• Paratuberculosis sero-status and milk production, SCC and calving interval in Irish dairy herds

      Hoogendam, K; Richardson, E; Mee, John F (Biomed Central, 2009-04-01)
      The objective of this study was to investigate the impact of paratuberculosis sero-status on milk yield, fat, protein, somatic cell count and calving interval in Irish dairy herds. Serum from all animals over 12 months of age (n = 2,602) in 34 dairy herds was tested for antibodies to Mycobacterium avium subsp. paratuberculosis using an ELISA. Herds were categorised by sero-status into positive, non-negative and negative, where a positive herd contained two or more positive cows, a non-negative herd contained only one positive cow and a negative herd contained no positive cows. Data at animal, parity and herd-level were analysed by multiple regression using general linear models. Positive herds (mean herd size = 129 cows) and non-negative herds (81 cows) were larger than negative herds (72 cows) (P < 0.01). Negative herds had the highest economic breeding index (EBI), while positive herds had the highest estimated breeding value (EBV) for milk yield. There was no significant effect of paratuberculosis sero-status at animal, parity or herd-level on milk yield, milk fat or protein production, somatic cell count score (SCCS) or calving interval. Negative herds tended to have a lower SCCS than positive and nonnegative herds (P = 0.087). This study only examined the effects of paratuberculosis sero-status but did not examine the clinical effects of Johne's disease at the farm or dairy industry levels.
    • Partitioning of starter bacteria and added exogenous enzyme activities between curd and whey during Cheddar cheese manufacture

      Doolan, I. A.; Nongonierma, A. B.; Kilcawley, Kieran N; Wilkinson, M.G. (Elsevier, 2013-07-26)
      Partitioning of starter bacteria and enzyme activities was investigated at different stages of Cheddar cheese manufacture using three exogenous commercial enzyme preparations added to milk or at salting. The enzyme preparations used were: Accelase AM317, Accelase AHC50, Accelerzyme CPG. Flow cytometric analysis indicated that AHC50 or AM317 consisted of permeabilised or dead cells and contained a range of enzyme activities. The CPG preparation contained only carboxypeptidase activity. Approximately 90% of starter bacteria cells partitioned with the curd at whey drainage. However, key enzyme activities partitioned with the bulk whey in the range of 22%–90%. An increased level of enzyme partitioning with the curd was observed for AHC50 which was added at salting, indicating that the mode of addition influenced partitioning. These findings suggest that further scope exists to optimise both bacterial and exogenous enzyme incorporation into cheese curd to accelerate ripening.
    • Pathogen profile of clinical mastitis in Irish milk-recording herds reveals a complex aetiology

      Keane, Orla M; Budd, Kathleen E; Flynn, James; McCoy, Finola (British Veterinary Association, 2013-05-21)
      Effective mastitis control requires knowledge of the predominant pathogen challenges on the farm. In order to quantify this challenge, the aetiological agents associated with clinical mastitis in 30 milk-recording dairy herds in Ireland over a complete lactation were investigated. Standard bacteriology was performed on 630 pretreatment quarter milk samples, of which 56 per cent were culture-positive, 42 per cent culture-negative and 2 per cent contaminated. Two micro-organisms were isolated from almost 5 per cent of the culture-positive samples. The bacteria isolated were Staphylococcus aureus (23 per cent), Streptococcus uberis (17 per cent), Escherichia coli (9 per cent), Streptococcus species (6 per cent), coagulase-negative Staphylococci (4 per cent) and other species (1 per cent). A wide variety of bacterial species were associated with clinical mastitis, with S aureus the most prevalent pathogen overall, followed by S uberis. However, the bacterial challenges varied widely from farm to farm. In comparison with previous reports, in the present study, the contagious pathogens S aureus and Streptococcus agalactiae were less commonly associated with clinical mastitis, whereas, the environmental pathogens S uberis and E coli were found more commonly associated with clinical mastitis. While S aureus remains the pathogen most commonly associated with intramammary infection in these herds, environmental pathogens, such as S uberis and E coli also present a considerable challenge.
    • Pathogenomic analysis of the common bovine Staphylococcus aureus clone (ET3): emergence of a virulent subtype with potential risk to public health

      Smyth, Cyril James; Hartigan, James Patrick (University of Chicago Press, 2012-07-02)
      A common clone (ET3) of Staphylococcus aureus is responsible for a large proportion of cases of bovine mastitis and occasionally causes zoonotic infections of humans. In the present study, we report the identification of a virulent clonal subtype (ST151) of ET3, which resulted in increased tissue damage and mortality in a mouse model of mastitis. ST151 has undergone extensive diversification in virulence and regulatory‐gene content, including the acquisition of genetic elements encoding toxins not made by other ET3 strains. Furthermore, ST151 had elevated levels of RNAIII and cytolytic toxin–gene expression, consistent with the enhanced virulence observed during experimental infection. Previously, the ST151 clone was shown to be hypersusceptible to the acquisition of vancomycin‐resistance genes from Enterococcus spp. Taken together, these data indicate the emergence of a virulent subtype of the common ET3 clone, which could present an enhanced risk to public health.
    • Pathways for nutrient loss to water with emphasis on phosphorus

      Tunney, Hubert; Kiely, G.; Morgan, G.; Moles, R.; Byrne, P.; Jordan, P.; Daly, Karen M.; Doody, Donnacha G.; Kurz, Isabelle; Bourke, David; O’Reilly, C.; Ryan, T. Declan; Holden, N.; Jennings, E.; Irvine, K.; Carton, Owen T. (Teagasc, 2007-06-01)
      The main objective of this project was to study phosphorus (P) loss from agricultural land under a range of conditions in Ireland, to quantify the main factors influencing losses and make recommendations on ways to reduce these losses. This report is a synthesis of the main conclusions and recommendations from the results of the studies. The final reports from the individual sub-projects in this project are available from the EPA (www.epa.ie).
    • Pathways for Nutrient Loss to Water; Slurry and Fertilizer Spreading

      Ryan, T. Declan; Holden, Nicholas M.; Carton, Owen T.; Fitzgerald, D.; Murphy, F. (Teagasc, 2008-07-08)
      There are almost 150,000 farms in Ireland and these contribute substantial quantities of N and P to inland and coastal waters. Some of these nutrients are carried from wet soils by overland flow and by leaching from dry soils. Farm practice can reduce the loss from farms by judicious management of nutrients. Improvements are required to diminish export of nutrients without impairing operations on the farm. Literature regarding nutrient loss from agriculture was reviewed in this project and maps were prepared to predict best slurry spreading times around Ireland. Two further maps were prepared to show slurry storage requirement on farms.
    • Pathways for Nutrient Loss to Water; Slurry and Fertilizer Spreading.

      Ryan, Declan; Holden, N.; Carton, Owen T.; Fitzgerald, D.; Murphy, F. (Teagasc, 2008-07-08)
      The objectives of this work were as follows: • To critically review information in existing literature and data. This would help to develop an improved understanding of the factors contributing to pollution by P and N. • To identify regional opportunities for spreading slurry • To estimate the regional opportunities for storing slurry These objectives were pursued in the following way. The first target was addressed by literature review, by an in-depth review of the Fertiliser Use Survey (Coulter et al., 2002) and by a revised statistical analysis of nutrient loss data from former trials at Johnstown Castle. For objective 2, a mapping exercise, using detailed rainfall data, indicated the climate risk element of slurry spreading. A similar approach was adopted for the third objective where climate and other data were used to plot maps of slurry storage requirement.
    • Pedotransfer functions for Irish soils – estimation of bulk density (ρb) per horizon type

      Reidy, Brian; Simo, Iolando; Sills, P.; Creamer, Rachel E. (European Geosciences Union, 2016-01-18)
      Soil bulk density is a key property in defining soil characteristics. It describes the packing structure of the soil and is also essential for the measurement of soil carbon stock and nutrient assessment. In many older surveys this property was neglected and in many modern surveys this property is omitted due to cost both in laboratory and labour and in cases where the core method cannot be applied. To overcome these oversights pedotransfer functions are applied using other known soil properties to estimate bulk density. Pedotransfer functions have been derived from large international data sets across many studies, with their own inherent biases, many ignoring horizonation and depth variances. Initially pedotransfer functions from the literature were used to predict different horizon type bulk densities using local known bulk density data sets. Then the best performing of the pedotransfer functions were selected to recalibrate and then were validated again using the known data. The predicted co-efficient of determination was 0.5 or greater in 12 of the 17 horizon types studied. These new equations allowed gap filling where bulk density data were missing in part or whole soil profiles. This then allowed the development of an indicative soil bulk density map for Ireland at 0–30 and 30–50 cm horizon depths. In general the horizons with the largest known data sets had the best predictions, using the recalibrated and validated pedotransfer functions.
    • Performance and carcass traits of progeny of Limousin sires differing in genetic merit

      Keane, Michael G.; Diskin, Michael G. (Teagasc, Oak Park, Carlow, Ireland, 2007)
      Genetic indices for growth and carcass classification are published for beef sires used in Ireland for artificial insemination (AI). The objective of this study was to compare growth and carcass traits of progeny of Limousin sires of low and high genetic index for growth. A total of 70 progeny (42 males and 28 females) out of predominantly Holstein-Friesian cows by 7 AI Limousin sires were reared together to slaughter. The 7 sires were classified as low (n=3) or high (n=4) index based on their published genetic index for growth. The male progeny were reared entire and all animals were slaughtered at about 20 months of age. Carcasses were classified for conformation and fatness, and a rib joint (ribs 6 to 10) was separated into fat, muscle and bone. Growth rate did not differ significantly between the index groups but tended to be higher for the high index progeny. This higher growth rate, combined with a significantly higher kill out proportion, resulted in carcass weight andcarcass weight per day of age being significantly higher for the high index progeny. Carcass conformation and fat class were not affected by genetic index, nor was the composition of the rib joint. Compared with males, females had a significantly lower growth rate and kill out proportion and, consequently, had a significantly lower carcass weight. The proportions of fat and bone in the rib joint were significantly higher, and the proportion of muscle was significantly lower for females than for males. It is concluded that carcass weight reflected sire group genetic index for growth but feed intake, carcass classification and rib joint composition were not affected.
    • Performance and feed intake of five beef suckler cow genotypes and pre-weaning growth of their progeny

      Murphy, B.M.; Drennan, Michael J; O'Mara, Frank P.; McGee, Mark (Teagasc, Oak Park, Carlow, Ireland, 2008)
      The effect of beef suckler cow genotype on feed intake, performance, milk yield and on pre-weaning growth of their progeny was determined over four lactations. The five cow genotypes examined were Limousin (L), Charolais (C), Limousin × Holstein-Friesian (LF), Limousin × (Limousin × Holstein-Friesian) (LLF) and Simmental × (Limousin × Holstein-Friesian) (SLF). The herd calved in spring and the progeny spent from April until weaning (October/ November) at pasture with their dams. Live weight (kg) at the start of the indoor winter period was greater (P < 0.001) for C (702) than L (616) cows who in turn were heavier than LF (552) and LLF (574), with SLF (582) being intermediate. Silage dry matter (DM) intake (kg /day) was greater (P < 0.01) for C and SLF cows than L and LLF, whereas LF were inter-mediate. Dry matter intake (kg/day) of zero-grazed grass did not differ (P > 0.05) between the genotypes but followed a similar trend to grass silage intake. The decrease in live weight over the indoor winter period was greater (P < 0.01) for L and C cows than for LLF and SLF, whereas LF were intermediate. The increase in live weight during the grazing season was greater (P < 0.01) for C cows than all except L, which were intermediate. Calving difficulty score was greater (P < 0.01) for C cows than LLF, L and SLF, whereas LF were intermediate. Birth weight of calves from LF cows was lower (P < 0.001) than C with L being intermediate, but greater than LLF, with SLF being intermediate. Milk yield (kg/day) was higher (P < 0.001) for LF (9.7) and SLF (8.7) cows than the other genotypes (5.5 to 7.0), which did not differ significantly. Pre-weaning live-weight gain was greater (P < 0.001) for progeny of LF cows than all other genotypes except SLF, which in turn were greater than L and C, with LLF being intermediate. In conclusion, calf pre-weaning growth was higher for cow genotypes with higher milk yield, which was also associated with higher cow DM intake.
    • The Performance of Cannabis Sativa (HEMP) as a Fibre Source for Medium Density Fibre Board (MDF).

      Crowley, J.G. (Teagasc, 2001-05-01)
      Industrial hemp (Cannabis sativa) was successfully grown over a three-year period without the use of agrochemicals, and with a relatively low input of nitrogen fertilizer at 120 kg/ha (96 units/ac). The yields achieved were encouraging at an average of 12.5 t/ha of whole stems at 15% m.c. over the three years. Sowing in early- to mid-April at a seed rate of half the conventional recommended rate of 50 kg/ha proved to be sufficient to achieve the maximum yield of stems where long fibre yield and finess (quality) are not required. For this study the hemp was produced as a raw material for the fibre board industry, where the whole stem and not just the long blast fibre is required. Hemp is relatively disease-free with Botrytis and Sclerotinia the only diseases encountered. For both, spraying is not possible due to the height of the crop. Infection rarely causes economic losses. Harvesting hemp proved difficult with conventional farm harvesting equipment. The development of the hemp crop as an industrial raw material will require the development of harvesting, chopping and storage techniques that can cope with the height, bulk and fibrous nature of the crop.
    • Peripheral and gastrointestinal immune systems of healthy cattle raised outdoors at pasture or indoors on a concentrate-based ration

      Lejeune, Alexandre; Monahan, Frank J; Moloney, Aidan P; Earley, Bernadette; Black, Alistair D; Campion, Deirdre P; Englishby, Tanya; Reilly, Petrina; O'Doherty, John; Sweeney, Torres (Biomed Central, 2010-03-31)
      Background: Despite an increasing preference of consumers for beef produced from more extensive pasture-based production systems and potential human health benefits from the consumption of such beef, data regarding the health status of animals raised on pasture are limited. The objective of this study was to characterise specific aspects of the bovine peripheral and the gastrointestinal muscosal immune systems of cattle raised on an outdoor pasture system in comparison to animals raised on a conventional intensive indoor concentrate-based system. Results: A number of in vitro functional tests of immune cells suggested subtle differences between the animals on the outdoor versus indoor production systems. There was a decrease in the number of neutrophils and monocytes engaged in phagocytosis in outdoor cattle (P < 0.01 and P < 0.05, respectively) in comparison to those indoors. Following mitogen stimulation, a lower level of interferon-γ was produced in leukocytes from the outdoor animals (P < 0.05). There was evidence of a gastrointestinal nematode infection in the outdoor animals with elevated levels of serum pepsinogen (P < 0.001), a higher number of eosinophils (P < 0.05) and a higher level of interleukin-4 and stem cell factor mRNA expression (P < 0.05) in the outdoor animals in comparison to the indoor animals. Lower levels of copper and iodine were measured in the outdoor animals in comparison to indoor animals (P < 0.001). Conclusion: Despite distinctly contrasting production systems, only subtle differences were identified in the peripheral immune parameters measured between cattle raised at pasture in comparison to animals raised on a conventional intensive indoor concentrate-based production system.
    • Phosphorus loss from soil to water.

      Tunney, Hubert; Carton, Owen T.; O'Donnell, T.; Fanning, A. (Teagasc, 1998-12-01)
      The work described under this project covers field work on phosphorus(P) loss from soil to water under field conditions. In addition two International Workshops on P loss to water, held in Ireland in 1995 and 1998, are also covered under this project. The results indicate that P loss to water is a complex process and it is influenced by a number of factors, including hydrology of the soil, rates and timing of P application and soil P levels. Most work on this subject indicates that there is a positive relationship between soil test P levels and P loss to water. There is need for further work to establish the relative contribution of the different variables involved in P loss from soil to water for different soils and farming conditions. This should help provide answers to the most sustainable methods to minimise losses of P to water and ensure that agricultural production is compatible with good water quality.
    • Phosphorus management on Irish dairy farms post controls introduced under the EU Nitrates Directive

      Buckley, Cathal; Wall, David P.; Moran, Brian; O'Neill, Stephen; Murphy, Paul N. C.; Department of Agriculture, Food and the Marine (Elsevier, 2015-11-08)
      The Republic of Ireland was one of a minority of EU member states to include direct controls on chemical phosphorus (P) fertilisers in its EU Nitrates Directive National Action Plan, first introduced in 2006. This study estimates farm gate phosphorus balances and use efficiencies across 150 specialist dairy farms over the seven year period since these controls were introduced (2006–2012) using nationally representative data. Results indicate that P balances declined by 50% over the study period from 11.9 in 2006 to 6.0 kg ha− 1 in 2012. This decline was driven by a reduction in chemical fertiliser imports of 6.5 kg ha− 1. This is equivalent to a reduction of 281 kg of P and represents a cost saving of €812 per annum across the average farm. Phosphorus use efficiency also improved over the period from 60% in 2006 to 78% in 2012, peaking in 2011 at 88.3%. This was achieved while increasing milk solids output per hectare and per cow. Results of a random effects panel data model indicated that P balance and use efficiency are significantly influenced by factors such as fertiliser prices, stocking rates, land use potential, use of milk recording technology, contact with extension services and rainfall patterns.
    • The phosphorus requirements for silage production on high fertility soils

      Power, V.; Tunney, Hubert; Jeffrey, D.W. (Teagasc (Agriculture and Food Development Authority), Ireland, 2005)
      The minimum phosphorus requirement for a mid-season ryegrass was investigated under cutting conditions over a 10-year period at each of three Teagasc sites (Clonroche, Johnstown Castle and Oak Park) in southeast Ireland. Treatments consisted of 0, 20, 30, 40, and 50 kg ha–1 year–1 P applied in autumn. Generally, there were three grass cuts each year and soil samples were taken after the third cut prior to the application of P. Nitrogen and potassium fertiliser was applied to ensure maximum grass yield. There was an emerging treatment effect over time as evidenced by the significance of the treatment × year interaction. The effect of site varied with year reflecting the variability in weather and number of cuts taken at the individual sites. A treatment effect on annual first-cut-silage yield was observed. The largest treatment difference for dry matter (DM) yield of first-cut silage was between the control and the P treated plots (0.32 t/ha). The results show that the draw down of soil-P reserves was adequate to maintain yield for a number of years without additional fertiliser P application. Initial soil tests indicated moderate to high soil test P levels (STP) as measured by the Morgan’s test. Application of P at equivalent to removal rates did not maintain STP. The results suggest that application of a regular small maintenance dressing of P, replacing realistic removals, is the most appropriate fertiliser application strategy.
    • Phosphorus Retention and sorption by constructed wetland soils.

      Dunne, E.; Culleton, Noel; O'Donovan, G.; Harrington, R. (Teagasc, 2005-01-01)
      Phosphorus plays a major role in the eutrophication of freshwater systems. Wetland systems either natural or constructed have an inherent ability to cycle and retain P. Physical, chemical and biological processes regulate P retention in wetland soils and sediments. Of those processes, sorption and precipitation are important in retaining P. Sorption is typically greater under aerobic soil/sediment conditions than anaerobic conditions. Under anaerobic conditions, Fe plays a major role in P dynamics, whereas Al is not affected by changes in redox. Precipitation of P as insoluble Ca bound P is a dominant transformation at high pH. Long-term P retention by wetland systems includes accretion and decomposition of organic and detrital material, and its associated P content. Case studies reviewed illustrated that P retention in natural and constructed wetland systems can vary by several orders of 30 magnitude depending on site-specific factors. The literature reviewed also indicates that using wetlands to retain P from agricultural practices is significant and variable.
    • Phylogenetic and functional potential links pH and N2O emissions in pasture soils

      Samad, Sainur; Biswas, Ambarish; Bakken, Lars R.; Clough, Timothy J.; de Klein, Cecilia A.M.; Richards, Karl G.; Lanigan, Gary J.; Morales, Sergio E. (Nature Publishing Group, 2016-10-26)
      Denitrification is mediated by microbial, and physicochemical, processes leading to nitrogen loss via N2O and N2 emissions. Soil pH regulates the reduction of N2O to N2, however, it can also affect microbial community composition and functional potential. Here we simultaneously test the link between pH, community composition, and the N2O emission ratio (N2O/(NO + N2O + N2)) in 13 temperate pasture soils. Physicochemical analysis, gas kinetics, 16S rRNA amplicon sequencing, metagenomic and quantitative PCR (of denitrifier genes: nirS, nirK, nosZI and nosZII) analysis were carried out to characterize each soil. We found strong evidence linking pH to both N2O emission ratio and community changes. Soil pH was negatively associated with N2O emission ratio, while being positively associated with both community diversity and total denitrification gene (nir & nos) abundance. Abundance of nosZII was positively linked to pH, and negatively linked to N2O emissions. Our results confirm that pH imposes a general selective pressure on the entire community and that this results in changes in emission potential. Our data also support the general model that with increased microbial diversity efficiency increases, demonstrated in this study with lowered N2O emission ratio through more efficient conversion of N2O to N2.
    • Physical and mechanical properties of soil for ridge formation, ridge geometry and yield in new planting and ridge formation methods of potato production

      Vucajnk, F.; Vidrih, M.; Bernik, R. (Teagasc, 2012-12)
      In 2008 and 2009, a trial was performed to enhance the physical and mechanical properties of light soil for ridge formation, to increase the cross-sectional area of loose soil in the ridge, to improve the marketable yield and time efficiency, and to lower the percentage of green tubers. Three different planting and ridge formation methods applied to potato production were compared. The first method involved simultaneous planting and small ridge formation, followed by final ridge formation with a PTO-driven potato cultivator immediately before potato emergence (CL method). The second method combined planting and simultaneous final ridge formation (P+FR method), while, in the third method (BF+P+FR method), a special bed former attached to the front of a tractor that pushed the loose soil off the tractor wheels was used. The trial design was a randomised complete block with three repetitions. The BF+P+FR method produced the best physical and mechanical properties of the soil for ridge formation, while the CL method produced the poorest. Due to greater distance of the seed tuber from the ridge centre, the CL method resulted in the largest yield and percentage of green tubers. In comparison with the other two methods, the CL method gave a lower percentage of marketable tubers and a higher percentage of non-marketable tubers. Moreover, the BF+P+FR and P+FR methods were more time-efficient during planting and ridge formation than the CL method.
    • Physical Impact of Livestock on the Hill Environment.

      Walsh, M.; Collins, J.F.; Guinan, L.; Clavin, D.J.; Nixon, D. (Teagasc, 2001-06-01)
      The overall objective of this work was to provide quantitative and objective information on the role of livestock on changes over time in vegetation and soils in the hill areas and to develop a suitable monitoring programme.
    • The physical, economic and policy drivers of land conversion to forestry in Ireland

      Upton, Vincent; O'Donoghue, Cathal; Ryan, Mary; Department of Agriculture, Food and the Marine (Elsevier, 2013-11-27)
      Land use change is fundamentally a product of the interaction of physical land characteristics, economic considerations and agricultural and environmental policies. Researchers are increasingly combining physical and socio-economic spatial data to investigate the drivers of land-use change in relation to policy and economic developments. Focusing on Ireland, this study develops a panel data set of annual afforestation over 2811 small-area boundaries between 1993 and 2007 from vector and raster data sources. Soil type and other physical characteristics are combined with the net returns of converting agricultural land to forestry, based on the micro-simulation of individual farm incomes, to investigate land conversion. A spatial econometric approach is adopted to model the data and a range of physical, economic and policy factors are identified as having a significant effect on afforestation rates. In addition to the financial returns, the availability and quality of land and the implementation of environmental protection policies are identified as important factors in land conversion. The implications of these factors for the goal of forest expansion are discussed in relation to conflicting current and future land use policies.