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Background: Brachiaria humidicola (Bh) has the ability to produce biological nitrification inhibitors (NIs) and release NIs from the root to the soil. Aims: To compare the effects of growing Bh with Brachiaria ruziziensis (Br, which is not able to produceNIs) on soil nitrogen (N) dynamics,Ngases and carbon dioxide (CO2) emissions and nitrifiers and denitrifiers following sheep urine application, a laboratory incubation was conducted in a He/O2 continuous flow denitrification system (DENIS). This incubation was conducted in the absence of light. Hence themeasured effects of Bh and Br on N cycling were the residual effect of biological NIs released into the soil prior to the incubation and released via root death. Methods: The treatmentswere: (1) Bhwith water application (Bh+W); (2) Bh with sheep urine (Bh + U); (3) Br with water application (Br + W); (4) Br with sheep urine (Br + U). Results: Results showed that soil NO3– concentration increased significantly in the soil with sheep urine application after the incubation. Soil nitrous oxide (N2O) and nitric oxide (NO) emissions increased immediately after the sheep urine application and peaked twice during the incubation. Cumulative emissions for the first peak were significantly lower from the Bh + U treatment (0.054 kg N ha–1) compared with the Br + U treatment (0.111 kg N ha–1), but no significant differences were observed in the total cumulative N2O and NO emissions between the Bh + U and Br + U treatment at the end of the incubation. Sheep urine addition did not affect the AOA, nirS and nosZ gene copies, but significantly increased the AOB gene copies after the incubation. Conclusions: We conclude that the residual effect of Bh to mitigate N2O emissions in a highly nitrifying soil is short-lived.

The benefits that nitrogen (N) fertilizers represent for the sustenance of the population at the global scale are undeniable. However, the nitrogen-use efficiency (NUE) in agriculture (the amount of nitrogen retrieved in food produced per unit of nitrogen applied) is extremely low. Volatilization, leaching, soil erosion and denitrification processes result in the loss of most of the applied N, which isleading to field recoveries that rarely exceed 50%. These losses that are driven by both biotic and abiotic factors cause several environmental damages including water eutrophication, greenhouse gases production and soil acidification. This chapter aims to provide an overview of the nitrogen cycle in agriculture and the N losses derived from the use of N-fertilizers as well as to give a comprehensive description of the factors that drive these losses including soil pH, soil temperature, soil moisture and oxygen availability, soil-carbon (C) content, the C:N ratio of applied substrates, soil pore spaces and composition of microbial communities.

Nitrogen (N) stabilizers such as urease inhibitors (UI) and nitrification inhibitors (NI) are promising tools to mitigate N losses from fertilized soils. To better understand the efficacy of UI and NI, a 2-year field trial was carried out in the North China Plain (NCP) to analyze the impact of UI and NI on NH3 loss and N transformations following urea fertilizer application. Additionally, a laboratory study using an automated continuous-flow incubation system was conducted under controlled conditions, using the same soil, to evaluate the mitigation potential of the N stabilizers on NO, N2O and CO2 emission. The results showed that a novel UI product, Limus® (BASF, Germany), containing active ingredients N-(n-butyl) thiophosphoric triamide (NBPT) and N-(n-propyl) thiophosphoric triamide (NPPT), limited ammonium formation rate and reduced NH3 loss in both maize (by 85 and 96% for year 1 and 2, respectively) and wheat (by 41 and 64%, for year 1 and 2, respectively) seasons. The 3, 4-dimethypyrazole phosphate (DMPP) amendment significantly retarded nitrate formation rate but the effectiveness was compromised by high ambient temperature; additionally, the NI amendment increased NH3 emission (by 16 and 24% for maize and wheat year 2, respectively). In the laboratory incubation experiment, addition of the UI reduced emissions of NO, N2O and CO2 by 89, 73 and 19%, respectively, while the addition of the NI reduced the respective emissions by 95, 83 and 24% over the 16 d incubation period. These results suggest that N stabilizers can play a significant role in the mitigation of the environmental impacts of intensive agriculture, and, in particular, that the UI amendment may have the better potential to reduce N losses in the climatic and soil conditions of the NCP, and that the NI should be avoided under high ambient temperatures.

To identify the production and consumption pathways and temporal dynamics of N2O emitted from soil, this study uses 15N-labelled substrate-N to quantify the underlying gross N transformation rates using the Ntrace analysis tool and link them to N-emissions. In three experiments twelve soil cores each were incubated in a lab incubation system to measure gaseous emissions, while parallel incubations under the same conditions were set up for destructive soil sampling at 7 time points. Using the triple labelling technique (applying NH4NO3 with either the NH4+-N or the NO3−-N, or both being 15N labelled), this study investigated the effects of 55, 70 and 85% water filled pore space (deemed to promote nitrification, both nitrification and denitrification, and denitrification, respectively) in a clay soil on gaseous N emissions and investigates the source and processes leading to N2O emissions. To assess the utilisation of applied NO3− vs. nitrified NO3− from applied NH4+, the 15N tracing tool Ntrace was used to quantify the rates of immobilisation of NO3− and NH4+, oxidation of NH4+, mineralisation of organic N and subsequent nitrification by the analysis of the 15N in the soil. Gross transformation rates were calculated, indicating the relative importance of added NO3− and NO3− derived from nitrified added NH4+. Results show an important contribution of heterotrophic nitrification (organic N oxidation to NO3−) which was highest at the 55% water filled pore space (WFPS), decreasing in its contribution to N-transformation processes with increasing WFPS, while nitrification (NH4+ oxidation to NO3−) was contributing the most at 70% WFPS. The contribution of denitrification increased with increasing WFPS, but only became dominant at 85% WFPS. While denitrification still showed to be most important at high and nitrification at lower WFPS, the actual % WFPS values were not as expected and highlight the fact that WFPS is a contributor, but not the sole/most important parameter determining the type of N-transformation processes taking place.

The objective of the present study was to evaluate the impact of the treatment of slurry liquid fraction (LF) acidified to pH 5.5 (ALF) on nitrification and denitrification processes after soil application. The impact of such treatment was compared with that of untreated LF, LF treated with a nitrification inhibitor (3,4-Dimethylpyrazole phosphate (DMPP)) (LF + DMPP). An incubation was conducted using the denitrification incubation system (DENIS/gas-flow-core technique) at a constant temperature of 20 °C and lasted for 32 days in order to follow nitrogen dynamics and gaseous emissions (N2O, NO, CO2) from soil. Inhibition of ammonium nitrification and nitrate accumulation was evident in both LF + DMPP and ALF at the top soil (0–3.75 cm) and those effects were stronger in the LF + DMPP. Denitrification was the main source of N2O emissions from soils amended with treated and untreated LF. Compared to the untreated LF, the ALF significantly reduced the total N lost as N2O from 0.10% to 0.05% of the applied N whereas the DMPP reduced the total N lost as N2O from 0.10% to 0.07%. Relative to the untreated LF, the ALF reduced the total N lost as NO emissions from 0.03% to 0.02% of the applied N whereas DMPP addition led to a stronger decrease from 0.03% to 0.01%. Both, ALF and LF + DMPP had no impact on CO2 emissions relative to the untreated LF. The ALF reduced CO2 emissions by 19% relative to the LF + DMPP. Our results demonstrate that slurry acidification affect not only nitrification but also the denitrification process. This suggests that slurry acidification is a valid technique to minimize N emissions.

To test the hypothesis that the inclusion of the forage herbs chicory (Cichorium intybus L.) or plantain (Plantago lanceolata L.) or both in a grass–legume pasture mix improves persistence of sown vegetation and reduces weed and invertebrate pest ingress, a study was undertaken in 31–44 intensively managed pastures in each of five regions in New Zealand (Northland, Waikato, Bay of Plenty, Taranaki and Canterbury). The regions were stratified according to farm type (dairy or sheep and beef), pasture type (sown with grasses, legumes and herbs or grasses and legumes) and pasture age (young: 1–2 years old; medium: 3–4 years old; and old: 5+ years since sowing, n = 171). Sown species ground cover and emergence from the soil seed bank was greater, and unsown species ground cover and emergence lower, in sheep and beef pastures sown with herbs than without herbs (78% vs 68% ground cover, respectively, averaged over all pasture ages), but there was no difference between pasture types on dairy farms. Invert...

Rationale Isotopic signatures of N2O can help distinguish between two sources (fertiliser N or endogenous soil N) of N2O emissions. The contribution of each source to N2O emissions after N‐application is difficult to determine. Here, isotopologue signatures of emitted N2O are used in an improved isotopic model based on Rayleigh‐type equations. Methods The effects of a partial (33% of surface area, treatment 1c) or total (100% of surface area, treatment 3c) dispersal of N and C on gaseous emissions from denitrification were measured in a laboratory incubation system (DENIS) allowing simultaneous measurements of NO, N2O, N2 and CO2 over a 12‐day incubation period. To determine the source of N2O emissions those results were combined with both the isotope ratio mass spectrometry analysis of the isotopocules of emitted N2O and those from the 15N‐tracing technique. Results The spatial dispersal of N and C significantly affected the quantity, but not the timing, of gas fluxes. Cumulative emissions are larger for treatment 3c than treatment 1c. The 15N‐enrichment analysis shows that initially ~70% of the emitted N2O derived from the applied amendment followed by a constant decrease. The decrease in contribution of the fertiliser N‐pool after an initial increase is sooner and larger for treatment 1c. The Rayleigh‐type model applied to N2O isotopocules data (δ15Nbulk‐N2O values) shows poor agreement with the measurements for the original one‐pool model for treatment 1c; the two‐pool models gives better results when using a third‐order polynomial equation. In contrast, in treatment 3c little difference is observed between the two modelling approaches. Conclusions The importance of N2O emissions from different N‐pools in soil for the interpretation of N2O isotopocules data was demonstrated using a Rayleigh‐type model. Earlier statements concerning exponential increase in native soil nitrate pool activity highlighted in previous studies should be replaced with a polynomial increase with dependency on both N‐pool sizes., Biotechnology and Biological Sciences Research Council (BBSRC), Grant/Award Number: BB/K001051/1.D.

Oil sands tailings ponds in Alberta (Canada) are strongly stratified ecosystems structured in an upper water layer and underlying mud layers that harbour a diversity of microorganisms, contributing to hydrocarbon degradation and elemental cycling. Until now not much is known about the biogeochemistry of the ponds and their spatial structure is not well explored yet. An understanding of microbial activity and community composition is important, in particular, in order to determine potential effects on pond properties and long term development. Therefore, the purpose of the present study was to identify reactive zones of iron, carbon and sulfur cycling in an active tailings pond, by comparing biogeochemical data along two depth profiles. For both profiles a zone of intense sulfur cycling was substantiated by maxima of: (a) dissolved and solid sulfides; (b) sulfate reduction rates and thiosulfate oxidation potentials; and (c) viable counts of sulfate reducers and relative abundances of functional genes. In addition, methanogenesis and microbial iron reduction were shown to be important electron accepting processes in the ponds. All processes coexisted in a zone of intense elemental cycling at a depth of 1–4 m below the water–mud interface, where fresh tailings are likely to accumulate. Microbial activity and biomass decreased with depth, where tailings had higher age and density. While the upper mud layers were influenced by the presence of different archaea, the microbial communities showed an increased presence of bacterial species at depth. Insights from qPCR, 35 S radiotracer technique and stable isotope analysis mirrored some differences between the profiles, regarding sulfur and carbon cycling. Despite this, both profiles showed remarkably similar patterns of microbial community composition and activity, revealing a good reproducibility of biogeochemical cycling within a few metres.

Jarosite minerals (AB3(TO4)2(OH)6) are iron hydroxysulfate minerals that can readily incorporate trace metals into their mineral structure. A range of metals can be incorporated into the jarosite structure, including oxyanions such as selenate (SeO42−). Selenium is a micronutrient, but is toxic in relatively low doses. Selenium is present in aqueous systems in its two oxyanion forms: selenate and selenite (SeO32−). The tetrahedral sulfate coordination site can be completely substituted for selenate in jarosite minerals (NaFe3(SO4)x(SeO4)2-x(OH)6). Bacteria have been observed to reduce Se oxyanions to both more reduced forms and insoluble elemental Se. This is a pathway for selenium immobilization at contaminated sites. This experiment investigates the reductive dissolution of two Se-jarosites (solid substitution containing high and low selenium concentrations) in the presence of Shewanella putrefaciens CN32. It was observed that both Fe(III) and selenate were metabolically reduced and released into solution through jarosite dissolution . Selenate was also found to be incorporated intracellularly and reduced to particulate Se which was released upon cell lysis. Compared to the abiotic samples, enhanced dissolution was found with both the live and dead bacteria treatments.

[EN] Emissions of gaseous forms of nitrogen from soil, such as nitrous oxide (N2O) and nitric oxide (NO), have shown great impact on global warming and atmospheric chemistry. Although in soil both nitrification and denitrification could cause N2O and NO emissions, most studies demonstrated that denitrification is the dominant process responsible for the increase of atmospheric N2O, while nitrification produces mostly NO. The use of nitrification inhibitors (NIs) has repeatedly been shown to reduce both N2O and NO emissions from agricultural soils; nevertheless, the efficiency of the mitigation effect varies greatly. It is generally assumed that nitrification inhibitors have no direct effect on denitrification. However, the indirect impact, due to the reduced substrate (nitrate) delivery to microsites where denitrification occurs, may have significant effects on denitrification product stoichiometry that may significantly lower soil borne N2O emissions. Soil-water status is considered to have a remarkable effect on the relative fluxes of nitrogen gases. The effect and mechanism of NI on N2O, NO and N-2 emission under different soil water-filled pore space (WFPS) is still not well explored. In the present study, we conducted a soil incubation experiment in an automated continuous-flow incubation system under a He/O-2 atmosphere. Ammonium sulfate was applied with and without NI (DMPP) to a permanent UK grassland soil under three different soil moisture conditions (50, 65, and 80% WFPS). With every treatment, glucose was applied to supply enough available carbon for denitrification. Emissions of CO2, N2O, NO and N-2 were investigated. Additionally, isotopic signatures of soil-emitted N2O were analyzed. Generally, higher WFPS led to higher N2O and NO emissions, while N-2 emissions were only detected at high soil moisture condition (80% WFPS). Different processes were responsible for N2O and NO emission in different phases of the incubation period. The application of DMPP did significantly reduce both N2O and NO emissions at all three soil moisture conditions. Furthermore, DMPP application increased N-2 emissions and decreased the N2O/(N2O + N-2) product ratio at 80% WFPS. (C) 2017 Elsevier Ltd. All rights reserved., Rothamsted Research is sponsored by the BBSRC. This study was in part funded by BBSRC project BB/K001051/1 and supported by the Chinese Scholarship Council (scholarship no. give number 201306350130).

This paper presents a comprehensive and critical review of research on different co-composting approaches to bioremediate hydrocarbon contaminated soil, organisms that have been found to degrade PAHs, and PAH breakdown products. Advantages and limitations of using certain groups of organisms and recommended areas of further research effort are identified. Studies investigating the use of composting techniques to treat contaminated soil are broad ranging and differ in many respects, which makes comparison of the different approaches very difficult. Many studies have investigated the use of specific bio-additives in the form of bacteria or fungi with the aim of accelerating contaminant removal; however, few have employed microbial consortia containing organisms from both kingdoms despite knowledge suggesting synergistic relationships exist between them in contaminant removal. Recommendations suggest that further studies should attempt to systemize the investigations of composting approaches to bio-remediate...

Microorganisms are the ultimate survivalists and account for the major portion of Earth’s biological diversity. They play critical roles in many global biogeochemical cycles (carbon, nitrogen, sulfur, and iron to name but a few). A gram of soil can contain 103–106 different bacterial species, and microorganisms (bacteria as well as archaea and fungi) have been observed in diverse terrestrial and aquatic environments ranging from deep oceanic hydrothermal vents to isolated voids in polar ice sheets. Given this extreme diversity across the globe, attention has been given to the development of techniques to identify and characterize bacterial communities, encouraged also by the prospect to find new species, enzymes, or proteins that can be used in industrial applications. Over the last 20 years, the science and application of molecular-based approaches has evolved from a perspective of determining the biological structure to elucidating the entire genome and its functions. This chapter will focus on discussing different widely used approaches and recent advancements made to detect and quantify “microbial activity” in contaminated environments using biochemical and molecular tools. Understanding how contaminants are biologically influenced in the environment will require a detailed understanding of both chemical and biological function within various environmental compartments. Combined these techniques can be used to address multiple environmental issues and will aid in the development of new remediation technologies.

The application of reactive nitrogen (N) in the form of synthetic/organic fertilizers plays a central role in supporting a larger human population, but also contributes to global warming through the emission of nitrous oxide (N2O). The use of nitrification inhibitors (NIs) has repeatedly been shown to minimize N2O emissions; however, their effectiveness in reducing N2O emissions varies greatly under different environmental conditions. A better understanding of how and to what extent NIs can mitigate fertilizer-related soil-borne N2O emissions under a range of different conditions is required. In the present study, we carried out a soil incubation experiment in a fully automated continuous-flow incubation system under conditions favoring either nitrification- or denitrification-derived N2O emissions. Additionally, the abundance of AOB amoA, and AOA amoA genes was quantified and N2O isotopic signatures were analyzed. We mixed a common NI (PIADIN®) with mineral fertilizer (ammonium sulfate) and examined the N2O mitigation potential of the NI in a fertilized sandy soil (low denitrification potential) and a sandy soil mixed with wheat straw (high denitrification potential) at 70% water holding capacity (WHC). In non-NI treatments, the addition of straw led to a drastic increase of CO2 and N2O emissions compared to the non-straw-amended soils, suggesting stimulated microbial activity and higher denitrification rate. The NI reduced N2O emissions in the straw-amended treatment by 41%, whereas in the treatment without straw this was only 17%. With the combination of N2O isotopic signatures and functional gene abundances, fungal denitrification was considered to be the major process contributing to the higher N2O fluxes specifically in straw-amended soils. Overall, our study indicated that NI can be used as an effective method for mitigating N2O emissions in cropland specifically when the denitrification potential is high, e.g. in moist N-fertilized and straw-amended soils.