Pseudoxanthomonas kalamensis sp. nov., a novel gammaproteobacterium isolated from Johnston Atoll, North Pacific Ocean

An aerobic, mesophilic bacterium, strain JA40T, was isolated from soil contaminated with polycyclic aromatic hydrocarbons and polychlorinated biphenyls collected from Johnston Atoll in the North Pacific Ocean. The strain formed yellow-pigmented colonies on heterotrophic media. The cells were Gram-negative, non-motile, non-sporulating rods. The strain reduced nitrite to nitrous oxide, the DNA G+C content was 64 mol% and the dominant fatty acids were 15 : 0 iso, 17 : 1 iso cis7 and 11 : 0 iso 3-OH. DNA sequencing of 1457 nt of the 16S rRNA gene established that JA40T belongs in the genus Pseudoxanthomonas within the Xanthomonadaceae branch of the Gammaproteobacteria. Strain JA40T can be differentiated from other mesophilic species in the genus on the basis of its physiological and biochemical characteristics and distinctive fatty acid profile. Thus strain JA40T (=ATCC BAA-1031T=CIP 108476T) is the type strain of a novel species of the genus Pseudoxanthomonas, for which the name Pseudoxanthomonas kalamensis sp. nov. is proposed.

Nitrous oxide fluxes in turfgrass: effects of nitrogen fertilization rates and types

Urban ecosystems are rapidly expanding and their effects on atmospheric nitrous oxide (N2O) inventories are unknown. Our objectives were to: (i) measure the magnitude, seasonal patterns, and annual emissions of N2O in turfgrass; (ii) evaluate effects of fertilization with a high and low rate of urea N; and (iii) evaluate effects of urea and ammonium sulfate on N2O emissions in turfgrass. Nitrogen fertilizers were applied to turfgrass: (i) urea, high rate (UH; 250 kg N ha(-1) yr(-1)); (ii) urea, low rate (UL; 50 kg N ha(-1) yr(-1)); and (iii) ammonium sulfate, high rate (AS; 250 kg N ha(-1) y(-1)); high N rates were applied in five split applications. Soil fluxes of N2O were measured weekly for 1 yr using static surface chambers and analyzing N2O by gas chromatography. Fluxes of N2O ranged from -22 microg N2O-N m(-2) h(-1) during winter to 407 microg N2O-N m(-2) h(-1) after fall fertilization. Nitrogen fertilization increased N2O emissions by up to 15 times within 3 d, although the amount of increase differed after each fertilization. Increases were greater when significant precipitation occurred within 3 d after fertilization. Cumulative annual emissions of N2O-N were 1.65 kg ha(-1) in UH, 1.60 kg ha(-1) in AS, and 1.01 kg ha(-1) in UL. Thus, annual N2O emissions increased 63% in turfgrass fertilized at the high compared with the low rate of urea, but no significant effects were observed between the two fertilizer types. Results suggest that N fertilization rates may be managed to mitigate N2O emissions in turfgrass ecosystems.

[Study on mechanism of enhanced UV-B radiation influencing on N2O emission from soil-winter wheat system]

To study the influencing mechanisms of enhanced UV-B radiation on the emission of N20 from soil-wheat system, outdoor pot experiments with simulating 20% supplemental level of UV-B were conducted. Results indicate that the enhanced UV-B had no significant impact on the emission of N20 from soil-wheat system in turning- green stage, but declined the N2O flux and the rate of the system's respiration in elongation stage. The impact mechanisms of enhanced UV-B radiation on the N2O flux were to directly change the nitrogen metabolism process of wheat plant, such as significantly increasing soluble protein, total nitrogen and total phosphorus in wheat leaves. But the effects of UV-B radiation on soil N2O emission may be indirect, namely, UV-B treatment by working on wheat plant significantly increased the soil available nitrogen, soil microbial biomass C and N, and also changed the ratio of soil microbial C: N(from 5.0 to 6.8) in winter-wheat rhizosphere.

Insight into Catalysis of Nitrous Oxide Reductase from High-resolution Structures of Resting and Inhibitor-bound Enzyme from Achromobacter cycloclastes

The difficult chemistry of nitrous oxide (N2O) reduction to gaseous nitrogen (N2) in biology is catalysed by the novel micro4-sulphide-bridged tetranuclear Cuz cluster of the N2O reductases (N2OR). Two spectroscopically distinct forms of this cluster have been identified as CuZ and CuZ*. We have obtained a 1.86 A resolution crystal structure of the pink-purple species of N2OR from Achromobacter cycloclastes (AcN2OR) isolated under aerobic conditions. This structure reveals a previously unobserved ligation with two oxygen atoms from H2O/OH- coordinated to Cu1 and Cu4 of the catalytic centre. We ascribe this structure to be that of the CuZ form of the cluster, since the previously reported structures of two blue species of N2ORs, also isolated aerobically, have characterised the redox inactive CuZ* form, revealing a single water molecule at Cu4. Exposure of the as-isolated AcN2OR to sodium iodide led to reduction of the electron-donating CuA site and the formation of a blue species. Structure determination of this adduct at 1.7 A resolution showed that iodide was bound at the CuZ site bridging the Cu1 and Cu4 ions. This structure represents the first observation of an inhibitor bound to the Cu1-Cu4 edge of the catalytic cluster, providing clear evidence for this being the catalytic edge in N2ORs. These structures, together with the published structural and spectroscopic data, give fresh insight into the mode of substrate binding, reduction and catalysis.

The Involvement of the Nociceptin Receptor in the Antinociceptive Action of Nitrous Oxide

Nociceptin and its receptor are widely expressed in the central nervous system and are involved in the modulation of nociception. We have previously reported that the minimum anesthetic alveolar concentrations for volatile anesthetics do not differ between nociceptin receptor knockout (NOP-/-) mice and wild-type (NOP+/+) mice. In the present study, we investigated whether the nociceptin system is involved in the antinociceptive action of nitrous oxide. Using the acetic acid-induced writhing test, we showed that nitrous oxide had significantly less analgesic action in NOP-/- mice than in NOP+/+ mice. Furthermore, when anesthetized with a mixture of halothane and nitrous oxide (70%), intraperitoneal injection of acetic acid resulted in an increase of plasma adrenocorticotropic hormone concentrations in NOP-/- mice but not in NOP+/+ mice. An immunohistochemical study showed that nitrous oxide exposure induced c-Fos expression in the spinal cords of NOP+/+ mice but not in those of NOP-/- mice. These results together suggest that the antinociceptive action of nitrous oxide is, at least partly, mediated by the nociceptin system.

The effect of Chinese tallow tree (Sapium sebiferum) ecotype on soil-plant system carbon and nitrogen processes

The EICA hypothesis predicts that shifts in allocation of invasive plants give rise to higher growth rates and lower herbivore defense levels in their introduced range than conspecifics in their native range. These changes in traits of invasive plants may also affect ecosystem processes. We conducted an outdoor pot experiment with Chinese tallow tree (Sapium sebiferum, Euphorbiaceae) seedlings from its native (Jiangsu, China, native ecotype) and introduced ranges (Texas, USA, invasive ecotype) to compare their relative performances in its native range and to examine ecotype effects on soil processes with and without fertilization. Consistent with predictions, plant (shoot and root) mass was significantly greater and leaf defoliation tended to be higher, while the root:shoot ratio was lower for the invasive ecotype relative to the native ecotype. Seasonal amounts of soil-plant system CO(2) and N(2)O emissions were higher for the invasive ecotype than for the native ecotype. Soil respiration rates and N(2)O emission increases from fertilization were also greater for the invasive ecotype than for the native ecotype, while shoot-specific respiration rates (g CO(2)-C g(-1) C day(-1)) did not differ between ecotypes. Further, soil inorganic N (ammonium and nitrate) was higher, but soil total N was lower for soils with the invasive ecotype than soils with the native ecotype. Compared with native ecotypes, therefore, invasive ecotypes may have developed a competition advantage in accelerating soil processes and promoting more nitrogen uptake through soil-plant direct interaction. The results of this study suggest that soil and ecosystem processes accelerated by variation in traits of invasive plants may have implications for their invasiveness.

[Alteration of renal hemodynamic in adriamycin-induced nephrosis rats administrated with Wulingsan]

OBJECTIVE

To investigate the effect of traditional classical compound Wulingsan on renal hemodynamic in rats with adriamycin (ADR)-induced nephrosis.

METHOD

After establishing a model of rats with adriamycin-induced nephrosis, we administrated wulin-san to the ADR rats via oral gavage for four weeks and measured mean arterial blood preasure (MABP) with manometer. Renal clearance of paraaminohippuric acid (PAH) and inulin were detected, then renal plasma flow (RPF) and glomerular filtration rate (GFR) were calculated. Renal vascular resistance (RVR) was calculated as the division of MABP by RPF. Renal endothelin (ET) and angiotensin II (Ang II) were detected with radioimmunity assay kits, and nitrous oxide (NO) was detected with biochemical kits.

RESULT

There was no significant change of GFR in ARD rats, but RPF and NO were decreased, which accompanied by enhanced RVR, ET and Ang II. RPF was increased in the administrated rats, in company with RVR, ET and Ang II decreased, whereas NO was not influenced after the administration.

CONCLUSION

Wulingsan can improve the renal hemodynamic in ADR rats, at least in part by modulating the levels of vasoactive factor.

Kinetic Modeling of Nitric-Oxide-Associated Reaction Network

PURPOSE

Nitric oxide and superoxide are the two important free radicals in the biological system. The coexistence of both free radicals in the physiological milieu gives rise to intricate oxidative and nitrosative reactions, which have been implicated in many physiological and/or pathophysiological conditions, such as vasodilatation and inflammation. It is difficult, if not impossible, to study the complexity of the nitric oxide/superoxide system using current experimental approaches. Computational modeling thus offers an alternative way for studying the problem.

METHODS

In this present study, key reaction pathways related to the generation, reaction and scavenging of both nitric oxide and superoxide were integrated into a reaction network. The network dynamics was investigated by numerical simulations to a set of coupled differential equations and by dynamical analysis. Two specific questions pertaining to the reaction kinetics of the reactive chemical species in the nitric oxide/superoxide system were studied: (1) how does the system respond dynamically when the generation rate of nitric oxide and superoxide varies? (2) how would antioxidants such as glutathione modulate the system dynamics?

RESULTS

While changing basal GSH levels does not alter the kinetics of nitric oxide, superoxide, and peroxynitrite, the kinetic profiles of N203, GSNO and GSH are sensitive to the variation of basal GSH levels. The kinetics of the potential nitrosative species, N203, is switch like, which is dependent on the level of GSH.

CONCLUSIONS

The model predicts that concurrent high nitric oxide and superoxide generation--such as in the inflammatory conditions--may result in nonlinear system dynamics, and glutathione may serve as a dynamic switch of N203 mediated nitrosation reaction.

Nitrous oxide emissions from corn-soybean systems in the midwest

Soil N2O emissions from three corn (Zea mays L.)-soybean [Glycine max (L.) Merr.] systems in central Iowa were measured from the spring of 2003 through February 2005. The three managements systems evaluated were full-width tillage (fall chisel plow, spring disk), no-till, and no-till with a rye (Secale cereale L. 'Rymin') winter cover crop. Four replicate plots of each treatment were established within each crop of the rotation and both crops were present in each of the two growing seasons. Nitrous oxide fluxes were measured weekly during the periods of April through October, biweekly during March and November, and monthly in December, January, and February. Two polyvinyl chloride rings (30-cm diameter) were installed in each plot (in and between plant rows) and were used to support soil chambers during the gas flux measurements. Flux measurements were performed by placing vented chambers on the rings and collecting gas samples 0, 15, 30, and 45 min following chamber deployment. Nitrous oxide fluxes were computed from the change in N2O concentration with time, after accounting for diffusional constraints. We observed no significant tillage or cover crop effects on N2O flux in either year. In 2003 mean N2O fluxes were 2.7, 2.2, and 2.3 kg N2O-N ha(-1) yr(-1) from the soybean plots under chisel plow, no-till, and no-till + cover crop, respectively. Emissions from the chisel plow, no-till, and no-till + cover crop plots planted to corn averaged 10.2, 7.9, and 7.6 kg N2O-N ha(-1) yr(-1), respectively. In 2004 fluxes from both crops were higher than in 2003, but fluxes did not differ among the management systems. Fluxes from the corn plots were significantly higher than from the soybean plots in both years. Comparison of our results with estimates calculated using the Intergovernmental Panel on Climate Change default emission factor of 0.0125 indicate that the estimated fluxes underestimate measured emissions by a factor of 3 at our sites.

Net global warming potential and greenhouse gas intensity in irrigated cropping systems in northeastern Colorado

The impact of management on global warming potential (GWP), crop production, and greenhouse gas intensity (GHGI) in irrigated agriculture is not well documented. A no-till (NT) cropping systems study initiated in 1999 to evaluate soil organic carbon (SOC) sequestration potential in irrigated agriculture was used in this study to make trace gas flux measurements for 3 yr to facilitate a complete greenhouse gas accounting of GWP and GHGI. Fluxes of CO2, CH4, and N2O were measured using static, vented chambers, one to three times per week, year round, from April 2002 through October 2004 within conventional-till continuous corn (CT-CC) and NT continuous corn (NT-CC) plots and in NT corn-soybean rotation (NT-CB) plots. Nitrogen fertilizer rates ranged from 0 to 224 kg N ha(-1). Methane fluxes were small and did not differ between tillage systems. Nitrous oxide fluxes increased linearly with increasing N fertilizer rate each year, but emission rates varied with years. Carbon dioxide efflux was higher in CT compared to NT in 2002 but was not different by tillage in 2003 or 2004. Based on soil respiration and residue C inputs, NT soils were net sinks of GWP when adequate fertilizer was added to maintain crop production. The CT soils were smaller net sinks for GWP than NT soils. The determinant for the net GWP relationship was a balance between soil respiration and N2O emissions. Based on soil C sequestration, only NT soils were net sinks for GWP. Both estimates of GWP and GHGI indicate that when appropriate crop production levels are achieved, net CO2 emissions are reduced. The results suggest that economic viability and environmental conservation can be achieved by minimizing tillage and utilizing appropriate levels of fertilizer.

Agricultural soil greenhouse gas emissions: a review of national inventory methods

Parties to the United Nations Framework Convention on Climate Change (UNFCCC) are required to submit national greenhouse gas (GHG) inventories, together with information on methods used in estimating their emissions. Currently agricultural activities contribute a significant portion (approximately 20%) of global anthropogenic GHG emissions, and agricultural soils have been identified as one of the main GHG source categories within the agricultural sector. However, compared to many other GHG sources, inventory methods for soils are relatively more complex and have been implemented only to varying degrees among member countries. This review summarizes and evaluates the methods used by Annex 1 countries in estimating CO2 and N2O emissions in agricultural soils. While most countries utilize the Intergovernmental Panel on Climate Change (IPCC) default methodology, several Annex 1 countries are developing more advanced methods that are tailored for specific country circumstances. Based on the latest national inventory reporting, about 56% of the Annex 1 countries use IPCC Tier 1 methods, about 26% use Tier 2 methods, and about 18% do not estimate or report N2O emissions from agricultural soils. More than 65% of the countries do not report CO2 emissions from the cultivation of mineral soils, organic soils, or liming, and only a handful of countries have used country-specific, Tier 3 methods. Tier 3 methods usually involve process-based models and detailed, geographically specific activity data. Such methods can provide more robust, accurate estimates of emissions and removals but require greater diligence in documentation, transparency, and uncertainty assessment to ensure comparability between countries. Availability of detailed, spatially explicit activity data is a major constraint to implementing higher tiered methods in many countries.

Long-term trends in nitrous oxide emissions, soil nitrogen, and crop yields of till and no-till cropping systems

No-till cropping can increase soil C stocks and aggregation but patterns of long-term changes in N2O emissions, soil N availability, and crop yields still need to be resolved. We measured soil C accumulation, aggregation, soil water, N2O emissions, soil inorganic N, and crop yields in till and no-till corn-soybean-wheat rotations between 1989 and 2002 in southwestern Michigan and investigated whether tillage effects varied over time or by crop. Mean annual NO3- concentrations in no-till were significantly less than in conventional till in three of six corn years and during one year of wheat production. Yields were similar in each system for all 14 years but three, during which yields were higher in no-till, indicating that lower soil NO3- concentrations did not result in lower yields. Carbon accumulated in no-till soils at a rate of 26 g C m(-2) yr(-1) over 12 years at the 0- to 5-cm soil depth. Average nitrous oxide emissions were similar in till (3.27 +/- 0.52 g N ha d(-1)) and no-till (3.63 +/- 0.53 g N ha d(-1)) systems and were sufficient to offset 56 to 61% of the reduction in CO2 equivalents associated with no-till C sequestration. After controlling for rotation and environmental effects by normalizing treatment differences between till and no-till systems we found no significant trends in soil N, N2O emissions, or yields through time. In our sandy loam soils, no-till cropping enhances C storage, aggregation, and associated environmental processes with no significant ecological or yield tradeoffs.

Growth and denitrifying activity of Xanthobacter autotrophicus CECT 7064 in the presence of selected pesticides

The effects of the application of nine pesticides used commonly in agriculture (aldrin, lindane, dimetoate, methylparathion, methidation, atrazine, simazine, captan and diflubenzuron) on growth, CO2 production, denitrifying activity [as nitrous oxide (N2O) released] and nitrite accumulation in the culture medium by Xanthobacter autotrophicus strain CECT 7064 (Spanish Type Culture Collection) (a micro-organism isolated from a submerged fixed-film) were studied. The herbicide atrazine and the insecticide dimetoate totally inhibited growth and biological activity of X. autotrophicus at 10 mg l(-1), while the rest of the tested pesticides delayed the growth of strain CECT 7064 but did not drastically affect the bacterial growth after 96 h of culture. The denitrifying activity of X. autotrophicus was negatively affected by the pesticides application with the exception of fungicide captan. The release of N2O was strongly inhibited by several pesticides (aldrin, lindane, methylparathion, methidation and diflubenzuron), while dimetoate, atrazine and simazine inhibited totally the denitrifying activity of the strain. The effects of the pesticides on denitrifying submerged fixed-film reactor are discussed.

DAYCENT national-scale simulations of nitrous oxide emissions from cropped soils in the United States

Until recently, Intergovernmental Panel on Climate Change (IPCC) emission factor methodology, based on simple empirical relationships, has been used to estimate carbon (C) and nitrogen (N) fluxes for regional and national inventories. However, the 2005 USEPA greenhouse gas inventory includes estimates of N2O emissions from cultivated soils derived from simulations using DAYCENT, a process-based biogeochemical model. DAYCENT simulated major U.S. crops at county-level resolution and IPCC emission factor methodology was used to estimate emissions for the approximately 14% of cropped land not simulated by DAYCENT. The methodology used to combine DAYCENT simulations and IPCC methodology to estimate direct and indirect N2O emissions is described in detail. Nitrous oxide emissions from simulations of presettlement native vegetation were subtracted from cropped soil N2O to isolate anthropogenic emissions. Meteorological data required to drive DAYCENT were acquired from DAYMET, an algorithm that uses weather station data and accounts for topography to predict daily temperature and precipitation at 1-km2 resolution. Soils data were acquired from the State Soil Geographic Database (STATSGO). Weather data and dominant soil texture class that lie closest to the geographical center of the largest cluster of cropped land in each county were used to drive DAYCENT. Land management information was implemented at the agricultural-economic region level, as defined by the Agricultural Sector Model. Maps of model-simulated county-level crop yields were compared with yields estimated by the USDA for quality control. Combining results from DAYCENT simulations of major crops and IPCC methodology for remaining cropland yielded estimates of approximately 109 and approximately 70 Tg CO2 equivalents for direct and indirect, respectively, mean annual anthropogenic N2O emissions for 1990-2003.

Radiation-induced effect of adenine (vitamin B4) on mitomycin C activity. In vitro experiments

The radiation-induced biological behavior of adenine (vitamin B4) was investigated in vitro under various conditions, implementing breast cancer cells (MCF-7 line) as a model. In aerated media (46% OH and 54% O2*-) at pH=7.4, adenine at low concentration (2 micromol) acted as an efficient radiation-protecting agent. At higher concentration, however, it inhibited cytostatic properties with regard to cancer cells. This double-track activity is based on its chemical structure. Similar features of adenine were also observed in air-free (46% OH, 44% e- aq, 10% H) as well as in media saturated with N2O (90% OH, 10% H), but with different efficiencies. In the presence of mitomycin C (MMC), adenine retained its double-track behavior. Hence, adenine and MMC compete for the e- aq, but the electronically excited adenine molecules can transfer electrons to MMC, leading to the additional formation of active MMC-. By implementation of formate for the conversion of OH and H into the transient *COO-, which subsequently transfers electron to MMC, a highest efficiency of MMC- was obtained.

Greenhouse gas emissions from forestry operations: a life cycle assessment

Most forest carbon assessments focus only on biomass carbon and assume that greenhouse gas (GHG) emissions from forestry activities are minimal. This study took an in-depth look at the direct and indirect emissions from Pacific Northwest (PNW) Douglas-fir [Pseudotsuga menziesii (Mirbel) Franco] forestry activities to support or deny this claim. Greenhouse gas budgets for 408 "management regimes" were calculated using Life Cycle Assessment (LCA) methodology. These management regimes were comprised of different combinations of three types of seedlings (P + 1, 1 + 1, and large plug), two types of site preparation (pile and burn, and chemical), 17 combinations of management intensity including fertilization, herbicide treatment, pre-commercial thinning (PCT), commercial thinning (CT), and nothing, and four different rotation ages (30, 40, 50, and 60 yr). Normalized to 50 yr, average direct GHG emissions were 8.6 megagrams (Mg) carbon dioxide equivalents (CO2e) ha(-1), which accounted for 84% of total GHG emissions from the average of 408 management regimes. Harvesting (PCT, CT, and clear cutting) contributed the most to total GHG emissions (5.9 Mg CO2e per 700 m3 harvested timber), followed by pile and burn site preparation (4.0 Mg CO2e ha(-1) or 32% of total GHG emissions) and then fertilization (1.9 Mg CO2e ha(-1) or 15% of total GHG emissions). Seedling production, seedling transportation, chemical site preparation, and herbicide treatment each contributed less than 1% of total GHG emissions when assessed per hectare of planted timberland. Total emissions per 100 m3 averaged 1.6 Mg CO2e ha(-1) over all 408 management regimes. An uncertainty analysis using Monte Carlo simulations revealed that there are significant differences between most alternative management regimes.

Assessing alternatives for mitigating net greenhouse gas emissions and increasing yields from rice production in China over the next twenty years

Assessments of the efficacy of mitigation of greenhouse gas (GHG) emissions from paddy rice systems have typically been analyzed based on field studies. Extrapolation of the mitigation potential of alternative management practices from field studies to a national scale may be enhanced by spatially explicit process models, like the DeNitrification and DeComposition (DNDC) model. Our objective was to analyze the impacts of mitigation alternatives, management of water, fertilizer, and rice straw, on net GHG emissions (carbon dioxide, methane, and nitrous oxide fluxes), yields, and water use. After constructing a GIS database of soil, climate, rice cropping area and systems, and management practices, we ran DNDC with 21-yr alternative management schemes for each of the approximately 2500 counties in China. Results indicate that, despite large-scale adoption of midseason drainage, there is still large potential for additional methane reductions from Chinese rice paddies of 20 to 60% over 2000-2020. However, changes in management for reducing CH4 emissions simultaneously affect soil carbon dynamics as well as N2O emissions and can thereby reorder the ranking of technical mitigation effectiveness. The order of net GHG emissions reduction effectiveness found here is upland rice > shallow flooding > ammonium sulfate > midseason drainage > off-season straw > slow-release fertilizer > continuous flooding. Most of the management alternatives produced yields comparable to the baseline; however, continuous flooding and upland rice significantly reduced yields. Water management strategies appear to be the most technically promising GHG mitigation alternatives, with shallow flooding providing additional benefits of both water conservation and increased yields.

Nitrate-dependent [Fe(II)EDTA]2− oxidation by Paracoccus ferrooxidans sp. nov., isolated from a denitrifying bioreactor

Enrichments with [Fe(II)EDTA]2- as electron donor and nitrate or nitrite as electron acceptor were established using an inoculum from a bioreactor performing denitrification. A nitrate-reducing, [Fe(II)EDTA]2- oxidizing strain was isolated and named strain BDN-1. The G + C content of strain BDN-1 was 67%, and the organism was closely affiliated to Paracoccus denitrificans, P. pantotrophus and P. versutus by 16S rRNA sequence comparison. Results from DNA-DNA hybridization, rep-PCR, and whole cell protein analysis gave congruent results confirming the genotypic and phenotypic differences between strain BDN-1 and the other species of Paracoccus. From these results, we considered strain BDN-1 as a novel species for which we propose the name Paracoccus ferrooxidans. Apart from [Fe(II)EDTA]2-, BDN-1 could also use thiosulfate and thiocyanate as inorganic electron donors. Nitrate, nitrite, N2O, [Fe(II)EDTA.NO]2- and oxygen could be used by strain BDN-1 as electron acceptors. Repeated transfer on a culture medium with bicarbonate as the sole carbon source confirmed that strain BDN-1 was a facultative autotroph. [Fe(II)EDTA]2- oxidation dependent denitrification was also performed by other Paracoccus species, that were closely affiliated to P. ferrooxidans.

Influence of freeze-thaw stress on the structure and function of microbial communities and denitrifying populations in soil

Microbial N2O release during the course of thawing of soil was investigated in model experiment focusing on denitrification, since freeze-thaw has been shown to cause significant physical and biological changes in soil, including a surge of N2O and CO2. The origin of these is still controversially discussed. The increase in denitrification after thawing may be attributed to the diffusion of organic substrates newly available to denitrifiers from disrupted soil aggregates, leading to an increase in microbial activity. Laboratory experiments with upper soil layer of a grassland were conducted in microcosms for real-time gas measurements during the entire phase of freeze and thaw. Shifts in microbial communities were evident on resolution of 16S and 18S rRNA genes and transcripts by denaturing gradient gel electrophoresis (DGGE). Microbial expression profiles were compared by RNA-arbitrarily primed PCR technique and subsequent resolution of amplified products on acrylamide gels. Differences in expression levels of periplasmic nitrate reductase gene (napA) and cytochrome cd1 nitrite reductase (nirS) were observed by most-probable-number-reverse transcription-PCR, with higher levels of expression occurring just after thawing began, followed by a decrease. napA and nirS DGGE profiles showed no change in banding patterns with fingerprints derived from DNA, whereas those derived from cDNA showed a clear succession of denitrifying bacteria, with the most complex pattern being observed at the end of the N2O surge. This study provides insight into the structural community changes and expression dynamics of denitrifiers as a result of freeze-thaw stress. Also, the results presented here support the belief that the gas fluxes observed during thawing is a result of freezing initiated high microbial activity.

N2O reduction by the mu4-sulfide-bridged tetranuclear CuZ cluster active site

Nitrous oxide (N2O) reduction is a chemical challenge both in the selective oxidation of organic substrates by N2O and in the removal of N2O as a green-house gas. The reduction of N2O is thermodynamically favorable but kinetically inert, and requires activating transition-metal centers. In biological systems, N2O reduction is the last step in the denitrification process of the bacterial nitrogen cycle and is accomplished by the enzyme nitrous oxide reductase, whose active site consists of a micro4-sulfide-bridged tetranuclear CuZ cluster which has many unusual spectroscopic features. Recent studies have developed a detailed electronic-structure description of the resting CuZ cluster, determined its catalytically relevant state, and provided insight into the role of this tetranuclear copper cluster in N2O activation and reduction.

In vivo emission of dinitrogen by earthworms via denitrifying bacteria in the gut

Earthworms emit the greenhouse gas nitrous oxide (N2O), and ingested denitrifiers in the gut appear to be the main source of this N2O. The primary goal of this study was to determine if earthworms also emit dinitrogen (N2), the end product of complete denitrification. When [15N]nitrate was injected into the gut, the earthworms Aporrectodea caliginosa and Lumbricus terrestris emitted labeled N2 (and also labeled N2O) under in vivo conditions; emission of N2 by these two earthworms was relatively linear and approximated 1.2 and 6.6 nmol N2 per h per g (fresh weight), respectively. Isolated gut contents also produced [15N]nitrate-derived N2 and N2O under anoxic conditions. N2 is formed by N2O reductase, and acetylene, an inhibitor of this enzyme, inhibited the emission of [15N]nitrate-derived N2 by living earthworms. Standard gas chromatographic analysis demonstrated that the amount of N2O emitted was relatively linear during initial incubation periods and increased in response to acetylene. The calculated rates for the native emissions of N2 (i.e., without added nitrate) by A. caliginosa and L. terrestris were 1.1 and 1.5 nmol N2 per h per g (fresh weight), respectively; these emission rates approximated that of N2O. These collective observations indicate that (i) earthworms emit N2 concomitant with the emission of N2O via the in situ activity of denitrifying bacteria in the gut and (ii) N2O is quantitatively an important denitrification-derived end product under in situ conditions.

Determinants of nitric oxide steady-state levels during anaerobic respiration by Neisseria gonorrhoeae

Nitric oxide (NO) is an important host defence molecule that varies its immune stimulatory effects depending on the concentrations at which it is produced, with low concentrations (< 1 microM) promoting an anti-inflammatory host response while higher concentrations (>1 microM) lead to inflammatory responses. Neisseria gonorrhoeae grows anaerobically by anaerobic respiration using nitrite reductase (Nir) to convert nitrite to NO and nitric oxide reductase (Nor) to convert NO to nitrous oxide. As N. gonorrhoeae can both produce and degrade NO, we have begun a study of NO metabolism in this bacterium to understand how gonococcal manipulation of NO concentration may influence the inflammatory response during infection. N. gonorrhoeae has an apparent Nir Km of 33 microM nitrite and an apparent Nor Km of 1.2 microM NO. The maximum specific activities for Nir and Nor were 135 nmoles nitrite reduced per minute per OD600 (pH 6.7) and 270 nmoles NO reduced per minute per OD600 (pH 7.5) respectively. N. gonorrhoeae established a steady-state concentration of NO after nitrite addition that was dependent on the nitrite concentration until saturation at 1 mM nitrite. The NO steady-state level decreased as pH increased, and the ratio of activities of Nir and Nor correlated to the NO steady-state level. When the NO donor DETA/NO was used to simulate host NO production, N. gonorrhoeae also established a NO steady-state level. The concentration of NO at steady state was found to be a function of the concentration of NO generated by DETA/NO, with N. gonorrhoeae reducing the NO from proinflammatory (>1 microM) to anti-inflammatory (approximately 100 nM) concentrations. The implications of the ability of N. gonorrhoeae to maintain an anti-inflammatory NO concentration is discussed in relation to asymptomatic infection in women.

Symbiotic Bradyrhizobium japonicum reduces N2O surrounding the soybean root system via nitrous oxide reductase

N(2)O reductase activity in soybean nodules formed with Bradyrhizobium japonicum was evaluated from N(2)O uptake and conversion of (15)N-N(2)O into (15)N-N(2). Free-living cells of USDA110 showed N(2)O reductase activity, whereas a nosZ mutant did not. Complementation of the nosZ mutant with two cosmids containing the nosRZDFYLX genes of B. japonicum USDA110 restored the N(2)O reductase activity. When detached soybean nodules formed with USDA110 were fed with (15)N-N(2)O, they rapidly emitted (15)N-N(2) outside the nodules at a ratio of 98.5% of (15)N-N(2)O uptake, but nodules inoculated with the nosZ mutant did not. Surprisingly, N(2)O uptake by soybean roots nodulated with USDA110 was observed even in ambient air containing a low concentration of N(2)O (0.34 ppm). These results indicate that the conversion of N(2)O to N(2) depends exclusively on the respiratory N(2)O reductase and that soybean roots nodulated with B. japonicum carrying the nos genes are able to remove very low concentrations of N(2)O.

Structure and activity of the denitrifying community in a maize-cropped field fertilized with composted pig manure or ammonium nitrate

One alternative to mineral fertilization is to use organic fertilizers. Our aim was to compare the impacts of 7-year applications of composted pig manure and ammonium nitrate on the structure and activity of the denitrifying community. Mineralization and organization of N, denitrification rates and N2O/N2 ratio were also investigated. Fourteen months after the last application, the potential denitrifying activity (+319%), N mineralization (+110%) and organization (+112%) were higher under pig compost than under ammonium nitrate fertilization. On the other hand, the N2O/(N2O+N2) ratio was lower (P<0.05, n=5) under organic fertilization. These effects of organic fertilization were in accordance with its higher total carbon content and microbial biomass. Fingerprints and clone library analyses showed that the structure of the denitrifying community was affected by the fertilization regime. Our results reveal that organic or mineral fertilizer applications could affect both structure and activity of the denitrifying community, with a possible influence on in situ N2O fluxes. These effects of the fertilization regime persisted for at least 14 months after the last application.