Autotrophic ammonia oxidation at low pH through urea hydrolysis.

Ammonia oxidation in laboratory liquid batch cultures of autotrophic ammonia oxidizers rarely occurs at pH values less than 7, due to ionization of ammonia and the requirement for ammonium transport rather than diffusion of ammonia. Nevertheless, there is strong evidence for autotrophic nitrification in acid soils, which may be carried out by ammonia oxidizers capable of using urea as a source of ammonia. To determine the mechanism of urea-linked ammonia oxidation, a ureolytic autotrophic ammonia oxidizer, Nitrosospira sp. strain NPAV, was grown in liquid batch culture at a range of pH values with either ammonium or urea as the sole nitrogen source. Growth and nitrite production from ammonium did not occur at pH values below 7. Growth on urea occurred at pH values in the range 4 to 7.5 but ceased when urea hydrolysis was complete, even though ammonia, released during urea hydrolysis, remained in the medium. The results support a mechanism whereby urea enters the cells by diffusion and intracellular urea hydrolysis and ammonia oxidation occur independently of extracellular pH in the range 4 to 7.5. A proportion of the ammonia produced during this process diffuses from the cell and is not subsequently available for growth if the extracellular pH is less than 7. Ureolysis therefore provides a mechanism for nitrification in acid soils, but a proportion of the ammonium produced is likely to be released from the cell and may be used by other soil organisms.     

Nitrification of archaeal ammonia oxidizers in acid soils is supported by hydrolysis of urea

The hydrolysis of urea as a source of ammonia has been proposed as a mechanism for the nitrification of ammonia-oxidizing bacteria (AOB) in acidic soil. The growth of Nitrososphaera viennensis on urea suggests that the ureolysis of ammonia-oxidizing archaea (AOA) might occur in natural environments. In this study, ¹⁵N isotope tracing indicates that ammonia oxidation occurred upon the addition of urea at a concentration similar to the in situ ammonium content of tea orchard soil (pH 3.75) and forest soil (pH 5.4) and was inhibited by acetylene. Nitrification activity was significantly stimulated by urea fertilization and coupled well with abundance changes in archaeal amoA genes in acidic soils. Pyrosequencing of 16S rRNA genes at whole microbial community level demonstrates the active growth of AOA in urea-amended soils. Molecular fingerprinting further shows that changes in denaturing gradient gel electrophoresis fingerprint patterns of archaeal amoA genes are paralleled by nitrification activity changes. However, bacterial amoA and 16S rRNA genes of AOB were not detected. The results strongly suggest that archaeal ammonia oxidation is supported by hydrolysis of urea and that AOA, from the marine Group 1.1a-associated lineage, dominate nitrification in two acidic soils tested.     

The effect of pellet size on the ammonia loss from urea applied to forest soil

Summary Using diluted phosphoric acid- and glycerol-treated polyurethane plastic foam discs as static ammonia absorbers, the extent of ammonia loss from applied urea was determined on forest soil under field conditions. The investigation, which primarily involved a comparison of urea materials of two different pellet sizes (2–4 mg and 2060 mg urea per pellet, respectively), extended over a period of 28 days. The urea was applied to the soil surface at a rate of 200 kg N per hectare.It was found that the gaseous ammonia loss from the large-pellet urea (tablets) was markedly lower than that from the small-pellet urea during the first two weeks of exposure. On extending the observation period to four weeks, this difference in cumulative ammonia loss decreased successively. After 28 days' exposure, at a daily mean temperature of 13°C, the volatile loss amounted to 20 and 22 per cent, respectively. An addition of 5% (w/w) of a solution of concentrated orthophosphoric acid, or a fine-crystalline ortho-boric acid to the large-pellet urea, resulted in a reduction of the loss to half the value. The possibilities of controlling the ammonia loss from urea by combining the large pellet size with the addition of urease inhibitors are discussed. re]19721012     

Effect of phenylphosphorodiamidate on urea hydrolysis,ammonia volatilization and rice growth in an alkali soil

Summary In order to improve nitrogen recovery by rice, the effect of a urease inhibitor phenylphosphorodiamidate (PPD) on the efficiency of fertilizer urea was studied in laboratory and greenhouse. Addition of PPD to urea (5% w/w) delayed urea hydrolysis by 3 to 4 days and reduced ammonia volatilization from 45% (without PPD) to 8.5% (with PPD). Ammonia volatilization obeyed first order kinetics. Urea hydrolysis was sufficiently strongly inhibited to match the nitrification potential of the soil. N application to rice by three different modes showed that a delayed mode (4 splits) was superior to two conventional modes (3 splits) in nitrogen recovery and fertilizer efficiency since it met nitrogen requirement of plants at reproductive stage. In 2 out of 3 modes of application, there was a 14% increase (relative) in grain yields and dry matter, and 6.8% increase in N uptake efficiency on application of PPD along with urea. The results indicate that urease inhibitors like PPD can be effectively used to block urea hydrolysis, reduce ammonia volatilization losses and improve N use efficiency by rice.     

The African lungfish, Protopterus dolloi, detoxifies ammonia to urea during environmental ammonia exposure

The African lungfish, Protopterus dolloi, was able to maintain a low level of blood plasma ammonia during exposure to high concentrations of environmental ammonia. After 6 d of exposure to 30 or 100 mM NH(4)Cl, the total ammonia concentrations in the blood plasma were 0.288 and 0.289 mM, respectively, which were only 1.7-fold greater than the control value of 0.163 mM. In addition, accumulation of ammonia occurred only in the muscle, but not in the liver. This was achieved in part through urea synthesis, as reflected by significant increases in urea contents in the muscle, liver, and plasma of the experimental animals. In contrast with plasma ammonia, the plasma urea concentrations of specimens exposed to 30 or 100 mM NH(4)Cl for 6 d increased 15.4-fold and 18.8-fold, respectively. Taken together, these results suggest that P. dolloi upregulated the rate of urea synthesis to detoxify ammonia during environmental ammonia exposure and that the increased rate of urea synthesis was fast enough to compensate for the rate of endogenous ammonia production plus the net influx of exogenous ammonia in these experimental animals. Simultaneously, there were increases in the rates of urea excretion in the experimental animals between day 2 and day 6 of environmental ammonia exposure. Interestingly, the rates of urea excretion in specimens exposed to 100 mM NH(4)Cl were lower than those exposed to 30 mM NH(4)Cl, despite the presumably greater load of ammonia to be detoxified to urea in the former situation. It would appear that P. dolloi was regulating the rate of urea excretion during ammonia exposure to retain urea, which might have some physiological functions under environmental stresses yet to be determined. There were decreases in the contents of glutamate, glutamine, and total free amino acids in the liver of the experimental animals, which indirectly suggest that a reduction in the rate of proteolysis and/or amino acid catabolism would have occurred that might lead to a decrease in ammonia production. Our results suggest that, unlike marine elasmobranchs and coelacanths, which synthesize and retain urea for osmoregulatory purposes, the ureogenic P. dolloi was adapted to synthesizing and excreting urea for the purpose of ammonia detoxification.     

Nitrification and ammonia volatilisation losses from urea and dicyandiamide-treated urea in a sandy loam soil

Summary Nitrification and ammonia volatilisation losses from urea and dicyandiamide (DCD)-treated urea were studied in a sandy loam soil. Laboratory experiments indicated that 20 ppm (of soil) DCD effectively inhibited nitrification of urea over sixty days. If the urea was treated with DCD (20 ppm), ammonia emission from the soil was extended over 105 days; with urea alone, it was negligible after 15 days. A field study indicated that DCD treatment increased volatilisation losses of ammonia tremondously if urea was applied to the soil surface; these losses were minimised if the urea was placed at 5 cm depth. It would seem that nitrification inhibitors must be combined with a placement technique.     

Odour and ammonia emissions from intensive poultry units in Ireland

Odour and ammonia emissions were measured from three broiler, two layer and two turkey houses in Ireland. The broiler units gave a large range of odour and ammonia emission rates depending on the age of the birds and the season. A considerable variation between the odour and ammonia emission rates was evident for the two layer units which may have been due to the different manure handling systems utilised in the houses. There was relatively little difference in the odour and ammonia emissions from the two turkey houses. As a precautionary principle, odour emission rates utilised in atmospheric dispersion models should use the maximum values for broilers and turkeys (1.22 and 10.5 ou(E) s(-1) bird(-1) respectively) and the mean value for the layers depending on the manure handling system used (0.47 or 1.35 ou(E) s(-1) bird(-1)).     

Odour and ammonia emissions from intensive pig units in Ireland

Odour and ammonia emissions were measured at four intensive pig units in Ireland. Odour samples were collected on-site and analysed for odour concentration using an olfactometer. Ammonia concentrations in the exhaust ventilation air were measured using a portable sensor. The geomean odour emission rates over the four pig units were 17.2, 44.4, 4.3, 9.9 and 16.8 ou(E) s(-1) animal(-1) for dry sows, farrowing sows, first stage weaners, second stage weaners and finishers, respectively. The mean ammonia emission rates, measured at two of the units, were 12.1, 17.1, 1.4, 2.9 and 10.0 g d(-1) animal(-1) for dry sows, farrowing sows, first stage weaners, second stage weaners and finishers, respectively. In general, the odour and ammonia emission rates were comparable to those reported in literature, although some odour emission rate figures were noticeably lower for finishing pigs in this study. The variability in the data highlights the need for individual site assessment.     

Nitrous oxide emissions from wastewater treatment processes

Nitrous oxide (N(2)O) emissions from wastewater treatment plants vary substantially between plants, ranging from negligible to substantial (a few per cent of the total nitrogen load), probably because of different designs and operational conditions. In general, plants that achieve high levels of nitrogen removal emit less N(2)O, indicating that no compromise is required between high water quality and lower N(2)O emissions. N(2)O emissions primarily occur in aerated zones/compartments/periods owing to active stripping, and ammonia-oxidizing bacteria, rather than heterotrophic denitrifiers, are the main contributors. However, the detailed mechanisms remain to be fully elucidated, despite strong evidence suggesting that both nitrifier denitrification and the chemical breakdown of intermediates of hydroxylamine oxidation are probably involved. With increased understanding of the fundamental reactions responsible for N(2)O production in wastewater treatment systems and the conditions that stimulate their occurrence, reduction of N(2)O emissions from wastewater treatment systems through improved plant design and operation will be achieved in the near future.     

A spatial micro-simulation analysis of methane emissions from Irish agriculture

Using micro-simulation modelling techniques this paper examines methane emissions across Irish farms. The effects of a carbon equivalent tax on average family farm income are analysed at both the farm and regional level. The spatial micro-simulation model developed uses a technique called simulated annealing to match the Irish Census of Agriculture data to a National Farm Survey. The main advantage of the spatial micro-simulation approach is the fact that it allows one to account for the heterogeneity in the farm population across space. The results of the modelling process are presented using GIS mapping techniques and highlight the fact that there would be significant regional variation in the burden of an agricultural tax that was based on a rate per unit of methane emissions. The results also demonstrate that if the methane tax revenue raised was redistributed in the form of an environmental subsidy to farmers participating in an agri-environmental scheme (the Rural Environment Protection Scheme (REPS)) it would encourage farmers to participate in the scheme and could also have the effect of moving low income farms up the earnings distribution ladder.     

Laboratory measurements and simulations of ammonia volatilization from urea applied to calcareous Chinese loess soils

Ammonia volatilization is the major pathway for mineral nitrogen loss in the calcareous soils of the Chinese loess plateau, with maximum losses reaching 50% of the fertilizer-N applied. A volatilization-diffusion experiment was carried out in the laboratory using a forced-draft system and soil columns of 15.5 cm depth. Urea was surface applied at rates of 210 kg N ha^-1 to a soil with 10% CaCO₃ and a pH of 7.7. The amount of ammonia volatilized as well as the concentration profiles of ammoniacal-nitrogen and soil pH in the upper 50 mm of the soil columns after 4, 7 and 10 days were measured and subsequently modelled. The mechanistic model of Rachhpal-Singh and Nye, originally developed for neutral, non-calcareous soils, was modified to include the pH-buffering action of the soil carbonates. Model parameters were independently determined or taken from the literature. Measured and predicted cumulative NH₃ losses agreed very well in the first 10 days following fertilizer application. However, in contrast to the simulations, NH₃-volatilization was still proceeding in the experiment even after 13 days, with cumulative losses reaching 60% of the applied N. In addition to the high initial soil pH, the low bulk density and high volumetric air content of the soil columns used for the experiment proved decisive for the high rates of ammonia volatilization, provoking a strong increase in the amount of ammoniacal-N diffusing towards the soil surface as gaseous NH₃. The simulations showed that due to the high soil pH, the buffering action of the soil carbonates played a comparatively smaller role.     

The molecular basis of speciation: from patterns to processes,rules to mechanisms

The empirical study of speciation has brought us closer to unlocking the origins of life’s vast diversity. By examining recently formed species, a number of general patterns, or rules, become apparent. Among fixed differences between species, sexual genes and traits are one of the most rapidly evolving and novel functional classes, and premating isolation often develops earlier than postmating isolation. Among interspecific hybrids, sterility evolves faster than inviability, the X-chromosome has a greater effect on incompatibilities than autosomes, and hybrid dysfunction affects the heterogametic sex more frequently than the homogametic sex (Haldane’s rule). Haldane’s rule, in particular, has played a major role in reviving interest in the genetics of speciation. However, the large genetic and reproductive differences between taxa and the multi-factorial nature of each rule have made it difficult to ascribe general mechanisms. Here, we review the extensive progress made since Darwin on understanding the origin of species. We revisit the rules of speciation, regarding them as landmarks as species evolve through time. We contrast these ‘rules’ of speciation to ‘mechanisms’ of speciation representing primary causal factors ranging across various levels of organization—from genic to chromosomal to organismal. To explain the rules, we propose a new ‘hierarchical faster-sex’ theory: the rapid evolution of sex and reproduction-related (SRR) genes (faster-SRR evolution), in combination with the preferential involvement of the X-chromosome (hemizygous X-effects) and sexually selected male traits (faster-male evolution). This unified theory explains a comprehensive set of speciation rules at both the prezyotic and postzygotic levels and also serves as a cohesive alternative to dominance, composite, and recent genomic conflict interpretations of Haldane’s rule.