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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    Health and welfare of rabbits farmed in different production systems
    Saxmose Nielsen, Søren ; Alvarez, Julio ; Bicout, Dominique Joseph ; Calistri, Paolo ; Depner, Klaus ; Drewe, Julian Ashley ; Garin‐bastuji, Bruno ; Gonzales Rojas, Jose Luis ; Gortázar Schmidt, Christian ; Michel, Virginie ; Miranda Chueca, Miguel Ángel ; Roberts, Helen Clare ; Sihvonen, Liisa Helena ; Spoolder, Hans ; Stahl, Karl ; Velarde Calvo, Antonio ; Viltrop, Arvo ; Buijs, Stephanie ; Edwards, Sandra ; Candiani, Denise ; Mosbach‐schulz, Olaf ; Stede, Yves Van Der; Winckler, Christoph - \ 2019
    EFSA Journal 18 (2019)1. - ISSN 1831-4732 - 96 p.
    animal welfare - animal production - rabbits - animal housing - animal behaviour - animal health
    The AGRI committee of the European Parliament requested EFSA to assess the welfare of rabbits farmed in different production systems, including organic production, and to update its 2005 scientific opinion about the health and welfare of rabbits kept for meat production. Considering reproducing does, kits and growing rabbits, this scientific opinion focusses on six different housing systems, namely conventional cages, structurally enriched cages, elevated pens, floor pens, outdoor/partially outdoor systems and organic systems. To compare the level of welfare in the different housing systems and rabbit categories, welfare impact scores for 20 welfare consequences identified from the literature were calculated, taking their occurrence, duration and severity into account. Based on the overall welfare impact score (sum of scores for the single welfare consequences), obtained via a 2-step expert knowledge elicitation process, the welfare of reproducing does is likely (certainty 66–90%) to be lower in conventional cages compared to the five other housing systems. In addition, it is likely to extremely likely (certainty 66–99%) that the welfare of kits is lower in outdoor systems compared to the other systems and that the welfare is higher in elevated pens than in the other systems. Finally, it is likely to extremely likely (certainty 66–99%) that the welfare of growing rabbits is lower in conventional cages compared to the other systems and that the welfare is higher in elevated pens than in the other systems. Ranking of the welfare consequences allowed an analysis of the main welfare consequences within each system and rabbit category. It was concluded that for reproducing does, as well as growing rabbits, welfare consequences related to behavioural restrictions were more prominent in conventional cages, elevated pens and enriched cages, whereas those related to health problems were more important in floor pens, outdoor and organic systems. Housing in organic rabbit farming is diverse, which can result in different welfare consequences, but the overall welfare impact scores suggest that welfare in organic systems is generally good.
    Mapping the quality of regions for cycling
    Goossen, C.M. - \ 2019
    In: International Cycling Conference 2017. - Dessau-Roßlau : Umweltbundesamt (Dokumentationen 03/2019) - p. 19 - 20.
    Hydrographic and Biological Survey of a Surface-Intensified Anticyclonic Eddy in the Caribbean Sea
    Boog, C.G. van der; Jong, M.F. de; Scheidat, M. ; Leopold, M.F. ; Geelhoed, S.C.V. ; Schulz, K. ; Dijkstra, H.A. ; Pietrzak, J.D. ; Katsman, C.A. - \ 2019
    Journal of Geophysical Research: Oceans 124 (2019)8. - ISSN 2169-9275 - p. 6235 - 6251.
    anticyclone - barrier layer - Caribbean Sea - ecology - hydrographic - thermohaline staircases

    In the Caribbean Sea, mesoscale anticyclonic ocean eddies impact the local ecosystem by mixing of low salinity river outflow with the nutrient-rich waters upwelling along the Venezuelan and Colombian coast. To gain insight into the physics and the ecological impact of these anticyclones, we performed a combined hydrographic and biological survey of one Caribbean anticyclone in February 2018. We found that the anticyclone had a radius of 90 km and was surface intensified with the strongest velocities (0.72 m/s) in the upper 150 m of the water column. Below, isopycnal displacements were found down to 700 dbar. The core of the anticyclone entrained waters from the Orinoco River plume and contained slightly elevated chlorophyll concentrations compared to the surroundings. At the edge of the anticyclone we observed higher densities of flying fish but not higher densities of predators like seabirds and cetaceans. Below the surface, a strong temperature inversion (0.98 °C) was present within a barrier layer. In addition, we found thermohaline staircases that originated from double diffusion processes within Tropical Atlantic Central Water.

    Towards a traceable climate service: Assessment of quality and usability of essential climate variables
    Zeng, Yijian ; Su, Zhongbo ; Barmpadimos, Iakovos ; Perrels, Adriaan ; Poli, Paul ; Boersma, K.F. ; Frey, Anna ; Ma, Xiaogang ; Bruin, Karianne de; Goosen, Hasse ; John, Viju O. ; Roebeling, Rob ; Schulz, Jörg ; Timmermans, Wim - \ 2019
    Remote Sensing 11 (2019)10. - ISSN 2072-4292
    Climate data record (CDRs) - Climate services - Essential climate variables (ECVs) - Quality assurance - Traceability - Usability assessment

    Climate services are becoming the backbone to translate climate knowledge, data & information into climate-informed decision-making at all levels, from public administrations to business operators. It is essential to assess the technical and scientific quality of the provided climate data and information products, including their value to users, to establish the relation of trust between providers of climate data and information and various downstream users. The climate data and information products (i.e., from satellite, in-situ and reanalysis) shall be fully traceable, adequately documented and uncertainty quantified and can provide sufficient guidance for users to address their specific needs and feedbacks. This paper discusses details on how to apply the quality assurance framework to deliver timely assessments of the quality and usability of Essential Climate Variable (ECV) products. It identifies an overarching structure for the quality assessment of single product ECVs (i.e., consists of only one single variable), multi-product ECVs (i.e., more than one single parameter), thematic products (i.e., water, energy and carbon cycles), as well as the usability assessment. To support a traceable climate service, other than rigorously evaluating the technical and scientific quality of ECV products, which represent the upstream of climate services, how the uncertainty propagates into the resulting benefit (utility) for the users of the climate service needs to be detailed.

    Fungicides: An Overlooked Pesticide Class?
    Zubrod, Jochen P. ; Bundschuh, Mirco ; Arts, Gertie ; Brühl, Carsten A. ; Imfeld, Gwenaël ; Knäbel, Anja ; Payraudeau, Sylvain ; Rasmussen, Jes J. ; Rohr, Jason ; Scharmüller, Andreas ; Smalling, Kelly ; Stehle, Sebastian ; Schulz, Ralf ; Schäfer, Ralf B. - \ 2019
    Environmental Science and Technology 53 (2019)7. - ISSN 0013-936X - p. 3347 - 3365.

    Fungicides are indispensable to global food security and their use is forecasted to intensify. Fungicides can reach aquatic ecosystems and occur in surface water bodies in agricultural catchments throughout the entire growing season due to their frequent, prophylactic application. However, in comparison to herbicides and insecticides, the exposure to and effects of fungicides have received less attention. We provide an overview of the risk of fungicides to aquatic ecosystems covering fungicide exposure (i.e., environmental fate, exposure modeling, and mitigation measures) as well as direct and indirect effects of fungicides on microorganisms, macrophytes, invertebrates, and vertebrates. We show that fungicides occur widely in aquatic systems, that the accuracy of predicted environmental concentrations is debatable, and that fungicide exposure can be effectively mitigated. We additionally demonstrate that fungicides can be highly toxic to a broad range of organisms and can pose a risk to aquatic biota. Finally, we outline central research gaps that currently challenge our ability to predict fungicide exposure and effects, promising research avenues, and shortcomings of the current environmental risk assessment for fungicides.

    Baseline and power analyses for the assessment of beach litter reductions in the European OSPAR region
    Schulz, Marcus ; Walvoort, Dennis J.J. ; Barry, Jon ; Fleet, David M. ; Loon, Willem M.G.M. van - \ 2019
    Environmental Pollution 248 (2019). - ISSN 0269-7491 - p. 555 - 564.
    Baseline value - Beach litter - litteR - Non-parametrical power analysis - Reduction target

    Marine litter pollution is a global environmental problem. Beach litter is a part of this problem, and is widely monitored in Europe. The European Marine Strategy Framework Directive (MSFD) requires a reduction of beach litter. A reduction of 30% has been proposed in the European Plastics Strategy. The aims of this study are to develop (a) a method to calculate sufficiently stable and precise baseline values for beach litter, and (b) to derive a method of power analysis to estimate the number of beach litter surveys, necessary to detect a given reduction, using these baseline values. Beach litter data from the OSPAR (Oslo Paris Convention) region were used, and tailor-made statistical methods were implemented in open source software, litteR. Descriptive statistics and Theil-Sen and Mann-Kendall trend analyses were calculated for the most abundant beach litter types, for 14 survey sites. The length of a baseline period necessary to obtain a specified precision of the mean baseline value, expressed as Coefficient of Variation (CV), was calculated. Power analyses were performed using Monte Carlo simulations combined with Wilcoxon tests to determine significant deviations of the simulated datasets from the baseline mean values. For most survey sites, the mean length of monitoring periods necessary to achieve a CV < 10% amounts to four to five years with four surveys a year. The mean number of surveys necessary to detect a statistically significant reduction of 30% with 80% power ranges from 14 to 20. Power analyses show that a reduction of 10% is difficult to detect, because more than 24 surveys are needed. In contrary, a reduction of 40–50% can be detected easily with a small (<12) number of surveys. The new methods could also be applied to other areas where similar beach litter surveys are performed.

    Beneficial use of dredged sediment to enhance salt marsh development by applying a ‘Mud Motor’
    Baptist, Martin J. ; Gerkema, T. ; Prooijen, B.C. van; Maren, D.S. van; Regteren, M. van; Schulz, K. ; Colosimo, I. ; Vroom, J. ; Kessel, T. van; Grasmeijer, B. ; Willemsen, P. ; Elschot, K. ; Groot, A.V. de; Cleveringa, J. ; Eekelen, E.M.M. van; Schuurman, F. ; Lange, H.J. de; Puijenbroek, M.E.B. van - \ 2019
    Ecological Engineering 127 (2019). - ISSN 0925-8574 - p. 312 - 323.
    Building with Nature - Nature-based solutions - Cohesive sediment - Dredging - Salt marshes - intertidal flats
    We test an innovative approach to beneficially re-use dredged sediment to enhance salt marsh development. A Mud Motor is a dredged sediment disposal in the form of a semi-continuous source of mud in a shallow tidal channel allowing natural processes to disperse the sediment to nearby mudflats and salt marshes. We describe the various steps in the design of a Mud Motor pilot: numerical simulations with a sediment transport model to explore suitable disposal locations, a tracer experiment to measure the transport fate of disposed mud, assessment of the legal requirements, and detailing the planning and technical feasibility. An extensive monitoring and research programme was designed to measure sediment transport rates and the response of intertidal mudflats and salt marshes to an increased sediment load. Measurements include the sediment transport in the tidal channel and on the shallow mudflats, the vertical accretion of intertidal mudflats and salt marsh, and the salt marsh vegetation cover and composition. In the Mud Motor pilot a total of 470,516 m 3
    of fine grained sediment (D50 of ∼10 μm) was disposed over two winter seasons, with an average of 22 sediment disposals per week of operation. Ship-based measurements revealed a periodic vertical salinity stratification that is inverted compared to a classical estuary and that is working against the asymmetric flood-dominated transport direction. Field measurements on the intertidal mudflats showed that the functioning of the Mud Motor, i.e. the successful increased mud transport toward the salt marsh, is significantly dependent on wind and wave forcing. Accretion measurements showed relatively large changes in surface elevation due to deposition and erosion of layers of
    watery mud with a thickness of up to 10 cm on a time scale of days. The measurements indicate notably higher sediment dynamics during periods of Mud Motor disposal. The salt marsh demonstrated significant vertical accretion though this has not yet led to horizontal expansion because there was more hydrodynamic stress than foreseen. In carrying out the pilot we learned that the feasibility of a Mud Motor depends on an assessment of additional travel time for the dredger, the effectiveness on salt marsh growth, reduced dredging volumes in a port, and many other practical issues. Our improved understanding on the transport processes in the channel and on the mudflats and salt marsh yields design lessons and guiding principles for future applications of sediment
    management in salt marsh development that include a Mud Motor approach
    Standard method performance requirements (SMPRs®) 2017.017 : Determination of 2-and 3-MCPD, 2-and 3-MCPD esters, and glycidyl esters in infant and adult/pediatric nutritional formula
    Kuhlmann, Jan ; Anderson, Warwick ; Bandong, Grace ; Bratinova, Stefanka ; Burger, Dominik ; Cook, Jo Marie ; Cruijsen, Hans ; Dominicis, Emiliano De; Vreeze, Marcel De; Ehling, Stefan ; Empl, Anna Maria ; Evers, Jaap ; Gude, Thomas ; Hanlon, Paul ; Jaudzems, Greg ; Koesukwiwat, Urairat ; Lesueur, Celine ; MacMahon, Shaun ; Manti, Vicky ; Mastovska, Katerina ; Mikkelsen, Aase ; Myers, Rick ; Paolillo, Paola ; Parisi, Salvatore ; Pinkston, J.D. ; Rankin, Robert ; Reuther, John ; Romano, Joe ; Schulz, Claudia ; Stanley, Glenn ; Stephenson, Cheryl ; Sullivan, Darryl ; Szpylka, John ; Tennyson, Steve ; Leeuwen, Stefan Van; Yadlapalli, Sudhakar ; Yeung, Jupiter - \ 2018
    Journal of AOAC International 101 (2018)1. - ISSN 1060-3271 - p. 324 - 326.
    Implementation of PROMETHEUS 4‐step approach for evidence use in EFSA scientific assessments: benefits, issues, needs and solutions
    Aiassa, Elisa ; Martino, Laura ; Barizzone, Fulvio ; Ciccolallo, Laura ; Garcia, Ana ; Georgiadis, Marios ; Guajardo, Irene Muñoz ; Tomcikova, Daniela ; Alexander, Jan ; Calistri, Paolo ; Gundert‐remy, Ursula ; Hart, Andrew David ; Hoogenboom, Ron Laurentius ; Messean, Antoine ; Naska, Androniki ; Navarro, Maria Navajas ; Noerrung, Birgit ; Ockleford, Colin ; Wallace, Robert John ; Younes, Maged ; Abuntori, Blaize ; Alvarez, Fernando ; Aryeetey, Monica ; Baldinelli, Francesca ; Barrucci, Federica ; Bau, Andrea ; Binaglia, Marco ; Broglia, Alessandro ; Castoldi, Anna Federica ; Christoph, Eugen ; Sesmaisons‐Lecarré, Agnes De; Georgiadis, Nikolaos ; Gervelmeyer, Andrea ; Istace, Frederique ; López‐Gálvez, Gloria ; Manini, Paola ; Maurici, Daniela ; Merten, Caroline ; Messens, Winy ; Mosbach‐Schulz, Olaf ; Putzu, Claudio ; Bordajandi, Luisa Ramos ; Smeraldi, Camilla ; Tiramani, Manuela ; Martínez, Silvia Valtueña ; Sybren, Vos ; Hardy, Anthony Richard ; Hugas, Marta ; Kleiner, Juliane ; Seze, Guilhem De - \ 2018
    EFSA Supporting Publications 15 (2018)4. - ISSN 2397-8325
    In 2014, the European Food Safety Authority (EFSA) started the PROMETHEUS (PROmoting METHods for Evidence Use in Scientific assessments) project to improve further and increase the consistency of the methods it uses in its scientific assessments. The project defined a set of principles for the scientific assessment process and a 4‐step approach (plan/carry out/verify/report) for their fulfilment, which was tested in ten case studies, one from each EFSA panel. The present report describes the benefits, issues, needs and solutions related to the implementation of the 4‐step approach in EFSA, identified in a dedicated workshop in October 2017. The key benefits of the approach, which was deemed applicable to all types of EFSA scientific assessment including assessments of regulated products, are: 1) increased ‘scientific value’ of EFSA outputs, i.e. the extent of impartiality, methodological rigour, transparency and engagement; 2) guarantee of fitness‐for‐purpose, as it implies tailoring the methods to the specificities of each assessment; 3) efficiency gain, since preparing a protocol for the assessment upfront helps more streamlined processes throughout the implementation phase; 4) innovation, as the approach promotes the pioneering practice of ‘planning before doing’ (well established in primary research) for broad scientific assessments in regulatory science; and 5) increased harmonisation and consistency of EFSA assessments. The 4‐step approach was also considered an effective system for detecting additional methodological and/or expertise needs and a useful basis for further defining a quality management system for EFSA's scientific processes. The identified issues and solutions related to the implementation of the approach are: a) lack of engagement and need for effective communication on benefits and added value; b) need for further advances especially in the field of problem formulation/protocol development, evidence appraisal and evidence integration; c) need for specialised expertise in the previous aspects; and specific needs for d) assessments of regulated products and e) outsourced projects.
    Quality assurance framework development based on six new ECV data products to enhance user confidence for climate applications
    Nightingale, Joanne ; Boersma, Klaas Folkert ; Muller, Jan Peter ; Compernolle, Steven ; Lambert, Jean Christopher ; Blessing, Simon ; Giering, Ralf ; Gobron, Nadine ; Smedt, Isabelle De ; Coheur, Pierre ; George, Maya ; Schulz, Jörg ; Wood, Alexander - \ 2018
    Remote Sensing 10 (2018)8. - ISSN 2072-4292
    Climate applications - Climate data records - CO - Earth observation satellites - Essential climate variables - FAPAR - HCHO - LAI - NO2 - Quality assurance - Surface albedo - Traceability - User requirements

    Data from Earth observation (EO) satellites are increasingly used to monitor the environment, understand variability and change, inform evaluations of climate model forecasts, and manage natural resources. Policymakers are progressively relying on the information derived from these datasets to make decisions on mitigating and adapting to climate change. These decisions should be evidence based, which requires confidence in derived products, as well as the reference measurements used to calibrate, validate, or inform product development. In support of the European Union's Earth Observation Programmes Copernicus Climate Change Service (C3S), the Quality Assurance for Essential Climate Variables (QA4ECV) project fulfilled a gap in the delivery of climate quality satellite-derived datasets, by prototyping a generic system for the implementation and evaluation of quality assurance (QA) measures for satellite-derived ECV climate data record products. The project demonstrated the QA system on six new long-term, climate quality ECV data records for surface albedo, leaf area index (LAI), fraction of absorbed photosynthetically active radiation (FAPAR), nitrogen dioxide (NO2), formaldehyde (HCHO), and carbon monoxide (CO). The provision of standardised QA information provides data users with evidence-based confidence in the products and enables judgement on the fitness-for-purpose of various ECV data products and their specific applications.

    A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits
    Hibrand Saint-Oyant, L. ; Ruttink, T. ; Hamama, L. ; Kirov, I. ; Lakhwani, D. ; Zhou, N.N. ; Bourke, P.M. ; Daccord, N. ; Leus, L. ; Schulz, D. ; Geest, H. van de; Hesselink, T. ; Laere, K. Van; Debray, K. ; Balzergue, S. ; Thouroude, T. ; Chastellier, A. ; Jeauffre, J. ; Voisine, L. ; Gaillard, S. ; Borm, T.J.A. ; Arens, P. ; Voorrips, R.E. ; Maliepaard, C. ; Neu, E. ; Linde, M. ; Paslier, M.C. Le; Bérard, A. ; Bounon, R. ; Clotault, J. ; Choisne, N. ; Quesneville, H. ; Kawamura, K. ; Aubourg, S. ; Sakr, S. ; Smulders, M.J.M. ; Schijlen, E. ; Bucher, E. ; Debener, T. ; Riek, J. De; Foucher, F. - \ 2018
    Nature Plants 4 (2018). - ISSN 2055-026X - p. 473 - 484.

    Rose is the world’s most important ornamental plant, with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Roses are outbred and can have various ploidy levels. Our objectives were to develop a high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short reads, and anchoring to a high-density genetic map, and to study the genome structure and genetic basis of major ornamental traits. We produced a doubled haploid rose line (‘HapOB’) from Rosa chinensis ‘Old Blush’ and generated a rose genome assembly anchored to seven pseudo-chromosomes (512 Mb with N50 of 3.4 Mb and 564 contigs). The length of 512 Mb represents 90.1–96.1% of the estimated haploid genome size of rose. Of the assembly, 95% is contained in only 196 contigs. The anchoring was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features, including the pericentromeric regions, through annotation of transposable element families and positioned centromeric repeats using fluorescent in situ hybridization. The rose genome displays extensive synteny with the Fragaria vesca genome, and we delineated only two major rearrangements. Genetic diversity was analysed using resequencing data of seven diploid and one tetraploid Rosa species selected from various sections of the genus. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and the number of flower petals. A rose APETALA2/TOE homologue is proposed to be the major regulator of petal number in rose. This reference sequence is an important resource for studying polyploidization, meiosis and developmental processes, as we demonstrated for flower and prickle development. It will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae.

    The ecological role of volatile mediated interactions belowground
    Schulz-Bohm, Kristin - \ 2018
    Wageningen University. Promotor(en): W. de Boer, co-promotor(en): P. Garbeva. - Wageningen : Wageningen University - ISBN 9789463438889 - 262

    In the porous network of soil, microbes are unevenly distributed. Interactions between soil (micro-) organisms that are physically separated could be mediated by volatile organic compounds (VOCs). VOCs are small, partially very smelly, molecules that can diffuse through air- and water-filled soil pores. Microbes, similar to plants, produce a diverse set of VOCs. The importance of these compounds in communication and competitiveness between microbes and plants in soil is increasingly recognized. However, our understanding on the relevance of VOCs-mediated interactions belowground is still limited. The aim of this thesis was to reveal novel insights into the ecological role of VOCs in microbial interactions and community dynamics in soil. A soil model system which more closely reflects conditions of soil environment in and around the rhizosphere was designed to study VOCs-mediated interactions between bacteria-bacteria, bacteria-fungi and plant-bacteria. Furthermore, novel aspects on the ecological role of VOCs in interactions of soil microorganisms such as protists were examined. Results of this thesis revealed that microbial interactions and shifts in the community composition strongly affect the volatile emission in soil. In this context, bacteria associated to the fungus can significantly influence the VOCs production and fitness of the fungal host. Moreover, within this thesis it was demonstrated that VOCs produced by microbes in the rhizosphere or plant roots can have a significant long distance effect on microorganisms in the surrounding nutrient-depleted bulk soil. For instance, VOCs released by bacterial interactions in the rhizosphere could stimulate the activity of distant starved bacteria. Furthermore, it was shown that plants can attract (beneficial) bacteria by root-VOCs. These results suggest that the rhizosphere effect might not be restricted to narrow zone – the few millimeters around the roots – but is further expanded by VOCs-mediated interactions. Interestingly, VOCs can also play a role as long-distance messenger in interactions between bacteria and protists. It was shown that bacterial VOCs such as terpenes affect protist activity and motility. This was mostly correlated to responses in direct feeding-interactions. Accordingly, bacterial VOCs could serve as signals for protists to find suitable prey. Overall, findings of this thesis provide novel information on the complexity of VOCs-mediated interactions in soil and contribute to our knowledge on the importance of VOCs-mediated (chemical) communication in ecosystem functioning belowground.

    Calling from distance : attraction of soil bacteria by plant root volatiles
    Schulz-Bohm, Kristin ; Gerards, Saskia ; Hundscheid, Maria ; Melenhorst, Jasper ; Boer, Wietse de; Garbeva, Paolina - \ 2018
    ISME Journal 12 (2018). - ISSN 1751-7362 - p. 1252 - 1262.
    Plants release a wide set of secondary metabolites including volatile organic compounds (VOCs). Many of those compounds are considered to function as defense against herbivory, pests, and pathogens. However, little knowledge exists about the role of belowground plant VOCs for attracting beneficial soil microorganisms. We developed an olfactometer system to test the attraction of soil bacteria by VOCs emitted by Carex arenaria roots. Moreover, we tested whether infection of C. arenaria with the fungal pathogen Fusarium culmorum modifies the VOCs profile and bacterial attraction. The results revealed that migration of distant bacteria in soil towards roots can be stimulated by plant VOCs. Upon fungal infection, the blend of root VOCs changed and specific bacteria with antifungal properties were attracted. Tests with various pure VOCs indicated that those compounds can diffuse over long distance but with different diffusion abilities. Overall, this work highlights the importance of plant VOCs in belowground long-distance plant–microbe interactions.
    Dynamics of Soil Bacterial Communities Over a Vegetation Season Relate to Both Soil Nutrient Status and Plant Growth Phenology
    Francioli, Davide ; Schulz, Elke ; Buscot, François ; Reitz, Thomas - \ 2018
    Microbial Ecology 75 (2018)1. - ISSN 0095-3628 - p. 216 - 227.
    B-ARISA fingerprinting - Inoculation of sterilized soil - Niche and neutral assemblage processes - Plant-soil interactions - Soil bacterial communities
    Soil microorganisms regulate element cycling and plant nutrition, mediate co-existence of neighbors, and stabilize plant communities. Many of these effects are dependent upon environmental conditions and, in particular, on nutrient quality and availability in soils. In this context, we set up a pot experiment in order to examine the combined effects of soil nutrient availability and microbial communities on plant-soil interactions and to investigate assemblage rules for soil bacterial communities under changed nutrient conditions. Four gamma-sterilized soils, strongly differing in their nutrient contents, were obtained from different fertilization treatments of a centenary field experiment and used to grow communities of grassland plants. The sterilized soils were either self- or cross-inoculated with microbial consortia from the same four soils. Molecular fingerprinting analyses were carried out at several time points in order to identify drivers and underlying processes of microbial community assemblage. We observed that the bacterial communities that developed in the inoculated sterilized soils differed from those in the original soils, displaying dynamic shifts over time. These shifts were illustrated by the appearance of numerous OTUs that had not been detected in the original soils. The community patterns observed in the inoculated treatments suggested that bacterial community assembly was determined by both niche-mediated and stochastic-neutral processes, whereby the relative impacts of these processes changed over the course of the vegetation season. Moreover, our experimental approach allowed us not only to evaluate the effects of soil nutrients on plant performance but also to recognize a negative effect of the microbial community present in the soil that had not been fertilized for more than 100 years on plant biomass. Our findings demonstrate that soil inoculation-based approaches are valid for investigating plant-soil-microbe interactions and for examining rules that shape soil microbial community assemblages under variable ecological conditions.
    Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
    Bowers, Robert M. ; Kyrpides, Nikos C. ; Stepanauskas, Ramunas ; Harmon-Smith, Miranda ; Doud, Devin ; Reddy, T.B.K. ; Schulz, Frederik ; Jarett, Jessica ; Rivers, Adam R. ; Eloe-Fadrosh, Emiley A. ; Tringe, Susannah G. ; Ivanova, Natalia N. ; Copeland, Alex ; Clum, Alicia ; Becraft, Eric D. ; Malmstrom, Rex R. ; Birren, Bruce ; Podar, Mircea ; Bork, Peer ; Weinstock, George M. ; Garrity, George M. ; Dodsworth, Jeremy A. ; Yooseph, Shibu ; Sutton, Granger ; Glöckner, Frank O. ; Gilbert, Jack A. ; Nelson, William C. ; Hallam, Steven J. ; Jungbluth, Sean P. ; Ettema, Thijs J.G. ; Tighe, Scott ; Konstantinidis, Konstantinos T. ; Liu, Wen Tso ; Baker, Brett J. ; Rattei, Thomas ; Eisen, Jonathan A. ; Hedlund, Brian ; McMahon, Katherine D. ; Fierer, Noah ; Knight, Rob ; Finn, Rob ; Cochrane, Guy ; Karsch-Mizrachi, Ilene ; Tyson, Gene W. ; Rinke, Christian ; Lapidus, Alla ; Meyer, Folker ; Yilmaz, Pelin ; Parks, Donovan H. ; Eren, A.M. - \ 2017
    Nature Biotechnology 35 (2017)8. - ISSN 1087-0156 - p. 725 - 731.

    We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity.

    Marine litter
    Fleet, D.M. ; Dau, K. ; Gutow, L. ; Schulz, M. ; Unger, Bianca ; Franeker, J.A. van - \ 2017
    Wilhelmshaven : Common Wadden Sea Secretariat (Wadden Sea Quality Status Report ) - 22 p.
    The results from the various investigations and monitoring programmes presented in this report demonstrate the continuous and widespread occurrence of litter in the Wadden Sea and adjacent offshore waters. Marine litter of different sizes and from diverse sources occurs on dunes and beaches, in and on inter- to subtidal sediments and in marine organisms, including protected seabirds and mammals. The OSPAR Beach Litter Monitoring and Monitoring on Litter in Fulmars’ Stomachs provide an evaluation of the temporal development of litter abundance in the southern North Sea. Both programmes clearly show that litter densities have not declined since the last Wadden Sea QSR in 2009, indicating that large amounts of litter are still entering the marine environment either directly within the Wadden Sea or from adjacent waters. The amount of litter entering the marine environment is continuously increasing
    (Jambeck et al., 2015). This increase is, however, not apparent in the results of the two monitoring programmes. Litter degrades in the marine environment and breaks down into ever smaller fragments. The fragmentation of plastic objects produces microplastics, which are not sufficiently assessed by current monitoring programmes. Densities of microplastics are expected to increase substantially in the future in all marine habitats. Accordingly, scientifically sound monitoring of these synthetic particles with standardized methods that allow for the comparison of results from different programmes will be indispensable.
    Marine litter is not restricted to specific habitats but occurs in all compartments of the marine environment with a constant exchange between them. Accordingly, monitoring litter densities in both coastal and offshore habitats is essential for a sound evaluation of litter pollution of the Wadden Sea. Many of the investigations presented in this report are on-off events, which do not provide information on temporal trends. However, they do demonstrate that the Wadden Sea is contaminated with marine litter and that litter densities in the Wadden Sea are not lower than in other coastal regions. The litter densities presented in this report provide a valuable baseline for future evaluations of temporal trends. The monitoring of litter in fulmars’ stomachs and the examinations of carcasses of harbour porpoise, harbour seals and eider ducks revealed that litter does not simply occur in the marine environment but actually interacts in a potentially harmful way with the marine biota. It is well established that the ingestion of litter can have deleterious and often lethal effects on marine organisms. It is yet unknown whether marine litter has demographically relevant implications for marine species. For evaluating this, the effects of marine litter must not be considered in isolation but always together with the effects of other environmental stressors such as ocean warming and acidification, eutrophication and the exploitation of natural stocks (see reports on climate change, geomorphology, eutrophication and fisheries). Several
    Wadden Sea Plan targets are compromised by the continuous pollution of the North Sea with marine litter. A proper management of the marine litter problem will require appropriate reduction measures and extended and optimized monitoring programmes in order to evaluate future developments.
    Modernizing Polish Agricultural economics teaching and research: An evaluation of academic cooperation
    Dalton, Graham ; Heijman, W.J.M. ; Majewski, Edward - \ 2017
    Acta Scientiarum Polonorum. Oeconomia 16 (2017)4. - ISSN 1644-0757 - p. 13 - 21.
    Tempus - MBA - Human Capital - AGRIMBA - Cost Benefits of Education
    Twenty-five years ago in response to the collapse of communism in Poland, an academic consortium was formed around two Polish Universities of Life Sciences (formerly Universities of Agriculture) for a Tempus project. The consortium has expanded from a project to revise curricula in agricultural economics within a market economy to much wider educational and research interests. The consortium’s main achievement has been in the organisation and accreditation of MBA programmes which has subsequently been augmented by a network for other educational and research programmes in a number of countries (AGRIMBA). This article explores the social net benefits of this example of investment in human capital relying on the concepts laid down by the Nobel Prize winners Theodore Schulz and Gary Becker.
    Innovative Participatory Research Methods in Earth System Governance
    Faling, M.F. ; Garard, Jennifer ; Schouten, Greetje ; Schulz, Karsten ; Veeger, Marieke ; Vervoort, J.M. ; Rutting, Lucas - \ 2017
    The Annual Review of Social Partnerships 12 (2017). - ISSN 2059-4291 - p. 76 - 80.
    Current environmental problems are often extremely complex, uncertain, and affecting multiple actors and institutions across sectors and scales. Earth System Governance (ESG) is a field of research that is highly relevant for understanding social interactions across scales and sectors and addressing complex problems. ESG refers to the broad collection of formal and informal rules, mechanisms, and networks ranging from the local to the global scale which deal with environmental changes1. ESG can be seen as both an empirical phenomenon and as a political project2. It refers to a social phenomenon observed in the interactions and activities of many international regimes, bureaucracies, local and transnational activists groups, and expert networks. At the same time, it is also a political effort to unite stakeholders, aiming to strengthen the institutions and networks addressing complex governance challenges associated with ESG. Participatory research is one very important way to appeal to ESG both as a social phenomenon - as a way to better understand the complex empirical dynamics associated with ESG – and as a political endeavour – by engaging different stakeholders in (academic) research and fostering processes of learning.
    The EFSA quantitative approach to pest risk assessment – methodological aspects and case studies
    Gilioli, G. ; Schrader, G. ; Grégoire, J.C. ; MacLeod, A. ; Mosbach-Schulz, O. ; Rafoss, T. ; Rossi, V. ; Urek, G. ; Werf, W. van der - \ 2017
    EPPO Bulletin 47 (2017)2. - ISSN 0250-8052 - p. 213 - 219.

    A new method for pest risk assessment and the identification and evaluation of risk-reducing options is currently under development by the European Food Safety Authority (EFSA) Plant Health Panel. The draft method has been tested on pests of concern to the European Union (EU). The method is adaptable and can focus either on all the steps and sub-steps of the assessment process or on specific parts if necessary. It is based on assessing changes in pest population abundance as the major driver of the impact on cultivated plants and on the environment. Like other pest risk assessment systems the method asks questions about the likelihood and magnitude of factors that contribute to risk. Responses can be based on data or expert judgment. Crucially, the approach is quantitative, and it captures uncertainty through the provision by risk assessors of quantile estimates of the probability distributions for the assessed variables and parameters. The assessment is based on comparisons between different scenarios, and the method integrates risk-reducing options where they apply to a scenario, for example current regulation against a scenario where risk-reducing options are not applied. A strategy has been developed to communicate the results of the risk assessment in a clear, comparable and transparent way, with the aim of providing the requestor of the risk assessment with a useful answer to the question(s) posed to the EFSA Plant Health Panel. The method has been applied to four case studies, two fungi, Ceratocystis platani and Cryphonectria parasitica, the nematode Ditylenchus destructor and the Grapevine flavescence dorée phytoplasma. Selected results from these case studies illustrate the types of output that the method can deliver.

    Genetic characterization of Western European noble crayfish populations (Astacus astacus) for advanced conservation management strategies
    Schrimpf, A. ; Piscione, M. ; Cammaerts, R. ; Collas, M. ; Herman, D. ; Jung, A. ; Ottburg, F. ; Roessink, I. ; Rollin, X. ; Schulz, R. ; Theissinger, K. - \ 2017
    Conservation Genetics 18 (2017)6. - ISSN 1566-0621 - p. 1299 - 1315.
    Artificial stocking - Management units - Microsatellite analysis - MtDNA sequences - Population genetic diversity - Species conservation

    One central goal of conservation biology is to conserve the genetic diversity of species in order to protect their adaptive potential. The main objective of this study was to identify management units (MUs) for the threatened noble crayfish (Astacus astacus) in Western Europe by utilizing sequence and microsatellite analysis to determine populations in need of focused conservation programs. With the analysis of noble crayfish from 31 sampling sites from Belgium, France, The Netherlands and Germany, and further comparison of this data with a European-wide dataset, we propose four distinct MUs: the French Meuse (MU 1), the French Rhine (MU 2), the Belgian Scheldt and Meuse (MU 3) as well as populations from the French Seine (MU 4). This knowledge enables advanced A. astacus conservation management practises in these catchments by distinguishing between outbreeding and inbreeding populations and by preserving the maximum genetic diversity. When required, a high genetic diversity can be conserved by strengthen existing populations via stocking with populations that either bear the most common haplotype or population-specific private haplotypes in order to maintain recent and regional adaptions. Above all, stocking with populations that exhibit haplotypes from outside Western Europe should be avoided in these catchments. This study supports the preservation of the genetic diversity of noble crayfish in Western Europe and provides thus a proposition for advanced conservation management.

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