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Resistance to insecticides used to control pests is an issue of increasing concern for agriculture. The grain aphid, Sitobion avenae, is a pest of cereals and grasses worldwide, and one of growing concern due to the evolution of resistance to certain insecticides. Resistance confers benefits to insects by enabling them to survive exposure to insecticide compounds; however, the mutations conferring resistance may also penalise the insect in pesticide-free environments due to fitness costs associated with the new phenotype. Here we tested the hypothesis of a reproductive penalty linked to the knockdown resistance mutation (kdr) to pyrethroid insecticides. The mutation occurs predominantly in a single SA3 clone. To date, only heterozygous-resistant forms (kdr-SR) have been detected in populations in Ireland and the UK, and this suggests that a fitness penalty may preclude the formation of both male and female heterozygous-resistant sexual forms. By designing an experiment which included a resistant and a non-resistant clone, we were able to simulate reduced daylight and temperature conditions which, in nature, trigger sexual reproduction and therefore study the responses of each clone. This allowed us to detect the switch from asexual females to sexual females and males and report on the conditions associated with the production of sexual forms. The results showed that both aphid clones were able to produce sexual forms with no difference in the onset of sexual reproduction, although reproductive strategies differed between clones. The later onset of male forms in the SA3 clone may decrease the likelihood of mating interactions to create fully resistant (kdr-RR) genotypes and this may constitute a fitness penalty due to pyrethroid resistance.

In a subset of dairy cows, prolonged pathological uterine inflammation results in purulent vaginal discharge (PVD), which can have negative consequences for both fertility and milk production. However, unlike for intensive systems, analysis of the effects of PVD in predominantly pasture-based herds is limited. The objective of this study was to assess the effect of PVD in spring-calving, pasture-based dairy cows on production and reproduction indices, stratified according to previous full-lactation milk yield. We assessed clinical disease as defined by vaginal mucus score (VMS) in 440 Holstein-Friesian cows from 5 farms. Cows were categorized as healthy (VMS 0) or having PVD (VMS 1–3) at 21 d postpartum. We recorded 305-d milk, milk protein, and milk fat yields (kg) before and after disease diagnosis, as well as fertility data, such as services per conception and the calving–conception period (CCP). Using SAS 9.4 (SAS Institute Inc., Cary, NC), we analyzed data using PROC MIXED, PROC PHREG, and PROC LOGISTIC to determine the least squares means differences and hazard and odds ratios between the groups, respectively. Overall, a 60% prevalence of PVD was recorded at 21 d postpartum. Milk yield and milk constituents were similar between all VMS categories and between healthy cows and cows with PVD. Although cows in the 4 VMS categories had statistically similar CCP, cows with PVD had a significantly longer CCP than healthy cows on average (9 d). The hazard ratio for cows with PVD was 0.66, indicating a 34% higher risk of a prolonged CCP than healthy cows. Odds ratio analysis determined that cows with PVD were 3 times more likely not to conceive at all, twice as likely not to conceive at first service, twice as likely not to conceive by 100 d postpartum, and 3 times more likely to fail to conceive before 150 d postpartum compared with healthy cows. Cows were retrospectively categorized as having low or high milk yield, based on whether they were above or below the median 305-d milk yield of the study population (6,571 kg) in the lactation before vaginal mucus scoring. Based on a univariate odds ratio, high-yield cows were 1.6 times more likely to present with PVD in the subsequent lactation. The number of services per conception did not differ between healthy and PVD cows in the low- and high-yield groups. In the high-yield group, cows with PVD were 4.9 times more likely not to conceive, 2.7 times more likely to require multiple services to conceive, 2.1 times more likely to remain not pregnant by 100 d postpartum, and 4.4 times more likely to remain not pregnant by 150 d postpartum. The CCP was also significantly longer in cows with PVD than their healthy counterparts (115.9 ± 4.9 and 104 ± 7.4 d, respectively). In conclusion, PVD significantly increased the CCP in all cows, but to a greater extent in cows with a high milk yield in the lactation before disease diagnosis.

Background and Aims Perennial grasses are a global resource as forage, and for alternative uses in bioenergy and as raw materials for the processing industry. Marginal lands can be valuable for perennial biomass grass production, if perennial biomass grasses can cope with adverse abiotic environmental stresses such as drought and waterlogging. Methods In this study, two perennial grass species, reed canary grass (Phalaris arundinacea) and cocksfoot (Dactylis glomerata) were subjected to drought and waterlogging stress to study their responses for insights to improving environmental stress tolerance. Physiological responses were recorded, reference transcriptomes established and differential gene expression investigated between control and stress conditions. We applied a robust non-parametric method, RoDEO, based on rank ordering of transcripts to investigate differential gene expression. Furthermore, we extended and validated vRoDEO for comparing samples with varying sequencing depths. Key Results This allowed us to identify expressed genes under drought and waterlogging whilst using only a limited number of RNA sequencing experiments. Validating the methodology, several differentially expressed candidate genes involved in the stage 3 step-wise scheme in detoxification and degradation of xenobiotics were recovered, while several novel stress-related genes classified as of unknown function were discovered. Conclusions Reed canary grass is a species coping particularly well with flooding conditions, but this study adds novel information on how its transcriptome reacts under drought stress. We built extensive transcriptomes for the two investigated C3 species cocksfoot and reed canary grass under both extremes of water stress to provide a clear comparison amongst the two species to broaden our horizon for comparative studies, but further confirmation of the data would be ideal to obtain a more detailed picture.

Control of septoria tritici blotch in Irish winter wheat crops has been reliant on the application of azoles fungicides for over a decade. The resulting intensive applications of azole fungicides have placed the Irish Zymoseptoria tritici populations under immense pressures to adapt. Evidence of this adaptation is observed in the decreasing sensitivity of the Irish population to the azole fungicide epoxiconazole, where the mean sensitivity has decreased almost 16x over the period 2006–2015. This decrease in sensitivity has occurred in a stepwise manner, with the sensitive proportion of the population being gradually replaced by those more resistant. The decrease in sensitivity was also accompanied by an increase in frequency of Z. tritici strains with an insert (120, 862 or 866 bp) in their CYP51 promoter region. Neither the 862 bp nor 866 bp inserts impacted the expression of CYP51 in either absence or presence of epoxiconcazole. Sequencing of the CYP51 gene in a sub-sample of the 2015 collection identified 25 different CYP51 haplotypes, the majority of which combined previously identified mutations, including V136A, I381V and S524 T. The presence of the 862 or 866 bp insert in the different strains, whilst not exclusive was strongly associated with specific CYP51 haplotypes. This was also reflected in their sensitivity to a range of azoles, most notably metconazole and tebuconazole. Strains with inserts in their MFS1 gene promoter region and identical in size to those known confer multiple drug resistance (MDR) phenotypes were also identified in the 2015 sub-collection. Although the frequencies of strains with those inserts known to confer moderate-high levels of MDR were extremely low, their presence further highlights the adaptability and continued erosion of azole sensitivity in the Irish Z. tritici population.

Festulolium are hybrids between species within the Lolium and Festuca genera. They are attractive candidates for hybridisation due to their complementary characteristics in the context of forage production and environmental challenges, with Lolium exhibiting greater digestibility and Festuca possessing superior resilience to abiotic stress. To establish the extent of the representation of these characteristics in different Festulolium hybrids, a five-year field experiment was undertaken in a mild Atlantic climate. Four alternative species combinations and six pure species (controls) were evaluated for dry matter yield and persistency from 2014 to 2018, and various nutritional parameters in the first silage cut were measured from 2015 to 2017. Festulolium hybrids derived from L. multiflorum were found to group with both Lolium and Festuca pure species for a mean ground score to evaluate persistency (P < 0.05). Hybrid types of the L. perenne lineage were found to have ground score values more alike to their Lolium component and distinct from the F. pratensis pure species. In terms of dry matter yield, the majority of L. multiflorum hybrids observed formed a higher yielding group with the tetraploid L. multiflorum pure species and distinct from diploid F. pratensis pure species, whereas all other hybrid types and controls shared groups in common. For the nutrient content parameters including dry matter digestibility, water soluble sugars, and buffering capacity, Lolium pure species exhibited more favourable values, whereas hybrids were largely found to display intermediate to low values. Festuca pure species consistently exhibited poorer values with the exception of crude protein content where F. pratensis displayed the highest values and also the 2017 measurement of buffering capacity. In conclusion, the Festulolium hybrids shared characteristics with both parental types, but they often showed a greater likeness to the Lolium component.

Binary grass-clover and multi-species swards can increase herbage yields or facilitate reduced inputs of inorganic fertiliser nitrogen (N) compared with perennial ryegrass monocultures. However, the efficiency of the ensilage process and the nutritive value of silage produced from multi-species swards has not been documented. Replicate samples from grass-red clover binary mixture and multi-species mixture swards were ensiled in laboratory silos to assess the ensilability, fermentation characteristics, conservation losses and silage nutritive value compared with grass monocultures produced using inorganic N fertiliser. The results suggest that assessment of the ensilability and subsequent ensilage characteristics of binary and multi-species mixtures should be based on direct sampling from such mixtures rather than being predicted from values obtained from monocultures of constituent species. Under favourable ensiling conditions, unwilted binary mixtures and multi-species mixtures are satisfactorily preserved as silage, comparable to a perennial ryegrass monoculture receiving inorganic N fertiliser. However, when ensiled under more challenging crop conditions the mixtures exhibited a greater requirement for their preservation to be aided, compared with the perennial ryegrass monoculture. Despite the application of inorganic N reducing the legume content of multi-species mixture swards, it had relatively little effect on herbage ensilability or silage preservation. For all species treatments, silage nutritive values were primarily dependent on the pre-ensiling values, although herbage digestibility values declined during ensilage where the ensilage process was inefficient. The current study suggests that in order to be satisfactorily preserved as silage, binary grass-clover and multi-species swards have a greater requirement for an adequate rapid field wilt and/or effective preservative application compared with perennial ryegrass produced using inorganic fertiliser N.

Binary- and multi-species sown mixtures may increase herbage yield and/or reduce inorganic nitrogen (N) requirement compared to perennial ryegrass (PRG) (Lolium perenne L.) swards. A split-plot design was used to compare yields of binary- and multi-species mixtures to single-species swards of three grasses and red clover managed for intensive silage production under varying N application rates. Perennial and Italian (Lolium multiflorum Lam.) ryegrasses had greater annual yields when grown as single species receiving 360 kg N/ha per year than in binary mixtures with red clover (Trifolium pratense L.) receiving 0 kg N/ha per year, whereas timothy (Phleum pratense L.) produced equally high yields in both situations. When no inorganic N was applied, the annual dry matter yield of Mix 1 (10,738 kg/ha; PRG, timothy, red clover and white clover (Trifolium repens L.) and Mix 2 (11,679 kg/ha; PRG, timothy, red clover, ribwort plantain (Plantago lanceolata L.) and chicory (Cichorium intybus L.)) was greater than that of a PRG sward (PRG/0N; 5,885 kg/ha) and derived more from the contribution of legumes than herbs. This yield advantage of mixtures declined as inorganic N input increased, as did the legume and herb proportions in the multi-species swards. When averaged across rates of inorganic N input, Mix 2 had a greater annual yield than Mix 1 (12,464 vs. 11,893 kg/ha). Mix 2 receiving no inorganic fertiliser N and both Mix 1 and Mix 2 receiving 120 kg N/ha per year matched the annual yield achieved by PRG receiving 360 kg N/ha per year. Our results indicate that the yield performance of binary- and multi-species grassland swards should be measured in situ rather than predicted from single-species swards of constituent species.

The environmental loss of nitrogen in agricultural landscapes has pervasive consequences, including human health implications, eutrophication, loss of habitat biodiversity and greenhouse gas emissions. The efficacy of mitigation strategies designed to control or prevent nitrate contamination of waterbodies requires an understanding of catchment scale pressures and processes. Groundwater and stream nitrate concentrations fluctuate over temporal scales ranging from the daily to the decadal. Identifying spatiotemporal trends and dominant drivers of nitrate in water is challenging as the drivers are intertwined. The effects of agronomic, meteorological and hydrogeological drivers on groundwater and stream nitrate were investigated over seven years in two well-drained agricultural catchments, dominated by tillage and grassland farming, respectively. A significant positive temporal trend in nitrate concentration was observed in the tillage catchment, whereas no long-term trend was observed in the grassland catchment. Agronomic, meteorological and hydrogeological factors were significantly related to temporal nitrate changes across both catchments. Clearly identifying the drivers influencing temporal changes in nitrate concentrations is critical to improving water quality. The study highlighted that to reduce groundwater nitrate levels in areas of high risk (thin soils, low clay content and shallow groundwater), nitrogen applications need to be reduced and/or tailored, particularly at times of restricted crop growth.

We investigated how protein quantity (10%-30%) and quality (casein and whey) interact with dietary fat (20%-55%) to affect metabolic health in adult mice. Although dietary fat was the main driver of body weight gain and individual tissue weight, high (30%) casein intake accentuated and high whey intake reduced the negative metabolic aspects of high fat. Jejunum and liver transcriptomics revealed increased intestinal permeability, low-grade inflammation, altered lipid metabolism, and liver dysfunction in casein-fed but not whey-fed animals. These differential effects were accompanied by altered gut size and microbial functions related to amino acid degradation and lipid metabolism. Fecal microbiota transfer confirmed that the casein microbiota increases and the whey microbiota impedes weight gain. These data show that the effects of dietary fat on weight gain and tissue partitioning are further influenced by the quantity and quality of the associated protein, primarily via effects on the microbiota.

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.

Background Miscanthus is a commercial lignocellulosic biomass crop owing to its high biomass productivity, resilience and photosynthetic capacity at low temperature. These qualities make Miscanthus a particularly good candidate for temperate marginal land, where yields can be limited by insufficient or excessive water supply. Differences in response to water stress have been observed among Miscanthus species, which correlated to origin. In this study, we compared the physiological and molecular responses among Miscanthus species under excessive (flooded) and insufficient (drought) water supply in glasshouse conditions. Results A significant biomass loss was observed under drought conditions in all genotypes. M. x giganteus showed a lower reduction in biomass yield under drought conditions compared to the control than the other species. Under flooded conditions, biomass yield was as good as or better than control conditions in all species. 4389 of the 67,789 genes (6.4%) in the reference genome were differentially expressed during drought among four Miscanthus genotypes from different species. We observed the same biological processes were regulated across Miscanthus species during drought stress despite the DEGs being not similar. Upregulated differentially expressed genes were significantly involved in sucrose and starch metabolism, redox, and water and glycerol homeostasis and channel activity. Multiple copies of the starch metabolic enzymes BAM and waxy GBSS-I were strongly up-regulated in drought stress in all Miscanthus genotypes, and 12 aquaporins (PIP1, PIP2 and NIP2) were also up-regulated in drought stress across genotypes. Conclusions Different phenotypic responses were observed during drought stress among Miscanthus genotypes from different species, supporting differences in genetic adaption. The low number of DEGs and higher biomass yield in flooded conditions supported Miscanthus use in flooded land. The molecular processes regulated during drought were shared among Miscanthus species and consistent with functional categories known to be critical during drought stress in model organisms. However, differences in the regulated genes, likely associated with ploidy and heterosis, highlighted the value of exploring its diversity for breeding.

Intensification of the food production system to meet increased global demand for food has led to veterinary pharmaceuticals becoming a critical component in animal husbandry. Anticoccidials are a group of veterinary products used to control coccidiosis in food-producing animals, with primary prophylactic use in poultry production. Excretion in manure and subsequent land-spreading provides a potential pathway to groundwater. Information on the fate and occurrence of these compounds in groundwater is scant, therefore these substances are potential emerging organic contaminants of concern. A study was carried out to investigate the occurrence of anticoccidial compounds in groundwater throughout the Republic of Ireland. Twenty-six anticoccidials (6 ionophores and 20 synthetic anticoccidials) were analysed at 109 sites (63 boreholes and 46 springs) during November and December 2018. Sites were categorised and selected based on the following source and pathway factors: (a) the presence/absence of poultry activity (b) predominant aquifer category and (c) predominant groundwater vulnerability, within the zone of contribution (ZOC) for each site. Seven anticoccidials, including four ionophores (lasalocid, monensin, narasin and salinomycin) and three synthetic anticoccidials (amprolium, diclazuril and nicarbazin), were detected at 24% of sites at concentrations ranging from 1 to 386 ng L−1. Monensin and amprolium were the two most frequently detected compounds, detected at 15% and 7% of sites, respectively. Multivariate statistical analysis has shown that source factors are the most significant drivers of the occurrence of anticoccidials, with no definitive relationships between occurrence and pathway factors. The study found that the detection of anticoccidial compounds is 6.5 times more likely when poultry activity is present within the ZOC of a sampling point, compared to the absence of poultry activity. This work presents the first detections of these contaminants in Irish groundwater and it contributes to broadening our understanding of the environmental occurrence and fate of anticoccidial veterinary products.

This paper describes a 3D finite element (FE) model developed to understand the dynamic response of a ballasted track in which the underlying capping layer is reinforced using recycled rubber tires. Track deflection, the lateral spreading of ballast and vertical stress transmitted from the capping layer to the subgrade are discussed by considering the effect of reinforcement provided by these infilled tires. In this respect, the capping layer is confined and has improved damping properties. The cellular structure of the rubber tire assembly can radially confine the infilled materials, and thus reduce excessive lateral spreading and vertical displacement that would otherwise occur in a conventional track. At the same time the tire and gravel composite layer acts like a stiff but flexible “mattress” that controls the stress transmitted to the underlying subgrade while making it more uniform. Typical soft and stiff subgrade materials were used to investigate the dynamic response of track, and the stress paths of subgrade at different depths have been studied. It is noted that the effect of the tire assembly on the stress distribution within the subgrade decreases with depth, and the tire-reinforced track deflects less than its unreinforced counterpart at any given train speed.

The nutritive value of sown binary- and multi-species grassland mixtures may differ from the values expected based on single-species swards of their constituent species. Field plots were established in a split-plot design to assess the nutritive value of binary- and multi-species mixtures compared to single-species swards of three grass species and red clover (RC) (Trifolium pratense L.) managed for intensive silage production. The nutritive value of grass–legume binary mixtures reflected the values of the constituent species grown on their own, and thus may be predicted from monoculture values. The relatively low digestibility (dry matter digestibility [DMD]) and crude protein (CP) content of the Italian ryegrass (Lolium multiflorum L.) sward compared to perennial ryegrass (Lolium perenne L.) and timothy (Phleum pratense L.) suggests that it may have a limited role in binary- or multi-species swards. Herbage nutritive value in the multi-species swards (Mix 1: perennial ryegrass, timothy, RC and white clover [Trifolium repens L.]; Mix 2: perennial ryegrass, timothy, RC, ribwort plantain [Plantago lanceolata L.] and chicory [Cichorium intybus L.]) appeared to be influenced more by the presence of legumes than herbs. Compared to perennial ryegrass, the multi-species swards had a slower rate of DMD decline prior to Cut 1, but subsequently had lower DMD values at the mid-season harvests. Both multi-species mixtures exhibited DMD, water-soluble carbohydrate (WSC) and CP values that would not have been predicted from their constituent species and thus need to be measured on herbage from field plots growing these mixtures.

Co-digestion of forage silage with cattle slurry can greatly extend the stability of methanogenesis as compared to mono-digestion of the silage. Biogas and methane yields of the mixtures of perennial ryegrass silage (grass harvested at two growth stages i.e. stem elongation vs. floral development) with cattle slurry and of red clover silage (clover harvested at two growth stages i.e. mid-vegetative vs. early seed-pod development) with cattle slurry were measured, and synergistic effects were investigated. Silage and slurry were incubated as sole substrates or as part of binary mixtures (forage silage:cattle slurry ratios of 1:0, 0.75:0.25, 0.5:0.5, 0.25:0.75 and 0:1 on a volatile solid basis). The maximum measured synergistic effects for perennial ryegrass silages with cattle slurry and red clover silages with cattle slurry were observed at 0.75:0.25 and 0.5:0.5 (forage silge:cattle slurry), respectively. The forage silage:cattle slurry ratio to produce the maximum synergistic effects differed with the forage species ensiled and its growth stage when harvested.

Anaerobic co-digestion of contrasting substrates can result in synergistic or antagonistic effects on methanogenesis. Biogas and methane yields of the mixtures of cattle slurry (CS1 and CS2) or pig slurry with grass silages (GS1 and GS2) were measured using in vitro anaerobic batch digesters, and synergistic and antagonistic effects were investigated. Slurries and silages were incubated as individual substrates or as part of binary mixtures (slurry:silage mass ratios of volatile solids (VS) of 1:0, 0.75:0.25, 0.5:0.5, 0.75:0.25 and 0:1). The biogas yields of CS1, CS2, pig slurry, GS1 and GS2 were 405.9, 380.4, 550.8, 673.7 and 610.6 L kg−1 of VS, respectively while the corresponding methane yields were 269.1, 246.4, 380.1, 427.7 and 359.0 L kg−1 of VS. The sequential replacement of either cattle slurry by either grass silage caused a progressive increase in biogas and methane yields, but there was not as clear-cut increase when pig slurry was replaced by grass silages. The methane yield for slurry and silage mixtures displayed non-linear blending and the maximum effect, which was always antagonistic, was at a 0.5:0.5 mass ratio of VS, and ranged from 5.7-7.6 % below the yields predicted from mono-digestion of individual substrates.

Nitrate (NO3−) leaching and nitrous oxide (N2O) emission from urine patches in grazed pastures are key sources of water and air pollution, respectively. Broadcast spraying of the nitrification inhibitor dicyandiamide (DCD) has been shown to reduce these losses, but it is expensive. As an alternative, it had been demonstrated that feeding DCD to cattle (after manual mixing with supplementary feeds) was a practical, effective and cheaper method to deliver high DCD rates within urine patches. This two-year study carried out on simulated urine patches in three application seasons (spring, summer, autumn) explored the efficacy of DCD feeding to cattle to reduce N losses from grazed pasture soil in a heavy-textured soil under temperate climatic conditions. In each application season, DCD fed to cows, then excreted with urine and applied at a rate of 30 kg DCD ha− 1 (treatment U + DCD30-f) was as effective as powdered DCD mixed with normal urine and applied at the same rate (treatment U + DCD30) at reducing cumulative N2O-N emissions and the N2O-N emission factor (EF3, expressed as % of N applied). Increasing DCD loading within urine patches from 10 to 30 kg DCD ha− 1 improved efficacy by significantly reducing the EF3 from 34% to 64%, which highlights that under local conditions, 10 kg DCD ha− 1 (the recommended rate for commercial use in New Zealand) was not the optimum DCD rate to curb N2O emissions. The modelling of EF3 in this study also suggests that N mitigation should be given more attention when soil moisture is going to be high, which can be predicted with short-term weather forecasting. DCD feeding, for instance in autumn when cows are not lactating and the risk of N losses is high, could then be reduced by focusing mainly on those forecasted wet periods.

The aims were to quantify the effects of applying fibrolytic enzymes at ensiling on conservation characteristics and specific methane (CH4) yields (SMY) per unit mass, and per unit land area. At two stages of primary growth, four replicate plots of two species (perennial ryegrass and timothy) were subjected to nine treatments, an untreated control and four fibrolytic enzymes (ENZ 1–4) applied at two enzyme dosage rates (low and high) prior to ensiling. Silage SMYs were subsequently determined in an in vitro batch anaerobic digestion test. Generally, applying fibrolytic enzymes at ensiling reduced total fibre compared to control silages, which consequently enhanced mass-SMY and area-SMY. However, the impact on fibre, mass-SMY and area-SMY differed depending on both grass species and growth stage at harvest, with no single enzyme being consistently superior. Thus the potential of enhanced methane output with added enzymes at ensiling is both fibrolytic enzyme and grass substrate specific.

Grazed pastures contribute significantly to anthropogenic emissions of N2O but the respective contributions of archaea, bacteria and fungi to codenitrification in such systems is unresolved. This study examined the relative contributions of bacteria and fungi to rates of denitrification and codenitrification under a simulated ruminant urine event. It was hypothesised that fungi would be primarily responsible for both codenitrification and total N2O and N2 emissions. The effects of bacterial (streptomycin), fungal (cycloheximide), and combined inhibitor treatments were measured in a laboratory mesocosm experiment, on soil that had received 15N labelled urea. Soil inorganic-N concentrations, N2O and N2 gas fluxes were measured over 51 days. On Days 42 and 51, when nitrification was actively proceeding in the positive control, the inhibitor treatments inhibited nitrification as evidenced by increased soil NH 4 + -N concentrations and decreased soil NO 2 − -N and NO 3 − -N concentrations. Codenitrification was observed to contribute to total fluxes of both N2O (≥ 33%) and N2 (≥ 3%) in urine-amended grassland soils. Cycloheximide inhibition decreased NH 4 + –15N enrichment and reduced N2O fluxes while reducing the contribution of codenitrification to total N2O fluxes by ≥ 66 and ≥ 42%, respectively. Thus, given archaea do not respond to significant urea deposition, it is proposed that fungi, not bacteria, dominated total N2O fluxes, and the codenitrification N2O fluxes, from a simulated urine amended pasture soil.

I sought to expose and challenge neocolonial values and practices in a Western institution through an Indigenous woman’s nuanced and detailed experience of paternalism, racism, and exploitation. Th...

This study aimed to provide new insights into the epidemiology of Salmonella in pig production, focusing on potential shedding patterns in breeding pigs throughout a full production cycle and the risk of transmission of infection from the sow to her offspring. A longitudinal study was conducted on five farrow-to-finish commercial pig farms. In each herd, shedding of Salmonella in faeces was monitored in breeders through service, gestation and lactation. Swabs of the farrowing room floor and pools of faeces from piglets were collected on two occasions during lactation. Environmental pen swabs were also taken in the weaning and finisher houses. Salmonella isolates were serotyped, tested for antimicrobial resistance (AMR) and typed by Multiple-Locus Variable number tandem repeat Analysis (MLVA). Shedding by breeding pigs was low in all stages of the production cycle; 5% of sows shed at service, the production stage with highest risk of shedding (p

peer-reviewed At the catchment scale, a complex mosaic of environmental, hydrogeological and physicochemical characteristics combine to regulate the distribution of groundwater and stream nitrate (NO3−). The efficiency of NO3− removal (via denitrification) versus the ratio of accumulated reaction products, dinitrogen (excess N2) & nitrous oxide (N2O), remains poorly understood. Groundwater was investigated in two well drained agricultural catchments (10 km2) in Ireland with contrasting subsurface lithologies (sandstone vs. slate) and landuse. Denitrification capacity was assessed by measuring concentration and distribution patterns of nitrogen (N) species, aquifer hydrogeochemistry, stable isotope signatures and aquifer hydraulic properties. A hierarchy of scale whereby physical factors including agronomy, water table elevation and permeability determined the hydrogeochemical signature of the aquifers was observed. This hydrogeochemical signature acted as the dominant control on denitrification reaction progress. High permeability, aerobic conditions and a lack of bacterial energy sources in the slate catchment resulted in low denitrification reaction progress (0–32%), high NO3− and comparatively low N2O emission factors (EF5g1). In the sandstone catchment denitrification progress ranged from 4 to 94% and was highly dependent on permeability, water table elevation, dissolved oxygen concentration solid phase bacterial energy sources. Denitrification of NO3 − to N2 occurred in anaerobic conditions, while at intermediate dissolved oxygen; N2O was the dominant reaction product. EF5g1 (mean: 0.0018) in the denitrifying sandstone catchment was 32% less than the IPCC default. The denitrification observations across catchments were supported by stable isotope signatures. Stream NO3− occurrence was 32% lower in the sandstone catchment even though N loading was substantially higher than the slate catchment. Teagasc Walsh Fellowship Programme

Water misting/showers are used in abattoir lairages to improve meat quality, and to cool and calm pigs after transport and during hot weather. One novel approach, which has not been investigated to date, is to add a disinfectant to the misting water as a means of topically reducing Salmonella on pigs prior to slaughter, thereby potentially controlling this organism in the abattoir. The objective of this study was therefore to evaluate misting with water or with Virkon® S (an approved disinfectant for use in the presence of animals), for their ability to topically reduce Salmonella on high seroprevalence pig herds before stunning and to reduce Enterobacteriaceae. Three experimental groups were investigated: control group (i.e., no misting); water group (misting with cold, 15–17 °C, water, herein referred to as water); and a disinfectant group (misting with 0.5% Virkon® S). As pigs entered the abattoir, each animal was swabbed along its back before being allocated to its experimental group. Each group was randomly assigned to one of 3 lairage pens that were separated by non-trial pens. After 30 min of misting with water or disinfectant, pigs were moved to the stunning area, where each pig was again swabbed, as above. Swabs were analyzed for the presence of Salmonella and enumeration of Enterobacteriaceae. Before misting, Salmonella prevalence on the pigs was 79.0%, 72.1% and 83.6% for the control, water and disinfectant groups, respectively. After misting, Salmonella prevalence increased to 94.3% in the water group; whereas for the disinfectant group, the prevalence increased marginally to 85.9%. No change in Salmonella prevalence was detected for the control group. In line with the Salmonella results, no significant differences were observed in Enterobacteriaceae counts in the control group at either time point (4.37 and 5.01 log10 CFU/cm2, respectively) or in the disinfectant group before and after misting (4.02 and 4.26 log10 CFU/cm2, respectively). However, a 2.3 log10 CFU/cm2 increase in Enterobacteriaceae was recorded for the water group after misting as compared to before misting (p Since misting with water alone increased topical Salmonella contamination on pigs before slaughter, a risk assessment based on known Salmonella data, meat quality and welfare is recommended to determine whether its use is justifiable. On the other hand, the findings from this study suggest that misting with Virkon® S at 0.5% could have a role in topical antisepsis of pigs contaminated with Salmonella prior to slaughter and as such this warrants further investigation.

This study investigated several cleaning and disinfection protocols for their ability to eliminate Salmonella and to reduce levels of Enterobacteriaceae, within the lairage pens of a commercial pig abattoir. Eight protocols were evaluated in each of 12 lairage pens at the end of the slaughtering day on 3 occasions (36 pens/protocol): (P1) high-pressure cold water wash (herein referred to as high-pressure wash); (P2) high-pressure wash followed by a quaternary ammonium compound (QAC)-based disinfectant without rinsing; (P3) high-pressure wash followed by a chlorocresol-based disinfectant without rinsing; (P4) high-pressure wash followed by a sodium hydroxide/sodium hypochlorite detergent with rinsing; (P5) P4 followed by P2; (P6) P4 followed by P3; (P7) P5 with drying for 24-48h; and (P8) P6 with drying for 24-48h. Two floor swabs and one wall swab were taken from each lairage pen before and after each protocol was applied, and examined for the presence of Salmonella and enumeration of Enterobacteriaceae. High-pressure washing alone (P1) did not reduce the prevalence of Salmonella in the lairage pens. When high-pressure washing, the probability of detecting Salmonella following application of the chlorocresol-based disinfectant (P3) was lower than with the QAC-based disinfectant, P2 (14.2% versus 34.0%, respectively; p

Staphylococcus aureus is an important cause of bovine mastitis, and intramammary infections caused by this pathogen are often characterized as mild, chronic, or persistent. The strains of Staph. aureus associated with mastitis belong to several distinct bovine-adapted bacterial lineages. Studies of host-pathogen interactions have demonstrated that significant differences exist between Staph. aureus strains and lineages in their ability to internalize and to elicit expression of chemokines and pro-inflammatory mediators in bovine cells in vitro. To determine the effect of bacterial strain on the response to intramammary infection in vivo, 14 disease-free, first-lactation cows were randomly allocated to 2 groups and challenged with Staph. aureus strain MOK023 (belonging to CC97) or MOK124 (belonging to CC151). Clinical signs of infection, as well as somatic cell count (SCC), bacterial load, IL-8 and IL-1β in milk, anti-Staph. aureus IgG in milk and serum, anti-Staph. aureus IgA in milk, and white blood cell populations in milk and blood were monitored for 30 d after the challenge. Cows infected with MOK023 generally developed subclinical mastitis, whereas cows infected with MOK124 generally developed clinical mastitis. Milk yield was reduced to a greater extent in response to infection with MOK124 compared with MOK023 in the first week of the study. Significantly higher SCC, IL-8, and IL-1β in milk as well as higher anti-Staph. aureus IgG and IgA in milk and anti-Staph. aureus IgG in serum were also observed in response to MOK124 compared with the response to MOK023. Higher proportions of neutrophils were observed in milk of animals infected with MOK124 than in animals infected with MOK023. Higher neutrophil concentration in blood was also observed in the MOK124 group compared with the MOK023 group. Overall, the results indicate that the outcome of mastitis mediated by Staph. aureus is strain dependent.

Nitrate (NO3−) leaching and nitrous oxide (N2O) emission from urine patches in grazed pastures are key sources of water and air pollution, respectively. Numerous studies have demonstrated that broadcast application of the nitrification inhibitor dicyandiamide (DCD) can abate such losses of reactive nitrogen (N). This research explored an alternative usage of DCD. It is the first field study that investigates the feeding of powdered DCD mixed with several typical cattle feeds as a practical and effective method to deliver a nitrification inhibitor to urine patches. DCD (in its dry powdered form) was manually mixed with three typical dairy cow feed types (barley concentrate, maize silage or grass silage) before being fed to the cattle in a Latin Square design experiment. DCD delivery to the small area covered by urine patches during grazing events was then measured as a DCD equivalent application rate (in kg DCD ha−1). The absence of a significant feed type effect (P > 0.1) on the urine patch DCD equivalent application rate suggests that the ingestion of any of the three supplementary feeds mixed with DCD should be similarly effective at delivering DCD to urine patches, despite the potential differences in aspects of feed digestibility and the impact on rumen pH and rate of DCD passage through the rumen. Importantly, there was a highly significant positive relationship (P ≤ 0.0001) between excreted DCD and N in urine and urine patches, which meant that the deposition rate of DCD matched the urinary N inputs in urine patches. Additionally, less total DCD was needed than is required with broadcast application. Added to the fact that DCD and urinary N are both deposited at the same time and intimately mixed in urine patches, feeding DCD to dairy cows after mixing with different feeds could represent a more effective and practical DCD application strategy than a DCD broadcast application at a single rate.

Pork is an important source of human salmonellosis and low-cost on-farm control measures may provide a useful element in reducing the prevalence of this pathogen in food. This study investigated the effectiveness of dietary supplementation with sodium butyrate administered to finisher pigs for ∼4-weeks prior to slaughter to control Salmonella shedding on highly contaminated farms. Two trials (A and B) were conducted on two commercial pig farms, which had a history of high Salmonella seroprevalence. In both trials, pens (14 pens of 12 pigs/pen in Trial A and 12 pens of 12-17 pigs/pen in Trial B) were randomly assigned to a control (finisher feed without additive) or a treatment group (the same feed with 3kg sodium butyrate/t) for 24-28days, depending on the trial. Faeces were collected from each pig on days 0, 12 and 24/28, and blood, caecal digesta and ileocaecal/mesenteric lymph nodes were collected from the slaughterhouse. Pigs were weighed at the start and end of the trials, feed intake was recorded, and carcass quality parameters were recorded at slaughter. In Trial A, Salmonella shedding was reduced in the treatment compared to the control group at the end of the trial (30% versus 57% probability of detecting Salmonella in faeces, respectively; p0.001). This reflected the serology results, with detection of a lower seroprevalence in the treatment compared to the control group using the 20% optical density cut-off (69.5% versus 89%; p=0.001). However, no effect on faecal shedding or seroprevalance was observed in Trial B, which may be explained by the detection of a concomitant infection with Lawsonia intracellularis. No significant differences in Salmonella recovery rates were observed in the caecal digesta or lymph nodes in either trial. Furthermore, feed intake, weight gain, and feed conversion efficiency (FCE) did not differ between groups (p0.05) in either trial. Numerical improvements in weight gain and FCE were found with sodium butyrate treatment, which gave a cost benefit of €0.04/kg of live-weight gain. Overall, results suggest that strategic feeding of sodium butyrate, at 3kg/t of feed, to finishing pigs for 24-28days prior to slaughter was effective in reducing Salmonella shedding and seroprevalance but perhaps only in the absence of co-infection with other pathogens. However, sodium butyrate supplementation at this rate did not influence intestinal carriage, nor did it reduce seroprevalence to below the cut-off used for the high Salmonella risk category in Ireland (50%), or significantly improve growth performance.

This six year experiment quantified the impacts of management factors on red clover yield, persistence, nutritive value and ensilability, and compared these to perennial ryegrass receiving inorganic N fertiliser. Within a randomised complete block design, field plots were used to evaluate a 2 (cultivar; Merviot and Ruttinova) x 2 (alone or with perennial ryegrass) x 2 (0 and 50 kg fertiliser N/ha in mid March) x 2 (harvest schedule) combination of factors relating to red clover, and a 2 (harvest schedule) x 4 (0, 50, 100 and 150 kg N/ha for each cut) combination of factors relating to perennial ryegrass. The Early and Late harvest schedules both involved four cuts per year but commenced a fortnight apart. Red clover treatments averaged 14,906 kg dry matter/ha per year. There was no yield decline evident across years despite a decline in the proportion of red clover. The Early harvest schedule and sowing ryegrass with red clover increased herbage yield and digestibility. March application of fertiliser N to red clover treatments reduced annual yield. Early harvest schedule increased and both fertiliser N and sowing with ryegrass decreased the proportion of red clover. Sowing with ryegrass improved indices of ensilability but reduced crude protein. Both red clover cultivars had similar performance characteristics. A selected red clover-based treatment, considered to exhibit superior overall production characteristics, out-yielded perennial ryegrass plus fertiliser N in mid-season. However, it had poorer digestibility and ensilability indices.

The survival, morphological, and growth responses of European beech (Fagus sylvatica L.) and pedunculate oak (Quercus robur L.) seedlings to different light intensities, from full sunlight to heavy shade, were studied over two growing seasons in a shadehouse experiment. Although shade treatments significantly affected seedling growth, they did not influence seedling survival. Both growth and biomass increased as light intensity increased. Diameter growth of oak seedlings was higher than that of beech. Beech and oak seedlings showed typical acclimation to shade, including greater specific leaf area and height to diameter ratios, and lower leaf thickness and root:shoot ratios with increasing shade. Beech seedlings exhibited greater specific leaf area, and lower leaf thickness and root:shoot ratios than oak seedlings. In spite of the greater growth at full sunlight, the results from this study suggest that beech and oak seedlings would have high survival rates and would acclimate well if underplanted below overstories that reduce the available light to as low as 28% of full light.

Mycotoxins are heterogeneously distributed analytes such that obtaining a representative sample of silage for analysis can be highly challenging. The objectives of this study were to: (1) identify the variability in mycotoxin concentrations, nutritional value characteristics and fermentation characteristics when 20 cores were taken from individual next-to-be-fed silage bales and five cores were taken from the next-to-be-fed section of the feed face of pit silages, (2) compare the values obtained from intensive sampling of the silage after simulated feed-out to values obtained by the above mentioned core sampling, and (3) describe the impact of reducing the number of core samples taken from the baled and pit silages. Round baled silages (n=10) or sections (2 m wide × 1 m height) of pit silages (n=10) were core sampled at twenty and five positions, respectively. After coring, baled silages were chopped, mixed and placed along a simulated feed trough. Silage in the simulated feed trough was then grab sampled (n=20) to produce an aggregate sample, and this was undertaken in triplicate. For pits, silage was mixed and placed along a simulated feed trough before being sampled, as per baled silage. Variation within or among either baled or pit silages, and for core or feed trough samples, was generally much higher for mycotoxins than for conventional chemical composition traits. Within silage (bale or pit) and among silages, variation was generally reduced when samples were collected from the feed trough, except for mycotoxins in pit silages which had higher variation in the feed trough compared with core samples. Increasing the number of core samples increased the likelihood of detecting a positive sample if present and precise estimates of the true chemical composition of the population. Representatively sampling a next-to-be-fed section or bale of silage for conventional chemical characteristics was achieved with 2-4 core samples or 1-2 feed trough samples. However, in contrast, when sampling silages for mycotoxins, collecting a representative sample using core or feed trough sampling methods sometimes required over 100 and over 20 samples, respectively.

Treated municipal sewage sludge ("biosolids") and dairy cattle slurry (DCS) may be applied to agricultural land as an organic fertiliser. This study investigates losses of nutrients in runoff water (nitrogen (N) and phosphorus (P)), metals (copper (Cu), nickel (Ni), lead (Pb), zinc (Zn), cadmium (Cd), chromium (Cr)), and microbial indicators of pollution (total and faecal coliforms) arising from the land application of four types of treated biosolids and DCS to field micro-plots at three time intervals (24, 48, 360 h) after application. Losses from biosolids-amended plots or DCS-amended plots followed a general trend of highest losses occurring during the first rainfall event and reduced losses in the subsequent events. However, with the exception of total and faecal coliforms and some metals (Ni, Cu), the greatest losses were from the DCS-amended plots. For example, average losses over the three rainfall events for dissolved reactive phosphorus and ammonium-nitrogen from DCS-amended plots were 5 and 11.2 mg L(-1), respectively, which were in excess of the losses from the biosolids plots. When compared with slurry treatments, for the parameters monitored biosolids generally do not pose a greater risk in terms of losses along the runoff pathway. This finding has important policy implications, as it shows that concern related to the reuse of biosolids as a soil fertiliser, mainly related to contaminant losses upon land application, may be unfounded.

SUMMARYIncreasing phosphorus (P) fertilizer use efficiency in grassland is desirable, since uncertainty exists over the reserves of finite phosphate rock and its future availability. This necessitates revaluation of the current P fertilizer recommendations for grassland to examine the potential to increase fertilizer P efficiency. The present paper reports results from a long-term grassland P experiment (17 years) on two sites in which annual P fertilizer application rates were 0, 15, 30 and 45 kg P/ha/year. The effect of P fertilizer rate on herbage production and mineral concentration in herbage were investigated in addition to the soil test P (Morgan's) trends and P balance over the duration of the experiment for each rate of P fertilizer. The results showed that the P response to herbage yield and P concentration was similar on both sites. The response of herbage yield to P fertilizer was limited to harvests early in the growing season. The P concentration in herbage was lower in mid-season than in spring or autumn. Annual P fertilizer applications > 30 kg P/ha/year were required to maintain soil P levels at their initial levels over the duration of the experiment.

A method was developed and validated for the simultaneous determination of 42 mycotoxins in oats. The method includes all the mycotoxins listed under Commission Regulation 1881/2006 and Commission Recommendation 165/2013, the emerging mycotoxins (beauvericin, alternariol, alternariol-methyl-ether and enniatins), and two masked metabolites, namely deoxynivalenol-3-glucoside and T-2-glucoside. The method also focuses on a wide range of analytes of toxicological interest. The sample preparation involved extraction with an aqueous acetic acid solution and acetonitrile, followed by QuEChERS with mechanically assisted vibrational shaking. No further clean-up steps were employed, and analysis was performed using ultra-high performance liquid chromatography coupled to tandem mass spectrometry (UHPLC-MS/MS). Trueness ranged between 78% and 158%, while precision ranged from 1.7% to 49.9% under within-laboratory reproducibility conditions. Beside the high degree of accuracy and sample throughput provided, the method can be applied to a large number of compounds currently not regulated, thus generating knowledge and for risk assessment purposes.

HighlightsJeev is a novel smartphone application for tracking the vaccination coverage of children.Jeev synergistically combines smartphones, QR codes, and national id cards.Jeev is scalable and power efficient. Immunization saves millions of lives against vaccine-preventable diseases. Yet, 24 million children born every year do not receive proper immunization during their first year. UNICEF and WHO have emphasized the need to strengthen the immunization surveillance and monitoring in developing countries to reduce childhood deaths. In this regard, we present a software application called Jeev to track the vaccination coverage of children in rural communities. Jeev synergistically combines the power of smartphones and the ubiquity of cellular infrastructure, QR codes, and national identification cards. We present the design of Jeev and highlight its unique features along with a detailed evaluation of its performance and power consumption using the National Immunization Survey datasets. We are in discussion with a non-profit organization in Haiti to pilot test Jeev in order to study its effectiveness and identify socio-cultural issues that may arise in a large-scale deployment.

SUMMARYGrazing season length (GSL) on grassland farms with ruminant production systems can influence farm economics, livestock disease transmission, environmental impact, milk and meat quality, and consumer choice. Bioclimatic variables are biologically meaningful climate variables that may enable predictions of the impact of future climate change on GSL on European farms. The present study investigated the spatial relationship between current GSL (months) measured by EUROSTAT on dairy, beef and sheep farms in 706, 774 and 878 regions, respectively, and bioclimatic variables. A stepwise multiple regression model revealed a highly significant association between observed GSL and bioclimatic variables across Europe. Mean GSL was positively associated with the mean temperature of the coldest quarter and isothermality, and negatively associated with precipitation in the wettest month. Extrapolating these relationships to future climate change scenarios, most European countries were predicted to have a net increase in GSL with the increase being largest (up to 2·5 months) in the north-east of Europe. However, there were also predictions of increased variability between regions and decreases in GSL of up to 1·5 months in some areas such as the west of France, the south-west of Norway and the west coast of Britain. The study quantified and mapped the potential impact of climate change on GSL for dairy, beef and sheep farms across Europe.

Application of cattle slurry to grassland can lead to gaseous losses of nitrogen (N). The dynamics of ammonia (NH 3 ) emissions are well documented, but emissions of nitrous oxide (N 2 O) and other trace gases from land application of cattle slurry, are not as well understood. Nitrification inhibitors such as dicyandiamide (DCD) help to retain soil N in the ammonium (NH 4 + ) form, which is expected to result in reduced N loss and increased N use efficiency. Emissions of methane (CH 4 ) could potentially be affected by DCD, since the enzyme ammonia monooxygenase (AMO), which DCD is thought to inhibit, can oxidise CH 4 as well as NH 3 . The objective of this study was to investigate the impacts of DCD on N 2 O and CH 4 emissions from grassland soils after slurry application. At one experimental site, Johnstown Castle (JC), County Wexford, Ireland, slurry was applied in March, June and October for two years, at a rate of 33 m 3 ha −1 , by either bandspread (BS) or splashplate (SP) application methods, with and without DCD. A second site at Hillsborough (HB), County Down, Ireland, was treated in the same way for one year only, using the SP application method. Emissions of N 2 O and CH 4 were measured using static chambers. Over the entire experiment DCD significantly reduced cumulative N 2 O emissions by 47 and 70% at both sites. Slurry spreading method had no significant effect on direct N 2 O emissions and there was no effect of DCD on CH 4 emissions throughout the experiment. Using an emission factor for indirect N 2 O emissions of 1%, modelled losses of NH 3 through volatilisation, resulted in an estimated 13 times greater indirect than direct N 2 O emissions. The results suggest that, under typical Irish field conditions, DCD can be used to decrease direct N 2 O emissions, without increasing CH 4 emissions, and bandspreading can be used as a method of decreasing NH 3 volatilisation, without increasing direct N 2 O or CH 4 emissions. Since direct N 2 O emissions were relatively small, targeting indirect N 2 O emissions through mitigation of NH 3 volatilisation and nitrate (NO 3 − ) leaching could be an effective way of decreasing total N 2 O emissions from slurry application at these sites.

It's necessary to determine risks of pollution arising from amendment of organic by-products (OBs) to energy crops. The impact of applying two OBs on the quality of overland flow (OLF) from plantations of short rotation coppiced willow was assessed. Municipal biosolids (BS) and distillery effluent (DE) were spread annually on six 0.1174 ha treatment plots at rates of 100% (W-BS100, W-DE100), 50% (W-BS50, W-DE50) and 0% (W-BS0, W-DE0). The 100% rate was the maximum load of 15 t P ha−1 as per the current Irish regulation based on crop uptake of P. Surface flows were sampled over 18 months and tested for pH, electrical conductivity, NO3−, PO43−, total P, K, Cu, Cd, Cr, Pb, Ni, and Zn. Results showed NO3−, Cu, Cd, Cr, Pb, Ni, and Zn concentrations in OLF were well below quality standard limits set out in European Union (EU) drinking water (DW) and surface water (SW) regulation. For P–PO43− and K, concentrations in OLF exceeded these limits. There were treatment responses for all OLF species, except P and Ni; in some cases there were large increases in OLF concentration as OB treatment rate increased. There was build-up in soil-P, -K and in heavy metals (HMs) following application of BS, but not distillery effluent (DE). Results suggest increased OB application could result in increased export from plots treated with OBs. Despite high PO43− and K OLF concentrations, the occurrence of OLF was rare and volumes lost from plots were low; actual exports of nutrient and HMs by this pathway were small. It was unlikely OLF streams transported particulate matter far from plots, and no preferential flow routes were available to the OLF streams. For these reasons, the OLF encountered during experiments did not pose any serious threat to the quality of nearby surface waters. Capsule Organic by-products (OBs), biosolid and distillery effluent, amended to short rotation coppice willow. Impact on quality of surface (overland) flows (OLF) assessed by analysis of nutrients and heavy metals (HMs). Evidence of export of all three major agricultural nutrients and some heavy metals. Concentrations of P and K exceeded DW regulation limits in some instances. However, small volumes and rare occurrence of OLF indicated no risk to nearby surface waters. The practice of OB amendment resulted in little risk to surface waters at these scales. If scaled up to plantation scale, in areas vulnerable to OLF, careful consideration must be made about P-loss (on a catchment scale) before amendments carried out.

The objective of this study was to determine the diagnostic value of maternal serology for the diagnosis of Salmonella Dublin bovine abortion and stillbirth. A retrospective, unmatched, case-control study was carried out using twenty year's data (1989-2009) from bovine foetal submissions to an Irish government veterinary laboratory. Cases (n = 214) were defined as submissions with a S. Dublin culture-positive foetus from a S. Dublin unvaccinated dam where results of maternal S. Dublin serology were available. Controls (n = 415) were defined as submissions where an alternative diagnosis other than S. Dublin was made in a foetus from an S. Dublin unvaccinated dam where the results of maternal S. Dublin serology were available. A logistic regression model was fitted to the data: the dichotomous dependent variable was the S. Dublin foetal culture result, and the independent variables were the maternal serum agglutination test (SAT) titre results. Salmonella serology correctly classified 87% of S. Dublin culture-positive foetuses at a predicted probability threshold of 0.44 (cut-off at which sensitivity and specificity are at a maximum, J = 0.67). The sensitivity of the SAT at the same threshold was 73.8% (95% CI: 67.4%-79.5%), and the specificity was 93.2% (95% CI: 90.3%-95.4%). The positive and negative predictive values were 84.9% (95% CI: 79.3%-88.6%) and 87.3% (95% CI: 83.5%-91.3%), respectively. This study illustrates that the use of predicted probability values, rather than the traditional arbitrary breakpoints of negative, inconclusive and positive, increases the diagnostic value of the maternal SAT. Veterinary laboratory diagnosticians and veterinary practitioners can recover from the test results, information previously categorized, particularly from those results declared to be inconclusive.

Intensively managed agricultural pastures contribute to N2O and N2 fluxes resulting in detrimental environmental outcomes and poor N use efficiency, respectively. Besides nitrification, nitrifier-denitrification and heterotrophic denitrification, alternative pathways such as codenitrification also contribute to emissions under ruminant urine-affected soil. However, information on codenitrification is sparse. The objectives of this experiment were to assess the effects of soil moisture and soil inorganic-N dynamics on the relative contributions of codenitrification and denitrification (heterotrophic denitrification) to the N2O and N2 fluxes under a simulated ruminant urine event. Repacked soil cores were treated with 15N enriched urea and maintained at near saturation (−1 kPa) or field capacity (−10 kPa). Soil inorganic-N, pH, dissolved organic carbon, N2O and N2 fluxes were measured over 63 days. Fluxes of N2, attributable to codenitrification, were at a maximum when soil nitrite (NO2−) concentrations were elevated. Cumulative codenitrification was higher (P = 0.043) at −1 kPa. However, the ratio of codenitrification to denitrification did not differ significantly with soil moisture, 25.5 ± 15.8 and 12.9 ± 4.8% (stdev) at −1 and −10 kPa, respectively. Elevated soil NO2− concentrations are shown to contribute to codenitrification, particularly at −1 kPa.

There are plans to use Irish energy crop plantations as repositories of organic by-products (OBs). It is first necessary to determine the risk of surface-water (SW) pollution from amendment of OBs to energy crops under typical Irish conditions. Therefore, the impact of application of two OBs on the quality of overland flow (OLF) emanating from plantations of Miscanthus × giganteus was assessed. Municipal biosolids (BS) and distillery effluent (DE) were spread annually (for four years) on six 0.1174 ha plots at “100%”, “50%” and “0%” treatment rates. The 100% rate was the maximum P-load of 15 t ha−1 allowed by regulation. Surface flows were sampled over 25 months and tested for pH, electrical conductivity, NO3−, P, K, Cu, Cd, Cr, Pb, Ni, and Zn. Results were compared to drinking-water (DW) and SW quality limits; total exports were used to assess risk to SW. The concentrations of nitrate and heavy metals were within DW limits. Concentrations of PO43− were above limits in all cases; K in OLF from M-DEx plots was above DW limits (in some cases). Despite high concentrations, all exports were relatively small, as OLF events were rare and involved small volumes. There was correlation between OB treatment and increases in OLF concentration in some cases, implying higher applications could result in larger exports. Results imply very low SW quality risks exist in areas that are not prone to OLF (at treatment rates and plot scales used). It is recommended further work is conducted to assess risks at catchment scales, particularly for P-loss.

SUMMARYMineralized soil nitrogen (N) is an important source of N for grassland production. Some soils can supply large quantities of plant-available N through mineralization of soil organic matter. Grass grown on such soils require less fertilizer N applications per unit yield. A reliable, accurate and user-friendly method to account for soil N supply potential across a large diversity of soils and growing conditions is needed to improve N management and N recommendations over time. In the current study, the effectiveness of chemical N tests and soil properties to predict soil N supply for grass uptake across 30 Irish soil types varying in N supply potential was investigated under controlled environmental conditions. The Illinois soil N test (ISNT) combined with soil C : N ratio provided a good estimate of soil N supply in soils with low residual mineral N. Total oxidized N (TON) had the largest impact on grass dry matter (DM) yield and N uptake across the 30 soil types, declining in its influence in later growth periods. This reflected the high initial mineral N levels in these soils, which declined over time. In the current study, a model with ISNT-N, C : N and TON (log TON) best explained variability in grass DM yield and N uptake. All three rapid chemical soil tests could be performed routinely on field samples to provide an estimate of soil N supply prior to making N fertilizer application decisions. It can be concluded that these soil tests, through their assessment of soil N supply potential, can be effective tools for N management on grassland; however, field studies are needed to evaluate this under more diverse growing conditions.

SUMMARYNitrification inhibitors are used in agriculture for the purpose of decreasing nitrogen (N) losses, by limiting the microbially mediated oxidation of ammonium (NH4+) to nitrate (NO3−). Successful inhibition of nitrification has been shown in numerous studies, but the extent to which inhibitors affect other N transformations in soil is largely unknown. In the present study, cattle slurry was applied to microcosms of three different grassland soils, with or without the nitrification inhibitor dicyandiamide (DCD). A solution containing NH4+and NO3−, labelled with15N either on the NH4+or the NO3−part, was mixed with the slurry before application. Gross N transformation rates were estimated using a15N tracing model. In all three soils, DCD significantly inhibited gross autotrophic nitrification, by 79–90%. Gross mineralization of recalcitrant organic N increased significantly with DCD addition in two soils, whereas gross heterotrophic nitrification from the same pool decreased with DCD addition in two soils. Fungal to bacterial ratios were not significantly affected by DCD addition. Total gross mineralization and immobilization increased significantly across the three soils when DCD was used, which suggests that DCD can cause non-target effects on soil N mineralization–immobilization turnover.

Phenotyping of genetic resources remains the bottleneck in the characterization of genetic resources, since the advent of modern next-generation sequencing technologies has made genotyping much more cost- and time-effective. This article reports on the phenotyping of agriculturally important traits in perennial ryegrass (Lolium perenne). In the present study, water-soluble carbohydrate (WSC), crude protein and dry matter contents were recorded for 1320 individuals, pooled into 132 samples from 33 perennial ryegrass ecotypes and cultivars at five different harvest time points across the 2004 growing season. While, in general, the cultivars had higher WSC contents than the ecotypes, individual ecotypes did show potential to be used in breeding programmes, as they had higher values than all other accessions at particular cutting time points. In correlation analyses, positive relationships were observed between dry matter and glucose contents both early and late in the growing season. Principal components analysis allowed the split either between cultivars and ecotypes or between tetraploid cultivars and the rest of the accessions at four of the five cutting time points. In the analysis of variance, cutting time was the most significant factor influencing the variation in traits.

Simple Summary Mortality of full-term calves at calving is an increasing problem in dairy industries internationally. Multiple herd management factors contribute to such losses. This case-control study identified factors which differed between herds with high and low calf mortality. These included breeding, dietary, health and calving factors. It was concluded that calving, not pre-calving, management appears to be the most important area of concern in herds with high perinatal mortality. This indicates that farmers and their veterinarians need to focus on calving management when investigating such problems and when attempting to reduce losses in herds with high rates of bovine perinatal mortality. Abstract Bovine perinatal mortality is an increasing problem in dairy industries internationally. The objective of this study was to determine the risk factors associated with high and low herd-level calf mortality. Thirty herds with a history of either high (case) or low (control) calf mortality were recruited. A herd-level questionnaire was used to gather information on management practices likely to impact bovine perinatal mortality. The questionnaire was divided into four subsections dealing with pre-calving (breeding, diet and body condition score, endemic infectious diseases) and calving factors. Most of the significant differences between case and control herds were found in calving management. For example, in case herds, pregnant cattle were less likely to be moved to the calving unit two or more days and more likely to be moved less than 12 hours pre-calving, they were also less likely to calve in group-calving facilities and their calves were more likely to receive intranasal or hypothermal resuscitation. These management procedures may cause social isolation and periparturient psychogenic uterine atony leading to dystocia, more weak calves requiring resuscitation and high perinatal calf mortality. The key finding is that calving, not pre-calving, management appears to be the most important area of concern in herds with high perinatal mortality.

The impact of landspreading organic byproduct (OB) on the quality of groundwater (GW) and soil underlying short rotation coppiced willow plantations was assessed. Organic byproduct, namely biosolid (BS) and distillery effluent (DE), was spread on six plots (each with a plot area of 0.059 ha) at OB treatment-rates of 100%, 50% and 0%. The OB treatment rate was defined by the maximum permissible soil-P load defined in Irish regulation. Groundwater was sampled each month and tested for pH, electrical conductivity (EC), NO3, PO43, total soluble phosphorous (TSP), K and six heavy metals (HMs) Cu, Cd, Cr, Pb, Ni, and Zn. Results were assessed in relation to Irish GW threshold values (GTVs), to assess overall quality using a “well bottom” approach. The background concentration of GW K and GW P (established in early 2008, prior to all OB spreading) were above permissible Irish statutory limits, in all cases. There was evidence of percolation of K and TSP to GW; K and PO43 concentrations breached GTVs across all plots. There was also evidence of percolation of Cu through soil profile, though Cu GW concentration did not breach GTV, and no risk to GW quality is necessarily implied. A potential (though small) risk of P- and K-percolation could impact GW quality in commercially scaled-up plantations; however, risk to GW quality from NO3, Cu, Cd, Cr, Pb, Ni, and Zn leaching in soil are minimal. Sites considered for energy crop should be assessed for soil conditions, and vulnerability to leaching, before OB amendment programs are initiated. The study was conducted over two years; the longer term impact of applications of BS and DE on soil organic-matter content, salinity and pH (and subsequent loss through soil profile) should be assessed. The implication of scaling up test-bed sized applications to larger commercial plantation scales needs to be considered. Capsule: Amendments of organic byproduct to short rotation coppice willow may lead to leaching of nutrients to groundwater in certain circumstances.

Journal article Chemical amendment of dairy cattle slurry has been shown to effectively reduce incidental phosphorus (P) losses in runoff; however, the effects of amendments on incidental nitrogen (N) losses are not as well documented. This study examined P and N losses in runoff during three simulated rainfall events 2, 10 and 28 days after a single application of unamended/chemically amended dairy cattle slurry. Twenty-five hydraulically isolated plots, each measuring 0.9 m by 0.4 m and instrumented with runoff collection channels, were randomly assigned the following treatments: (i) grass-only, (ii) slurry-only (the study-control), (iii) slurry amended with industrial grade liquid alum comprising 8% Al2O3, (iv) slurry amended with industrial grade liquid poly-aluminum chloride (PAC) comprising 10% Al2O3, and (v) slurry amended with lime. During the first rainfall event, lime was ineffective but alum and PAC effectively reduced dissolved reactive P (DRP) (by 95 and 98%, respectively) and total P (TP) flow-weighted-mean-concentrations (by 82 and 93%, respectively) in runoff compared to the study-control. However, flow-weighted-mean-concentrations of ammonium-N (NH4-N) in runoff were increased with alum- (81%) and lime-treated (11%) slurry compared to the study-control whereas PAC reduced the NH4-N by 82%. Amendments were not observed to have a significant effect on NO3-N losses during this study. Slurry amendments reduced P losses for the duration of the study, whereas the effect of amendments on N losses was not significant following the first event. Antecedent volumetric water content of the soil or slope of the plots did not appear to affect runoff volume. However, runoff volumes (and consequently loads of P and N) were observed to increase for the chemically amended plots compared to the control and soil-only plots. This work highlights the importance of considering both P and N losses when implementing a specific nutrient mitigation measure. Teagasc (Walsh Fellowship) peer-reviewed