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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Oesterdam sand nourishment : Ecological and morphological development of a local sand nourishment
Boersema, Matthijs P. ; Werf, Jebbe van der; Salvador de Paiva, João N. ; Brink, Anneke M. van den; Soissons, Laura ; Walles, Brenda ; Bouma, Tjeerd J. ; Vet, P.L.M. de; Ysebaert, Tom J.W. ; Paree, Edwin ; Bijleveld, Mariska ; Zanten, Eric van; Westenbrugge, Kees van; Stronkhorst, Joost ; Jong, Dick de - \ 2018
Vlissingen : Centre of Expertise Delta Technology - 78
Boer wil verduurzamen om uit de crisis te komen
Wiskerke, Han - \ 2018

De Staat van de Boer; de agrarische sector is dringend toe aan een andere koers. Wat blijkt: boeren willen best veranderen en vergroenen, als er tenminste duidelijkhedi komt in het beleid.

Het Boerenland smacht naar een visionair
Wiskerke, Han - \ 2018

Volgens De Wageningse hoogleraar Han Wiskerke de uitkomsten van 'De Staat van de Boer'vooral kansen voor een structurele hervorming van de agrarische sector. Maar dan moet er nu wel iemand met een heldere toekomstvisie opstaan.

Exploring contacts facilitating transmission of influenza A(H5N1) virus between poultry farms in West Java, Indonesia : A major role for backyard farms?
Wibawa, Hendra ; Karo-Karo, Desniwaty ; Pribadi, Eko Sugeng ; Bouma, Annemarie ; Bodewes, Rogier ; Vernooij, Hans ; Diyantoro, ; Sugama, Agus ; Muljono, David H. ; Koch, Guus ; Tjatur Rasa, Fadjar Sumping ; Stegeman, Arjan - \ 2018
Preventive Veterinary Medicine 156 (2018). - ISSN 0167-5877 - p. 8 - 15.
Avian influenza - Contact structure - H5N1 - Indonesia - Poultry - Transmission
Highly pathogenic avian influenza virus (HPAIV) H5N1 has been reported in Asia, including Indonesia since 2003. Although several risk factors related to the HPAIV outbreaks in poultry in Indonesia have been identified, little is known of the contact structure of farms of different poultry production types (backyard chickens, broilers, layers, and ducks). This study aims to quantify the contact rates associated with the movement of people, and movements of live birds and products and equipment that affect the risk of HPAIV H5N1 transmission between poultry farms in Indonesia. On 124 poultry farms in 6 districts in West Java, logbooks were distributed to record the movements of farmers/staff and visitors and their poultry contacts. Most movements in backyard chicken, commercial native chicken, broiler and duck farms were visits to and from other poultry farms, whilst in layer farms visits to and from poultry companies, visits to egg collection houses and visit from other poultry farms were most frequent. Over 75% of persons visiting backyard chicken and duck farms had previously visited other poultry farms on the same day. Visitors of backyard chicken farms had the highest average contact rate, either direct contact with poultry on other farms before the visits (1.35 contact/day) or contact during their visits in the farms (10.03 contact/day). These results suggest that backyard chicken farms are most at risk for transmission of HPAIV compared to farms of the other poultry production types. Since visits of farm-to-farm were high, backyard farms could also a potential source for HPAIV transmission to commercial poultry farms.
The combined influence of body size and density on cohesive sediment resuspension by bioturbators
Cozzoli, Francesco ; Bouma, Tjeerd J. ; Ottolander, Pauline ; Lluch, Maria Salvador ; Ysebaert, Tom ; Herman, Peter M.J. - \ 2018
Scientific Reports 8 (2018)1. - ISSN 2045-2322
We propose an empirical framework to scale the effects of bioturbation on sediment resuspension to population bioturbation activity, approximated as population metabolic rate. Individual metabolic rates have been estimated as functions of body size and extrapolated to population level. We used experimental flumes to test this approach across different types of marine, soft-sediment bioturbators. We observed that a large part of the variance in biota-mediated sediment resuspension can be explained by a positive relationship with population metabolic rate. Other mechanisms can strongly influence the outcome, such as bioturbation of deep sediment strata, biotic interactions with hydrodynamic stress and overlapping areas of influence must be further investigated. By relating the biota-mediated changes in resuspended sediment to metabolism, we can place our observations within the broader context of the metabolic theory of ecology and to formulate general expectations about changes in biota-mediated sediment resuspension in response to changes in population structure and climate change.
Exposure of coastal ecosystems to river plume spreading across a near-equatorial continental shelf
Tarya, A. ; Hoitink, A.J.F. ; Vegt, M. van der; Katwijk, M.M. van; Hoeksema, B.W. ; Bouma, T.J. ; Lamers, L.P.M. ; Christianen, M.J.A. - \ 2018
Continental Shelf Research 153 (2018). - ISSN 0278-4343 - p. 1 - 15.
Coral reef - Exposure risk - Hydrodynamic model - River plume - Seagrass
The Berau Continental Shelf (BCS) in East Kalimantan, Indonesia, harbours various tropical marine ecosystems, including mangroves, seagrass meadows and coral reefs. These ecosystem are located partly within reach of the Berau River plume, which may affect ecosystem health through exposure to land-derived sediments, nutrients and pollutants carried by the plume. This study aims (1) to assess the exposure risk of the BCS coastal ecosystems to river plume water, measured as exposure time to three different salinity levels, (2) to identify the relationships between these salinity levels and the abundance and diversity of coral and seagrass ecosystems, and (3) to determine a suitable indicator for the impacts of salinity on coral reef and seagrass health. We analysed hydrodynamic models, classified salinity levels, and quantified the correlations between the salinity model parameters and ecological metrics for the BCS systems. An Empirical Orthogonal Functions (EOF) analysis revealed three modes of river plume dispersal patterns, which strongly reflect monsoon seasonality. The first mode, explaining 39% of the variability, was associated with the southward movement of the plume due to northerly winds, while the second and third modes (explaining 29% and 26% of the variability, respectively) were associated with the northeastward migration of the plume related to southwesterly and southerly winds. Exposure to low salinity showed higher correlations with biological indicators than mean salinity, indicating that low salinity is a more suitable indicator for coastal ecosystem health. Significant correlations (R2) were found between exposure time to low salinity (days with salinity values below 25 PSU) with coral cover, coral species richness, seagrass cover, the number of seagrass species, seagrass leaf phosphorus, nitrogen, C:N ratio and iron content. By comparing the correlation coefficients and the slopes of the regression lines, our study suggests that coral reefs are more susceptible to low salinity levels exposure than seagrass meadows. Regarding the risk of corals being exposed to low salinity, nearshore and northern barrier reefs were classified as “high risk” the middle barrier reef as “medium to high risk” and southern barrier reefs as “medium risk”. Further offshore, the oceanic reefs were classified as “low risk”. Regarding the seagrass meadows, the nearshore region was categorized as “high risk” the barrier reef as “medium to low risk” and oceanic reefs as “low risk”. This study contributes to assessing the potential impacts of salinity on the BCS ecosystems, and further provides a knowledge base for marine conservation planning.
Comment on : B. Minasny & A.B. Mc Bratney. 2018. Limited effect of organic matter on soil available water capacity
Bouma, J. - \ 2018
European Journal of Soil Science 69 (2018)1. - ISSN 1351-0754 - p. 154 - 154.
Understanding the conditionality of ecosystem services : The effect of tidal flat morphology and oyster reef characteristics on sediment stabilization by oyster reefs
Salvador de Paiva, João N. ; Walles, Brenda ; Ysebaert, Tom ; Bouma, Tjeerd J. - \ 2018
Ecological Engineering 112 (2018). - ISSN 0925-8574 - p. 89 - 95.
Biogeomorphology - Coastal protection - Crassostrea gigas - Ecosystem engineering - Ecosystem-based management
Ecosystem-based coastal protection by means of conserving, restoring or creating intertidal ecosystems that attenuate waves and stabilize shorelines, offers a promising way to climate proof coastlines for the future. The Pacific oyster (Crassostrea gigas) is an ecosystem engineering species, which is known for its wave attenuating and sediment trapping ecosystem services, but it remains unknown to which extent this is conditional. We aim to test the hypothesis that the ecosystem engineering effect concerning sediment trapping and stability by oyster reefs is conditional, and can be predicted based on i) local physical forcing, ii) morphological characteristics of the tidal flat, and iii) biological characteristics of the oyster reef. Analyses of long-term sediment accretion patterns on natural intertidal oyster reefs at the Oosterschelde basin (The Netherlands) showed that this ecosystem engineering effect is strongest on tidal flats under erosional conditions, lower aspect ratio (i.e., relative long and narrow reefs), relatively closed reefs (i.e., few open patches) and higher coverage of oysters within reef patches. The ability of C. gigas to shape the environment thus depends both on biotic and abiotic conditions, meaning that oyster reefs only work under specific conditions for erosion control. Overall, our results provide baseline understanding for ecosystem management aimed at affecting sediment dynamics, thereby contributing to a better understanding for designing ecosystem-based solutions under different abiotic and biotic conditions. In addition, present study provides a clear example of how we need to gain a better understanding of the conditionality of ecosystem services in general, to be able to create and restore ecosystems for obtaining their services.
A new look at soil phenoforms – Definition, identification, mapping
Rossiter, David ; Bouma, J. - \ 2018
Geoderma 314 (2018). - ISSN 0016-7061 - p. 113 - 121.
The soil genoform vs. soil phenoform distinction was suggested twenty years ago by Droogers and Bouma to recognize management-induced differences among pedons with the same long-term pedogenesis and included in the same soil map unit, these changes being sufficient to cause important and persistent differences in soil functions. To support the recent increased interest in soil change and soil health, we propose conceptual and operational definitions of soil genoforms and soil phenoforms, and suggest techniques to identify and map them. We define soil genoforms as soil classes as identified by the soil classification system used as the basis for detailed soil mapping in a given area. This avoids the difficulty of defining when human intervention has been sufficient to create new genoforms – by definition this is when new lowest-level classes are recognized in the classification system, based on diagnostic horizons and properties. We then define soil phenoforms as persistent variants of a genoform with sufficient physical or chemical differences to substantially affect soil functions. Soil phenoforms must be persistent enough that substantial management interventions are necessary to change them, thus seasonal and rotational variants are excluded from the concept. Soil phenoforms can be identified by measurements of indicator soil properties at locations within a soil genoform with different management and investigating if these are different enough to affect soil functions, notably soil hydrology and crop yield. Digital mapping of soil phenoforms will likely use maps of current and historical management as predictors. In areas with intensive or changed management, mapping should be repeated every few years to identify areas of changed soil phenoforms and new genoforms.
Supporting local institutions for inclusive green growth : Developing an Evidence Gap Map
Berkhout, Ezra ; Bouma, Jetske ; Terzidis, Nikolaos ; Voors, Maarten - \ 2018
NJAS Wageningen Journal of Life Sciences 84 (2018). - ISSN 1573-5214 - p. 51 - 71.
Evidence Gap Map - Evidence-based policy-making - Inclusive green growth - Local institutions - Rigorous evaluations - Structured literature search

We conduct a structured search of the academic literature that assesses the impact of development interventions that aim to build and strengthen local-level institutions to facilitate Inclusive Green Growth. Inclusive Green Growth extends the standard growth perspective to include welfare enhancements both the poor ('inclusive') and for future ('green') generations. We restrict our search to studies in the domain of agriculture and poverty alleviation in the developing world. We access ten online databases and various working paper series and focus on summarising evidence from quantitative studies that use rigorous evaluation methods. Together, this yields 158 studies. We then retain 66 studies that contain a credible counterfactual. We visualize the interventions and outcomes in an Evidence Gap Map, highlighting both the available evidence and remaining knowledge gaps. Most studies suggest that strengthening local institutions can improve the delivery and targeting of public services and overall satisfaction with local governance. There are however, clear limitations and knowledge gaps highlighting priorities for future work. Few studies assess impacts on final outcomes such as household income or agricultural productivity and no studies assess inclusive and green outcomes jointly. We discuss the key benefits of a structured literature search and Evidence Gap Map for policy-makers and development practitioners and illustrate how it serves as a knowledge repository and identifies where evidence is lacking, thus setting the agenda for future work.

Pedotransfer Functions in Earth System Science : Challenges and Perspectives
Looy, Kris Van; Bouma, Johan ; Herbst, Michael ; Koestel, John ; Minasny, Budiman ; Mishra, Umakant ; Montzka, Carsten ; Nemes, Attila ; Pachepsky, Yakov A. ; Padarian, José ; Schaap, Marcel G. ; Tóth, Brigitta ; Verhoef, Anne ; Vanderborght, Jan ; Ploeg, Martine J. van der; Weihermüller, Lutz ; Zacharias, Steffen ; Zhang, Yonggen ; Vereecken, Harry - \ 2017
Reviews of Geophysics 55 (2017)4. - ISSN 8755-1209 - p. 1199 - 1256.
Biogeochemical processes - Extrapolation - Heat flow - Hydraulic properties - Land surface model - Soil properties
Soil, through its various functions, plays a vital role in the Earth's ecosystems and provides multiple ecosystem services to humanity. Pedotransfer functions (PTFs) are simple to complex knowledge rules that relate available soil information to soil properties and variables that are needed to parameterize soil processes. In this paper, we review the existing PTFs and document the new generation of PTFs developed in the different disciplines of Earth system science. To meet the methodological challenges for a successful application in Earth system modeling, we emphasize that PTF development has to go hand in hand with suitable extrapolation and upscaling techniques such that the PTFs correctly represent the spatial heterogeneity of soils. PTFs should encompass the variability of the estimated soil property or process, in such a way that the estimation of parameters allows for validation and can also confidently provide for extrapolation and upscaling purposes capturing the spatial variation in soils. Most actively pursued recent developments are related to parameterizations of solute transport, heat exchange, soil respiration, and organic carbon content, root density, and vegetation water uptake. Further challenges are to be addressed in parameterization of soil erosivity and land use change impacts at multiple scales. We argue that a comprehensive set of PTFs can be applied throughout a wide range of disciplines of Earth system science, with emphasis on land surface models. Novel sensing techniques provide a true breakthrough for this, yet further improvements are necessary for methods to deal with uncertainty and to validate applications at global scale.
’s Nachts spuiten kan potentiële schade aan gewas reduceren : Schade door gewasbescherming niet zeldzaam
Bouma, E. ; Kierkels, T. ; Heuvelink, E. - \ 2017
Onder Glas 14 (2017)1. - p. 26 - 27.
Telers merken regelmatig dat het gewas een terugslag krijgt bij bespuitingen met gewasbeschermingsmiddelen. Komt dat door de werkzame stof, door de hulpstoffen of door iets anders? Niet alle vragen zijn te beantwoorden, maar er is wel een algemene werkwijze die potentiële schade kan reduceren: ’s nachts spuiten.
Windparken moeten beter over de EU verspreid worden
Kalverla, Peter - \ 2017
Different cross protection scopes of two avian influenza H5N1 vaccines against infection of layer chickens with a heterologous highly pathogenic virus
Poetri, Okti Nadia ; Boven, Michiel van; Koch, Guus ; Stegeman, Arjan ; Claassen, Ivo ; Wisaksana, I.W. ; Bouma, Annemarie - \ 2017
Research in Veterinary Science 114 (2017). - ISSN 0034-5288 - p. 143 - 152.
Archetti-Horsfall ratio - Avian influenza - Cross protection - H5N1

Avian influenza (AI) virus strains vary in antigenicity, and antigenic differences between circulating field virus and vaccine virus will affect the effectiveness of vaccination of poultry. Antigenic relatedness can be assessed by measuring serological cross-reactivity using haemagglutination inhibition (HI) tests. Our study aims to determine the relation between antigenic relatedness expressed by the Archetti-Horsfall ratio, and reduction of virus transmission of highly pathogenic H5N1 AI strains among vaccinated layers. Two vaccines were examined, derived from H5N1 AI virus strains A/Ck/WJava/Sukabumi/006/2008 and A/Ck/CJava/Karanganyar/051/2009. Transmission experiments were carried out in four vaccine and two control groups, with six sets of 16 specified pathogen free (SPF) layer chickens. Birds were vaccinated at 4 weeks of age with one strain and challenge-infected with the homologous or heterologous strain at 8 weeks of age. No transmission or virus shedding occurred in groups challenged with the homologous strain. In the group vaccinated with the Karanganyar strain, high cross-HI responses were observed, and no transmission of the Sukabumi strain occurred. However, in the group vaccinated with the Sukabumi strain, cross-HI titres were low, virus shedding was not reduced, and multiple transmissions to contact birds were observed. This study showed large differences in cross-protection of two vaccines based on two different highly pathogenic H5N1 virus strains. This implies that extrapolation of in vitro data to clinical protection and reduction of virus transmission might not be straightforward.

Top-down vs. bottom-up control on vegetation composition in a tidal marsh depends on scale
Elschot, Kelly ; Vermeulen, Anke ; Vandenbruwaene, Wouter ; Bakker, Jan P. ; Bouma, Tjeerd J. ; Stahl, Julia ; Castelijns, Henk ; Temmerman, Stijn - \ 2017
PLoS One 12 (2017)2. - ISSN 1932-6203

The relative impact of top-down control by herbivores and bottom-up control by environmental conditions on vegetation is a subject of debate in ecology. In this study, we hypothesize that top-down control by goose foraging and bottom-up control by sediment accretion on vegetation composition within an ecosystem can co-occur but operate at different spatial and temporal scales. We used a highly dynamic marsh system with a large population of the Greylag goose (Anser anser) to investigate the potential importance of spatial and temporal scales on these processes. At the local scale, Greylag geese grub for below-ground storage organs of the vegetation, thereby creating bare patches of a few square metres within the marsh vegetation. In our study, such activities by Greylag geese allowed them to exert topdown control by setting back vegetation succession. However, we found that the patches reverted back to the initial vegetation type within 12 years. At large spatial (i.e. several square kilometres) and temporal scales (i.e. decades), high rates of sediment accretion surpassing the rate of local sea-level rise were found to drive long-term vegetation succession and increased cover of several climax vegetation types. In summary, we conclude that the vegetation composition within this tidal marsh was primarily controlled by the bottom-up factor of sediment accretion, which operates at large spatial as well as temporal scales. Topdown control exerted by herbivores was found to be a secondary process and operated at much smaller spatial and temporal scales.

A modeling approach to assess coastal management effects on benthic habitat quality : A case study on coastal defense and navigability
Cozzoli, Francesco ; Smolders, Sven ; Eelkema, Menno ; Ysebaert, Tom ; Escaravage, Vincent ; Temmerman, Stijn ; Meire, Patrick ; Herman, Peter M.J. ; Bouma, Tjeerd J. - \ 2017
Estuarine Coastal and Shelf Science 184 (2017). - ISSN 0272-7714 - p. 67 - 82.
Coastal management - Estuary - Hydrodynamic modeling - Macrozoobenthos - Species distribution modeling

The natural coastal hydrodynamics and morphology worldwide is altered by human interventions such as embankments, shipping and dredging, which may have consequences for ecosystem functionality. To ensure long-term ecological sustainability, requires capability to predict long-term large-scale ecological effects of altered hydromorphology. As empirical data sets at relevant scales are missing, there is need for integrating ecological modeling with physical modeling. This paper presents a case study showing the long-term, large-scale macrozoobenthic community response to two contrasting human alterations of the hydromorphological habitat: deepening of estuarine channels to enhance navigability (Westerschelde) vs. realization of a storm surge barrier to enhance coastal safety (Oosterschelde). A multidisciplinary integration of empirical data and modeling of estuarine morphology, hydrodynamics and benthic ecology was used to reconstruct the hydrological evolution and resulting long-term (50 years) large-scale ecological trends for both estuaries over the last. Our model indicated that hydrodynamic alterations following the deepening of the Westerschelde had negative implications for benthic life, while the realization of the Oosterschelde storm surge barriers had mixed and habitat-dependent responses, that also include unexpected improvement of environmental quality. Our analysis illustrates long-term trends in the natural community caused by opposing management strategies. The divergent human pressures on the Oosterschelde and Westerschelde are examples of what could happen in a near future for many global coastal ecosystems. The comparative analysis of the two basins is a valuable source of information to understand (and communicate) the future ecological consequences of human coastal development.

Soil Capability: Exploring the Functional Potentials of Soils
Bouma, J. ; Ittersum, M.K. van; Stoorvogel, J.J. ; Batjes, N.H. ; Droogers, P. ; Pulleman, M.M. - \ 2017
In: Global Soil Security / Field, Damien J., Morgan, Christine L.S., McBratney, Alex B., Springer International Publishing (Progress in Soil Science ) - ISBN 9783319433936 - p. 27 - 44.
Soil capability index (CPI) - Land evaluation - Soil functions - Potential yield - Water-limited yield
Capability, a term that has been well defined in welfare economics, can be applied to soil by defining the intrinsic capacity of a soil to contribute to ecosystem services, including biomass production. Seven soil functions are used to define capabilities, and combining different functions in storylines provides integrated expressions for capability considering the different functions. Applied to biomass production in a sustainable production system, potential production (Yp) is defined as a function of radiation, temperature, CO2 and plant physiology. Yp is independent of soil and provides an absolute point of reference. Yw represents water-limited yield, reflecting actual water regimes and assuming that soil fertility is adequate and pests and diseases don’t occur. Ya represents actual yield. A soil capability index (SCI) is defined as SCI = (Ya/Yw) × 100 for a biomass production storyline for rainfed production systems. Some examples are presented. Using simulation modelling, Yp can be simulated for a given climate and Yw can be simulated for a given soil in a probabilistic manner using weather data for 30 years as a form of quantitative land evaluation. Ya can be measured. Not only capability, as such, is important, however, but also the way in which capability can be realized under practical conditions. Then, a management support system is needed to guide a farmer real time through the growing season, also taking into account long-term effects. Capability is defined for a given type of soil (the genoform), but sometimes management has had significant effects on soil properties, requiring a phenoform approach, as is illustrated.
How to characterize 'good' and 'greening' in the EU Common Agricultural Policy (CAP) : The case of clay soils in the Netherlands
Bouma, J. ; Wosten, Henk - \ 2016
Soil Use and Management 32 (2016)4. - ISSN 0266-0032 - p. 546 - 552.
Bypass flow - Internal catchment - Macropores - Modelling - Tile drainage - Trafficability

The change in the Common Agricultural Policy (CAP) of the European Union from product to producer support, including requirements for 'good agricultural and environmental conditions' and 'greening', is excellent. However, these requirements are now defined in rather general terms. Questions can be raised about suitable indicators, and there is a recognized need for effective management recommendations to support farmers in achieving the required 'good' conditions. These recommendations are bound to be quite different for different soils in different countries. A study of Dutch clay soils was based on a storyline describing current problems and management options for improvement, which were quantified using a soil-water-crop simulation model. Indicators were defined for agricultural conditions and suggestions made for the use of the model in a predictive mode to help farmers improve their soil management. Environmental conditions were judged by current environmental guidelines for water and air. When modelling, implicit assumptions that soils are homogeneous were shown to be unrealistic for these clay soils, requiring development of innovative methods and procedures, presenting a challenge for soil research.

Hoogleraren: visverbod op grote delen Noordzee
Lindeboom, Han - \ 2016
Ruimte voor de natuur in zee
Lindeboom, Han - \ 2016
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