The aim of the Teagasc Crops, Environment and Land Use Programme is to develop and transfer cost-effective crop production systems, along with evidence-based knowledge to support and underpin the development of an environmentally sustainable, competitive and profitable agri-food sector.

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  • Ensifer-mediated Arabidopsis thaliana Root Transformation (E-ART): A Protocol to Analyse the Factors that Support Ensifer-mediated Transformation (EMT) of Plant Cells

    Rathore, Deeraj Singh; Doohan, Fiona M.; Mullins, Ewen; Teagasc Walsh Fellowship Programme (Bio-protocol LLC, 2017-10-05)
    Ensifer adhaerens OV14, a soil borne alpha-proteobacteria of the Rhizobiaceae family, fortifies the novel plant transformation technology platform termed ‘Ensifer-mediated transformation’ (EMT). EMT can stably transform both monocot and dicot species, and the host range of EMT is continuously expanding across a diverse range of crop species. In this protocol, we adapted a previously published account that describes the use of Arabidopsis thaliana roots to investigate the interaction of A. thaliana and Agrobacterium tumefaciens. In our laboratory, we routinely use A. thaliana root explants to examine the factors that enhance the utility of EMT. In addition, the E-ART protocol can be used to study the transcriptional response of E. adhaerens and host plant following exposure to explant tissue, the transformability of different Ensifer adhaerens strains/mutants as well as testing the susceptibility of A. thaliana mutant lines as a means to decipher the mechanisms underpinning EMT.
  • Quantitative trait loci associated with different polar metabolites in perennial ryegrass - providing scope for breeding towards increasing certain polar metabolites

    Foito, Alexandre; Hackett, Christine A; Stewart, Derek; Velmurugan, Janaki; Milbourne, Dan; Byrne, Stephen L; Barth, Susanne; Department of Agriculture, Food and the Marine; RSF 06–346 (Biomed Central, 2017-10-10)
    Background Recent advances in the mapping of biochemical traits have been reported in Lolium perenne. Although the mapped traits, including individual sugars and fatty acids, contribute greatly towards ruminant productivity, organic acids and amino acids have been largely understudied despite their influence on the ruminal microbiome. Results In this study, we used a targeted gas-chromatography mass spectrometry (GC-MS) approach to profile the levels of 25 polar metabolites from different classes (sugars, amino acids, phenolic acids, organic acids and other nitrogen-containing compounds) present in a L. perenne F2 population consisting of 325 individuals. A quantitative trait (QTL) mapping approach was applied and successfully identified QTLs regulating seven of those polar metabolites (L-serine, L-leucine, glucose, fructose, myo-inositol, citric acid and 2, 3-hydroxypropanoic acid).Two QTL mapping approaches were carried out using SNP markers on about half of the population only and an imputation approach using SNP and DArT markers on the entire population. The imputation approach confirmed the four QTLs found in the SNP-only analysis and identified a further seven QTLs. Conclusions These results highlight the potential of utilising molecular assisted breeding in perennial ryegrass to modulate a range of biochemical quality traits with downstream effects in livestock productivity and ruminal digestion.
  • 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.
  • Carbon cycling in temperate grassland under elevated temperature

    Jansen-Willems, Anne B.; Lanigan, Gary; Grunhage, Ludger; Muller, Christoph (Wiley, 2016-11-01)
    An increase in mean soil surface temperature has been observed over the last century, and it is predicted to further increase in the future. The effect of increased temperature on ecosystem carbon fluxes in a permanent temperate grassland was studied in a long-term (6 years) field experiment, using multiple temperature increments induced by IR lamps. Ecosystem respiration (R-eco) and net ecosystem exchange (NEE) were measured and modeled by a modified Lloyd and Taylor model including a soil moisture component for R-eco (average R2 of 0.78) and inclusion of a photosynthetic component based on temperature and radiation for NEE (R2 = 0.65). Modeled NEE values ranged between 2.3 and 5.3 kg CO2 m−2 year−1, depending on treatment. An increase of 2 or 3°C led to increased carbon losses, lowering the carbon storage potential by around 4 tonnes of C ha−1 year−1. The majority of significant NEE differences were found during night-time compared to daytime. This suggests that during daytime the increased respiration could be offset by an increase in photosynthetic uptake. This was also supported by differences in δ13C and δ18O, indicating prolonged increased photosynthetic activity associated with the higher temperature treatments. However, this increase in photosynthesis was insufficient to counteract the 24 h increase in respiration, explaining the higher CO2 emissions due to elevated temperature.
  • Vegetative propagation of dieback-tolerant Fraxinus excelsior on

    Douglas, Gerry C.; Namara, J.M.; O'Connell, K.; Dunne, L.; Grant, Jim; European Co-Operation in Science and Technology; FP1103 (Swedish University of Agricultural Sciences, 2017)
    Ash trees which are tolerant to Hymenoscyphus fraxineus may be selected in all age classes among heavily infected populations. They may be produced also by controlled crossings of disease tolerant trees, because the genetic component of inheritance for disease tolerance is high. For mature and juvenile plant material, the deployment of disease tolerant genotypes could be potentially achieved by vegetatively propagating selected genotypes. We describe a system to vegetatively propagate selected ash genotypes and we discuss the prospects and options for using vegetative propagation on all age classes of trees. Mature trees were rejuvenated through the process of micropropagation to establish mother plants in large trays which were cut back repeatedly (hedged) to produce at least two crops of cuttings per year. The rooting capacity of ten genotypes was tested by a commercial nursery over a period of three years, to assess the feasibility of using hedged mother plants for efficient propagation. Commercial practise was to treat cuttings with 0.25% IBA, insert them in plug pots and maintain them covered with fine plastic within low plastic tunnels in a non heated greenhouse and without supplementary heating at the cutting base. In the first year, the mean rooting rate was 53 % for the first crop of cuttings and 35 % for the second. In the second and third years the rooting rates improved to over 80% for each crop of cuttings as experience was gained in handling the material. Rooting rate varied among the genotypes. We assessed the growth and development of micropropagated ash trees in the field from an observation clonal trial, consisting of four mature genotypes which had been established in 2002 in five replicate plots. The micropropagated trees were generally similar in height and dbh to seed derived control trees and developed normally. These observations are discussed in the context of using vegetative propagation as a tool in breeding and for the large scale deployment of ash with tolerance to H. fraxineus.
  • Ash dieback on the island of Ireland

    McCracken, A.R.; Douglas, Gerry C.; Ryan, C.; Destefanis, M.; Cooke, L.R.; European Co-Operation in Science and Technology (Swedish University of Agricultural Sciences, 2017)
    On the island of Ireland it is estimated that there are over half a million kilometres of hedgerows (400,000+ km in the Republic of Ireland (Rep. Ireland) and 113,000+ in Northern Ireland (Northern Ireland). Ash (Fraxinus excelsior) is the second most important component, after hawthorn (Crataegus monogyna), in large proportions of this hedgerow network. In the Rep. Ireland over 20,000 ha of ash have been planted since 1990, primarily for sawlogs and to provide material for the manufacture of hurleys, which are used in an important national sport called hurling, and for camogie sticks used to play camogie. Ash dieback, caused by Hymenoscyphus fraxineus, was first identified on the island in October 2012 and since then has been detected at 306 sites (195 in Rep. Ireland and 111 in Northern Ireland). In the vast majority of cases the outbreaks have been on young, imported trees planted within the previous 5 – 6 years and it was evident that the pathogen had been introduced on trees for planting. On a small number of occasions there was evidence of the pathogen cycling within a plantation or moving from the plantation to infect neighbouring hedgerow trees. One possible mechanism by which the pathogen can build up sufficient inoculum is by the formation of apothecia on infected woody tissue high up on the plants. Rep. Ireland and Northern Ireland have strict policies of eradication and containment, as set out in the All-Ireland Chalara Control Strategy. To date over 2.1 million trees have been destroyed as part of an eradication strategy. It is considered that this prompt and far-reaching action has had a significant impact, significantly mitigating and preventing the rapid establishment of the pathogen and limiting its spread. The interventions since the disease was first confirmed have helped to protect the considerable investment in ash plantations of the last 20 years. The pathogen has not, however, been eradicated from the island of Ireland and it remains to be seen how widespread, and how quickly ash dieback will become established on the island of Ireland. The latest figures from the Republic of Ireland are that 733 hectares of ash plantation has been reconstituted with another species as a result of Chalara and this has cost our state €2.6 million so far; in addition, Chalara has been found and confirmed in all 26 counties of the Republic of Ireland to a greater or lesser extent. As a result the current policies and procedures regarding Chalara are under review.
  • Multiple viral infections in Agaricus bisporus - Characterisation of 18 unique RNA viruses and 8 ORFans identified by deep sequencing

    Deakin, Gregory; Dobbs, Edward; Bennett, Julie M.; Jones, Ian M.; Grogan, Helen M.; Burton, Kerry S.; Teagasc Walsh Fellowship Programme; European Commission; 201043; 286836 (Nature Publishing Group, 2017-05-26)
    Thirty unique non-host RNAs were sequenced in the cultivated fungus, Agaricus bisporus, comprising 18 viruses each encoding an RdRp domain with an additional 8 ORFans (non-host RNAs with no similarity to known sequences). Two viruses were multipartite with component RNAs showing correlative abundances and common 3′ motifs. The viruses, all positive sense single-stranded, were classified into diverse orders/families. Multiple infections of Agaricus may represent a diverse, dynamic and interactive viral ecosystem with sequence variability ranging over 2 orders of magnitude and evidence of recombination, horizontal gene transfer and variable fragment numbers. Large numbers of viral RNAs were detected in multiple Agaricus samples; up to 24 in samples symptomatic for disease and 8–17 in asymptomatic samples, suggesting adaptive strategies for co-existence. The viral composition of growing cultures was dynamic, with evidence of gains and losses depending on the environment and included new hypothetical viruses when compared with the current transcriptome and EST databases. As the non-cellular transmission of mycoviruses is rare, the founding infections may be ancient, preserved in wild Agaricus populations, which act as reservoirs for subsequent cell-to-cell infection when host populations are expanded massively through fungiculture.
  • Can the agronomic performance of urea equal calcium ammonium nitrate across nitrogen rates in temperate grassland?

    Forrestal, Patrick J.; Harty, M.A.; Carolan, R.; Watson, C.J.; Lanigan, Gary; Wall, D.P.; Hennessy, Deirdre; Richards, Karl G. (Wiley, 2017-03-23)
    In temperate grassland, urea has been shown to have lower nitrous oxide emissions compared to ammonium nitrate-based fertilizer and is less expensive. However, nitrogen (N) loss via ammonia volatilization from urea raises questions regarding yield performance and efficiency. This study compares the yield and N offtake of grass fertilized with urea, calcium ammonium nitrate (CAN) and urea treated with the urease inhibitor N-(n-butyl) thiophosphoric triamide (NBPT) at six site-years. Five annual fertilizer N rates (100–500 kg N/ha) were applied in five equal splits of 20–100 kg N/ha during the growing season. On average, urea produced slightly better yields than CAN in spring (103.5% of CAN yield) and slightly poorer yields in summer (98.4% of CAN yield). There was no significant difference in annual grass yield between urea, CAN and urea + NBPT. Urea had the lowest cost per tonne of DM grass yield produced. However, the urea treatment had lower N offtake than CAN and this difference was more pronounced as the N rate increased. There was no difference in N offtake between urea + NBPT and CAN. While this study shows that urea produced yields comparable to CAN, urea apparent fertilizer N recovery (AFNR) tends to be lower. Urea selection in place of CAN will increase national ammonia emissions which is problematic for countries with targets to reduce ammonia emissions. Promisingly, NBPT allows the agronomic performance of urea to consistently equal CAN across N rates by addressing the ammonia loss limitations of urea.
  • Gross nitrogen transformations in grassland soil react differently to urea stabilisers under laboratory and field conditions

    Harty, M.A.; McGeough, K.L.; Carolan, R.; Muller, C.; Laughlin, R.J.; Lanigan, Gary; Richards, Karl G.; Watson, C.J. (Elsevier, 2017-02-10)
    A laboratory and a field study were conducted on a permanent grassland soil in Northern Ireland to investigate the effects of urea in combination with N process inhibitors such as the urease inhibitor N-(butyl) thiophosphoric triamide (NBPT) and/or the nitrification inhibitor dicyandiamide (DCD) on soil N dynamics. Urea enriched with n-butyl 15N to 60 atom % was applied to soil at a rate of 100 μg N g−1 dry soil in the laboratory and 100 kg N ha−1 in the field. A numerical 15N tracing model was used to quantify several simultaneously occurring gross N transformation rates in both studies. The changes in soil nitrate (NO3−) and ammonium (NH4+) concentrations and 15N enrichment over a 25-day period as well as the concentration and 15N enrichment of plant N at harvest were used to model soil gross N transformations. The results showed that the effect of N process inhibitors varied firstly between laboratory and field studies and secondly whether the inhibitors were applied individually or in combination. Overall DCD had a greater effect on the major soil N transformations than NBPT; reducing oxidation of NH4+, total nitrification, net NO3− produced, total mineralisation and the net adsorption of NH4+ at both laboratory and field scale. The effect of DCD was similar for these transformations whether applied alone or co-applied with NBPT. In contrast NBPT had no significant effect on oxidation of NH4+, total nitrification, total mineralisation or total immobilisation compared to urea in the field, while the effect on these transformations in the laboratory was significant. The contrasting effects of inhibitors on gross N transformations between laboratory and field may relate to the differences in experimental conditions, e.g. soil preparation, environmental conditions and the contribution of plant biomass. To obtain a more realistic assessment of gross soil N transformations in situ, it is essential that laboratory experiments are supplemented with field studies.
  • Groundwater nitrate reduction versus dissolved gas production: A tale of two catchments

    McAleer, E.B.; Coxon, C.E.; Richards, Karl G.; Jahangir, M.M.R.; Grant, Jim; Mellander, Per-Erik (Elsevier, 2017-02-20)
    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.
  • Ammonia emissions from urea, stabilized urea and calcium ammonium nitrate: insights into loss abatement in temperate grassland

    Forrestal, Patrick J.; Harty, M.; Carolan, R.; Lanigan, Gary; Watson, C.J.; Laughlin, R. J.; McNeill, G.; Chambers, B.J.; Richards, Karl G. (Wiley, 2015-11-17)
    Fertilizer nitrogen (N) contributes to ammonia (NH3) emissions, which European Union member states have committed to reduce. This study focused on evaluating NH3-N loss from a suite of N fertilizers over multiple applications, and gained insights into the temporal and seasonal patterns of NH3-N loss from urea in Irish temperate grassland using wind tunnels. The fertilizers evaluated were calcium ammonium nitrate (CAN), urea and urea with the N stabilizers N-(n-butyl) thiophosphoric triamide (NBPT), dicyandiamide (DCD), DCD+NBPT and a maleic and itaconic acid polymer (MIP). 200 (and 400 for urea only) kg N/ha/yr was applied in five equal applications over the growing season at two grassland sites (one for MIP). Mean NH3-N losses from CAN were 85% lower than urea and had highly variable loss (range 45% points). The effect of DCD on NH3 emissions was variable. MIP did not decrease NH3-N loss, but NBPT caused a 78.5% reduction and, when combined with DCD, a 74% reduction compared with urea alone. Mean spring and summer losses from urea were similar, although spring losses were more variable with both the lowest and highest losses. Maximum NH3-N loss usually occurred on the second day after application. These data highlight the potential of stabilized urea to alter urea NH3-N loss outcomes in temperate grassland, the need for caution when using season as a loss risk guide and that urea hydrolysis in temperate grassland initiates quickly. Micrometeorological measurements focused specifically on urea are needed to determine absolute NH3-N loss levels in Irish temperate grassland.
  • Temperate Grassland Yields and Nitrogen Uptake Are Influenced by Fertilizer Nitrogen Source

    Harty, Mary A.; Forrestal, Patrick J.; Carolan, Rachael; Watson, Catherine J.; Hennessy, Deirdre; Lanigan, Gary; Wall, David P.; Richards, Karl G. (American Society of Agronomy, 2017-01-25)
    In temperate grasslands, N source influences greenhouse gas emissions. Nitrification and urea hydrolysis inhibitors can reduce these losses. The objective of this study was to evaluate the impact of N source, urease inhibitors, and nitrification inhibitors on temperate grassland yields and N uptake. Experiments were conducted at three locations over 2 years (6 site-years) on the island of Ireland, covering a range of soils and climatic conditions. Results showed that calcium ammonium nitrate (CAN), urea+N-(n-butyl) thiophosphoric triamide (NBPT), urea+NBPT+dicyandiamide (DCD), and urea had equal annual dry matter yield. Urea+DCD had lower dry matter yield than CAN for 3 site-years. Calcium ammonium nitrate and urea+NBPT consistently had the same N uptake, urea+DCD had lower N uptake than CAN in 4 of 6 site-years, urea had lower N uptake than CAN in 2 site-years, and urea+NBPT+DCD had lower N uptake than CAN in 1 site-year. Urea+NBPT is a cost-effective alternative to CAN, which is consistently equal in terms of yield and N uptake in temperate grassland.
  • Effects of urease and nitrification inhibitors on yields and emissions in grassland and spring barley

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

    Fischer, K.; Burchill, W.; Lanigan, Gary; Kaupenjohann, M.; Chambers, B. J.; Richards, Karl G.; Forrestal, Patrick J. (Wiley, 2015-09-03)
    Deposition of urine and dung in pasture-based livestock production systems is a major source of ammonia (NH3) volatilization, contributing to the eutrophication and acidification of water bodies and to indirect nitrous oxide emissions. The objectives of this study were to (i) measure NH3 volatilization from dung and urine in three seasons, (ii) test the effect of spiking urine with the nitrification inhibitor dicyandiamide (DCD) on NH3 volatilization and (iii) generate NH3 emission factors (EFs) for dung, urine and urine + DCD in temperate maritime grassland. Accordingly, simulated dung, urine and urine spiked with DCD (at 30 kg DCD/ha equivalent rate) patches were applied to temperate grassland. Treatments were applied three times in 2014 with one measurement of NH3 loss being completed in spring, summer and autumn. The NH3-N EF was highest in spring, which was most likely due to the near absence of rainfall throughout the duration of loss measurement. The EFs across the experiments ranged between 2.8 and 5.3% (mean 3.9%) for dung, 8.7 and 14.9% (mean 11.2%) for urine and 9.5 and 19.5% (mean 12.9%) for urine + DCD, showing that ammonia loss from dung was significantly lower than from urine. Aggregating country-specific emission data such as those from the current experiment with data from climatically similar regions (perhaps in a weighted manner which accounts for the relative abundance of certain environmental conditions) along with modelling is a potentially resource-efficient approach for refining national ammonia inventories.
  • An evaluation of urine patch simulation methods for nitrous oxide emission measurement

    Forrestal, Patrick J.; Krol, Dominika; Lanigan, Gary; Jahangir, M.M.R.; Richards, Karl G. (Cambridge University Press, 2016-11-28)
    Global nitrous oxide (N2O) inventory estimates for pasture systems are refined based on measurements of N2O loss from simulated urine patches. A variety of methods are used for patch simulation but they frequently use a uniform wetted area (UWA), often smaller than a bovine urine patch. However, natural patches follow non-uniform infiltration patterns expanding naturally from a point of deposit with a non-wetted zone of influence. Using 2 litres of urine the UWA method was compared, using a 0·156 m2 collar, with a naturally expanding effective area (NEEA) method, using a 0·462 m2 collar under high (HL) and low (LL) N2O loss conditions. The method chosen affects urine nitrogen (N) loading to the soil. Under HL the UWA method induced a N2O-N loss of 280·6 mg/patch, significantly less than the 434·8 mg/patch loss for the NEEA method, for the same simulated urination. Under LL there was no method effect. Efforts should be made to employ patch simulation methods, which mimic natural deposits and can be achieved, at least in part, by: (a) Using a urine volume and N content similar to that of the animal of interest. (b) Allowing natural infiltration of the chosen urine volume to permit tapering towards the edges. (c) Measuring from the zone of influence in addition to the wetted area, i.e. the patch effective area.
  • Methods for the Identification of Important Areas of Plant Diversity in Ireland

    Walsh, Aidan; Teagasc Walsh Fellowship Programme (2016-06)
    The loss of biodiversity is an on-going global issue that not only results in the extinction of species but also threatens the ecosystem services and goods on which humanity depends. The global community has responded with ambitious targets to halt and reverse the loss of biodiversity. The causes of biodiversity loss are well understood and conservation measures can be deployed to protect biodiversity. However, conservation resources are limited and to be effective must be targeted to the most important areas of biodiversity. Using vascular plant distribution records for Ireland this research examined the distribution of plant species of conservation concern to determine if additional conservation measures should be targeted to these species. In an attempt to aid the targeting of conservation measures to the most important areas of biodiversity this research also investigated methods for the identification of priority areas for plant conservation. In an initial study vascular plant distribution records were collated and mapped for the island of Ireland. The tetrad scale (2km x 2km) data provided incomplete coverage for Ireland. Records for plant species of conservation concern were extracted and mapped at the tetrad scale for Ireland. The coincidence of the locations of the species of conservation concern and the distribution of areas designated for the protection of biodiversity in Ireland was examined. Between 22 – 40% of the locations of these species were found to occur outside of designated areas and for some individual species all of the locations occurred outside designated areas. The results indicated the importance of both designated areas and the wider countryside for biodiversity conservation. In particular the presence of species of conservation concern in non-designated areas highlights the need for conservation measures outside of designated areas. Subsequent research investigated a method for the identification of the most important areas of plant diversity at the tetrad and hectad (10km x 10km) scales in Ireland. A criteria-based scoring method was developed to characterise the landscape in terms of conservation value and identify the important areas of plant diversity. The effect of each of the criteria on priority area identification and on the representation of species (that is the extent to which species occur within a set of sites) within the priority areas was examined. The outcomes of this research identified a combination of criteria that allowed the identification of priority areas of high conservation value that contained a high species representation level. A subsequent investigation examined an alternative method for the identification of priority areas for conservation. A complementarity-based method using linear programming was used to identify the minimum number of priority areas in which species representation was guaranteed. Additional linear programs were formulated to identify restricted numbers of priority areas in which species representation was maximised. This research also developed a means of incorporating the outputs of the scoring method into the linear programming method. A combination of the plant distribution data, spatial environmental data, and a logistic regression method was used to build models to predict the distribution of the plant species of conservation concern group (SCC). The associations between the environmental data and SCC occurrence were examined and the predictive performance of both models was investigated using plant records in County Waterford. To conclude, this research showed that the tetrad-scale plant distribution coverage is patchy for most of Ireland. However, even with incomplete data the research indicated that conservation measures could be targeted to sites outside of protected areas. The plant distribution data can be used to characterise the landscape in terms of conservation value and both the scoring method and linear programming method can be used to identify priority areas for conservation. The scoring method and linear programming method can be combined to efficiently identify priority areas of high conservation value and the research showed the potential use of species distribution modelling for conservation planning in Ireland.
  • Morphological and physiological responses of Fagus sylvatica and Quercus robur seedlings to light availability

    Sevillano, Ignacio; COFORD; Teagasc Walsh Fellowship Programme (2016-06)
    The need to develop forest management systems other than clearfelling has resulted in a requirement for improved understanding of the potential of continuous cover forestry (CCF). One suggested method for the conversion of forest stands into CCF systems and for bringing under-performing forests into productivity is thinning in conjunction with underplanting. This study was an attempt to provide information on species suitability for underplanting of two important trees in European forestry: pedunculate oak (Quercus robur L.) and European beech (Fagus sylvatica L.). To determine the morphological, physiological and growth responses of these two species to different light conditions, beech and oak seedlings previously grown at full light for two years were covered by shading nets that provide different shade levels (62%, 51% or 28% of full light) or continued to be exposed to full light. The different shade levels were intended to mimic a range of underplanted conditions and the process of acclimation to shade was studied to provide information on the ecology and adaptation of underplanted seedlings. In addition to the controlled-shade experiment another study to determine the physiological responses of beech natural regeneration to shade was conducted under natural light conditions (from open gaps to closed canopy). Both oak and beech displayed similar acclimation in response to shade for most of the traits investigated. At the plant level, seedling acclimation to shade included higher biomass allocation to above than below-ground parts and greater energy investment on height than diameter growth. At the leaf level, seedlings grown under shade reduced their leaf thickness and photosynthetic rates per unit area and increased their specific leaf area. This increase in specific leaf area seems to be one mechanism that allows seedlings to perform well under shade conditions. Another acclimation to low light conditions was to increase the efficiency of the photosystem II under shade. Photosynthetic rates were higher and leaves were retained for longer in seedlings grown at full light than under shade. Hence, this probably led to a greater growth in the full light than under shade. Despite this greater growth at full light, the results of this study suggest that beech and oak seedlings would be able to acclimate and perform well if underplanted below overstories that reduce the available light to as low as 28% of full light without having any significant adverse effect on the quality of the final crop.
  • Broadleaf thinning in Ireland - a review of European silvicultural best practice

    Hawe, Jerry; Short, Ian; Department of Agriculture, Food and the Marine (Society of Irish Foresters, 2016)
    A substantial first-rotation broadleaf plantation resource in Ireland is progressively entering a thinning phase. Silvicultural best practice in support of such a management intervention needs to be developed for this new woodland resource to achieve its maximum commercial potential. National research trials are key to the provision of information for the development of best practice. Determining the current state-of-the-art is a prerequisite to the design and implementation of appropriate research trials. This study reviews the literature concerning the fundamental principles of broadleaf thinning with particular regard to timing, intensity and impacts on crop tree growth response, focussing on a range of commonly planted broadleaf species in Ireland. The overall aim of this review is to gain a fuller understanding of the most effective thinning methodology to be employed to maximise the production of high quality hardwood timber. In doing so it is intended that the information presented may support ongoing and future research trials with regard to potential silvicultural treatments to apply, data types and analysis and the likely results of practical application to commercial forestry.
  • A temporal assessment of nematode community structure and diversity in the rhizosphere of cisgenic Phytophthora infestans-resistant potatoes

    Ortiz, Vilma; Phelan, Sinead; Mullins, Ewen; European Union; KBBE.2011.3.5-01 (Biomed Central, 2016-12-01)
    Background Nematodes play a key role in soil processes with alterations in the nematode community structure having the potential to considerably influence ecosystem functioning. As a result fluctuations in nematode diversity and/or community structure can be gauged as a ‘barometer’ of a soil’s functional biodiversity. However, a deficit exists in regards to baseline knowledge and on the impact of specific GM crops on soil nematode populations and in particular in regard to the impact of GM potatoes on the diversity of nematode populations in the rhizosphere. The goal of this project was to begin to address this knowledge gap in regards to a GM potato line, cisgenically engineered for resistance to Phytophthora infestans (responsible organism of the Irish potato famine causing late blight disease). For this, a 3 year (2013, 2014, 2015) field experimental study was completed, containing two conventional genotypes (cvs. Desiree and Sarpo Mira) and a cisgenic genotype (cv. Desiree + Rpi-vnt1). Each potato genotype was treated with different disease management strategies (weekly chemical applications and corresponding no spray control). Hence affording the opportunity to investigate the temporal impact of potato genotype, disease management strategy (and their interaction) on the potato rhizosphere nematode community. Results Nematode structure and diversity were measured through established indices, accounts and taxonomy with factors recording a significant effect limited to the climatic conditions across the three seasons of the study and chemical applications associated with the selected disease management strategy. Based on the metrics studied, the cultivation of the cisgenic potato genotype exerted no significant effect (P > 0.05) on nematode community diversity or structure. The disease management treatments led to a reduction of specific trophic groups (e.g. Predacious c–p = 4), which of interest appeared to be counteracted by a potato genotype with vigorous growth phenotype e.g. cv. Sarpo Mira. The fluctuating climates led to disparate conditions, with enrichment conditions (bacterial feeding c–p = 1) dominating during the wet seasons of 2014 and 2015 versus the dry season of 2013 which induced an environmental stress (functional guild c–p = 2) on nematode communities. Conclusions Overall the functional guild indices in comparison to other indices or absolutes values, delivered the most accurate quantitative measurement with which to determine the occurrence of a specific disturbance relative to the cultivation of the studied cisgenic P. infestans-resistant potatoes.
  • Digital Soil Mapping in the Irish Soil Information System

    Corstanje, R.; Mayr, T.; Fealy, Reamonn; Zawadzka, J.; Lopapa, G.; Creamer, Rachel E.; Schulte, Rogier P. O. (International Union of Soil Sciences, 2009-12)
    Harmonised soil data across Europe with a 1:250 000 geo-referenced soil database will allow for exchange of data across member states and the provide the information needed by the European Commission and European Environment Agency for reporting on issues relating to soil quality under a fu-ture Soil Framework Directive. Within this context, the Environmental Protection Agency of the Republic of Ireland commissioned a project run by Teagasc to produce a 1:250 000 soil map of the Republic of Ire-land. Delivery of this map and associated database is a collaborative effort between Teagasc, the National Soil Resources Institute at Cranfield in the UK and University College Dublin.

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