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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Ems‐Dollard ecosystem model to study changing turbidity and higher trophic level response
Brinkman, A.G. ; Tamis, J.E. - \ 2018
Den Helder : Wageningen Marine Research (Wageningen Marine Research report C058/17) - 286
Plant responses to variable timing of aboveground clipping and belowground herbivory depend on plant age
Wang, Minggang ; Bezemer, T.M. ; Putten, Wim H. Van Der; Brinkman, E.P. ; Biere, Arjen - \ 2018
Journal of Plant Ecology 11 (2018)5. - ISSN 1752-9921 - p. 696 - 708.
Aims
Plants use different types of responses such as tolerance and
induced defense to mitigate the effects of herbivores. The direction
and magnitude of both these plant responses can vary with
plant age. However, most studies have focused on aboveground
herbivory, whereas important feeding occurs belowground. Here,
we tested the hypothesis that plant tolerance and defense following
shoot damage or root herbivory depends on plant age.
Methods
In order to test our hypothesis, we exposed the perennial grass species
Holcus lanatus to defoliation and root nematode inoculation at
three growth stages (young, intermediate and old plants), and examined
responses of plant traits related to tolerance (regrowth following
defoliation) and defense (leaf and root nitrogen and phenolics).
Important Findings
Defoliation overall reduced plant shoot and root biomass as well as
foliar concentrations of phenolics regardless of plant age at defoliation.
In contrast, defoliation increased foliar N concentrations, but
only when defoliation occurred at intermediate and old plant age.
Inoculation with root-feeding nematodes reduced root N concentrations
after a prolonged period of growth, but only when nematodes
had been inoculated when plants were young. The relative
shoot regrowth rate of plants increased immediately after defoliation
but this was independent of the plant age at which defoliation
occurred, i.e. was not stronger in plants that were defoliated at a
more advanced age, as hypothesized. Similarly, relative root growth
rates increased shortly after defoliation, but this was only observed
for plants defoliated when they were young. We conclude that plant
responses to aboveground and belowground herbivory in traits
related to both defense and tolerance are affected by plant age, but
do not generally change with plant age.
Changing soil legacies to direct restoration of plant communities
Brinkman, E.P. ; Raaijmakers, Ciska E. ; Boer, Wietse De; Putten, Wim H. Van Der - \ 2017
AoB Plants 9 (2017)5. - ISSN 2041-2851
It is increasingly acknowledged that soil biota may influence interactions among plant species; however, little is known about how to change historical influences of previous land management on soil biota, the so-called ‘biotic soil legacy effect’. We used a two-phase plant community-soil feedback approach to study how plant species typical to original (i.e. undisturbed) and degraded fen meadows may influence effects of the soil community on Carex species that are dominant in fen meadows. In phase 1, soil from original, degraded, successfully and unsuccessfully restored fen meadows was conditioned by growing plants typical to original or to degraded fen meadows. In phase 2, interactions between Carex and neighbouring plant species were studied to quantify plant community-soil feedback effects in different neighbour plant mixtures. Soil conditioning with plants typical to original fen meadows resulted in significantly more Carex biomass than with plants typical to degraded fen meadows. These effects were strongest when the soil originated from unsuccessfully restored fen meadows. However, biomass of plants typical of degraded fen meadows was also higher in soil conditioned by typical fen meadow plants. We conclude that soil legacy effects of plants from degraded fen meadows can be altered by growing typical fen meadow plant species in that soil, as this enhances priority effects that favour growth of other typical fen meadow plants. As also plant species from degraded fen meadows benefitted from soil conditioning, further studies are needed to reveal if plant species can be chosen that change negative soil legacy effects for rare and endangered fen meadow plant species, but not for plant species that are typical to degraded fen meadows.
Challenges in multicultural teamwork – students’ experiences and perceptions
Fortuin, K.P.J. ; Brinkman, B. ; Lie, R. ; Pap, Adri ; Popov, V. - \ 2017
Characterizing a thermostable Cas9 for bacterial genome editing and silencing
Mougiakos, Ioannis ; Mohanraju, Prarthana ; Bosma, Elleke F. ; Vrouwe, Valentijn ; Finger Bou, Max ; Naduthodi, Mihris I.S. ; Gussak, Alex ; Brinkman, Rudolf B.L. ; Kranenburg, Richard Van; Oost, John Van Der - \ 2017
Nature Communications 8 (2017)1. - ISSN 2041-1723
CRISPR-Cas9-based genome engineering tools have revolutionized fundamental research and biotechnological exploitation of both eukaryotes and prokaryotes. However, the mesophilic nature of the established Cas9 systems does not allow for applications that require enhanced stability, including engineering at elevated temperatures. Here we identify and characterize ThermoCas9 from the thermophilic bacterium Geobacillus thermodenitrificans T12. We show that in vitro ThermoCas9 is active between 20 and 70 °C, has stringent PAM-preference at lower temperatures, tolerates fewer spacer-protospacer mismatches than SpCas9 and its activity at elevated temperatures depends on the sgRNA-structure. We develop ThermoCas9-based engineering tools for gene deletion and transcriptional silencing at 55 °C in Bacillus smithii and for gene deletion at 37 °C in Pseudomonas putida. Altogether, our findings provide fundamental insights into a thermophilic CRISPR-Cas family member and establish a Cas9-based bacterial genome editing and silencing tool with a broad temperature range.
4. Ontwikkeling kwelder Ameland-Oost : Evaluatie bodemdalingsonderzoek 1986-2016
Elschot, Kelly ; Groot, Alma de; Dijkema, Kees ; Sonneveld, Cor ; Wal, Jan Tjalling van der; Vries, Pepijn de; Brinkman, A.G. ; Duin, Willem van; Molenaar, W. ; Krol, J. ; Kuiters, A.T. ; Vries, Daisy de; Wegman, R.M.A. ; Slim, P.A. ; Koppenaal, E.C. ; Vlas, J. de - \ 2017
In: Monitoring effecten van bodemdaling op Oost-Ameland / de Vlas, J., - p. 185 - 328.
Long-term trends in nutrient budgets of the western Dutch Wadden Sea (1976 - 2012)
Jung, A.S. ; Brinkman, A.G. ; Folmer, E.O. ; Herman, Peter M.J. ; Veer, Henk W. van der; Philippart, C.J.M. - \ 2017
coastal sea - Dutch Wadden Sea - nutrient budging
Long-term trends in nutrient budgets of the western Dutch Wadden Sea (1976–2012)
Jung, A.S. ; Brinkman, A.G. ; Folmer, E.O. ; Herman, Peter M.J. ; Veer, Henk W. van der; Philippart, C.J.M. - \ 2017
Journal of Sea Research 127 (2017). - ISSN 1385-1101 - p. 82 - 94.
Wadden Sea - Coastal North Sea - Nutrient exchange - Nitrogen - Phosphorus - Eutrophication - Nutrient budgets
Long-term field observations of nitrogen [N] and phosphorus [P] concentrations were used to construct nutriënt budgets for the western Dutch Wadden Sea between 1976 and 2012. Nutrients come into the western Dutch Wadden Sea via river runoff, through exchange with the coastal zone of the North Sea, neighbouring tidal basins and through atmospheric deposition (for N). The highest concentrations in phosphorus and nitrogen were observed
in themid-1980s. Improved phosphorus removal atwaste water treatment plants, management of fertilization in agriculture and removal of phosphates from detergents led to reduced riverine nutrient inputs and, consequently, reduced nutrient concentrations in theWadden Sea. The budgets suggest that the period of the initial net import of phosphorus and nitrogen switched to a net export in 1981 for nitrogen and in 1992 for phosphorus. Such different behaviour in nutrient budgets during the rise and fall of external nutriënt concentrations may be the result of different sediment-water exchange dynamics for P and N. It is hypothesized that during the period of increasing eutrophication (1976–1981) P, and to a lesser degree N, were stored in sediments as organic and inorganic nutrients. In the following period (1981–1992) external nutrient concentrations
(especially in the North Sea) decreased, but P concentrations in the Wadden Sea remained high due to prolonged sediment release, whilst denitrification removed substantial amounts of N. From1992 onwards, P andN budgetswere closed by net loss,most probably because P stores were then depleted and denitrification continued. Under the present conditions (lower rates of sediment import and depleted P stores), nutrient concentrations in this area are expected to be more strongly influenced by wind-driven exchange with the North Sea and precipitation-driven discharge from Lake IJssel. This implies that the consequences of climate change will be more important, than during the 1970s and 1980s.
Timing of simulated aboveground herbivory influences population dynamics of root-feeding nematodes
Wang, M. ; Biere, A. ; Putten, W.H. van der; Bezemer, T.M. ; Brinkman, E.P. - \ 2017
Plant and Soil 415 (2017)1-2. - ISSN 0032-079X - p. 215 - 228.
Plant damage inflicted by aboveground herbivores can occur at different stages of plant development and can induce plant responses that affect the growth of belowground herbivores. This study explores impacts of aboveground herbivory at different plant development stages on the population dynamics of root-feeding nematodes.
Becoming Globally Competent through Student Mobility
Popov, V. ; Brinkman, B. ; Oudenhoven, J.P. van - \ 2017
In: Competence-based Vocational and Professional Education / Mulder, Martin, Cham, Switzerland : Springer International Publishing (Technical and Vocational Education and Training: Issues, Concerns and Prospects ) - ISBN 9783319417110 - p. 1007 - 1028.
Flow through a filter plate backed by a packed bed of spheres
Sman, R.G.M. van der - \ 2017
Chemical Engineering Science 158 (2017). - ISSN 0009-2509 - p. 154 - 163.
Filtration - Fluid flow - Orifice - Simulation

In this paper we perform direct numerical simulation (DNS) on the problem of fluid flow through a filter plate backed by a packed bed of spheres, resembling a cake layer on top of a membrane. For both the complete problem, and its single components (the filter plate and a bed of spheres of finite height) we have observed three flow regimes, depending on the Reynolds number. In each regime the flow resistance is showing a different scaling with the Reynolds number. In the Stokes flow regime the total flow resistance can be decomposed in linear independent components. The interior flows inside the filter holes and inside the packed bed follow the same correlations as hold for the single component. However, at the transition zone between filter plate and packed bed, there is a diverging flow in the first row of the packed bed, whose contribution in the flow resistance scales with the fractional hole to the power −1.5. Similar scaling exponent has been found earlier for the viscous-inertial regime with Reynolds numbers larger than 10, which has been modelled using the porous medium approach. Our findings suggest that also in the Stokes flow and the weakly flow regime the problem can also be solved with the same porous medium approach using the Navier-Stokes equation having Darcy–Brinkman terms incorporated. This investigation provides a good basis for developing more accurate analytical models for the flow resistance of membrane filters with a cake layer on top.

Becoming globally competent through student mobility
Brinkman, B. ; Popov, V. - \ 2016
Development of intercultural competencies during international internships using a rubric
Gulikers, J.T.M. ; Runhaar, P.R. ; Brinkman, B. - \ 2016
Where, when and how plant–soil feedback matters in a changing world
Putten, Wim H. van der; Bradford, Mark A. ; Brinkman, E.P. ; Voorde, Tess F.J. van de; Veen, G.F. - \ 2016
Functional Ecology 30 (2016). - ISSN 0269-8463 - p. 1109 - 1121.
biodiversity loss - carbon and nutrient cycling - climate change - community composition - invasive plants - land use - plant–soil feedback triangle - range expansion

It is increasingly acknowledged that plant–soil feedbacks may play an important role in driving the composition of plant communities and functioning of terrestrial ecosystems. However, the mechanistic understanding of plant–soil feedbacks, as well as their roles in natural ecosystems in proportion to other possible drivers, is still in its infancy. Such knowledge will enhance our capacity to determine the contribution of plant–soil feedback to community and ecosystem responses under global environmental change. Here, we review how plant–soil feedbacks may develop under extreme drought and precipitation events, CO2 and nitrogen enrichment, temperature increase, land use change and plant species loss vs. gain. We present a framework for opening the ‘black box of soil’ considering the responses of the various biotic components (enemies, symbionts and decomposers) of plant–soil feedback to the global environmental changes, and we discuss how to integrate these components to understand and predict the net effects of plant–soil feedbacks under the various scenarios of change. To gain an understanding of how plant–soil feedback plays out in realistic settings, we also use the framework to discuss its interaction with other drivers of plant community composition, including competition, facilitation, herbivory, and soil physical and chemical properties. We conclude that understanding the role that plant–soil feedback plays in shaping the responses of plant community composition and ecosystem processes to global environmental changes requires unravelling the individual contributions of enemies, symbionts and decomposers. These biotic factors may show different response rates and strengths, thereby resulting in different net magnitudes and directions of plant–soil feedbacks under various scenarios of global change. We also need tests of plant–soil feedback under more realistic conditions to determine its contribution to changes in patterns and processes in the field, both at ecologically and evolutionary relevant time-scales.

Ecosysteemeffecten van lokaal veranderde slibgehaltes in de westelijke Waddenzee
Brinkman, A.G. - \ 2015
Den Helder : IMARES (Rapport / IMARES C157/15) - 121 p.
algen - schaaldieren - troebelheid - modellen - silt - aquatische ecosystemen - waddenzee - algae - shellfish - turbidity - models - aquatic ecosystems - wadden sea
Door middel van modelberekeningen is onderzocht hoe gevoelig primaire (algen) en secundaire (schelpdier‐)productie in de westelijke Waddenzee is voor een veranderde troebelheid. De studie is onderdeel van een gezamenlijke studie van Deltares‐IMARES naar antropogene invloeden op de primaire en secundaire productie. In de voorliggende studie worden ten behoeve van die analyse veel grotere troebelheidsveranderingen verondersteld dan welke in de praktijk kunnen voorkomen.
Blueprint for an Ems-Dollard ecoystem model study
Brinkman, A.G. - \ 2015
Den Helder : IMARES (Report / IMARES C158/15) - 39 p.
aquatic ecosystems - estuaries - aquatic ecology - models - eems-dollard - aquatische ecosystemen - estuaria - aquatische ecologie - modellen
Since in the ecological model study as performed in that research phytoplankton and phytobenthos were included, but no higher trophic levels, it was suggested to perform another ecosystem model study that does include higher trophic levels. In this report, such a model set‐up is presented. First, a short overview of existing (model‐)knowledge will be presented, including their strengths and shortcomings. Next, the present EcoWasp‐model is introduced, and possible improvements or needed extensions are mentioned. Also, the developed WasMo‐model (Gerla et al, 2014) will be mentioned.
Plant-feeding nematodes in coastal sand dunes: occurrence, host specificity and effects on plant growth
Brinkman, E.P. ; Duyts, H. ; Karssen, G. ; Stoel, C.D. ; Putten, W.H. van der - \ 2015
Plant and Soil 397 (2015)1. - ISSN 0032-079X - p. 17 - 30.
Ammophila arenaria - Ectoparasite - Endoparasite - Foredune - Generalist - Specialist
Aims Coastal sand dunes have a well-established abiotic gradient from beach to land and a corresponding spatial gradient of plant species representing succession in time. Here, we relate the distribution of plant-feeding nematodes with dominant plant species in the field to host specialization and impacts on plant species under controlled greenhouse conditions. Methods We assessed plant-feeding nematodes in soil and roots of six plant species that dominate the vegetation at successional positions along the gradient. In controlled conditions, we determined performance of all plant-feeding nematodes on each plant species and their effects on plant biomass. Results Specialist feeding type nematodes were confined to plant species in either foredunes or landward dunes. Generalist feeding type nematodes were found in highest numbers in the landward dunes. Most tested nematode species decreased root, but not shoot or rhizome biomass. Conclusions Host plant suitability determined occurrence of some plant-feeding nematodes in dunes, but abiotic and biotic soil conditions may play a role as well. Generalist feeding type nematodes were able to reproduce on all plant species. Feeding specialists, which are more protected by plant roots, might prefer host plants in the foredunes for the same reason as their host plants: to escape from natural enemies.
Voorstel draagkrachtmodel Zwarte Zee-eend in de Voordelta
Brinkman, A.G. - \ 2015
Den Burg : IMARES (Rapport / IMARES C053/15) - 57
Ems-Dollard primary production research Concise summary
Brinkman, A.G. ; Jacobs, P. ; Jak, R.G. ; Riegman, R. - \ 2015
IJmuiden : IMARES Wageningen UR (Report / IMARES Wageningen UR C163/14) - 78
kaderrichtlijn water - waterbeleid - waterkwaliteit - modder - troebelheid - ecologie - eems - eems-dollard - water framework directive - water policy - water quality - mud - turbidity - ecology - river ems
The Water Framework Directive (WFD) requires EU member states to achieve good ecological and chemical status of all designated water bodies (rivers, lakes, transitional and coastal waters) by 2015. Therefore Rijkswaterstaat Waterdienst has initiated the project ‘Research mud dynamics Ems Estuary’ . The aim of this project, carried out by Deltares and IMARES, is to (1) improve our knowledge on the mud dynamics in the Ems Estuary, (2) to identify the reasons for the increase in turbidity and (3) to quantify measures to improve the ecological status of the estuary.
Ems-Dollard primary production research: Full data report
Brinkman, A.G. ; Riegman, R. ; Jacobs, P. ; Kuhn, S. ; Meijboom, A. - \ 2015
IJmuiden : IMARES Wageningen UR (Report / IMARES Wageningen UR C160/14) - 297
kaderrichtlijn water - richtlijnen (directives) - waterbeleid - waterkwaliteit - modder - troebelheid - ecologie - eems - eems-dollard - water framework directive - directives - water policy - water quality - mud - turbidity - ecology - river ems
The Water Framework Directive (WFD) requires EU member states to achieve good ecological and chemical status of all designated water bodies (rivers, lakes, transitional and coastal waters) by 2015. Therefore Rijkswaterstaat Waterdienst has initiated the project ‘Research mud dynamics Ems Estuary’ . The aim of this project, carried out by Deltares and IMARES, is to (1) improve our knowledge on the mud dynamics in the Ems Estuary, (2) to identify the reasons for the increase in turbidity and (3) to quantify measures to improve the ecological status of the estuary.
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