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

  • Source partitioning using N2O isotopomers and soil WFPS to establish dominant N2O production pathways from different pasture sward compositions

    Bracken, Conor J.; Lanigan, Gary J.; Richards, Karl G.; Müller, Christoph; Tracy, Saoirse R.; Grant, James; Krol, Dominika J.; Sheridan, Helen; Lynch, Mary Bridget; Grace, Cornelia; et al. (Elsevier BV, 2021-08)
    Nitrous oxide (N2O) is a potent greenhouse gas (GHG) emitted from agricultural soils and is influenced by nitrogen (N) fertiliser management and weather and soil conditions. Source partitioning N2O emissions related to management practices and soil conditions could suggest effective mitigation strategies. Multispecies swards can maintain herbage yields at reduced N fertiliser rates compared to grass monocultures and may reduce N losses to the wider environment. A restricted-simplex centroid experiment was used to measure daily N2O fluxes and associated isotopomers from eight experimental plots (7.8 m2) post a urea-N fertiliser application (40 kg N ha−1). Experimental pastures consisted of differing proportions of grass, legume and forage herb represented by perennial ryegrass (Lolium perenne), white clover (Trifolium repens) and ribwort plantain (Plantago lanceolata), respectively. N2O isotopomers were measured using a cavity ring down spectroscopy (CRDS) instrument adapted with a small sample isotope module (SSIM) for the analysis of gas samples ≤20 mL. Site preference (SP = δ15Nα – δ15Nβ) and δ15Nbulk ((δ15Nα + δ15Nβ) / 2) values were used to attribute N2O production to nitrification, denitrification or a mixture of both nitrification and denitrification over a range of soil WFPS (%). Daily N2O fluxes ranged from 8.26 to 86.86 g N2O-N ha−1 d−1. Overall, 34.2% of daily N2O fluxes were attributed to nitrification, 29.0% to denitrification and 36.8% to a mixture of both. A significant diversity effect of white clover and ribwort plantain on predicted SP and δ15Nbulk indicated that the inclusion of ribwort plantain may decrease N2O emission through biological nitrification inhibition under drier soil conditions (31%–75% WFPS). Likewise, a sharp decline in predicted SP indicates that increased white clover content could increase N2O emissions associated with denitrification under elevated soil moisture conditions (43%–77% WFPS). Biological nitrification inhibition from ribwort plantain inclusion in grassland swards and management of N fertiliser source and application timing to match soil moisture conditions could be useful N2O mitigation strategies.
  • Biomass pools in intensively managed hedgerows can be a net emission of carbon dioxide

    Black, Kevin; Lanigan, Gary; Ward, Mark; Kavanagh, Ian; O’hÚallacháin, Daire; Sullivan, Lilian O; Department of Environment, Climate and Communications, Ireland; Department of Agriculture, Food and the Marine, Ireland (Research Square Platform LLC, 2022-06-22)
    Perennial landscape features, such as hedgerows, can play a role in enhancing terrestrial carbon (C) sinks, especially in North-western Europe, where they form a large part of the agricultural landscape. To date, there are few studies relating aerial imagery to ground-truthed biomass measurements and relating changes in biomass to hedgerow management. This study sought to develop relationships between measured biomass of hedgerows and digital elevation model (DEM) data from drones and aircraft. Furthermore, changes in hedgerow above-ground and below-ground biomass stocks were assessed using a two-point sampling approach. The developed inventory framework was then applied to a pilot study area of 419,701 hectares in Ireland. Robust relationships were developed relating DEM data to volume and above-ground biomass. Model equations were also developed linking above-ground and below-ground biomass. However, these were less robust due to the confounding impact of hedgerow management. Aboveground biomass was linearly correlated with hedge volume with irregular, unmanaged hedgerows observed to contain significantly higher amounts of aboveground biomass compared to regular, highly managed hedgerows. When the models were extrapolated to the county level, hedgerow biomass C pools are suggested to be a net emission of -0.3 tC. ha-1.yr-1 due to removals and management.
  • Ammonia emissions from agriculture and their contribution to fine particulate matter: A review of implications for human health

    Wyer, Katie E.; Kelleghan, David B.; Blanes-Vidal, Victoria; Schauberger, Günther; Curran, Thomas P.; Irish Department of Agriculture, Food, and the Marine; 2019R554 (Elsevier, 2022-12-01)
    Atmospheric ammonia (NH3) released from agriculture is contributing significantly to acidification and atmospheric NH3 may have on human health is much less readily available. The potential direct impact of NH3 on the health of the general public is under-represented in scientific literature, though there have been several studies which indicate that NH3 has a direct effect on the respiratory health of those who handle livestock. These health impacts can include a reduced lung function, irritation to the throat and eyes, and increased coughing and phlegm expulsion. More recent studies have indicated that agricultural NH3 may directly influence the early on-set of asthma in young children. In addition to the potential direct impact of ammonia, it is also a substantial contributor to the fine particulate matter (PM2.5) fraction (namely the US and Europe); where it accounts for the formation of 30% and 50% of all PM2.5 respectively. PM2.5 has the ability to penetrate deep into the lungs and cause long term illnesses such as Chronic Obstructive Pulmonary Disease (COPD) and lung cancer. Hence, PM2.5 causes economic losses which equate to billions of dollars (US) to the global economy annually. Both premature deaths associated with the health impacts from PM2.5 and economic losses could be mitigated with a reduction in NH3 emissions resulting from agriculture. As agriculture contributes to more than 81% of all global NH3 emissions, it is imperative that food production does not come at a cost to the world's ability to breathe; where reductions in NH3 emissions can be easier to achieve than other associated pollutants.
  • Optimising soil P levels reduces N2O emissions in grazing systems under different N fertilisation

    O’Neill, Rosie Mary; Gebremichael, Amanuel Woldeselassie; Lanigan, Gary J.; Renou‐Wilson, Florence; Müller, Christoph; Richards, Karl G.; Department of Agriculture, Australian Government, Food, and the Marine; Teagasc Walsh Scholarship Scheme; 15S655 (Wiley, 2022-07-27)
    The effect of long-term soil phosphorus (P) on in situ nitrous oxide (N2O) emissions from temperate grassland soil ecosystems is not well understood. Grasslands typically receive large nitrogen (N) inputs both from animal deposition and fertiliser application, with a large proportion of this N being lost to the environment. Understanding optimum nutrient stoichiometry by applying N fertilisers in a relative balance with P will help to reduce N losses by enabling maximum N-uptake by plants and microbes. This study investigates the N2O response from soils of long-term high and low P management receiving three forms of applied N at two different rates: a nitrate-based fertiliser (KNO3) and an ammonium-based fertiliser ([NH4]2SO4) (both at 40 Kg N ha−1), and a synthetic urine (750 Kg N ha−1). Low soil P significantly increased N2O emissions from KNO3 and (NH4)2SO4 fertilisers by over 50% and numerically increased N2O from urine by over 20%, which is suggested to be representative of the lack of significant effect of N fertilisation on N-uptake observed in the low P soils. There was a significant positive effect of soil P on grass N-uptake observed in the synthetic urine and KNO3 treatments, but not in the (NH4)2SO4 treatment. Low P soils had a significantly lower pH than high P soilss and responded differently to applied synthetic urine. There was also a significant effect of P level on potential nitrification which was nearly three times that of low P, but no significant difference between potential denitrification and P level. The results from this study highlight the importance of synergy between relative nutrient applications as a deficiency of one nutrient, such as P in this case, could be detrimental to the system as a whole. Optimising soil P can result in greater N uptake (over 12, 23 and 66% in (NH4)2SO4, KNO3 and synthetic urine treatments, respectively) and in reduced emissions by up to 50% representing a win-win scenario for farmers.
  • The effect of machine traffic zones associated with field headlands on soil structure in a survey of 41 tilled fields in a temperate maritime climate

    Ward, Mark; McDonell, Kevin; Metzger, Konrad; Forristal, Patrick Dermot; Teagasc Walsh Fellowship fund (Elsevier, 2021-06-30)
    Machinery traffic imposes a negative effect on soil structure, leading to soil compaction. Studies to date have primarily focused on the influence of applied wheel loads on soil structure. Few studies have assessed the impact of commercial farm operations on soil structure and crop performance, particularly on field headlands in a temperate maritime climate such as Ireland. A survey was conducted on 41 conventionally managed field sites to investigate the effect of field position (field edge, turning, transition and in-field zones) in relation to machinery operations on soil structure. Soil texture classes ranged from sandy loam to clay loam. All sites used plough-based crop establishment. Soil structural condition was assessed visually using the visual evaluation of soil structure method (VESS) for the topsoil (0−250 mm), and Double Spade below plough depth (250−400 mm). Quantitative soil measurements such as shear strength, bulk density and porosity using soil cores post-harvest, and soil cone penetration resistance were taken at two time points in the crop growth cycle. For most measurements of soil structure, the in-field zone of least machinery traffic produced the best scores (Sq 2.81 & DS 2.48), and the turning zone returned the poorest scores in the 0−250 mm soil layer (Sq 3.31 & DS 2.91). The strongest quantitative scores for the in-field and turning zones, respectively, were for trowel penetration resistance in the upper (2.49 & 3.20) and lower (3.41 & 4.05) soil depth layers and for shear vane (38.17 & 53.59 kPa) for the same zones. The visual assessments and some of the quantitative measurements (0−250 mm soil layer) followed the zone order trend of: turning, field edge, transition and in-field, for increasing machinery traffic. The results show that the visual soil indicators used in this study are more sensitive than quantitative soil measurements such as soil bulk density (ρb) or porosity (TP and MP) at detecting soil structural differences between zones, particularly below plough depth (>250 mm soil depth).
  • Stem-nesting Hymenoptera in Irish farmland: empirical evaluation of artificial trap nests as tools for fundamental research and pollinator conservation

    Hodge, Simon; Bottero, Irene; Dean, Robin; Maher, Stephanie; Stout, Jane; European Union; 773921 (International Commission for Plant Pollinator Relations, 2022-08-03)
    Insect pollinators are suffering global declines, necessitating the evaluation and development of methods for long-term monitoring and applied field research. Accordingly, this study evaluated the use of trap nests (“bee hotels”) as tools for investigating the ecology of cavity nesting Hymenoptera within Irish agricultural landscapes. Three trap nests consisting of 110 mm diameter plastic pipe containing 100 cardboard nest tubes of varying diameter were placed at eight apple orchards and eight oilseed rape sites and left in the field for five months. Sealed nest tubes occurred at 15 of the 16 sites, and in 77% of the 48 nests. However, only 7% of the 4800 individual nest tubes were sealed, and only 4% produced cavity-nesting Hymenoptera. Three cavity nesting bee species (Hylaeus communis, Osmia bicornis, Megachile versicolor) and two solitary wasp species (Ancistrocerus trifasciatus, A. parietinus) emerged from nest tubes. There were significant differences among species in terms of emergence date and the diameter of nest tubes from which they emerged, the latter allowing the calculation of niche width and niche overlap, and informing choice of tube size in future studies/conservation efforts. Trap nests, therefore, offer a valuable tool for fundamental ecological research and a model system for investigating interactions between stem-nesting species within their wider ecological networks. The ability of trap nests to actually increase farmland pollinator abundance and diversity as part of agri-environment schemes requires additional investigation. However, used in sufficient numbers, these trap nests provide valuable biogeographical data for cavity nesting Hymenoptera and offer a viable means for long term monitoring of these species in Irish farmland.
  • Assessing the long-term impact of urease and nitrification inhibitor use on microbial community composition, diversity and function in grassland soil

    Duff, Aoife M.; Forrestal, Patrick; Ikoyi, Israel; Brennan, Fiona; Teagasc (Elsevier, 2022-07-31)
    Reductions in ammonia (NH3) and nitrous oxide (N2O) emissions from agricultural systems are critical for achievement of sustainability targets that underpin international efforts on climate and biodiversity. Urease inhibitors (UI) such as N-(n-butyl) thiophosphoric triamide (NBPT) and nitrification inhibitors (NI) such as dicyandiamide (DCD) slow down microbial and chemical N transformation rates in soil, resulting in decreased environmental N losses. To date there has been minimal assessment of the long-term non-target impacts of UI and NI on soil microbial communities and biological function in grasslands. Utilising a temperate grassland field experiment where fertilisers (with or without inhibitors) were repeatedly applied over a five year period, we assessed the impact of individual or combined inhibitor use on microbial community composition, abundance and function via a combination of functional assays, quantitative polymerase chain reaction (qPCR) assays and amplicon sequence analysis. We also investigated the effect of N inhibitor use on the N functional community, and whether the form of applied N fertiliser (i.e. calcium ammonium nitrate (CAN) or Urea) affected microbial community composition and function. Treatments included a Control (no N); CAN; Urea; Urea + NBPT (UI); Urea + DCD (NI); and Urea + DCD + NBPT (NI & UI). There was no impact of either UI or NI use on non-target microbial community composition or abundance. Function and the abundance of N cycling communities were mainly unaffected by fertilisation or the use of inhibitors. The observed effect of NI was primarily on the nitrification process. There was a significant reduction in nitrification potential associated with the use of NI, and in the case of the Urea + DCD treatment a reduction in COMAMMOX nitrifier abundance, and an increase in potential N mineralisation and N2O emissions. Finally, there was a significant impact of fertilisation and fertiliser type (i.e. CAN or Urea) on the fungal community structure but no impact on bacterial community structure. These results provide a knowledge base that will inform policy regarding the utilisation of N inhibitors as a mitigation measure for reducing gaseous N losses in grasslands.
  • Effects of concentrate supplementation and genotype on milk production and nitrogen utilisation efficiency in late-lactation, spring-calving grazing dairy cows

    Doran, M.J.; Mulligan, F.J.; Lynch, M.B.; Fahey, A.G.; Rajauria, G.; Brady, E.L.; Pierce, K.M.; Department of Agriculture, Food, and the Marine (Ireland); 15/S/675 (Elsevier, 2022-07-31)
    The study objectives were to evaluate the effects of (1) concentrate supplementation (CS), (2) cow genotype, and (3) a potential interaction between CS and cow genotype on milk production, dry matter (DM) intake (DMI) and cow nitrogen (N) utilisation efficiency (NUE) in late lactation (+208 ± 14.1 days in milk), spring-calving grazing dairy cows. The experiment was a complete randomised block design with a 2 × 2 factorial arrangement of treatments and was conducted over a 52-day period. There were two feeding strategies (pasture-only (PO) and pasture + 2.7 kg DM CS) and two genotype groups [lower milk genotype (LM; milk kg PTA = -48 ± 59.9, fat kg PTA = +7 ± 4.7 and protein kg PTA = +3 ± 3.2) and higher milk genotype (HM; milk kg PTA = +190 ± 109.7, fat kg PTA = +12 ± 5.7 and protein kg PTA = +9 ± 3.6)]. Cows in their respective genotype group were randomly assigned to one of two feeding strategies, resulting in four treatment groups (n = 12). Cows grazed full time and were allocated 17 kg DM pasture/cow per d. No interactions were observed for any parameters measured. Cows offered CS had increased daily yields of fat + protein (+0.18 kg), lactose (+0.13 kg) and ECM (+2.46 kg) compared to cows offered PO. The HM cows had increased yields of daily fat + protein (+0.13 kg) and lactose (+0.1 kg) compared to the LM cows. Cows offered CS had decreased daily protein (-0.14%) but increased lactose (+0.08%) concentration compared to cows offered PO. The HM cows had decreased daily fat (-0.2%), protein (-0.16%) and casein (-0.07%) concentration compared to the LM cows. Cows offered CS had a reduced daily pasture DMI (-1.41 kg) but an increased daily total DMI (+1.29 kg) and feed N intake (+0.085 kg) compared to cows offered PO. Cows offered CS had decreased NUE (-0.1%) compared to cows offered PO. In conclusion, offering cows 2.7 kg DM CS per day improved milk production in late lactation but resulted in a poorer NUE. The poorer NUE was due to no difference in milk N output and an increase in the partitioning of feed N to urine. The HM cows had an increased milk response to CS with respect to milk fat + protein kg compared to the MR obtained from LM cows.
  • Datafile: Plant diversity enhanced nematode-based soil quality indices and changed soil nematode community structure in intensively-managed agricultural grasslands

    Ikoyi, Israel; Grange, Guylain; Finn, John; Brennan, Fiona P.; European Union Horizon programme; Teagasc Walsh Scholarship scheme; 818368 (MASTER) (2023)
    Plant productivity, decomposition and nutrient cycling are controlled by plant-soil-biota interactions. However, it remains poorly understood how plant species diversity and diversity interactions impact belowground communities that modulate these processes in intensively-managed grassland systems. In managed grassland communities, comprising species selected for agronomic performance, we investigated how plant species diversity affected the soil nematode community and associated ecological indices with a focus on assessing abovegroundbelowground interactions. A total of 27 nematode taxa were identified from 61 experimental field plots in which plant species diversity was systematically manipulated from a pool of six plant species within three functional groups (FGs; grasses, legumes, herbs). In general, there were strong effects of plant species identity on the nematode community; interspecific interaction effects did not consistently occur, but where they did were best related to plant community evenness. The equi-proportional six-species plant community had a significantly higher nematode diversity, maturity index (MI), structure index (SI) and proportion of sensitive taxa (omnivore and predators) but a lower enrichment index (EI) than the individual monocultures. The two legumes (Trifolium pratense and Trifolium repens) had the highest EI but lowest abundance of fungivores and channel index, indicating a bacterial- dominated decomposition pathway. Moreover, the community structure of nematodes in the equiproportional six-species community was significantly different from that in the monocultures. This change in community structure was associated with factors highly correlated with plant diversity, including higher aboveground biomass yield and total nitrogen in harvested biomass as well as lower biomass of weed species. Overall, our results show that multi-species forage sward mixtures that include grasses, legumes, and herbs can have a positive effect on the soil nematode community and nematode-based soil quality indices. This is of practical relevance for farmers and for EU agricultural policy targeted at sustainability, soil health and farming for biodiversity benefits.
  • Evaluation of the fertiliser replacement value of phosphorus-saturated filter media

    Arenas-Montaño, V.; Fenton, O.; Moore, B.; Healy, M.G.; European Union - Marie Skłodowska-Curie grant agreement; 675120 (Elsevier, 2021-04-01)
    The use of filter media to adsorb phosphorus (P) from nutrient-rich waters is an effective, simple and low-cost method to recover and reuse P as an inorganic fertiliser replacement. Although it is assumed that the saturated filter media can be applied to cropland as a safe fertiliser replacement, there is presently a lack of information on the fertiliser replacement value (FRV) of such products and their negative effects on plants and soil. Therefore, the aims of this paper were to evaluate the (1) P removal capacity and plant response to soil application of waste media from three sectors (industry, agriculture, and construction and demolition), and natural and synthetic materials (2) potentially confounding risks arising from the reuse of media as a fertiliser replacement, and (3) factors affecting their fertilising efficiency once applied to soil. The predominant factors affecting the FRV of P-saturated media were their adsorption capacity and chemical composition, soil pH, and composition of water used for saturation. Some measures to overcome the negative impacts of the land application of P-saturated media include selecting the most appropriate soil-filter material combinations, the use of P solubilising microorganisms, and mixing with manure before land application. Despite confounding factors and a lack of information on the performance of some media under comparable study conditions, this study found that there is a significant potential for P-saturated filter media to partially replace the use of P mineral fertilisers and aid in the attainment of a “circular economy” in agriculture.
  • Challenges and opportunities to capture dietary effects in on-farm greenhouse gas emissions models of ruminant systems

    Vibart, Ronaldo; de Klein, Cecile; Jonker, Arjan; van der Weerden, Tony; Bannink, André; Bayat, Ali R.; Crompton, Les; Durand, Anais; Eugène, Maguy; Klumpp, Katja; et al. (Elsevier, 2021-05-15)
    This paper reviews existing on-farm GHG accounting models for dairy cattle systems and their ability to capture the effect of dietary strategies in GHG abatement. The focus is on methane (CH4) emissions from enteric and manure (animal excreta) sources and nitrous oxide (N2O) emissions from animal excreta. We identified three generic modelling approaches, based on the degree to which models capture diet-related characteristics: from ‘none’ (Type 1) to ‘some’ by combining key diet parameters with emission factors (EF) (Type 2) to ‘many’ by using process-based modelling (Type 3). Most of the selected on-farm GHG models have adopted a Type 2 approach, but a few hybrid Type 2 / Type 3 approaches have been developed recently that combine empirical modelling (through the use of CH4 and/or N2O emission factors; EF) and process-based modelling (mostly through rumen and whole tract fermentation and digestion). Empirical models comprising key dietary inputs (i.e., dry matter intake and organic matter digestibility) can predict CH4 and N2O emissions with reasonable accuracy. However, the impact of GHG mitigation strategies often needs to be assessed in a more integrated way, and Type 1 and Type 2 models frequently lack the biological foundation to do this. Only Type 3 models represent underlying mechanisms such as ruminal and total-tract digestive processes and excreta composition that can capture dietary effects on GHG emissions in a more biological manner. Overall, the better a model can simulate rumen function, the greater the opportunity to include diet characteristics in addition to commonly used variables, and thus the greater the opportunity to capture dietary mitigation strategies. The value of capturing the effect of additional animal feed characteristics on the prediction of on-farm GHG emissions needs to be carefully balanced against gains in accuracy, the need for additional input and activity data, and the variability encountered on-farm.
  • An analysis of the spatio-temporal occurrence of anthelmintic veterinary drug residues in groundwater

    Mooney, D.; Richards, K.G.; Danaher, M.; Grant, J.; Gill, L.; Mellander, P.-E.; Coxon, C.E.; Science Foundation Ireland; 13/RC/2092 (Elsevier, 2021-05-15)
    Anthelmintics are antiparasitic drugs used to control helminthic parasites such as nematodes and trematodes in animals, particularly those exposed through pasture-based production systems. Even though anthelmintics have been shown to be excreted into the environment in relatively high amounts as unmetabolized drug or transformation products (TPs), there is still only limited information available on their environmental occurrence, particularly in groundwater, which has resulted in them being considered as potential emerging contaminants of concern. A comprehensive study was carried out to investigate the occurrence of 40 anthelmintic residues (including 13 TPs) in groundwaters (and associated surface waters) throughout the Republic of Ireland. The study focused on investigating the occurrence of these contaminants in karst and fractured bedrock aquifers, with a total of 106 sites (88 groundwaters and 18 surface waters) samples during spring 2017. Seventeen anthelmintic compounds consisting of eight parent drugs and nine TPs were detected at 22% of sites at concentrations up to 41 ng L−1. Albendazole and its TPs were most frequently detected residues, found at 8% of groundwater sites and 28% of surface water sites. Multivariate statistical analysis identified several source and pathway factors as being significantly related to the occurrence of anthelmintics in groundwater, however there was an evident localised effect which requires further investigation. An investigation of the temporal variations in occurrence over a 13 month period indicated a higher frequency and concentration of anthelmintics during February/March and again later during August/September 2018, which coincided with periods of increased usage and intensive meteorological events. This work presents the first detections of these contaminants in Irish groundwater and it contributes to broadening our understanding of anthelmintics in the environment. It also provides insight to seasonal trends in occurrence, which is critical for assessing potential future effects and implications of climate change.
  • Metagenomic and HT-qPCR analysis reveal the microbiome and resistome in pig slurry under storage, composting, and anaerobic digestion

    Do, Thi Thuy; Nolan, Stephen; Hayes, Nicky; O'Flaherty, Vincent; Burgess, Catherine; Brennan, Fiona; Walsh, Fiona; Health Research Board, Ireland; JPI-EC-AMR JTC 2017 (Elsevier, 2022-07-15)
    Direct application of pig slurry to agricultural land, as a means of nutrient recycling, introduces pathogens, antibiotic resistant bacteria, or genes, to the environment. With global environmental sustainability policies mandating a reduction in synthetic fertilisation and a commitment to a circular economy it is imperative to find effective on-farm treatments of slurry that maximises its fertilisation value and minimises risk to health and the environment. We assessed and compared the effect of storage, composting, and anaerobic digestion (AD) on pig slurry microbiome, resistome and nutrient content. Shotgun metagenomic sequencing and HT-qPCR arrays were implemented to understand the dynamics across the treatments. Our results identified that each treatment methods have advantages and disadvantages in removal pollutants or increasing nutrients. The data suggests that storage and composting are optimal for the removal of human pathogens and anaerobic digestion for the reduction in antibiotic resistance (AMR) genes and mobile genetic elements. The nitrogen content is increased in storage and AD, while reduced in composting. Thus, depending on the requirement for increased or reduced nitrogen the optimum treatment varies. Combining the results indicates that composting provides the greatest gain by reducing risk to human health and the environment. Network analysis revealed reducing Proteobacteria and Bacteroidetes while increasing Firmicutes will reduce the AMR content. KEGG analysis identified no significant change in the pathways across all treatments. This novel study provides a data driven decision tree to determine the optimal treatment for best practice to minimise pathogen, AMR and excess or increasing nutrient transfer from slurry to environment.
  • Diffuse reflectance mid infra-red spectroscopy combined with machine learning algorithms can differentiate spectral signatures in shallow and deeper soils for the prediction of pH and organic matter content

    Bachionde Santana, Felipe; Grunsky, Eric C.; Fitzsimons, Mairéad M.; Gallagher, Vincent; Daly, Karen; Teagasc; Geological Survey Ireland (Elsevier, 2022-11-30)
    Precision and sustainable agriculture requires information about soil pH and organic matter (OM) content at higher spatial and temporal scales than current agronomic sampling and analytical methods allow. This study examined the accuracy of spectral models using high throughput screening (HTS) in diffuse reflectance mode in mid Infra-red (MIR)/DRIFT combined with machine learning algorithms to predict soil pH(CaCl2) and %OM in shallow and deeper topsoils compared to laboratory methods. Models were developed from an archive of samples taken on a 4 km2 grid from the northern half of Ireland (Terra Soil project), which includes 18,859 samples (9,396 shallow + 9,463 deeper). The application of Cubist models showed that for different depths there are minor different spectral group associations with pH and %OM values. These differences resulted in a loss of accuracy in the extrapolation of the topsoil model to predict values from deeper topsoils or vice versa. Therefore we recommend the use of samples from both depths to build a calibration model.The proposed methodology was able to determine %OM and pH using a unique multivariate regression model for both depths, with RMSEP values of 1.12 and 0.89 %; RPIQ values of 42.34 and 38.48; R2val of 0.9989 and 0.9993 for %OM determinations in shallow and deeper topsoils, respectively. For pH determinations the RMSEP values obtained were 0.25 and 0.34; RPIQ values of 6.04 and 4.94; R2val 0.9385 and 0.8954. Both regression models are classified as excellent predictions models, yielding RPIQ values >4.05 for shallow and deeper topsoils. The results demonstrated the high potential of HTS-DRIFT combined with machine learning algorithms as a rapid, accurate, and cost-effective method to build large soil spectral libraries, displaying predicted results similar to two separate soil laboratory methods (pH and LOI).
  • Coupled steroid and phosphorus leaching from cattle slurry at lysimeter scale

    Manley, Amber; Collins, Adrian L.; Joynes, Adrian; Mellander, Per-Erik; Jordan, Phil; Walsh Fellowship; Soil to Nutrition strategic programme under Project 3; 2016115; BBS/E/C/000I0330 (Elsevier, 2022-05-31)
    Water quality degradation can be caused by excessive agricultural nutrient transfers from fertilised soils exposed to wet weather. Mitigation measures within the EU Nitrates Directive aim to reduce this pressure by including ‘closed’ fertiliser spreading periods during wet months. For organic fertilisers such as slurry and manure, this closed period requires sufficient on-farm winter storage and good weather conditions to relieve storage at the end of the period. Therefore, robust scientific evidence is needed to support the measure. Incidental nutrient transfers of recently applied organic fertilisers in wet weather can also be complicated by synchronous transfers from residual soil stores and tracing is required for risk assessments. The combination of nutrient monitoring and biomarker analyses may aid this and one such biomarker suite is faecal steroids. Accordingly, this study investigated the persistence of steroids and their association with phosphorus during leaching episodes. The focus was on the coupled behaviour of steroids and total phosphorus (TP) concentrations in sub-surface hydrological pathways. Cattle slurry was applied to monolith lysimeters either side of a closed period and concentrations of both steroids and TP were monitored in the leachate. The study showed no significant effect of the treatment (average p = 0.17), though tracer concentrations did significantly change over time (average p = 0.001). While the steroidal concentration ratio was validated for herbivorous faecal pollution in the leachate, there was a weak positive correlation between the steroids and TP. Further investigation at more natural scales (hillslope/catchment) is required to confirm tracer behaviours/correlations and to compliment this sub-surface pathway study.
  • Mitigating ammonia and greenhouse gas emissions from stored cattle slurry using agricultural waste, commercially available products and a chemical acidifier

    Kavanagh, I.; Fenton, O.; Healy, M.G.; Burchill, W.; Lanigan, G.J.; Krol, D.J.; Irish Department of Agriculture, Food and the Marine; Teagasc Walsh Scholarship Programme; RSF 13/S/430 (Elsevier, 2021-04-20)
    The production of bovine slurry and its subsequent storage are significant sources of ammonia (NH3) and greenhouse gases (GHGs). Chemical acidification of manures has been shown to significantly reduce these emissions. Waste products, derived from food processing and on-farm practices, may be used as “natural” acidifiers. However, the efficacy of these products in reducing pH and any subsequent emissions are unknown. Commercial “slurry improvers” or “additives” may also be a viable mitigation option; however, their effectiveness is questionable. This study investigated the efficacy and cost of a range of waste and commercial amendments and a chemical acidifier, ferric chloride (FeCl3), to identify the most effective amendment for NH3 and GHG emissions reduction. Ammonia abatement potential was observed for 5% sugar beet molasses (67% reduction), 7% apple pulp (49% reduction), and 7% grass silage (38% reduction). Methane (CH4) emissions were reduced only by spent brewers’ grain, sugarbeet molasses, and grass silage effluent at the higher inclusions (i.e. amounts added), with reductions ranging from 15% to 70%. Carbon dioxide (CO2) emissions were significantly increased with the addition of waste amendments. Commercially available additives had little impact on emissions, with the exception of one treatment, which reduced CH4 by approximately 10%. Ferric chloride reduced NH3 emissions by 20%–68%, CH4 by 6%–65%, and CO2 by 6%–38%, depending on the inclusion. All waste amendments had low marginal abatement costs ranging from -€0.46 to €0.88 kg−1 NH3 abated compared to FeCl3 and commercial amendments (€1.80 to €231 kg−1 NH3). This incubation experiment demonstrated that a range of on-farm and industry waste streams could be valorised to reduce NH3 emissions. However, many of these may result in higher CH4 and CO2 emissions due to input of labile carbon sources. Therefore, based on the results of the current study, it is recommended that sugarbeet molasses and ferric chloride, at 5% and 1.1% inclusions respectively, be examined in field experiments.
  • Drainage class and soil phosphorus availability shape microbial communities in Irish grasslands

    Graça, Jessica; Daly, Karen; Bondi, Giulia; Ikoyi, Israel; Crispie, Fiona; Cabrera-Rubio, Raul; Cotter, Paul D.; Schmalenberger, Achim; Department of Agriculture, Food and the Marine; RSF13S468 (Elsevier, 2021-06-30)
    Soil drainage and phosphorus (P) availability are considered indicators of management intensity in pasture-based agriculture supporting livestock. However, microbial adaptations to P-availability according to soil drainage class are rarely investigated. We hypothesized that well-drained grasslands with high P-availability will sustain a distinctive soil microbiota when compared to poorly-drained grasslands with low-P availability. The relationship between soil drainage, plant available P and grassland microbial communities was evaluated among well-drained sites with high- or low-P and poorly-drained sites with high- or low-P, using fingerprinting, next-generation sequencing and quantitative PCR. Bacterial community structures were primarily affected by drainage as well as significantly separated between a combination of drainage and P availability i.e. low-P and poorly drained versus high-P and well drained. Abundance of the bacterial phylum Actinobacteria was significantly higher in well-drained high-P soils while Firmicutes were more abundant in well-drained low-P soils. Soil fungal communities responded to both drainage status and plant available P. Fungal phyla such as Basidiomycota responded strongly towards availability of P, while Glomeromycota were most abundant in poorly drained low-P soils. The diversity of the alkaline phosphatase gene phoD responded more clearly to drainage than availability of P. Of the other environmental factors, soil pH significantly affected the bacterial and fungal communities structure analyzed. This study suggests that while bacteria and fungi are affected by a combination of soil drainage and P availability in Irish grassland soils, drainage has a more profound influence on bacterial communities than P availability.
  • An examination of maximum legal application rates of dairy processing and associated STRUBIAS fertilising products in agriculture

    Shi, W.; Fenton, O.; Ashekuzzaman, S.M.; Daly, k.; Leahy, J.J.; Khalaf, N.; Hu, Y.; Chojnacka, K.; Numviyimana, C.; Healy, M.G.; et al. (Elsevier, 2022-01-01)
    The dairy industry produces vast quantities of dairy processing sludge (DPS), which can be processed further to develop second generation products such as struvite, biochars and ashes (collectively known as STRUBIAS). These bio-based fertilizers have heterogeneous nutrient and metal contents, resulting in a range of possible application rates. To avoid nutrient losses to water or bioaccumulation of metals in soil or crops, it is important that rates applied to land are safe and adhere to the maximum legal application rates similar to inorganic fertilizers. This study collected and analysed nutrient and metal content of all major DPS (n = 84) and DPS-derived STRUBIAS products (n = 10), and created an application calculator in MS Excel™ to provide guidance on maximum legal application rates for ryegrass and spring wheat across plant available phosphorus (P) deficient soil to P-excess soil. The sample analysis showed that raw DPS and DPS-derived STRUBIAS have high P contents ranging from 10.1 to 122 g kg−1. Nitrogen (N) in DPS was high, whereas N concentrations decreased in thermo-chemical STRUBIAS products (chars and ash) due to the high temperatures used in their formation. The heavy metal content of DPS and DPS-derived STRUBIAS was significantly lower than the EU imposed limits. Using the calculator, application rates of DPS and DPS-derived STRUBIAS materials (dry weight) ranged from 0 to 4.0 tonnes ha−1 y−1 for ryegrass and 0–4.5 tonnes ha−1 y−1 for spring wheat. The estimated heavy metal ingestion to soil annually by the application of the DPS and DPS-derived STRUBIAS products was lower than the EU guideline on soil metal accumulation. The calculator is adaptable for any bio-based fertilizer, soil and crop type, and future work should continue to characterise and incorporate new DPS and DPS-derived STRUBIAS products into the database presented in this paper. In addition, safe application rates pertaining to other regulated pollutants or emerging contaminants that may be identified in these products should be included. The fertilizer replacement value of these products, taken from long-term field studies, should be factored into application rates.
  • A landscape classification map of Ireland and its potential use in national land use monitoring

    Carlier, J.; Doyle, M.; Finn, John; Ó hUallacháin, D.; Moran, J.; Department of Agriculture, Food and the Marine Research Stimulus Fund; 2019R425 (Elsevier, 2021-07-01)
    This study presents a novel landscape classification map of the Republic of Ireland and is the first to identify broad landscape classes by incorporating physiographic and land cover data. The landscape classification responds to commitments to identify and classify the Irish landscape as a signatory to the European Landscape Convention. The methodology applied a series of clustering iterations to determine an objective multivariate classification of physiographic landscape units and land cover datasets. The classification results determined nine statistically significant landscape classes and the development of a landscape classification map at a national scale. A statistical breakdown of land cover area and diversity of each class was interpreted, and a comparison was extended using independent descriptive variables including farmland use intensity, elevation, and dominant soil type. Each class depicts unique spatial and composition characteristics, from coastal, lowland and elevated, to distinct and dominating land cover types, further explained by the descriptive variables. The significance of individual classes and success of the classification is discussed with particular reference to the wider applicability of the map. The transferability of the methodology to other existing physiographic maps and environmental datasets to generate new landscape classifications is also considered. This novel work facilitates the development of a strategic framework to efficiently monitor, compare and analyse ecological and other land use data that is spatially representative of the distribution and extent of land cover in the Irish countryside.
  • The effect of machine traffic zones associated with field headlands on soil structure in a survey of 41 tilled fields in a temperate maritime climate

    Ward, Mark; McDonnell, Kevin; Metzger, Konrad; Forristal, Patrick Dermot; Teagasc Walsh Fellowship (Elsevier, 2021-06-30)
    Machinery traffic imposes a negative effect on soil structure, leading to soil compaction. Studies to date have primarily focused on the influence of applied wheel loads on soil structure. Few studies have assessed the impact of commercial farm operations on soil structure and crop performance, particularly on field headlands in a temperate maritime climate such as Ireland. A survey was conducted on 41 conventionally managed field sites to investigate the effect of field position (field edge, turning, transition and in-field zones) in relation to machinery operations on soil structure. Soil texture classes ranged from sandy loam to clay loam. All sites used plough-based crop establishment. Soil structural condition was assessed visually using the visual evaluation of soil structure method (VESS) for the topsoil (0−250 mm), and Double Spade below plough depth (250−400 mm). Quantitative soil measurements such as shear strength, bulk density and porosity using soil cores post-harvest, and soil cone penetration resistance were taken at two time points in the crop growth cycle. For most measurements of soil structure, the in-field zone of least machinery traffic produced the best scores (Sq 2.81 & DS 2.48), and the turning zone returned the poorest scores in the 0−250 mm soil layer (Sq 3.31 & DS 2.91). The strongest quantitative scores for the in-field and turning zones, respectively, were for trowel penetration resistance in the upper (2.49 & 3.20) and lower (3.41 & 4.05) soil depth layers and for shear vane (38.17 & 53.59 kPa) for the same zones. The visual assessments and some of the quantitative measurements (0−250 mm soil layer) followed the zone order trend of: turning, field edge, transition and in-field, for increasing machinery traffic. The results show that the visual soil indicators used in this study are more sensitive than quantitative soil measurements such as soil bulk density (ρb) or porosity (TP and MP) at detecting soil structural differences between zones, particularly below plough depth (>250 mm soil depth).

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