Improving the low-wind performance of the AERMOD atmospheric dispersion model for predicting short-range impacts of livestock ammonia emissions.

Short-range impacts to sensitive ecosystems as a result of ammonia emitted by livestock farms are often assessed using atmospheric dispersion modelling systems such as AERMOD. These assessments evaluate mean annual atmospheric concentrations of ammonia and nitrogen deposition rates at the ecosystem location for comparison with ecosystem damage thresholds. However, predictions of mean annual atmospheric concentrations can be dominated by periods of stable night-time conditions, which can contribute significantly to mean concentrations. AERMOD has been demonstrated to overestimate concentrations in certain stable low-wind conditions and so the model could potentially overestimate the short-range impacts of livestock ammonia emissions. This paper tests several modifications to the parameterisation of AERMOD (v12345) that aim to improve model predictions in low-wind conditions. The modifications are first described and then are applied to three pig farm case studies in the USA, Denmark and Spain to assess whether the modifications improve long-term mean ammonia concentration predictions through improved model performance. For these three case studies, most of the modifications tested improved model performance as a result of reducing the long-term mean concentration predictions, with the largest effect for low- or ground-level sources (e.g. slurry lagoons or naturally ventilated housing).

Fertilization Management: Assessing New Techniques and Key Interactions to Increase Crop Yields With Less N2O Emissions

El óxido nitroso (N2O) es un potente gas de efecto invernadero (GHG) proveniente mayoritariamente de la fertilización nitrogenada de los suelos agrícolas. Identificar estrategias de manejo de la fertilización que reduzcan estas emisiones sin suponer un descenso de los rendimientos es vital tanto a nivel económico como medioambiental. Con ese propósito, en esta Tesis se han evaluado: (i) estrategias de manejo directo de la fertilización (inhibidores de la nitrificación/ureasa); y (ii) interacciones de los fertilizantes con (1) el manejo del agua, (2) residuos de cosecha y (3) diferentes especies de plantas. Para conseguirlo se llevaron a cabo meta-análisis, incubaciones de laboratorio, ensayos en invernadero y experimentos de campo. Los inhibidores de la nitrificación y de la actividad ureasa se proponen habitualmente como medidas para reducir las pérdidas de nitrógeno (N), por lo que su aplicación estaría asociada al uso eficiente del N por parte de los cultivos (NUE). Sin embargo, su efecto sobre los rendimientos es variable. Con el objetivo de evaluar en una primera fase su efectividad para incrementar el NUE y la productividad de los cultivos, se llevó a cabo un meta-análisis. Los inhibidores de la nitrificación dicyandiamide (DCD) y 3,4-dimetilepyrazol phosphate (DMPP) y el inhibidor de la ureasa N-(n-butyl) thiophosphoric triamide (NBPT) fueron seleccionados para el análisis ya que generalmente son considerados las mejores opciones disponibles comercialmente. Nuestros resultados mostraron que su uso puede ser recomendado con el fin de incrementar tanto el rendimiento del cultivo como el NUE (incremento medio del 7.5% y 12.9%, respectivamente). Sin embargo, se observó que su efectividad depende en gran medida de los factores medioambientales y de manejo de los estudios evaluados. Una mayor respuesta fue encontrada en suelos de textura gruesa, sistemas irrigados y/o en cultivos que reciben altas tasas de fertilizante nitrogenado. En suelos alcalinos (pH ≥ 8), el inhibidor de la ureasa NBPT produjo el mayor efecto. Dado que su uso representa un coste adicional para los agricultores, entender las mejores prácticas que permitan maximizar su efectividad es necesario para posteriormente realizar comparaciones efectivas con otras prácticas que incrementen la productividad de los cultivos y el NUE. En base a los resultados del meta-análisis, se seleccionó el NBPT como un inhibidor con gran potencial. Inicialmente desarrollado para reducir la volatilización de amoniaco (NH3), en los últimos años algunos investigadores han demostrado en estudios de campo un efecto mitigador de este inhibidor sobre las pérdidas de N2O provenientes de suelos fertilizados bajo condiciones de baja humedad del suelo. Dada la alta variabilidad de los experimentos de campo, donde la humedad del suelo cambia rápidamente, ha sido imposible entender mecanísticamente el potencial de los inhibidores de la ureasa (UIs) para reducir emisiones de N2O y su dependencia con respecto al porcentaje de poros llenos de agua del suelo (WFPS). Por lo tanto se realizó una incubación en laboratorio con el propósito de evaluar cuál es el principal mecanismo biótico tras las emisiones de N2O cuando se aplican UIs bajo diferentes condiciones de humedad del suelo (40, 60 y 80% WFPS), y para analizar hasta qué punto el WFPS regula el efecto del inhibidor sobre las emisiones de N2O. Un segundo UI (i.e. PPDA) fue utilizado para comparar el efecto del NBPT con el de otro inhibidor de la ureasa disponible comercialmente; esto nos permitió comprobar si el efecto de NBPT es específico de ese inhibidor o no. Las emisiones de N2O al 40% WFPS fueron despreciables, siendo significativamente más bajas que las de todos los tratamientos fertilizantes al 60 y 80% WFPS. Comparado con la urea sin inhibidor, NBPT+U redujo las emisiones de N2O al 60% WFPS pero no tuvo efecto al 80% WFPS. La aplicación de PPDA incrementó significativamente las emisiones con respecto a la urea al 80% WFPS mientras que no se encontró un efecto significativo al 60% WFPS. Al 80% WFPS la desnitrificación fue la principal fuente de las emisiones de N2O en todos los tratamientos mientras que al 60% tanto la nitrificación como la desnitrificación tuvieron un papel relevante. Estos resultados muestran que un correcto manejo del NBPT puede suponer una estrategia efectiva para mitigar las emisiones de N2O. Con el objetivo de trasladar nuestros resultados de los estudios previos a condiciones de campo reales, se desarrolló un experimento en el que se evaluó la efectividad del NBPT para reducir pérdidas de N y aumentar la productividad durante un cultivo de cebada (Hordeum vulgare L.) en secano Mediterráneo. Se determinó el rendimiento del cultivo, las concentraciones de N mineral del suelo, el carbono orgánico disuelto (DOC), el potencial de desnitrificación, y los flujos de NH3, N2O y óxido nítrico (NO). La adición del inhibidor redujo las emisiones de NH3 durante los 30 días posteriores a la aplicación de urea en un 58% y las emisiones netas de N2O y NO durante los 95 días posteriores a la aplicación de urea en un 86 y 88%, respectivamente. El uso de NBPT también incrementó el rendimiento en grano en un 5% y el consumo de N en un 6%, aunque ninguno de estos incrementos fue estadísticamente significativo. Bajo las condiciones experimentales dadas, estos resultados demuestran el potencial del inhibidor de la ureasa NBPT para mitigar las emisiones de NH3, N2O y NO provenientes de suelos arables fertilizados con urea, mediante la ralentización de la hidrólisis de la urea y posterior liberación de menores concentraciones de NH4 + a la capa superior del suelo. El riego por goteo combinado con la aplicación dividida de fertilizante nitrogenado disuelto en el agua de riego (i.e. fertirriego por goteo) se considera normalmente una práctica eficiente para el uso del agua y de los nutrientes. Algunos de los principales factores (WFPS, NH4 + y NO3 -) que regulan las emisiones de GHGs (i.e. N2O, CO2 y CH4) y NO pueden ser fácilmente manipulados por medio del fertirriego por goteo sin que se generen disminuciones del rendimiento. Con ese propósito se evaluaron opciones de manejo para reducir estas emisiones en un experimento de campo durante un cultivo de melón (Cucumis melo L.). Los tratamientos incluyeron distintas frecuencias de riego (semanal/diario) y tipos de fertilizantes nitrogenados (urea/nitrato cálcico) aplicados por fertirriego. Fertirrigar con urea en lugar de nitrato cálcico aumentó las emisiones de N2O y NO por un factor de 2.4 y 2.9, respectivamente (P < 0.005). El riego diario redujo las emisiones de NO un 42% (P < 0.005) pero aumentó las emisiones de CO2 un 21% (P < 0.05) comparado con el riego semanal. Analizando el Poder de Calentamiento global en base al rendimiento así como los factores de emisión del NO, concluimos que el fertirriego semanal con un fertilizante de tipo nítrico es la mejor opción para combinar productividad agronómica con sostenibilidad medioambiental en este tipo de agroecosistemas. Los suelos agrícolas en las áreas semiáridas Mediterráneas se caracterizan por su bajo contenido en materia orgánica y bajos niveles de fertilidad. La aplicación de residuos de cosecha y/o abonos es una alternativa sostenible y eficiente desde el punto de vista económico para superar este problema. Sin embargo, estas prácticas podrían inducir cambios importantes en las emisiones de N2O de estos agroecosistemas, con impactos adicionales en las emisiones de CO2. En este contexto se llevó a cabo un experimento de campo durante un cultivo de cebada (Hordeum vulgare L.) bajo condiciones Mediterráneas para evaluar el efecto de combinar residuos de cosecha de maíz con distintos inputs de fertilizantes nitrogenados (purín de cerdo y/o urea) en estas emisiones. La incorporación de rastrojo de maíz incrementó las emisiones de N2O durante el periodo experimental un 105%. Sin embargo, las emisiones de NO se redujeron significativamente en las parcelas enmendadas con rastrojo. La sustitución parcial de urea por purín de cerdo redujo las emisiones netas de N2O un 46 y 39%, con y sin incorporación de residuo de cosecha respectivamente. Las emisiones netas de NO se redujeron un 38 y un 17% para estos mismos tratamientos. El ratio molar DOC:NO3 - demostró predecir consistentemente las emisiones de N2O y NO. El efecto principal de la interacción entre el fertilizante nitrogenado y el rastrojo de maíz se dio a los 4-6 meses de su aplicación, generando un aumento del N2O y una disminución del NO. La sustitución de urea por purín de cerdo puede considerarse una buena estrategia de manejo dado que el uso de este residuo orgánico redujo las emisiones de óxidos de N. Los pastos de todo el mundo proveen numerosos servicios ecosistémicos pero también suponen una importante fuente de emisión de N2O, especialmente en respuesta a la deposición de N proveniente del ganado mientras pasta. Para explorar el papel de las plantas como mediadoras de estas emisiones, se analizó si las emisiones de N2O dependen de la riqueza en especies herbáceas y/o de la composición específica de especies, en ausencia y presencia de una deposición de orina. Las hipótesis fueron: 1) las emisiones de N2O tienen una relación negativa con la productividad de las plantas; 2) mezclas de cuatro especies generan menores emisiones que monocultivos (dado que su productividad será mayor); 3) las emisiones son menores en combinaciones de especies con distinta morfología radicular y alta biomasa de raíz; y 4) la identidad de las especies clave para reducir el N2O depende de si hay orina o no. Se establecieron monocultivos y mezclas de dos y cuatro especies comunes en pastos con rasgos funcionales divergentes: Lolium perenne L. (Lp), Festuca arundinacea Schreb. (Fa), Phleum pratense L. (Php) y Poa trivialis L. (Pt), y se cuantificaron las emisiones de N2O durante 42 días. No se encontró relación entre la riqueza en especies y las emisiones de N2O. Sin embargo, estas emisiones fueron significativamente menores en ciertas combinaciones de especies. En ausencia de orina, las comunidades de plantas Fa+Php actuaron como un sumidero de N2O, mientras que los monocultivos de estas especies constituyeron una fuente de N2O. Con aplicación de orina la comunidad Lp+Pt redujo (P < 0.001) las emisiones de N2O un 44% comparado con los monocultivos de Lp. Las reducciones de N2O encontradas en ciertas combinaciones de especies pudieron explicarse por una productividad total mayor y por una complementariedad en la morfología radicular. Este estudio muestra que la composición de especies herbáceas es un componente clave que define las emisiones de N2O de los ecosistemas de pasto. La selección de combinaciones de plantas específicas en base a la deposición de N esperada puede, por lo tanto, ser clave para la mitigación de las emisiones de N2O. ABSTRACT Nitrous oxide (N2O) is a potent greenhouse gas (GHG) directly linked to applications of nitrogen (N) fertilizers to agricultural soils. Identifying mitigation strategies for these emissions based on fertilizer management without incurring in yield penalties is of economic and environmental concern. With that aim, this Thesis evaluated: (i) the use of nitrification and urease inhibitors; and (ii) interactions of N fertilizers with (1) water management, (2) crop residues and (3) plant species richness/identity. Meta-analysis, laboratory incubations, greenhouse mesocosm and field experiments were carried out in order to understand and develop effective mitigation strategies. Nitrification and urease inhibitors are proposed as means to reduce N losses, thereby increasing crop nitrogen use efficiency (NUE). However, their effect on crop yield is variable. A meta-analysis was initially conducted to evaluate their effectiveness at increasing NUE and crop productivity. Commonly used nitrification inhibitors (dicyandiamide (DCD) and 3,4-dimethylepyrazole phosphate (DMPP)) and the urease inhibitor N-(n-butyl) thiophosphoric triamide (NBPT) were selected for analysis as they are generally considered the best available options. Our results show that their use can be recommended in order to increase both crop yields and NUE (grand mean increase of 7.5% and 12.9%, respectively). However, their effectiveness was dependent on the environmental and management factors of the studies evaluated. Larger responses were found in coarse-textured soils, irrigated systems and/or crops receiving high nitrogen fertilizer rates. In alkaline soils (pH ≥ 8), the urease inhibitor NBPT produced the largest effect size. Given that their use represents an additional cost for farmers, understanding the best management practices to maximize their effectiveness is paramount to allow effective comparison with other practices that increase crop productivity and NUE. Based on the meta-analysis results, NBPT was identified as a mitigation option with large potential. Urease inhibitors (UIs) have shown to promote high N use efficiency by reducing ammonia (NH3) volatilization. In the last few years, however, some field researches have shown an effective mitigation of UIs over N2O losses from fertilized soils under conditions of low soil moisture. Given the inherent high variability of field experiments where soil moisture content changes rapidly, it has been impossible to mechanistically understand the potential of UIs to reduce N2O emissions and its dependency on the soil water-filled pore space (WFPS). An incubation experiment was carried out aiming to assess what is the main biotic mechanism behind N2O emission when UIs are applied under different soil moisture conditions (40, 60 and 80% WFPS), and to analyze to what extent the soil WFPS regulates the effect of the inhibitor over N2O emissions. A second UI (i.e. PPDA) was also used aiming to compare the effect of NBPT with that of another commercially available urease inhibitor; this allowed us to see if the effect of NBPT was inhibitor-specific or not. The N2O emissions at 40% WFPS were almost negligible, being significantly lower from all fertilized treatments than that produced at 60 and 80% WFPS. Compared to urea alone, NBPT+U reduced the N2O emissions at 60% WFPS but had no effect at 80% WFPS. The application of PPDA significantly increased the emissions with respect to U at 80% WFPS whereas no significant effect was found at 60% WFPS. At 80% WFPS denitrification was the main source of N2O emissions for all treatments. Both nitrification and denitrification had a determinant role on these emissions at 60% WFPS. These results suggest that adequate management of the UI NBPT can provide, under certain soil conditions, an opportunity for N2O mitigation. We translated our previous results to realistic field conditions by means of a field experiment with a barley crop (Hordeum vulgare L.) under rainfed Mediterranean conditions in which we evaluated the effectiveness of NBPT to reduce N losses and increase crop yields. Crop yield, soil mineral N concentrations, dissolved organic carbon (DOC), denitrification potential, NH3, N2O and nitric oxide (NO) fluxes were measured during the growing season. The inclusion of the inhibitor reduced NH3 emissions in the 30 d following urea application by 58% and net N2O and NO emissions in the 95 d following urea application by 86 and 88%, respectively. NBPT addition also increased grain yield by 5% and N uptake by 6%, although neither increase was statistically significant. Under the experimental conditions presented here, these results demonstrate the potential of the urease inhibitor NBPT in abating NH3, N2O and NO emissions from arable soils fertilized with urea, slowing urea hydrolysis and releasing lower concentrations of NH4 + to the upper soil layer. Drip irrigation combined with split application of N fertilizer dissolved in the irrigation water (i.e. drip fertigation) is commonly considered best management practice for water and nutrient efficiency. Some of the main factors (WFPS, NH4 + and NO3 -) regulating the emissions of GHGs (i.e. N2O, carbon dioxide (CO2) and methane (CH4)) and NO can easily be manipulated by drip fertigation without yield penalties. In this study, we tested management options to reduce these emissions in a field experiment with a melon (Cucumis melo L.) crop. Treatments included drip irrigation frequency (weekly/daily) and type of N fertilizer (urea/calcium nitrate) applied by fertigation. Crop yield, environmental parameters, soil mineral N concentrations, N2O, NO, CH4, and CO2 fluxes were measured during the growing season. Fertigation with urea instead of calcium nitrate increased N2O and NO emissions by a factor of 2.4 and 2.9, respectively (P < 0.005). Daily irrigation reduced NO emissions by 42% (P < 0.005) but increased CO2 emissions by 21% (P < 0.05) compared with weekly irrigation. Based on yield-scaled Global Warming Potential as well as NO emission factors, we conclude that weekly fertigation with a NO3 --based fertilizer is the best option to combine agronomic productivity with environmental sustainability. Agricultural soils in semiarid Mediterranean areas are characterized by low organic matter contents and low fertility levels. Application of crop residues and/or manures as amendments is a cost-effective and sustainable alternative to overcome this problem. However, these management practices may induce important changes in the nitrogen oxide emissions from these agroecosystems, with additional impacts on CO2 emissions. In this context, a field experiment was carried out with a barley (Hordeum vulgare L.) crop under Mediterranean conditions to evaluate the effect of combining maize (Zea mays L.) residues and N fertilizer inputs (organic and/or mineral) on these emissions. Crop yield and N uptake, soil mineral N concentrations, dissolved organic carbon (DOC), denitrification capacity, N2O, NO and CO2 fluxes were measured during the growing season. The incorporation of maize stover increased N2O emissions during the experimental period by c. 105 %. Conversely, NO emissions were significantly reduced in the plots amended with crop residues. The partial substitution of urea by pig slurry reduced net N2O emissions by 46 and 39 %, with and without the incorporation of crop residues respectively. Net emissions of NO were reduced 38 and 17 % for the same treatments. Molar DOC:NO3 - ratio was found to be a robust predictor of N2O and NO fluxes. The main effect of the interaction between crop residue and N fertilizer application occurred in the medium term (4-6 month after application), enhancing N2O emissions and decreasing NO emissions as consequence of residue incorporation. The substitution of urea by pig slurry can be considered a good management strategy since N2O and NO emissions were reduced by the use of the organic residue. Grassland ecosystems worldwide provide many important ecosystem services but they also function as a major source of N2O, especially in response to N deposition by grazing animals. In order to explore the role of plants as mediators of these emissions, we tested whether and how N2O emissions are dependent on grass species richness and/or specific grass species composition in the absence and presence of urine deposition. We hypothesized that: 1) N2O emissions relate negatively to plant productivity; 2) four-species mixtures have lower emissions than monocultures (as they are expected to be more productive); 3) emissions are lowest in combinations of species with diverging root morphology and high root biomass; and 4) the identity of the key species that reduce N2O emissions is dependent on urine deposition. We established monocultures and two- and four-species mixtures of common grass species with diverging functional traits: Lolium perenne L. (Lp), Festuca arundinacea Schreb. (Fa), Phleum pratense L. (Php) and Poa trivialis L. (Pt), and quantified N2O emissions for 42 days. We found no relation between plant species richness and N2O emissions. However, N2O emissions were significantly reduced in specific plant species combinations. In the absence of urine, plant communities of Fa+Php acted as a sink for N2O, whereas the monocultures of these species constituted a N2O source. With urine application Lp+Pt plant communities reduced (P < 0.001) N2O emissions by 44% compared to monocultures of Lp. Reductions in N2O emissions by species mixtures could be explained by total biomass productivity and by complementarity in root morphology. Our study shows that plant species composition is a key component underlying N2O emissions from grassland ecosystems. Selection of specific grass species combinations in the context of the expected nitrogen deposition regimes may therefore provide a key management practice for mitigation of N2O emissions.

Soil moisture content determines the effect of the urease inhibitor NBPT on N2O emissions

Among the mitigation strategies to prevent nitrogen (N) losses from ureic fertilizers, urease inhibitors (UIs) have been demonstrated to promote high N use efficiency by reducing ammonia (NH3) volatilization. In the last few years, some field experiments have also shown its effectiveness in reducing nitrous oxide (N2O) losses from fertilized soils under conditions of low soil moisture. An incubation experiment was carried out with the aim of assessing the main biotic mechanisms behind N2O emissions once that the UIs N-(n-butyl) thiophosphoric triamid (NBPT) and phenil phosphorodiamidate (PPDA) were applied with Urea (U) under different soil moisture conditions (40, 60 and 80 % water-filled pore space, WFPS). In the same study we tried to analyze to what extent soil WFPS regulates the effect of these inhibitors on N2O emissions. The use of PPDA in our study allowed us to compare the effect of NBPT with that of another commercially available urease inhibitor, aiming to see if the results were inhibitor-specific or not. Based on the results from this experiment, a WFPS (i.e. 60 %) was chosen for a second study (i.e. mesocosm experiment) aiming to assess the efficiency of the UIs to indirectly affect N2O emissions through influencing the pool of soil mineral N. The N2O emissions at 40 % WFPS were almost negligible, being significantly lower from all fertilized treatments than that produced at 60 and 80 % WFPS. When compared to U alone, NBPT+U reduced the N2O emissions at 60 % WFPS but had no effect at 80 % WFPS. The application of PPDA significantly increased the emissions with respect to U at 80 % WFPS whereas no significant effect was found at 60 %. At 80 % WFPS, denitrification was the main source of N2O emissions for all treatments. In the mesocosm study, the application of NBPT+U was an effective strategy to reduce N2O emissions (75 % reduction compared to U alone), due to a lower soil ammonium (NH4 +) content induced by the inhibitor. These results suggest that adequate management of the UI NBPT could provide, under certain soil conditions, an opportunity for mitigation of N2O emissions from fertilized soils.

Modelling agro-forestry scenarios for ammonia abatement in the landscape

Ammonia emissions from livestock production can have negative impacts on nearby protected sites and ecosystems that are sensitive to eutrophication and acidification. Trees are effective scavengers of both gaseous and particulate pollutants from the atmosphere making tree belts potentially effective landscape features to support strategies aiming to reduce ammonia impacts. This research used the MODDAS-THETIS a coupled turbulence and deposition turbulence model, to examine the relationships between tree canopy structure and ammonia capture for three source types?animal housing, slurry lagoon, and livestock under a tree canopy. By altering the canopy length, leaf area index, leaf area density, and height of the canopy in the model the capture efficiencies varied substantially. A maximum of 27% of the emitted ammonia was captured by tree canopy for the animal housing source, for the slurry lagoon the maximum was 19%, while the livestock under trees attained a maximum of 60% recapture. Using agro-forestry systems of differing tree structures near ?hot spots? of ammonia in the landscape could provide an effective abatement option for the livestock industry that complements existing source reduction measures.

Cost-effective mitigation of ammonia emissions from fertilizer use in Spanish agroecosystems

Mitigación GEI sistemas agrícolas

Ammonia and Greenhouse Gases Emission from Slurry Storage with impermeable Cover and Landspreading of Cattle Slurry

Intensive farm systems handle large volume of livestock wastes, resulting in adverse environmental effects, such as gaseous losses into the atmosphere in form of ammonia (NH3) and greenhouse gases (GHG), i.e. methane (CH4), carbon dioxide (CO2) and nitrous oxide (N2O). In this study, the manure management continuum of slurry storage with impermeable cover and following cattle slurry band spreading and incorporation to soil was assessed for NH3 and GHG emissions. The experiment was conducted in an outdoor covered storage (flexible bag system) (study I), which collected the slurry produced in 7 dairy cattle farms (2,000 m3 slurry) during 12 days in the northern Spain.

Comparison of micrometeorological techinques for estimating ammonia emission from covered slurry storage and land spreading of cattle slurry

The micrometeorological mass-balance integrated horizontal flux (IHF) technique has been commonly employed for measuring ammonia (NH3) emissions inon-field experiments. However, the inverse-dispersion modeling technique, such as the backward Lagrangian stochastic (bLS) modeling approach, is currently highlighted as offering flexibility in plot design and requiring a minimum number of samplers (Ro et al., 2013). The objective of this study was to make a comparison between the bLS technique with the IHF technique for estimating NH3 emission from flexible bag storage and following landspreading of dairy cattle slurry. Moreover, considering that NH3 emission in storage could have been non uniform, the effect on bLS estimates of a single point and multiple downwind concentration measurements was tested, as proposed by Sanz et al. (2010).

Ammonia and methane gas emissions from pig slurry: variability induced through feeding strategies

Esta Tesis doctoral fue desarrollada para estudiar las emisiones de amoniaco (NH3) y metano (CH4) en purines de cerdos, y los efectos ocasionados por cambios en la formulación de la dieta. Con este propósito, fueron llevados a cabo tres estudios. El experimento 1 fue realizado con el objetivo de analizar los factores de variación de la composición de purines y establecer ecuaciones de predicción para emisiones potenciales de NH3 y CH4. Fueron recogidas setenta y nueve muestras de piensos y purines durante dos estaciones del año (verano y invierno) de granjas comerciales situadas en dos regiones de España (Centro y Mediterráneo). Se muestrearon granjas de gestación, maternidad, lactación y cebo. Se determinó la composición de piensos y purines, y la emisión potencial de NH3 y CH4. El contenido de nutrientes de los piensos fue usado como covariable en el análisis. La espectroscopia de reflectancia del infrarrojo cercano (NIRS) se evaluó como herramienta de predicción de la composición y potencial emisión de gases del purín. Se encontró una amplia variabilidad en la composición de piensos y purines. Las granjas del Mediterráneo tenían mayor pH (P<0,001) y concentración de cenizas (P =0,02) en el purín que las del Centro. El tipo de granja también afectó al contenido de extracto etéreo (EE) del purín (P =0,02), observando los valores más elevados en las instalaciones de animales jóvenes. Los resultados sugieren un efecto tampón de la fibra de la dieta en el pH del purín y una relación directa (P<0,05) con el contenido de fibra fecal. El contenido de proteína del pienso no afectó al contenido de nitrógeno del purín, pero disminuyó (P=0,003) la concentración de sólidos totales (ST) y de sólidos volátiles (SV). Se obtuvieron modelos de predicción de la emisión potencial de NH3 (R2=0,89) y CH4 (R2=0,61) partir de la composición del purín. Los espectros NIRS mostraron una buena precisión para la estimación de la mayor parte de los constituyentes, con coeficientes de determinación de validación cruzada (R2cv) superiores a 0,90, así como para la predicción del potencial de emisiones de NH3 y CH4 (R2cv=0,84 y 0,68, respectivamente). El experimento 2 fue realizado para investigar los efectos del nivel de inclusión de dos fuentes de sub-productos fibrosos: pulpa de naranja (PN) y pulpa de algarroba (PA), en dietas iso-fibrosas de cerdos de cebo, sobre la composición del purín y las emisiones potenciales de NH3 y CH4. Treinta cerdos (85,4±12,3 kg) fueron alimentados con cinco dietas iso-nutritivas: control comercial trigo/cebada (C) y cuatro dietas experimentales incluyendo las dos fuentes de sub-productos a dos niveles (75 y 150 g/kg) en una estructura 2 × 2 factorial. Después de 14 días de periodo de adaptación, heces y orina fueron recogidas separadamente durante 7 días para medir la digestibilidad de los nutrientes y el nitrógeno (N) excretado (6 réplicas por dieta) en cerdos alojados individualmente en jaulas metabólicas. Las emisiones de NH3 y CH4 fueron medidas después de la recogida de los purínes durante 11 y 100 días respectivamente. La fuente y el nivel de subproductos fibrosos afectó a la eficiencia digestiva de diferentes formas, ya que los coeficientes de digestibilidad total aparente (CDTA) para la materia seca (MS), materia orgánica (MO), fracciones fibrosas y energía bruta (EB) aumentaron con la PN pero disminuyeron con la inclusión de PA (P<0,05). El CDTA de proteína bruta (PB) disminuyó con la inclusión de las dos fuentes de fibra, siendo más bajo al mayor nivel de inclusión. La concentración fecal de fracciones fibrosas aumentó (P<0,05) con el nivel de inclusión de PA pero disminuyó con el de PN (P<0,01). El nivel más alto de las dos fuentes de fibra en el pienso aumentó (P<0,02) el contenido de PB fecal pero disminuyó el contenido de N de la orina (de 205 para 168 g/kg MS, P<0,05) en todas las dietas suplementadas comparadas con la dieta C. Adicionalmente, las proporciones de nitrógeno indigerido, nitrógeno soluble en agua, nitrógeno bacteriano y endógeno excretado en heces no fueron afectados por los tratamientos. Las características iniciales del purín no difirieron entre las diferentes fuentes y niveles de fibra, excepto para el pH que disminuyó con la inclusión de altos niveles de sub-productos. La emisión de NH3 por kg de purín fue más baja en todas las dietas suplementadas con fibras que en la dieta C (2,44 vs.1,81g de promedio, P<0,05). Además, purines de dietas suplementadas con alto nivel de sub-productos tendieron (P<0,06) a emitir menos NH3 por kg de nitrógeno total y mostraron un potencial más bajo para emitir CH4, independientemente de la fuente de fibra. El experimento 3 investigó los efectos de la fuente de proteína en dietas prácticas. Tres piensos experimentales fueron diseñados para sustituir una mescla de harina y cascarilla de soja (SOJ) por harina de girasol (GIR) o por DDGS del trigo (DDGST). La proporción de otros ingredientes fue modificada para mantener los contenidos de nutrientes similares a través de las dietas. El cambio en la fuente de proteína dio lugar a diferencias en el contenido de fibra neutro detergente ligada a proteína bruta (FNDPB), fibra soluble (FS) y lignina ácido detergente (LAD) en la dieta. Veinticuatro cerdos (ocho por dieta), con 52,3 o 60,8 kg en la primera y segunda tanda respectivamente, fueron alojados individualmente en jaulas metabólicas. Durante un periodo de 7 días fue determinado el balance de MS, el CDTA de los nutrientes y la composición de heces y orina. Se realizó el mismo procedimiento del experimento 2 para medir las emisiones de NH3 y CH4 de los purines de cada animal. Ni la ingestión de MS ni el CDTA de la MS o de la energía fueron diferentes entre las dietas experimentales, pero el tipo de pienso afectó (P<0.001) la digestibilidad de la PB, que fue mayor para GIR (0,846) que para SOJ (0,775), mientras que la dieta DDGST mostró un valor intermedio (0,794). La concentración fecal de PB fue por tanto influenciada (P<0,001) por el tratamiento, observándose la menor concentración de PB en la dieta GIR y la mayor en la dieta SOJ. La proporción de N excretado en orina o heces disminuyó de 1,63 en la dieta GIR hasta 0,650 en la dieta SOJ, como consecuencia de perdidas más bajas en orina y más altas en heces, con todas las fracciones de nitrógeno fecales creciendo en paralelo a la excreción total. Este resultado fue paralelo a una disminución de la emisión potencial de NH3 (g/kg purín) en la dieta SOJ con respecto a la dieta GIR (desde 1,82 a 1,12, P<0,05), dando valores intermedios (1,58) para los purines de la dieta DDGST. Por otro lado, el CDTA de la FS y de la fibra neutro detergente (FND) fueron afectados (P<0,001 y 0,002, respectivamente) por el tipo de dieta, siendo más bajas en la dieta GIR que en la dieta SOJ; además, se observó un contenido más alto de FND (491 vs. 361g/kg) en la MS fecal para la dieta GIR que en la dieta SOJ, presentando la dieta DDGST valores intermedios. El grado de lignificación de la FND (FAD/FND x 100) de las heces disminuyó en el orden GIR>DDGST>SOJ (desde 0,171 hasta 0,109 y 0,086, respectivamente) en paralelo a la disminución del potencial de emisión de CH4 por g de SV del purín (desde 301 a 269 y 256 mL, respectivamente). Todos los purines obtenidos en estos tres experimentos y Antezana et al. (2015) fueron usados para desarrollar nuevas calibraciones con la tecnología NIRS, para predecir la composición del purín y el potencial de las emisiones de gases. Se observó una buena precisión (R2cv superior a 0,92) de las calibraciones cuando muestras de los ensayos controlados (2, 3 y Antezana et al., 2015) fueron añadidas, aumentando el rango de variación. Una menor exactitud fue observada para TAN y emisiones de NH3 y CH4, lo que podría explicarse por una menor homogeneidad en la distribución de las muestras cuando se amplía el rango de variación del estudio. ABSTRACT This PhD thesis was developed to study the emissions of ammonia (NH3) and methane (CH4) from pig slurry and the effects caused by changes on diet formulation. For these proposes three studies were conducted. Experiment 1 aimed to analyse several factors of variation of slurry composition and to establish prediction equations for potential CH4 and NH3 emissions. Seventy-nine feed and slurry samples were collected at two seasons (summer and winter) from commercial pig farms sited at two Spanish regions (Centre and Mediterranean). Nursery, growing-fattening, gestating and lactating facilities were sampled. Feed and slurry composition were determined, and potential CH4 and NH3 emissions measured. Feed nutrient contents were used as covariates in the analysis. Near infrared reflectance spectroscopy (NIRS) was evaluated as a predicting tool for slurry composition and potential gaseous emissions. A wide variability was found both in feed and slurry composition. Mediterranean farms had a higher pH (P<0.001) and ash (P=0.02) concentration than those located at the centre of Spain. Also, type of farm affected ether extract (EE) content of the slurry (P=0.02), with highest values obtained for the youngest animal facilities. Results suggested a buffer effect of dietary fibre on slurry pH and a direct relationship (P<0.05) with fibre constituents of manure. Dietary protein content did not affect slurry nitrogen content (N) but decreased (P=0.003) in total solid (TS) and volatile solids (VS) concentration. Prediction models of potential NH3 emissions (R2=0.89) and biochemical CH4 potential (B0) (R2=0.61) were obtained from slurry composition. Predictions from NIRS showed a high accuracy for most slurry constituents with coefficient of determination of cross validation (R2cv) above 0.90 and a similar accuracy of prediction of potential NH3 and CH4 emissions (R2cv=0.84 and 0.68, respectively) thus models based on slurry composition from commercial farms. Experiment 2 was conducted to investigate the effects of increasing the level of two sources of fibrous by-products, orange pulp (OP) and carob meal (CM), in iso-fibrous diets for growing-finishing pig, slurry composition and potential NH3 and CH4 emissions. Thirty pigs (85.4±12.3 kg) were fed five iso-nutritive diets: a commercial control wheat/barley (C) and four experimental diets including two sources of fibrous by-products OP and CM and two dietary levels (75 and 150 g/kg) in a 2 × 2 factorial arrangement. After a 14-day adaptation period, faeces and urine were collected separately for 7 days to measure nutrient digestibility and the excretory patterns of N from pigs (6 replicates per diet) housed individually in metabolic pens. For each animal, the derived NH3 and CH4 emissions were measured in samples of slurry over an 11 and 100-day storage periods, respectively. Source and level of the fibrous by-products affected digestion efficiency in a different way as the coefficients of total tract apparent digestibility (CTTAD) for dry matter (DM), organic matter (OM), fibre fractions and gross energy (GE) increased with OP but decreased with CM (P<0.05). Crude protein CTTAD decreased with the inclusion of both sources of fibre, being lower at the highest dietary level. Faecal concentration of fibre fractions increased (P<0.05) with the level of inclusion of CM but decreased with that of OP (P<0.01). High dietary level for both sources of fibre increased (P<0.02) CP faecal content but urine N content decreased (from 205 to 168 g/kg DM, P<0.05) in all the fibre-supplemented compared to C diet. Additionally, the proportions of undigested dietary, water soluble, and bacterial and endogenous debris of faecal N excretion were not affected by treatments. The initial slurry characteristics did not differ among different fibre sources and dietary levels, except pH, which decreased at the highest by-product inclusion levels. Ammonia emission per kg of slurry was lower in all the fibre-supplemented diets than in C diet (2.44 vs. 1.81g as average, P<0.05). Additionally, slurries from the highest dietary level of by-products tended (P<0.06) to emit less NH3 per kg of initial total Kjeldahl nitrogen (TKN) and showed a lower biochemical CH4 potential , independently of the fibre source. Experiment 3 investigated the effects of protein source in practical diets. Three experimental feeds were designed to substitute a mixture of soybean meal and soybean hulls (SB diet) with sunflower meal (SFM) or wheat DDGS (WDDGS). The proportion of other ingredients was also modified in order to maintain similar nutrient contents across diets. Changes in protein source led to differences in dietary content of neutral detergent insoluble crude protein (NDICP), soluble fibre (SF) and acid detergent lignin (ADL). Twenty-four pigs (eight per diet), weighing 52.3 or 60.8 kg at the first and second batch respectively, were housed individually in metabolic pens to determine during a 7-day period DM balance, CTTAD of nutrients, and faecal and urine composition. Representative slurry samples from each animal were used to measure NH3 and CH4 emissions over an 11 and or 100-day storage period, respectively. Neither DM intake, nor DM or energy CTTAD differed among experimental diets, but type of feed affected (P<0.001) CP digestibility, which was highest for SFM (0.846) than for SB (0.775) diet, with WDDGS-based diet giving an intermediate value (0.794). Faecal DM composition was influenced (P<0.001) accordingly, with the lowest CP concentration found for diet SFM and the highest for SB. The ratio of N excreted in urine or faeces decreased from SFM (1.63) to SB diet (0.650), as a consequence of both lower urine and higher faecal losses, with all the faecal N fractions increasing in parallel to total excretion. This result was parallel to a decrease of potential NH3 emission (g/kg slurry) in diet SB with respect to diet SFM (from 1.82 to 1.12, P<0.05), giving slurry from WDDGS-based diet an intermediate value (1.58). Otherwise, SF and insoluble neutral detergent fibre (NDF) CTTAD were affected (P<0.001 and P=0.002, respectively) by type of diet, being lower for SFM than in SB-diet; besides, a higher content of NDF (491 vs. 361 g/kg) in faecal DM was observed for SFM with respect to SB based diet, with WDDGS diet being intermediate. Degree of lignification of NDF (ADL/NDF x 100) of faeces decreased in the order SFM>WDDGS>SB (from 0.171 to 0.109 and 0.086, respectively) in parallel to a decrease of biochemical CH4 potential per g of VS of slurry (from 301 to 269 and 256 ml, respectively). All slurry samples obtained from these three experiments and Antezana et al. (2015) were used to develop new calibrations with NIRS technology, to predict the slurry composition and potential gaseous emissions of samples with greater variability in comparison to experiment 1. Better accuracy (R2cv above 0.92) was observed for calibrations when samples from controlled trials experiments (2, 3 and Antezana et al., 2015) were included, increasing the range of variation. A lower accuracy was observed for TAN, NH3 and CH4 gaseous emissions, which might be explained by the less homogeneous distribution with a wider range of data.

Ammonia acquisition in enteric bacteria: Physiological role of the ammonium/methylammonium transport B (AmtB) protein

Homologues of the amtB gene of enteric bacteria exist in all three domains of life. Although their products are required for transport of the ammonium analogue methylammonium in washed cells, only in Saccharomyces cerevisiae have they been shown to be necessary for growth at low NH4+ concentrations. We now demonstrate that an amtB strain of Escherichia coli also grows slowly at low NH4+ concentrations in batch culture, but only at pH values below 7. In addition, we find that the growth defect of an S. cerevisiae triple-mutant strain lacking the function of three homologues of the ammonium/methylammonium transport B (AmtB) protein [called methylammonium/ammonium permeases (MEP)] that was observed at pH 6.1 is relieved at pH 7.1. These results provide direct evidence that AmtB participates in acquisition of NH4+/NH3 in bacteria as well as eucarya. Because NH3 is the species limiting at low pH for a given total concentration of NH4+ + NH3, results with both organisms indicate that AmtB/MEP proteins function in acquisition of the uncharged form. We confirmed that accumulation of [14C]methylammonium depends on its conversion to γ-N-methylglutamine, an energy-requiring reaction catalyzed by glutamine synthetase, and found that at pH 7, constitutive expression of AmtB did not relieve the growth defects of a mutant strain of Salmonella typhimurium that appears to require a high internal concentration of NH4+/NH3. Hence, contrary to previous views, we propose that AmtB/MEP proteins increase the rate of equilibration of the uncharged species, NH3, across the cytoplasmic membrane rather than actively transporting—that is, concentrating—the charged species, NH4+.

Identifying potential mechanisms enabling acidophily in the ammonia-oxidizing archaeon "Candidatus Nitrosotalea devanaterra"

FUNDING INFORMATION This work, including the efforts of Luis Sayavedra-Soto, was funded by National Science Foundation (NSF) (0541797). This work, including the efforts of Laura E. Lehtovirta-Morley, James I. Prosser, and Graeme W. Nicol, was funded by Natural Environment Research Council (NERC) (NE/I027835/1). Graeme W. Nicol is also supported by the AXA Research Fund.

Molecular adaptation of Ammonia Monooxygenase during independent pH specialization in Thaumarchaeota

Acknowledgements. This work was funded by Natural Environment Research Council Fellowship NE/J019151/1 and by institutional funding from within the University of Aberdeen.

Isolation of 'Candidatus Nitrosocosmicus franklandus', a novel ureolytic soil archaeal ammonia oxidiser with tolerance to high ammonia concentration

Acknowledgements. The authors would like to thank Mr Kevin Mackenzie and Mrs Gillian Milne (University of Aberdeen) for technical support with scanning electron microscopy, and Dr Robin Walker for access to the Woodlands Field experimental plots at the SRUC,Craibstone Estate, Aberdeen. This work was financially supported by Natural Environmental Research Council (standard grants NE/I027835/1 and NE/L006286/1 and fellowship NE/J019151/1), EC Marie Curie ITN NORA, Grant Agreement No. 316472, the AXA Research Fund and the Centre for Genome Enabled Biology and Medicine, University of Aberdeen.

A different approach to treatment of phenylketonuria: Phenylalanine degradation with recombinant phenylalanine ammonia lyase

Phenylketonuria (PKU), with its associated hyperphenylalaninemia (HPA) and mental retardation, is a classic genetic disease and the first to have an identified chemical cause of impaired cognitive development. Treatment from birth with a low phenylalanine diet largely prevents the deviant cognitive phenotype by ameliorating HPA and is recognized as one of the first effective treatments of a genetic disease. However, compliance with dietary treatment is difficult and when it is for life, as now recommended by an internationally used set of guidelines, is probably unrealistic. Herein we describe experiments on a mouse model using another modality for treatment of PKU compatible with better compliance using ancillary phenylalanine ammonia lyase (PAL, EC 4.3.1.5) to degrade phenylalanine, the harmful nutrient in PKU; in this treatment, PAL acts as a substitute for the enzyme phenylalanine monooxygenase (EC 1.14.16.1), which is deficient in PKU. PAL, a robust enzyme without need for a cofactor, converts phenylalanine to trans-cinnamic acid, a harmless metabolite. We describe (i) an efficient recombinant approach to produce PAL enzyme, (ii) testing of PAL in orthologous N-ethyl-N′-nitrosourea (ENU) mutant mouse strains with HPA, and (iii) proofs of principle (PAL reduces HPA)—both pharmacologic (with a clear dose–response effect vs. HPA after PAL injection) and physiologic (protected enteral PAL is significantly effective vs. HPA). These findings open another way to facilitate treatment of this classic genetic disease.

Correlation of breath ammonia with blood urea nitrogen and creatinine during hemodialysis

We have spectroscopically determined breath ammonia levels in seven patients with end-stage renal disease while they were undergoing hemodialysis at the University of California, Los Angeles, dialysis center. We correlated these measurements against simultaneously taken blood samples that were analyzed for blood urea nitrogen (BUN) and creatinine, which are the accepted standards indicating the level of nitrogenous waste loading in a patient's bloodstream. Initial levels of breath ammonia, i.e., at the beginning of dialysis, are between 1,500 ppb and 2,000 ppb (parts per billion). These levels drop very sharply in the first 15–30 min as the dialysis proceeds. We found the reduction in breath ammonia concentration to be relatively slow from this point on to the end of dialysis treatment, at which point the levels tapered off at 150 to 200 ppb. For each breath ammonia measurement, taken at 15–30 min intervals during the dialysis, we also sampled the patient's blood for BUN and creatinine. The breath ammonia data were available in real time, whereas the BUN and creatinine data were available generally 24 h later from the laboratory. We found a good correlation between breath ammonia concentration and BUN and creatinine. For one of the patients, the correlation gave an R2 of 0.95 for breath ammonia and BUN correlation and an R2 of 0.83 for breath ammonia and creatinine correlation. These preliminary data indicate the possibility of using the real-time breath ammonia measurements for determining efficacy and endpoint of hemodialysis.

Rhizosphere Bacteria Enhance Selenium Accumulation and Volatilization by Indian Mustard1

Indian mustard (Brassica juncea L.) accumulates high tissue Se concentrations and volatilizes Se in relatively nontoxic forms, such as dimethylselenide. This study showed that the presence of bacteria in the rhizosphere of Indian mustard was necessary to achieve the best rates of plant Se accumulation and volatilization of selenate. Experiments with the antibiotic ampicillin showed that bacteria facilitated 35% of plant Se volatilization and 70% of plant tissue accumulation. These results were confirmed by inoculating axenic plants with rhizosphere bacteria. Compared with axenic controls, plants inoculated with rhizosphere bacteria had 5-fold higher Se concentrations in roots (the site of volatilization) and 4-fold higher rates of Se volatilization. Plants with bacteria contained a heat-labile compound in their root exudate; when this compound was added to the rhizosphere of axenic plants, Se accumulation in plant tissues increased. Plants with bacteria had an increased root surface area compared with axenic plants; the increased area was unlikely to have caused their increased tissue Se accumulation because they did not accumulate more Se when supplied with selenite or selenomethionine. Rhizosphere bacteria also possibly increased plant Se volatilization because they enabled plants to overcome a rate-limiting step in the Se volatilization pathway, i.e. Se accumulation in plant tissues.