Now showing items 1-20 of 536

    • 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).
    • FitForests – Looking at how Ireland’s Forests are shaping up to climate change

      Farrelly, Niall; Department of Agriculture, Food and the Marine (2022)
      Climate change is already having impacts on the health of the world’s forests. Healthy forests are critical to mitigate climate change. So how are Ireland’s forests shaping up? The FitForest is a DAFM-funded project which aim to address knowledge gaps in species and provenance selection to identify those that may be more adapted to future climatic conditions. High diversity among populations that may have phenotypic plasticity and/ or adaptive potential may be better adapted to capitalize on changing environmental conditions. This adaptive capacity is commonly assessed by studying the traits of trees which convey some inherent advantage over other populations which allows them to prosper in certain environments (e.g. late bud flush or water use efficiency). The project is a collaboration between a team of researchers from Teagasc, the Agri- Food and Biosciences Institute (NI), UCD, and climatologists from NUI-Maynooth.
    • The Application Of Genomics To Sitka Spruce Tree Improvement.

      Farrelly, Niall; Cashell, Ronan; Tobin, Brian; Zang, Shui; Department of Agriculture, Food and the Marine (2020)
      The GenESIS research is a new four year project funded by DAFM and features researchers from Teagasc, UCD, Trinity College Dublin, NUI Galway, National Botanic Gardens assisted by Coillte and hopes to document the genetics of Sitka spruce forests in Ireland and develop genotyping tools to assist tree-breeding efforts. The new research involves the development of a new genotyping platform that will be utilised for assessing differences in the genetic makeup of trees, used to assess diversity in Sitka spruce populations, for DNA fingerprinting, and also for genomic selection which has the potential to accelerating tree breeding efforts.

      Farrelly, Niall; Teagasc (2018)
      Teagasc forestry researcher, Dr Niall Farrelly, indicates that the removal of poor quality trees at first and second thinning is essential to focus production on trees with potential to achieve construction grade timber. It also puts more money in your pocket. • An analysis after two thinnings shows that thinning more heavily resulted in the production of a larger volume of commercial pallet wood. • The heaviest (Grade D) thinning has produced more than twice the volume of Pallet wood compared to the light (Grade B) thinning. • Income from timber sales in the heaviest thinning (Grade D) was almost 60% higher than for the light thinning (Grade B). • Timber quality measured by the volume of 5 metre+ straight logs was greatly enhanced by thinning with the greatest proportion of straight trees (by volume) in the heaviest (Grade D) thinning. • The heaviest (Grade D) thinning produced larger trees, a higher proportion of trees with straighter stems and the largest volume of commercial Pallet wood and offers the potential for earlier saw log timber production. On this basis heavier (Grade D) thinning is likely to be the most financially attractive thinning/ harvesting management option.
    • 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.
    • Potential of urban green spaces for supporting horticultural production: a national scale analysis

      Walsh, Lael E; Mead, Bethan R; Hardman, Charlotte A; Evans, Daniel; Liu, Lingxuan; Falagán, Natalia; Kourmpetli, Sofia; Davies, Jess; Global Food Security; Scottish Government; et al. (IOP Publishing, 2022-01-14)
      As urban areas and land-use constraints grow, there is increasing interest in utilizing urban spaces for food production. Several studies have uncovered significant potential for urban growing to supplement production of fruit and vegetables, focusing on one or two cities as case studies, whilst others have assessed the global scale potential. Here, we provide a national-scale analysis of the horticultural production potential of urban green spaces, which is a relevant scale for agri-food and urban development policy making using Great Britain (GB) as a case study. Urban green spaces available for horticultural production across GB are identified and potential yields quantified based on three production options. The distribution of urban green spaces within 26 urban towns and cities across GB are then examined to understand the productive potential compared to their total extent and populations. Urban green spaces in GB, at their upper limit, have the capacity to support production that is 8× greater than current domestic production of fruit and vegetables. This amounts to 38% of current domestic production and imports combined, or >400% if exotic fruits and vegetables less suited to GB growing conditions are excluded. Most urban green spaces nationally are found to fall within a small number of categories, with private residential gardens and amenity spaces making up the majority of space. By examining towns and cities across GB in further detail, we find that the area of green space does not vary greatly between urban conurbations of different sizes, and all are found to have substantial potential to meet the dietary needs of the local urban population. This study highlights that national policies can be suitably developed to support urban agriculture and that making use of urban green spaces for food production could help to enhance the resilience of the national-scale food system to shocks in import pathways, or disruptions to domestic production and distribution.
    • 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.
    • Environmental and cultivar variability in composition, content and biological activity of phenolic acids and alkylresorcinols of winter wheat grains from a multi-site field trial across Europe

      Kowalska, Iwona; Moldoch, Jaroslaw; Pawelec, Sylwia; Podolska, Grażyna; von Cossel, Moritz; Derycke, Veerle; Haesaert, Geert; Lana, Marcos A.; da Silva Lopes, Marta; Riche, Andrew B.; et al. (Elsevier, 2022-09-30)
      Different factors such as the genotype, environmental conditions, temperature stress, solar radiation and others can influence the phytochemical status of plants. The concentration of phenolic acids and alkylresorciols (ARs) as well as their chemical composition and biological activity have been determined in twelve winter wheat cultivars grown at eight European locations. This was the first winter wheat multi-location field trial of the European Consortium for Open Field Experimentation (ECOFE). Extracts from grain were analyzed using a UPLC-PDA-ESI-MS system (phenolic acids), UPLC-PDA-MS/MS (alkylresorcinols) and TLC-DPPH• test with ImageJ program (antiradical activity). The phenolic acid profile consisted of five hydroxybenzoic acid and four hydroxycinnamic acid derivatives, among which ferulic and sinapic acids were predominated. The ARs profile consisted of nine AR derivatives, among which 5-n-heneicosylresorcinol (C21:0) and 5-n-nonadecanylresorcinol (C19:0) were predominated. Our study showed significant differences in phenolic acids and AR content between wheat cultivars, as well as between locations. We observed a positive correlation between the biological activity of extracts and the total amount of phenolic acids and ARs. Two cultivars, Chambo and Julius (average of all sites) and samples from the Spanish site (average of all cultivars) showed the highest content and composition of nutritional substances.
    • 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.
    • Transmission of mushroom virus X and the impact of virus infection on the transcriptomes and proteomes of different strains of Agaricus bisporus

      O'Connor, Eoin; Doyle, Sean; Amini, Aniça; Grogan, Helen; Fitzpatrick, David A.; Teagasc Walsh Scholarship; Science Foundation Ireland; 10564231; SFI 12/RI/2346(3) (Elsevier, 2021-09-30)
      Cultivation of Agaricus bisporus is a large horticultural industry for many countries worldwide, where a single variety is almost grown exclusively. Mushroom virus X (MVX), a complex of multiple positive-sense single stranded RNA (ss(+)RNA) viruses, is a major pathogen of typical A. bisporus crops. MVX can manifest a variety of symptoms in crops and is highly infective and difficult to eradicate once established in host mycelium. Currently our knowledge regarding the molecular response of A. bisporus fruit bodies to MVX infection is limited. In order to study the response of different A. bisporus strains with different susceptibilities to MVX, we designed a model system to evaluate the in-vitro transmission of viruses in A. bisporus hyphae over a time-course, at two crucial phases in the crop cycle. The symptom expression of MVX in these varieties and the transcriptomic and proteomic response of fruit bodies to MVX-infection were examined. Transmission studies revealed the high potential of MVX to spread to uninfected mycelium yet not into the fruit bodies of certain strains in a crop. MVX affected colour and quality of multiple fruit bodies. Gene expression is significantly altered in all strains and between times of inoculation in the crop. Genes related to stress responses displayed differential expression. Proteomic responses revealed restriction of cellular signalling and vesicle transport in infected fruit bodies. This in-depth analysis examining many factors relevant to MVX infection in different A. bisporus strains, will provide key insights into host responses for this commercially important food crop.
    • 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.