Johnstown Castle is Ireland’s leading research centre for soils and the rural environment. The centre conducts research on soils; nutrient efficiency; recovery and losses; air and water quality; the agricultural environment and agro-ecology. The research results generated are used widely by advisors, farmers, scientists and policy makers.

Recent Submissions

  • Easy phylotyping of Escherichia coli via the EzClermont web app and command-line tool

    Waters, Nicholas R.; Abram, Florence; Brennan, Fiona; Holmes, Ashleigh; Pritchard, Leighton; The James Hutton Institute; National University of Ireland, Galway (Microbiology Society, 2020-09-01)
    The Clermont PCR method for phylotyping Escherichia coli remains a useful classification scheme even though genome sequencing is now routine, and higher-resolution sequence typing schemes are now available. Relating present-day whole-genome E. coli classifications to legacy phylotyping is essential for harmonizing the historical literature and understanding of this important organism. Therefore, we present EzClermont – a novel in silico Clermont PCR phylotyping tool to enable ready application of this phylotyping scheme to whole-genome assemblies. We evaluate this tool against phylogenomic classifications, and an alternative software implementation of Clermont typing. EzClermont is available as a web app at www.ezclermont.org, and as a command-line tool at https://nickp60.github.io/EzClermont/.
  • Mid-infrared spectroscopy as an alternative to laboratory extraction for the determination of lime requirement in tillage soils

    Metzger, Konrad; Zhang, Chaosheng; Ward, Mark; Daly, Karen; Teagasc Walsh Fellowship Programme; Department for Agriculture Food and the Marine; RMIS 6837; 15/ICTAGRI 2 (Elsevier BV, 2020-04)
    Lime is a crucial soil conditioner to bring agricultural soils to optimum pH values for nutrient availability. Lime recommendations are typically determined in laboratory extractions, the most common being the “Shoemaker- McLean and Pratt” (SMP) buffer method, that requires carcinogenic reagents soon to be abolished under the EU legislation. As an alternative to wet chemistry, mid-infrared (MIR) spectroscopy has shown to be a cost-and time effective method at predicting soil properties. The capability and feasibility of diffuse reflectance infrared spectroscopy (DRIFTS) to predict lime requirement (LR) in tillage fields is examined. Samples from 41 cereal tillage fields (n = 655) are used to build a calibration for DRIFTS using partial least squares regression (PLSR). The samples were split into calibration set (31 fields, n=495) and validation set (10 fields, n= 160). After preprocessing with trim, smoothing and standard normal variate, a calibration model using 6 latent variables, provided R2 of 0.89 and root mean square error of cross-validation (RMSECV) of 1.56 t/ha. Prediction of all fields from the validation set resulted in R2 of 0.76 and root mean square error of prediction (RMSEP) of 1.68 t/ ha. The predictions of the single fields ranged from R2 values of 0.41 to 0.72, RMSEP of 0.48 to 4.2 t/ha and ratios of performance to inter-quartile distance (RPIQ) of 0.45 to 3.56. It was shown that the signals of soil constituents having an influence on the LR were picked up in the spectra and were identified in the loading weights of the PLSR. While the error is too high to predict the variability of LR within the field, MIR prediction using field averages provided a viable alternative to current laboratory methods for blanket spreading of lime on tillage fields.
  • Predicting the Distribution of High Nature Value farmland in Ireland: IDEAL-HNV

    Finn, John; Sullivan, Caroline; O’hÚallacháin, Daire; green, stuart; Clifford, Brian; Matin, Shafique; Meredith, David; Moran, James (2020-08-28)
    Conference presentation outlining the IDEAL-HNV project
  • Environmental footprint family to address local to planetary sustainability and deliver on the SDGs

    Vanham, Davy; Leip, Adrian; Galli, Alessandro; Kastner, Thomas; Bruckner, Martin; Uwizeye, Aimable; van Dijk, Kimo; Ercin, Ertug; Dalin, Carole; Brandão, Miguel; et al. (Elsevier BV, 2019-07-29)
    The number of publications on environmental footprint indicators has been growing rapidly, but with limited efforts to integrate different footprints into a coherent framework. Such integration is important for comprehensive understanding of environmental issues, policy formulation and assessment of trade-offs between different environmental concerns. Here, we systematize published footprint studies and define a family of footprints that can be used for the assessment of environmental sustainability. We identify overlaps between different footprints and analyse how they relate to the nine planetary boundaries and visualize the crucial information they provide for local and planetary sustainability. In addition, we assess how the footprint family delivers on measuring progress towards Sustainable Development Goals (SDGs), considering its ability to quantify environmental pressures along the supply chain and relating them to the water-energy-food-ecosystem (WEFE) nexus and ecosystem services. We argue that the footprint family is a flexible framework where particular members can be included or excluded according to the context or area of concern. Our paper is based upon a recent workshop bringing together global leading experts on existing environmental footprint indicators.
  • Biogeography of arbuscular mycorrhizal fungal spore traits along an aridity gradient, and responses to experimental rainfall manipulation

    Deveautour, Coline; Chieppa, Jeff; Nielsen, Uffe N.; Boer, Matthias M.; Mitchell, Christopher; Horn, Sebastian; Power, Sally A.; Guillen, Alberto; Bennett, Alison E.; Powell, Jeff R.; et al. (Elsevier BV, 2020-08)
    Spore size, colour and melanin content are hypothesised to be functional in relation to environmental stress. Here, we studied AM fungal spores in arid environments of Australia and in an experimental platform simulating altered rainfall. We used microscopy and image analysis to measure spore colour and size, and a quantitative colorimetric assay to estimate melanin content in spores. In arid sites, melanin content tended to increase with increasing aridity. We observed a large range of spore colours at all sites but found a higher proportion of both dark and light spores, and fewer intermediate colours, in drier sites. Spore abundance and size varied among sites, but neither were related to aridity. In the experimental platform established in a grassland, we found no evidence that altered rainfall influenced spore traits. This study identifies traits associated with environmental stress to inform future work into AM fungal life history and assembly processes.
  • A Functional Land Management conceptual framework under soil drainage and land use scenarios

    Coyle, Cait; Creamer, Rachel E.; Schulte, Rogier P.O.; O'Sullivan, Lilian; Jordan, Phil; Institute of Technology, Sligo (Elsevier BV, 2015-11-15)
    Agricultural soils offer multiple soil functions, which contribute to a range of ecosystem services, and the demand for the primary production function is expected to increase with a growing world population. Other key functions on agricultural land have been identified as water purification, carbon sequestration, habitat biodiversity and nutrient cycling, which all need to be considered for sustainable intensification. All soils perform all functions simultaneously, but the variation in the capacity of soils to supply these functions is reviewed in terms of defined land use types (arable, bio-energy, broadleaf forest, coniferous forest, managed grassland, other grassland and Natura 2000) and extended to include the influence of soil drainage characteristics (well, moderately/imperfect, poor and peat). This latter consideration is particularly important in the European Atlantic pedo-climatic zone; the spatial scale of this review. This review develops a conceptual framework on the multi-functional capacity of soils, termed Functional Land Management, to facilitate the effective design and assessment of agri-environmental policies. A final functional soil matrix is presented as an approach to show the consequential changes to the capacity of the five soil functions associated with land use change on soils with contrasting drainage characteristics. Where policy prioritises the enhancement of particular functions, the matrix indicates the potential trade-offs for individual functions or the overall impact on the multi-functional capacity of soil. The conceptual framework is also applied by land use area in a case study, using the Republic of Ireland as an example, to show how the principle of multi-functional land use planning can be readily implemented.
  • The challenge of managing soil functions at multiple scales: An optimisation study of the synergistic and antagonistic trade-offs between soil functions in Ireland

    Valujeva, Kristine; O’Sullivan, Lilian; Gutzler, Carsten; Fealy, Reamonn; Schulte, Rogier P.; European Commission (Elsevier, 2016-08-09)
    Recent forecasts show a need to increase agricultural production globally by 60% from 2005 to 2050, in order to meet a rising demand from a growing population. This poses challenges for scientists and policy makers to formulate solutions on how to increase food production and simultaneously meet environmental targets such as the conservation and protection of water, the conservation of biodiversity, and the mitigation of greenhouse gas emissions. As soil and land are subject to growing pressure to meet both agronomic and environmental targets, there is an urgent need to understand to what extent these diverging targets can be met simultaneously. Previously, the concept of Functional Land Management (FLM) was developed as a framework for managing the multifunctionality of land. In this paper, we deploy and evaluate the concept of FLM, using a real case-study of Irish agriculture. We investigate a number of scenarios, encompassing combinations of intensification, expansion and land drainage, for managing three soil functions, namely primary productivity, water purification and carbon sequestration. We use proxy-indicators (milk production, nitrate concentrations and area of new afforestation) to quantify the ‘supply’ of these three soil functions, and identify the relevant policy targets to frame the ‘demand’ for these soil functions. Specifically, this paper assesses how soil management and land use management interact in meeting these multiple targets simultaneously, by employing a non-spatial land use model for livestock production in Ireland that assesses the supply of soil functions for contrasting soil drainage and land use categories. Our results show that, in principle, it is possible to manage these three soil functions to meet both agronomic and environmental objectives, but as we add more soil functions, the management requirements become increasingly complex. In theory, an expansion scenario could meet all of the objectives simultaneously. However, this scenario is highly unlikely to materialise due to farm fragmentation, low land mobility rates and the challenging afforestation rates required for achieving the greenhouse gas reduction targets. In the absence of targeted policy interventions, an unmanaged combination of scenarios is more likely to emerge. The challenge for policy formation on future land use is how to move from an unmanaged combination scenario towards a managed combination scenario, in which the soil functions are purposefully managed to meet current and future agronomic and environmental targets, through a targeted combination of intensification, expansion and land drainage. Such purposeful management requires that the supply of each soil function is managed at the spatial scale at which the corresponding demand manifests itself. This spatial scale may differ between the soil functions, and may range from farm scale to national scale. Finally, our research identifies the need for future research to also consider and address the misalignment of temporal scales between the supply and demand of soil functions.
  • Using machine learning to estimate herbage production and nutrient uptake on Irish dairy farms

    Nikoloski, Stevanche; Murphy, Philip; Kocev, Dragi; Džeroski, Sašo; Wall, David; Teagasc Walsh Fellowship Programme; European Union; 635201 (Elsevier for American Dairy Science Association, 2019-08-22)
    Nutrient management on grazed grasslands is of critical importance to maintain productivity levels, as grass is the cheapest feed for ruminants and underpins these meat and milk production systems. Many attempts have been made to model the relationships between controllable (crop and soil fertility management) and noncontrollable influencing factors (weather, soil drainage) and nutrient/productivity levels. However, to the best of our knowledge not much research has been performed on modeling the interconnections between the influencing factors on one hand and nutrient uptake/herbage production on the other hand, by using data-driven modeling techniques. Our paper proposes to use predictive clustering trees (PCT) learned for building models on data from dairy farms in the Republic of Ireland. The PCT models show good accuracy in estimating herbage production and nutrient uptake. They are also interpretable and are found to embody knowledge that is in accordance with existing theoretical understanding of the task at hand. Moreover, if we combine more PCT into an ensemble of PCT (random forest of PCT), we can achieve improved accuracy of the estimates. In practical terms, the number of grazings, which is related proportionally with soil drainage class, is one of the most important factors that moderates the herbage production potential and nutrient uptake. Furthermore, we found the nutrient (N, P, and K) uptake and herbage nutrient concentration to be conservative in fields that had medium yield potential (11 t of dry matter per hectare on average), whereas nutrient uptake was more variable and potentially limiting in fields that had higher and lower herbage production. Our models also show that phosphorus is the most limiting nutrient for herbage production across the fields on these Irish dairy farms, followed by nitrogen and potassium.
  • Relating growth potential and biofilm formation of Shigatoxigenic Escherichia coli to in planta colonisation and the metabolome of ready- to-eat crops

    Merget, Bernhard; Forbes, Ken J; Brennan, Fiona P.; McAteer, Sean P; Shepherd, Tom; Strachan, Norval J; Holden, Nicola; FSA; Scottish Rural & Environment Science & Analytical Services Division; FS101056 (Cold Spring Harbor Laboratory, 2019-01-17)
    Contamination of fresh produce with pathogenic Escherichia coli, including Shigatoxigenic E. coli (STEC), represents a serious risk to human health. Colonisation is governed by multiple bacterial and plant factors that can impact on the probability and suitability of bacterial growth. Thus, we aimed to determine whether the growth potential of STEC for plants associated with foodborne outbreaks (two leafy vegetables and two sprouted seed species), is predictive for colonisation of living plants as assessed from growth kinetics and biofilm formation in plant extracts. Fitness of STEC was compared to environmental E. coli, at temperatures relevant to plant growth. Growth kinetics in plant extracts varied in a plant-dependent and isolate-dependent manner for all isolates, with spinach leaf lysates supporting the fastest rates of growth. Spinach extracts also supported the highest levels of biofilm formation. Saccharides were identified as the major driver of bacterial growth, although no single metabolite could be correlated with growth kinetics. The highest level of in planta colonisation occurred on alfalfa sprouts, though internalisation was 10-times more prevalent in the leafy vegetables than in sprouted seeds. Marked differences in in planta growth meant that growth potential could only be inferred for STEC for sprouted seeds. In contrast, biofilm formation in extracts related to spinach colonisation. Overall, the capacity of E. coli to colonise, grow and internalise within plants or plant-derived matrices were influenced by the isolate type, plant species, plant tissue type and temperature, complicating any straight-forward relationship between in vitro and in planta behaviours. Importance Fresh produce is an important vehicle for STEC transmission and experimental evidence shows that STEC can colonise plants as secondary hosts, but differences in the capacity to colonise occur between different plant species and tissues. Therefore, an understanding of the impact of these plant factors have on the ability of STEC to grow and establish is required for food safety considerations and risk assessment. Here, we determined whether growth and the ability of STEC to form biofilms in plants extracts could be related to specific plant metabolites or could predict the ability of the bacteria to colonise living plants. Growth rates for sprouted seeds (alfalfa and fenugreek) exhibited a positive relationship between plant extracts and living plants, but not for leafy vegetables (lettuce and spinach). Therefore, the detailed variations at the level of the bacterial isolate, plant species and tissue type all need to be considered in risk assessment.
  • 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.
  • Farming for Nature. The Role of Results-Based Payments

    O'Rourke, Eileen; Finn, John (Teagasc and National Parks and Wildlife Service (NPWS), 2020)
    Agricultural habitats cover approximately half the European Union (EU) and an estimated 50% of all species and several habitats of conservation concern in the EU depend on agricultural management. Reversing the loss of European biodiversity is clearly dependent on the conservation of farmland biodiversity. Results-based approaches are the focus of a growing discussion about improved biodiversity conservation and environmental performance of EU agri-environmental policies. This book outlines lessons learned from a collection of Irish case studies that have implemented results-based approaches and payments for the conservation of farmland habitats and species. The case studies include prominent projects and programmes: the Burren Programme, AranLIFE, KerryLIFE, the NPWS Farm Plan Scheme and Result-Based Agri-environmental Payment Schemes (RBAPS) project. This work is intended for an international audience of practitioners, policymakers and academics interested in results-based approaches for the conservation of biodiversity and the provision of ecosystem services.
  • The Complex Pathway towards Farm-Level Sustainable Intensification: An Exploratory Network Analysis of Stakeholders’ Knowledge and Perception

    Micha, Evgenia; Fenton, Owen; Daly, Karen M.; Kakonyi, Gabriella; Ezzati, Golnaz; Moloney, Thomas; Thornton, Steven; European Union; 675120 (MDPI AG, 2020-03-25)
    Farm-level sustainable intensification of agriculture (SIA) has become an important concept to ensuring food security while minimising negative externalities. However, progress towards its achievement is often constrained by the different perceptions and goals of various stakeholders that affect farm management decisions. This study examines farm-level SIA as a dynamic system with interactive components that are determined by the interests of the stakeholders involved. A systems thinking approach was used to identify and describe the pathways towards farm-level SIA across the three main pillars of sustainability. An explanatory network analysis of fuzzy cognitive maps (FCMs) that were collectively created by representative groups of farmers, farm advisors and policy makers was performed. The study shows that SIA is a complex dynamic system, affected by cognitive beliefs and particular knowledge within stakeholder groups. The study concludes that, although farm-level SIA is a complex process, common goals can be identified in collective decision making.
  • Assessing the role of artificially drained agricultural land for climate change mitigation in Ireland

    Paul, Carsten; Fealy, Reamonn; Fenton, Owen; Lanigan, Gary; O'Sullivan, Lilian; Schulte, Rogier P.; Irish Dairy Research Fund; Teagasc Greenhouse Gas Working Group; Department of Agriculture, Food and the Marine (Elsevier, 2017-12-19)
    In 2014 temperate zone emission factor revisions were published in the IPCC Wetlands Supplement. Default values for direct CO2 emissions of artificially drained organic soils were increased by a factor of 1.6 for cropland sites and by factors ranging from 14 to 24 for grassland sites. This highlights the role of drained organic soils as emission hotspots and makes their rewetting more attractive as climate change mitigation measures. Drainage emissions of humic soils are lower on a per hectare basis and not covered by IPCC default values. However, drainage of great areas can turn them into nationally relevant emission sources. National policy making that recognizes the importance of preserving organic and humic soils’ carbon stock requires data that is not readily available. Taking Ireland as a case study, this article demonstrates how a dataset of policy relevant information can be generated. Total area of histic and humic soils drained for agriculture, resulting greenhouse gas emissions and climate change mitigation potential were assessed. For emissions from histic soils, calculations were based on IPCC emission factors, for humic soils, a modified version of the ECOSSE model was used. Results indicated 370,000 ha of histic and 426,000 ha of humic soils under drained agricultural land use in Ireland (8% and 9% of total farmed area). Calculated annual drainage emissions were 8.7 Tg CO2e from histic and 1.8 Tg CO2e from humic soils (equal to 56% of Ireland’s agricultural emissions in 2014, excluding emissions from land use). If half the area of drained histic soils was rewetted, annual saving would amount to 3.2 Tg CO2e. If on half of the deep drained, nutrient rich grasslands drainage spacing was decreased to control the average water table at −25 cm or higher, annual savings would amount to 0.4 Tg CO2e.
  • Clay illuviation provides a long-term sink for C sequestration in subsoils

    Torres-Sallan, Gemma; Schulte, Rogier P.; Lanigan, Gary; Byrne, Kenneth; Reidy, Brian; Simó, Iolanda; Six, Johan; Creamer, Rachel; Irish Soil Information System project; Teagasc; et al. (Springer Nature, 2017-04-06)
    Soil plays a key role in the global carbon (C) cycle. Most current assessments of SOC stocks and the guidelines given by Intergovernmental Panel on Climate Change (IPCC) focus on the top 30 cm of soil. Our research shows that, when considering only total quantities, most of the SOC stocks are found in this top layer. However, not all forms of SOC are equally valuable as long-term stable stores of carbon: the majority of SOC is available for mineralisation and can potentially be re-emitted to the atmosphere. SOC associated with micro-aggregates and silt plus clay fractions is more stable and therefore represents a long-term carbon store. Our research shows that most of this stable carbon is located at depths below 30 cm (42% of subsoil SOC is located in microaggregates and silt and clay, compared to 16% in the topsoil), specifically in soils that are subject to clay illuviation. This has implications for land management decisions in temperate grassland regions, defining the trade-offs between primary productivity and C emissions in clay-illuviated soils, as a result of drainage. Therefore, climate smart land management should consider the balance between SOC stabilisation in topsoils for productivity versus sequestration in subsoils for climate mitigation.
  • An Analysis of Abatement Potential of Greenhouse Gas Emissions in Irish Agriculture 2021-2030

    Lanigan, Gary; Donnellan, Trevor; Hanrahan, Kevin; Carsten, Paul; Shalloo, Laurence; Krol, Dominika; Forrestal, Patrick J.; Farrelly, Niall; O’Brien, Donal; Ryan, Mary; et al. (Teagasc, 2018-06-10)
    This report has been prepared by the Teagasc Working Group on GHG Emissions, which brings together and integrates the extensive and diverse range of organisational expertise on agricultural greenhouse gases. The previous Teagasc GHG MACC was published in 2012 in response to both the EU Climate and Energy Package and related Effort Sharing Decision and in the context of the establishment of the Food Harvest 2020 production targets.
  • 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.
  • Real-time forecasting of pesticide concentrations in soil

    McGrath, Gavan; Rao, P. Suresh C.; Mellander, Per-Erik; Kennedy, Ivan; Rose, Michael; van Zwieten, Lukas; Grains Research and Development Corporation grant; Lee A. Reith Endowment in the Lyles School of Civil Engineering at Purdue University; Environmental Protection Agency; DAN00180; et al. (Elsevier, 2019-01-31)
    Forecasting pesticide residues in soils in real time is essential for agronomic purposes, to manage phytotoxic effects, and in catchments to manage surface and ground water quality. This has not been possible in the past due to both modelling and measurement constraints. Here, the analytical transient probability distribution (pdf) of pesticide concentrations is derived. The pdf results from the random ways in which rain events occur after pesticide application. First-order degradation kinetics and linear equilibrium sorption are assumed. The analytical pdfs allow understanding of the relative contributions that climate (mean storm depth and mean rainfall event frequency) and chemical (sorption and degradation) properties have on the variability of soil concentrations into the future. We demonstrated the two uncertain reaction parameters can be constrained using Bayesian methods. An approach to a Bayesian informed forecast is then presented. With the use of new rapid tests capable of providing quantitative measurements of soil concentrations in the field, real-time forecasting of future pesticide concentrations now looks possible for the first time. Such an approach offers new means to manage crops, soils and water quality, and may be extended to other classes of pesticides for ecological risk assessment purposes.
  • An integrated assessment of nitrogen source, transformation and fate within an intensive dairy system to inform management change

    Clagnan, Elisa; Thornton, Steven F; Rolfe, Stephen A.; Wells, Naomi; Knoeller, Kay; Murphy, John; Tuohy, Patrick; Daly, Karen M.; Healy, Mark G.; Ezzati, Golnaz; et al. (PLoS ONE, 2019-07-23)
    From an environmental perspective optimised dairy systems, which follow current regulations, still have low nitrogen (N) use efficiency, high N surplus (kg N ha-1) and enable ad-hoc delivery of direct and indirect reactive N losses to water and the atmosphere. The objective of the present study was to divide an intensive dairy farm into N attenuation capacity areas based on this ad-hoc delivery. Historical and current spatial and temporal multi-level datasets (stable isotope and dissolved gas) were combined and interpreted. Results showed that the farm had four distinct attenuation areas: high N attenuation: characterised by ammonium-N (NH4+-N) below 0.23 mg NH4+-N l-1 and nitrate (NO3--N) below 5.65 mg NO3--N l-1 in surface, drainage and groundwater, located on imperfectly to moderately-well drained soils with high denitrification potential and low nitrous oxide (N2O) emissions (av. 0.0032 mg N2O-N l-1); moderate N attenuation: characterised by low NO3--N concentration in drainage water but high N2O production (0.0317 mg N2O-N l-1) and denitrification potential lower than group 1 (av. δ15N-NO3-: 16.4‰, av. δ18O-NO3-: 9.2‰), on well to moderately drained soils; low N attenuation—area 1: characterised by high NO3--N (av. 6.90 mg NO3--N l-1) in drainage water from well to moderately-well drained soils, with low denitrification potential (av. δ15N-NO3-: 9.5‰, av. δ18O-NO3-: 5.9‰) and high N2O emissions (0.0319 mg N2O l-1); and low N attenuation—area 2: characterised by high NH4+-N (av. 3.93 mg NH4+-N l-1 and high N2O emissions (av. 0.0521 mg N2O l-1) from well to imperfectly drained soil. N loads on site should be moved away from low attenuation areas and emissions to air and water should be assessed.
  • 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.
  • The ALFAM2 database on ammonia emission from field-applied manure: Description and illustrative analysis

    Hafner, Sasha D.; Pacholski, Andreas; Bittman, Shabtai; Burchill, William; Bussink, Wim; Chantigny, Martin; Carozzi, Marco; Génermont, Sophie; Häni, Christoph; Hansen, Martin N.; et al. (Elsevier, 2017-12-27)
    Ammonia (NH3) emission from animal manure contributes to air pollution and ecosystem degradation, and the loss of reactive nitrogen (N) from agricultural systems. Estimates of NH3 emission are necessary for national inventories and nutrient management, and NH3 emission from field-applied manure has been measured in many studies over the past few decades. In this work, we facilitate the use of these data by collecting and organizing them in the ALFAM2 database. In this paper we describe the development of the database and summarise its contents, quantify effects of application methods and other variables on emission using a data subset, and discuss challenges for data analysis and model development. The database contains measurements of emission, manure and soil properties, weather, application technique, and other variables for 1895 plots from 22 research institutes in 12 countries. Data on five manure types (cattle, pig, mink, poultry, mixed, as well as sludge and “other”) applied to three types of crops (grass, small grains, maize, as well as stubble and bare soil) are included. Application methods represented in the database include broadcast, trailing hose, trailing shoe (narrow band application), and open slot injection. Cattle manure application to grassland was the most common combination, and analysis of this subset (with dry matter (DM) limited to <15%) was carried out using mixed- and fixed-effects models in order to quantify effects of management and environment on ammonia emission, and to highlight challenges for use of the database. Measured emission in this subset ranged from <1% to 130% of applied ammonia after 48 h. Results showed clear, albeit variable, reductions in NH3 emission due to trailing hose, trailing shoe, and open slot injection of slurry compared to broadcast application. There was evidence of positive effects of air temperature and wind speed on NH3 emission, and limited evidence of effects of slurry DM. However, random-effects coefficients for differences among research institutes were among the largest model coefficients, and showed a deviation from the mean response by more than 100% in some cases. The source of these institute differences could not be determined with certainty, but there is some evidence that they are related to differences in soils, or differences in application or measurement methods. The ALFAM2 database should be useful for development and evaluation of both emission factors and emission models, but users need to recognize the limitations caused by confounding variables, imbalance in the dataset, and dependence among observations from the same institute. Variation among measurements and in reported variables highlights the importance of international agreement on how NH3 emission should be measured, along with necessary types of supporting data and standard protocols for their measurement. Both are needed in order to produce more accurate and useful ammonia emission measurements. Expansion of the ALFAM2 database will continue, and readers are invited to contact the corresponding author for information on data submission. The latest version of the database is available at http://www.alfam.dk.

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