Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Trafficking intensity index for soil compaction management in grasslands
    Bondi, Giulia ; O‘Sullivan, Lilian ; Fenton, Owen ; Creamer, Rachel ; Marongiu, Irene ; Wall, David P. - \ 2020
    Soil Use and Management (2020). - ISSN 0266-0032
    compaction - grazing - machinery - soil - soil structural quality - trafficking pressure

    Good soil structure provides multiple benefits for society but in grass-based production systems is underpinned by trafficking management regime. For Irish soils, there is no soil trafficking intensity index that considers the effect of geo-climatic variability or differences in drainage classes on soil compaction risk. Grazing and machinery activity data were compiled across 38 managed grasslands along with common soil structural quality indicators in order to develop and validate a ‘soil trafficking intensity index for compaction (STICi)’. Two component indices of STICi were developed: (a) a grazing trafficking index (Gi, kg × year ha−1) and (b) a machinery trafficking index (Mi, kg × year ha−1). The average annual grazing trafficking pressure observed was 213,914 kg × year ha−1, and the average annual machinery trafficking pressure was 4,412 kg × year ha−1. These figures represent thresholds above which soils are at higher risk of compaction. Mi spanned a wider range (−2.1 ≤ Mi ≤ 2.8) compared with Gi (−1.32 ≤ Gi ≤ 1.06). STICi and components, when disaggregated by soil drainage class, were able to detect changes in direct indicators of soil structural quality, such as bulk density, total porosity, water holding capacity, water conductivity and visual soil assessment. STICi (Mi and Gi) were also related to indirect indicators, such as, soil carbon content, earthworms and microbial biomass. In general, poorly drained sites showed higher vulnerability to machinery trafficking intensity compared with grazing trafficking pressure. At national scale, STICi can be utilized to identify soils at risk of compaction and underpin targeted management advice for supporting sustainable grassland production.

    Scaling carbon fluxes from eddy covariance sites to globe : Synthesis and evaluation of the FLUXCOM approach
    Jung, Martin ; Schwalm, Christopher ; Migliavacca, Mirco ; Walther, Sophia ; Camps-Valls, Gustau ; Koirala, Sujan ; Anthoni, Peter ; Besnard, Simon ; Bodesheim, Paul ; Carvalhais, Nuno ; Chevallier, Frederic ; Gans, Fabian ; Goll, Daniel S. ; Haverd, Vanessa ; Köhler, Philipp ; Ichii, Kazuhito ; Jain, Atul K. ; Liu, Junzhi ; Lombardozzi, Danica ; Nabel, Julia E.M.S. ; Nelson, Jacob A. ; O'Sullivan, Michael ; Pallandt, Martijn ; Papale, Dario ; Peters, Wouter ; Pongratz, Julia ; Rödenbeck, Christian ; Sitch, Stephen ; Tramontana, Gianluca ; Walker, Anthony ; Weber, Ulrich ; Reichstein, Markus - \ 2020
    Biogeosciences 17 (2020)5. - ISSN 1726-4170 - p. 1343 - 1365.

    FLUXNET comprises globally distributed eddy-covariance-based estimates of carbon fluxes between the biosphere and the atmosphere. Since eddy covariance flux towers have a relatively small footprint and are distributed unevenly across the world, upscaling the observations is necessary to obtain global-scale estimates of biosphere-atmosphere exchange. Based on cross-consistency checks with atmospheric inversions, sun-induced fluorescence (SIF) and dynamic global vegetation models (DGVMs), here we provide a systematic assessment of the latest upscaling efforts for gross primary production (GPP) and net ecosystem exchange (NEE) of the FLUXCOM initiative, where different machine learning methods, forcing data sets and sets of predictor variables were employed. Spatial patterns of mean GPP are consistent across FLUXCOM and DGVM ensembles ( at 1 spatial resolution) while the majority of DGVMs show, for 70 of the land surface, values outside the FLUXCOM range. Global mean GPP magnitudes for 2008-2010 from FLUXCOM members vary within 106 and 130 PgC class with the largest uncertainty in the tropics. Seasonal variations in independent SIF estimates agree better with FLUXCOM GPP (mean global pixel-wise) than with GPP from DGVMs (mean global pixel-wise). Seasonal variations in FLUXCOM NEE show good consistency with atmospheric inversion-based net land carbon fluxes, particularly for temperate and boreal regions. Interannual variability of global NEE in FLUXCOM is underestimated compared to inversions and DGVMs. The FLUXCOM version which also uses meteorological inputs shows a strong co-variation in interannual patterns with inversions (for 2001-2010). Mean regional NEE from FLUXCOM shows larger uptake than inversion and DGVM-based estimates, particularly in the tropics with discrepancies of up to several hundred grammes of carbon per square metre per year. These discrepancies can only partly be reconciled by carbon loss pathways that are implicit in inversions but not captured by the flux tower measurements such as carbon emissions from fires and water bodies. We hypothesize that a combination of systematic biases in the underlying eddy covariance data, in particular in tall tropical forests, and a lack of site history effects on NEE in FLUXCOM are likely responsible for the too strong tropical carbon sink estimated by FLUXCOM. Furthermore, as FLUXCOM does not account for fertilization effects, carbon flux trends are not realistic. Overall, current FLUXCOM estimates of mean annual and seasonal cycles of GPP as well as seasonal NEE variations provide useful constraints of global carbon cycling, while interannual variability patterns from FLUXCOM are valuable but require cautious interpretation. Exploring the diversity of Earth observation data and of machine learning concepts along with improved quality and quantity of flux tower measurements will facilitate further improvements of the FLUXCOM approach overall.

    Sources of Uncertainty in Regional and Global Terrestrial CO2 Exchange Estimates
    Bastos, A. ; O'Sullivan, M. ; Ciais, P. ; Makowski, D. ; Sitch, S. ; Friedlingstein, P. ; Chevallier, F. ; Rödenbeck, C. ; Pongratz, J. ; Luijkx, I.T. ; Patra, P.K. ; Peylin, P. ; Canadell, J.G. ; Lauerwald, R. ; Li, W. ; Smith, N.E. ; Peters, W. ; Goll, D.S. ; Jain, A.K. ; Kato, E. ; Lienert, S. ; Lombardozzi, D.L. ; Haverd, V. ; Nabel, J.E.M.S. ; Poulter, B. ; Tian, H. ; Walker, A.P. ; Zaehle, S. - \ 2020
    Global Biogeochemical Cycles 34 (2020)2. - ISSN 0886-6236
    atmospheric inversions - carbon cycle - dynamic global vegetation models - global carbon budget

    The Global Carbon Budget 2018 (GCB2018) estimated by the atmospheric CO2 growth rate, fossil fuel emissions, and modeled (bottom-up) land and ocean fluxes cannot be fully closed, leading to a “budget imbalance,” highlighting uncertainties in GCB components. However, no systematic analysis has been performed on which regions or processes contribute to this term. To obtain deeper insight on the sources of uncertainty in global and regional carbon budgets, we analyzed differences in Net Biome Productivity (NBP) for all possible combinations of bottom-up and top-down data sets in GCB2018: (i) 16 dynamic global vegetation models (DGVMs), and (ii) 5 atmospheric inversions that match the atmospheric CO2 growth rate. We find that the global mismatch between the two ensembles matches well the GCB2018 budget imbalance, with Brazil, Southeast Asia, and Oceania as the largest contributors. Differences between DGVMs dominate global mismatches, while at regional scale differences between inversions contribute the most to uncertainty. At both global and regional scales, disagreement on NBP interannual variability between the two approaches explains a large fraction of differences. We attribute this mismatch to distinct responses to El Niño–Southern Oscillation variability between DGVMs and inversions and to uncertainties in land use change emissions, especially in South America and Southeast Asia. We identify key needs to reduce uncertainty in carbon budgets: reducing uncertainty in atmospheric inversions (e.g., through more observations in the tropics) and in land use change fluxes, including more land use processes and evaluating land use transitions (e.g., using high-resolution remote-sensing), and, finally, improving tropical hydroecological processes and fire representation within DGVMs.

    Global carbon budget 2019
    Friedlingstein, Pierre ; Jones, Matthew W. ; O'Sullivan, Michael ; Andrew, Robbie M. ; Hauck, Judith ; Peters, Glen P. ; Peters, Wouter ; Pongratz, Julia ; Sitch, Stephen ; Quéré, Corinne Le; Bakker, Dorothee C.E. ; Canadell1, Josep G. ; Ciais1, Philippe ; Jackson, Robert B. ; Anthoni, Peter ; Barbero, Leticia ; Bastos, Ana ; Bastrikov, Vladislav ; Becker, Meike ; Bopp, Laurent ; Buitenhuis, Erik ; Chandra, Naveen ; Chevallier, Frédéric ; Chini, Louise P. ; Currie, Kim I. ; Feely, Richard A. ; Gehlen, Marion ; Gilfillan, Dennis ; Gkritzalis, Thanos ; Goll, Daniel S. ; Gruber, Nicolas ; Gutekunst, Sören ; Harris, Ian ; Haverd, Vanessa ; Houghton, Richard A. ; Hurtt, George ; Ilyina, Tatiana ; Jain, Atul K. ; Joetzjer, Emilie ; Kaplan, Jed O. ; Kato, Etsushi ; Goldewijk, Kees Klein ; Korsbakken, Jan Ivar ; Landschützer, Peter ; Lauvset, Siv K. ; Lefèvre, Nathalie ; Lenton, Andrew ; Lienert, Sebastian ; Lombardozzi, Danica ; Marland, Gregg ; McGuire, Patrick C. ; Melton, Joe R. ; Metzl, Nicolas ; Munro, David R. ; Nabel, Julia E.M.S. ; Nakaoka, Shin Ichiro ; Neill, Craig ; Omar, Abdirahman M. ; Ono, Tsuneo ; Peregon, Anna ; Pierrot, Denis ; Poulter, Benjamin ; Rehder, Gregor ; Resplandy, Laure ; Robertson, Eddy ; Rödenbeck, Christian ; Séférian, Roland ; Schwinger, Jörg ; Smith, Naomi ; Tans, Pieter P. ; Tian, Hanqin ; Tilbrook, Bronte ; Tubiello, Francesco N. ; Werf, Guido R. Van Der; Wiltshire, Andrew J. ; Zaehle, Sönke - \ 2019
    Earth System Science Data 11 (2019)4. - ISSN 1866-3508 - p. 1783 - 1838.

    Accurate assessment of anthropogenic carbon dioxide (CO2) emissions and their redistribution among the atmosphere, ocean, and terrestrial biosphere-the "global carbon budget"-is important to better understand the global carbon cycle, support the development of climate policies, and project future climate change. Here we describe data sets and methodology to quantify the five major components of the global carbon budget and their uncertainties. Fossil CO2 emissions (EFF) are based on energy statistics and cement production data, while emissions from land use change (ELUC), mainly deforestation, are based on land use and land use change data and bookkeeping models. Atmospheric CO2 concentration is measured directly and its growth rate (GATM) is computed from the annual changes in concentration. The ocean CO2 sink (SOCEAN) and terrestrial CO2 sink (SLAND) are estimated with global process models constrained by observations. The resulting carbon budget imbalance (BIM), the difference between the estimated total emissions and the estimated changes in the atmosphere, ocean, and terrestrial biosphere, is a measure of imperfect data and understanding of the contemporary carbon cycle. All uncertainties are reported as ±1σ. For the last decade available (2009-2018), EFF was 9:5±0:5 GtC yr-1, ELUC 1:5±0:7 GtC yr-1, GATM 4:9±0:02 GtC yr-1 (2:3±0:01 ppm yr-1), SOCEAN 2:5±0:6 GtC yr-1, and SLAND 3:2±0:6 GtC yr-1, with a budget imbalance BIM of 0.4 GtC yr-1 indicating overestimated emissions and/or underestimated sinks. For the year 2018 alone, the growth in EFF was about 2.1% and fossil emissions increased to 10:0±0:5 GtC yr-1, reaching 10 GtC yr-1 for the first time in history, ELUC was 1:5±0:7 GtC yr-1, for total anthropogenic CO2 emissions of 11:5±0:9 GtC yr-1 (42:5±3:3 GtCO2). Also for 2018, GATM was 5:1±0:2 GtC yr-1 (2:4±0:1 ppm yr-1), SOCEAN was 2:6±0:6 GtC yr-1, and SLAND was 3:5±0:7 GtC yr-1, with a BIM of 0.3 GtC. The global atmospheric CO2 concentration reached 407:38±0:1 ppm averaged over 2018. For 2019, preliminary data for the first 6-10 months indicate a reduced growth in EFF of C0:6% (range of.0:2% to 1.5 %) based on national emissions projections for China, the USA, the EU, and India and projections of gross domestic product corrected for recent changes in the carbon intensity of the economy for the rest of the world. Overall, the mean and trend in the five components of the global carbon budget are consistently estimated over the period 1959-2018, but discrepancies of up to 1 GtC yr-1 persist for the representation of semi-decadal variability in CO2 fluxes. A detailed comparison among individual estimates and the introduction of a broad range of observations shows (1) no consensus in the mean and trend in land use change emissions over the last decade, (2) a persistent low agreement between the different methods on the magnitude of the land CO2 flux in the northern extra-tropics, and (3) an apparent underestimation of the CO2 variability by ocean models outside the tropics. This living data update documents changes in the methods and data sets used in this new global carbon budget and the progress in understanding of the global carbon cycle compared with previous publications of this data set (Le Quéré et al., 2018a, b, 2016, 2015a, b, 2014, 2013). The data generated by this work are available at (Friedlingstein et al., 2019).

    Evolutionary diversity is associated with wood productivity in Amazonian forests
    Coelho de Souza, Fernanda ; Dexter, Kyle G. ; Phillips, Oliver L. ; Pennington, Toby R. ; Neves, Danilo ; Sullivan, Martin J.P. ; Alvarez-Davila, Esteban ; Alves, Átila ; Amaral, Ieda ; Andrade, Ana ; Aragao, Luis E.O.C. ; Araujo-Murakami, Alejandro ; Arets, Eric J.M.M. ; Arroyo, Luzmilla ; Aymard C, Gerardo A. ; Bánki, Olaf ; Baraloto, Christopher ; Barroso, Jorcely G. ; Boot, Rene G.A. ; Brienen, Roel J.W. ; Brown, Foster ; Camargo, José Luís C. ; Castro, Wendeson ; Chave, Jerome ; Cogollo, Alvaro ; Comiskey, James A. ; Cornejo-Valverde, Fernando ; Costa, Antonio Lola da; Camargo, Plínio B. de; Fiore, Anthony Di; Feldpausch, Ted R. ; Galbraith, David R. ; Gloor, Emanuel ; Goodman, Rosa C. ; Gilpin, Martin ; Herrera, Rafael ; Higuchi, Niro ; Honorio Coronado, Eurídice N. ; Jimenez-Rojas, Eliana ; Killeen, Timothy J. ; Laurance, Susan ; Laurance, William F. ; Lopez-Gonzalez, Gabriela ; Lovejoy, Thomas E. ; Malhi, Yadvinder ; Marimon, Beatriz S. ; Marimon-Junior, Ben Hur ; Mendoza, Casimiro ; Monteagudo-Mendoza, Abel ; Neill, David A. ; Vargas, Percy Núñez ; Peñuela Mora, Maria C. ; Pickavance, Georgia C. ; Pipoly, John J. ; Pitman, Nigel C.A. ; Poorter, Lourens ; Prieto, Adriana ; Ramirez, Freddy ; Roopsind, Anand ; Rudas, Agustin ; Salomão, Rafael P. ; Silva, Natalino ; Silveira, Marcos ; Singh, James ; Stropp, Juliana ; Steege, Hans ter; Terborgh, John ; Thomas-Caesar, Raquel ; Umetsu, Ricardo K. ; Vasquez, Rodolfo V. ; Célia-Vieira, Ima ; Vieira, Simone A. ; Vos, Vincent A. ; Zagt, Roderick J. ; Baker, Timothy R. - \ 2019
    Nature Ecology & Evolution 3 (2019). - ISSN 2397-334X - p. 1754 - 1761.

    Higher levels of taxonomic and evolutionary diversity are expected to maximize ecosystem function, yet their relative importance in driving variation in ecosystem function at large scales in diverse forests is unknown. Using 90 inventory plots across intact, lowland, terra firme, Amazonian forests and a new phylogeny including 526 angiosperm genera, we investigated the association between taxonomic and evolutionary metrics of diversity and two key measures of ecosystem function: aboveground wood productivity and biomass storage. While taxonomic and phylogenetic diversity were not important predictors of variation in biomass, both emerged as independent predictors of wood productivity. Amazon forests that contain greater evolutionary diversity and a higher proportion of rare species have higher productivity. While climatic and edaphic variables are together the strongest predictors of productivity, our results show that the evolutionary diversity of tree species in diverse forest stands also influences productivity. As our models accounted for wood density and tree size, they also suggest that additional, unstudied, evolutionarily correlated traits have significant effects on ecosystem function in tropical forests. Overall, our pan-Amazonian analysis shows that greater phylogenetic diversity translates into higher levels of ecosystem function: tropical forest communities with more distantly related taxa have greater wood productivity.

    Demands on land : Mapping competing societal expectations for the functionality of agricultural soils in Europe
    Schulte, Rogier P.O. ; O'Sullivan, Lilian ; Vrebos, Dirk ; Bampa, Francesca ; Jones, Arwyn ; Staes, Jan - \ 2019
    Environmental Science & Policy 100 (2019). - ISSN 1462-9011 - p. 113 - 125.
    Agriculture - EU - LANDMARK - Policy - Soil - Sustainability

    The Common Agricultural Policy (CAP) of the European Union (EU) has been highly successful in securing the supply of food from Europe's agricultural land. However, new expectations have emerged from society on the functions that agricultural land should deliver, including the expectations that land should regulate and purify water, should sequester carbon to contribute to the mitigation of climate change, should provide a home for biodiversity and allow for the sustainable cycling of nutrients in animal and human waste streams. Through a series of reforms of the CAP, these expectations, or ‘societal demands’ have translated into a myriad of EU and national level policies aimed at safeguarding the sustainability and multifunctionality of European agriculture, resulting in a highly complex regulatory environment for land managers. The current reform of the CAP aims to simultaneously simplify and strengthen policy making on environmental protection and climate action, through the development of Strategic Plans at national level, which allow for more targeted and context-specific policy formation. In this paper, we contribute to the knowledge base underpinning the development of these Strategic Plans by mapping the variation in the societal demands for soil functions across EU Member States, based on an extensive review of the existing policy environment relating to sustainable and multifunctional land management. We show that the societal demands for primary production, water regulation and purification, carbon sequestration, biodiversity and nutrient cycling vary greatly between Member States, as determined by population, farming systems and livestock densities, geo-environmental conditions and landscape configuration. Moreover, the total societal demands for multifunctionality differs between Member States, with the lowest demands found in Member States that have designated the higher shares of EU CAP funding towards ‘Pillar 2′ expenditure, aimed at environmental protection and regional development. We review which lessons can be learnt from these observations, in the context of the proposals for the new CAP for the period 2021–2027, which include enhanced conditionality of direct income support for farmers and the instigation of eco-schemes in Pillar 1, in addition to Agri-Environmental and Climate Measures in Pillar 2. We conclude that the devolution of planning to Strategic Plans at national level provides an opportunity for more effective and targeted incentivisation of sustainable land management, provided that these plans take account for variations in the societal demand for soil functions, as well as the capacity of contrasting soils to deliver on this multifunctionality.

    Digging deeper : Understanding the contribution of subsoil carbon for climate mitigation, a case study of Ireland
    Simo, I. ; Schulte, R. ; O'Sullivan, L. ; Creamer, R. - \ 2019
    Environmental Science & Policy 98 (2019). - ISSN 1462-9011 - p. 61 - 69.
    Agricultural soils - Soil carbon mapping - Soil organic carbon stocks

    In an attempt to counter the progress of climate change, the European Commission 2030 climate and energy framework developed a binding target to cut GHG emissions within the territory by at least 40% below 1990 levels, by 2030. In the past, this did not include the role of soils in providing a sink for carbon. As of 2014, the European Commission legislative proposed to integrate greenhouse gas emissions and removals from LULUCF in the 2030 climate and energy framework, allowing for the contribution of carbon sinks in national inventories. To calculate the potential of these sinks it is essential to firstly understand what stocks exist at a national scale and identify the so-called ‘carbon hotspots’ in the landscape to reduce the potential leaks in the system. This is further enhanced by identifying soils which provide the potential for further sequestration of carbon, due to their soil texture and aggregate composition. Moreover, deeper soil horizons may have a high capacity to sequester significant amounts of SOC as the turnover time and chemical recalcitrance of soil organic matter (SOM)increases with depth (Lorenz and Lal, 2005). This study highlights the need to dig deeper and assess soil carbon stocks below the standard 30 cm depth, applied in many calculations and models, in order to derive sufficiently accurate estimations of soil organic carbon (SOC)stocks and the total quantity of stable SOC at depth. Using Ireland as a case study, SOC stock maps are produced with the objective of identifying and securing existing information for SOC and to show the spatial distribution and geographical variation of SOC stock at different depths. Using empirical data from a national soil survey, SOC measurements from the surface 30 cm, 50 cm and 1 m were compared across all soil types. The results indicate a large variation between soils when comparing the SOC of the first 30 cm only, while the proportion of total SOC stock contained within 0–50 cm was more consistent within subgroups of soil types, and accounts for 90% of the carbon found to 1 m. Luvisols and Stagnosols have been previously identified as soils capable of sequestering larger stores of SOC in their subsoils. These soil types were spatially mapped and the stock converted to CO 2 emission equivalents. On average, up to 40 t ha −1 of stable SOC is contained at a depth below 30 cm. At national level, this adds up to 69 Mt of SOC. This research provides a spatially targeted approach that combines efforts to reduce CO 2 emissions from carbon hotspots while also augmenting the sequestration of stable carbon at depth in soils with clay illuviation and wetness (stagnic)diagnostic horizons.

    Harvesting European knowledge on soil functions and land management using multi-criteria decision analysis
    Bampa, Francesca ; O'Sullivan, Lilian ; Madena, Kirsten ; Sandén, Taru ; Spiegel, Heide ; Henriksen, Christian Bugge ; Ghaley, Bhim Bahadur ; Jones, Arwyn ; Staes, Jan ; Sturel, Sylvain ; Trajanov, Aneta ; Creamer, Rachel E. ; Debeljak, Marko - \ 2019
    Soil Use and Management 35 (2019)1. - ISSN 0266-0032 - p. 6 - 20.
    DEX model - farmers and multi-stakeholders - locally relevant advice - participatory research - soil quality

    Soil and its ecosystem functions play a societal role in securing sustainable food production while safeguarding natural resources. A functional land management framework has been proposed to optimize the agro-environmental outputs from the land and specifically the supply and demand of soil functions such as (a) primary productivity, (b) carbon sequestration, (c) water purification and regulation, (d) biodiversity and (e) nutrient cycling, for which soil knowledge is essential. From the outset, the LANDMARK multi-actor research project integrates harvested knowledge from local, national and European stakeholders to develop such guidelines, creating a sense of ownership, trust and reciprocity of the outcomes. About 470 stakeholders from five European countries participated in 32 structured workshops covering multiple land uses in six climatic zones. The harmonized results include stakeholders’ priorities and concerns, perceptions on soil quality and functions, implementation of tools, management techniques, indicators and monitoring, activities and policies, knowledge gaps and ideas. Multi-criteria decision analysis was used for data analysis. Two qualitative models were developed using Decision EXpert methodology to evaluate “knowledge” and “needs”. Soil quality perceptions differed across workshops, depending on the stakeholder level and regionally established terminologies. Stakeholders had good inherent knowledge about soil functioning, but several gaps were identified. In terms of critical requirements, stakeholders defined high technical, activity and policy needs in (a) financial incentives, (b) credible information on improving more sustainable management practices, (c) locally relevant advice, (d) farmers’ discussion groups, (e) training programmes, (f) funding for applied research and monitoring, and (g) strengthening soil science in education.

    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. - \ 2018
    Ambio 47 (2018)2. - ISSN 0044-7447 - p. 216 - 230.
    Functional Land Management - Policy framework - Soil functions - Stakeholder workshops - Sustainability - Think-Do-Gap
    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.
    Assessing the role of artificially drained agricultural land for climate change mitigation in Ireland
    Paul, Carsten ; Fealy, Réamonn ; Fenton, Owen ; Lanigan, Gary ; O'Sullivan, Lilian ; Schulte, Rogier P.O. - \ 2018
    Environmental Science & Policy 80 (2018). - ISSN 1462-9011 - p. 95 - 104.
    Greenhouse gas - Histosol - IWMS - LULUCF - Organic soil - Peatland
    In 2014 temperate zone emission factor revisions were published in the IPCC Wetlands Supplement. Default values for direct CO2 emissions of artificially drained organic soils were increased by a factor of 1.6 for cropland sites and by factors ranging from 14 to 24 for grassland sites. This highlights the role of drained organic soils as emission hotspots and makes their rewetting more attractive as climate change mitigation measures. Drainage emissions of humic soils are lower on a per hectare basis and not covered by IPCC default values. However, drainage of great areas can turn them into nationally relevant emission sources. National policy making that recognizes the importance of preserving organic and humic soils’ carbon stock requires data that is not readily available. Taking Ireland as a case study, this article demonstrates how a dataset of policy relevant information can be generated. Total area of histic and humic soils drained for agriculture, resulting greenhouse gas emissions and climate change mitigation potential were assessed. For emissions from histic soils, calculations were based on IPCC emission factors, for humic soils, a modified version of the ECOSSE model was used. Results indicated 370,000 ha of histic and 426,000 ha of humic soils under drained agricultural land use in Ireland (8% and 9% of total farmed area). Calculated annual drainage emissions were 8.7 Tg CO2e from histic and 1.8 Tg CO2e from humic soils (equal to 56% of Ireland's agricultural emissions in 2014, excluding emissions from land use). If half the area of drained histic soils was rewetted, annual saving would amount to 3.2 Tg CO2e. If on half of the deep drained, nutrient rich grasslands drainage spacing was decreased to control the average water table at −25 cm or higher, annual savings would amount to 0.4 Tg CO2e.
    Application of dexter’s soil physical quality index: An irish case study
    Fenton, O. ; Vero, S. ; Schulte, R.P.O. ; O’sullivan, L. ; Bondi, G. ; Creamer, R.E. - \ 2017
    Irish Journal of Agricultural and Food Research 56 (2017)1. - ISSN 0791-6833 - p. 45 - 53.
    Agriculture - Soil - Soil physical quality - Soil quality - Soil structure

    Historically, due to a lack of measured soil physical data, the quality of Irish soils was relatively unknown. Herein, we investigate the physical quality of the national representative profiles of Co. Waterford. To do this, the soil physical quality (SPQ) S-Index, as described by Dexter (2004a,b,c) using the S-theory (which seeks the inflection point of a soil water retention curve [SWRC]), is used. This can be determined using simple (S-Indirect) or complex (S-Direct) soil physical data streams. Both are achievable using existing data for the County Waterford profiles, but until now, the suitability of this S-Index for Irish soils has never been tested. Indirect-S provides a generic characterisation of SPQ for a particular soil horizon, using simplified and modelled information (e.g. texture and SWRC derived from pedo-transfer functions), whereas Direct-S provides more complex site-specific information (e.g. texture and SWRC measured in the laboratory), which relates to properties measured for that exact soil horizon. Results showed a significant correlation between S-Indirect (Si) and S-Direct (Sd). Therefore, the S-Index can be used in Irish soils and presents opportunities for the use of Si at the national scale. Outlier horizons contained >6% organic carbon (OC) and bulk density (Bd) values <1 g/cm3 and were not suitable for Si estimation. In addition, the S-Index did not perform well on excessively drained soils. Overall correlations of Si with Bd and of Si with OC% for the dataset were detected. Future work should extend this approach to the national scale dataset in the Irish Soil Information System.

    Soil protection for a sustainable future : options for a soil monitoring network for Ireland
    O'Sullivan, L. ; Bampa, F. ; Knights, K. ; Creamer, R.E. - \ 2017
    Soil Use and Management 33 (2017)2. - ISSN 0266-0032 - p. 346 - 363.
    drainage class - indicators - land use - natural resource - protection - Soil monitoring - sustainability

    The increased recognition of the importance of soil is reflected in the UN Post-2015 Development Agenda with sustainable development goals that directly and indirectly relate to soil quality and protection. Despite a lack of legally binding legislation for soil protection, the European Commission remains committed to the objective of soil protection. However, the achievement of a legally binding framework for soil protection relies on the implementation of a soil monitoring network (SMN) that can detect changes to soil quality over time. As beneficiaries do not pay for the provision of soil information, the options for soil monitoring are limited. The use of existing data sets should be considered first. Using Ireland as an example, this research explored the opportunities for a SMN for Ireland considering three existing national data sets. The options for a SMN are considered in terms of their spatial and stratified distribution, the parameters to be measured and an economic analysis of the options proposed. This research finds that for Ireland, either a 10 or a 16 km2 grid interval stratified by land use and drainage class offers the best potential in relation to the spatial distribution of existing data sets to reflect local data at a national level. With existing data, the stratified SIS data using the 16 km2 grid offers the best value for money, with baseline costs for analysis, excluding field costs, of between €706 481 and €2.8 million. Acknowledging the impossibility of measuring all parameters with ideal frequency, this study proposes a two-tier system for optimized monitoring frequency. Parameters must anticipate future policy requirements. Finally, the implementation of a SMN must be accompanied by standardized methods, defined thresholds and action mandates to maintain soil quality within allowable limits.

    The BROWSE model for predicting exposures of residents and bystanders to agricultural use of plant protection products: An overview
    Butler Ellis, M.C. ; De Zande, Jan C. Van; Berg, Frederik Van Den; Kennedy, Marc C. ; O'sullivan, Christine M. ; Jacobs, Cor M. ; Fragkoulis, Georgios ; Spanoghe, Pieter ; Gerritsen-ebben, Rianda ; Frewer, Lynn J. ; Charistou, Agathi - \ 2017
    Biosystems Engineering 154 (2017). - ISSN 1537-5110 - p. 92 - 104.
    New models have been developed, with the aim of improving the estimate of exposure of residents and bystanders to agricultural pesticides for regulatory purposes. These are part of a larger suite of models also covering operators and workers. The population that is modelled for residents and bystanders relates to people (both adults and children) who have no association with the application (i.e. not occupational exposure) but are adjacent to the treated area during and/or after the application process. The scenarios that the models aim to describe are based on consideration of both best practice and of real practice, as shown in surveys and from expert knowledge obtained in stakeholder consultations.

    The work has focused on three causes of exposure identified as having potential for improvement: boom sprayers, orchard sprayers and vapour emissions.

    An overview of the models is given, and a description of model input values and proposed defaults. The main causes of uncertainty in the models are also discussed. There are a number of benefits of the BROWSE model over current models of bystander and resident exposure, which includes the incorporation of mitigation measures for reducing exposure and the use of probabilistic modelling to avoid an over-conservative approach.

    It is expected that the levels of exposure that the BROWSE model predicts will, in some cases, be higher than those predicted by the current UK regulatory model. This is largely because the modelled scenarios have been updated to account for current practice and current scientific knowledge.
    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 - \ 2016
    Environmental Science & Policy 56 (2016). - ISSN 1462-9011 - p. 39 - 48.
    Agriculture - Ecosystem service - Soil functions - Sustainable intensification

    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.

    Impact of fitting dominance and additive effects on accuracy of genomic prediction of breeding values in layers
    Heidaritabar, M. ; Wolc, A. ; Arango, J. ; Zeng, J. ; Settar, P. ; Fulton, J.E. ; O'Sullivan, N.P. ; Bastiaansen, J.W.M. ; Fernando, R.L. ; Garrick, D.J. ; Dekkers, J.C.M. - \ 2016
    Journal of Animal Breeding and Genetics 133 (2016). - ISSN 0931-2668 - p. 334 - 346.
    Additive effect - Dominance effect - Genomic selection - Layer

    Most genomic prediction studies fit only additive effects in models to estimate genomic breeding values (GEBV). However, if dominance genetic effects are an important source of variation for complex traits, accounting for them may improve the accuracy of GEBV. We investigated the effect of fitting dominance and additive effects on the accuracy of GEBV for eight egg production and quality traits in a purebred line of brown layers using pedigree or genomic information (42K single-nucleotide polymorphism (SNP) panel). Phenotypes were corrected for the effect of hatch date. Additive and dominance genetic variances were estimated using genomic-based [genomic best linear unbiased prediction (GBLUP)-REML and BayesC] and pedigree-based (PBLUP-REML) methods. Breeding values were predicted using a model that included both additive and dominance effects and a model that included only additive effects. The reference population consisted of approximately 1800 animals hatched between 2004 and 2009, while approximately 300 young animals hatched in 2010 were used for validation. Accuracy of prediction was computed as the correlation between phenotypes and estimated breeding values of the validation animals divided by the square root of the estimate of heritability in the whole population. The proportion of dominance variance to total phenotypic variance ranged from 0.03 to 0.22 with PBLUP-REML across traits, from 0 to 0.03 with GBLUP-REML and from 0.01 to 0.05 with BayesC. Accuracies of GEBV ranged from 0.28 to 0.60 across traits. Inclusion of dominance effects did not improve the accuracy of GEBV, and differences in their accuracies between genomic-based methods were small (0.01-0.05), with GBLUP-REML yielding higher prediction accuracies than BayesC for egg production, egg colour and yolk weight, while BayesC yielded higher accuracies than GBLUP-REML for the other traits. In conclusion, fitting dominance effects did not impact accuracy of genomic prediction of breeding values in this population.

    Making the most of our land : Managing soil functions from local to continental scale
    Schulte, Rogier P.O. ; Bampa, Francesca ; Bardy, Marion ; Coyle, Cait ; Creamer, Rachel E. ; Fealy, Reamonn ; Gardi, Ciro ; Ghaley, Bhim Bahadur ; Jordan, Phil ; Laudon, Hjalmar ; O'Donoghue, Cathal ; Ó'hUallacháin, Daire ; O'Sullivan, Lilian ; Rutgers, Michiel ; Six, Johan ; Toth, Gergely L. ; Vrebos, Dirk - \ 2015
    Frontiers in Environmental Science 3 (2015)DEC. - ISSN 2296-665X
    Ecosystem services - Functional Land Management - Policy - Soil functions - Sustainable intensification

    The challenges of achieving both food security and environmental sustainability have resulted in a confluence of demands on land within the European Union (EU): we expect our land to provide food, fiber and fuel, to purify water, to sequester carbon, and provide a home to biodiversity as well as external nutrients in the form of waste from humans and intensive livestock enterprises. All soils can perform all of these five functions, but some soils are better at supplying selective functions. Functional Land Management is a framework for policy-making aimed at meeting these demands by incentivizing land use and soil management practices that selectively augment specific soil functions, where required. Here, we explore how the demands for contrasting soil functions, as framed by EU policies, may apply to very different spatial scales, from local to continental scales. At the same time, using Ireland as a national case study, we show that the supply of each soil function is largely determined by local soil and land use conditions, with large variations at both local and regional scales. These discrepancies between the scales at which the demands and supply of soil functions are manifested, have implications for soil and land management: while some soil functions must be managed at local (e.g., farm or field) scale, others may be offset between regions with a view to solely meeting national or continental demands. In order to facilitate the optimization of the delivery of soil functions at national level, to meet the demands that are framed at continental scale, we identify and categorize 14 policy and market instruments that are available in the EU. The results from this inventory imply that there may be no need for the introduction of new specific instruments to aid the governance of Functional Land Management. We conclude that there may be more merit in adapting existing governance instruments by facilitating differentiation between soils and landscapes.

    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. - \ 2015
    Land Use Policy 47 (2015). - ISSN 0264-8377 - p. 42 - 54.
    Carbon price - Food security and environmental sustainability - Functional Land Management - GIS and policy frameworks - Land drainage - Soil functions

    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.

    Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera
    Sun, Z. ; Harris, H.M.B. ; McCann, A. ; Guo, C. ; Argimón, S. ; Zhang, W. ; Yang, X. ; Jeffery, I.B. ; Cooney, J.C. ; Kagawa, T.F. ; Liu, W. ; Song, Y. ; Salvetti, E. ; Wrobel, A. ; Rasinkangas, P. ; Parkhill, J. ; Rea, M.C. ; O'Sullivan, O. ; Ritari, J. ; Douillard, F.P. ; Paul Ross, R. ; Yang, R. ; Briner, A.E. ; Felis, G.E. ; Vos, W.M. de; Barrangou, R. ; Klaenhammer, T.R. ; Caufield, P.W. ; Cui, Y. ; Zhang, H. ; O'Toole, P.W. - \ 2015
    Nature Communications 6 (2015). - ISSN 2041-1723 - 13 p.
    Lactobacilli are a diverse group of species that occupy diverse nutrient-rich niches associated with humans, animals, plants and food. They are used widely in biotechnology and food preservation, and are being explored as therapeutics. Exploiting lactobacilli has been complicated by metabolic diversity, unclear species identity and uncertain relationships between them and other commercially important lactic acid bacteria. The capacity for biotransformations catalysed by lactobacilli is an untapped biotechnology resource. Here we report the genome sequences of 213 Lactobacillus strains and associated genera, and their encoded genetic catalogue for modifying carbohydrates and proteins. In addition, we describe broad and diverse presence of novel CRISPR-Cas immune systems in lactobacilli that may be exploited for genome editing. We rationalize the phylogenomic distribution of host interaction factors and bacteriocins that affect their natural and industrial environments, and mechanisms to withstand stress during technological processes. We present a robust phylogenomic framework of existing species and for classifying new species
    Bystander and Resident exposure to spray drift from orchard applications: field measurements, including a comparison of spray drift collectors
    Butler Ellis, M.C. ; Lane, A. ; O'Sullivan, C.M. ; Alanis, R. ; Harris, A. ; Stallinga, H. ; Zande, J.C. van de - \ 2014
    In: International Advances in Pesticide Application, Oxford, UK. - Wellesbourne, Warwick CV35 9EF, UK : Association of Applied Biologists Warwick Enterprise Park - p. 187 - 194.
    Case Study: Nile
    Roest, C.W.J. ; Schoumans, O.F. ; Siderius, C. ; Walsum, P.E.V. van; Jaspers, A.M.J. - \ 2010
    In: The adaptive Water Resources Management Handbook, 2010 / Mysiak, J., Henrikson, H.J., Sullivan, C., Bromley, J., Pahl-Wostl, C., London : Earthscan - ISBN 9781844077922 - 216 p.
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