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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  • Gain in Nitrogen Yield from Grass-Legume Mixtures is Robust Over a Wide Range of Legume Proportions and Environmental Conditions

    Suter, Matthias; Finn, John A.; Connolly, John; Loges, Ralph; Lüscher, Andreas (Elsevier BV, 2015-08-19)
    Global food security is currently challenged and requires sustainable intensification of agriculture through initiatives that include more efficient use of nitrogen (N) and increased protein self-sufficiency through home-grown crops. Such challenges were addressed in a continental-scale field experiment conducted over three years, in which the amount of total nitrogen yield (Ntot) and the gain in N yield in mixtures as compared to grass monocultures (Ngainmix) was quantified from four-species grass-legume stands with greatly varying legume proportions. Stands consisted of monocultures and mixtures of two N2 fixing legumes and two non-fixing grasses. The amount of Ntot of mixtures was significantly greater (P ≤ 0.05) than that of grass monocultures at the majority of evaluated sites in all three years. Ntot and thus Ngainmix increased with increasing legume proportion up to one third of legumes. With higher percentages of legumes, Ntot and Ngainmix did not further increase. Thus, across sites and years, mixtures with one third proportion of legumes had 57% higher Ntot than grass monocultures and attained ∼95% of the maximum Ntot acquired by any stand. The relative N gain in mixture (Ngainmix/Ntotmix) was most severely impaired by minimum site temperature (R = 0.64, P = 0.010). Nevertheless, Ngainmix/Ntotmix was not correlated to site productivity (P = 0.500), suggesting that, within climatic restrictions, balanced grass-legume mixtures can benefit from comparable relative gains in N yield across largely differing productivity levels. We conclude that higher N output (Ntot or forage protein per unit area) can be achieved with grass-legume mixtures than with pure grass alone for a given amount of N fertilizer applied; conversely, the same N output can be achieved by mixed swards with less input of N. Therefore, the use of grass-legume mixtures can substantially contribute to resource-efficient agricultural grassland systems over a wide range of productivity levels, implying important savings in N fertilizers and greenhouse gas emissions.
  • Functional Land Management for managing soil functions: A case-study of the trade-off between primary productivity and carbon storage in response to the intervention of drainage systems in Ireland

    O'Sullivan, L.; Creamer, R.E.; Fealy, R.; Lanigan, G.; Simo, I.; Fenton, O.; Carfrae, J.; Schulte, R.P.O.; Department of Agriculture, Food and the Marine (Elsevier BV, 2015-09)
    Globally, there is growing demand for increased agricultural outputs. At the same time, the agricultural industry is expected to meet increasingly stringent environmental targets. Thus, there is an urgent pressure on the soil resource to deliver multiple functions simultaneously. The Functional Land Management framework (Schulte et al., 2014) is a conceptual tool designed to support policy making to manage soil functions to meet these multiple demands. This paper provides a first example of a practical application of the Functional Land Management concept relevant to policy stakeholders. In this study we examine the trade-offs, between the soil functions ‘primary productivity’ and ‘carbon cycling and storage’, in response to the intervention of land drainage systems applied to ‘imperfectly’ and ‘poorly’ draining managed grasslands in Ireland. These trade-offs are explored as a function of the nominal price of ‘Certified Emission Reductions’ or ‘carbon credits’. Also, these trade-offs are characterised spatially using ArcGIS to account for spatial variability in the supply of soil functions. To manage soil functions, it is essential to understand how individual soil functions are prioritised by those that are responsible for the supply of soil functions – generally farmers and foresters, and those who frame demand for soil functions – policy makers. Here, in relation to these two soil functions, a gap exists in relation to this prioritisation between these two stakeholder groups. Currently, the prioritisation and incentivisation of these competing soil functions is primarily a function of CO2 price. At current CO2 prices, the agronomic benefits outweigh the monetised environmental costs. The value of CO2 loss would only exceed productivity gains at either higher CO2 prices or at a reduced discount period rate. Finally, this study shows large geographic variation in the environmental cost: agronomic benefit ratio. Therein, the Functional Land Management framework can support the development of policies that are more tailored to contrasting biophysical environments and are therefore more effective than ‘blanket approaches’ allowing more specific and effective prioritisation of contrasting soil functions.
  • Groundwater nitrate reduction versus dissolved gas production: A tale of two catchments

    McAleer, E.B.; Coxon, C.E.; Richards, K.G.; Jahangir, M.M.R; Grant, J.; Mellander, Per.E.; Teagasc Walsh Fellowship Programme (Elsevier BV, 2017-05-15)
    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.
  • Predicting microbial water quality with models: Over-arching questions for managing risk in agricultural catchments

    Oliver, David M.; Porter, Kenneth D.H.; Pachepsky, Yakov A.; Muirhead, Richard W.; Reaney, Sim M.; Coffey, Rory; Kay, David; Milledge, David G.; Hong, Eunmi; Anthony, Steven G.; et al. (Elsevier BV, 2016-02)
    The application of models to predict concentrations of faecal indicator organisms (FIOs) in environmental systems plays an important role for guiding decision-making associated with the management of microbial water quality. In recent years there has been an increasing demand by policy-makers for models to help inform FIO dynamics in order to prioritise efforts for environmental and human-health protection. However, given the limited evidence-base on which FIO models are built relative to other agricultural pollutants (e.g. nutrients) it is imperative that the end-user expectations of FIO models are appropriately managed. In response, this commentary highlights four over-arching questions associated with: (i) model purpose; (ii) modelling approach; (iii) data availability; and (iv) model application, that must be considered as part of good practice prior to the deployment of any modelling approach to predict FIO behaviour in catchment systems. A series of short and longer-term research priorities are proposed in response to these questions in order to promote better model deployment in the field of catchment microbial dynamics.
  • A Functional Land Management conceptual framework under soil drainage and land use scenarios

    Coyle, Cait; Creamer, Rachel E.; Schulte, Rogier P.O.; O'Sullivan, Lilian; Jordan, Phil; Institute of Technology, Sligo (Elsevier BV, 2015-11-15)
    Agricultural soils offer multiple soil functions, which contribute to a range of ecosystem services, and the demand for the primary production function is expected to increase with a growing world population. Other key functions on agricultural land have been identified as water purification, carbon sequestration, habitat biodiversity and nutrient cycling, which all need to be considered for sustainable intensification. All soils perform all functions simultaneously, but the variation in the capacity of soils to supply these functions is reviewed in terms of defined land use types (arable, bio-energy, broadleaf forest, coniferous forest, managed grassland, other grassland and Natura 2000) and extended to include the influence of soil drainage characteristics (well, moderately/imperfect, poor and peat). This latter consideration is particularly important in the European Atlantic pedo-climatic zone; the spatial scale of this review. This review develops a conceptual framework on the multi-functional capacity of soils, termed Functional Land Management, to facilitate the effective design and assessment of agri-environmental policies. A final functional soil matrix is presented as an approach to show the consequential changes to the capacity of the five soil functions associated with land use change on soils with contrasting drainage characteristics. Where policy prioritises the enhancement of particular functions, the matrix indicates the potential trade-offs for individual functions or the overall impact on the multi-functional capacity of soil. The conceptual framework is also applied by land use area in a case study, using the Republic of Ireland as an example, to show how the principle of multi-functional land use planning can be readily implemented.
  • Exploring the sensitivity of visual soil evaluation to traffic-induced soil compaction

    Emmet-Booth, J.P.; Holden, N.M.; Fenton, O; Bondi, G; Forristal, P.D.; Irish Department of Agriculture, Food and the Marine; 13/S/468 (Elsevier, 2019-10-24)
    Visual Soil Evaluation (VSE) techniques are useful for assessing the impact of land management, particularly the identification and remediation of soil compaction. Despite an increasing body of VSE research, comparatively few studies have explored the sensitivity of VSE for capturing experimentally imposed compaction to estimate sensitivity and limit of detection. The aim of this research was to examine the ability of VSE techniques to indicate soil structure at different soil profile depths and to measure the associated soil productive function (yield) response to imposed compaction. A two-year experiment was conducted on sites with loam and sandy soils. Varying levels of wheeled traffic were imposed on plots in a randomised block design, prior to sowing winter barley (Hordeum vulgare L.). Quantitative crop and soil measurements were taken throughout the season in conjunction with VSE techniques, which assessed to 25 cm (VESS), 40 cm (Double Spade) and 80 cm (SubVESS) depth. Graduated changes were observed by soil and some crop quantitative measurements as traffic treatment varied. VESS and Double Spade successfully identified a graduated treatment effect at all sites to 40 cm depth, although diagnosis translated into a yield response for the loam but not the sandy soil. Correlation between VESS Sq scores and crop yield were found. SubVESS gave mixed signals and indicated impacts lower in the profile in certain instances. These impacts were not captured by quantitative soil measurements.This work highlights the capacity for VSE techniques to indicate soil structural damage, which may cause a crop yield response, therefore allowing appropriate soil management strategies to be deployed before yield penalties occur.
  • The challenge of managing soil functions at multiple scales: An optimisation study of the synergistic and antagonistic trade-offs between soil functions in Ireland

    Valujeva, Kristine; O’Sullivan, Lilian; Gutzler, Carsten; Fealy, Reamonn; Schulte, Rogier P.; European Commission (Elsevier, 2016-08-09)
    Recent forecasts show a need to increase agricultural production globally by 60% from 2005 to 2050, in order to meet a rising demand from a growing population. This poses challenges for scientists and policy makers to formulate solutions on how to increase food production and simultaneously meet environmental targets such as the conservation and protection of water, the conservation of biodiversity, and the mitigation of greenhouse gas emissions. As soil and land are subject to growing pressure to meet both agronomic and environmental targets, there is an urgent need to understand to what extent these diverging targets can be met simultaneously. Previously, the concept of Functional Land Management (FLM) was developed as a framework for managing the multifunctionality of land. In this paper, we deploy and evaluate the concept of FLM, using a real case-study of Irish agriculture. We investigate a number of scenarios, encompassing combinations of intensification, expansion and land drainage, for managing three soil functions, namely primary productivity, water purification and carbon sequestration. We use proxy-indicators (milk production, nitrate concentrations and area of new afforestation) to quantify the ‘supply’ of these three soil functions, and identify the relevant policy targets to frame the ‘demand’ for these soil functions. Specifically, this paper assesses how soil management and land use management interact in meeting these multiple targets simultaneously, by employing a non-spatial land use model for livestock production in Ireland that assesses the supply of soil functions for contrasting soil drainage and land use categories. Our results show that, in principle, it is possible to manage these three soil functions to meet both agronomic and environmental objectives, but as we add more soil functions, the management requirements become increasingly complex. In theory, an expansion scenario could meet all of the objectives simultaneously. However, this scenario is highly unlikely to materialise due to farm fragmentation, low land mobility rates and the challenging afforestation rates required for achieving the greenhouse gas reduction targets. In the absence of targeted policy interventions, an unmanaged combination of scenarios is more likely to emerge. The challenge for policy formation on future land use is how to move from an unmanaged combination scenario towards a managed combination scenario, in which the soil functions are purposefully managed to meet current and future agronomic and environmental targets, through a targeted combination of intensification, expansion and land drainage. Such purposeful management requires that the supply of each soil function is managed at the spatial scale at which the corresponding demand manifests itself. This spatial scale may differ between the soil functions, and may range from farm scale to national scale. Finally, our research identifies the need for future research to also consider and address the misalignment of temporal scales between the supply and demand of soil functions.
  • Can herbage nitrogen fractionation in Lolium perenne be improved by herbage management?

    Hoekstra, Nyncke J.; Struik, Paul; Lantinga, Egbert A.; Van Amburgh, Michael; Schulte, Rogier P.; Teagasc Walsh Fellowship Programme (Elsevier, 2009-08-20)
    The high degradability of grass protein is an important factor in the low nitrogen (N) utilization of grazing bovines in intensive European grassland systems. We tested the hypothesis that protein degradability as measured by the Cornell Net Carbohydrate and Protein System (CNCPS) protein fractionation scheme, can be manipulated by herbage management tools, with the aim to reduce N loss to the environment. A field experiment comprising the factorial combinations of three fertilizer N application rates (0, 90 and 390 kg N ha−1 year−1), three regrowth periods (2–3, 4–5, and 6–7 weeks), two perennial ryegrass (Lolium perenne L.) cultivars [Aberdart (high sugar content) and Respect (low sugar content)] and two cutting heights (approximately 8 and 12 cm) was conducted at Teagasc, Johnstown Castle Research Centre, Wexford, Ireland. The plots were sampled during four seasons [September/October 2002 (late season), April 2003 (early season), May/June 2003 (mid season) and September 2003 (late season)] and protein fractions were determined in both sheath and lamina material. The protein was highly soluble and on average 19% and 28% of total N was in the form of non-protein N, 16% and 19% in the form of buffer-soluble protein, 52% and 40% in the form of buffer-insoluble protein, and 12% and 13% in the form of potentially available cell wall N for lamina and sheath material, respectively. In both materials only 0.9% of total N was present as unavailable cell wall N. In general the herbage management tools investigated did not have much effect on protein fractionation. The effects of regrowth period, cultivar and cutting height were small and inconsistent. High N application rates significantly increased protein degradability, especially during late season. This is relevant, as it has been shown that enhanced protein degradation increases the potential N loss through urine excretion at a time when urine-N excreted onto pasture is prone to leaching. However, the effect was most evident for sheath material, which forms only a small proportion of the animals' intake. It was concluded that there appears to be little scope for manipulating the herbage-N fractionation through herbage management. The consequences for modelling herbage quality could be positive as there does not seem to be a need to model the individual N fractions; in most cases the N fractions can be expressed as a fixed proportion of total N instead.
  • Predicting microbial water quality with models: Over-arching questions for managing risk in agricultural catchments

    Oliver, David M.; Porter, Kenneth D.H.; Pachepsky, Yakov A.; Muirhead, Richard W.; Reaney, Sim M.; Coffey, Rory; Kay, David; Milledge, David G.; Hong, Eunmi; Anthony, Steven G.; et al. (Elsevier, 2015-12-03)
    The application of models to predict concentrations of faecal indicator organisms (FIOs) in environmental systems plays an important role for guiding decision-making associated with the management of microbial water quality. In recent years there has been an increasing demand by policy-makers for models to help inform FIO dynamics in order to prioritise efforts for environmental and human-health protection. However, given the limited evidence-base on which FIO models are built relative to other agricultural pollutants (e.g. nutrients) it is imperative that the end-user expectations of FIO models are appropriately managed. In response, this commentary highlights four over-arching questions associated with: (i) model purpose; (ii) modelling approach; (iii) data availability; and (iv) model application, that must be considered as part of good practice prior to the deployment of any modelling approach to predict FIO behaviour in catchment systems. A series of short and longer-term research priorities are proposed in response to these questions in order to promote better model deployment in the field of catchment microbial dynamics.
  • Transcriptome sequencing of Festulolium accessions under salt stress

    Teshome, A.; Byrne, S. L; Didion, T.; De Vega, J.; Jensen, C. S; Klaas, M.; Barth, S.; European Union; Marie Sklodowska-Curie Actions; FP7-KBBE-2011-5-289461; et al. (Biomed Central, 2019-05-31)
    Objectives The objective of this study was to establish transcriptome assemblies of Festulolium hybrids under salt stress, and identify genes regulated across the hybrids in response to salt stress. The development of transcriptome assemblies for Festulolium hybrids and cataloguing of genes regulated under salt stress will facilitate further downstream studies. Results Plants were grown at three salt concentrations (0.5%, 1% and 1.5%) and phenotypic and transcriptomic data was collected. Salt stress was confirmed by progressive loss of green leaves as salt concentration increased from 0 to 1.5%. We generated de-novo transcriptome assemblies for two Festulolium pabulare festucoid genotypes, for a single Festulolium braunii genotype, and a single F. pabulare loloid genotype. We also identified 1555 transcripts that were up regulated and 1264 transcripts that were down regulated in response to salt stress in the Festulolium hybrids. Some of the identified transcripts showed significant sequence similarity with genes known to be regulated during salt and other abiotic stresses.
  • Using machine learning to estimate herbage production and nutrient uptake on Irish dairy farms

    Nikoloski, Stevanche; Murphy, Philip; Kocev, Dragi; Džeroski, Sašo; Wall, David; Teagasc Walsh Fellowship Programme; European Union; 635201 (Elsevier for American Dairy Science Association, 2019-08-22)
    Nutrient management on grazed grasslands is of critical importance to maintain productivity levels, as grass is the cheapest feed for ruminants and underpins these meat and milk production systems. Many attempts have been made to model the relationships between controllable (crop and soil fertility management) and noncontrollable influencing factors (weather, soil drainage) and nutrient/productivity levels. However, to the best of our knowledge not much research has been performed on modeling the interconnections between the influencing factors on one hand and nutrient uptake/herbage production on the other hand, by using data-driven modeling techniques. Our paper proposes to use predictive clustering trees (PCT) learned for building models on data from dairy farms in the Republic of Ireland. The PCT models show good accuracy in estimating herbage production and nutrient uptake. They are also interpretable and are found to embody knowledge that is in accordance with existing theoretical understanding of the task at hand. Moreover, if we combine more PCT into an ensemble of PCT (random forest of PCT), we can achieve improved accuracy of the estimates. In practical terms, the number of grazings, which is related proportionally with soil drainage class, is one of the most important factors that moderates the herbage production potential and nutrient uptake. Furthermore, we found the nutrient (N, P, and K) uptake and herbage nutrient concentration to be conservative in fields that had medium yield potential (11 t of dry matter per hectare on average), whereas nutrient uptake was more variable and potentially limiting in fields that had higher and lower herbage production. Our models also show that phosphorus is the most limiting nutrient for herbage production across the fields on these Irish dairy farms, followed by nitrogen and potassium.
  • Equivalence analysis to support environmental safety assessment: Using nontarget organism count data from field trials with cisgenically modified potato

    van der Voet, Hilko; Goedhart, Paul W.; Lazebnik, Jenny; Kessel, Geert J. T.; Mullins, Ewen; van Loon, Joop J. A.; Arpaia, Salvatore; European Union; 289706 (Wiley, 2019-02-14)
    This paper considers the statistical analysis of entomological count data from field experiments with genetically modified (GM) plants. Such trials are carried out to assess environmental safety. Potential effects on nontarget organisms (NTOs), as indicators of biodiversity, are investigated. The European Food Safety Authority (EFSA) gives broad guidance on the environmental risk assessment (ERA) of GM plants. Field experiments must contain suitable comparator crops as a benchmark for the assessment of designated endpoints. In this paper, a detailed protocol is proposed to perform data analysis for the purpose of assessing environmental safety. The protocol includes the specification of a list of endpoints and their hierarchical relations, the specification of intended levels of data analysis, and the specification of provisional limits of concern to decide on the need for further investigation. The protocol emphasizes a graphical representation of estimates and confidence intervals for the ratio of mean abundances for the GM plant and its comparator crop. Interpretation relies mainly on equivalence testing in which confidence intervals are compared with the limits of concern. The proposed methodology is illustrated with entomological count data resulting from multiyear, multilocation field trials. A cisgenically modified potato line (with enhanced resistance to late blight disease) was compared to the original conventional potato variety in the Netherlands and Ireland in two successive years (2013, 2014). It is shown that the protocol encompasses alternative schemes for safety assessment resulting from different research questions and/or expert choices. Graphical displays of equivalence testing at several hierarchical levels and their interpretation are presented for one of these schemes. The proposed approaches should be of help in the ERA of GM or other novel plants.
  • Relating growth potential and biofilm formation of Shigatoxigenic Escherichia coli to in planta colonisation and the metabolome of ready- to-eat crops

    Merget, Bernhard; Forbes, Ken J; Brennan, Fiona; McAteer, Sean P; Shepherd, Tom; Strachan, Norval J; Holden, Nicola; FSA; Scottish Rural & Environment Science & Analytical Services Division; FS101056 (Cold Spring Harbor Laboratory, 2019-01-17)
    Contamination of fresh produce with pathogenic Escherichia coli, including Shigatoxigenic E. coli (STEC), represents a serious risk to human health. Colonisation is governed by multiple bacterial and plant factors that can impact on the probability and suitability of bacterial growth. Thus, we aimed to determine whether the growth potential of STEC for plants associated with foodborne outbreaks (two leafy vegetables and two sprouted seed species), is predictive for colonisation of living plants as assessed from growth kinetics and biofilm formation in plant extracts. Fitness of STEC was compared to environmental E. coli, at temperatures relevant to plant growth. Growth kinetics in plant extracts varied in a plant-dependent and isolate-dependent manner for all isolates, with spinach leaf lysates supporting the fastest rates of growth. Spinach extracts also supported the highest levels of biofilm formation. Saccharides were identified as the major driver of bacterial growth, although no single metabolite could be correlated with growth kinetics. The highest level of in planta colonisation occurred on alfalfa sprouts, though internalisation was 10-times more prevalent in the leafy vegetables than in sprouted seeds. Marked differences in in planta growth meant that growth potential could only be inferred for STEC for sprouted seeds. In contrast, biofilm formation in extracts related to spinach colonisation. Overall, the capacity of E. coli to colonise, grow and internalise within plants or plant-derived matrices were influenced by the isolate type, plant species, plant tissue type and temperature, complicating any straight-forward relationship between in vitro and in planta behaviours. Importance Fresh produce is an important vehicle for STEC transmission and experimental evidence shows that STEC can colonise plants as secondary hosts, but differences in the capacity to colonise occur between different plant species and tissues. Therefore, an understanding of the impact of these plant factors have on the ability of STEC to grow and establish is required for food safety considerations and risk assessment. Here, we determined whether growth and the ability of STEC to form biofilms in plants extracts could be related to specific plant metabolites or could predict the ability of the bacteria to colonise living plants. Growth rates for sprouted seeds (alfalfa and fenugreek) exhibited a positive relationship between plant extracts and living plants, but not for leafy vegetables (lettuce and spinach). Therefore, the detailed variations at the level of the bacterial isolate, plant species and tissue type all need to be considered in risk assessment.
  • The impact of cattle dung pats on earthworm distribution in grazed pastures

    Bacher, M. G.; Fenton, O.; Bondi, G.; Creamer, R. E.; Karmarkar, M.; Schmidt, O.; Department of Agriculture, Food and the Marine; 13/S/468 (Springer Science and Business Media LLC, 2018-12-19)
    Background Grazed grassland management regimes can have various effects on soil fauna. For example, effects on earthworms can be negative through compaction induced by grazing animals, or positive mediated by increases in sward productivity and cattle dung pats providing a food source. Knowledge gaps exist in relation to the behaviour of different earthworm species i.e. their movement towards and aggregation under dung pats, the legacy effects of pats and the spatial area of recruitment. The present study addressed these knowledge gaps in field experiments, over 2 years, using natural and simulated dung pats on two permanent, intensively grazed pastures in Ireland. Results Dung pats strongly affected spatial earthworm distribution, with up to four times more earthworms aggregating beneath pats, than in the control locations away from pats. In these earthworm communities comprising 11 species, temporally different aggregation and dispersal patterns were observed, including absence of individual species from control locations, but no clear successional responses. Epigeic species in general, but also certain species of the anecic and endogeic groups were aggregating under dung. Sampling after complete dung pat disappearance (27 weeks after application) suggested an absence of a dung pat legacy effect on earthworm communities. Based on species distributions, the maximum size of the recruitment area from which earthworms moved to pats was estimated to be 3.8 m2 per dung pat. Since actual grazing over 6 weeks would result in the deposition of about 300 dung pats per ha, it is estimated that a surface area of 1140 m2 or about 11% of the total grazing area can be influenced by dung pats in a given grazing period. Conclusions This study showed that the presence of dung pats in pastures creates temporary hot spots in spatial earthworm species distribution, which changes over time. The findings highlight the importance of considering dung pats, temporally and spatially, when sampling earthworms in grazed pastures. Published comparisons of grazed and cut grasslands probably reached incorrect conclusions by ignoring or deliberately avoiding dung pats. Furthermore, the observed intense aggregation of earthworms beneath dung pats suggests that earthworm functions need to be assessed separately at these hot spots.
  • Pooled DNA sequencing to identify SNPs associated with a major QTL for bacterial wilt resistance in Italian ryegrass (Lolium multiflorum Lam.)

    Knorst, Verena; Byrne, Stephen; Yates, Steven; Asp, Torben; Widmer, Franco; Studer, Bruno; Kölliker, Roland; Swiss National Science Foundation; 31003A_138358 (Springer Science and Business Media LLC, 2018-11-30)
    Italian ryegrass (Lolium multiflorum Lam.) is one of the most important forage grass species in temperate regions. Its yield, quality and persistency can significantly be reduced by bacterial wilt, a serious disease caused by Xanthomonas translucens pv. graminis. Although a major QTL for bacterial wilt resistance has previously been reported, detailed knowledge on underlying genes and DNA markers to allow for efficient resistance breeding strategies is currently not available. We used pooled DNA sequencing to characterize a major QTL for bacterial wilt resistance of Italian ryegrass and to develop inexpensive sequence-based markers to efficiently target resistance alleles for marker-assisted recurrent selection. From the mapping population segregating for the QTL, DNA of 44 of the most resistant and 44 of the most susceptible F1 individuals was pooled and sequenced using the Illumina HiSeq 2000 platform. Allele frequencies of 18 × 106 single nucleotide polymorphisms (SNP) were determined in the resistant and susceptible pool. A total of 271 SNPs on 140 scaffold sequences of the reference parental genome showed significantly different allele frequencies in both pools. We converted 44 selected SNPs to KASP™ markers, genetically mapped these proximal to the major QTL and thus validated their association with bacterial wilt resistance. This study highlights the power of pooled DNA sequencing to efficiently target binary traits in biparental mapping populations. It delivers genome sequence data, SNP markers and potential candidate genes which will allow to implement marker-assisted strategies to fix bacterial wilt resistance in outcrossing breeding populations of Italian ryegrass.
  • Characterization of Potato Virus Y Isolates and Assessment of Nanopore Sequencing to Detect and Genotype Potato Viruses

    Della Bartola, Michele; Byrne, Stephen; Mullins, Ewen; Department of Agriculture, Food and the Marine; 15/S/618 SCOPE (MDPI AG, 2020-04-23)
    Potato virus Y (PVY) is the most economically important virus infecting cultivated potato (Solanum tuberosum L.). Accurate diagnosis is crucial to regulate the trade of tubers and for the sanitary selection of plant material for propagation. However, high genetic diversity of PVY represents a challenge for the detection and classification of isolates. Here, the diversity of Irish PVY isolates from a germplasm collection and commercial sites was investigated using conventional molecular and serological techniques. Recombinant PVY isolates were prevalent, with PVYNTNa being the predominant genotype. In addition, we evaluated Nanopore sequencing to detect and reconstruct the whole genome sequence of four viruses (PVY, PVX, PVS, PLRV) and five PVY genotypes in a subset of eight potato plants. De novo assembly of Nanopore sequencing reads produced single contigs covering greater than 90% of the viral genome and sharing greater than 99.5% identity to the consensus sequences obtained with Illumina sequencing. Interestingly, single near full genome contigs were obtained for different isolates of PVY co-infecting the same plant. Mapping reads to available reference viral genomes enabled us to generate near complete genome sequences sharing greater than 99.90% identity to the Illumina-derived consensus. This is the first report describing the use of Oxford Nanopore’s MinION to detect and genotype potato viruses. We reconstructed the genome of PVY and other RNA viruses; indicating the technologies potential for virus detection in potato production systems, and for the study of genetic diversity of highly heterogeneous viruses such as PVY.
  • Transforming Sitka Spruce Plantations

    Wilson, Edward R.; Ní Dhubháin, Aine; Short, Ian; Teagasc Walsh Fellowship Programme (Teagasc, 2020)
    The TranSSFor project is comparing conventional thinning in Sitka spruce plantations with two alternative thinning regimes.
  • Farming for Nature. The Role of Results-Based Payments

    O'Rourke, Eileen; Finn, John A. (Teagasc and National Parks and Wildlife Service (NPWS), 2020)
    Agricultural habitats cover approximately half the European Union (EU) and an estimated 50% of all species and several habitats of conservation concern in the EU depend on agricultural management. Reversing the loss of European biodiversity is clearly dependent on the conservation of farmland biodiversity. Results-based approaches are the focus of a growing discussion about improved biodiversity conservation and environmental performance of EU agri-environmental policies. This book outlines lessons learned from a collection of Irish case studies that have implemented results-based approaches and payments for the conservation of farmland habitats and species. The case studies include prominent projects and programmes: the Burren Programme, AranLIFE, KerryLIFE, the NPWS Farm Plan Scheme and Result-Based Agri-environmental Payment Schemes (RBAPS) project. This work is intended for an international audience of practitioners, policymakers and academics interested in results-based approaches for the conservation of biodiversity and the provision of ecosystem services.
  • Comparison of three inventory protocols for use in privately-owned plantations under transformation to Continuous Cover Forestry

    Spazzi, Jonathan; O Tuama, Padraig; Wilson, Edward R.; Short, Ian (Society of Irish Foresters, 2019)
    Interest is growing in Continuous Cover Forestry (CCF) as a management approach among private forest owners in Ireland. Developments in forest policy are directed at promoting CCF as a means of enhancing forest resilience, sustaining forest production and delivering diverse ecosystem services. In 2019 the Department of Agriculture, Food and the Marine (DAFM) introduced a new pilot funding measure to support the adoption of CCF management in suitable private forests. Currently the area of forest under CCF management is relatively small (estimated at around 1% of the total forest area) and several barriers to wider adoption have been identified. These include the lack of a simple template for the transformation of planted forests to CCF and a monitoring protocol with known inventory costs and outputs. In this study three inventory protocols were compared in terms of their ease of use, the types of data outputs and cost effectiveness in a forest stand at an early stage of transformation to CCF. These protocols were compared to a complete enumeration approach. The inventory protocols being tested were developed by the UK Forestry Commission (FCIN45), a group of French and Belgian researchers (VISUAL) and the Irregular Silviculture Network (ISN). Results indicate that by using modern technology and careful design, a cost-effective inventory protocol can be implemented to collect information of sufficient accuracy to inform management decisions. Advantages and limitations of each protocol are discussed. The ultimate outcome would be the development and adoption of a common inventory and monitoring approach to enable private owners to critically compare stand management and performance. This is essential to support and guide forest managers and forest owners during the transformation process.
  • Nitrogen and Phosphorus Availability From Various Composted Wastes For Use In Irish Agriculture And Horticulture

    Lee, Alan; Teagasc Walsh Fellowship Programme (2016-02)
    Current environmental EU legislation promotes recycling and recovery from organic waste products. Compost has been identified as an alternative to inorganic fertilisers and animal slurries as a nutrient source for crop plants. This study aimed to investigate nitrogen (N) and phosphorus (P) availability from various composted waste through detailed characterisations, complemented by short term lab incubations and long term plant growth experiments. Twenty-five composts were selected and classified by their groups. The composts were characterised by multiple different analytical techniques. Two incubation studies were conducted. One investigating N and P mineralisation potential of the composts and the second on the effects or soil type on P mineralisation. Two large glasshouse based pot experiments were then conducted. A subsequent stability study of two separate methods on mechanical biological treated waste was also investigated for a potential relationship. Characterisation of the composts highlighted the difference between compost feedstocks with the manure waste being distinctly separate from the other groups. The biowaste groups identified as either food waste or brown bin waste. The incubation experiment highlighted that N mineralisation was more predictable than P. From the pot experiment only manure waste mineralised N above 10%. All of the other groups mineralised minute amounts. Prediction of N mineralisation was found to be more accurate from lignin and neutral detergent fibre content over the more traditional C/N ratio. Mineralisation of small amounts of organic N occurred in summer months. There was a distinct lack of a relationship between the P incubation and pot experiment. Plant uptake of P was higher than expected for all treatments. The manure waste composts were higher in cumulative P uptake than inorganic fertiliser. Stability in composts was found not to affect mineralisation or induce immobilisation. The effects of soil type on composts were most pronounced in composts lower in fulvic acid. The composts with higher humic acid were not found to significantly mineralise a higher amount of P. The stability study investigating oxygen uptake rate (OUR) and respiration index (AT4) on the mechanical biological treated waste showed a high correlation between the two methods where AT4 was below 40 mg O2.g DM-1. The findings point to a possible reassessment of compost quality guidelines for composts. The availability of P is far greater and therefore should be considered the primary nutrient available from compost. The stability parameter for manure waste compost may also need assessing as it is unachievable in reasonable composting time frame. The biowaste compost has proven to be high in P. There is also the potential to develop quite specifically produced composts based on their feedstock and composting length for particular agronomic or environmental needs. Compost application is a feasible source of nutrients and organic matter due to escalating fertiliser prices and more stringent regulations surrounding fertilisers and slurries.

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