• An Immortalized Genetic Mapping Population for Perennial Ryegrass: A Resource for Phenotyping and Complex Trait Mapping

      Velmurugan, Janaki; Milbourne, Dan; Connolly, Vincent; Heslop-Harrison, J. S.; Anhalt, Ulrike C. M.; Lynch, M. B.; Barth, Susanne; Teagasc Walsh Fellowship Programme (Frontiers, 2018-05-31)
      To address the lack of a truly portable, universal reference mapping population for perennial ryegrass, we have been developing a recombinant inbred line (RIL) mapping population of perennial ryegrass derived via single seed descent from a well-characterized F2 mapping population based on genetically distinct inbred parents in which the natural self-incompatibility (SI) system of perennial ryegrass has been overcome. We examined whether it is possible to create a genotyping by sequencing (GBS) based genetic linkage map in a small population of the F6 generation of this population. We used 41 F6 genotypes for GBS with PstI/MspI-based libraries. We successfully developed a genetic linkage map comprising 6074 SNP markers, placing a further 22080 presence and absence variation (PAV) markers on the map. We examined the resulting genetic map for general and RIL specific features. Overall segregation distortion levels were similar to those experienced in the F2 generation, but segregation distortion was reduced on linkage group 6 and increased on linkage group 7. Residual heterozygosity in the F6 generation was observed at a level of 5.4%. There was a high proportion of chromosomes (30%) exhibiting the intact haplotype of the original inbred parents of the F1 genotype from which the population is derived, pointing to a tendency for chromosomes to assort without recombining. This could affect the applicability of these lines and might make them more suitable for situations where repressed recombination is an advantage. Inter- and intra-chromosomal linkage disequilibrium (LD) analysis suggested that the map order was robust. We conclude that this RIL population, and subsequent F7 and F8 generations will be useful for genetic analysis and phenotyping of agronomic and biological important traits in perennial ryegrass.
    • Impact of agronomic practices of an intensive dairy farm on nitrogen concentrations in a karst aquifer in Ireland

      Huebsch, Manuela; Horan, Brendan; Blum, P.; Richards, Karl G.; Grant, Jim; Fenton, Owen; Teagasc Walsh Fellowship Programme (Elsevier, 24/09/2013)
      Exploring the relationship between agricultural nitrogen loading on a dairy farm and groundwater reactive nitrogen concentration such as nitrate is particularly challenging in areas underlain by thin soils and karstified limestone aquifers. The objective of this study is to relate changes in detailed agronomic N-loading, local weather conditions, hydrogeological and geological site characteristics with groundwater N occurrence over an 11-year period on an intensive dairy farm with free draining soils and a vulnerable limestone aquifer. In addition, the concept of vertical time lag from source to receptor is considered. Statistical analysis used regression with automatic variable selection. Four scenarios were proposed to describe the relationships between paddock and groundwater wells using topographic and hydrogeological assumptions. Monitored nitrate concentrations in the studied limestone aquifer showed a general decrease in the observed time period (2002–2011). Statistical results showed that a combination of improved agronomic practices and site specific characteristics such as thicknesses of the soil and unsaturated zone together with hydrogeological connections of wells and local weather conditions such as rainfall, sunshine and soil moisture deficit were important explanatory variables for nitrate concentrations. Statistical results suggested that the following agronomic changes improved groundwater quality over the 11-year period: reductions in inorganic fertiliser usage, improvements in timing of slurry application, the movement of a dairy soiled water irrigator to less karstified areas of the farm and the usage of minimum cultivation reseeding on the farm. In many cases the explanatory variables of farm management practices tended to become more important after a 1- or 2-year time lag. Results indicated that the present approach can be used to elucidate the effect of farm management changes to groundwater quality and therefore the assessment of present and future legislation implementations.
    • The impact of cattle dung pats on earthworm distribution in grazed pastures

      Bacher, M. G.; Fenton, Owen; Bondi, G.; Creamer, Rachel; Karmarkar, M.; Schmidt, O.; Department of Agriculture, Food and the Marine; 13/S/468 (Springer Science and Business Media LLC, 2018-12-19)
      Background Grazed grassland management regimes can have various effects on soil fauna. For example, effects on earthworms can be negative through compaction induced by grazing animals, or positive mediated by increases in sward productivity and cattle dung pats providing a food source. Knowledge gaps exist in relation to the behaviour of different earthworm species i.e. their movement towards and aggregation under dung pats, the legacy effects of pats and the spatial area of recruitment. The present study addressed these knowledge gaps in field experiments, over 2 years, using natural and simulated dung pats on two permanent, intensively grazed pastures in Ireland. Results Dung pats strongly affected spatial earthworm distribution, with up to four times more earthworms aggregating beneath pats, than in the control locations away from pats. In these earthworm communities comprising 11 species, temporally different aggregation and dispersal patterns were observed, including absence of individual species from control locations, but no clear successional responses. Epigeic species in general, but also certain species of the anecic and endogeic groups were aggregating under dung. Sampling after complete dung pat disappearance (27 weeks after application) suggested an absence of a dung pat legacy effect on earthworm communities. Based on species distributions, the maximum size of the recruitment area from which earthworms moved to pats was estimated to be 3.8 m2 per dung pat. Since actual grazing over 6 weeks would result in the deposition of about 300 dung pats per ha, it is estimated that a surface area of 1140 m2 or about 11% of the total grazing area can be influenced by dung pats in a given grazing period. Conclusions This study showed that the presence of dung pats in pastures creates temporary hot spots in spatial earthworm species distribution, which changes over time. The findings highlight the importance of considering dung pats, temporally and spatially, when sampling earthworms in grazed pastures. Published comparisons of grazed and cut grasslands probably reached incorrect conclusions by ignoring or deliberately avoiding dung pats. Furthermore, the observed intense aggregation of earthworms beneath dung pats suggests that earthworm functions need to be assessed separately at these hot spots.
    • Impact of chemical amendment of dairy cattle slurry on phosphorus, suspended sediment and metal loss to runoff from a grassland soil

      Brennan, Raymond B.; Fenton, Owen; Grant, Jim; Healy, Mark G.; Teagasc Walsh Fellowship Programme (Elsevier, 01/11/2011)
      Emerging remediation technologies such as chemical amendment of dairy cattle slurry have the potential to reduce phosphorus (P) solubility and consequently reduce P losses arising from land application of dairy cattle slurry. The aim of this study was to determine the effectiveness of chemical amendment of slurry to reduce incidental losses of P and suspended sediment (SS) from grassland following application of dairy cattle slurry and to examine the effect of amendments on metal concentrations in runoff water. Intact grassed-soil samples were placed in two laboratory runoff boxes, each 200-cm-long by 22.5-cm-wide by 5-cm-deep, before being amended with dairy cattle slurry (the study control) and slurry amended with either: (i) alum, comprising 8% aluminium oxide (Al2O3) (1.11:1 aluminium (Al):total phosphorus (TP) of slurry) (ii) poly-aluminium chloride hydroxide (PAC) comprising 10% Al2O3 (0.93:1 Al:TP) (iii) analytical grade ferric chloride (FeCl2) (2:1 Fe:TP), (iv) and lime (Ca(OH)2) (10:1 Ca:TP). When compared with the study control, PAC was the most effective amendment, reducing dissolved reactive phosphorus (DRP) by up to 86% while alum was most effective in reducing SS (88%), TP (94%), particulate phosphorus (PP) (95%), total dissolved phosphorus (TDP) (81%), and dissolved unreactive phosphorus (DUP) (86%). Chemical amendment of slurry did not appear to significantly increase losses of Al and Fe compared to the study control, while all amendments increased Ca loss compared to control and grass-only treatment. While chemical amendments were effective, the reductions in incidental P losses observed in this study were similar to those observed in other studies where the time from slurry application to the first rainfall event was increased. Timing of slurry application may therefore be a much more feasible way to reduce incidental P losses. Future work must examine the long-term effects of amendments on P loss to runoff and not only incidental losses.
    • Impact of chemically amended pig slurry on greenhouse gas emissions, soil properties and leachate

      O'Flynn, Cornelius J.; Healy, Mark G.; Lanigan, Gary; Troy, Shane M.; Somers, Cathal; Fenton, Owen; Irish Research Council for Science, Engineering and Technology (Elsevier, 10/07/2013)
      The effectiveness of chemical amendment of pig slurry to ameliorate phosphorus (P) losses in runoff is well studied, but research mainly has concentrated only on the runoff pathway. The aims of this study were to investigate changes to leachate nutrient losses, soil properties and greenhouse gas (GHG) emissions due to the chemical amendment of pig slurry spread at 19 kg total phosphorus (TP), 90 kg total nitrogen (TN), and 180 kg total carbon (TC) ha-1. The amendments examined were: (1) commercial grade liquid alum (8% Al2O3) applied at a rate of 0.88:1 [Al:TP] (2) commercial-grade liquid ferric chloride (38% FeCl3) applied at a rate of 0.89:1 [Fe:TP] and (3) commercial-grade liquid poly-aluminium chloride (PAC) (10% Al2O3) applied at a rate of 0.72:1 [Al:TP]. Columns filled with sieved soil were incubated for 8 mo at 10oC and were leached with 160 ml (19 mm) distilled water wk-1. All amendments reduced the Morgan’s phosphorus and water extractable P content of the soil to that of the soil-only treatment, indicating that they have the ability to reduce P loss in leachate following slurry application. There were no significant differences between treatments for nitrogen (N) or carbon (C) in leachate or soil, indicating no deleterious impact on reactive N emissions or soil C cycling. Chemical amendment posed no significant change to GHG emissions from pig slurry, and in the cases of alum and PAC, reduced cumulative N2O and CO2 losses. Chemical amendment of land applied pig slurry can reduce P in runoff without any negative impact on nutrient leaching and GHG emissions. Future work must be conducted to ascertain if more significant reductions in GHG emissions are possible with chemical amendments.
    • The Impact of Chemically Amended Pig Slurry on Surface Runoff, Leachate and Greenhouse Gasses

      O'Flynn, Cornelius J.; Irish Research Council (2013-05)
      In Ireland, the pig industry is concentrated in a small number of counties. Pig farms typically have a high stocking rate. Therefore, the disposal of slurry in a cost-effective and environmentally-responsible way is a serious issue for farmers. Slurry is commonly applied to land, but this may not be possible if the land is at, or approaching, phosphorus (P) saturation. As pig farmers dispose of slurry in the vicinity of their properties, most of the nearby land is at P saturation, so alternative treatment methods need to be utilised (e.g. constructed wetlands, anaerobic digestion, filtration) or the slurry needs to be transported to another location. These alternatives are not currently financially viable in Ireland. Existing legislation (S.I. 610 of 2010) and recent changes in the implementation of legislation governing the timing and quantities of slurry that may be applied to land, means that pig farmers will no longer be able to exceed the maximum legal application rate to land (from January 2017). European policy aiming to intensify pig production will only accentuate this problem. If pig farmers are forced, in exceptional circumstances, to land apply slurry to unsuitable land, surface and subsurface losses of nutrients and suspended solids (SS) may occur. This could be potentially problematic if the land is located in a critical source area (CSA), an area that is highly likely to pollute receiving waters. In these circumstances, a possible novel solution is to chemically amend the pig slurry prior to landspreading. This would mean that pig farmers may, in exceptional circumstances, utilise the land in the vicinity of their farms for landspreading, without releasing excessive nutrients and SS into receiving waters. However, knowledge gaps exist concerning the type of amendments to be used, the characteristics of the soil on which they can be most effectively used, and their impact on incidental (short-term) and chronic (long-term) losses of nutrients, SS and greenhouse gas (GHG) to surface and subsurface water and the atmosphere. Therefore, the aims of this project were to: (1) identify the most appropriate chemical amendments, and their addition rates, to reduce P losses in runoff from pig slurry based on effectiveness, cost and feasibility; (2) investigate the impacts of these chemical amendments on nutrient losses in leachate, soil properties and GHG emissions; and (3) identify suitable soil types on which to landspread chemically-amended pig slurry. Laboratory bench-scale experiments were designed to identify the amendments which had the potential to reduce P in overland runoff and to quantify the stoichiometric rates at which to add them to the slurry. Based on effectiveness, cost and feasibility, the amendments identified were alum, which reduced dissolved reactive phosphorus (DRP) in overlying water by 86%, poly-aluminium chloride (PAC) (73%) and ferric chloride (FeCl3) (71%). Following these bench-scale experiments, rainfall simulation experiments were conducted to quantify the impact of chemical amendments to slurry on surface runoff losses at various time intervals from the time of application. Poly-aluminium chloride performed best in these experiments. For the first time, the effect of these amendments on GHG emissions, soil properties and leachate was also examined. Chemical amendment did not adversely affect GHG emissions, soil properties or leachate from pig slurry, but FeCl3 increased nitrous oxide (N2O) and carbon dioxide (CO2) losses. Finally, a 3-mo incubation experiment was conducted using a range of soil types to examine the effect of amendments on the long-term plant availability of P in soil and P solubility. Alum reduced more water extractable P than PAC, but also resulted in less plant available P. Considering cost, surface runoff and subsurface leachate losses, GHG emissions and impacts on soil chemistry, PAC was found to be the most suitable amendment with which to chemically amend pig slurry. There is the potential, in combination with existing programmes of measures, to employ chemical amendment as a measure to mitigate the environmental impact arising from the landspreading of pig slurry. This should be conducted in targeted areas of the CSA and should take into account soil type and its chemical properties. Before implementation, these tests must first be validated in long-term testing at field-scale over a wide variety of soil types, and include repeated application and incorporation. At present, there is no provision in legislation for chemical amendments to be used as a mitigation measure in the land application of pig slurry, but if they are to be utilised, a regulatory framework will need to be introduced by the relevant bodies.
    • The impact of grazing cattle on soil physical properties and nutrient concentrations in overland flow from pasture, Part B

      Kurz, Isabelle; O’Reilly, Conor; Tunney, Hubert; Bourke, David; Environmental Protection Agency (Teagasc, 01/06/2007)
      The loss of nutrients from agricultural land to water bodies is a serious concern in many countries. To gain information on the contribution of grazing animals to diffuse nutrient losses from pasture areas to water, this study looked at the impact of cattle on nutrient concentrations in overland flow and on soil hydrology (bulk density, macroporosity and resistance to penetration). Rainfall simulations to produce overland flow were conducted and soil physical measurements were taken on experimental plots assigned to one of two treatments: 1) cattle had unrestricted access to the plot; 2) cattle could graze the plot but they could neither walk on the plot area nor deposit excrements on it. Areas to which the cattle had free access were characterised by 57%-83% lower macroporosity, by 8%-17% higher bulk density and by 27%-50% higher resistance to penetration than areas from which the cattle were excluded. The nutrients in overland flow from grassland that were affected by the presence of grazing animals were mainly the particulate nitrogen, the organic phosphorus and the potassium concentrations. Overall, the presence of cattle had a longer lasting effect on the soil hydrological parameters measured than on the nutrient concentrations in overland flow.
    • Impact of P inputs on source-sink P dynamics of sediment along an agricultural ditch network

      Ezzati, G.; Fenton, Owen; Healy, M.G.; Christianson, L.; Feyereisen, G.W.; Thornton, S.; Chen, Q.; Fan, B.; Ding, J.; Daly, Karen; et al. (Elsevier BV, 2020-03)
      Phosphorus (P) loss from intensive dairy farms is a pressure on water quality in agricultural catchments. At farm scale, P sources can enter in-field drains and open ditches, resulting in transfer along ditch networks and delivery into nearby streams. Open ditches could be a potential location for P mitigation if the right location was identified, depending on P sources entering the ditch and the source-sink dynamics at the sediment-water interface. The objective of this study was to identify the right location along a ditch to mitigate P losses on an intensive dairy farm. High spatial resolution grab samples for water quality, along with sediment and bankside samples, were collected along an open ditch network to characterise the P dynamics within the ditch. Phosphorus inputs to the ditch adversely affected water quality, and a step change in P concentrations (increase in mean dissolved reactive phosphorus (DRP) from 0.054 to 0.228 mg L−1) midway along the section of the ditch sampled, signalled the influence of a point source entering the ditch. Phosphorus inputs altered sediment P sorption properties as P accumulated along the length of the ditch. Accumulation of bankside and sediment labile extractable P, Mehlich 3 P (M3P) (from 13 to 97 mg kg−1) resulted in a decrease in P binding energies (k) to < 1 L mg−1 at downstream points and raised the equilibrium P concentrations (EPC0) from 0.07 to 4.61 mg L−1 along the ditch. The increase in EPC0 was in line with increasing dissolved and total P in water, demonstrating the role of sediment downstream in this ditch as a secondary source of P to water. Implementation of intervention measures are needed to both mitigate P loss and remediate sediment to restore the sink properties. In-ditch measures need to account for a physicochemical lag time before improvements in water quality will be observed.
    • Impact of pig slurry amendments on phosphorus, suspended sediment and metal losses in laboratory runoff boxes under simulated rainfall

      O'Flynn, Cornelius J.; Fenton, Owen; Wilson, Paul; Healy, Mark G.; Irish Research Council for Science, Engineering and Technology (Elsevier, 30/12/2012)
      Losses of phosphorus (P) when pig slurry applications to land are followed by a rainfall event or losses from soils with high P contents can contribute to eutrophication of receiving waters. The addition of amendments to pig slurry spread on high P Index soils may reduce P and suspended sediment (SS) losses. This hypothesis was tested at laboratory-scale using runoff boxes under simulated rainfall conditions. Intact grassed soil samples, 100 cm-long, 22.5 cm-wide and 5 cm-deep, were placed in runoff boxes and pig slurry or amended pig slurry was applied to the soil surface. The amendments examined were: (1) commercial grade liquid alum (8% Al2O3) applied at a rate of 0.88:1 [Al:total phosphorus (TP)] (2) commercial-grade liquid ferric chloride (38% FeCl3) applied at a rate of 0.89:1 [Fe:TP] and (3) commercial-grade liquid poly-aluminium chloride (PAC) (10% Al2O3) applied at a rate of 0.72:1 [Al:TP]. The grassed soil was then subjected to three rainfall events (10.3 ± 0.15 mm h−1) at time intervals of 48, 72, and 96 h following slurry application. Each sod received rainfall on 3 occasions. Results across three rainfall events showed that for the control treatment, the average flow weighted mean concentration (FWMC) of TP was 0.61 mg L−1, of which 31% was particulate phosphorus (PP), and the average FWMC of SS was 38.1 mg L−1. For the slurry treatment, there was an average FWMC of 2.2 mg TP L−1, 47% of which was PP, and the average FWMC of SS was 71.5 mg L−1. Ranked in order of effectiveness from best to worst, PAC reduced the average FWMC of TP to 0.64 mg L−1 (42% PP), FeCl3 reduced TP to 0.91 mg L−1 (52% PP) and alum reduced TP to 1.08 mg L−1 (56% PP). The amendments were in the same order when ranked for effectiveness at reducing SS: PAC (74%), FeCl3 (66%) and alum (39%). Total phosphorus levels in runoff plots receiving amended slurry remained above those from soil only, indicating that, although incidental losses could be mitigated by chemical amendment, chronic losses from the high P index soil in the current study could not be reduced.
    • The Impact of Policy Instruments on Soil Multifunctionality in the European Union

      Vrebos, Dirk; Bampa, Francesca; Creamer, Rachel E.; Gardi, Ciro; Ghaley, Bhim Bahadur; Jones, Arwyn; Rutgers, Michiel; Sandén, Taru; Staes, Jan; Meire, Patrick; et al. (MDPI, 2017-03-09)
      Agricultural ecosystems provide a range of benefits that are vital to human well-being. These benefits are dependent on several soil functions that are affected in different ways by legislation from the European Union, national, and regional levels. We evaluated current European Union soil-related legislation and examples of regional legislation with regard to direct and indirect impacts on five soil functions: the production of food, fiber, and fuel; water purification and regulation; carbon sequestration and climate regulation; habitat for biodiversity provisioning; and the recycling of nutrients/agro-chemicals. Our results illustrate the diversity of existing policies and the complex interactions present between different spatial and temporal scales. The impact of most policies, positive or negative, on a soil function is usually not established, but depends on how the policy is implemented by local authorities and the farmers. This makes it difficult to estimate the overall state and trends of the different soil functions in agricultural ecosystems. To implement functional management and sustainable use of the different soil functions in agricultural ecosystems, more knowledge is needed on the policy interactions as well as on the impact of management options on the different soil functions.
    • Impact of Soil Type, Biology and Temperature on the Survival of Non-Toxigenic Escherichia Coli O157

      Moynihan, Emma; Richards, Karl G.; Ritz, Karl; Tyrrel, Sean; Brennan, Fiona P.; Teagasc Walsh Fellowship Programme (Royal Irish Academy, 14/06/2013)
      The occurrence of microbial enteropathogens in the environment can represent a serious risk to human health. The fate of enteropathogens introduced into the soil environment is dependent on a wide range of complex interacting environmental factors. While the effect of abiotic factors on enteropathogen survival has been widely examined, the interaction of enteropathogens with the soil microbial community is poorly understood. This study investigated the effect of soil biology and soil type on the survival of a non-toxigenic strain of Escherichia coli O157 under different temperature regimes. Soil microcosms of two soil types, with and without an intact microbial community, were inoculated with the enteropathogen surrogate, and survival was determined over a 64-day period, encompassing a shift from cold to ambient temperatures. In both soil types bacterial numbers decreased in soil with an intact microflora, while in the absence of an intact community E. coli populations increased. This effect was temperature specific, with E. coli populations remaining stable at low temperature, regardless of treatment. Soil type was of importance in survival at both cold and ambient temperatures. This work highlights the signifi cance of the soil microbial community in suppressing enteropathogens in soil, and of investigating die-off in a multi-factorial manner.
    • The impact of the grazing animal on phosphorus, nitrogen, potassium and suspended solids loss from grazed pastures, Part A

      Tunney, Hubert; Kurz, Isabelle; Bourke, David; O'Reilly, Colin; Jeffrey, D.W.; Dowding, P.; Foy, B.; Kilpatrick, D.J.; Haygarth, P. (Teagasc, 01/06/2007)
      In Ireland 90% of the 4.2 million ha of farmland is grassland. Phosphorus deficiency limited grassland production in Ireland and this was corrected by chemical fertiliser use in the 1960s and 1970s. The increased inputs of fertilisers led to increased intensification of grassland with a doubling of grass yield and of grazing animal numbers, from about 3 million to over 6 million livestock units. There is little information on relative contribution of increased chemical fertiliser use compared to increased grazing animal numbers on phosphorus loss to water. The main objective of this study was to obtain information on nutrient loss, particularly phosphorus, in overland flow from cut and grazed grassland plots, with a range of soil test phosphorus levels over three years and implications.
    • Implications of the proposed Soil Framework Directive on agricultural systems in Atlantic Europe – a review

      Creamer, Rachel E.; Brennan, Fiona P.; Fenton, Owen; Healy, Mark G.; Lalor, Stanley T. J.; Lanigan, Gary; Regan, J. T.; Griffiths, Bryan (Wiley; British Society of Soil Science, 28/07/2010)
      The main threats to soils outlined in the pending Soil Framework Directive (SFD) are: contamination, loss of organic matter, erosion, compaction, sealing, salinization and desertification. The first four threats are pertinent to agricultural systems in Atlantic Europe, but vary in their extent between countries depending on the spatial soil distribution. Loss of soil biodiversity has not been included as a potential threat in the SFD due to lack of information that is currently available both spatially and temporally to facilitate any legislation to protect it. This paper gives emphasis to the four main threats outlined above associated with Agricultural systems in Atlantic Europe. Each soil threat is discussed in relation to the agricultural management calendar for cultivated and grazed grassland soils. The paper discusses current soil protection policies and possible changes to such legislation with the adoption of the SFD by member states.
    • Improving and disaggregating N2O emission factors for ruminant excreta on temperate pasture soils

      Krol, Dominika; Carolan, Rachael; Minet, E.; McGeough, K. L.; Watson, C. J.; Forrestal, Patrick J.; Lanigan, Gary; Richards, Karl G.; Department of Agriculture, Food and the Marine, Ireland; RSF10/RD/SC/716; et al. (Elsevier, 11/06/2016)
      Cattle excreta deposited on grazed grasslands are a major source of the greenhouse gas (GHG) nitrous oxide (N2O). Currently, many countries use the IPCC default emission factor (EF) of 2% to estimate excreta-derived N2O emissions. However, emissions can vary greatly depending on the type of excreta (dung or urine), soil type and timing of application. Therefore three experiments were conducted to quantify excreta-derived N2O emissions and their associated EFs, and to assess the effect of soil type, season of application and type of excreta on the magnitude of losses. Cattle dung, urine and artificial urine treatments were applied in spring, summer and autumn to three temperate grassland sites with varying soil and weather conditions. Nitrous oxide emissions were measured from the three experiments over 12 months to generate annual N2O emission factors. The EFs from urine treated soil was greater (0.30–4.81% for real urine and 0.13–3.82% for synthetic urine) when compared with dung (− 0.02–1.48%) treatments. Nitrous oxide emissions were driven by environmental conditions and could be predicted by rainfall and temperature before, and soil moisture deficit after application; highlighting the potential for a decision support tool to reduce N2O emissions by modifying grazing management based on these parameters. Emission factors varied seasonally with the highest EFs in autumn and were also dependent on soil type, with the lowest EFs observed from well-drained and the highest from imperfectly drained soil. The EFs averaged 0.31 and 1.18% for cattle dung and urine, respectively, both of which were considerably lower than the IPCC default value of 2%. These results support both lowering and disaggregating EFs by excreta type.
    • In situ denitrification rates in shallow groundwater beneath a springbarley - mustard cover crop system

      Jahangir, Mohammad M. R.; Minet, E.; Johnston, Paul; Coxon, Catherine E.; Richards, Karl G. (European Geosciences Union, 28/04/2014)
    • In situ N2O emissions are not mitigated by hippuric and benzoic acids under denitrifying conditions

      Krol, Dominika; Forrestal, Patrick J.; Lanigan, Gary; Richards, Karl G. (Elsevier, 29/12/2014)
      Ruminant urine patches deposited onto pasture are a significant source of greenhouse gas nitrous oxide (N2O) from livestock agriculture. Increasing food demand is predicted to lead to a rise in ruminant numbers globally, which, in turn will result in elevated levels of urine-derived N2O. Therefore mitigation strategies are urgently needed. Urine contains hippuric acid and together with one of its breakdown products, benzoic acid, has previously been linked to mitigating N2O emissions from urine patches in laboratory studies. However, the sole field study to date found no effect of hippuric and benzoic acid concentration on N2O emissions. Therefore the aim of this study was to investigate the in situ effect of these urine constituents on N2O emissions under conditions conducive to denitrification losses. Unadulterated bovine urine (0 mM of hippuric acid, U) was applied, as well as urine amended with either benzoic acid (96 mM, U + BA) or varying rates of hippuric acid (8 and 82 mM, U + HA1, U + HA2). Soil inorganic nitrogen (N) and N2O fluxes were monitored over a 66 day period. Urine application resulted in elevated N2O flux for 44 days. The largest N2O fluxes accounting for between 13% (U) and 26% (U + HA1) of total loss were observed on the day of urine application. Between 0.9 and 1.3% of urine-N was lost as N2O. Cumulative N2O loss from the control was 0.3 kg N2O–N ha− 1 compared with 11, 9, 12, and 10 kg N2O–N ha− 1 for the U, U + HA1, U + HA2, and U + BA treatments, respectively. Incremental increases in urine HA or increase in BA concentrations had no effect on N2O emissions. Although simulation of dietary manipulation to reduce N2O emissions through altering individual urine constituents appears to have no effect, there may be other manipulations such as reducing N content or inclusion of synthetic inhibitory products that warrant further investigation.
    • Incidental phosphorus and nitrogen loss from grassland plots receiving chemically amended dairy cattle slurry

      Brennan, Raymond B.; Healy, Mark G.; Grant, Jim; Ibrahim, Tristan G.; Fenton, Owen; Teagasc Walsh Fellowship Programme (Elsevier, 2012-12)
      Chemical amendment of dairy cattle slurry has been shown to effectively reduce incidental phosphorus (P) losses in runoff; however, the effects of amendments on incidental nitrogen (N) losses are not as well documented. This study examined P and N losses in runoff during three simulated rainfall events 2, 10 and 28 days after a single application of unamended/chemically amended dairy cattle slurry. Twenty-five hydraulically isolated plots, each measuring 0.9 m by 0.4 m and instrumented with runoff collection channels, were randomly assigned the following treatments: (i) grass-only, (ii) slurry-only (the study-control), (iii) slurry amended with industrial grade liquid alum comprising 8% Al2O3, (iv) slurry amended with industrial grade liquid poly-aluminum chloride (PAC) comprising 10% Al2O3, and (v) slurry amended with lime. During the first rainfall event, lime was ineffective but alum and PAC effectively reduced dissolved reactive P (DRP) (by 95 and 98%, respectively) and total P (TP) flow-weighted-mean-concentrations (by 82 and 93%, respectively) in runoff compared to the study-control. However, flow-weighted-mean-concentrations of ammonium–N (NH4–N) in runoff were increased with alum- (81%) and lime-treated (11%) slurry compared to the study-control whereas PAC reduced the NH4–N by 82%. Amendments were not observed to have a significant effect on NO3–N losses during this study. Slurry amendments reduced P losses for the duration of the study, whereas the effect of amendments on N losses was not significant following the first event. Antecedent volumetric water content of the soil or slope of the plots did not appear to affect runoff volume. However, runoff volumes (and consequently loads of P and N) were observed to increase for the chemically amended plots compared to the control and soil-only plots. This work highlights the importance of considering both P and N losses when implementing a specific nutrient mitigation measure.
    • Indirect emissions of N2O, CO2 and CH4 via groundwater in contrasting agricultural systems

      Jahangir, Mohammad M. R.; Johnston, Paul; Richards, Karl G.; Irish Research Council; Department of Agriculture, Food and the Marine, Ireland (10/03/2014)
      The dynamics of dissolved carbon (C) and nitrogen (N) in groundwater is a key ‘‘missing piece’’ in our understanding of global C and N balances. In addition, quantification of dissolved nitrous oxide (N2O), carbon dioxide (CO2) and methane (CH4) in groundwater beneath an agricultural system is of huge importance for global greenhouse gas (GHG) budget estimation. This research aimed to (i) measure the amount of dissolved C and N losses from two terrestrial ecosystems to the aquatic ecosystems via groundwater, and (ii) estimate the contribution of indirect emissions of GHG to the atmosphere.
    • The influence of aggregate size fraction and horizon position on microbial community composition

      Fox, Aaron; Ikoyi, Israel; Torres-Sallan, Gemma; Lanigan, Gary; Schmalenberger, Achim; Wakelin, Steve; Creamer, Rachel; Teagasc Walsh Fellowship Programme; Environmental Protection Agency; Agricultural GHG Research Initiative for Ireland; et al. (Elsevier, 2018-03-09)
      The influence of horizon position and aggregate size on bacterial and fungal community composition was determined. From nine sites, soils were collected from the top three horizon positions (H1, H2 and H3). Physical fractionation separated samples into large macroaggregate (LM, >2000 μm), macroaggregate (MAC, >250 μm), microaggregate (MIC, <250 μm), and silt and clay (SC, 53 μm) fractions. In all samples, the structure of the bacterial and fungal community composition was assessed via restriction fragment length polymorphism (T-RFLP), and for the four aggregate sizes from the top two horizons positions an in-depth analysis of the bacterial community was conducted using next generation sequencing (NGS). Bacterial and fungal communities both differed between aggregate-sizes. Changes in the composition of the bacterial and fungal communities also occurred among horizon positions, with a significant interaction between aggregate size and horizon position evident for the bacterial community. Using NGS, it was shown that aggregate-size had a significant effect on the bacterial community in both horizon positions at both the phyla and family taxonomic levels. MAC and MIC significantly differed in the % relative abundance of bacterial groups, potentially indicating differing predation pressures. These results indicate that both horizon position and aggregate size support distinct microbial communities. Understanding these parameters is critical in our comprehension of the patterns of microbial diversity in soil.
    • Influence of soil moisture on codenitrification fluxes from a urea-affected pasture soil

      Clough, Timothy J.; Lanigan, Gary; de Klein, Cecile; Samad, Sainur; Morales, Sergio; Rex, David; Bakken, Lars R.; Johns, Charlotte; Condron, Leo; Grant, Jim; et al. (Nature, 2017-05-19)
      Intensively managed agricultural pastures contribute to N2O and N2 fluxes resulting in detrimental environmental outcomes and poor N use efficiency, respectively. Besides nitrification, nitrifier-denitrification and heterotrophic denitrification, alternative pathways such as codenitrification also contribute to emissions under ruminant urine-affected soil. However, information on codenitrification is sparse. The objectives of this experiment were to assess the effects of soil moisture and soil inorganic-N dynamics on the relative contributions of codenitrification and denitrification (heterotrophic denitrification) to the N2O and N2 fluxes under a simulated ruminant urine event. Repacked soil cores were treated with 15N enriched urea and maintained at near saturation (−1 kPa) or field capacity (−10 kPa). Soil inorganic-N, pH, dissolved organic carbon, N2O and N2 fluxes were measured over 63 days. Fluxes of N2, attributable to codenitrification, were at a maximum when soil nitrite (NO2−) concentrations were elevated. Cumulative codenitrification was higher (P = 0.043) at −1 kPa. However, the ratio of codenitrification to denitrification did not differ significantly with soil moisture, 25.5 ± 15.8 and 12.9 ± 4.8% (stdev) at −1 and −10 kPa, respectively. Elevated soil NO2− concentrations are shown to contribute to codenitrification, particularly at −1 kPa.