Nitrosospira spp. can produce nitrous oxide via a nitrifier denitrification pathway

Nitrous oxide (N2O) emission from soils is a major contributor to the atmospheric loading of this potent greenhouse gas. It is thought that autotrophic ammonia oxidizing bacteria (AOB) are a significant source of soil-derived N2O and a denitrification pathway (i.e. reduction of NO2- to NO and N2O), so-called nitrifier denitrification, has been demonstrated as a N2O production mechanism in Nitrosomonas europaea. It is thought that Nitrosospira spp. are the dominant AOB in soil, but little information is available on their ability to produce N2O or on the existence of a nitrifier denitrification pathway in this lineage. This study aims to characterize N2O production and nitrifier denitrification in seven strains of AOB representative of clusters 0, 2 and 3 in the cultured Nitrosospira lineage. Nitrosomonas europaea ATCC 19718 and ATCC 25978 were analysed for comparison. The aerobically incubated test strains produced significant (P < 0.001) amounts of N2O and total N2O production rates ranged from 2.0 amol cell(-1) h(-1), in Nitrosospira tenuis strain NV12, to 58.0 amol cell(-1) h(-1), in N. europaea ATCC 19718. Nitrosomonas europaea ATCC 19718 was atypical in that it produced four times more N2O than the next highest producing strain. All AOB tested were able to carry out nitrifier denitrification under aerobic conditions, as determined by production of N-15-N2O from applied N-15-NO2-. Up to 13.5% of the N2O produced was derived from the exogenously applied N-15-NO2-. The results suggest that nitrifier denitrification could be a universal trait in the betaproteobacterial AOB and its potential ecological significance is discussed.

Effect of earthworm Eisenia fetida and wetland plants on nitrification and denitrification potentials in vertical flow constructed wetland.

The response of nitrification potentials, denitrification potentials, and N removal efficiency to the introduction of earthworms and wetland plants in a vertical flow constructed wetland system was investigated. Addition of earthworms increased nitrification and denitrification potentials of substrate in non-vegetated constructed wetland by 236% and 8%, respectively; it increased nitrification and denitrification potentials in rhizosphere in vegetated constructed wetland (Phragmites austrail, Typha augustifolia and Canna indica), 105% and 5%, 187% and 12%, and 268% and 15% respectively. Denitrification potentials in rhizosphere of three wetland plants were not significantly different, but nitrification potentials in rhizosphere followed the order of C. indica > T. augustifolia > P. australis when addition of earthworms into constructed wetland. Addition of earthworms to the vegetated constructed significantly increased the total number of bacteria and fungi of substrates (P < 0.05). The total number of bacteria was significantly correlated with nitrification potentials (r = 913, P < 0.01) and denitrification potentials (r = 840, P < 0.01), respectively. The N concentration of stems and leaves of C. indica were significantly higher in the constructed wetland with earthworms (P < 0.05). Earthworms had greater impact on nitrification potentials than denitrification potentials. The removal efficiency of N was improved via stimulated nitrification potentials by earthworms and higher N uptake by wetland plants.

Impact of sewage sludge applications on the biogeochemistry of soils

This report describes an investigation into the bioavailability and fate of trace metals and their subsequent impact on important soil microbiological functions such as nitrification, denitrification and methane oxidation in low and high Cu containing soils in the presence and absence of residual organic matter from sewage sludge additions made 10 years earlier. The soils being studied are part of long term sewage sludge trials and include a low Cu soil ( 13.3mg Cu/ kg soil, 4.18 LOI %), left un- amended to serve as a control soil, soil amended with a high Cu sewage sludge ( 278.3mg Cu/ kg soil, 6.52 LOI %) and soil amended with a low Cu sewage sludge ( 46.3mg Cu/ kg soil, 6.18 LOI %). Soil was also amended with inorganic metal salts ( 273.4mg Cu/ kg soil, 4.52 LOI %) to further investigate the impact of Cu in the absence of additional organic matter contained in applied sewage sludge. Data from the first two years of a project are presented which has included field- based studies at long term sewage sludge trials based in Watlington, Oxford, UK and laboratory based studies at the Institute of Grassland & Environmental Research, North Wyke, Devon, UK.

Hydrological controls on soil redox dynamics in a peat-based, restored wetland

Increasing areas of altered wetland are being restored by re-flooding the soil. Evidence in the literature indicates that this practice can induce the redox-mediated release of soil nutrients, thereby increasing the risk of diffuse water pollution. However, for the sake of improving wedand management decisions, there is a need for more detailed studies of the underlying relationship between the hydrological and redox dynamics that explain this risk; this is particularly the case in agricultural peatlands that are commonly targeted for the creation of lowland wet grassland. A 12-month field study was conducted to evaluate the relationship between hydrological fluctuations and soil redox potential (Eh) in a nutrient-rich peat field (32 g N kg(-1) and 1100 mg P kg(-1) in the surface 0-30 cm soil) that had been restored as lowland wet grassland from intensive arable production. Field tensiometers were installed at the 30-, 60- and 90-cm soil depths, and Pt electrodes at the 10-, 30-, 60- and 90-cm depths, for daily logging of soil water tension and Eh, respectively. The values for soil water tension displayed a strong negative relationship (P < 0.001) with monthly dip well observations of water table height. Calculations of soil water potential from the logged tension values were used, therefore, to provide a detailed profile of field water level and, together with precipitation data, explained some of the variation in Eh. For example, during the summer, alternating periods of aerobism (Eh > 330 mV) in the surface, 0-10 cm layer of peat coincided with intense precipitation events. Redox potential throughout the 30-100 cm profile also fluctuated seasonally; indeed, at all depths Eh displayed a strong, negative relationship (P < 0.001) with water table height over the 12-month study period. However, Eh throughout the 30-100 cm profile remained relatively low (< 230 mV), indicating permanently reduced conditions that are associated with denitrification and reductive dissolution of Fe-bound P. The implications of these processes in the N- and P-rich peat for wetland plant diversity and water quality are discussed. (c) 2006 Elsevier B.V. All rights reserved.

Assessing the sources and magnitude of diurnal nitrate variability in the San Joaquin River (California) with an in-situ optical nitrate sensor and dual nitrate isotopes

We investigated diurnal nitrate (NO3-) concentration variability in the San Joaquin River using an in situ optical NO3- sensor and discrete sampling during a 5-day summer period characterized by high algal productivity. Dual NO3- isotopes (delta N-15(NO3) and delta O-18(NO3)) and dissolved oxygen isotopes (delta O-18(DO)) were measured over 2 days to assess NO3- sources and biogeochemical controls over diurnal time-scales. Concerted temporal patterns of dissolved oxygen (DO) concentrations and delta O-18(DO) were consistent with photosynthesis, respiration and atmospheric O-2 exchange, providing evidence of diurnal biological processes independent of river discharge. Surface water NO3- concentrations varied by up to 22% over a single diurnal cycle and up to 31% over the 5-day study, but did not reveal concerted diurnal patterns at a frequency comparable to DO concentrations. The decoupling of delta N-15(NO3) and delta O-18(NO3) isotopes suggests that algal assimilation and denitrification are not major processes controlling diurnal NO3- variability in the San Joaquin River during the study. The lack of a clear explanation for NO3- variability likely reflects a combination of riverine biological processes and time-varying physical transport of NO3- from upstream agricultural drains to the mainstem San Joaquin River. The application of an in situ optical NO3- sensor along with discrete samples provides a view into the fine temporal structure of hydrochemical data and may allow for greater accuracy in pollution assessment.

Presubmergence and green manure affect the transformations of nitrogen-15-labeled urea under lowland soil conditions

The effect of presubmergence and green manuring on various processes involved in [N-15]-urea transformations were studied in a growth chamber after [N-15]-urea application to floodwater. Presubmergence for 14 days increased urea hydrolysis rates and floodwater pH, resulting in higher NH3 volatilization as compared to without presubmergence. Presubmergence also increased nitrification and subsequent denitrification but lower N assimilation by floodwater algae caused higher gaseous losses. Addition of green manure maintained higher NH4+-N concentration in floodwater mainly because of lower nitrification rates but resulted in highest NH3 volatilization losses. Although green manure did not affect the KCl extractable NH4+-N from applied fertilizer, it maintained higher NH4+-N content due to its decomposition and increased mineralization of organic N. After 32 days about 36.9% (T-1), 23.9% (T-2), and 36.4% (T-3) of the applied urea N was incorporated in the pool of soil organic N in treatments. It was evident that the presubmergence has effected the recovery of applied urea N.

Modelling the inorganic nitrogen behaviour in a small Mediterranean forested catchment, Fuirosos (Catalonia)

The aim of this work was to couple a nitrogen (N) sub-model to already existent hydrological lumped (LU4-N) and semi-distributed (LU4-R-N and SD4-R-N) conceptual models, to improve our understanding of the factors and processes controlling nitrogen cycling and losses in Mediterranean catchments. The N model adopted provides a simplified conceptualization of the soil nitrogen cycle considering mineralization, nitrification, immobilization, denitrification, plant uptake, and ammonium adsorption/desorption. It also includes nitrification and denitrification in the shallow perched aquifer. We included a soil moisture threshold for all the considered soil biological processes. The results suggested that all the nitrogen processes were highly influenced by the rain episodes and that soil microbial processes occurred in pulses stimulated by soil moisture increasing after rain. Our simulation highlighted the riparian zone as a possible source of nitrate, especially after the summer drought period, but it can also act as an important sink of nitrate due to denitrification, in particular during the wettest period of the year. The riparian zone was a key element to simulate the catchment nitrate behaviour. The lumped LU4-N model (which does not include the riparian zone) could not be validated, while both the semi-distributed LU4-R-N and SD4-R-N model (which include the riparian zone) gave satisfactory results for the calibration process and acceptable results for the temporal validation process.

High resolution simulation of recent Arctic and Antarctic stratospheric chemical ozone loss compared to observations

Simulations of polar ozone losses were performed using the three-dimensional high-resolution (1∘ × 1∘) chemical transport model MIMOSA-CHIM. Three Arctic winters 1999–2000, 2001–2002, 2002–2003 and three Antarctic winters 2001, 2002, and 2003 were considered for the study. The cumulative ozone loss in the Arctic winter 2002–2003 reached around 35% at 475 K inside the vortex, as compared to more than 60% in 1999–2000. During 1999–2000, denitrification induces a maximum of about 23% extra ozone loss at 475 K as compared to 17% in 2002–2003. Unlike these two colder Arctic winters, the 2001–2002 Arctic was warmer and did not experience much ozone loss. Sensitivity tests showed that the chosen resolution of 1∘ × 1∘ provides a better evaluation of ozone loss at the edge of the polar vortex in high solar zenith angle conditions. The simulation results for ozone, ClO, HNO3, N2O, and NO y for winters 1999–2000 and 2002–2003 were compared with measurements on board ER-2 and Geophysica aircraft respectively. Sensitivity tests showed that increasing heating rates calculated by the model by 50% and doubling the PSC (Polar Stratospheric Clouds) particle density (from 5 × 10−3 to 10−2 cm−3) refines the agreement with in situ ozone, N2O and NO y levels. In this configuration, simulated ClO levels are increased and are in better agreement with observations in January but are overestimated by about 20% in March. The use of the Burkholder et al. (1990) Cl2O2 absorption cross-sections slightly increases further ClO levels especially in high solar zenith angle conditions. Comparisons of the modelled ozone values with ozonesonde measurement in the Antarctic winter 2003 and with Polar Ozone and Aerosol Measurement III (POAM III) measurements in the Antarctic winters 2001 and 2002, shows that the simulations underestimate the ozone loss rate at the end of the ozone destruction period. A slightly better agreement is obtained with the use of Burkholder et al. (1990) Cl2O2 absorption cross-sections.

Upland streamwater nitrate dynamics across decadal to sub-daily timescales: a case study of Plynlimon, Wales

Streamwater nitrate dynamics in the River Hafren, Plynlimon, mid-Wales were investigated over decadal to sub-daily timescales using a range of statistical techniques. Long-term data were derived from weekly grab samples (1984–2010) and high-frequency data from 7-hourly samples (2007–2009) both measured at two sites: a headwater stream draining moorland and a downstream site below plantation forest. This study is one of the first to analyse upland streamwater nitrate dynamics across such a wide range of timescales and report on the principal mechanisms identified. The data analysis provided no clear evidence that the long-term decline in streamwater nitrate concentrations was related to a decline in atmospheric deposition alone, because nitrogen deposition first increased and then decreased during the study period. Increased streamwater temperature and denitrification may also have contributed to the decline in stream nitrate concentrations, the former through increased N uptake rates and the latter resultant from increased dissolved organic carbon concentrations. Strong seasonal cycles, with concentration minimums in the summer, were driven by seasonal flow minimums and seasonal biological activity enhancing nitrate uptake. Complex diurnal dynamics were observed, with seasonal changes in phase and amplitude of the cycling, and the diurnal dynamics were variable along the river. At the moorland site, a regular daily cycle, with minimum concentrations in the early afternoon, corresponding with peak air temperatures, indicated the importance of instream biological processing. At the downstream site, the diurnal dynamics were a composite signal, resultant from advection, dispersion and nitrate processing in the soils of the lower catchment. The diurnal streamwater nitrate dynamics were also affected by drought conditions. Enhanced diurnal cycling in Spring 2007 was attributed to increased nitrate availability in the post-drought period as well as low flow rates and high temperatures over this period. The combination of high-frequency short-term measurements and long-term monitoring provides a powerful tool for increasing understanding of the controls of element fluxes and concentrations in surface waters.

Effect of cattle urine addition on the surface emissions and subsurface concentrations of greenhouse gases in a UK peat grassland

Grazing systems represent a substantial percentage of the global anthropogenic flux of nitrous oxide (N2O) as a result of nitrogen addition to the soil. The pool of available carbon that is added to the soil from livestock excreta also provides substrate for the production of carbon dioxide (CO2) and methane (CH4) by soil microorganisms. A study into the production and emission of CO2, CH4 and N2O from cattle urine amended pasture was carried out on the Somerset Levels and Moors, UK over a three-month period. Urine-amended plots (50 g N m−2) were compared to control plots to which only water (12 mg N m−2) was applied. CO2 emission peaked at 5200 mg CO2 m−2 d−1 directly after application. CH4 flux decreased to −2000 μg CH4 m−2 d−1 two days after application; however, net CH4 flux was positive from urine treated plots and negative from control plots. N2O emission peaked at 88 mg N2O m−2 d−1 12 days after application. Subsurface CH4 and N2O concentrations were higher in the urine treated plots than the controls. There was no effect of treatment on subsurface CO2 concentrations. Subsurface N2O peaked at 500 ppm 12 days after and 1200 ppm 56 days after application. Subsurface NO3− concentration peaked at approximately 300 mg N kg dry soil−1 12 days after application. Results indicate that denitrification is the key driver for N2O release in peatlands and that this production is strongly related to rainfall events and water-table movement. N2O production at depth continued long after emissions were detected at the surface. Further understanding of the interaction between subsurface gas concentrations, surface emissions and soil hydrological conditions is required to successfully predict greenhouse gas production and emission.

Anthropogenic nutrient sources and loads from a Mediterranean catchment into a coastal lagoon: Mar Menor, Spain

The Mar Menor is a coastal lagoon increasingly threatened by urban and agricultural pressures. The main watercourse draining into the lagoon is the Rambla del Albujón. A fortnightly campaign carried out over one annual cycle enabled us to characterize the treated urban sewage effluents and agricultural sources which contribute to the nutrient fluxes in the watercourse. Multivariate analysis provided information for establishing chemical signatures and for assessing the relative influence of the various sources on the water quality at the outlet. Mass balances were used to examine net gains and losses, and cross-correlations with rainfall to analyze climatic influence and control factors in the trends of the nutrient flux. The rainfall pattern was significantly cross-correlated with nitrate and phosphorus fluxes from agricultural sources, while fluctuations in the resident population explained the phosphorus flux trend in urban sources. 50% of dissolved inorganic nitrogen was from agricultural sources, while 70% of total phosphate and 91% of total organic carbon were from urban point sources. The net amounts of all the nutrients fell as a result of plant uptake and/or denitrification in the channel. The control of urban point sources (phosphorus-enriched) is suggested as a promptly action for improving the health of the coastal lagoon.

Novel European free-living, non-diazotrophic Bradyrhizobium isolates from contrasting soils that lack nodulation and nitrogen fixation genes - a genome comparison

The slow-growing genus Bradyrhizobium is biologically important in soils, with different representatives found to perform a range of biochemical functions including photosynthesis, induction of root nodules and symbiotic nitrogen fixation and denitrification. Consequently, the role of the genus in soil ecology and biogeochemical transformations is of agricultural and environmental significance. Some isolates of Bradyrhizobium have been shown to be non-symbiotic and do not possess the ability to form nodules. Here we present the genome and gene annotations of two such free-living Bradyrhizobium isolates, named G22 and BF49, from soils with differing long-term management regimes (grassland and bare fallow respectively) in addition to carbon metabolism analysis. These Bradyrhizobium isolates are the first to be isolated and sequenced from European soil and are the first free-living Bradyrhizobium isolates, lacking both nodulation and nitrogen fixation genes, to have their genomes sequenced and assembled from cultured samples. The G22 and BF49 genomes are distinctly different with respect to size and number of genes; the grassland isolate also contains a plasmid. There are also a number of functional differences between these isolates and other published genomes, suggesting that this ubiquitous genus is extremely heterogeneous and has roles within the community not including symbiotic nitrogen fixation.