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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    How the COVID-19 pandemic highlights the necessity of animal research
    Genzel, Lisa ; Adan, Roger ; Berns, Anton ; Beucken, Jeroen van den; Blokland, Arjan ; Boddeke, Erik H.W.G.M. ; Bogers, Willy M. ; Bontrop, Ronald ; Bulthuis, R. ; Bousema, Teun ; Clevers, Hans ; Coenen, Tineke C.J.J. ; Dam, Anne Marie van; Deen, Peter M.T. ; Dijk, K.W. van; Eggen, Bart J.L. ; Elgersma, Ype ; Erdogan, Izel ; Englitz, Bernard ; Fentener van Vlissingen, J.M. ; Fleur, Susanne la; Fouchier, Ron ; Fitzsimons, Carlos P. ; Frieling, Wilbert ; Haagmans, Bart ; Heesters, Balthasar A. ; Henckens, Marloes ; Herfst, Sander ; Hol, Elly ; Hove, Daniel van den; Jonge, Marien I. de; Jonkers, Jos ; Joosten, Leo A.B. ; Kalsbeek, Andries ; Kamermans, Maarten ; Kampinga, Harm H. ; Kas, Martien J. ; Keijer, J. ; Kersten, Sander ; Kiliaan, Amanda J. ; Kooij, Taco W.A. ; Kooijman, Sander ; Koopman, Werner J.H. ; Korosi, Aniko ; Krugers, Harm J. ; Kuiken, Thijs ; Kushner, Steven A. ; Langermans, Jan A.M. ; Lesscher, Heidi ; Lucassen, Paul J. ; Lutgens, Esther ; Netea, Mihai G. ; Noldus, Lucas P.J.J. ; Meer, Jos W.M. van der; Meye, Frank J. ; Mul, Joram D. ; Oers, Kees van; Olivier, Jocelien D.A. ; Pasterkamp, R.J. ; Philippens, Ingrid H.C.H.M. ; Prickaerts, Jos ; Pullox, Bart J.A. ; Rensen, Patrick C.N. ; Rheenen, Jacco van; Rij, Ronald P. van; Ritsma, Laila ; Rockx, Barry H.G. ; Roozendaal, Benno ; Schothorst, Evert M. van; Stittelaar, K. ; Stockhofe, Norbert ; Swaab, Dick F. ; Swart, Rik L. de; Vanderschuren, Louk J.M.J. ; Vries, Taco de; Vrij, Femke de; Wezel, Richard van; Wierenga, Corette J. ; Wiesmann, Maximilian ; Willuhn, Ingo ; Zeeuw, Chris I. de; Homberg, Judith R. - \ 2020
    Current Biology 30 (2020)18. - ISSN 0960-9822 - p. R1014 - R1018.
    Recently, a petition was offered to the European Commission calling for an immediate ban on animal testing. Although a Europe-wide moratorium on the use of animals in science is not yet possible, there has been a push by the non-scientific community and politicians for a rapid transition to animal-free innovations. Although there are benefits for both animal welfare and researchers, advances on alternative methods have not progressed enough to be able to replace animal research in the foreseeable future. This trend has led first and foremost to a substantial increase in the administrative burden and hurdles required to make timely advances in research and treatments for human and animal diseases. The current COVID-19 pandemic clearly highlights how much we actually rely on animal research. COVID-19 affects several organs and systems, and the various animal-free alternatives currently available do not come close to this complexity. In this Essay, we therefore argue that the use of animals is essential for the advancement of human and veterinary health. In this Essay, Genzel et al. make the case for animal research in light of the COVID-19 pandemic.
    Ammonia emission of the MeadowFloor CL for dairy barns : A case-control study in the Environmental Research Barn of Dairy Campus
    Winkel, A. ; Bokma, S. ; Hol, J.M.G. ; Blanken, K. - \ 2020
    Wageningen : Wageningen Livestock Research (Report / Wageningen Livestock Research 1275) - 25
    In this study, measurements of ammonia emission have been carried out in a cubicle room of the environmental research barn of Dairy Campus equipped with the MeadowFloor CL of the company Proflex and a slurry scraper of the company JOZ. An identical room, equipped with a conventional concrete slatted floor, served as control. This study shows that the MeadowFloor CL yields a 35% reduction of ammonia emission.---In deze studie zijn emissiemetingen van ammoniak uitgevoerd aan een ligboxenafdeling in de Milieustal van Dairy Campus uitgerust met de MeadowFloor CL van de firma Proflex en een mestschuif van de firma JOZ. Een identieke afdeling uitgerust met een conventionele betonroostervloer zonder schuif diende als referentie. Uit deze studie blijkt dat de MeadowFloor CL een 35% reductie van de emissie van ammoniak bewerkstelligt.
    Ontwerp Boerderij van de Toekomst
    Visser, Chris de; Sukkel, Wijnand ; Kempenaar, Corné ; Wal, Tamme van der; Wolf, Pieter de; Visser, Andries ; Smit, Bert ; Schoorlemmer, Herman ; Schoutsen, Maureen ; Klompe, Koen ; Veldhuisen, Bram ; Selin-Noren, Isabella ; Dijk, Chris van; Hol, Stefan ; Voort, Marcel van der; Janssens, Bas - \ 2020
    Wageningen : Stichting Wageningen Research, Wageningen Plant Research, Business unit Open Teelten (Rapport / Stichting Wageningen Research, Wageningen Plant Research, Business unit Open Teelten WPR-823) - 45
    Methane production from insect, worm and mushroom waste streams and combinations
    Elissen, Hellen ; Hol, Stefan ; Weide, Rommie van der - \ 2019
    Wageningen : Stichting Wageningen Research, Wageningen Plant Research, Business Unit Field Crops (Report WPR 817) - 25
    In literature, the synergistic effect of several substrates on feedstocks for anaerobic digestion/methane production is described for several substrates. Champost from mushroom production, vermicompost from worm composting/vermiculture and BSF (black soldier fly) larvae frass from insect production were therefore tested for this report for their synergistic effect. It was found that insect frass had a very high biogas/methane production as a single substrate. Addition of the frass led to a concentration dependent biogas production in mixtures with ‘old’ digestate higher than was expected based on the results of the single substrates. Champost resulted in some biogas production but from vermicompost hardly any biogas could be produced. Also, no synergistic or concentration effects could be noted from the latter two.
    A low proportion of rare bacterial taxa responds to abiotic changes compared with dominant taxa
    Kurm, Viola ; Geisen, Stefan ; Gera Hol, Wilhelmina H. - \ 2019
    Environmental Microbiology 21 (2019)2. - ISSN 1462-2912 - p. 750 - 758.

    In many studies, rare bacterial taxa have been found to increase in response to environmental changes. These changes have been proposed to contribute to the insurance of ecosystem functions. However, it has not been systematically tested if rare taxa are more likely to increase in abundance than dominant taxa. Here, we study whether rare soil bacterial taxa are more likely to respond to environmental disturbances and if rare taxa are more opportunistic than dominant taxa. To test this, we applied nine different disturbance treatments to a grassland soil and observed changes in bacterial community composition over 7 days. While 12% of the dominant taxa changed in abundance, only 1% of the rare taxa showed any effect. Rare taxa increased in response to a single disturbance treatment only, while dominant taxa responded to up to five treatments. We conclude that rare taxa are not more likely to contribute to community dynamics after disturbances than dominant taxa. Nevertheless, as rare taxa outnumber abundant taxa with here 230 taxa that changed significantly, the chance is high that some of these rare taxa might act as ecologically important keystone taxa. Therefore, rare and abundant taxa might both contribute to ecosystem insurance.

    'Proefbedrijf Lelystad heeft expertise kringlooplandbouw'
    Visser, Chris de; Wolf, Pieter de; Hol, Stefan - \ 2019
    Wilde zwijnen op hol
    Jansman, Hugh - \ 2019
    Ammonia and odour emission from a veal calves housing system with V-shaped manure belt and ‘Groene Vlag’ slatted floor
    Mosquera, J. ; Hattum, T. van; Nijeboer, G.M. ; Hol, J.M.G. ; Dooren, H.J.C. van; Bokma, S. - \ 2019
    Wageningen : Wageningen Livestock Research (Wageningen Livestock Research report 1171) - 30
    This report presents the results of measurements performed at one animal facility for veal calves using the control-case approach, to estimate the ammonia and odour emission reduction of a floor (Groene Vlag) combined with a V-shaped manure belt under the floor compared to the traditional wooden slatted floor. These measurements were commissioned by Bettink Service Team and by Beerepoot Stalinrichtingen BV. Ammonia emissions were significantly lower (53%) than the emission from the traditional floor measured simultaneously within the same farm (case-control approach). Odour emissions were significantly lower (47%) than the emission from the traditional floor measured simultaneously within the same farm (case-control approach).
    Gasvormige emissies uit vrijloopstallen met houtsnipperbodems : ammoniak-, lachgas- en methaanemissie op stalniveau
    Dooren, H.J.C. van; Hol, J.M.G. ; Blanken, K. ; Galama, P.J. - \ 2019
    Wageningen : Wageningen Livestock Research (Wageningen Livestock Research rapport 1163) - 46
    Measurements of emission of ammonia, methane and laughing gas from compost bedded pack barnsfor dairy cows are presented. Ammonia emission was reduced by 31% but methane emissionincreased by 34% and emission of laughing gas were 14 times higher than a references slurry based housing system.
    Competition and predation as possible causes of bacterial rarity
    Kurm, Viola ; Putten, Wim H. van der; Weidner, Simone ; Geisen, Stefan ; Snoek, Basten L. ; Bakx, Tanja ; Gera Hol, Wilhelmina H. - \ 2019
    Environmental Microbiology 21 (2019)4. - ISSN 1462-2912 - p. 1356 - 1368.

    We assembled communities of bacteria and exposed them to different nutrient concentrations with or without predation by protists. Taxa that were rare in the field were less abundant at low nutrient concentrations than common taxa, independent of predation. However, some taxa that were rare in the field became highly abundant in the assembled communities, especially under ample nutrient availability. This high abundance points at a possible competitive advantage of some rare bacterial taxa under nutrient-rich conditions. In contrast, the abundance of most rare bacterial taxa decreased at low resource availability. Since low resource availability will be the prevailing situation in most soils, our data suggests that under those conditions poor competitiveness for limiting resources may contribute to bacterial rarity. Interestingly, taxa that were rare in the field and most successful under predator-free conditions in the lab also tended to be more reduced by predation than common taxa. This suggests that predation contributes to rarity of bacterial taxa in the field. We further discuss whether there may be a trade-off between competitiveness and predation resistance. The substantial variability among taxa in their responses to competition and predation suggests that other factors, for example abiotic conditions and dispersal ability, also influence the local abundance of soil bacteria.

    Cultivation-success of rare soil bacteria is not influenced by incubation time and growth medium
    Kurm, Viola ; Putten, Wim H. Van Der; Hol, W.H.G. - \ 2019
    PLoS ONE 14 (2019)1. - ISSN 1932-6203

    Rare bacterial species have recently attracted interest due to their many potential beneficial functions. However, only little is known about their cultivability. In this study we test the hypotheses that the use of flow cell-sorting for cultivation results in a high proportion of rare soil bacterial isolates relative to bacterial taxa that are abundant in soil. Moreover, we investigate whether different oligotrophic cultivation media and a prolonged incubation time increase the number of cultivated rare species. In a cultivation study we used flow cell sorting to select for small cells and to separate single cells, and grew bacteria on different oligotrophic media with prolonged incubation times. The abundance of the isolates in the field was assessed by comparing them to a 454-sequencing dataset from the same soil. Consequentially, all bacterial isolates were classified as either rare (<0.01% relative abundance) or abundant (>0.01% relative abundance) in the field soil. We found more bacterial taxa among the isolates that were abundant in soil than would be expected by the proportion of abundant species in the field. Neither incubation time nor growth medium had an influence on the recovery of rare species. However, we did find differences in time until visible growth on the plate between different phylogenetic classes of the isolates. These results indicate that rare cultivable species are active and not more likely to be dormant than abundant species, as has been suggested as a reason for their rarity. Moreover, future studies should be aware of the influence incubation time might have on the phylogenetic composition of the isolate collection.

    Rekentool voor het bepalen van de effecten van voer- en management-maatregelen op de ammoniakemissie bij varkens: ontwikkeling en validatie
    Aarnink, Andre ; Pas, Loes van de; Peet-Schwering, Carola van der; Hol, Annemieke ; Binnendijk, Gisabeth ; Dinh, Phung Le; Hafner, Sasha ; Ogink, Nico - \ 2018
    Wageningen : Wageningen Livestock Research (Wageningen Livestock Research rapport 1086) - 118
    A calculation model was developed to determine the effect of housing, dietary and management measures on the ammonia emission from houses for growing-finishing pigs, weaned piglets and pregnant sows. On Pig Innovation Centre Sterksel measurements were done for further development and validation of the model.
    Data from: Soil microbial species loss affects plant biomass and survival of an introduced bacterial strain, but not inducible plant defences
    Kurm, V. ; Putten, W.H. van der; Pineda, Ana ; Hol, G.W.H. - \ 2018
    Wageningen University & Research
    induced systemic resistence - low abundant soil microbes - PGPR - Arabidopsis thaliana - Myzus persicae - Pseudomonas fluorescens
    Background and Aims: Plant growth-promoting rhizobacteria (PGPR) strains can influence plant-insect interactions. However, little is known about the effect of changes in the soil bacterial community in general and especially the loss of rare soil microbes on these interactions. Here, the influence of rare soil microbe-reduction on induced systemic resistance (ISR) in a wild ecotype of Arabidopsis thaliana against the aphid Myzus persicae was investigated. - Methods: To create a gradient of microbial abundances, soil was inoculated with a serial dilution of a microbial community and responses of Arabidopsis plants that originated from the same site as the soil microbes were tested. Plant biomass, transcription of genes involved in plant defences, and insect performance were measured. In addition, the effects of the PGPR strain Pseudomonas fluorescens SS101 on plant and insect performance were tested under influence of the various soil dilution treatments. - Key Results: Plant biomass showed a hump-shaped relationship with soil microbial community dilution, independent of aphid or Pseudomonas treatments. Both aphid infestation and inoculation with Pseudomonas reduced plant biomass, and led to downregulation of PR1 (salicylic acid-responsive gene) and CYP79B3 (involved in synthesis of glucosinolates). Aphid performance and gene transcription were unaffected by soil dilution. - Conclusions: Neither the loss of rare microbial species, as caused by soil dilution, nor Pseudomonas, affect the resistance of A. thaliana against M. persicae. However, both Pseudomonas survival and plant biomass respond to rare species loss. Thus, loss of rare soil microbial species can have a significant impact on both above- and belowground organisms.
    Causes and consequences of soil bacterial rarity
    Kurm, Viola - \ 2018
    Wageningen University. Promotor(en): W.H. van der Putten, co-promotor(en): W.H.G. Hol. - Wageningen : Wageningen University - ISBN 9789463432498 - 206

    In the highly diverse community of soil bacteria most species occur at extremely low numbers and are consequently called the “rare biosphere”. In this thesis I studied why these species are rare whereas others are common. I found that many rare bacterial species can grow rapidly and are doing well in competition, but that rare species could be more vulnerable to predation. This might account for their rarity in soil. Still growth, competitiveness and predation resistance differed greatly between rare species. In addition, I tested if rare soil bacterial species can protect plants from insect attack by stimulating resistance mechanisms in the plant. However, there was no effect of rare bacteria on plant resistance. Rather plant response varied with different bacterial communities regardless of whether rare species were present or not. Overall, my thesis demonstrates that there are likely no general causes of bacterial rarity or general consequences for plant health.

    Soil microbial species loss affects plant biomass and survival of an introduced bacterial strain, but not inducible plant defences
    Kurm, Viola ; Putten, Wim H. van der; Pineda, Ana ; Hol, G.W.H. - \ 2018
    Annals of Botany 121 (2018)2. - ISSN 0305-7364 - p. 311 - 319.
    Arabidopsis thaliana - induced systemic resistance - low-abundance soil microbes - Myzus persicae - PGPR
    Background and Aims: Plant growth-promoting rhizobacteria (PGPR) strains can influence plant-insect interactions. However, little is known about the effect of changes in the soil bacterial community in general and especially the loss of rare soil microbes on these interactions. Here, the influence of rare soil microbe reduction on induced systemic resistance (ISR) in a wild ecotype of Arabidopsis thaliana against the aphid Myzus persicae was investigated. Methods: To create a gradient of microbial abundances, soil was inoculated with a serial dilution of a microbial community and responses of Arabidopsis plants that originated from the same site as the soil microbes were tested. Plant biomass, transcription of genes involved in plant defences, and insect performance were measured. In addition, the effects of the PGPR strain Pseudomonas fluorescens SS101 on plant and insect performance were tested under the influence of the various soil dilution treatments. Key Results: Plant biomass showed a hump-shaped relationship with soil microbial community dilution, independent of aphid or Pseudomonas treatments. Both aphid infestation and inoculation with Pseudomonas reduced plant biomass, and led to downregulation of PR1 (salicylic acid-responsive gene) and CYP79B3 (involved in synthesis of glucosinolates). Aphid performance and gene transcription were unaffected by soil dilution. Conclusions: Neither the loss of rare microbial species, as caused by soil dilution, nor Pseudomonas affect the resistance of A. Thaliana against M. persicae. However, both Pseudomonas survival and plant biomass respond to rare species loss. Thus, loss of rare soil microbial species can have a significant impact on both above- and belowground organisms.
    A model for estimating seasonal trends of ammonia emission from cattle manure applied to grassland in the Netherlands
    Huijsmans, J.F.M. ; Vermeulen, G.D. ; Hol, J.M.G. ; Goedhart, P.W. - \ 2018
    Atmospheric Environment 173 (2018). - ISSN 1352-2310 - p. 231 - 238.
    Ammonia emission - Application techniques - Grassland - Manure - Model - Weather
    Field data on ammonia emission after liquid cattle manure (‘slurry’) application to grassland were statistically analysed to reveal the effect of manure and field characteristics and of weather conditions in eight consecutive periods after manure application. Logistic regression models, modelling the emission expressed as a percentage of the ammonia still present at the start of each period as the response variable, were developed separately for broadcast spreading, narrow band application (trailing shoe) and shallow injection. Wind speed, temperature, soil type, total ammoniacal nitrogen (TAN) content and dry matter content of the manure, application rate and grass height were selected as significant explanatory variables. Their effects differed for each application method and among periods. Temperature and wind speed were generally the most important drivers for emission. The fitted regression models were used to reveal seasonal trends in NH3 emission employing historical meteorological data for the years 1991–2014. The overall average emission was higher in early and midsummer than in early spring and late summer. This seasonal trend was most pronounced for broadcast spreading followed by narrow band application, and was almost absent for shallow injection. However, due to the large variation in weather conditions, emission on a particular day in early spring can be higher than on a particular day in summer. The analysis further revealed that, in a specific scenario and depending on the application technique, emission could be reduced with 20–30% by restricting manure application to favourable days, i.e. with weather conditions with minimal emission levels.
    Ammoniakemissie uit natuurlijk geventileerde hellingstallen voor vleesvee
    Aarnink, Andre ; Hol, J.M.G. ; Bokma, Sjoerd - \ 2017
    Wageningen : Wageningen Livestock Research (Rapport / Wageningen Livestock Research 1078) - 33
    In this study the gaseous and dust emissions from straw bedded sloped floor housing for beef cattle were studied. It is concluded that ammonia emissions are probably higher than the present emission factor for beef cattle. The emission of methane is comparable to that for dairy cattle and the emissions of nitrous oxide and particulate matter are low
    Transient negative biochar effects on plant growth are strongest after microbial species loss
    Hol, W.H.G. ; Vestergård, Mette ; Hooven, Freddy ten; Duyts, Henk ; Voorde, Tess F.J. van de; Bezemer, T.M. - \ 2017
    Soil Biology and Biochemistry 115 (2017). - ISSN 0038-0717 - p. 442 - 451.
    Biochar - Medicago sativa - Serial dilution - Soil inoculation - Vicia villosa

    Biochar has been explored as an organic amendment to improve soil quality and benefit plant growth. The overall positive effects of biochar on crop yields are generally attributed to abiotic changes, while the alternative causal pathway via changes in soil biota is unexplored. We compared plant growth effects of legumes in sterile soil inoculated with dilutions of soil and soil microbial suspensions to determine the direct effects of biochar-induced changes in soil biota on plant growth. Suspensions and soil were from soil amended with biochar and soil without biochar. By comparing consecutive plant growth phases on the same inoculated soils, we also determined the temporal effects of soil biota from biochar-amended and control soils. Biota from biochar-amended soil was less beneficial for Medicago sativa growth, especially with small amounts of inocula. Flowering was delayed in the presence of biota from biochar plots. Inoculum with either soil or soil suspension gave similar results for plant biomass, indicating that microorganisms play a major role. Vicia villosa growth did not respond to the various inocula, even though the inoculum quantity strongly affected nematode community composition and protozoan abundance. In a later growing phase the negative effect of biochar-associated biota on Medicago growth mostly disappeared, which leads to the conclusion that the benefits of biochar application via abiotic changes may outweigh the negative effects of biochar on soil biota.

    Ammoniakemissie bij met water verdunde mest toegediend met een sleepvoetenmachine op grasland : resultaten 2016-2017
    Huijsmans, J.F.M. ; Hol, J.M.G. ; Schooten, H.A. van; Verwijs, B.R. - \ 2017
    Lelystad : Wageningen Plant Research (Rapport / Wageningen Plant Research WPR-754) - 34
    Detecting soil microbial community shifts via remote sensing
    Hol, Gera ; Bartholomeus, H.M. - \ 2017
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