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Bacteria and fungi have been shown to produce nitrous oxide (NO) during denitrification, but their contribution after nitrate (NO) application to soil is not clearly established. In a microcosm experiment, the relative contribution of bacteria and fungi to NO and carbon dioxide (CO) production by four contrasting soils representing different land uses after KNO addition was studied. The soils were daily wetted to 80% water-filled pore space (WFPS) and kept under greenhouse conditions for 10 days. The fungicide cycloheximide and the bactericide streptomycin were used to determine the possible microbial origin of the NO and CO emissions. Non-target effects of the antibiotics on the emission of NO and CO were evaluated using the inhibitor additivity ratio (IAR). The abundance of the bacterial and fungal communities was estimated by quantitative PCR (qPCR) of the bacterial 16S rRNA gene and the fungal internal transcribed spacer (ITS) region, respectively. The gene copy number of bacterial denitrifiers was calculated after quantification of the nirK, nirS, norB, nosZI and nosZII genes. After 10 d, regardless of the soil type, the cumulative NO emission from the soils treated with cycloheximide or streptomycin were similar. In all the four soils, NO fluxes were greater (on average 1.8 ± 0.3 times) in soils amended with the fungicide than with the bactericide during incubation for the first 48–96 h. Greater NO emissions (on average 1.7 ± 0.2 times) were detected in soils where bacteria were inhibited in comparison to those treated with the fungicide from 96 to 240 h. On average, 68.5% of the total CO emitted during the 10-d incubation period was produced in soils treated with the fungicide and 31.5% in those treated with the bactericide. The greater contribution of bacteria to the production of NO than fungi during the first 48–96 h was possibly due to a faster used of nitrate. Variations in the abundance of bacterial 16S rRNA genes, the ITS region, and the nirK, nirS, norB and nosZI bacterial denitrification genes indicated that the antibiotics used to prevent the growth of bacteria and fungi were effective during incubation. These results suggest that both bacteria and fungi should be considered when designing and applying greenhouse gas mitigation strategies in soils and that their relative contribution to produce NO and CO can vary with time and nitrate availability., This study was supported by the ERDF-cofinanced grant AGL2017–85676R from Ministerio de Economía, Industria y Competitividad. ACH thanks the Federation of European Microbiological Societies (FEMS) Research Grant 2017–2 program (FEMS-RG-2017-0067) and Ministerio de Educación Cultura y Deporte (MECD) for grant FPU 2014/01633. The authors would also like to acknowledge the UK Biotechnology and Biological Sciences Research Council (BBSRC) funded projects BBS/E/C/000I0310, BBS/E/C/000I0320 and BBS/E/C/000J0100 and UK Natural Environment Research Council (NERC) funded projects NE/M013847/1 and NE/M015351/1.

Maintaining an adequate phosphorus (P) supply for plants and microorganisms is central to agricultural production; however, the long-term effects of organic manure and inorganic fertilizer application on soil P cycling remain unclear. Organic P cycling in a sandy loam soil receiving medium and high rates of farmyard manure (FYM) with and without mineral fertilisers was studied in a long-term field experiment with 14C/33P isotope labelling and metagenomic shotgun sequencing. FYM application alone negatively affected soil total P and organic P (Po) accumulation by enhancing crop offtake, enhancing Po mineralisation and stimulating P loss from the topsoil by reducing its P sorption potential. The P mineralisation/immobilisation rates detected by the 33P pool dilution method were significantly correlated with the abundance of microbial P cycling genes. Soil available C and N concentrations were related to gross P mineralisation/immobilisation rates and the abundance of P uptake/scavenging genes. Microbial genes related to P uptake and metabolism were more abundant than P scavenging genes, while P scavenging genes may work efficiently as both of them can sustain similar P mineralisation and immobilisation rates. The addition of FYM also promoted phosphatase activity reflecting the increased supply of Po in these soils. Our study demonstrates that long-term FYM application alters soil Po stocks and cycling, and that microbial functional gene abundance was coupled with P cycling rates.

Land application of farmyard manure (FYM) is a widespread agronomic practice used to enhance soil fertility, but its long-term effects on soil microbial carbon (C) and nitrogen (N) cycling have not been investigated in detail. Topsoils (0–23 cm) and subsoils (23–38 cm) were collected from a field trial on a sandy-textured soil where FYM had been applied at high (50–25 t ha−1 yr−1, 28 yr) and low rates (10 t ha−1 yr−1, 16 yr), and compared to soil treated only with synthetic NPK fertilisers. The turnover rate of key components of soil organic matter (SOM; proteins, peptides, amino acids, cellulose, and glucose) were evaluated by 14C labelling and measuring cellobiohydrolase, β-glucosidase, β-1,4-N-acetylglucosaminidase, L-leucine aminopeptidase, protease, and deaminase activities, whereas gross NH4+ and NO3− production and consumption were determined by 15N-isotope pool dilution. Microbial communities were determined using phospholipid fatty acid (PLFA) profiling. Our results indicate that long-term FYM addition significantly enhanced the accumulation of soil C and N, soil organic N (SON) turnover, exoenzyme activity, and gross NO3− production and assimilation. Rates of protein, peptide, and amino acid processing rate were 169–248, 87–147, and 85–305 mg N kgDWsoil−1 d−1, respectively, gross NH4+ and NO3− production and consumption were 1.8–5.8 mg N kgDWsoil−1 d−1, and the highest rates were shown under the high FYM treatment in topsoil and subsoil. The half-life of cellulose and glucose decomposition under the high FYM treatment were 16.4% and 31.0% lower than them in the synthetic NPK fertiliser treatment, respectively, indicating higher rates of C cycling under high manure application as also evidenced by the higher rate of CO2 production. This was ascribed to an increase in microbial biomass rather than a change in microbial community structure. Based on the high pool sizes and high turnover rate, this suggests that peptides may represent one of the dominant forms of N taken up by soil microorganisms. We conclude that long-term FYM application builds SOM reserves and induces faster rates of nutrient cycling by boosting microbial biomass rather than by changing its community composition.

Summary Background The length of time that people with HIV on antiretroviral therapy (ART) with viral load suppression will be able to continue before developing viral rebound is unknown. We aimed to investigate the rate of first viral rebound in people that have achieved initial suppression with ART, to determine factors associated with viral rebound, and to use these estimates to predict long-term durability of viral suppression. Methods The UK Collaborative HIV Cohort (UK CHIC) Study is an ongoing multicentre cohort study that brings together in a standardised format data on people with HIV attending clinics around the UK. We included participants who started ART with three or more drugs and who had achieved viral suppression (≤50 copies per mL) by 9 months after the start of ART (baseline). Viral rebound was defined as the first single viral load of more than 200 copies per mL or treatment interruption (for ≥1 month). We investigated factors associated with viral rebound with Poisson regression. These results were used to calculate the rate of viral rebound according to several key factors, including age, calendar year at start of ART, and time since baseline. Results Of the 16 101 people included, 4519 had a first viral rebound over 58 038 person-years (7·8 per 100 person-years, 95% CI 7·6–8·0). Of the 4519 viral rebounds, 3105 (69%) were defined by measurement of a single viral load of more than 200 copies per mL, and 1414 (31%) by a documented treatment interruption. The rate of first viral rebound declined substantially over time until 7 years from baseline. The other factors associated with viral rebound were current age at follow-up and calendar year at ART initiation (p

The use of in-situ sensors capable of real-time monitoring of soil nitrogen (N) may facilitate improvements in agricultural N-use efficiency (NUE) through better fertiliser management. The optimal design of such sensor networks, consisting of clusters of sensors each attached to a data logger, depends upon the spatial variation of soil N and the relative cost of the data loggers and sensors. The primary objective of this study was to demonstrate how in-situ networks of N sensors could be optimally designed to enable the cost-efficient monitoring of soil N within a grassland field (1.9 ha). In the summer of 2014, two nested sampling campaigns (June & July) were undertaken to assess spatial variation in soil amino acids, ammonium (NH4+) and nitrate (NO3−) at a range of scales that represented the within (less than 2 m) and between (greater than 2 m) data logger/sensor cluster variability. Variance at short range (less than 2 m) was found to be dominant for all N forms. Variation at larger scales (greater than 2 m) was not as large but was still considered an important spatial component for all N forms, especially NO3−. The variance components derived from the nested sampling were used to inform the efficient design of theoretical in-situ networks of NH4+ and NO3− sensors based on the costs of a commercially available data logger and ion-selective electrodes (ISEs). Based on the spatial variance observed in the June nested sampling, and given a budget of £5000, the NO3− field mean could be estimated with a 95% confidence interval width of 1.70 μg N g−1 using 2 randomly positioned data loggers each with 5 sensors. Further investigation into “aggregate-scale” (less than 1 cm) spatial variance revealed further large variation at the sub 1-cm scale for all N forms. Sensors, for which the measurement represents an integration over a sensor-soil contact area of diameter less than 1 cm, would be subject to this aggregate-scale variability. As such, local replication at scales less than 1 cm would be needed to maintain the precision of the resulting field mean estimation. Adoption of in-situ sensor networks will depend upon the development of suitable low‐cost sensors, demonstration of the cost-benefit and the construction of a decision support system that utilises the generated data to improve the NUE of fertiliser N management.

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.

Out-wintering pads offer a reduced cost system for wintering cattle, minimising damage to pasture, providing animal welfare and production benefits, and generate, potentially, a more manageable effluent and lower ammonia emissions. The objectives of the present study were (i) to contribute to improved understanding of the factors impacting on effluent quality, ammonia emissions and animal welfare via observations on four farm-based out-wintering pads (ComOWPs) in England, Wales and Ireland and more detailed studies undertaken on four experimental OWPs (ExpOWPs) constructed at Rothamsted Research North Wyke, Devon, England and (ii) to corroborate the effluent quality data from both the ComOWPs and the ExpOWPs, with findings in the literature. Woodchip size, feeding management and area allowance were the treatment factors applied on the ExpOWPs. These three factors were randomised across the four ExpOWPs, over four 6–7 week periods. Effluent quality from the ExpOWPs was sampled frequently in a flow proportional way and analysed for total N (TN); total P (TP); total solids (TS); ammonium-N (NH4+-N); nitrate-N (NO3−-N). Beef cattle were periodically weighed for determination of live weight gain (LWG). An approximate nitrogen balance was calculated as a means of understanding its partitioning and fate during and after the ExpOWPs use. Effluent quality from the ComOWPs was sampled frequently, also in a flow-proportional way, and analysed for TN, TP, TS, NH4+-N, NO3−-N, total K and COD. Effluent quality data from the ExpOWPs showed no significant differences (P > 0.05) between treatments, with average concentrations of 1095 mg l−1, and 806 mg l−1, for TN and NH4+-N, respectively. Average effluent concentrations from the ComOWPs were 356 mg l−1 TN and 124 mg l−1 NH4+-N. Ammonia emissions from the ExpOWPs showed no significant differences (P > 0.05) between the treatments, with average mean emission rates of 2.5 g m−2 d−1 NH3-N, respectively. A positive correlation was established between NH3-N emission rate and wind speed. Emission rates from the ComOWPs ranged from 0.7 to 1.6 g m−2 d−1 NH3-N. Average daily LWG on the ExpOWPs was 1.33 kg steer−1 d−1. The effluent from both the ComOWPs and ExpOWPs were more similar with dirty water and of consistently lower strength than beef cattle slurry, as supported by findings in the literature, and therefore, it is suggested to be subject to the regulatory requirements of dirty water rather than slurry.

Current research on macronutrient cycling in UK agricultural systems aims to optimise soil and nutrient management for improved agricultural production and minimise effects on the environment and provision of ecosystem services. Nutrient use inefficiencies can cause environmental pollution through the release of greenhouse gases into the atmosphere and of soluble and particulate forms of N, P and carbon (C) in leachate and run-off into watercourses. Improving nutrient use efficiencies in agriculture calls for the development of sustainable nutrient management strategies: more efficient use of mineral fertilisers, increased recovery and recycling of waste nutrients, and, better exploitation of the substantial inorganic and organic reserves of nutrients in the soil. Long-term field experimentation in the UK has provided key knowledge of the main nutrient transformations in agricultural soils. Emerging analytical technologies, especially stable isotope labelling, that better characterise macronutrient forms and bioavailability and improve the quantification of the complex relationships between the macronutrients in soils at the molecular scale, are augmenting this knowledge by revealing the underlying processes. The challenge for the future is to determine the relationships between the dynamics of N, P and C across scales, which will require both new modelling approaches and integrated approaches to macronutrient cycling.

Little is known about the mechanisms that drive the movement of livestock-derived organic matter (LD-OM) in soil–water systems. This work investigates the partitioning of LD-OM in soil and identifies specific inorganic compounds and organic biomarkers that can be used to trace the movement of dissolved and soil-associated LD-OM fractions. Dairy cow slurry was applied to soil in lysimeters prior to a simulated rainfall event; leachate from the base of the lysimeters was collected at regular intervals during and after the rainfall until leaching ceased. Soil cores were taken after the rainfall for the analysis of soil-associated LD-OM derived compounds at different depths. Bulk elemental analysis (C and N) of leachate and soil samples showed that, in isolation, it lacked the sensitivity to trace the movement of LD-OM. Analysis of N species ( NH 4 + , NO 3 - and NO 2 - ) and organic compounds using fluorescence spectroscopy was used to investigate the dissolved fraction of the LD-OM and showed that NH 4 + and low molecular weight proteinaceous fractions could be used to trace the dissolved component of slurry through soils. Pyrolysis–gas chromatography–mass spectrometry (Py–GC–MS) of bulk soil and high temperature (HT) GC–MS of total lipid extracts (TLEs) of the lysimeter soils and leachates were used to investigate the soil bound fraction. Stanols with 5β configuration were observed in the top 10 cm of soil and not in the leachates and therefore were determined as indicators of soil-bound LD-OM. The results provide new information about compounds that can be used to define the pathways of LD-OM transport in soil. Their application includes the investigation of sources of faecal contamination of water courses via (i) the dissolved fractions of LD-OM fractions and (ii) the redistribution of soil-associated LD-OM by erosion of surface soil layers.

Global demand for food is increasing as is the recognition that this must be achieved with minimal negative impacts on the environment or other ecosystem services (ESs). Here we develop an understanding of the relationships among ESs delivered within temperate agricultural grassland systems in lowland Europe. We reviewed the refereed literature on pair-wise interactions between nine different ESs. These were agricultural production, climate regulation, air quality regulation, water quality regulation, hydrological regulation, soil erosion regulation, nutrient cycling, biodiversity conservation, and landscape quality. For each pair, we sought information on how each ES responds to changes in the other. Each interaction was assigned to one of five categories: (i) no direct relationship between the driving ES on the responding ES, (ii) the driving ES has a negative impact on the responding ES, (iii) the driving ES has a positive impact on the responding ES, (iv) the evidence of direction of effect is inconclusive, because of either inadequate information or contradictions in the literature, and (v) there is no current evidence in the current literature for a relationship. Negative relationships resulted only from the effects of increasing the intensity of agricultural production on other ESs. Available evidence infers that erosion regulation and good nutrient cycling were the only two driving ESs shown to enhance agricultural production implying that their protection will enhance our ability to meet future food needs. In order for agriculture to become more sustainable, we need to develop agricultural methods that can minimize the negative impacts of these win–lose relationships.

The application of untreated or treated animal manure to soils can result in increased N and C gaseous emissions contributing to ecosystem change and global warming. In the present study, dairy cattle slurry (liquid manure) was subjected first to pre-treatment by separation using a screw press to obtain a liquid (LF) and a solid fraction (SF). Then, the different fractions and the whole slurry (WS) were combined with two nitrification inhibitors (NI), dicyandiamide (DCD) or 3,4-dimethylpyrazole phosphate (DMPP), were applied to soil to assess the effect of slurry treatment by separation and NI addition on soil N dynamics and CH4, CO2, NH3, NO and N2O emissions. The WS and the two slurry fractions, combined or not with DCD or DMPP, were applied to soil at an equivalent field dosage of 120 kg total N ha(-1). Controls including a soil only, soil-DCD and soil-DMPP treatments were also included. The mixtures were incubated for 93-d at 20 degrees C. Results obtained show that NI inhibited nitrification between 16 and 30-d in WS and LF, with DMPP having a longer effect over time compared to DCD. There was no significant effect of NI on nitrification for the SF treatment. Nitrification inhibitors did not significantly affect (P>0.05) the CH4, CO2 and N2O emissions, but significantly decreased (P

There is a lack of information on ammonia (NH 3 ) emissions from cattle housing systems in Mediterranean countries, with most published data deriving from NW Europe. An investigation was carried out in NW Portugal to quantify NH 3 emissions for the main types of dairy cattle buildings in Portugal, i.e. naturally ventilated buildings and outdoor concrete yards, and to derive robust emission factors (EFs) for these conditions and compare with EFs used elsewhere in Europe. Measurements were made throughout a 12-month period using the passive flux sampling method in the livestock buildings and the equilibrium concentration technique in outdoor yards. The mean NH 3 emission factor for the whole housing system (buildings + outdoor yards) was 43.7 g NH 3 –N LU −1 day −1 and for outdoor concrete yards used by dairy cattle was 26.6 g NH 3 –N LU −1 day −1 . Expressing NH 3 emission in terms of the quantity of liquid milk produced gave similar values across the three dairy farms studied (with a mean of 2.3 kg N ton-milk −1 produced) and may have advantages when comparing different farming systems. In dairy houses with outdoor yards, NH 3 emissions from the yard area contributed to 69–92% of total emissions from this housing system. Emissions were particularly important during spring and summer seasons from outdoor yards with NH 3 emitted in this period accounting for about 72% of annual emissions from outdoor yards. Mean NH 3 emission factors derived for this freestall housing system and outdoor concrete yards used by dairy cattle in Portugal were higher than those measured in northern Europe. In addition, values of animal N excretion estimated in this study were greater than official National standard values. If these emissions are typical for Portuguese dairy systems, then the current National inventory underestimates emissions from this source in NW of Portugal, because of the use of lower standard values of N excretion by dairy cattle.

The highest emissions of CO2 from soils and most pronounced priming effect (PE) from soils generally occur immediately after slurry application. However, the influence of different particle size slurry fractions on net soil C respiration dynamics and PE has not been studied. Therefore, a slurry separation technique based on particle sizes was used in the present study. Six distinct fractions (>2000, 425–2000, 250–425, 150–250, 45–150, 250 μm fractions. The overall contribution of slurry C to total CO2 emissions was higher in smaller slurry particle size treatments in the first days after application. The addition of the various slurry fractions to soil caused both significant positive and negative PEs on the soil organic matter mineralization. The timing and type (positive or negative) of PE depended on the slurry particle size. Clearly, farm based separation pre-treatment leading to two or more fractions with different particle sizes has also the potential to reduce or modify short-term CO2 emissions immediately after slurry application to soil.

Measurements of ammonia (NH 3 ), nitrous oxide (N 2 O) and methane (CH 4 ) were made from 11 outdoor concrete yards used by livestock. Measurements of NH 3 emission were made using the equilibrium concentration technique while closed chambers were used to measure N 2 O and CH 4 emissions. Outdoor yards used by livestock proved to be an important source of NH 3 emission. Greatest emission rates were measured from dairy cow feeding yards, with a mean of 690 mg NH 3 -N m −2 h −1 . Smaller emission rates were measured from sheep handling areas, dairy cow collecting yards, beef feeding yards and a pig loading area, with respective mean emission rates of 440, 280, 220 and 140 mg NH 3 -N m −2 h −1 . Emission rates of N 2 O and CH 4 were much smaller and for CH 4 , in particular, emission rates were influenced greatly by the presence or absence of dung on the measurement area.

In this study we evaluated how typical split applications of cattle slurry (SL) or mineral fertilizer (AN) (in spring, summer and autumn) affected greenhouse gas (GHG) emissions from a grassland soil. Field measurements were carried out between May and November 2011 using the closed chamber technique. The experiment was located in the South West of England, an area which is typically characterized by high annual precipitation (>1000 mm year−1) and cool temperatures (average annual air temperature of 9.6 °C). The unusual dry climatic conditions observed during the late spring and summer, and the rainfall events identified in autumn affected soil water filled pore space (WFPS) resulting in low nitrous oxide (N2O) fluxes during the experiment. After the first two applications, climatic conditions dried the soil to values below 60%WFPS, the threshold level for losses of N2O by nitrification. In contrast, the frequent rainfall events observed after the third application (in autumn) increased the WFPS and promoted losses of N2O by denitrification. In terms of fertilizer type, AN resulted in higher cumulative N2O emissions compared with SL after the third application, probably because the SL treatment resulted in more anaerobic soil conditions and ammonia (NH3) volatilization resulted in a smaller mineral N pool in the soil available for N2O production and emission. Ammonia (NH3) emission modelling estimated losses of N by volatilization of NH3 between 25% and 38% of N applied after slurry surface broadcast application. Plant N offtake represented nearly all of the total N applied in AN plots following the first two applications and 59% of that applied in the third, whereas in SL plots an average of 64% of the total N applied in the three applications was harvested in the grass. Nitrogen gas (N2) fluxes were not measured but the large rainfall events observed after the third application gradually increased the soil WFPS to saturation and could also have resulted in losses of N by complete denitrification, especially from the AN treatment. Thus, applications of AN and SL resulted in total N2O-N losses during the 6-month measurement period of 0.21 and 0.17 kg N ha−1, respectively (representing only 0.02% and 0.003% of the N applied). Methane (CH4) production was observed in the first two or three days after SL spreading. For the remaining days, and also in plots treated with AN, the soil acted as a sink of CH4 (consumption). Total net CH4 cumulative values of −0.09 and 0.92 kg CH4 ha−1 were observed in AN and SL, respectively. CH4 consumption and production rates were related to changes in the %WFPS. Thus, dry soil conditions (below 60%WFPS) enhanced the CH4 consumption in AN plots and reduced the rate of CH4 production in SL plots during May and June. Total net cumulative carbon dioxide (CO2) fluxes of 1.24 and 0.35 Mg CO2-C ha−1 were observed in AN and SL plots during the 6-months measurements.

Cardenas, L. M., Chadwick, D. R., Scholefield, D., Fychan, A. R., Marley, C. L., Jones, R., Bol, R., Well, R., Vallejo, A. (2007). The effect of diet manipulation on nitrous oxide and methane emissions from manure application to grassland soils. Atmospheric Environment, 41 (33), 7096-7107