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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    Endogenous regime change : Lessons from transition pathways in Dutch dairy farming
    Runhaar, Hens ; Fünfschilling, Lea ; Pol-Van Dasselaar, Agnes van den; Moors, Ellen H.M. ; Temmink, Rani ; Hekkert, Marko - \ 2020
    Environmental Innovation and Societal Transitions 36 (2020). - ISSN 2210-4224 - p. 137 - 150.
    Governance - Grazing - Institutional logics - Productivist agriculture - The Netherlands - Transformation

    Sustainability transitions are commonly considered impossible without regime change. Theoretical work on regime change has mainly focused on niches and landscapes and less on change ‘from within’. Empirical analysis helps theorising endogenous regime change. Conceptualising regimes as semi-coherent entities composed of multiple ‘institutional logics’, we analyse the endogenous regime change in Dutch dairy farming. Practices in this sector have become more and more market-driven. This dominant logic however was increasingly challenged by institutional logics centring round cultural identity and sustainability. Tensions particularly centred round the increased indoor housing of cows. The contestation of this practice eventually led to a first ‘crack’ in the regime, as it weakened the dominance of the market logic and enabled opportunities for more sustainability. Our case study shows that the presence of alternative institutional logics is necessary to crack the regime, but opportunities to patch it back together are similarly crucial to enable sustainability transitions.

    Maize silage as enrichment material improves the welfare of growing-finishing pigs in environmentally-friendly pens
    Ocepek, Marko ; Goold, Conor M. ; Busančić, Mirjana ; Aarnink, André J.A. - \ 2020
    Applied Animal Behaviour Science 230 (2020). - ISSN 0168-1591
    Drinker position - Maize silage - Pig behaviour - Straw

    Provision of enrichment in welfare- and environmentally-friendly pig pens is important for sustainable pig production. The primary aim of the present experiment was to investigate the effects of maize silage as a singular enrichment compared to a combination of maize silage and chopped straw on behaviours important for determining pig welfare (play, locomotion, exploration, social contact, aggression, manipulation, eating, drinking, lying/sleeping, sitting/standing and nosing objects) in growing-finishing pigs (pigs, n = 432; batch, n = 2; pens n = 12 per batch). Secondly, the impact of drinker position (IN: two drinkers placed in the inside area; OUT: two drinkers in the outside area; IN_OUT: a drinker in each of the inside and outside areas; n = 8 pens per group) on pig behaviour was assessed. There were no statistically significant influences of enrichment treatments on behaviour. The OUT group performed less manipulation behaviour than the IN (mean difference = 2.65; 90 % highest density interval (HDI): 0.46, 4.84) and IN-OUT (mean difference = 2.88 HDI: 0.69, 5.15) groups, and drank more than the IN-OUT group (mean difference = -3.87; HDI: -6.76, -0.90). In addition, we found that a one standard deviation (∼ 2 days) increase in observation days/pig age significantly decreased manipulation (log coefficient = -0.32; HDI: -0.42, -0.22) and aggressive behaviours (log coefficient = -0.46; HDI: -0.57, -0.36), but there was an increase in drinking (log coefficient = 0.13; HDI: 0.09, 0.18) and nosing objects (log coefficient = 0.12; HDI: 0.06, 0.18). Significant associations were also found for batch (season), as well as correlations between behaviours. In summary, our results showed that pig behaviours during the growing-fattening period were similarly expressed in the maize silage and combined maize silage and chopped straw treatments, suggesting that maize silage in environmentally-friendly pig pens is adequate in ensuring welfare standards. Furthermore, placing drinkers in the outside area reduced manipulation between pen-mates, thus, could improve pig welfare.

    In utero behavioral imprinting to predation risk in pups of the bank vole
    Sievert, Thorbjörn ; Kerkhoven, Arjane ; Haapakoski, Marko ; Matson, Kevin D. ; Ylönen, Olga ; Ylönen, Hannu - \ 2020
    Behavioral Ecology and Sociobiology 74 (2020)2. - ISSN 0340-5443
    Alarm pheromone - Cross-generational effects - Odor - Olfaction - Predation risk

    Abstract: In the predator–prey arms race, survival-enhancing adaptive behaviors are essential. Prey can perceive predator presence directly from visual, auditory, or chemical cues. Non-lethal encounters with a predator may trigger prey to produce special body odors, alarm pheromones, informing conspecifics about predation risks. Recent studies suggest that parental exposure to predation risk during reproduction affects offspring behavior cross-generationally. We compared behaviors of bank vole (Myodes glareolus) pups produced by parents exposed to one of three treatments: predator scent from the least weasel (Mustela nivalis nivalis); scent from weasel-exposed voles, i.e., alarm pheromones; or a control treatment without added scents. Parents were treated in semi-natural field enclosures, but pups were born in the lab and assayed in an open-field arena. Before each behavioral test, one of the three scent treatments was spread throughout the test arena. The tests followed a full factorial design (3 parental treatments × 3 area treatments). Regardless of the parents’ treatment, pups exposed to predator odor in the arena moved more. Additionally, pups spend more time in the center of the arena when presented with predator odor or alarm pheromone compared with the control. Pups from predator odor–exposed parents avoided the center of the arena under control conditions, but they spent more time in the center when either predator odor or alarm pheromone was present. Our experiment shows that cross-generational effects are context-sensitive, depending on the perceived risk. Future studies should examine cross-generational behavioral effects in ecologically meaningful environments instead of only neutral ones. Significance statement: We exposed bank voles to odors signaling predation risk to assess the effects parental predation exposure on the behavior of their offspring. Besides predator odor, we also assessed the role of a conspecific alarm cue as a novel way of spreading the predation risk information. Pup behaviors were assessed in the open-field arena, a standard way of assessing animal behavior in a wide range of contexts. We found that also alarm pheromone increased the time pups spend in the center of the arena similarly to predator odor. While previous studies suggested that offspring would be more fearful, our results indicate that the cross-generational effects are very context-dependent; i.e., they differ significantly depending on which scent cue is presented in the open-field arena. This shows the need for better tools or measurements to translate laboratory results into ecologically meaningful frameworks.

    Assessing the nutrient cycling potential in agricultural soils using decision modelling
    Trajanov, Aneta ; Schröder, Jaap ; Wall, David ; Delgado, Antonio ; Schulte, Rogier ; Debeljak, Marko - \ 2019
    In: Proceedings of the 15th International Symposium on Operational Research, SOR 2019. - SLOVENIAN SOCIETY INFORMATIKA (Proceedings of the 15th International Symposium on Operational Research, SOR 2019 ) - ISBN 9789616165556 - p. 23 - 27.
    Decision model - DEXi - Nutrient cycling - Recommendations - Soil functions

    One of the essential functions that agricultural soils provide is nutrient cycling. The capacity of soils to provide this function is influenced by the interactions between soil properties, climate and management. Understanding these interactions can help in assessing the soil nutrient cycling potential on a field and in identifying best management options. To optimize this process, we developed a multi-attribute decision model using the DEXi modelling tool. The outputs from this model may be used to obtain recommendations for farmers and other stakeholders and assist them with the selection of management practices fostering the nutrient cycling potential of soils.

    Global patterns and drivers of ecosystem functioning in rivers and riparian zones
    Tiegs, Scott D. ; Costello, David M. ; Isken, Mark W. ; Woodward, Guy ; McIntyre, Peter B. ; Gessner, Mark O. ; Chauvet, Eric ; Griffiths, Natalie A. ; Flecker, Alex S. ; Acuña, Vicenç ; Albariño, Ricardo ; Allen, Daniel C. ; Alonso, Cecilia ; Andino, Patricio ; Arango, Clay ; Aroviita, Jukka ; Barbosa, Marcus V.M. ; Barmuta, Leon A. ; Baxter, Colden V. ; Bell, Thomas D.C. ; Bellinger, Brent ; Boyero, Luz ; Brown, Lee E. ; Bruder, Andreas ; Bruesewitz, Denise A. ; Burdon, Francis J. ; Callisto, Marcos ; Canhoto, Cristina ; Capps, Krista A. ; Castillo, María M. ; Clapcott, Joanne ; Colas, Fanny ; Colón-Gaud, Checo ; Cornut, Julien ; Crespo-Pérez, Verónica ; Cross, Wyatt F. ; Culp, Joseph M. ; Danger, Michael ; Dangles, Olivier ; Eyto, Elvira De; Derry, Alison M. ; Villanueva, Veronica Díaz ; Douglas, Michael M. ; Elosegi, Arturo ; Encalada, Andrea C. ; Entrekin, Sally ; Espinosa, Rodrigo ; Ethaiya, Diana ; Ferreira, Verónica ; Ferriol, Carmen ; Flanagan, Kyla M. ; Fleituch, Tadeusz ; Follstad Shah, Jennifer J. ; Barbosa, André Frainer ; Friberg, Nikolai ; Frost, Paul C. ; Garcia, Erica A. ; Lago, Liliana García ; Soto, Pavel Ernesto García ; Ghate, Sudeep ; Giling, Darren P. ; Gilmer, Alan ; Gonçalves, José Francisco ; Gonzales, Rosario Karina ; Graça, Manuel A.S. ; Grace, Mike ; Grossart, Hans Peter ; Guérold, François ; Gulis, Vlad ; Hepp, Luiz U. ; Higgins, Scott ; Hishi, Takuo ; Huddart, Joseph ; Hudson, John ; Imberger, Samantha ; Iñiguez-Armijos, Carlos ; Iwata, Tomoya ; Janetski, David J. ; Jennings, Eleanor ; Kirkwood, Andrea E. ; Koning, Aaron A. ; Kosten, Sarian ; Kuehn, Kevin A. ; Laudon, Hjalmar ; Leavitt, Peter R. ; Lemes Da Silva, Aurea L. ; Leroux, Shawn J. ; LeRoy, Carri J. ; Lisi, Peter J. ; MacKenzie, Richard ; Marcarelli, Amy M. ; Masese, Frank O. ; McKie, Brendan G. ; Medeiros, Adriana Oliveira ; Meissner, Kristian ; Miliša, Marko ; Mishra, Shailendra ; Miyake, Yo ; Moerke, Ashley ; Mombrikotb, Shorok ; Mooney, Rob ; Moulton, Tim ; Muotka, Timo ; Negishi, Junjiro N. ; Neres-Lima, Vinicius ; Nieminen, Mika L. ; Nimptsch, Jorge ; Ondruch, Jakub ; Paavola, Riku ; Pardo, Isabel ; Patrick, Christopher J. ; Peeters, Edwin T.H.M. ; Pozo, Jesus ; Pringle, Catherine ; Prussian, Aaron ; Quenta, Estefania ; Quesada, Antonio ; Reid, Brian ; Richardson, John S. ; Rigosi, Anna ; Rincón, José ; Rîşnoveanu, Geta ; Robinson, Christopher T. ; Rodríguez-Gallego, Lorena ; Royer, Todd V. ; Rusak, James A. ; Santamans, Anna C. ; Selmeczy, Géza B. ; Simiyu, Gelas ; Skuja, Agnija ; Smykla, Jerzy ; Sridhar, Kandikere R. ; Sponseller, Ryan ; Stoler, Aaron ; Swan, Christopher M. ; Szlag, David ; Teixeira-De Mello, Franco ; Tonkin, Jonathan D. ; Uusheimo, Sari ; Veach, Allison M. ; Vilbaste, Sirje ; Vought, Lena B.M. ; Wang, Chiao Ping ; Webster, Jackson R. ; Wilson, Paul B. ; Woelfl, Stefan ; Xenopoulos, Marguerite A. ; Yates, Adam G. ; Yoshimura, Chihiro ; Yule, Catherine M. ; Zhang, Yixin X. ; Zwart, Jacob A. - \ 2019
    Science Advances 5 (2019)1. - ISSN 2375-2548 - p. 14966 - 14973.

    River ecosystems receive and process vast quantities of terrestrial organic carbon, the fate of which depends strongly on microbial activity. Variation in and controls of processing rates, however, are poorly characterized at the global scale. In response, we used a peer-sourced research network and a highly standardized carbon processing assay to conduct a global-scale field experiment in greater than 1000 river and riparian sites. We found that Earth's biomes have distinct carbon processing signatures. Slow processing is evident across latitudes, whereas rapid rates are restricted to lower latitudes. Both the mean rate and variability decline with latitude, suggesting temperature constraints toward the poles and greater roles for other environmental drivers (e.g., nutrient loading) toward the equator. These results and data set the stage for unprecedented "next-generation biomonitoring" by establishing baselines to help quantify environmental impacts to the functioning of ecosystems at a global scale.

    A case study on prediction of sensitivity of tomato sepals to fungal infection using hyperspectral imaging
    Chauhan, A. ; Harchioui, Najim El; Hogeveen-van Echtelt, Esther ; Mensink, M.G.J. ; Brdar, Sanja ; Panic, Marko ; Grbovic, Zeljana - \ 2019
    In: Book of Abstracts European Federation for Information Technology in Agriculture, Food and the Environment (EFITA) 2019. - EFITA - p. 42 - 42.
    User stories: Marko Ruis: Lectoraat / GKC / DWW
    Ruis, Markus - \ 2019
    Substrate conformational dynamics facilitate structure-specific recognition of gapped DNA by DNA polymerase
    Craggs, Timothy D. ; Sustarsic, Marko ; Plochowietz, Anne ; Mosayebi, Majid ; Kaju, Hendrik ; Cuthbert, Andrew ; Hohlbein, Johannes ; Domicevica, Laura ; Biggin, Philip C. ; Doye, Jonathan P.K. ; Kapanidis, Achillefs N. - \ 2019
    Nucleic acids research 47 (2019)20. - ISSN 0305-1048 - p. 10788 - 10800.

    DNA-binding proteins utilise different recognition mechanisms to locate their DNA targets; some proteins recognise specific DNA sequences, while others interact with specific DNA structures. While sequence-specific DNA binding has been studied extensively, structure-specific recognition mechanisms remain unclear. Here, we study structure-specific DNA recognition by examining the structure and dynamics of DNA polymerase I Klenow Fragment (Pol) substrates both alone and in DNA-Pol complexes. Using a docking approach based on a network of 73 distances collected using single-molecule FRET, we determined a novel solution structure of the single-nucleotide-gapped DNA-Pol binary complex. The structure resembled existing crystal structures with regards to the downstream primer-template DNA substrate, and revealed a previously unobserved sharp bend (∼120°) in the DNA substrate; this pronounced bend was present in living cells. MD simulations and single-molecule assays also revealed that 4-5 nt of downstream gap-proximal DNA are unwound in the binary complex. Further, experiments and coarse-grained modelling showed the substrate alone frequently adopts bent conformations with 1-2 nt fraying around the gap, suggesting a mechanism wherein Pol recognises a pre-bent, partially-melted conformation of gapped DNA. We propose a general mechanism for substrate recognition by structure-specific enzymes driven by protein sensing of the conformational dynamics of their DNA substrates.

    Chitin-Binding Protein of Verticillium nonalfalfae Disguises Fungus from Plant Chitinases and Suppresses Chitin-Triggered Host Immunity
    Volk, Helena ; Marton, Kristina ; Flajšman, Marko ; Radišek, Sebastjan ; Tian, Hui ; Hein, Ingo ; Podlipnik, Črtomir ; Thomma, Bart P.H.J. ; Košmelj, Katarina ; Javornik, Branka ; Berne, Sabina - \ 2019
    Molecular Plant-Microbe Interactions 32 (2019)10. - ISSN 0894-0282 - p. 1378 - 1390.
    Fungal effectors - Fungus–plant interactions - Mechanisms of pathogenicity

    During fungal infections, plant cells secrete chitinases, which digest chitin in the fungal cell walls. The recognition of released chitin oligomers via lysin motif (LysM)-containing immune host receptors results in the activation of defense signaling pathways. We report here that Verticillium nonalfalfae, a hemibiotrophic xylem-invading fungus, prevents these digestion and recognition processes by secreting a carbohydrate-binding motif 18 (CBM18)-chitin-binding protein, VnaChtBP, which is transcriptionally activated specifically during the parasitic life stages. VnaChtBP is encoded by the Vna8.213 gene, which is highly conserved within the species, suggesting high evolutionary stability and importance for the fungal lifestyle. In a pathogenicity assay, however, Vna8.213 knockout mutants exhibited wilting symptoms similar to the wild-type fungus, suggesting that Vna8.213 activity is functionally redundant during fungal infection of hop. In a binding assay, recombinant VnaChtBP bound chitin and chitin oligomers in vitro with submicromolar affinity and protected fungal hyphae from degradation by plant chitinases. Moreover, the chitin-triggered production of reactive oxygen species from hop suspension cells was abolished in the presence of VnaChtBP, indicating that VnaChtBP also acts as a suppressor of chitin-triggered immunity. Using a yeast-two-hybrid assay, circular dichroism, homology modeling, and molecular docking, we demonstrated that VnaChtBP forms dimers in the absence of ligands and that this interaction is stabilized by the binding of chitin hexamers with a similar preference in the two binding sites. Our data suggest that, in addition to chitin-binding LysM (CBM50) and Avr4 (CBM14) fungal effectors, structurally unrelated CBM18 effectors have convergently evolved to prevent hydrolysis of the fungal cell wall against plant chitinases and to interfere with chitin-triggered host immunity.

    Assessing the climate regulation potential of Agricultural soils using a decision support tool adapted to stakeholders' needs and possibilities
    Broek, Marijn Van de; Henriksen, Christian Bugge ; Ghaley, Bhim Bahadur ; Lugato, Emanuele ; Kuzmanovski, Vladimir ; Trajanov, Aneta ; Debeljak, Marko ; Sandén, Taru ; Spiegel, Heide ; Decock, Charlotte ; Creamer, Rachel ; Six, Johan - \ 2019
    Frontiers in Environmental Science 7 (2019). - ISSN 2296-665X
    Soils perform many functions that are vital to societies, among which their capability to regulate global climate has received much attention over the past decades. An assessment of the extent to which soils perform a specific function is not only important to appropriately value their current capacity, but also to make well-informed decisions about how and where to change soil management to align the delivered soil functions with societal demands. To obtain an overview of the capacity of soils to perform different functions, accurate and easy-to-use models are necessary. A problem with most currently-available models is that data requirements often exceed data availability, while generally a high level of expert knowledge is necessary to apply these models. Therefore, we developed a qualitative model to assess how agricultural soils function with respect to climate regulation. The model is driven by inputs about agricultural management practices, soil properties and environmental conditions. To reduce data requirements on stakeholders, the 17 input variables are classified into either (1) three classes: low, medium and high or (2) the presence or absence of a management practice. These inputs are combined using a decision tree with internal integration rules to obtain an estimate of the magnitude of N2O emissions and carbon sequestration. These two variables are subsequently combined into an estimate of the capacity of a soil to perform the climate regulation function. The model was tested using data from long-term field experiments across Europe. This showed that the model is generally able to adequately assess this soil function across a range of environments under different management practices. In a next step, this model will be combined with models to assess other soil functions (soil biodiversity, primary productivity, nutrient cycling and water regulation and purification). This will allow the assessment of trade-offs between these soil functions for agricultural land across Europe.
    No systematic effects of sampling direction on climate-growth relationships in a large-scale, multi-species tree-ring data set
    Gut, Urs ; Árvai, Mátyás ; Bijak, Szymon ; Camarero, J.J. ; Cedro, Anna ; Cruz-García, Roberto ; Garamszegi, Balázs ; Hacket-Pain, Andrew ; Hevia, Andrea ; Huang, Weiwei ; Isaac-Renton, Miriam ; Kaczka, Ryszard J. ; Kazimirović, Marko ; Kędziora, Wojciech ; Kern, Zoltán ; Klisz, Marcin ; Kolář, Tomáš ; Körner, Michael ; Kuznetsova, Veronica ; Montwé, David ; Petritan, Any Mary ; Petritan, Ion Catalin ; Plavcová, Lenka ; Rehschuh, Romy ; Rocha, Eva ; Rybníček, Michal ; Sánchez-Salguero, Raúl ; Schröder, Jens ; Schwab, Niels ; Stajić, Branko ; Tomusiak, Robert ; Wilmking, Martin ; Sass-Klaassen, Ute ; Buras, Allan - \ 2019
    Dendrochronologia 57 (2019). - ISSN 1125-7865
    Climate signal - Correlation analysis - Dendro-provenancing - Directional growth - Principal Component Gradient Analysis - Tree-rings

    Ring-width series are important for diverse fields of research such as the study of past climate, forest ecology, forest genetics, and the determination of origin (dendro-provenancing) or dating of archaeological objects. Recent research suggests diverging climate-growth relationships in tree-rings due to the cardinal direction of extracting the tree cores (i.e. direction-specific effect). This presents an understudied source of bias that potentially affects many data sets in tree-ring research. In this study, we investigated possible direction-specific growth variability based on an international (10 countries), multi-species (8 species) tree-ring width network encompassing 22 sites. To estimate the effect of direction-specific growth variability on climate-growth relationships, we applied a combination of three methods: An analysis of signal strength differences, a Principal Component Gradient Analysis and a test on the direction-specific differences in correlations between indexed ring-widths series and climate variables. We found no evidence for systematic direction-specific effects on tree radial growth variability in high-pass filtered ring-width series. In addition, direction-specific growth showed only marginal effects on climate-growth correlations. These findings therefore indicate that there is no consistent bias caused by coring direction in data sets used for diverse dendrochronological applications on relatively mesic sites within forests in flat terrain, as were studied here. However, in extremely dry, warm or cold environments, or on steep slopes, and for different life-forms such as shrubs, further research is advisable.

    Modeling of Soil Functions for Assessing Soil Quality: Soil Biodiversity and Habitat Provisioning
    Leeuwen, J.P. van; Creamer, Rachel ; Cluzeau, Daniel ; Debeljak, Marko ; Gatti, Fabio ; Henriksen, Christian Bugge ; Kuzmanovski, Vladimir ; Menta, Cristina ; Pérès, Guénola ; Picaud, Calypso ; Saby, N.P.A. ; Trajanov, Aneta ; Trinsoutrot-Gattin, Isabelle ; Visioli, Giovanna ; Rutgers, M. - \ 2019
    Frontiers in Environmental Science 7 (2019). - ISSN 2296-665X - 13 p.
    Soil biodiversity and habitat provisioning is one of the soil functions that agricultural land provides to society. This paper describes assessment of the soil biodiversity function (SB function) as a proof of concept to be used in a decision support tool for agricultural land management. The SB function is defined as “the multitude of soil organisms and processes, interacting in an ecosystem, providing society with a rich biodiversity source and contributing to a habitat for aboveground organisms.” So far, no single measure provides the full overview of the soil biodiversity and how a soil supports a habitat for a biodiverse ecosystem. We have assembled a set of attributes for a proxy-indicator system, based on four “integrated attributes”: (1) soil nutrient status, (2) soil biological status, (3) soil structure, and (4) soil hydrological status. These attributes provide information to be used in a model for assessing the capacity of a soil to supply the SB function. A multi-criteria decision model was developed which comprises of 34 attributes providing information to quantify the four integrated attributes and subsequently assess the SB function for grassland and for cropland separately. The model predictions (in terms of low—moderate—high soil biodiversity status) were compared with expert judgements for a collection of 137 grassland soils in the Netherlands and 52 French soils, 29 grasslands, and 23 croplands. For both datasets, the results show that the proposed model predictions were statistically significantly correlated with the expert judgements. A sensitivity analysis indicated that the soil nutrient status, defined by attributes such as pH and organic carbon content, was the most important integrated attribute in the assessment of the SB function. Further progress in the assessment of the SB function is needed. This can be achieved by better information regarding land use and farm management. In this way we may make a valuable step in our attempts to optimize the multiple soil functions in agricultural landscapes, and hence the multifaceted role of soils to deliver a bundle of ecosystem services for farmers and citizens, and support land management and policy toward a more sustainable society.
    A Field-Scale Decision Support System for Assessment and Management of Soil Functions
    Debeljak, Marko ; Trajanov, Aneta ; Kuzmanovski, Vladimir ; Schroder, J.J. ; Sandén, Taru ; Spiegel, Heide ; Wall, David ; Broek, Marijn van de; Rutgers, Michiel ; Bampa, Francesca ; Creamer, Rachel ; Henriksen, Christian Bugge - \ 2019
    Frontiers in Environmental Science 7 (2019). - ISSN 2296-665X
    Agricultural decision support systems (DSS) 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 modelling 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 advises 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.
    ‘Opening up’ science policy: engaging with RRI in Brazil
    Reyes-Galindo, Luis ; Monteiro, Marko ; Macnaghten, Phil - \ 2019
    Journal of Responsible Innovation 6 (2019)3. - ISSN 2329-9460 - p. 353 - 360.
    Brazil - governance of science and technology - RRI - science and technology policy

    This article presents initial results from the Brazilian team in the Responsible Research and Innovation in Practice (RRI-Practice) collaboration, concurrently running in 22 countries. The project invites reflection from institutional actors through a variety of participatory exercises that focus on RRI’s potential for ‘opening up’ and impacting national science and innovation policy. After summarising the operational challenges faced during the research process, we focus on the main empirical findings. We conclude that despite its potential for opening up policy deliberation, RRI faces the inherent hurdles of surpassing longstanding Brazilian institutional traditions of hierarchical governance, autonomy and the dominance of linear models of innovation.

    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.

    Removing the no-analogue bias in modern accelerated tree growth leads to stronger medieval drought
    Scharnweber, Tobias ; Heußner, Karl Uwe ; Smiljanic, Marko ; Heinrich, Ingo ; Maaten-Theunissen, Marieke van der; Maaten, Ernst van der; Struwe, Thomas ; Buras, Allan ; Wilmking, Martin - \ 2019
    Scientific Reports 9 (2019)1. - ISSN 2045-2322

    In many parts of the world, especially in the temperate regions of Europe and North-America, accelerated tree growth rates have been observed over the last decades. This widespread phenomenon is presumably caused by a combination of factors like atmospheric fertilization or changes in forest structure and/or management. If not properly acknowledged in the calibration of tree-ring based climate reconstructions, considerable bias concerning amplitudes and trends of reconstructed climatic parameters might emerge or low frequency information is lost. Here we present a simple but effective, data-driven approach to remove the recent non-climatic growth increase in tree-ring data. Accounting for the no-analogue calibration problem, a new hydroclimatic reconstruction for northern-central Europe revealed considerably drier conditions during the medieval climate anomaly (MCA) compared with standard reconstruction methods and other existing reconstructions. This demonstrates the necessity to account for fertilization effects in modern tree-ring data from affected regions before calibrating reconstruction models, to avoid biased results.

    Plant functional trait change across a warming tundra biome
    Bjorkman, Anne D. ; Myers-Smith, Isla H. ; Elmendorf, Sarah C. ; Normand, Signe ; Rüger, Nadja ; Beck, Pieter S.A. ; Blach-Overgaard, Anne ; Blok, Daan ; Cornelissen, J.H.C. ; Forbes, Bruce C. ; Georges, Damien ; Goetz, Scott J. ; Guay, Kevin C. ; Henry, Gregory H.R. ; Hillerislambers, Janneke ; Hollister, Robert D. ; Karger, Dirk N. ; Kattge, Jens ; Manning, Peter ; Prevéy, Janet S. ; Rixen, Christian ; Schaepman-Strub, Gabriela ; Thomas, Haydn J.D. ; Vellend, Mark ; Wilmking, Martin ; Wipf, Sonja ; Carbognani, Michele ; Hermanutz, Luise ; Lévesque, Esther ; Molau, Ulf ; Petraglia, Alessandro ; Soudzilovskaia, Nadejda A. ; Spasojevic, Marko J. ; Tomaselli, Marcello ; Vowles, Tage ; Alatalo, Juha M. ; Alexander, Heather D. ; Anadon-Rosell, Alba ; Angers-Blondin, Sandra ; Beest, Mariska te; Berner, Logan ; Björk, Robert G. ; Buchwal, Agata ; Buras, Allan ; Christie, Katherine ; Heijmans, Monique M.P.D. ; Ozinga, Wim A. - \ 2018
    Nature 526 (2018). - ISSN 0028-0836 - p. 57 - 62.
    The tundra is warming more rapidly than any other biome on Earth, and the potential ramifications are far-reaching because of global feedback effects between vegetation and climate. A better understanding of how environmental factors shape plant structure and function is crucial for predicting the consequences of environmental change for ecosystem functioning. Here we explore the biome-wide relationships between temperature, moisture and seven key plant functional traits both across space and over three decades of warming at 117 tundra locations. Spatial temperature–trait relationships were generally strong but soil moisture had a marked influence on the strength and direction of these relationships, highlighting the potentially important influence of changes in water availability on future trait shifts in tundra plant communities. Community height increased with warming across all sites over the past three decades, but other traits lagged far behind predicted rates of change. Our findings highlight the challenge of using space-for-time substitution to predict the functional consequences of future warming and suggest that functions that are tied closely to plant height will experience the most rapid change. They also reveal the strength with which environmental factors shape biotic communities at the coldest extremes of the planet and will help to improve projections of functional changes in tundra ecosystems with climate warming.
    Contrasting regional habitats for urban sustainability experimentation in Europe
    Heiligenberg, Harm van den; Heimeriks, Gaston ; Hekkert, Marko ; Raven, Rob ; Sol, Jifke - \ 2018
    Sustainability 10 (2018)5. - ISSN 2071-1050
    Countercultures - Experimentation - Geography of transitions - Regional innovation - Sustainability

    The sustainability challenge requires experimentation with innovations, followed by an upscaling process towards a broader regime change in the long term. In Europe we observe various regional hotspots for sustainability experimentation which suggests that there are favorable spatial contexts. Little is known about why different kinds of experiments flourish or fail in various spatial contexts. In this paper we explore these contexts by using the habitat concept. A habitat is regarded as the configuration of favorable local and regional context factors for experimentation. To capture the diversity of these habitats we have constructed archetypical experimentation patterns. These patterns are built up of five dimensions: knowledge, governance, informal institutions, regional innovation advantages, and social learning. In a comparative case study in four city regions in Europe we find a large contrast in habitats. Countercultures play an important role, as they shape a beneficial context for experimentation through alternative ideas and lifestyles. We also find indications that it is important that a combination of several habitat factors is present, and that these factors have aligned and evolved over several years of experimentation, thus leading to a more mature habitat. The research suggests that regional stakeholders can positively influence most of the habitat factors shaping future upscaling. However, there are also some important factors, such as regional knowledge and skills, which have a path-dependent nature and are more difficult to improve in the short term.

    Does sex matter? Gender-specificity and its influence on site-chronologies in the common dioecious shrub Juniperus communis
    Shetti, Rohan ; Buras, Allan ; Smiljanic, Marko ; Hallinger, Martin ; Grigoriev, Andrey A. ; Wilmking, Martin - \ 2018
    Dendrochronologia 49 (2018). - ISSN 1125-7865 - p. 118 - 126.
    Basal area increment - Boreal shrub - Principle component gradient analysis - Ring-width - Sexual dimorphism
    In recent years an increasing number of studies have shown shrubs to be reliable proxies of environmental conditions in regions where Trees − due to harsh climate conditions − are absent. Although many shrubs are monoecious, some are dioecious, which poses certain questions related to gender-specific growth as observed for trees in previous studies. Here, we address the questions whether dioecious shrubs, similar to trees, show growth differences between male and female plants, and − if so − whether this difference needs to be considered in terms of sample selection. We chose Juniperus communis. L., the most widely distributed woody plant, and a common and well-studied dioecious shrub species in the northern hemisphere, especially in the Boreal, Subarctic tundra and Alpine regions. Our samples were collected from four sites − three from the Ural Mountains and one site from Kirkenes in Norway. To see if there were differences in radial growth between sexes we performed four different analyses. First, we used multivariate explorative statistics to see if there were gender biased sub-populations and generally found no differences. Secondly, to compare growth over the lifetime of shrubs we computed cumulative annual increments of basal area which revealed no gender-specific growth patterns. Thirdly, to test if differences in radial growth between male and female shrubs affect the resulting site-chronology, we compared individual shrub chronologies with the site-chronology and found a significant differentiation between normalized correlations of gender-specific chronologies to the site-chronology. This significant difference was restricted to an overall comparison, but not evident at individual site-level. Lastly, we compared correlations of gender-specific chronologies and a mean site-chronology with monthly climate records to find only very few meaningful differences in their responses. In summary, we could not detect any clear gender-specific growth pattern in Juniperus communis but observed a trend towards more non-climatic signals in female junipers which may affect the resulting site-chronology.
    Biomonitoring of intermittent rivers and ephemeral streams in Europe : Current practice and priorities to enhance ecological status assessments
    Stubbington, Rachel ; Chadd, Richard ; Cid, Núria ; Csabai, Zoltán ; Miliša, Marko ; Morais, Manuela ; Munné, Antoni ; Pařil, Petr ; Pešić, Vladimir ; Tziortzis, Iakovos ; Verdonschot, Ralf C.M. ; Datry, Thibault - \ 2018
    Science of the Total Environment 618 (2018). - ISSN 0048-9697 - p. 1096 - 1113.
    Bioassessment - Bioindicators - River typology - Temporary rivers - Temporary streams - Water Framework Directive
    Intermittent rivers and ephemeral streams (IRES) are common across Europe and dominate some Mediterranean river networks. In all climate zones, IRES support high biodiversity and provide ecosystem services. As dynamic ecosystems that transition between flowing, pool, and dry states, IRES are typically poorly represented in biomonitoring programmes implemented to characterize EU Water Framework Directive ecological status. We report the results of a survey completed by representatives from 20 European countries to identify current challenges to IRES status assessment, examples of best practice, and priorities for future research. We identify five major barriers to effective ecological status classification in IRES: 1. the exclusion of IRES from Water Framework Directive biomonitoring based on their small catchment size; 2. the lack of river typologies that distinguish between contrasting IRES; 3. difficulties in defining the 'reference conditions' that represent unimpacted dynamic ecosystems; 4. classification of IRES ecological status based on lotic communities sampled using methods developed for perennial rivers; and 5. a reliance on taxonomic characterization of local communities. Despite these challenges, we recognize examples of innovative practice that can inform modification of current biomonitoring activity to promote effective IRES status classification. Priorities for future research include reconceptualization of the reference condition approach to accommodate spatiotemporal fluctuations in community composition, and modification of indices of ecosystem health to recognize both taxon-specific sensitivities to intermittence and dispersal abilities, within a landscape context.
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