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

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

      Byrne, Andrew W.; Sleeman, D. Paddy; O'Keeffe, James; Davenport, John; Department of Agriculture, Food and the Marine, Ireland; Teagasc Walsh Fellowship Programme (Royal Irish Academy, 30/04/2012)
      The badger is an ecologically and economically important species. Detailed knowledge of aspects of the ecology of this animal in Ireland has only emerged through research over recent decades. Here, we review what is known about the species' Irish populations and compare these findings with populations in Britain and Europe. Like populations elsewhere, setts are preferentially constructed on south or southeast facing sloping ground in well-drained soil types. Unlike in Britain, Irish badger main setts are less complex and most commonly found in hedgerows. Badgers utilise many habitat types, but greater badger densities have been associated with landscapes with high proportions of pasture and broadleaf woodlands. Badgers in Ireland tend to have seasonally varied diets, with less dependence on earthworms than some other populations in northwest Europe. Recent research suggests that females exhibit later onset and timing of reproductive events, smaller litter sizes and lower loss of blastocysts than populations studied in Britain. Adult social groups in Ireland tend to be smaller than in Britain, though significantly larger than social groups from continental Europe. Although progress has been made in estimating the distribution and density of badger populations, national population estimates have varied widely in the Republic of Ireland. Future research should concentrate on filling gaps in our knowledge, including population models and predictive spatial modelling that will contribute to vaccine delivery, management and conservation strategies.
    • Ecosystem function enhanced by combining four functional types of plant species in intensively-managed grassland mixtures: a three-year continental-scale field experiment

      Finn, John; Kirwan, Laura; Connolly, John; Sebastia, Maria Teresa; Helgadottir, Aslaug; Baadshaug, Ole; Belanger, Gilles; Black, Alistair D; Brophy, C.; Collins, Rosemary; et al. (Wiley-Blackwell, 22/02/2013)
      1. A co-ordinated continental-scale field experiment across 31 sites was used to compare the biomass yield of monocultures and four-species mixtures associated with intensively managed agricultural grassland systems. To increase complementarity in resource use, each of the four species in the experimental design represented a distinct functional type derived from two levels of each of two functional traits, nitrogen acquisition (N2-fixing legume or non-fixing grass) crossed with temporal development (fast-establishing or temporally persistent). Relative abundances of the four functional types in mixtures were systematically varied at sowing to vary the evenness of the same four species in mixture communities at each site, and sown at two levels of seed density. 2. Across multiple years, the total yield (including weed biomass) of the mixtures exceeded that of the average monoculture in >97% of comparisons. It also exceeded that of the best monoculture (transgressive overyielding) in about 60% of sites, with a mean yield ratio of mixture to best-performing monoculture of 1.07 across all sites. Analyses based on yield of sown species only (excluding weed biomass) demonstrated considerably greater transgressive overyielding (significant at about 70% of sites, ratio of mixture to best-performing monoculture = 1.18). 3. Mixtures maintained a resistance to weed invasion over at least three years. In mixtures, median values indicate <4% of weed biomass in total yield, whereas the median percentage of weeds in monocultures increased from 15% in year 1 to 32% in year 3. 4. Within each year, there was a highly significant relationship (P<0.0001) between sward evenness and the diversity effect (excess of mixture performance over that predicted from the monoculture performances of component species). At lower evenness values, increases in community evenness resulted in an increased diversity effect, but the diversity effect was not significantly different from the maximum diversity effect across a wide range of higher evenness values. The latter indicates the robustness of the diversity effect to changes in species’ relative abundances. 5. Across sites with three complete years of data (24 of the 31 sites), the effect of interactions between the fast-establishing and temporal persistent trait levels of temporal development was highly significant and comparable in magnitude to effects of interactions between N2-fixing and non-fixing trait levels of nitrogen acquisition. 6. Synthesis and applications. The design of grassland mixtures is relevant to farm-level strategies to achieve sustainable intensification. Experimental evidence indicated significant yield benefits of four-species agronomic mixtures which yielded more than the highest-yielding monoculture at most sites. The results are relevant for agricultural practice, and show how grassland mixtures can be designed to improve resource complementarity, increase yields and reduce weed invasion. The yield benefits were robust to considerable changes in the relative proportions of the four species, which is extremely useful for practical management of grassland swards.
    • Effect of Agricultural Practices on Nitrate Leaching

      Ryan, Michael; McNamara, Kevin; Brophy, C.; Connolly, John; Carton, Owen T.; Richards, Karl G.; Environmental Protection Agency (Teagasc, 01/12/2005)
      A farm-scale study, carried out at Teagasc, Moorepark (Curtin’s farm), examined the effect of four managements (treatments) on nitrate-nitrogen (NO3-N) leaching over the period 2001-`05. Leaching was measured in these treatments: (T1) plots receiving dirty water and N fertilizer which were grazed; (T2) 2-cut silage and grazing plots receiving slurry and fertilizer N; (T3) grazed plots receiving fertilizer N and (T4) 1-cut silage and grazing plots receiving slurry and fertilizer N. The soil is a free-draining sandy loam overlying Karstic fissured limestone. The mean direct N inputs (kg/ha) for T1-T4 in 2001-`04 were 311, 309, 326, 331, respectively, with stocking rates (LU/ha) of 2.12 - ~2.47. Eight ceramic cups per plot, in 3 replicate plots of each treatment, were used to collect water, on a weekly basis, from 1.0 m deep using 50 kPa suction. There were 33, 37, 26 and 24 sampling dates in the 4 years, respectively. The NO3-N and NH4-N concentrations (mg/l) were determined in the water samples. The annual average and weekly concentration of these parameters was statistically analysed for all years, using a repeated measures analysis. The aggregated data were not normally distributed. There was an interaction between treatment and year (p<0.001). Significant differences (p=0.05) in NO3-N concentrations showed between the treatments in years 1, 2, 4 but not in year 3. For the NH4-N data there was no interaction between treatment and year, p=0.12, or main effect of treatment, p=0.54 but there were differences between years, p=0.01. Mean weekly concentrations were analysed separately for each year. For NO3-N, in years 1, 2 and 4 there was an interaction between treatment and week (p<0.001). With NH4-N, there was an interaction between treatment and week in all 4 years. Dirty water was significantly higher than grazed and 1 cut silage in NO3-N concentrations in year 1; in year 2, dirty water and 2 cut silage were significantly higher than the other treatments while in year 4, dirty water and grazed were significantly higher than the other two treatments. The overall four-year weighted mean NO3-N and NH4-N concentrations were 8.2 and 0.297 mg/l. The NCYCLE (UK) model was adapted for Irish conditions as NCYCLE_IRL. The NCYCLE empirical approach proved to be suitable to predict N fluxes from Irish grassland systems in most situations. Experimental data appeared to agree quite well, in most cases, with the outputs from NCYCLE_IRL. The model was not capable of predicting data from some of the leaching experiments, which suggests that the observed leaching phenomena in these experiments could be governed by non-average conditions or other parameters not accounted for in NCYCLE_IRL. An approach that took into account denitrification, leaching and herbage yield would probably explain the differences found. NCYCLE_IRL proved to be a useful tool to analyse N leaching from grazed and cut grassland systems in Ireland.
    • Effect of an agri-environmental measure on nitrate leaching from a beef farming system in Ireland

      Richards, Karl G.; Jahangir, Mohammad M. R.; Drennan, Michael J; Lenehan, J.J.; Connolly, John; Brophy, C.; Carton, Owen T. (Elsevier, 07/01/2015)
      Agricultural nitrogen (N) management remains a key environmental challenge. Improving N management is a matter of urgency to reduce the serious ecological consequences of the reactive N. Nitrate (NO3−–N) leaching was measured under suckler beef production systems stocked at two intensities: (1) intensive, 210 kg organic N ha−1 with two cut silage harvests; and (2) rural environmental protection scheme (REPS), 170 kg organic N ha−1 with one cut silage harvest. Three replicate plots of each treatment were instrumented with ceramic cups (8 per plot), randomly placed within each plot at a depth of 1 m to collect soil solution for NO3−–N at 50 kPa suction to collecting vessels one week prior to sampling. Samples were taken on a total of 53 sampling dates over 3 winter drainage periods (2002/03, 2003/04 and 2004/05). Over the course of the experiment the mean annual soil solution NO3−–N concentration exceeded the MAC twice out of 15 means (5 treatments over 3 years). The REPS grazing and silage sub treatments had significantly lower mean annual soil solution total oxidized N (TON) concentrations than the respective intensive treatments in years 2 and 3. Annual total NO3−–N losses over the three years in intensive and REPS systems ranged from 55 to 71 and 15 to 20 kg N ha−1, respectively. Mean N surpluses in intensive and REPS systems were 210 and 95 kg ha−1, respectively with the corresponding mean N inputs of 272 and 124 kg N ha−1. The reduction in N inputs under the REPS system results in lower N leaching losses and contributed to a significant reduction in pressures on water quality.
    • The effect of cattle slurry in combination with nitrate and the nitrification inhibitor dicyandiamide on in situ nitrous oxide and dinitrogen emissions

      McGeough, K. L.; Laughlin, Ronald J.; Watson, C. J.; Muller, Christoph; Ernfors, M.; Cahalan, E.; Richards, Karl G.; Department of Agriculture, Food and the Marine, Ireland; RSF 07 519 (European Geosciences Union, 04/12/2012)
      A field study was conducted to determine the effect of the nitrification inhibitor dicyandiamide (DCD) on N2O and N2 emissions after cattle slurry (CS) application in the presence of nitrate (NO3) fertiliser on seven different occasions (between March 2009 and March 2011). N2O emissions from CS in the presence of NO3 fertiliser were very high (0.4–8.7% of applied N) over a 20-day period, under mild moist conditions. Emissions were significantly larger from the CS treatment compared to an NH4+-N source, supplying the same rate of N as in the slurry. This study supports the view that organic fertilisers should not be applied at the same time as nitrate-based fertilisers, as significant increases in N2O emissions occur. The average N2O mole fraction (N2O/(N2O + N2)) over all seven application dates was 0.34 for CSNO3 compared to 0.24 for the NH4ClNO3 treatment, indicating the dominance of N2 emissions. The rate of nitrification in CSNO3 was slower than in NH4ClNO3, and DCD was found to be an effective nitrification inhibitor in both treatments. However, as N2O emissions were found to be predominantly associated with the NO3 pool, the effect of DCD in lowering N2O emissions is limited in the presence of a NO3 fertiliser. To obtain the maximum cost-benefit of DCD in lowering N2O emissions, under mild moist conditions, it should not be applied to a nitrate containing fertiliser (e.g. ammonium nitrate or calcium ammonium nitrate), and therefore the application of DCD should be restricted to ammonium-based organic or synthetic fertilisers.
    • Effect of chemical amendments to dairy soiled water and time between application and rainfall on phosphorus and sediment losses in runoff

      Serrenho, Ana; Fenton, Owen; Murphy, Paul N. C.; Grant, Jim; Healy, Mark G.; Department of Agriculture, Food and the Marine, Ireland; RSF 07 525 (Elsevier, 15/07/2012)
      Dairy soiled water (DSW) is a dilute, low nutrient effluent produced on Irish dairy farms through the regular washing down of milking parlours and holding areas. In Ireland, there is no closed period for the land application of DSW except where heavy rain is forecast within 48 h. Chemical amendments have the potential to decrease phosphorus (P) and suspended sediment (SS) loss from DSW applied to land. This study examined the impact of three time intervals (12, 24 and 48 h) between DSW application and rainfall and five treatments (control, unamended DSW, and DSW amended with lime, alum or ferric chloride (FeCl2)) on P and sediment losses from an intact grassland soil in runoff boxes. Rainfall was simulated at 10.5 ± 1 mm h− 1. Phosphorus concentrations (1–1.6 mg L− 1) in runoff from DSW application, while not quantitative measures of P loss to surface waters in the field, indicated the importance of incidental P losses and that the current 48 h restriction in Ireland is prudent. Unamended DSW application increased P loss by, on average, 71%, largely due to an increase in particulate phosphorus (PP) loss. All three amendments were effective in decreasing P and SS losses in runoff and, apart from the SS results for lime, were significantly different (p < 0.05) to the control at at least one time point. Lime (a 64% reduction in total phosphorus (TP) in comparison with DSW only) was less effective than alum or FeCl2, likely due to the lower solubility of CaCO3 in water. Chemical amendment showed potential to decrease P losses from land application of DSW, but the efficacy of such amendments would need to be assessed in field trials and a cost–benefit analysis conducted to further examine whether they could be practically implemented on farms.
    • The Effect of Chemical Amendments Used for Phosphorus Abatement on Greenhouse Gas and Ammonia Emissions from Dairy Cattle Slurry: Synergies and Pollution Swapping

      Brennan, Raymond B.; Healy, Mark G.; Fenton, Owen; Lanigan, Gary; European Union; Teagasc Walsh Fellowship Programme; FP7-KBBE-2010-4 (PLoS, 08/06/2015)
      Land application of cattle slurry can result in incidental and chronic phosphorus (P) loss to waterbodies, leading to eutrophication. Chemical amendment of slurry has been proposed as a management practice, allowing slurry nutrients to remain available to plants whilst mitigating P losses in runoff. The effectiveness of amendments is well understood but their impacts on other loss pathways (so-called ‘pollution swapping’ potential) and therefore the feasibility of using such amendments has not been examined to date. The aim of this laboratory scale study was to determine how the chemical amendment of slurry affects losses of NH3, CH4, N2O, and CO2. Alum, FeCl2, Polyaluminium chloride (PAC)- and biochar reduced NH3 emissions by 92, 54, 65 and 77% compared to the slurry control, while lime increased emissions by 114%. Cumulative N2O emissions of cattle slurry increased when amended with alum and FeCl2 by 202% and 154% compared to the slurry only treatment. Lime, PAC and biochar resulted in a reduction of 44, 29 and 63% in cumulative N2O loss compared to the slurry only treatment. Addition of amendments to slurry did not significantly affect soil CO2 release during the study while CH4 emissions followed a similar trend for all of the amended slurries applied, with an initial increase in losses followed by a rapid decrease for the duration of the study. All of the amendments examined reduced the initial peak in CH4 emissions compared to the slurry only treatment. There was no significant effect of slurry amendments on global warming potential (GWP) caused by slurry land application, with the exception of biochar. After considering pollution swapping in conjunction with amendment effectiveness, the amendments recommended for further field study are PAC, alum and lime. This study has also shown that biochar has potential to reduce GHG losses arising from slurry application.
    • Effect of organic, conventional and mixed cultivation practices on soil microbial community structure and nematode abundance in a cultivated onion crop

      Reilly, Kim; Cullen, Eileen; Lola-Luz, Theodora; Stone, Dote; Valverde, Juan; Gaffney, Michael; Brunton, Nigel; Grant, Jim; Griffiths, Bryan; Department of Agriculture, Food and the Marine, Ireland; et al. (Wiley, 07/06/2013)
      BACKGROUND: Responses of the soil microbial and nematode community to organic and conventional agricultural practices were studied using the Teagasc Kinsealy Systems Comparison trial as the experimental system. The trial is a long term field experiment which divides conventional and organic agriculture into component pest-control and soil treatment practices. We hypothesised that management practices would affect soil ecology and used community level physiological profiles (CLPP), microbial and nematode counts, and denaturing gradient gel electrophoresis (DGGE) to characterise soil microbial communities in plots used for onion (Allium cepa L.) cultivation. RESULTS: Microbial activity and culturable bacterial counts were significantly higher under fully organic management. Culturable fungi, actinomycete and nematode counts showed a consistent trend towards higher numbers under fully organic management but these data were not statistically significant. No differences were found in the fungal/bacterial ratio. DGGE banding patterns and sequencing of excised bands showed clear differences between treatments. Putative onion fungal pathogens were predominantly sequenced under conventional soil treatment practices whilst putative soil suppressive bacterial species were predominantly sequenced from the organic pest-control treatment plots. CONCLUSION: Organic management increased microbial activity and diversity. Sequence data was indicative of differences in functional groups and warrants further investigation.
    • The effect of precipitation and application rate on dicyandiamide persistence and efficiency in two Irish grassland soils

      Cahalan, E.; Minet, E.; Emfors, M.; Muller, Christoph; Devaney, D.; Forrestal, Patrick J.; Richards, Karl G.; Department of Agriculture, Food and the Marine, Ireland; RSF 07519; RSF 07545 (Wiley, 14/07/2015)
      The nitrification inhibitor dicyandiamide (DCD) has had variable success in reducing nitrate (NO3-) leaching and nitrous oxide (N2O) emissions from soils receiving nitrogen (N) fertilisers. Factors such as soil type, temperature and moisture have been linked to the variable efficacy of DCD. Since DCD is water soluble it can be leached from the rooting zone where it is intended to inhibit nitrification. Intact soil columns (15 cm diameter by 35 cm long) were taken from luvic gleysol and haplic cambisol grassland sites and placed in growth chambers. DCD was applied at 15 or 30 kg DCD ha-1, with high or low precipitation. Leaching of DCD, mineral N and the residual soil DCD concentrations were determined over eight weeks High precipitation increased DCD in leachate and decreased recovery in soil. A soil x DCD rate interaction was detected for the DCD unaccounted (proxy for degraded DCD). In the cambisol degradation of DCD was high (circa 81%) and unaffected by DCD rate. In contrast DCD degradation in the gleysol was lower and differentially affected by rate, 67 and 46% for the 15 and 30 kg ha-1 treatments, respectively. Differences DCD degradation rates between soils may be related to differences in organic matter content and associated microbiological activity. Variable degradation rates of DCD in soil, unrelated to temperature or moisture, may contribute to varying DCD efficacy. Soil properties should be considered when tailoring DCD strategies for improving nitrogen use efficiency and crop yields, through the reduction of reactive nitrogen loss.
    • The effect of renovation of long-term temperate grassland on N2O emissions and N leaching from contrasting soils

      Krol, Dominika; Jones, M. B.; Williams, M.; Richards, Karl G.; Bourdin, F.; Lanigan, Gary; Department of Agriculture, Food and the Marine, Ireland; 07 RSF 527 (Elsevier, 19/04/2016)
      Renovation of long-term grassland is associated with a peak in soil organic N mineralisation which, coupled with diminished plant N uptake can lead to large gaseous and leaching N losses. This study reports on the effect of ploughing and subsequent N fertilisation on the N2O emissions and DON/NO3− leaching, and evaluates the impact of ploughing technique on the magnitude and profile of N losses. This study was carried out on isolated grassland lysimeters of three Irish soils representing contrasting drainage properties (well-drained Clonakilty, moderately-drained Elton and poorly-drained Rathangan). Lysimeters were manually ploughed simulating conventional (CT) and minimum tillage (MT) as two treatments. Renovation of grassland increased N2O flux to a maximum of 0.9 kg N2O–N ha− 1 from poorly-drained soil over four days after treatment. Although there was no difference between CT and MT in the post-ploughing period, the treatment influenced subsequent N2O after fertiliser applications. Fertilisation remained the major driver of N losses therefore reducing fertilisation rate post-planting to account for N mineralised through grassland renovation could reduce the losses in medium to longer term. Leaching was a significant loss pathway, with the cumulative drainage volume and N leached highly influenced by soil type. Overall, the total N losses (N2O + N leached) were lowest from poorly and moderately draining soil and highest for the well draining soil, reflecting the dominance of leaching on total N losses and the paramount importance of soil properties.
    • Effects of multi-species swards on dry matter production and the incidence of unsown species at three Irish sites

      Connolly, John; Finn, John; Black, Alistair D; Kirwan, Laura; Brophy, C.; Luscher, A.; European Union; Science Foundation Ireland; COST Action 852; 09/RFP/EOB2546 (Teagasc (Agriculture and Food Development Authority), Ireland, 2009)
      Recent ecological research provides evidence that an increased number of plant species in natural grasslands is associated with increased biomass productivity, and provides a wide range of other ecosystem benefits. This suggests that increases in species diversity in agricultural ecosystems may similarly lead to increased benefits. The work reported below was part of the COST 852 Agrodiversity experiment, carried out at 34 sites across Europe. In Ireland, the effects of four-species grass-clover mixtures on herbage production, species persistence and unsown species suppression at three sites over multiple years, were investigated under growing conditions that were intensive relative to unfertilised natural grassland systems. The design included a range of four-species mixtures and monocultures of perennial ryegrass, timothy, cocksfoot, white clover, red clover and Caucasian clover. Several harvests were taken at each site for two or three years. Species diversity had a strong, persistent and positive effect on overall yield and the yield of sown species, and enhanced resistance to the growth of unsown species. Mixtures generally yielded well when compared with the best monoculture, and sometimes out yielded it. These effects on total yield declined over time but were still important at the end of the experiments. The diversity effects on sown species yield and on resistance to unsown species increased with time. Diversity effects were robust to changes in species composition, and persisted for the duration of the experiments across mixtures and over time. Virtually every mixture had a higher yield, and suppressed unsown species better, than monocultures of perennial ryegrass. These patterns were broadly consistent across sites. The persistence of species varied widely and was not consistent across sites.
    • Effects of over-winter green cover on groundwater nitrate and dissolved organic carbon concentrations beneath tillage land

      Premrov, Alina; Coxon, Catherine E.; Hackett, Richard; Kirwan, Laura; Richards, Karl G. (Elsevier, 13/09/2012)
      Application of over-winter green cover (e.g. cover crops) as a measure for reducing nitrate losses from tillage land has been frequently investigated, especially in the unsaturated zone. Monitoring of groundwater is less common in these studies. Studies on groundwater responses to different land treatments can be challenging because they can be influenced by various conditions, such as recharge, seasonal variations, and aquifer properties, often occurring at different time scales than surface water processes. The aim of this study was to evaluate groundwater nitrate (NO3−single bondN) and dissolved organic carbon (DOC) concentration responses to different over-winter green covers: mustard, natural regeneration and no cover. A field experiment was designed and run for three years on tillage land underlain by a vulnerable sand and gravel aquifer in the south-east of Ireland. Results showed that over-winter green cover growth on tillage land can be an effective measure to reduce groundwater NO3−single bondN concentrations. A significant decrease in groundwater NO3−single bondN concentrations was observed under the mustard cover compared to no cover. All treatments, including no cover, showed a decline in groundwater NO3−single bondN concentrations over time. A significant increase in groundwater DOC was also observed under the mustard cover. Although the overall groundwater DOC concentrations were low, the increased DOC occurrence in groundwater should be accounted for in carbon balances and could potentially enhance groundwater denitrification in cases where aquifer conditions may favour it.
    • Effects of urease and nitrification inhibitors on yields and emissions in grassland and spring barley

      Forrestal, Patrick J.; Wall, David; Carolan, Rachael; Harty, Mary A.; Roche, Leanne; Krol, Dominika; Watson, C. J.; Lanigan, Gary; Richards, Karl G.; Department of Agriculture, Food and the Marine, Ireland; et al. (International Fertiliser Society, 09/12/2016)
      In trials conducted in the temperate maritime climate of Ireland on a range of acidic soils, calcium ammonium nitrate (CAN) and urea gave comparable yield performance. There was little evidence of reduced yields by using urea for grassland or spring barley. Our finding that urea produced annual yields that were not significantly different from CAN differs from previous studies which found that yields from urea were lower than those from ammonium nitrate or nitrate based fertiliser in the UK. However, there are also published results from trials conducted in temperate Irish grassland showing equal yield performance of CAN and urea in the 1970s. Based on yield performance and the cost of fertiliser there is scope to dramatically increase the level of urea usage in straight and blended fertilisers in the temperate maritime climate of Ireland in both grassland and spring barley. Such an increase will bring substantial benefits in terms of reducing direct nitrous oxide (N2O) emissions from fertiliser applied to soil, particularly in poorly draining soils subject to high levels of precipitation. Nitrogen recovery by plants tends to be more sensitive to differences in fertiliser efficiency than is yield. Although yields did not differ between urea and CAN; urea had a lower nitrogen recovery indicating that urea usage will also result in a reduced level of fertiliser use efficiency. Reduced efficiency is less tangible to farmers who tend to be primarily concerned with dependable yield results. Reduced efficiency is a problem nonetheless, particularly as it is closely linked to NH3 emissions in urea usage. European countries including Ireland have committed to reduce national NH3 emissions to comply with the revised National Emission Ceilings Directive (2001/81/EC) in Europe. Increased urea usage, which looks attractive from a yield, cost and direct N2O perspective in Ireland, runs counter to meeting these commitments. Additionally, NH3 is a source of indirect N2O emissions that will negate some of the N2O savings from urea. Due to the issues of yield dependability, fertiliser efficiency, N2O and NH3 emissions the urease inhibitor N-(n-butyl) thiophosphoric triamide (NBPT) is a particularly attractive option for making urea use more efficient by addressing its key weakness in the area of variable NH3 loss and efficiency. The urease inhibitor NBPT along with the nitrification inhibitor dicyandiamide (DCD) were tested with urea in comparison with calcium ammonium nitrate (CAN). The nitrification inhibitor DCD was very effective in reducing fertiliser N associated N2O emissions. Indeed, its usage allowed N2O levels to be reduced to levels comparable to where no application of N fertiliser was made at some site-years. However, at the DCD incorporation rate tested, DCD contributed to variability in NH3 loss from urea and suppressed both yield response and fertiliser efficiency. Use of the urease inhibitor NBPT in addition to DCD went a substantial way to resolving these shortcomings. Continuing work is needed to tailor the rate of existing and new urease and nitrification inhibitors to optimise the balance between suppression of gaseous N emissions, agronomic performance and economic considerations.
    • 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.
    • 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.
    • Enteropathogen survival in soil from different land-uses is predominantly regulated by microbial community composition

      Moynihan, Emma; Richards, Karl G.; Brennan, Fiona P.; Tyrrel, Sean; Ritz, Karl; Teagasc Post-doctoral Fellowship Scheme; Teagasc Walsh Fellowship Programme (Elsevier, 23/01/2015)
      Microbial enteropathogens can enter the environment via landspreading of animal slurries and manures. Biotic interactions with the soil microbial community can contribute to their subsequent decay. This study aimed to determine the relative impact of biotic, specifically microbial community structure, and physico-chemical properties associated with soils derived from 12 contrasting land-uses on enteropathogen survival. Phenotypic profiles of microbial communities (via phospholipid fatty acid (PLFA) profiling), and total biomass (by fumigation-extraction), in the soils were determined, as well as a range of physicochemical properties. The persistence of Salmonella Dublin, Listeria monocytogenes, and Escherichia coli was measured over 110 days within soil microcosms. Physicochemical and biotic data were used in stepwise regression analysis to determine the predominant factor related to pathogen-specific death rates. Phenotypic structure, associated with a diverse range of constituent PLFAs, was identified as the most significant factor in pathogen decay for S. Dublin, L. monocytogenes, non-toxigenic E. coli O157 but not for environmentally-persistent E. coli. This demonstrates the importance of entire community-scale interactions in pathogen suppression, and that such interactions are context-specific.
    • Environmental aspects of soil phosphorus testing

      Daly, Karen M.; Casey, A. (Teagasc (Agriculture and Food Development Authority), Ireland, 2005)
      Soil phosphorus testing in Ireland uses Morgan’s reagent from samples taken to 10 cm depth for agronomic recommendations. However, its suitability as an environmental indicator has been questioned in terms of sample depth and extraction solution. Seven grassland sites were sampled to depths of 2, 5 and 10 cm and extracted for Morgan’s P, the standard agronomic test, as well as iron-oxide impregnated paper strip P (FeOP), calcium chloride extractable P (CaCl2-P) and water soluble P (WSP), all proposed as environmental soil tests. Extractable soil P decreased with increasing sample depth, as did variances in each test, such that, 2 cm samples had highest concentrations and variances. The current standard sample depth (10 cm) was linearly related to corresponding data from samples taken to 2 and 5 cm, indicating that surface soil P can be consistently estimated from the current standard depth. When soil tests were compared with dissolved reactive P (DRP) in overland flow collected from two field sites, certain soil tests were better indicators of P loss than others. The relative difference in Morgan’s P values at the standard sample depth (10 cm) was reflected in the relative difference in P loss between the two sites. Average values of DRP collected from two sites ranged from 0.032 to 0.067 mg/l at the low P site and 0.261 to 0.620 at the high P site. Average DRP values from the high P site and maximum DRP values from the low P site were simulated using water-soluble P extraction at water to soil ratios 5 to 250 l/kg. In this study, Morgan’s P to 10 cm gave a good indication of the relative difference in DRP loss between the two sites.
    • 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.
    • Essential elements and heavy metal concentrations in a small area of the Castlecomer Plateau, Co. Kilkenny, Ireland: Implications for animal performance.

      Canty, M.J.; McCormack, Stephen; Lane, E.A.; Collins, D.M.; More, Simon J (Teagasc (Agriculture and Food Development Authority), Ireland, 2011)
      Many ruminants are solely or mostly dependant for their nutrients, including essential elements, on the forage available to them, either in its natural state or conserved as hay or silage. A soil and herbage survey was carried out in April and September 2007, in a 3.1 km × 3.0 km grid, incorporating 106 and 46 sampling points, respectively, on the Castlecomer Plateau, Co. Kilkenny, Ireland. The aim was to determine the nutrient and heavy metal status of soil and herbage in the sampling area, and to examine the concentrations observed for their potential to impact on animal performance. Low soil pH and high soil lime requirements were identified within the sampling area. The concentrations of Ca, Cu, Se and Zn were low in both soil and herbage. These conditions are similar to those found on other farms in Ireland. Fluoride was detected in 61 of the 97 herbage samples in April 2007, but only four exceeded 40 mg/kg dry matter, the maximum tolerable level for cattle. Mineral imbalances (Ca, Cu, Se and Zn) observed in pastures caused by low soil mineral status, exacerbated by low soil pH, could impair animal performance in the area studied.