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

  • Efficacy of Woodchip Biochar and Brown Coal Waste as Stable Sorbents for Abatement of Bioavailable Cadmium, Lead and Zinc in Soil

    Amoah-Antwi, C.; Kwiatkowska-Malina, J.; Szara, E.; Thornton, S.; Fenton, Owen; Malina, G.; European Union; 675120 (Springer Science and Business Media LLC, 2020-10-03)
    Organic sorbents alter physicochemical soil properties and mitigate heavy metal (HM) bioavailability. However, some sorbents are labile and, therefore, introduce the risk of HM release into soil after mineralisation. Before field application, new stable organic sorbents such as woodchip biochar (BIO) and brown coal waste (BCW) need to be tested and compared with standard organic amendments like farmyard manure (FYM). An incubated pot experiment was conducted to investigate the efficacy of FYM, BIO and BCW (added to soil in pots at 5 and 10% w/w) to alter soil physicochemical properties and mitigate bioavailability of Cd, Pb and Zn spiked in treatments at different doses (in mg kg−1 ); 0 (not spiked), 1 (1 Cd, 70 Pb, 100 Zn) and 2 (3 Cd, 500 Pb, 700 Zn), and incubated for 9 weeks. At the end of the experiment, the EDTAextractable HM fractions, pH, cation exchange capacity (CEC) and specific surface area (SSA, to check trends) were determined in all treated soils. Results showed that FYM, BCW and BIO generally improved all soil properties (except reduced pH from BCW and apparent SSA reduction from FYM) and accounted for respective maximum abatements of Cd (50.2, 69.9 and 25.5%), Pb (34.2, 64.3 and 17.4%) and Zn (14.9, 17.7 and 11.8%) bioavailability in soil. FYM and BCW were more effective at 10% w/w especially in the low contaminated soil, whereas the highest efficacy for BIO was at 5% w/w and in the high contaminated soil. The efficacies of sorption by the organic sorbents varied for different HMs and were in the orders: BCW > FYM > BIO for Cd, FYM > BCW > BIO for Pb and BIO > BCW > FYM for Zn. Soil pH and CEC were strongly correlated with HM bioavailability in all treatments and implied that immobilisation of HMs occurred via complex formation, ion exchange and pH-dependent specific adsorption. All three sorbents were beneficial as soil amendments, and in terms of HM mitigation, BCW had the highest efficacy, followed by FYM and then BIO. Considering the documented high soil stability of BCW and BIO, these results are promising for further trialling at field scale.
  • Spatial evaluation and trade‐off analysis of soil functions through Bayesian networks

    Vrebos, Dirk; Jones, Arwyn; Lugato, Emanuele; O’Sullivan, Lillian; Schulte, Rogier; Staes, Jan; Meire, Patrick; European Union; 635201 (Wiley, 2020-08-23)
    There is increasing recognition that soils fulfil many functions for society. Each soil can deliver a range of functions, but some soils are more effective at some functions than others due to their intrinsic properties. In this study we mapped four different soil functions on agricultural lands across the European Union. For each soil function, indicators were developed to evaluate their performance. To calculate the indicators and assess the interdependencies between the soil functions, data from continental long‐term simulation with the DayCent model were used to build crop‐specific Bayesian networks. These Bayesian Networks were then used to calculate the soil functions' performance and trade‐offs between the soil functions under current conditions. For each soil function the maximum potential was estimated across the European Union and changes in trade‐offs were assessed. By deriving current and potential soil function delivery from Bayesian networks a better understanding is gained of how different soil functions and their interdependencies can differ depending on soil, climate and management. Highlights When increasing a soil function, how do trade‐offs affect the other functions under different conditions? Bayesian networks evaluate trade‐offs between soil functions and estimate their maximal delivery. Maximizing a soil function has varied effects on other functions depending on soil, climate and management. Differences in trade‐offs make some locations more suitable for increasing a soil function then others.
  • Biodiversity and ecosystem function: making sense of numerous species interactions in multi-species communities

    Brophy, Caroline; Dooley, Áine; Kirwan, Laura; Finn, John A.; McDonnell, Jack; Bell, Thomas; Cadotte, Marc W.; Connolly, John; Science Foundation Ireland; 09/RFP/EOB2546 (Wiley, 2017-06-30)
    Understanding the biodiversity and ecosystem function relationship can be challenging in species‐rich ecosystems. Traditionally, species richness has been relied on heavily to explain changes in ecosystem function across diversity gradients. Diversity–Interactions models can test how ecosystem function is affected by species identity, species interactions, and evenness, in addition to richness. However, in a species‐rich system, there may be too many species interactions to allow estimation of each coefficient, and if all interaction coefficients are estimable, they may be devoid of any sensible biological meaning. Parsimonious descriptions using constraints among interaction coefficients have been developed but important variability may still remain unexplained. Here, we extend Diversity–Interactions models to describe the effects of diversity on ecosystem function using a combination of fixed coefficients and random effects. Our approach provides improved standard errors for testing fixed coefficients and incorporates lack‐of‐fit tests for diversity effects. We illustrate our methods using data from a grassland and a microbial experiment. Our framework considerably reduces the complexities associated with understanding how species interactions contribute to ecosystem function in species‐rich ecosystems.
  • Comparative assessment of ecosystem C exchange in Miscanthusand reed canary grass during early establishment

    Ní Choncubhair, Órlaith; Osborne, Bruce; Finnan, John; Lanigan, Gary; Department of Agriculture, Food and the Marine; 07527 (Wiley, 2016-05-12)
    Land‐use change to bioenergy crop production can contribute towards addressing the dual challenges of greenhouse gas mitigation and energy security. Realisation of the mitigation potential of bioenergy crops is, however, dependent on suitable crop selection and full assessment of the carbon (C) emissions associated with land conversion. Using eddy covariance‐based estimates, ecosystem C exchange was studied during the early‐establishment phase of two perennial crops, C3 reed canary grass (RCG) and C4 Miscanthus, planted on former grassland in Ireland. Crop development was the main determinant of net carbon exchange in the Miscanthus crop, restricting significant net C uptake during the first 2 years of establishment. The Miscanthus ecosystem switched from being a net C source in the conversion year to a strong net C sink (−411 ± 63 g C m−2) in the third year, driven by significant above‐ground growth and leaf expansion. For RCG, early establishment and rapid canopy development facilitated a net C sink in the first 2 years of growth (−319 ± 57 (post‐planting) and −397 ± 114 g C m−2, respectively). Peak seasonal C uptake occurred three months earlier in RCG (May) than Miscanthus (August), however Miscanthus sustained net C uptake longer into the autumn and was close to C‐neutral in winter. Leaf longevity is therefore a key advantage of C4 Miscanthus in temperate climates. Further increases in productivity are projected as Miscanthus reaches maturity and are likely to further enhance the C sink potential of Miscanthus relative to RCG.
  • Exploring the sensitivity of visual soil evaluation to traffic-induced soil compaction

    Emmet-Booth, J.P.; Holden, N.M.; Fenton, Owen; Bondi, G.; Forristal, P.D.; Department of Agriculture, Food and the Marine; 13/S/468 (Elsevier BV, 2020-03)
    Visual Soil Evaluation (VSE) techniques are useful for assessing the impact of land management, particularly the identification and remediation of soil compaction. Despite an increasing body of VSE research, comparatively few studies have explored the sensitivity of VSE for capturing experimentally imposed compaction to estimate sensitivity and limit of detection. The aim of this research was to examine the ability of VSE techniques to indicate soil structure at different soil profile depths and to measure the associated soil productive function (yield) response to imposed compaction. A two-year experiment was conducted on sites with loam and sandy soils. Varying levels of wheeled traffic were imposed on plots in a randomised block design, prior to sowing winter barley (Hordeum vulgare L.). Quantitative crop and soil measurements were taken throughout the season in conjunction with VSE techniques, which assessed to 25 cm (VESS), 40 cm (Double Spade) and 80 cm (SubVESS) depth. Graduated changes were observed by soil and some crop quantitative measurements as traffic treatment varied. VESS and Double Spade successfully identified a graduated treatment effect at all sites to 40 cm depth, although diagnosis translated into a yield response for the loam but not the sandy soil. Correlation between VESS Sq scores and crop yield were found. SubVESS gave mixed signals and indicated impacts lower in the profile in certain instances. These impacts were not captured by quantitative soil measurements. This work highlights the capacity for VSE techniques to indicate soil structural damage, which may cause a crop yield response, therefore allowing appropriate soil management strategies to be deployed before yield penalties occur.
  • The arrival of a red invasive seaweed to a nutrient over-enriched estuary increases the spatial extent of macroalgal blooms

    Bermejo, Ricardo; MacMonagail, Michéal; Heesch, Svenja; Mendes, Ana; Edwards, Maeve; Fenton, Owen; Knöller, Kay; Daly, Eve; Morrison, Liam; Environmental Protection Agency; et al. (Elsevier BV, 2020-06)
    The red seaweed Agarophyton vermiculophyllum is an invasive species native to the north-west Pacific, which has proliferated in temperate estuaries of Europe, North America and Africa. Combining molecular identification tools, historical satellite imagery and one-year seasonal monitoring of biomass and environmental conditions, the presence of A. vermiculophyllum was confirmed, and the invasion was assessed and reconstructed. The analysis of satellite imagery identified the first bloom in 2014 and revealed that A. vermiculophyllum is capable of thriving in areas, where native bloom-forming species cannot, increasing the size of blooms (ca. 10%). The high biomass found during the peak bloom (>2 kg m−2) and the observation of anoxic events indicated deleterious effects. The monitoring of environmental conditions and biomass variability suggests an essential role of light, temperature and phosphorous in bloom development. The introduction of this species could be considered a threat for local biodiversity and ecosystem functioning in a global change context.
  • Sward composition and soil moisture conditions affect nitrous oxide emissions and soil nitrogen dynamics following urea-nitrogen application

    Bracken, Conor J.; Lanigan, Gary J.; Richards, Karl G.; Müller, Christoph; Tracy, Saoirse R.; Grant, James; Krol, Dominika; Sheridan, Helen; Lynch, Mary Bridget; Grace, Cornelia; et al. (Elsevier BV, 2020-06)
    Increased emissions of N2O, a potent greenhouse gas (GHG), from agricultural soils is a major concern for the sustainability of grassland agriculture. Emissions of N2O are closely associated with the rates and forms of N fertilisers applied as well as prevailing weather and soil conditions. Evidence suggests that multispecies swards require less fertiliser N input, and may cycle N differently, thus reducing N loss to the environment. This study used a restricted simplex-centroid experimental design to investigate N2O emissions and soil N cycling following application of urea-N (40 kg N ha−1) to eight experimental swards (7.8 m2) with differing proportions of three plant functional groups (grass, legume, herb) represented by perennial ryegrass (PRG, Lolium perenne), white clover (WC, Trifolium repens) and ribwort plantain (PLAN, Plantago lanceolata), respectively. Swards were maintained under two contrasting soil moisture conditions to examine the balance between nitrification and denitrification. Two N2O peaks coincided with fertiliser application and heavy rainfall events; 13.4 and 17.7 g N2O-N ha−1 day−1 (ambient soil moisture) and 39.8 and 86.9 g N2O-N ha−1 day−1 (wet soil moisture). Overall, cumulative N2O emissions post-fertiliser application were higher under wet soil conditions. Increasing legume (WC) proportions from 0% to 60% in multispecies swards resulted in model predicted N2O emissions increasing from 22.3 to 96.2 g N2O-N ha−1 (ambient soil conditions) and from 59.0 to 219.3 g N2O-N ha−1 (wet soil conditions), after a uniform N application rate. Soil N dynamics support denitrification as the dominant source of N2O especially under wet soil conditions. Significant interactions of PRG or WC with PLAN on soil mineral N concentrations indicated that multispecies swards containing PLAN potentially inhibit nitrification and could be a useful mitigation strategy for N loss to the environment from grassland agriculture.
  • Nitrogen fertilisers with urease inhibitors reduce nitrous oxide and ammonia losses, while retaining yield in temperate grassland

    Krol, Dominika; Forrestal, P. J.; Wall, David P.; Lanigan, G. J.; Sanz-Gomez, J.; Richards, K. G.; Irish Research Council; EPSPD/2016/54 (Elsevier, 2020-04-02)
    Nitrogen fertilisation, although a cornerstone of modern agricultural production, negatively impacts the environment through gaseous losses of nitrous oxide (N2O), a potent greenhouse gas (GHG), and ammonia (NH3), a known air pollutant. The aim of this work was to assess the feasibility of urea treated with urease inhibitors to reduce gaseous N losses in temperate grassland, while maintaining or improving productivity compared to conventional fertiliser formulations. Urease inhibitors were N-(n-butyl)-thiophosphoric triamide (NBPT) (urea + NBPT) and N-(n-propyl)-thiophosphoric triamide (NPPT) (urea+ NBPT + NPPT), while conventional fertilisers were urea and calcium ammonium nitrate (CAN). N2O emission factors were 0.06%, 0.07%, 0.09% and 0.58% from urea + NBPT, urea, urea + NBPT + NPPT and CAN, respectively, with CAN significantly higher than all the urea formulations, which were not significantly different from each other. Ammonia loss measured over one fertiliser application was significantly larger from urea, at 43%, compared with other formulations at 13.9%, 13.8% and 5.2% from urea + NBPT, urea + NBPT + NPPT and CAN, respectively. Changing fertiliser formulation had no significant impact on grass yield or N uptake in four out of five harvests. In the last harvest urea + NBPT significantly out-yielded urea, but not CAN or urea + NBPT + NPPT. Overall, urea treated with either one or both urease inhibitors significantly reduced emissions of N2O and NH3, while preserving yield quantity and quality. Therefore, changing fertiliser formulation to these products should be encouraged as a strategy to reduce GHG and air pollution from agricultural practices in temperate climate.
  • Exploring Climate‐Smart Land Management for Atlantic Europe

    Schulte, Rogier P. O.; O'Sullivan, Lilian; Coyle, Cait; Farrelly, Niall; Gutzler, Carsten; Lanigan, Gary; Torres‐Sallan, Gemma; Creamer, Rachel E.; Dairy Research Trust; Department of Agriculture, Food and the Marine (Wiley, 2016-09)
    Core Ideas Managing soil organic carbon is an essential aspect of climate‐smart agriculture. Combining component research, we derive a soil carbon management concept for Ireland. Optimized soil carbon management is differentiated in accordance with soil type. Existing policy tools can be tailored to incentivize climate‐smart land management. Soils can be a sink or source of carbon, and managing soil carbon has significant potential to partially offset agricultural greenhouse gas emissions. While European Union (EU) member states have not been permitted to account for this offsetting potential in their efforts to meet the EU 2020 reduction targets, this policy is now changing for the period 2020 to 2030, creating a demand for land management plans aimed at maximizing the offsetting potential of land. In this letter, we derive a framework for climate‐smart land management in the Atlantic climate zone of the EU by combining the results from five component research studies on various aspects of the carbon cycle. We show that the options for proactive management of soil organic carbon differ according to soil type and that a spatially tailored approach to land management will be more effective than blanket policies.
  • The elusive role of soil quality in nutrient cycling: a review

    Schröder, J. J.; Schulte, R. P. O.; Creamer, R. E.; Delgado, A.; Leeuwen, J.; Lehtinen, T.; Rutgers, M.; Spiegel, H.; Staes, J.; Tóth, G.; et al. (Wiley, 2016-09-16)
    Cycling of nutrients, including nitrogen and phosphorus, is one of the ecosystem services we expect agricultural soils to deliver. Nutrient cycling incorporates the reuse of agricultural, industrial and municipal organic residues that, misleadingly, are often referred to as ‘wastes’. The present review disentangles the processes underlying the cycling of nutrients to better understand which soil properties determine the performance of that function. Four processes are identified (i) the capacity to receive nutrients, (ii) the capacity to make and keep nutrients available to crops, (iii) the capacity to support the uptake of nutrients by crops and (iv) the capacity to support their successful removal in harvested crop. Soil properties matter but it is imperative that, as constituents of ‘soil quality’, they should be evaluated in the context of management options and climate and not as ends in their own right. The effect of a soil property may vary depending on the prevailing climatic and hydrologic conditions and on other soil properties. We recognize that individual soil properties may be enhancing one of the processes underlying the cycling of nutrients but simultaneously weakening others. Competing demands on soil properties are even more obvious when considering other soil functions such as primary production, purification and flow regulation of water, climate modification and habitat provision, as shown by examples. Consequently, evaluations of soil properties and management actions need to be site-specific, taking account of local aspects of their suitability and potential challenges.
  • Data and code: Beneficial effects of multi-species mixtures on N2O emissions from intensively managed grassland swards

    Cummins, Saoirse; Finn, John; Richards, Karl; Lanigan, Gary; Grange, Guylain; Brophy, Caroline; Cardenas, Laura M.; Misselbrook, Tom H.; Reynolds, Chris K.; Krol, Dominika; et al. (2021)
    We provide the data and statistical code that produced the results presented in Cummins et al. (2021). Three files are available to download: - The data file ‘Cummins_etal_2021_N2O.csv’: contains the annual N2O emissions and N2O emissions intensities (see Readme file for details) measured from sown grassland comprising one to six species within one to three functional groups (grass, legume and herb). - An accompanying readme file ‘Readme_Cummins_etal_2021_N2O.txt’: this contains the metadata for the data in ‘Cummins_etal_2021_N2O.csv’. - Statistical code (SAS software) ‘’: SAS code to repeat the analyses as in the final models of the published paper.
  • 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, and as a command-line tool at
  • 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.

View more