• Annual replication is essential in evaluating the response of the soil microbiome to the genetic modification of maize in different biogeographical regions

      Szoboszlay, Márton; Näther, Astrid; Mullins, Ewen; Tebbe, Christoph C.; European Union; 289706 (Public Library of Science (PLoS), 2019-12-17)
      The importance of geographic location and annual variation on the detection of differences in the rhizomicrobiome caused by the genetic modification of maize (Bt-maize, event MON810) was evaluated at experimental field sites across Europe including Sweden, Denmark, Slovakia and Spain. DNA of the rhizomicrobiome was collected at the maize flowering stage in three consecutive years and analyzed for the abundance and diversity of PCR-amplified structural genes of Bacteria, Archaea and Fungi, and functional genes for bacterial nitrite reductases (nirS, nirK). The nirK genes were always more abundant than nirS. Maize MON810 did not significantly alter the abundance of any microbial genetic marker, except for sporadically detected differences at individual sites and years. In contrast, annual variation between sites was often significant and variable depending on the targeted markers. Distinct, site-specific microbial communities were detected but the sites in Denmark and Sweden were similar to each other. A significant effect of the genetic modification of the plant on the community structure in the rhizosphere was detected among the nirK denitrifiers at the Slovakian site in only one year. However, most nirK sequences with opposite response were from the same or related source organisms suggesting that the transient differences in community structure did not translate to the functional level. Our results show a lack of effect of the genetic modification of maize on the rhizosphere microbiome that would be stable and consistent over multiple years. This demonstrates the importance of considering annual variability in assessing environmental effects of genetically modified crops.
    • The Complex Pathway towards Farm-Level Sustainable Intensification: An Exploratory Network Analysis of Stakeholders’ Knowledge and Perception

      Micha, Evgenia; Fenton, Owen; Daly, Karen M.; Kakonyi, Gabriella; Ezzati, Golnaz; Moloney, Thomas; Thornton, Steven; European Union; 675120 (MDPI AG, 2020-03-25)
      Farm-level sustainable intensification of agriculture (SIA) has become an important concept to ensuring food security while minimising negative externalities. However, progress towards its achievement is often constrained by the different perceptions and goals of various stakeholders that affect farm management decisions. This study examines farm-level SIA as a dynamic system with interactive components that are determined by the interests of the stakeholders involved. A systems thinking approach was used to identify and describe the pathways towards farm-level SIA across the three main pillars of sustainability. An explanatory network analysis of fuzzy cognitive maps (FCMs) that were collectively created by representative groups of farmers, farm advisors and policy makers was performed. The study shows that SIA is a complex dynamic system, affected by cognitive beliefs and particular knowledge within stakeholder groups. The study concludes that, although farm-level SIA is a complex process, common goals can be identified in collective decision making.
    • Ecosystem function enhanced by combining four functional types of plant species in intensively-managed grassland mixtures: a three-year continental-scale field experiment

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

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

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

      Bhaskar A.V., Vijaya; Baresel, Jörg Peter; Weedon, Odette; Finckh, Maria R.; German BMBF; European Union; 031A350C; 727217 (Springer Nature, 2019-06-21)
      Early vigour traits of wheat composite cross populations (CCPs) based on high yielding (Y) or high quality (Q) or Y*Q varietal intercross evolving under organic or conventional conditions in parallel populations were studied hydroponically. To eliminate storage and year effects, frozen F6, F10, F11 and F15 seeds were multiplied in one field, resulting in the respective Fx.1 generations. This eliminated generation and growing system effects on seed size for the F6.1 F10.1 and F15.1. Due to a severe winter kill affecting the F11, the generation effect persisted, leading to larger seeds and markedly different seedling traits in the F11.1 compared to the F10.1 and F15.1. Seedling traits were similar among parallel populations. Shoot length and weight increased in both systems until the F11.1 across farming systems and remained constant thereafter. Over time, seminal root length and root weight of organic CCPs increased and total- and specific- root length decreased significantly compared to the conventional CCPs. Rooting patterns under organic conditions suggests better ability to reach deeper soil nutrients. In both systems, Q and YQ CCPs were more vigorous than Y CCPs, confirming genetic differences among populations. Overall, heterogeneous populations appear very plastic and selection pressure was stronger in organic systems.
    • 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.
    • Exploring the potential of grass feedstock from marginal land in Ireland: Does marginal mean lower yield?

      Meehan, Peter; Burke, Brendan; Doyle, Deirdre; Barth, Susanne; Finnan, John; European Union; KBBE-2011-5-289461 (Elsevier, 2017-11-02)
      The production of biomass feedstock from marginal land has attracted much attention as a means of avoiding conflict between the production of food and fuel. Yield potentials from marginal lands have generally not been quantified although it is generally assumed that lower biomass yields can be expected from marginal lands. A three year study was conducted in Ireland in order to determine if grass yields of perennial rhizomatous grasses (cocksfoot, tall fescue, reed canary grass, festulolium) for anaerobic digestion from three marginal land sites (very wet site, very dry site, site prone to flooding) could match yields from better soils. Randomised complete block designs were established on each site in 2012 with two varieties of each grass species as treatments. Three grass harvests were taken from each site in 2013 and in 2014. There was no significant difference between yields from the control site and those from the very dry site and the site prone to flooding. Biomass yields from the very wet site were 85% of those from the control site. Highest yields were obtained from festulolium which were significantly higher than yields from perennial ryegrass. An energy analysis showed that maximising the production of grass from low lying mineral marginal grassland in Ireland could provide enough energy to meet the energy requirements of both the private car fleet and the heavy goods vehicle fleet while avoiding conflict with food production which could be concentrated on conventional land.
    • A Field-Scale Decision Support System for Assessment and Management of Soil Functions

      Debeljak, Marko; Trajanov, Aneta; Kuzmanovski, Vladimir; Schröder, Jaap; Sandén, Taru; Spiegel, Heide; Wall, David; Van de Broek5, Marijn; Rutgers, Michiel; Bampa, France; et al. (Frontiers Media SA, 2019-08-05)
      Agricultural decision support systems (DSSs) are mostly focused on increasing the supply of individual soil functions such as, e.g., primary productivity or nutrient cycling, while neglecting other important soil functions, such as, e.g., water purification and regulation, climate regulation and carbon sequestration, soil biodiversity, and habitat provision. Making right management decisions for long-term sustainability is therefore challenging, and farmers and farm advisors would greatly benefit from an evidence-based DSS targeted for assessing and improving the supply of several soil functions simultaneously. To address this need, we designed the Soil Navigator DSS by applying a qualitative approach to multi-criteria decision modeling using Decision Expert (DEX) integrative methodology. Multi-criteria decision models for the five main soil functions were developed, calibrated, and validated using knowledge of involved domain experts and knowledge extracted from existing datasets by data mining. Subsequently, the five DEX models were integrated into a DSS to assess the soil functions simultaneously and to provide management advices for improving the performance of prioritized soil functions. To enable communication between the users and the DSS, we developed a user-friendly computer-based graphical user interface, which enables users to provide the required data regarding their field to the DSS and to get textual and graphical results about the performance of each of the five soil functions in a qualitative way. The final output from the DSS is a list of soil mitigation measures that the end-users could easily apply in the field in order to achieve the desired soil function performance. The Soil Navigator DSS has a great potential to complement the Farm Sustainability Tools for Nutrients included in the Common Agricultural Policy 2021–2027 proposal adopted by the European Commission. The Soil Navigator has also a potential to be spatially upgraded to assist decisions on which soil functions to prioritize in a specific region or member state. Furthermore, the Soil Navigator DSS could be used as an educational tool for farmers, farm advisors, and students, and its potential should be further exploited for the benefit of farmers and the society as a whole.
    • Functional Land Management: Bridging the Think-Do-Gap using a multi-stakeholder science policy interface

      O'Sullivan, Lilian; Wall, David; Creamer, Rachel E.; Bampa, Francesca; Schulte, Rogier P.; European Union; National Development Plan 2007–2013.; 635201; 677407; 13S468 (Springer, 2017-11)
      Functional Land Management (FLM) is proposed as an integrator for sustainability policies and assesses the functional capacity of the soil and land to deliver primary productivity, water purification and regulation, carbon cycling and storage, habitat for biodiversity and recycling of nutrients. This paper presents the catchment challenge as a method to bridge the gap between science, stakeholders and policy for the effective management of soils to deliver these functions. Two challenges were completed by a wide range of stakeholders focused around a physical catchment model—(1) to design an optimised catchment based on soil function targets, (2) identify gaps to implementation of the proposed design. In challenge 1, a high level of consensus between different stakeholders emerged on soil and management measures to be implemented to achieve soil function targets. Key gaps including knowledge, a mix of market and voluntary incentives and mandatory measures were identified in challenge 2.
    • Functional Land Management: Bridging the Think-Do-Gap using a multi-stakeholder science policy interface

      O’Sullivan, Lilian; Wall, David; Creamer, Rachel; Bampa, Francesca; Schulte, Rogier P. O.; National Development Plan 2007–2013; European Union; 13S468; 635201; 677407 (Springer Science and Business Media LLC, 2017-11-24)
      Functional Land Management (FLM) is proposed as an integrator for sustainability policies and assesses the functional capacity of the soil and land to deliver primary productivity, water purification and regulation, carbon cycling and storage, habitat for biodiversity and recycling of nutrients. This paper presents the catchment challenge as a method to bridge the gap between science, stakeholders and policy for the effective management of soils to deliver these functions. Two challenges were completed by a wide range of stakeholders focused around a physical catchment model—(1) to design an optimised catchment based on soil function targets, (2) identify gaps to implementation of the proposed design. In challenge 1, a high level of consensus between different stakeholders emerged on soil and management measures to be implemented to achieve soil function targets. Key gaps including knowledge, a mix of market and voluntary incentives and mandatory measures were identified in challenge 2.
    • Future global pig production systems according to the Shared Socioeconomic Pathways

      Lassaletta, Luis; Estellés, Fernando; Beusen, Arthur; Bouwman, Lex; Calvet, Salvador; van Grinsven, Hans J.M.; Doelman, Jonathan; Stehfest, Elke; Uwizeye, Aimable; Westhoek, Henk; et al. (Elsevier, 2019-02-08)
      Global pork production has increased fourfold over the last 50 years and is expected to continue growing during the next three decades. This may have considerable implications for feed use, land requirements, and nitrogen emissions. To analyze the development of the pig production sector at the scale of world regions, we developed the IMAGE-Pig model to describe changes in feed demand, feed conversion ratios (FCRs), nitrogen use efficiency (NUE) and nitrogen excretion for backyard, intermediate and intensive systems during the past few decades as a basis to explore future scenarios. For each region and production system, total production, productive characteristics and dietary compositions were defined for the 1970–2005 period. The results show that due to the growing pork production total feed demand has increased by a factor of two (from 229 to 471Tg DM). This is despite the improvement of FCRs during the 1970–2005 period, which has reduced the feed use per kg of product. The increase of nitrogen use efficiency was slower than the improvement of FCRs due to increasing protein content in the feed rations. As a result, total N excretion increased by more than a factor of two in the 1970–2005 period (from 4.6 to 11.1 Tg N/year). For the period up to 2050, the Shared Socio-economic Pathways (SSPs) provide information on levels of human consumption, technical development and environmental awareness. The sustainability of pig production systems for the coming decades will be based not only on the expected efficiency improvements at the level of animal breeds, but also on four additional pillars: (i) use of alternative feed sources not competing with human food, (ii) reduction of the crude protein content in rations, (iii) the proper use of slurries as fertilizers through coupling of crop and livestock production and (iv) moderation of the human pork consumption.
    • Genetic Analysis Using a Multi-Parent Wheat Population Identifies Novel Sources of Septoria Tritici Blotch Resistance

      Riaz, Adnan; KockAppelgren, Petra; Hehir, James Gerard; Kang, Jie; Meade, Fergus; Cockram, James; Milbourne, Dan; Spink, John; Mullins, Ewen; Byrne, Stephen; et al. (MDPI AG, 2020-08-04)
      Zymoseptoria tritici is the causative fungal pathogen of septoria tritici blotch (STB) disease of wheat (Triticum aestivum L.) that continuously threatens wheat crops in Ireland and throughout Europe. Under favorable conditions, STB can cause up to 50% yield losses if left untreated. STB is commonly controlled with fungicides; however, a combination of Z. tritici populations developing fungicide resistance and increased restrictions on fungicide use in the EU has led to farmers relying on fewer active substances. Consequently, this serves to drive the emergence of Z. tritici resistance against the remaining chemistries. In response, the use of resistant wheat varieties provides a more sustainable disease management strategy. However, the number of varieties offering an adequate level of resistance against STB is limited. Therefore, new sources of resistance or improved stacking of existing resistance loci are needed to develop varieties with superior agronomic performance. Here, we identified quantitative trait loci (QTL) for STB resistance in the eight-founder “NIAB Elite MAGIC” winter wheat population. The population was screened for STB response in the field under natural infection for three seasons from 2016 to 2018. Twenty-five QTL associated with STB resistance were identified in total. QTL either co-located with previously reported QTL or represent new loci underpinning STB resistance. The genomic regions identified and the linked genetic markers serve as useful resources for STB resistance breeding, supporting rapid selection of favorable alleles for the breeding of new wheat cultivars with improved STB resistance.
    • Genomic prediction of crown rust resistance in Lolium perenne

      Arojju, Sai Krishna; Conaghan, Patrick; Barth, Susanne; Milbourne, Dan; Casler, Michael D.; Hodkinson, Trevor R.; Michel, Thibauld; Byrne, Stephen; Department of Agriculture Food and the Marine; European Union; et al. (Springer Science and Business Media LLC, 2018-05-29)
      Background Genomic selection (GS) can accelerate genetic gains in breeding programmes by reducing the time it takes to complete a cycle of selection. Puccinia coronata f. sp lolli (crown rust) is one of the most widespread diseases of perennial ryegrass and can lead to reductions in yield, persistency and nutritional value. Here, we used a large perennial ryegrass population to assess the accuracy of using genome wide markers to predict crown rust resistance and to investigate the factors affecting predictive ability. Results Using these data, predictive ability for crown rust resistance in the complete population reached a maximum of 0.52. Much of the predictive ability resulted from the ability of markers to capture genetic relationships among families within the training set, and reducing the marker density had little impact on predictive ability. Using permutation based variable importance measure and genome wide association studies (GWAS) to identify and rank markers enabled the identification of a small subset of SNPs that could achieve predictive abilities close to those achieved using the complete marker set. Conclusion Using a GWAS to identify and rank markers enabled a small panel of markers to be identified that could achieve higher predictive ability than the same number of randomly selected markers, and predictive abilities close to those achieved with the entire marker set. This was particularly evident in a sub-population characterised by having on-average higher genome-wide linkage disequilibirum (LD). Higher predictive abilities with selected markers over random markers suggests they are in LD with QTL. Accuracy due to genetic relationships will decay rapidly over generations whereas accuracy due to LD will persist, which is advantageous for practical breeding applications.
    • Genotyping by Sequencing and Plastome Analysis Finds High Genetic Variability and Geographical Structure in Dactylis glomerata L. in Northwest Europe Despite Lack of Ploidy Variation

      Hodkinson, Trevor R.; Perdereau, Aude; Klaas, Manfred; Cormican, Paul; Barth, Susanne; European Union; 289461 (MDPI AG, 2019-06-28)
      Large collections of the forage and bioenergy grass Dactylis glomerata were made in northwest (NW) Europe along east to west and north to south clines for genetic resource conservation and to inform breeding programmes of genetic diversity, genepools, and ploidy. Leaves were sampled for genetic analysis and seed and rhizome for ex-situ conservation. Genotyping by sequencing (GBS) was used to assay nuclear DNA diversity and plastome single nucleotide polymorphism (SNP) discovery was undertaken using a long-read PCR and MiSeq approach. Nuclear and plastid SNPs were analysed by principal component analysis (PCA) to compare genotypes. Flow cytometry revealed that all samples were tetraploid, but some genome size variation was recorded. GBS detected an average of approximately 10,000 to 15,000 SNPs per country sampled. The highest average number of private SNPs was recorded in Poland (median ca. 2000). Plastid DNA variation was also high (1466 SNPs, 17 SNPs/kbp). GBS data, and to a lesser extent plastome data, also show that genetic variation is structured geographically in NW Europe with loose clustering matching the country of plant origin. The results reveal extensive genetic diversity and genetic structuring in this versatile allogamous species despite lack of ploidy variation and high levels of human mediated geneflow via planting.
    • The Impact of Policy Instruments on Soil Multifunctionality in the European Union

      Vrebos, Dirk; Bampa, Francesca; Creamer, Rachel E.; Gardi, Ciro; Ghaley, Bhim Bahadur; Jones, Arwyn; Rutgers, Michiel; Sandén, Taru; Staes, Jan; Meire, Patrick; et al. (MDPI, 2017-03-09)
      Agricultural ecosystems provide a range of benefits that are vital to human well-being. These benefits are dependent on several soil functions that are affected in different ways by legislation from the European Union, national, and regional levels. We evaluated current European Union soil-related legislation and examples of regional legislation with regard to direct and indirect impacts on five soil functions: the production of food, fiber, and fuel; water purification and regulation; carbon sequestration and climate regulation; habitat for biodiversity provisioning; and the recycling of nutrients/agro-chemicals. Our results illustrate the diversity of existing policies and the complex interactions present between different spatial and temporal scales. The impact of most policies, positive or negative, on a soil function is usually not established, but depends on how the policy is implemented by local authorities and the farmers. This makes it difficult to estimate the overall state and trends of the different soil functions in agricultural ecosystems. To implement functional management and sustainable use of the different soil functions in agricultural ecosystems, more knowledge is needed on the policy interactions as well as on the impact of management options on the different soil functions.
    • Methodological tests of the use of trace elements as tracers to assess root activity

      Hoekstra, Nyncke J.; Finn, John; Buchmann, Nina; Gockele, A.; Landert, L.; Prill, N.; Scherer-Lorenzen, M.; Luscher, L.; European Union; Irish Research Council; et al. (Springer, 2014-03)
      Background and aims There is increasing interest in how resource utilisation in grassland ecosystems is affected by changes in plant diversity and abiotic conditions. Research to date has mainly focussed on aboveground responses and there is limited insight into belowground processes. The aim of this study was to test a number of assumptions for the valid use of the trace elements caesium, lithium, rubidium and strontium as tracers to assess the root activity of several grassland species. Methods We carried out a series of experiments addressing the reliability of soil labelling, injection density, incubation time, application rate and the comparability of different tracers in a multiple tracer method. Results The results indicate that it is possible to achieve a reliable labelling of soil depths. Tracer injection density affected the variability but not the mean level of plant tracer concentrations. Tracer application rates should be based on pilot studies, because of site- and species-specific responses. The trace elements did not meet prerequisites to be used in a multiple tracer method. Conclusions The use of trace elements as tracers is potentially a very useful tool to give insight into plant root activity at different soil depths. This work highlights some of the main benefits and pitfalls of the method and provides specific recommendations to assist the design of tracer experiments and interpretation of the results.
    • Multiple factors control the environmental effectiveness of agri-environment schemes: implications for design and evaluation

      Finn, John; Kurz, Isabelle; Bourke, David; European Union; European Commission; SSPE-CT-2003-502070 (School of Agriculture, Food Science and Veterinary Medicine, University College Dublin in association with Teagasc, 2008)
      Achieving and evaluating the environmental effectiveness of agri-environment schemes (AESs) has proven difficult. The design and ex ante evaluation of AESs is a crucial phase for ensuring effectiveness, but seems to receive relatively little attention. We propose a programme theory (a structured description of the various cause-and-effect relationships that underpin and achieve a policy initiative) for AESs that considers multiple factors that drive environmental performance at farm-scale (appropriate farm-level objectives, farmer compliance, implementation by institutions, and cause-and-effect relationship between management prescriptions and environmental objectives), and factors that determine how farm-scale performance aggregates to produce scheme-scale performance (participation rate, targeting, and threshold effects). These factors can be used as assessment criteria with which to pinpoint specific causes of AES failure, and thereby offer a practical approach to complement the design and evaluation of the environmental effects of AESs.
    • Nitrogen yield advantage from grass-legume mixtures is robust over a wide range of legume proportions and environmental conditions

      Suter, Matthias; Connolly, John; Finn, John; Loges, R.; Kirwan, Laura; Sebastia, Maria Teresa; Luscher, A.; European Union (Wiley, 28/01/2015)
      Current challenges to global food security require sustainable intensification of agriculture through initiatives that include more efficient use of nitrogen (N), increased protein self-sufficiency through home-grown crops, and reduced N losses to the environment. 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 of 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 legume percentages, Ntot and Ngainmix did not continue to increase. Thus, across sites and years, mixtures with one third proportion of legumes attained ~95% of the maximum Ntot acquired by any stand and had 57% higher Ntot than grass monocultures.Realized legume proportion in stands and the relative N gain in mixture (Ngainmix/Ntot in mixture) were most severely impaired by minimum site temperature (R = 0.70, P = 0.003 for legume proportion; R = 0.64, P = 0.010 for Ngainmix/Ntot in mixture). Nevertheless, the relative N gain in mixture 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 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 thus greenhouse gas emissions and a considerable potential for climate change mitigation.
    • Plastid genome sequencing reveals biogeographical structure and extensive population genetic variation in wild populations of Phalaris arundinacea L. in north‐western Europe

      Perdereau, Aude; Klass, Manfred; Barth, Susanne; Hodkinson, Trevor R.; European Union; 289461 (Wiley, 2016-03-31)
      New and comprehensive collections of the perennial rhizomatous reed canary grass (Phalaris arundinacea) were made in NW Europe along north‐to‐south and east‐to‐west clines from Denmark, Germany, Ireland, Poland, Sweden and the United Kingdom. Rhizome, seed and leaf samples were taken for analysis and genetic resource conservation. A subsample covering the geographical range was characterized using plastid genome sequencing and SNP discovery generated using a long‐read PCR and MiSeq sequencing approach. Samples were also subject to flow cytometry and all found to be tetraploid. New sequences were assembled against a Lolium perenne (perennial ryegrass) reference genome, and an average of approximately 60% of each genome was aligned (81 064 bp). Genetic variation was high among the 48 sequenced genotypes with a total of 1793 SNPs, equating to 23 SNPs per kbp. SNPs were subject to principal coordinate and Structure analyses to detect population genetic groupings and to examine phylogeographical pattern. Results indicate substantial genetic variation and population genetic structuring of this allogamous species at a broad geographical scale in NW Europe with plastid genetic diversity organized more across an east‐to‐west than a north‐to‐south cline.