uptake activity was, however, relatively insensitive to persulfate and tetrathionate ions.     

Purification and characterization of ATPase from Nitrobacter winogradskyi

An ATPase was purified from Nitrobacter winogradskyi, and some of its molecular and enzymatic properties were determined. The enzyme was composed of two subunits of 64 and 59 kDa, respectively. The enzyme had its pH optimum at 9.5 and showed a specific activity of 7 units per mg protein. This activity was about 14% and 18% of that of F1-ATPases obtained from Escherichia coli and Sulfolobus acidocaldarius, respectively. The enzyme was 29% and 6% inhibited by 100 microM dicyclohexylcarbodiimide (DCCD) and 100 microM NaN3, respectively. It was not inhibited by 20 mM NaNO3.     

Microbial nitrate respiration--genes, enzymes and environmental distribution

Nitrate is a key node in the network of the assimilatory and respiratory nitrogen pathways. As one of the ‘fixed’ forms of nitrogen, nitrate plays an essential role in both nature and industry. For bacteria, it is both a nitrogen source and an electron acceptor. In agriculture and wastewater treatment, nitrate respiration by microorganisms is an important issue with respect to economics, greenhouse gas emission and public health. Several microbial processes compete for nitrate: denitrification, dissimilatory nitrate reduction to ammonium and anaerobic ammonium oxidation. In this review we provide an up to date overview of the organisms, genes and enzymes involved in nitrate respiration. We also address the molecular detection of these processes in nature. We show that despite rapid progress in the experimental and genomic analyses of pure cultures, knowledge on the mechanism of nitrate reduction in natural ecosystems is still largely lacking.     

Nitrogen fixation and nitrate reduction in the root nodules of legumes

Published data on, and hypotheses regarding the effect of NO⁻₃ on functioning of legume root nodules are reviewed. It is concluded that a short-term reversible effect of NO⁻₃ may act via an increased resistance to O₂ diffusion in nodules; this is coupled to decreased bacteroid respiration. For longer exposures to NO⁻₃ nodule activity is irreversibly lost, but how this relates to carbohydrate deprivation or NO-₂ accumulation is unclear. Complicating factors include denitrification reactions and the interaction of NO⁻₂ with leghaemoglobin.     

The specific functions of menaquinone and demethylmenaquinone in anaerobic respiration with fumarate,dimethylsulfoxide, trimethylamine N-oxide and nitrate by Escherichia coli

The respiratory activities of E. coli with H₂ as donor and with nitrate, fumarate, dimethylsulfoxide (DMSO) or trimethylamine N-oxide (TMAO) as acceptor were measured using the membrane fraction of quinone deficient strains. The specific activities of the membrane fraction lacking naphthoquinones with fumarate, DMSO or TMAO amounted to 2% of those measured with the membrane fraction of the wild-type strain. After incorporation of vitamin K₁ [instead of menaquinone (MK)] into the membrane fraction deficient of naphthoquinones, the activities with fumarate or DMSO were 92% or 17%, respectively, of the activities which could be theoretically achieved. Incorporation of demethylmenaquinone (DMK) did not lead to a stimulation of the activities of the mutant. In contrast, the electron transport activity with TMAO was stimulated by the incorporation of either vitamin K₁ or DMK. Nitrate respiration was fully active in membrane fractions lacking either naphthoquinones or Q, but was 3% of the wild-type activity, when all quinones were missing. Nitrate respiration was stimulated on the incorporation of either vitamin K₁ or Q into the membrane fraction lacking quinones, while the incorporation of DMK was without effect. These results suggest that MK is specifically involved in the electron transport chains catalyzing the reduction of fumarate or DMSO, while either MK or DMK serve as mediators in TMAO reduction. Nitrate respiration requires either Q or MK.Abbreviations DMK demethylmenaquinone - MK menaquinone - Q ubiquinone - DMSO dimethylsulfoxide - TMAO trimethylamine N-oxide - DMS dimethylsulfide - TMA trimethylamine - BV benzylviologen     

Denitrification, nitrate turnover, and aerobic respiration by benthic foraminiferans in the oxygen minimum zone off Chile

Population density, nitrate turnover, and oxygen respiration of benthic foraminiferans were investigated in the oxygen minimum zone (OMZ) off the Chilean coast. Live foraminiferans were found predominantly in the upper 3 mm of the sediment, and the nitrate accumulating species Nonionella cf. stella and Stainforthia sp. dominated with a combined standing stock of 2.0 × 10⁶ Rose Bengal stained specimens m^− 2. The rate of denitrification in cells of N. cf. stella analyzed with nitrous oxide microsensors during acetylene inhibition was 84 ± 33 pmol C individual^− 1 d^− 1. Multiplied with the standing stock of N. cf. stella and Stainforthia sp. this yielded a minimum benthic denitrification rate of 173 µmol N m^− 2 d^− 1 by foraminiferans. Foraminiferal denitrification, which seemed to account for almost all benthic denitrification at the investigated site will be overlooked by most conventional methods measuring benthic denitrification. Compared to the denitrification rates, the potential rates of nitrate accumulation and oxygen respiration by N. cf. stella were an order of magnitude higher (864 pmol N individual^− 1 d^− 1 and 760 ± 87 pmol C individual^− 1 d^− 1, respectively), which seems an adaptation to the infrequent availability of nitrate and oxygen in the sediment surface.     

Anaerobic degradation of 3-halobenzoates by a denitrifying bacterium

A denitrifying bacterium was isolated from a river sediment after enrichment on 3-chlorobenzoate under anoxic, denitrifying conditions. The bacterium, designated strain 3CB-1, degraded 3-chlorobenzoate, 3-bromobenzoate, and 3-iodobenzoate with stoichiometric release of halide under conditions supporting anaerobic growth by denitrification. The 3-halobenzoates and 3-hydroxybenzoate were used as growth substrates with nitrate as the terminal electron acceptor. The doubling time when growing on 3-halobenzoates ranged from 18 to 25 h. On agar plates with 1 mM 3-chlorobenzoate as the sole carbon source and 30 mM nitrate as the electron acceptor, strain 3CB-1 formed small colonies (1–2 mm in diameter) in 2 to 3 weeks. Anaerobic degradation of both 3-chlorobenzoate and 3-hydroxybenzoate was dependent on nitrate as an electron acceptor and resulted in nitrate reduction corresponding to the stoichiometric values for complete oxidation of the substrate to CO₂. 3-Chlorobenzoate was not degraded in the presence of oxygen. 3-Bromobenzoate and 3-iodobenzoate were also degraded under denitrifying conditions with stoichiometric release of halide, but 3-fluorobenzoate was not utilized by the bacterium. Utilization of 3-chlorobenzoate was inducible, while synthesis of enzymes for 3-hydroxybenzoate degradation was constitutively low, but inducible. Degradation was specific to the position of the halogen substituent, and strain 3CB-1 did not utilize 2- or 4-chlorobenzoate. Received: 6 November 1998 / Accepted: 19 January 1999     

Close genetic relationship between Nitrobacter hamburgensis nitrite oxidoreductase and Escherichia coli nitrate reductases

The nitrite oxidoreductase (NOR) from the facultative nitrite-oxidizing bacterium Nitrobacter hamburgensis X14 was investigated genetically. In order to develop a probe for the gene norB, the N-terminal amino acid sequence of the NOR -subunit (NorB) was determined. Based on that amino acid sequence, an oligo-nucleotide was derived that was used for the identification and cloning of gene norB. Sequence analysis of DNA fragments revealed three adjacent open reading frames in the order norA, norX, norB. The DNA sequences of norX and norB represented complete genes while the open reading frame of norA was truncated by the cloning site. The deduced amino acid sequence of protein NorB contained four cysteine clusters with striking homology to those of iron-sulfur centers of bacterial ferredoxins. NorB shares significant sequence similarity to the -subunits (NarH, NarY) of the two dissimilatory nitrate reductases (NRA, NRZ) of Escherichia coli. Additionally, the derived amino acid sequence of the truncated open reading frame of norA showed striking resemblance to the -subunits (NarG, NarZ) of the E. coli nitrate reductases.