Abiotic nitrate incorporation, anaerobic microsites, and the ferrous wheel

Nitrate has long been thought to be chemically unreactive in soil. This view was challenged by the report of an apparently abiotic process whereby nitrate (NO₃ ^?) is incorporated into organic compounds (Dail et al. 2001). In Colman et al. (2007), we examined how common this process might be by testing for it in 45 soils collected from across a range of ecosystem types. We found no evidence of this process occurring in any of the soils, but found evidence of an analytical artifact that creates the appearance of incorporation. We suggested that prior evidence of this process might be due in part or in total to this analytical artifact. Davidson et al. (2008), however, challenged our results and conclusions, suggesting that we failed to observe the abiotic incorporation because we eliminated the anaerobic microsites they argue are necessary for the process. We address the criticisms, and show that they actually raise questions about the robustness of the only study to have reported abiotic NO₃ ^? incorporation in sterile soils. We argue that this area of research needs new artifact-free experiments if the controversy is going to be resolved.     

Delayed, ferrous iron-dependent peroxidation of rat liver microsomes

Measurement of both chemiluminescence (CL) and the formation of 2-thiobarbituric acid-reacting substances (TBAR) has been used to study the delayed, nonenzymatic lipid peroxidation (LP) initiated in rat liver microsomes by ferrous chloride. Following Fe2+ addition, the CL technique revealed a burst of light emission (peak, Phase II) which was preceded by a period of little or no detectable photon production (delay, Phase I) and succeeded by an increased emission (Phase III). Analysis of TBAR indicated a low rate of LP during the delay which increased more than fivefold during a 1-min period and which corresponded to the CL peak. The delay length depended on both the Fe2+ concentration and the microsome concentration; increased Fe2+ yielded longer delays while increased microsome concentration decreased the delay. As reported by others [J. R. Bucher, M. Tien, and S. D. Aust (1983) Biochem. Biophys. Res. Commun. 111, 777-784; J. M. Braughler, L. A. Duncan, and R. L. Chase (1986) J. Biol. Chem. 261, 10282-10289], Fe3+ also decreased the delay. The ferric-nitrilotriacetate (Fe3+-NTA) complex was found to be more efficient than "free" Fe3+ [Fe(NO3)3]; a 100 microM concentration of the 1:1 Fe3+-NTA complex eliminated the delay due to 100 microM Fe2+, whereas 400 microM Fe(NO3)3 reduced the delay from 17.5 to 2.5 min. Incubation under reduced O2 tension demonstrated a requirement for O2 during the delay. The use of antioxidants [butylated hydroxytoluene, (+)-catechin, promethazine, and uric acid] and inhibitors of the Haber-Weiss reaction (mannitol, Tris buffer, dimethyl sulfoxide, catalase, and superoxide dismutase) indicated that the initiating species has characteristics of a weak oxidizing radical capable of either hydrogen or electron abstraction from suitable target molecules. We hypothesize that the delay that is sensitive to the Fe2+:microsome ratio is due to reductive elimination of the initiating species by "free" Fe2+. The nature of the initiating species has yet to be determined; however, the argument is presented that the perferryl ion (Fe3+-O2-.) may possess the characteristics required for the initiator.     

Photo and thermal reactions of ferrous hydroxide

The reactions of ferrous ion near neutral pH are of interest because of its known presence in the Archaean oceans. We have confirmed the long wavelength ultraviolet photochemical and the thermal reactions of ferrous hydroxide to form hydrogen. We have shown that a claim of the reduction of carbon dioxide to formaldehyde at neutral pH is mistaken. By the use of¹⁴C labelled compounds, we have found that less than 1 ppm of carbon dioxide is reduced to formaldehyde and less than 10 ppm of formate ion is so reduced. The thermal reaction to form hydrogen has a small activation energy of 7 kcal mole^–1. We conclude that thermal and photochemical formation of hydrogen from ferrous ion in the Archaean ocean could be comparable at pH 8–9. At lower pH, toward its limit at pH 5, the photochemical reaction would predominate. Both the thermal and photochemical reactions are specific for ferrous hydroxide, being far slower for the phosphate (>50- and 7-fold) and the bicarbonate (2- and 30-fold) complexes.     

湿地林土壤的Fe2+,Eh及pH值的变化

通过在不同含水量 (田间持水量的 6 0 % :对照处理 ;田间持水量的 2 5 0 % :淹水处理 )和不同温度 (2 0℃ ,2 5℃ ,30℃ )条件下的室内培养 ,对江苏省里下河地区池杉湿地林土壤的二价铁离子 (Fe2 )浓度 ,氧化还原电位 (Eh)及 p H值进行了研究。结果表明 ,与对照处理相比 ,淹水土壤的 p H值和 Fe2 浓度明显提高 (P<0 .0 1) ,而 Eh值则明显降低 (P<0 .0 1)。在淹水条件下 ,高温处理的土壤 p H值和 Fe2 浓度明显高于低温处理土壤 (P<0 .0 1) ,Eh值则相反。研究表明 ,土壤 Eh值与 p H值之间存在着密切的 3次方程式关系 (P<0 .0 0 1)。就里下河地区湿地林土壤而言 ,Eh值下降至 2 0 0 m V以下时 ,才会有大量的铁元素被还原为Fe2 。     

Nitrosylation of rabbit ferrous heme-hemopexin

Hemopexin (HPX) serves as a trap for toxic plasma heme, ensuring its complete clearance by transportation to the liver. Moreover, HPX-heme has been postulated to play a key role in the homeostasis of nitric oxide (NO). Here, the thermodynamics for NO binding to rabbit ferrous HPX-heme as well as the EPR and optical absorption spectroscopic properties of rabbit ferrous nitrosylated HPX-heme (HPX-heme-NO) are reported. The value of the dissociation equilibrium constant for NO binding to rabbit ferrous HPX-heme (i.e., H) is (1.4±0.2)×10^–7 M, at pH 7.0 and 10.0 °C; the value of H is unaffected by sodium chloride. At pH 7.0, rabbit ferrous HPX-heme-NO is a six-coordinate heme-iron species, characterized by an X-band EPR spectrum with an axial geometry and by =146 mM^–1 cm^–1 at 419 nm. At pH 4.0, rabbit ferrous HPX-heme-NO is a five-coordinate heme-iron species, characterized by an X-band EPR spectrum with three-line splitting centered at 334 mT and by =74 mM^–1 cm^–1 at 387 nm. The pK_a value of the reversible pH-induced six- to five-coordinate spectroscopic transition is 4.8±0.1 in the absence of sodium chloride and 4.3±0.1 in the presence of 1.5×10^–1 M sodium chloride. This result is in agreement with the effect of sodium chloride on rabbit HPX-heme stability. The present data have been analyzed in parallel with those of a related heme model compound and heme-protein systems.     

Characterization of arsenopyrite oxidizing Thiobacillus. Tolerance to arsenite,arsenate, ferrous and ferric iron

Two strains of Thiobacillus, T. ferrooxidans and T. thiooxidans, have been isolated from a bacterial inoculum cultivated during a one-year period in a 1001 continuous laboratory pilot for treatment of an arsenopyrite/pyrite concentrate. The optimum pH for the growth of both strains has been found to be between 1.7 and 2.5. Because of the high metal toxicity in bioleach pulps, the tolerance of T. ferrooxidans and T. thiooxidans with respect to iron and arsenic has been studied. The growth of both strains is inhibited with 10 g/l of ferric ion, 5 g/l of arsenite and 40 g/l of arsenate. 20 g/l of ferrous iron is toxic to T. ferrooxidans but 30 g/l is necessary to impede the growth of T. thiooxidans.     

Isolation and characterization of an acidophilic, heterotrophic bacterium capable of oxidizing ferrous iron.

A heterotrophic bacterium, isolated from an acidic stream in a disused pyrite mine which contained copious growths of "acid streamers," displayed characteristics which differentiated it from previously described mesophilic acidophiles. The isolate was obligately acidophilic, with a pH range of 2.0 to 4.4 and an optimum pH of 3.0. The bacterium was unable to fix carbon dioxide but oxidized ferrous iron, although at a slower rate than either Thiobacillus ferrooxidans or Leptospirillum ferrooxidans. Elemental sulfur and manganese(II) were not oxidized. In liquid media, the isolate produced macroscopic streamerlike growths. Microscopic examination revealed that the bacterium formed long (greater than 100 microns) filaments which tended to disintegrate during later growth stages, producing single, motile cells and small filaments. The isolate did not appear to utilize the energy from ferrous iron oxidation. Both iron (ferrous or ferric) and an organic substrate were necessary to promote growth. The isolate displayed a lower tolerance to heavy metals than other iron-oxidizing acidophiles, and growth was inhibited by exposure to light. There was evidence of extracellular sheath production by the isolate. In this and some other respects, the isolate resembles members of the Sphaerotilus-Leptothrix group of filamentous bacteria. The guanine-plus-cytosine content of the isolate was 62 mol%, which is less than that recorded for Sphaerotilus-Leptothrix spp. and greater than those of L. ferrooxidans and most T. ferrooxidans isolates.     

Isolation and characterization of an acidophilic, heterotrophic bacterium capable of oxidizing ferrous iron.

A heterotrophic bacterium, isolated from an acidic stream in a disused pyrite mine which contained copious growths of "acid streamers," displayed characteristics which differentiated it from previously described mesophilic acidophiles. The isolate was obligately acidophilic, with a pH range of 2.0 to 4.4 and an optimum pH of 3.0. The bacterium was unable to fix carbon dioxide but oxidized ferrous iron, although at a slower rate than either Thiobacillus ferrooxidans or Leptospirillum ferrooxidans. Elemental sulfur and manganese(II) were not oxidized. In liquid media, the isolate produced macroscopic streamerlike growths. Microscopic examination revealed that the bacterium formed long (greater than 100 microns) filaments which tended to disintegrate during later growth stages, producing single, motile cells and small filaments. The isolate did not appear to utilize the energy from ferrous iron oxidation. Both iron (ferrous or ferric) and an organic substrate were necessary to promote growth. The isolate displayed a lower tolerance to heavy metals than other iron-oxidizing acidophiles, and growth was inhibited by exposure to light. There was evidence of extracellular sheath production by the isolate. In this and some other respects, the isolate resembles members of the Sphaerotilus-Leptothrix group of filamentous bacteria. The guanine-plus-cytosine content of the isolate was 62 mol%, which is less than that recorded for Sphaerotilus-Leptothrix spp. and greater than those of L. ferrooxidans and most T. ferrooxidans isolates.     

Inhibition of Clostridium perfringens by heated combinations of nitrite, sulfur, and ferrous or ferric ions.

Heating mixtures of sodium nitrite, cysteine, and either ferrous sulfate or ferric chloride at 121 C for 20 min at pH 6.5 or 6.3 produced a potent inhibitor of Clostridium perfringens vegetative cells and spores when added to previously heat-sterilized fluid thioglycolate medium. When the mixtures containing FeSO4 at pH 5.2 or FeCl3 at pH 2.7 were heated, the inhibitory effect was not produced. These responses seem to eliminate the possibility that cysteine nitrosothiol is the agent responsible for the heated-nitrite inhibition known as the Perigo effect. The variable pH responses also cast doubt upon the role of the black Roussin salt as the agent of the Perigo effect.     

Inhibition of Clostridium perfringens by heated combinations of nitrite, sulfur, and ferrous or ferric ions.

Heating mixtures of sodium nitrite, cysteine, and either ferrous sulfate or ferric chloride at 121 C for 20 min at pH 6.5 or 6.3 produced a potent inhibitor of Clostridium perfringens vegetative cells and spores when added to previously heat-sterilized fluid thioglycolate medium. When the mixtures containing FeSO4 at pH 5.2 or FeCl3 at pH 2.7 were heated, the inhibitory effect was not produced. These responses seem to eliminate the possibility that cysteine nitrosothiol is the agent responsible for the heated-nitrite inhibition known as the Perigo effect. The variable pH responses also cast doubt upon the role of the black Roussin salt as the agent of the Perigo effect.     

Interaction of cytochrome c, ferrous ion, and phosphate. Electron transfer within a stoichiometric complex.

The rate and extent of electron transfer from ferrous ion to ferricytochrome c are enhanced by the presence of inorganic orthophosphate at concentrations comparable to those of reductant and oxidant. Evidence, obtained by the method of continuous variations, shows that the electron transfer occurs within a stoichiometric complex composed of cytochrome c, ferrous ion, and phosphate in molar proportions of about 1:1:1. The incorporation of the anion into this complex appears to result in a modulation of the extent and rate of cytochrome c reduction. The rate of electron transfer obeys a first order rate law, characterized by an apparent first order rate constant of 1.4 min-1. The complex has kinetic significance only; equilibrium dialysis, gel filtration, and sedimentation velocity experiments yielded no evidence for stable binding of phosphate and iron, or of aggregation, on a significant scale. The extent of reduction is limited (for reasons not yet known) to about one-half of the available cytochrome molecules. Reduction in excess of 50% can be achieved only when both, ferrous ion and phosphate, are present in excess of the cytochrome concentration. Kinetic data indicate that reduction to extents over and below 50% occurs by different mechanisms.     

The heme-iron geometry of ferrous nitrosylated heme-serum lipoproteins,hemopexin, and albumin: a comparative EPR study

Serum high and low density lipoproteins, albumin, and hemopexin (HDL, LDL, SA, and HPX, respectively) serve as traps of toxic plasma heme and participate in its complete clearance by transportation to the liver. Moreover, SA-(heme) and HPX-heme have been proposed to facilitate NO scavenging in vivo. Here, the EPR-spectroscopic properties of ferrous nitrosylated heme-human high and low density lipoproteins (HDL-heme-NO and LDL-heme-NO, respectively) as well as of ferrous nitrosylated heme-rabbit serum hemopexin (HPX-heme-NO) are reported and analyzed in parallel with those of ferrous nitrosylated heme-human serum albumin (SA-heme-NO). HDL-heme-NO and LDL-heme-NO as well as SA-heme-NO, in the absence of allosteric effectors (i.e., N-form), are five-coordinate heme-iron species, characterized by the three-line splitting observed in the high magnetic field region of the X-band EPR spectrum. On the other hand, SA-heme-NO, in the presence of drugs (i.e., B-form), and HPX-heme-NO are six-coordinate heme-iron species, characterized by an X-band EPR spectrum with an axial geometry. The heme-iron coordination state of HDL-heme-NO, LDL-heme-NO, SA-heme-NO, and HPX-heme-NO is in keeping with values of ferric heme dissociation rate constants which decrease in the following order: LDL>HDL>SA>HPX. Altogether, these observations suggest that HPX displays a cleft much more suitable for heme binding than other heme-carriers.     

Activation of mammalian tyrosinase by ferrous ions

Kinetic experiments are reported showing that mammalian tyrosinase from B16 mouse melanoma is significantly activated by catalytic amounts of ferrous ions. Monitoring of tyrosine oxidation by both dopachrome formation and oxygen consumption showed that ferrous ions at micromolar concentrations induce a marked enzymatic activity with 0.01 U/ml of highly purified tyrosinase, whereas no detectable reaction occurs in the absence of metal over a sufficiently prolonged period of time. The extent of the activating effect, which is specific for the reduced form of iron, is proportional to the concentration of the added metal with a typical saturation profile, no further effect being observed beyond a threshold value. Changing the buffer system from phosphate to hepes or tris results in a marked decrease of the Fe2(+)-induced activation. Scavengers of active oxygen species, such as superoxide dismutase, catalase, formate and mannitol have no detectable effect on the tyrosinase activity. These results are accounted for in terms of an activation mechanism involving reduction of the cupric ions at the active site of the resting enzyme.     

Interactions of ferrous ions with peroxidized lecithin-liposomes

Oxidation of Fe2+ in the presence of peroxidized lecithin-liposomes small unilamellar vesicles suspended in various media (pH = 5.5) is described. Peroxidation of lecithin was induced by UV light and assayed by three methods: estimation of conjugated dienes, accumulation of hydroperoxides and by the thiobarbituric acid test. The oxidation of Fe2+ was accelerated by phosphate and citrate buffers, but in acetate buffer it was dependent on lipid peroxidases concentration and exhibited saturation kinetics.