Enzymology of the oxidation of ammonia to nitrite by bacteria

The enzymes which catalyze the oxidation of ammonia to nitrite by autotrophic bacteria are reviewed. A comparison is made with enzymes which catalyze the same reactions in methylotrophs and organotrophic heterotrophic bacteria.     

Utilization and leaching of nitrate from two Deschampsia-dominated heathland sites: a lysimeter study using intact soil columns*

High deposition levels of atmospheric ammonia in the Netherlands have led to the major replacement of dwarf shrubs by grasses and to elevated nitrification rates in acid heathland soils. In order to study the efficacy of a naturally established grass-heath of Deschampsia flexuosa at capturing NO^- ₃, an outdoor 'mesocosm' lysimeter experiment was set up with relatively large and undisturbed soil columns from two Deschampsia-dominated heathland sites. One of the sites (Ede) had a relatively high rate of nitrate production, whereas the other (Hoorneboeg [HB]) showed practically no nitrate formation. For part of the Ede columns, the fate of labeled nitrate, split-applied at two rates (30 or 150 kg ha^-1 yr^-1) during two seasons, was studied. D. flexuosa was highly effective in acquiring fertilizer nitrate, as demonstrated by (1) distinct rises in foliar NRA, especially at high N; (2) increased ¹⁵N enrichments in all plant components with N rate; (3) significant increases in organic-N and carboxylate concentration in several plant compartments; and (4) clear shifts in biomass allocation in favour of the aboveground tissues.After 18 months at low N, an average 39 and 23% of the applied N was immobilized in the plant and soil compartments, respectively; at high N rate, corresponding recoveries were 33 and 20%. Total leaching of nitrate (beyond a depth of 35 cm) from the unfertilized Ede columns corresponded to an annual loss of 1.9 kmol N ha^-1, whereas leaching was virtually zero from HB columns. Relatively high amounts of N leached from the fertilized columns with apparent fertilizer recovery in the leachate reaching an average 60% at high N. However,¹⁵ N analyses revealed only recoveries of 2.0% (low N) and 7.2% (high N) of the applied N in the leachate. From columns where the plant cover had been removed, apparent and real leaching losses reached values of >100 and 10% of the applied N, respectively. Hence, soil-derived N appeared by far the major source of leaching. Unplanted and unfertilized HB columns displayed high rates of nitrification and leached high amounts of nitrate, suggesting a plant-induced repression of the in situ nitrification at this site.On average, planted columns had lost 37% (low N) and 40% (high N) of the applied N, whereas unplanted lysimeters had lost 89% (for both low and high N). The N not recovered was presumed lost by denitrification due to favourable conditions with respect to nitrate concentration, moisture, carbon supply, and temperature.     

Soils,a sink for N2O? A review

Soils are the main sources of the greenhouse gas nitrous oxide (N₂O). The N₂O emission at the soil surface is the result of production and consumption processes. So far, research has concentrated on net N₂O production. However, in the literature, there are numerous reports of net negative fluxes of N₂O, (i.e. fluxes from the atmosphere to the soil). Such fluxes are frequent and substantial and cannot simply be dismissed as experimental noise.
Net N₂O consumption has been measured under various conditions from the tropics to temperate areas, in natural and agricultural systems. Low mineral N and large moisture contents have sometimes been found to favour N₂O consumption. This fits in with denitrification as the responsible process, reducing N₂O to N₂. However, it has also been reported that nitrifiers consume N₂O in nitrifier denitrification. A contribution of various processes could explain the wide range of conditions found to allow N₂O consumption, ranging from low to high temperatures, wet to dry soils, and fertilized to unfertilized plots. Generally, conditions interfering with N₂O diffusion in the soil seem to enhance N₂O consumption. However, the factors regulating N₂O consumption are not yet well understood and merit further study.
Frequent literature reports of net N₂O consumption suggest that a soil sink could help account for the current imbalance in estimated global budgets of N₂O. Therefore, a systematic investigation into N₂O consumption is necessary. This should concentrate on the organisms, reactions, and environmental factors involved.     

滨海湿地生态系统微生物驱动的氮循环研究进展

滨海湿地生态系统介于陆地生态系统和海洋生态系统之间,其类型多种多样,环境差异极大,微生物种类丰富。近年来,随着人为氮源的大量输入,造成滨海湿地生态系统富营养化污染问题日趋严重。本文主要总结了滨海湿地生态系统微生物驱动的固氮、硝化、反硝化、厌氧氨氧化、NO_3~-还原成铵等主要氮循环过程,并综述了通过功能基因(如nifH、amoA、hzo、nirS、nirK、nrfA)检测微生物群落多样性及其环境影响因素的相关研究,旨在更好理解微生物驱动氮循环过程以去除氮,以期为减轻富营养化和危害性藻类爆发提供科学依据。     

Morphological analysis of pore size and connectivity in a thick mixed‐culture biofilm

Morphological parameters are commonly used to predict transport and metabolic kinetics in biofilms. Yet, quantification of biofilm morphology remains challenging because of imaging technology limitations and lack of robust analytical approaches. We present a novel set of imaging and image analysis techniques to estimate internal porosity, pore size distributions, and pore network connectivity to a depth of 1 mm at a resolution of 10 µm in a biofilm exhibiting both heterotrophic and nitrifying activities. Optical coherence tomography (OCT) scans revealed an extensive pore network with diameters as large as 110 µm directly connected to the biofilm surface and surrounding fluid. Thin‐section fluorescence in situ hybridization microscopy revealed that ammonia‐oxidizing bacteria (AOB) distributed through the entire thickness of the biofilm. AOB were particularly concentrated in the biofilm around internal pores. Areal porosity values estimated from OCT scans were consistently lower than those estimated from multiphoton laser scanning microscopy, though the two imaging modalities showed a statistically significant correlation (r = 0.49, p < 0.0001). Estimates of areal porosity were moderately sensitive to gray‐level threshold selection, though several automated thresholding algorithms yielded similar values to those obtained by manually thresholding performed by a panel of environmental engineering researchers (±25% relative error). These findings advance our ability to quantitatively describe the geometry of biofilm internal pore networks at length scales relevant to engineered biofilm reactors and suggest that internal pore structures provide crucial habitat for nitrifier growth.     

Modeling nitrous oxide emission from rivers: a global assessment

Estimates of global riverine nitrous oxide (N₂O) emissions contain great uncertainty. We conducted a meta‐analysis incorporating 169 observations from published literature to estimate global riverine N₂O emission rates and emission factors. Riverine N₂O flux was significantly correlated with NH₄, NO₃ and DIN (NH₄ + NO₃) concentrations, loads and yields. The emission factors EF(a) (i.e., the ratio of N₂O emission rate and DIN load) and EF(b) (i.e., the ratio of N₂O and DIN concentrations) values were comparable and showed negative correlations with nitrogen concentration, load and yield and water discharge, but positive correlations with the dissolved organic carbon : DIN ratio. After individually evaluating 82 potential regression models based on EF(a) or EF(b) for global, temperate zone and subtropical zone datasets, a power function of DIN yield multiplied by watershed area was determined to provide the best fit between modeled and observed riverine N₂O emission rates (EF(a): R² = 0.92 for both global and climatic zone models, n = 70; EF(b): R² = 0.91 for global model and R² = 0.90 for climatic zone models, n = 70). Using recent estimates of DIN loads for 6400 rivers, models estimated global riverine N₂O emission rates of 29.6–35.3 (mean = 32.2) Gg N₂O–N yr⁻¹ and emission factors of 0.16–0.19% (mean = 0.17%). Global riverine N₂O emission rates are forecasted to increase by 35%, 25%, 18% and 3% in 2050 compared to the 2000s under the Millennium Ecosystem Assessment's Global Orchestration, Order from Strength, Technogarden, and Adapting Mosaic scenarios, respectively. Previous studies may overestimate global riverine N₂O emission rates (300–2100 Gg N₂O–N yr⁻¹) because they ignore declining emission factor values with increasing nitrogen levels and channel size, as well as neglect differences in emission factors corresponding to different nitrogen forms. Riverine N₂O emission estimates will be further enhanced through refining emission factor estimates, extending measurements longitudinally along entire river networks and improving estimates of global riverine nitrogen loads.     

Is there any effect of renal failure on the hepatic regeneration capacity following partial hepatectomy in rats?

The effects of renal dysfunction on liver regeneration capacity have not been fully elucidated before, although many patients with renal failure are subjected to hepatectomy due to hepatobiliary diseases. In this study, we sought to determine the effects of renal dysfunction on the hepatic regeneration capacity using rat chronic renal failure model. After establishing chronic renal failure (CRF group) by semi-total renal resection, the rats were subjected to 70% partial hepatectomy (PHx). Rats without renal failure were used as control (Sham group). The hepatic regeneration rate, histology of the liver, clearance of indocyanine green into the bile, and the expression of hepatic regeneration-associated genes in the liver were evaluated. The hepatic regeneration rate was lower in CRF group as compared to Sham group on day 1 after PHx. Mitotic index evaluated by histologic examination on day 1 after PHx was also significantly lower in CRF group. However, no difference in these indices was observed on day 2 and 7 between Sham and CRF. Indocyanine green clearance rate was almost identical between Sham and CRF on day 7 following PHx. The baseline expressions of the hepatic regeneration-associated genes, such as IL-6, TNF-alpha, HGF, c-fos, and c-jun, in the liver of CRF were significantly lower than those of Sham. However, the rate of upregulation of these genes was not significantly different between Sham and CRF. These results clearly demonstrate that the renal dysfunction, although initially delays the onset, does not suppress the total hepatic regeneration capacity following partial hepatectomy. The function of the regenerated liver on day 7 after PHx also was not different. Our results provide a possibility that the hepatectomy can be indicated even for the patient with a chronic renal failure.