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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    Farm dust resistomes and bacterial microbiomes in European poultry and pig farms
    Luiken, Roosmarijn E.C. ; Gompel, Liese Van; Bossers, Alex ; Munk, Patrick ; Joosten, Philip ; Hansen, Rasmus Borup ; Knudsen, Berith E. ; García-Cobos, Silvia ; Dewulf, Jeroen ; Aarestrup, Frank M. ; Wagenaar, Jaap A. ; Smit, Lidwien A.M. ; Mevius, Dik J. ; Heederik, Dick J.J. ; Schmitt, Heike - \ 2020
    Environment International 143 (2020). - ISSN 0160-4120
    Air - Farm - Metagenomics - Microbiome - One health - Resistome

    Background: Livestock farms are a reservoir of antimicrobial resistant bacteria from feces. Airborne dust-bound bacteria can spread across the barn and to the outdoor environment. Therefore, exposure to farm dust may be of concern for animals, farmers and neighboring residents. Although dust is a potential route of transmission, little is known about the resistome and bacterial microbiome of farm dust. Objectives: We describe the resistome and bacterial microbiome of pig and poultry farm dust and their relation with animal feces resistomes and bacterial microbiomes, and on-farm antimicrobial usage (AMU). In addition, the relation between dust and farmers’ stool resistomes was explored. Methods: In the EFFORT-study, resistomes and bacterial microbiomes of indoor farm dust collected on Electrostatic Dust fall Collectors (EDCs), and animal feces of 35 conventional broiler and 44 farrow-to-finish pig farms from nine European countries were determined by shotgun metagenomic analysis. The analysis also included 79 stool samples from farmers working or living at 12 broiler and 19 pig farms and 46 human controls. Relative abundance of and variation in resistome and bacterial composition of farm dust was described and compared to animal feces and farmers’ stool. Results: The farm dust resistome contained a large variety of antimicrobial resistance genes (ARGs); more than the animal fecal resistome. For both poultry and pigs, composition of dust resistomes finds (partly) its origin in animal feces as dust resistomes correlated significantly with fecal resistomes. The dust bacterial microbiome also correlated significantly with the dust resistome composition. A positive association between AMU in animals on the farm and the total abundance of the dust resistome was found. Occupational exposure to pig farm dust or animal feces may contribute to farmers’ resistomes, however no major shifts in farmers resistome towards feces or dust resistomes were found in this study. Conclusion: Poultry and pig farm dust resistomes are rich and abundant and associated with the fecal resistome of the animals and the dust bacterial microbiome.

    Aromatic Potential of Diverse Non-Conventional Yeast Species for Winemaking and Brewing
    Gamero, Amparo ; Dijkstra, Annereinou ; Smit, Bart ; Jong, Catrienus de - \ 2020
    Fermentation 6 (2020)2. - ISSN 2311-5637
    Traditionally, Saccharomyces species are those used to conduct industrial alcoholic fermentations. Recently, an increasing interest has arisen with respect to the potential of so-called non-conventional yeasts to improve wine and beer aroma profiles, keeping the particular terroir of each region or for the development of craft beers. In this study, the potential of diverse non-conventional yeasts to improve aroma in winemaking and brewing was investigated, testing several pure and mixed culture combinations. In addition, a comparison between microscale and labscale was carried out in order to assess the value of microwine and microbeer as screening tools. The results indicated that non-Saccharomyces yeasts were good candidates to enhance or diversify aroma profiles in alcoholic beverages, especially regarding acetate ester yield and fruity aromas. However, mixed cultures with Saccharomyces spp. are normally required to achieve a successful fermentation. The adjustment of pithing ratios is crucial for this purpose. Microscale is presented as an effective and efficient screening tool to compare different culture combinations, although scaling-up will always be necessary in order to get results closer to real winemaking or brewing processes
    Clinical and Pathological Findings in SARS-CoV-2 Disease Outbreaks in Farmed Mink (Neovison vison)
    Molenaar, Robert Jan ; Vreman, Sandra ; Hakze-van der Honing, Renate W. ; Zwart, Rob ; Rond, Jan de; Weesendorp, Eefke ; Smit, Lidwien A.M. ; Koopmans, Marion ; Bouwstra, Ruth ; Stegeman, Arjan ; Poel, Wim H.M. van der - \ 2020
    Veterinary Pathology (2020). - ISSN 0300-9858
    COVID-19 - mink - pneumonia - respiratory disease - severe acute respiratory syndrome coronavirus 2 - zoonoses

    SARS-CoV-2, the causative agent of COVID-19, caused respiratory disease outbreaks with increased mortality in 4 mink farms in the Netherlands. The most striking postmortem finding was an acute interstitial pneumonia, which was found in nearly all examined mink that died at the peak of the outbreaks. Acute alveolar damage was a consistent histopathological finding in mink that died with pneumonia. SARS-CoV-2 infections were confirmed by detection of viral RNA in throat swabs and by immunohistochemical detection of viral antigen in nasal conchae, trachea, and lung. Clinically, the outbreaks lasted for about 4 weeks but some animals were still polymerase chain reaction–positive for SARS-CoV-2 in throat swabs after clinical signs had disappeared. This is the first report of the clinical and pathological characteristics of SARS-CoV-2 outbreaks in mink farms.

    Description and determinants of the faecal resistome and microbiome of farmers and slaughterhouse workers : A metagenome-wide cross-sectional study
    Gompel, Liese Van; Luiken, Roosmarijn E.C. ; Hansen, Rasmus B. ; Munk, Patrick ; Bouwknegt, Martijn ; Heres, Lourens ; Greve, Gerdit D. ; Scherpenisse, Peter ; Jongerius-Gortemaker, Betty G.M. ; Tersteeg-Zijderveld, Monique H.G. ; García-Cobos, Silvia ; Dohmen, Wietske ; Dorado-García, Alejandro ; Wagenaar, Jaap A. ; Urlings, Bert A.P. ; Aarestrup, Frank M. ; Mevius, Dik J. ; Heederik, Dick J.J. ; Schmitt, Heike ; Bossers, Alex ; Smit, Lidwien A.M. - \ 2020
    Environment International 143 (2020). - ISSN 0160-4120
    Antimicrobial resistance - Farmers - Microbiome - Occupational exposure - Resistome - Slaughterhouse workers

    Background: By studying the entire human faecal resistome and associated microbiome, the diversity and abundance of faecal antimicrobial resistance genes (ARGs) can be comprehensively characterized. Prior culture-based studies have shown associations between occupational exposure to livestock and carriage of specific antimicrobial resistant bacteria. Using shotgun metagenomics, the present study investigated 194 faecal resistomes and bacteriomes from humans occupationally exposed to ARGs in livestock (i.e. pig and poultry farmers, employees and family members and pig slaughterhouse workers) and a control population (Lifelines cohort) in the Netherlands. In addition, we sought to identify determinants for the human resistome and bacteriome composition by applying a combination of multivariate (NMDS, PERMANOVA, SIMPER and DESeq2 analysis) and multivariable regression analysis techniques. Results: Pig slaughterhouse workers and pig farmers carried higher total ARG abundances in their stools compared to broiler farmers and control subjects. Tetracycline, β-lactam and macrolide resistance gene clusters dominated the resistome of all studied groups. No significant resistome alpha diversity differences were found among the four populations. However, the resistome beta diversity showed a separation of the mean resistome composition of pig and pork exposed workers from broiler farmers and controls, independent of their antimicrobial use. We demonstrated differences in resistome composition between slaughter line positions, pig versus poultry exposed workers, as well as differences between farmers and employees versus family members. In addition, we found a significant correlation between the bacteriome and resistome, and significant differences in the bacteriome composition between and within the studied subpopulations. Finally, an in-depth analysis of pig and poultry farms – of which also farm livestock resistomes were analysed – showed positive associations between the number of on-farm working hours and human faecal AMR loads. Conclusion: We found that the total normalized faecal ARG carriage was larger in persons working in the Dutch pork production chain compared to poultry farmers and controls. Additionally, we showed significant differences in resistome and bacteriome composition of pig and pork exposed workers compared to a control group, as well as within-population (farms, slaughterhouse) compositional differences. The number of on-farm working hours and the farm type (pig or broiler) that persons live or work on are determinants for the human faecal resistome. Overall, our results may suggest direct or indirect livestock contact as a determinant for human ARG carriage. Future studies should further focus on the connection between the human and livestock resistome (i.e. transmission routes) to substantiate the evidence for livestock-associated resistome acquisition.

    Natuur Impuls Oosterschelde : Toepassingsmogelijkheden van slibrijk sediment voor natuurbouw
    Ysebaert, Tom ; Walles, Brenda ; Werf, Jebbe van der; Vet, Lodewijk de; Hansen, Jill ; Duren, Luca van; Smit, Jaco de; Bouma, Tjeerd ; Stronkhorst, Joost - \ 2020
    Yerseke : Wageningen Marine Research (Wageningen Marine Research report C038/20) - 137
    Ook planten worden ziek
    Gommers, Charlotte - \ 2020
    In: Cahier Biowetenschappen & Maatschappij / Govers, F., Pieterse, C., Termorshuizen, A., Smit, A., Den Haag : Stichting Biowetenschappen en Maatschappij (BWM) (Cahier Biowetenschappen & Maatschappij 2) - ISBN 9789073196988 - p. 8 - 11.
    We zijn veel met onze eigen gezondheid bezig, zeker als we geïnfecteerd raken met een virus of anderszins door een ziekte worden overvallen. Maar ook de gezondheid van planten moeten we goed bewaken, want akkergewassen, bomen en sierplanten worden continu belaagd door ziekteverwekkers en insecten. Soms zijn die belagers er jarenlang niet, om dan opeens weer toe te slaan. Waar komen ze vandaan, wat is hun impact en hoe worden ze geïdentificeerd door de plantendokters van nu?
    Uitgelicht: Dubbele dreiging
    Willemen, Doriet - \ 2020
    In: Cahier Biowetenschappen & Maatschappij / Govers, F., Pieterse, C., Termorshuizen, A., Smit, A., Den Haag : Stichting Biowetenschappen en Maatschappij (BWM) (Cahier Biowetenschappen & Maatschappij 2) - ISBN 9789073196988 - p. 12 - 12.
    Ziekteverwekkers en hun trukendozen
    Govers, F. ; Termorshuizen, A.J. ; Pieterse, Corné - \ 2020
    In: Cahier Biowetenschappen & Maatschappij / Govers, F., Pieterse, C., Termorshuizen, A., Smit, A., Den Haag : Stichting Biowetenschappen en Maatschappij (BWM) (Cahier Biowetenschappen & Maatschappij 2) - ISBN 9789073196988 - p. 14 - 17.
    Voorkómen is beter
    Rossing, W.A.H. - \ 2020
    In: Cahier Biowetenschappen & Maatschappij / Govers, F., Pieterse, C., Termorshuizen, A., Smit, A., Den Haag : Stichting Biowetenschappen en Maatschappij (BWM) (Cahier Biowetenschappen & Maatschappij 2) - ISBN 9789073196988 - p. 35 - 37.
    Preventie is het codewoord in de plantgezondheid: hoe kunnen we ziektes vóór zijn, hoe kunnen we voorkomen dat het gewas wordt belaagd? Aanpassing van de omgeving van de plant is één manier: zorgen dat de barrières om bij de plant te komen, hoog zijn. Ook ín de plant kunnen we barricades opwerpen, door resistente planten te selecteren en te veredelen. Verder kunnen we met voorbehandeling van het zaad de plant een goede start geven en wapenen tegen indringers. En dan hebben we tegenwoordig ook nog apps die alarm slaan zodra de omstandigheden bevorderlijk zijn voor ziekteverwekkers.
    Uitgelicht: hongersnood en volksverhuizing
    Willemen, Doriet - \ 2020
    In: Cahier Biowetenschappen & Maatschappij / Govers, F., Pieterse, C., Termorshuizen, A., Smit, A., Den Haag : Stichting Biowetenschappen en Maatschappij (BWM) (Cahier Biowetenschappen & Maatschappij 2) - ISBN 9789073196988 - p. 30 - 30.
    Uitgelicht: vampierplanten
    Willemen, Doriet - \ 2020
    In: Plantgezondheid / Govers, F., Pieterse, C., Termorshuizen, A., Smit, A., Den Haag : Stichting Biowetenschappen en Maatschappij (BWM) (Cahier Biowetenschappen & Maatschappij 2) - ISBN 9789073196988 - p. 84 - 84.
    Uitgelicht: echt of vals?
    Willemen, Doriet - \ 2020
    In: Plantgezondheid / Govers, F., Pieterse, C., Termorshuizen, A., Smit, A., Den Haag : Stichting Biowetenschappen en Maatschappij (BWM) (Cahier Biowetenschappen & Maatschappij 2) - ISBN 9789073196988 - p. 38 - 38.
    Blik op de toekomst : Preciesielandbouw
    Polder, G. ; Zedde, H.J. van de; Franke, G.J. - \ 2020
    In: Plantgezondheid / Govers, F., Pieterse, C., Termorshuizen, A., Smit, A., Den Haag : Stichting Biowetenschappen en Maatschappij (BWM) (Cahier Biowetenschappen & Maatschappij 2) - ISBN 9789073196988 - p. 82 - 85.
    Wetenschappers zoeken nieuwe manieren om de plantgezondheid in de toekomst te waarborgen. Genetici kunnen de plant steeds subtieler bewapenen door kleine wijzigingen in het erfelijk materiaal aan te brengen. Andere wetenschappers onderzoeken hoe de micro-organismen in de bodem de plant te hulp kunnen schieten. Ook zijn er geautomatiseerde systemen in ontwikkeling die de plantenbelagers in een vroeg stadium detecteren en bestrijden. Waarschijnlijk blijft er voldoende perspectief voor de boeren. Zeker als de overheid ervoor zorgt dat zij een betere prijs voor hun producten krijgen.
    Wat als de ziekte toeslaat? : Biologische bestrijding: benut wat de natuur biedt
    Messelink, G.J. ; Köhl, J. - \ 2020
    In: Plantgezondheid / Govers, F., Pieterse, C., Termorshuizen, A., Smit, A., Den Haag : Stichting Biowetenschappen en Maatschappij (BWM) (Cahier Biowetenschappen & Maatschappij 2) - ISBN 9789073196988 - p. 52 - 55.
    Als alles gericht is op preventie, waarom zijn er dan nog steeds plantenziekten? Helaas is resistentie tegen lang niet alle plantenbelagers beschikbaar. En soms kan een plantenbelager dankzij genetische mutatie de resistentie omzeilen. Wat dan resteert is een directe vorm van bestrijding, biologisch dan wel chemisch. De discussie of we zonder chemische bestrijding kunnen, wordt momenteel volop gevoerd; de overheid wil er in ieder geval binnen tien jaar afscheid van nemen. De suikerbiet kunnen we dan kwijtraken, gezien de grote druk van allerlei ziekten en plagen. Aardappelteelt blijft wel mogelijk, maar de opbrengsten zullen sterk achteruitgaan. Biologische bestrijding zou een alternatief kunnen zijn, maar zijn er wel voldoende goedwerkende ‘groene middelen’ beschikbaar?
    Uitgelicht: plantenziekten: soms mooi en nuttig
    Willemen, Doriet - \ 2020
    In: Plantgezondheid / Govers, F., Pieterse, C., Termorshuizen, A., Smit, A., Den Haag : Stichting Biowetenschappen en Maatschappij (BWM) (Cahier Biowetenschappen & Maatschappij 2) - ISBN 9789073196988 - p. 44 - 44.
    Vermindert plantendiversiteit de kans op ziektes?
    Mommer, L. - \ 2020
    In: Cahier Biowetenschappen & Maatschappij / Govers, F., Pieterse, C., Termorshuizen, A., Smit, A., Den Haag : Stichting Biowetenschappen en Maatschappij (BWM) (Cahier Biowetenschappen & Maatschappij 2) - ISBN 9789073196988 - p. 32 - 33.
    Wat als de ziekte toeslaat? : Een 'vaccin' voor de iep
    Postma, J. - \ 2020
    In: Plantgezondheid / Govers, F., Pieterse, C., Termorshuizen, A., Smit, A., Den Haag : Stichting Biowetenschappen en Maatschappij (BWM) (Cahier Biowetenschappen & Maatschappij 2) - ISBN 9789073196988 - p. 56 - 57.
    Als alles gericht is op preventie, waarom zijn er dan nog steeds plantenziekten? Helaas is resistentie tegen lang niet alle plantenbelagers beschikbaar. En soms kan een plantenbelager dankzij genetische mutatie de resistentie omzeilen. Wat dan resteert is een directe vorm van bestrijding, biologisch dan wel chemisch. De discussie of we zonder chemische bestrijding kunnen, wordt momenteel volop gevoerd; de overheid wil er in ieder geval binnen tien jaar afscheid van nemen. De suikerbiet kunnen we dan kwijtraken, gezien de grote druk van allerlei ziekten en plagen. Aardappelteelt blijft wel mogelijk, maar de opbrengsten zullen sterk achteruitgaan. Biologische bestrijding zou een alternatief kunnen zijn, maar zijn er wel voldoende goedwerkende ‘groene middelen’ beschikbaar?
    Plantgezondheid : Hoe voorkomen we dat planten ziek worden?
    Govers, F. ; Pieterse, Corné ; Termorshuizen, Aad ; Smit, Astrid - \ 2020
    Den Haag : Stichting Biowetenschappen en Maatschappij (BWM) (Cahier 2) - ISBN 9789073196988 - 100 p.
    Beter bewaren
    Gabriëls, S.H.E.J. ; Woltering, E.J. - \ 2020
    In: Plantgezondheid / Govers, F., Pieterse, C., Termorshuizen, A., Smit, A., Stichting Biowetenschappen en Maatschappij (Cahier Biowetenschappen en Maatschappij 2020/2) - ISBN 9789073196988 - p. 31 - 31.
    SARS-CoV-2 infection in farmed minks, the Netherlands, April and May 2020
    Oreshkova, Nadia ; Molenaar, Robert Jan ; Vreman, Sandra ; Harders, Frank ; Oude Munnink, Bas B. ; Hakze-van der Honing, Renate W. ; Gerhards, Nora ; Tolsma, Paulien ; Bouwstra, Ruth ; Sikkema, Reina S. ; Tacken, Mirriam G.J. ; Rooij, Myrna M.T. de; Weesendorp, Eefke ; Engelsma, Marc Y. ; Bruschke, Christianne J.M. ; Smit, Lidwien A.M. ; Koopmans, Marion ; Poel, Wim H.M. van der; Stegeman, Arjan - \ 2020
    Eurosurveillance 25 (2020)23. - ISSN 1025-496X
    interstitial pneumonia - mink - SARS-CoV-2 - transmission

    Respiratory disease and increased mortality occurred in minks on two farms in the Netherlands, with interstitial pneumonia and SARS-CoV-2 RNA in organ and swab samples. On both farms, at least one worker had coronavirus disease-associated symptoms before the outbreak. Variations in mink-derived viral genomes showed between-mink transmission and no infection link between the farms. Inhalable dust contained viral RNA, indicating possible exposure of workers. One worker is assumed to have attracted the virus from mink.

    Stadslandbouw en plantenziekten
    Veen, E.J. ; Jansma, J.E. ; Vermeulen, T. ; Vlasakker, Paulien van de - \ 2020
    In: Plantgezondheid / Govers, Francine, Pieterse, Corné, Termorshuizen, Aad, Smit, Astrid, Stichting Biowetenschappen en Maatschappij (BWM) (Cahiers bio-wetenschappen en maatschappij 2) - p. 88 - 89.
    Plantgezondheid : Hoe voorkomen we dat planten ziek worden?
    Govers, Francine ; Pieterse, Corné ; Termorshuizen, Aad ; Smit, Astrid - \ 2020
    Den Haag : Stichting Biowetenschappen en Maatschappij (BWM) (Cahiers bio-wetenschappen en maatschappij 39e jaargang, kwartaal 2) - ISBN 9789073196988 - 96
    Methanol based chain elongation with acetate to n-butyrate and isobutyrate at varying selectivities dependent on pH
    Leeuw, Kasper de; Smit, Sanne de; Oossanen, Sabine van; Moerland, Merijn ; Buisman, Cees ; Strik, David - \ 2020
    Wageningen University & Research
    PRJEB36205 - ERP119366 - metagenome
    Biomass fermentation technologies offer alternative methods to produce platform chemicals that currently originate from fossil sources. This research showed that an enriched microbiome was capable to produce iso-butyric acid via methanol based chain elongation of acetate. A long term continuous reactor experiment showed that the selectivity for isobutyrate (i-C4) and/or n-butyrate (n-C4) could be reversibly adjusted by changing the reactor pH. A reactor pH of 6.75 led to formation of (carbon per total carbon of products) of 0.78 n-C4 and 0.024 i-C4, whereas a reactor pH of 5.2 led to a selectivity of 0.25 n-C4 and 0.63 i-C4 . This shift in product spectrum was also represented by a shift in microbial composition. The results suggest that an Eubacterium genus is responsible for the formation of n-C4, whereas a Clostridium luticellarii strain is responsible for the formation of a mixture of i-C4 and n¬¬-C4. The formation of n and i-C4 at a low pH was observed to be coupled according to the thermodynamics of isomerization. At a reactor pH of 5.5 and 5.2 the product ratio of i-C4:n-C4 approached the ratio of 0.684 i-C4 : 0.316 n-C4, which is the theoretical ratio that would be achieved when i-C4 and n-C4 would be formed at amounts determined by the equilibrium of isomerization. Various batch experiments at pH 5.5 and 5.2 confirmed that addition of either n-C4 or i-C4 at the start of the batch would immediately lead to the formation of the other butyrate component. Moreover, batch experiments performed at pH 6.5 immediately produced mainly n-C4 and led to the development of a completely different microbiome. The imposed pH as a strong selective pressure can immediately facilitate changes in product selectivities for n-C4 and i-C4 during methanol based chain elongation of acetate.
    Methanol-Based Chain Elongation with Acetate to n-Butyrate and Isobutyrate at Varying Selectivities Dependent on pH
    Leeuw, Kasper D. de; Smit, Sanne M. de; Oossanen, Sabine van; Moerland, Marinus J. ; Buisman, Cees J.N. ; Strik, David P.B.T.B. - \ 2020
    ACS sustainable chemistry & engineering 8 (2020)22. - ISSN 2168-0485
    Biobased chemicals - Chain elongation - Isobutyrate - Methanol - n-Butyrate - Open-culture fermentation - Selection pressure

    Biomass fermentation technologies offer alternative methods to produce platform chemicals that currently originate from fossil sources. This research showed that an enriched microbiome was capable to produce isobutyrate (i-C4) from acetate via methanol-based chain elongation. A long-term continuous reactor experiment showed that the selectivity for i-C4 and/or n-butyrate (n-C4) could be reversibly adjusted by changing the reactor pH. A reactor pH of 6.75 led to formation of (carbon per total carbon of products) 0.78 n-C4 and 0.024 i-C4, whereas a reactor pH of 5.2 led to a selectivity of 0.24 n-C4 and 0.65 i-C4. This shift in product spectrum was also represented by a shift in microbial composition. The results suggest that a Eubacterium genus is responsible for the formation of n-C4, whereas a Clostridium luticellarii strain is responsible for the formation of a mixture of i-C4 and n-C4. The formation of n-C4 and i-C4 at a low pH was observed to be coupled according to the thermodynamics of isomerization. At a reactor pH of 5.5 and 5.2, the product ratio of i-C4:n-C4 approached 0.69 i-C4:0.31 n-C4, which is the theoretical ratio that would be achieved when determined by the equilibrium of isomerization. Various batch experiments at pH 5.5 and 5.2 confirmed that addition of either n-C4 or i-C4 at the start of the batch would directly lead to the formation of the other butyrate component. Moreover, batch experiments performed at pH 6.5 produced mainly n-C4 and led to the development of a completely different microbiome. The imposed pH is a strong selection pressure that can facilitate changes in product selectivities for n-C4 and i-C4 during methanol-based chain elongation of acetate.

    Seagrass coastal protection services reduced by invasive species expansion and megaherbivore grazing
    James, Rebecca K. ; Christianen, Marjolijn J.A. ; Katwijk, Marieke M. van; Smit, Jaco C. de; Bakker, Elisabeth S. ; Herman, Peter M.J. ; Bouma, Tjeerd J. - \ 2020
    Journal of Ecology (2020). - ISSN 0022-0477
    coastal protection - conservation - ecosystem services - exotic species - marine ecology - marine vegetation - storm resilience - tropical ecology

    Seagrasses provide an important ecosystem service by creating a stable erosion-resistant seabed that contributes to effective coastal protection. Variable morphologies and life-history strategies, however, are likely to impact the sediment stabilization capacity of different seagrass species. We question how opportunistic invasive species and increasing grazing by megaherbivores may alter sediment stabilization services provided by established seagrass meadows, using the Caribbean as a case study. Utilizing two portable field-flumes that simulate unidirectional and oscillatory flow regimes, we compared the sediment stabilization capacity of natural seagrass meadows in situ under current- and wave-dominated regimes. Monospecific patches of a native (Thalassia testudinum) and an invasive (Halophila stipulacea) seagrass species were compared, along with the effect of three levels of megaherbivore grazing on T. testudinum: ungrazed, lightly grazed and intensively grazed. For both hydrodynamic regimes, the long-leaved, dense meadows of the climax species, T. testudinum provided the highest stabilization. However, the loss of above-ground biomass by intensive grazing reduced the capacity of the native seagrass to stabilize the surface sediment. Caribbean seagrass meadows are presently threatened by the rapid spread of the invasive opportunistic seagrass, H. stipulacea. The dense meadows of H. stipulacea were found to accumulate fine sediment, and thereby, appear to be effective in reducing bottom shear stress during calm periods. This fine sediment within the invasive meadows, however, is easily resuspended by hydrodynamic forces, and the low below-ground biomass of H. stipulacea make it susceptible to uprooting during storm events, potentially leaving large regions vulnerable to erosion. Overall, this present study highlights that intensive megaherbivore grazing and opportunistic invasive species threaten the coastal protection services provided by mildly grazed native species. Synthesis. Seagrass meadows of dense, long-leaved species stabilize the sediment surface and maintain the seabed integrity, thereby contributing to coastal protection. These services are threatened by intensive megaherbivore grazing, which reduces the stability of the surface sediment, and opportunistic invasive species, which are susceptible to uprooting in storms and thereby can leave the seabed vulnerable to erosion.

    Het succes verklaard: Biologische landbouw in Flevoland bloeit en groeit
    Dekking, A.J.G. ; Jansma, J.E. ; Smit, A.B. ; Janssens, S.R.M. - \ 2020
    Ekoland 40 (2020)5. - ISSN 0926-9142 - p. 26 - 27.
    Specification and regulation of vascular tissue identity in the Arabidopsis embryo
    Smit, Margot E. ; Llavata-Peris, Cristina I. ; Roosjen, Mark ; Beijnum, Henriette van; Novikova, Daria ; Levitsky, Victor ; Sevilem, Iris ; Roszak, Pawel ; Slane, Daniel ; Jürgens, Gerd ; Mironova, Victoria ; Brady, Siobhan M. ; Weijers, Dolf - \ 2020
    Development 147 (2020)8. - ISSN 0950-1991
    Arabidopsis - Auxin - Embryo - Gene regulatory network - Vascular development

    Development of plant vascular tissues involves tissue identity specification, growth, pattern formation and cell-type differentiation. Although later developmental steps are understood in some detail, it is still largely unknown how the tissue is initially specified. We used the early Arabidopsis embryo as a simple model to study this process. Using a large collection of marker genes, we found that vascular identity was specified in the 16-cell embryo. After a transient precursor state, however, there was no persistent uniform tissue identity. Auxin is intimately connected to vascular tissue development. We found that, although an AUXIN RESPONSE FACTOR5/MONOPTEROS (ARF5/MP)-dependent auxin response was required, it was not sufficient for tissue specification. We therefore used a large-scale enhanced yeast one-hybrid assay to identify potential regulators of vascular identity. Network and functional analysis of candidate regulators suggest that vascular identity is under robust, complex control. We found that one candidate regulator, the G-class bZIP transcription factor GBF2, can modulate vascular gene expression by tuning MP output through direct interaction. Our work uncovers components of a gene regulatory network that controls the initial specification of vascular tissue identity.

    Fecal Carriage of Extended-Spectrum-β-Lactamase/AmpC-Producing Escherichia coli in Horses
    Hordijk, Joost ; Farmakioti, Evangelia ; Smit, Lidwien A.M. ; Duim, Birgitta ; Graveland, Haitske ; Theelen, Mathijs J.P. ; Wagenaar, Jaap A. - \ 2020
    Applied and Environmental Microbiology 86 (2020)8. - ISSN 0099-2240
    AmpC - antimicrobial resistance - equidae - ESBL - fecal carriage - risk factor

    A nationwide study on the occurrence of extended-spectrum β-lactamase (ESBL)/AmpC in nonhospitalized horses in the Netherlands was performed. Molecular characterization was done, and questionnaires were analyzed to identify factors associated with carriage. In total, 796 horse owners were approached; 281 of these submitted a fecal sample from their horse(s), resulting in 362 samples. All samples were cultured qualitatively in Luria-Bertani (LB) broth and subsequently on MacConkey agar, both supplemented with 1 mg/liter cefotaxime (LB+ and MC+). Positive samples were subsequently cultured quantitatively on MC+. Initial extended-spectrum-β-lactamase (ESBL)/AmpC screening was performed by PCR, followed by whole-genome sequencing on selected strains. Associations between ESBL/AmpC carriage and questionnaire items were analyzed using a univariate generalized estimating equation (GEE) regression analysis, followed by a multiple GEE model for relevant factors. In total, 39 of 362 samples (11%) were determined to be positive for ESBL/AmpC. blaCTX-M-1-carrying isolates were obtained from 77% of positive samples (n = 30). Other ESBL/AmpC genes observed included blaCTX-M-2, blaCTX-M-14, blaCTX-M-15, blaCTX-M-32, blaSHV-12, blaCMY-2, and blaACT-10 A high association between the presence of blaCTX-M-1 and IncHI1 plasmids was observed (46% of samples; n = 18). Based on core genome analysis (n = 48 isolates), six Escherichia coli clusters were identified, three of which represented 80% of the isolates. A negative association between ESBL/AmpC carriage and horses being in contact with other horses at a different site was observed. The presence of a dog on the premises and housing in a more densely human-populated region were positively associated.IMPORTANCE Extended-spectrum β-lactamases (ESBLs) are widespread in human and animal populations and in the environment. Many different ESBL variants exist. The dissemination of ESBLs within and between populations and the environment is also largely influenced by genetic mobile elements (e.g., plasmids) that facilitate spread of these ESBLs. In order to identify potential attributable ESBL sources for, e.g., the human population, it is important to identify the different ESBL variants, the bacteria carrying them, and the potential risk factors for ESBL carriage from other potential sources. This nationwide study focuses on ESBL carriage in the open horse population and investigated the molecular characteristics, geographical distribution throughout the Netherlands, and potential risk factors for fecal ESBL carriage in horses. These data can be used for future attribution studies in order to reduce potential transmission of ESBL-producing bacteria between sources.

    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
    Bodemmaatregelen op dalgrond in de Veenkoloniën: effecten op bodemkwaliteit, opbrengst en financiële meerwaarde : Analyse van de resultaten van de systeemproef Bodemkwaliteit Veenkoloniën 2014-2017
    Haan, Janjo de; Asperen, Paulien van; Visser, Johnny ; Burgt, Geert Jan van der; Smit, Elsbeth ; Dawson, Andrew ; Klompe, Koen - \ 2020
    Wageningen : Stichting Wageningen Research, Wageningen Plant Research, Businessunit WUR Open Teelten (Rapport / Stichting Wageningen Research, Wageningen Plant Research, Businessunit WUR Open Teelten WPR-831) - 69
    In een langjarig experiment op proefbedrijf Valthermond wordt op dalgrond met gemiddeld 11% organische stof een vijftal maatregelen in een vierjarige akkerbouwvruchtwisseling vergeleken met de standaard werkwijze, in vier herhalingen. De maatregelen Tagetes, Compost, sturen Ca/Mg-verhouding, Steenmeel zijn elk op hun eigen wijze gericht op verbetering van de bodemkwaliteit. Ook een combinatie van alle maatregelen is onderzocht. Over de maatregelen heen liggen varianten van grondbewerking (NKG en Spitten) in duplo. Na vier jaar blijkt de maatregel Tagetes (de teelt van zomergerst vervangen door een hoofdteelt Tagetes) zowel meer opbrengst op te leveren in de aardappelteelt als economisch rendabel te zijn, ondanks de opbrengstderving door het wegvallen van de verkoop van gerst. De andere strategieën hebben weinig of geen effect op de opbrengst en de kosten zijn hoger dan de eventuele extra inkomsten door opbrengstverhoging. NKG lijkt een positief effect te hebben op de opbrengst maar dat is nog niet statistisch significant. Wel leidt NKG tot kostenbesparing ten opzichte van Spitten door lagere machinekosten en lager brandstofverbruik. Veranderingen in bodemkwaliteit zijn nog nauwelijks waargenomen. Dat komt naar verwachting mede doordat die effecten meer tijd nodig hebben om zich te tonen. De nitraatnorm voor grondwater wordt meestal overschreden, onafhankelijk van de maatregel. Waar de norm wel gehaald wordt ligt het aan bodem en grondwater, niet aan de bemestingsstrategie. Het onderzoek wordt voortgezet.
    Opportunities for improving the dairy sector in Romania
    Zaalmink, Wim ; Bergevoet, Ron ; Daatselaar, Co ; Smit, Bert - \ 2020
    Wageningen : Wageningen Economic Research (Wageningen Economic Research report 2020-015) - ISBN 9789463953160 - 52
    Romania is a milk importing country. Dairy farming in the country is small-scale but offers good prospects. The level of agricultural knowledge among farmers is still low due to insufficient agricultural education. Dutch businesses are active in Romania to develop dairy farming but are running up against this low level of knowledge. This report describes the experiences of transferring knowledge to farmers and advisors in central Transylvania.
    Measurement and genetic architecture of lifetime depression in the Netherlands as assessed by LIDAS (Lifetime Depression Assessment Self-report)
    Fedko, Iryna O. ; Hottenga, Jouke Jan ; Helmer, Quinta ; Mbarek, Hamdi ; Huider, Floris ; Amin, Najaf ; Beulens, Joline W. ; Bremmer, Marijke A. ; Elders, Petra J. ; Galesloot, Tessel E. ; Kiemeney, Lambertus A. ; Loo, Hanna M. Van; Picavet, H.S.J. ; Rutters, Femke ; Spek, Ashley Van Der; De Wiel, Anne M. Van; Duijn, Cornelia Van; Geus, Eco J.C. De; Feskens, Edith J.M. ; Hartman, Catharina A. ; Oldehinkel, Albertine J. ; Smit, Jan H. ; Verschuren, W.M.W. ; Penninx, Brenda W.J.H. ; Boomsma, Dorret I. ; Bot, Mariska - \ 2020
    Psychological Medicine (2020). - ISSN 0033-2917
    LIDAS - Lifetime Depression Assessment Self-report - major depressive disorder - online assessment tool - prevalence

    BackgroundMajor depressive disorder (MDD) is a common mood disorder, with a heritability of around 34%. Molecular genetic studies made significant progress and identified genetic markers associated with the risk of MDD; however, progress is slowed down by substantial heterogeneity as MDD is assessed differently across international cohorts. Here, we used a standardized online approach to measure MDD in multiple cohorts in the Netherlands and evaluated whether this approach can be used in epidemiological and genetic association studies of depression.MethodsWithin the Biobank Netherlands Internet Collaboration (BIONIC) project, we collected MDD data in eight cohorts involving 31 936 participants, using the online Lifetime Depression Assessment Self-report (LIDAS), and estimated the prevalence of current and lifetime MDD in 22 623 unrelated individuals. In a large Netherlands Twin Register (NTR) twin-family dataset (n 18 000), we estimated the heritability of MDD, and the prediction of MDD in a subset (n = 4782) through Polygenic Risk Score (PRS).ResultsEstimates of current and lifetime MDD prevalence were 6.7% and 18.1%, respectively, in line with population estimates based on validated psychiatric interviews. In the NTR heritability estimates were 0.34/0.30 (s.e. = 0.02/0.02) for current/lifetime MDD, respectively, showing that the LIDAS gives similar heritability rates for MDD as reported in the literature. The PRS predicted risk of MDD (OR 1.23, 95% CI 1.15-1.32, R2 = 1.47%).ConclusionsBy assessing MDD status in the Netherlands using the LIDAS instrument, we were able to confirm previously reported MDD prevalence and heritability estimates, which suggests that this instrument can be used in epidemiological and genetic association studies of depression.

    Perceptions of Care Sport Connectors’ Tasks for Strengthening the Connection Between Primary Care, Sports and Physical Activity: A Delphi Study
    Smit, Eva ; Leenaars, Karlijn E.F. ; Wagemakers, Annemarie ; Velden, Koos Van Der; Molleman, Gerard R.M. - \ 2020
    International Journal of Integrated Care 20 (2020)1. - ISSN 1568-4156 - p. 2 - 2.
    Introduction: Care sport connectors stimulate physical activity and facilitate collaboration between the primary care and physical activity sectors in the Netherlands. To strengthen intersectoral collaboration between the primary care and sports sectors, it is necessary to study which tasks a care sport connector must fulfil according to their own and other professionals’ perceptions.

    Methods: A Delphi study was conducted with 182 professionals from the primary care, public health and physical activity sectors. Rounds 1 and 2 included questions about task perception, willingness to collaborate and expectations of care sport connectors. Rounds 3 and 4 were used to reach consensus.

    Results: All professions acknowledged physical activity promotion tasks, but they are not all willing to collaborate. They expect a broad range of roles from care sport connectors: informative, executive, guiding and intermediate. Care sport connectors reached consensus on two roles: informative and intermediate.

    Discussion: Care sport connectors have an important role in strengthening intersectoral collaboration. All the professions acknowledged a task concerning physical activity promotion and accepted a broker role. Thus, a public health mind-set seems to be present to some extent. However, challenges remain, such as the lack of willingness to collaborate among primary care professionals and sports policies not (yet) supporting intersectoral collaboration.
    Biologische landbouw in Flevoland : Omvang en productstromen
    Dekking, Arjan ; Jansma, Jan-Eelco ; Janssens, Bas ; Smit, Bert - \ 2020
    Wageningen : Stichting Wageningen Research (WR), business unit Wageningen Plant Research (Rapport / Stichting Wageningen Research (WR), business unit Wageningen Plant Research WPR-822) - 40
    Effect extra CO2 inkoop op emissie van de glastuinbouw in 2030
    Velden, N.J.A. van der; Smit, P.X. - \ 2020
    Wageningen : Wageningen Economic Research (Wageningen Economic Research nota 2020-005) - 15
    Effect of growth conditions on the efficiency of cell disruption of Neochloris oleoabundans
    Safi, C. ; Olivieri, G. ; Engelen-Smit, N. ; Spekking, W. ; Veloo, R. ; Broek, L.A.M. van den; Sijtsma, L. - \ 2020
    Bioresource Technology 300 (2020). - ISSN 0960-8524
    Cell disintegration - Enzymes - High-pressure homogenization - Nitrogen deplete - Nitrogen replete

    The impact of four different growth conditions on the cell disruption efficiency of Neochloris oleoabundans was investigated. A mechanical and biological cell disruption methods were evaluated separately and combined. It has been established that microalgae grown in marine water under nitrogen deprivation were the most resistant against cell disruption methods and released the lowest amount of proteins. The release of lipids, however, followed the “hindered molecule diffusion phenomenon” because it did not follow the same release pattern as proteins. The enzymatic treatment was efficient enough to release the majority of the proteins without combining it with high-pressure homogenization. Regarding energy input, Neochloris oleoabundans grown in marine water under nitrogen deprivation required the highest energy input to release proteins (Ep = 13.76 kWh.kg−1) and to break the cells by high-pressure homogenization (Ex – HPH = 1.14 kWh.kg−1) or by the combination of enzymes and High-pressure homogenization (Ex – ENZ = 2.79 kWh.kg−1).

    A PXY-Mediated Transcriptional Network Integrates Signaling Mechanisms to Control Vascular Development in Arabidopsis
    Smit, Margot ; Mcgregor, Shauni ; Sun, Heng ; Gough, Catherine ; Bågman, Anne-Maarit ; Soyars, Cara L. ; Kroon, Johan T.M. ; Gaudinier, Allison ; Williams, Clara J. ; Yang, Xiyan ; Nimchuk, Zachary L. ; Weijers, Dolf ; Turner, Simon R. ; Brady, Siobhan M. ; Etchells, Peter - \ 2020
    The Plant Cell 32 (2020)2. - ISSN 1040-4651
    Vascular meristems generate the majority of biomass in higher plants. They constitute a bifacial stem cell population from which xylem and phloem are specified on opposing sides by positional signals. The PHLOEM INTERCALATED WITH XYLEM (PXY) receptor kinase promotes vascular cell division and organisation. However, how these functions are specified and integrated is unknown. Here, a putative PXY-mediated transcriptional regulatory network comprised of 690 transcription factor-promoter interactions was mapped. Among these interactions was a feed-forward loop containing transcription factors WUSCHEL HOMEOBOX RELATED 14 (WOX14) and TARGET OF MONOPTEROS 6 (TMO6), which each regulate the expression of a third transcription factor, LATERAL ORGAN BOUNDARIES DOMAIN 4 (LBD4). PXY signalling in turn regulates the WOX14, TMO6, LBD4 loop to control vascular proliferation. Genetic interaction between LBD4 and PXY suggests that LBD4 marks the phloem-procambium boundary, thus defining the shape of the vascular bundle. These data collectively support a novel mechanism that influences recruitment of cells into the phloem lineage, and defines the role of PXY signalling in this context to the arrangement of vascular tissue.
    Overview of in vivo and ex vivo endpoints in murine food allergy models: Suitable for evaluation of the sensitizing capacity of novel proteins?
    Castan, Laure ; Bøgh, Katrine Lindholm ; Maryniak, Natalia Z. ; Epstein, M. ; Kazemi, Sahar ; O'Mahony, Liam ; Bodinier, Marie ; Smit, Joost ; Bilsen, Jolanda H.M. Van; Blanchard, Carine ; Głogowski, Robert ; Kozakova, Hana ; Schwarzer, Martin ; Noti, Mario ; Wit, N.J.W. de; Bouchaud, Grégory ; Bastiaan-Net, S. - \ 2020
    Allergy 75 (2020)2. - ISSN 0105-4538 - p. 289 - 301.
    Significant efforts are necessary to introduce new dietary protein sources to feed a growing world population while maintaining food supply chain sustainability. Such a sustainable protein transition includes the use of highly modified proteins from side streams or the introduction of new protein sources that may lead to increased clinically relevant allergic sensitization. With food allergy being a major health problem of increasing concern, understanding the potential allergenicity of new or modified proteins is crucial to ensure public health protection. The best predictive risk assessment methods currently relied on are in vivo models, making the choice of endpoint parameters a key element in evaluating the sensitizing capacity of novel proteins. Here, we provide a comprehensive overview of the most frequently used in vivo and ex vivo endpoints in murine food allergy models, addressing their strengths and limitations for assessing sensitization risks. For optimal laboratory‐to‐laboratory reproducibility and reliable use of predictive tests for protein risk assessment, it is important that researchers maintain and apply the same relevant parameters and procedures. Thus, there is an urgent need for a consensus on key food allergy parameters to be applied in future food allergy research in synergy between both knowledge institutes and clinicians.
    Hecaton
    Wijfjes, R. ; Smit, S. - \ 2019
    Wageningen : Wageningen University & Research
    Code repository for Hecaton, a tool for CNV detection in plants
    Veehouderij en Gezondheid Omwonenden III: Longontsteking in de nabijheid van geitenhouderijen in Gelderland, Overijssel en Utrecht
    Smit, Lidwien ; Huss, Anke ; Jacobs, José ; Baliatsas, Christos ; Dückers, Michel ; Boender, Gert Jan ; McCarthy, Catharine ; Hagenaars, Thomas ; IJzermans, Joris ; Heederik, Dick - \ 2019
    Utrecht : Institute for Risk Assessment Sciences (IRAS), Universiteit Utrecht - 39
    Glastuinbouw: Barometer Duurzame landbouw Noord-Brabant
    Venema, G.S. ; Dolman, M.A. ; Smit, A.B. ; Jukema, G.D. ; Wisman, J.H. ; Jager, J.H. - \ 2019
    Wageningen Economic Research - 38 p.
    De factsheet Glastuinbouw maakt onderdeel uit van de Barometer Duurzame landbouw Noord-Brabant. In opdracht van de provincie Noord-Brabant wordt op basis van feiten over een breed terrein een zo actueel mogelijk beeld gegeven van de primaire agrarische sectoren. Ook wordt inzicht gegeven in opgetreden ontwikkelingen in de laatste decennia, en wordt een vergelijk gemaakt met de nationale ontwikkeling.
    Barometer Duurzame landbouw Noord-Brabant
    Venema, G.S. ; Dolman, M.A. ; Smit, A.B. ; Jukema, G.D. ; Wisman, J.H. ; Jager, J.H. - \ 2019
    Wageningen Economic Research - 32 p.
    Melkveehouderij: Barometer Duurzame landbouw Noord-Brabant
    Venema, G.S. ; Dolman, M.A. ; Smit, A.B. ; Jukema, G.D. ; Wisman, J.H. ; Jager, J.H. - \ 2019
    Wageningen Economic Research - 36 p.
    De factsheet Melkveehouderij maakt onderdeel uit van de Barometer Duurzame landbouw Noord-Brabant. In opdracht van de provincie Noord-Brabant wordt op basis van feiten over een breed terrein een zo actueel mogelijk beeld gegeven van de primaire agrarische sectoren. Ook wordt inzicht gegeven in opgetreden ontwikkelingen in de laatste decennia, en wordt een vergelijk gemaakt met de nationale ontwikkeling.
    Overig tuinbouw en blijvende teelt: Barometer Duurzame landbouw Noord-Brabant
    Venema, G.S. ; Dolman, M.A. ; Smit, A.B. ; Jukema, G.D. ; Wisman, J.H. ; Jager, J.H. - \ 2019
    Wageningen Economic Research - 29 p.
    De factsheet Overige tuinbouw en blijvende teelt maakt onderdeel uit van de Barometer Duurzame landbouw Noord-Brabant. In opdracht van de provincie Noord-Brabant wordt op basis van feiten over een breed terrein een zo actueel mogelijk beeld gegeven van de primaire agrarische sectoren. Ook wordt inzicht gegeven in opgetreden ontwikkelingen in de laatste decennia, en wordt een vergelijk gemaakt met de nationale ontwikkeling.
    Overige veehouderij: Barometer Duurzame landbouw Noord-Brabant
    Venema, G.S. ; Dolman, M.A. ; Smit, A.B. ; Jukema, G.D. ; Wisman, J.H. ; Jager, J.H. - \ 2019
    Wageningen Economic Research - 29 p.
    De factsheet Overige veehouderij maakt onderdeel uit van de Barometer Duurzame landbouw Noord-Brabant. In opdracht van de provincie Noord-Brabant wordt op basis van feiten over een breed terrein een zo actueel mogelijk beeld gegeven van de primaire agrarische sectoren. Ook wordt inzicht gegeven in opgetreden ontwikkelingen in de laatste decennia, en wordt een vergelijk gemaakt met de nationale ontwikkeling.
    Pluimveehouderij: Barometer Duurzame landbouw Noord-Brabant
    Venema, G.S. ; Dolman, M.A. ; Smit, A.B. ; Jukema, G.D. ; Wisman, J.H. ; Jager, J.H. - \ 2019
    Wageningen Economic Research - 34 p.
    De factsheet Pluimveehouderij maakt onderdeel uit van de Barometer Duurzame landbouw Noord-Brabant. In opdracht van de provincie Noord-Brabant wordt op basis van feiten over een breed terrein een zo actueel mogelijk beeld gegeven van de primaire agrarische sectoren. Ook wordt inzicht gegeven in opgetreden ontwikkelingen in de laatste decennia, en wordt een vergelijk gemaakt met de nationale ontwikkeling.
    Akkerbouw en vollegrondsgroenteteelt: Barometer Duurzame landbouw Noord-Brabant
    Venema, G.S. ; Dolman, M.A. ; Smit, A.B. ; Jukema, G.D. ; Wisman, J.H. ; Jager, J.H. - \ 2019
    Wageningen Economic Research - 43 p.
    De factsheet Akkerbouw en vollegrondsgroenteteelt maakt onderdeel uit van de Barometer Duurzame landbouw Noord-Brabant. In opdracht van de provincie Noord-Brabant wordt op basis van feiten over een breed terrein een zo actueel mogelijk beeld gegeven van de primaire agrarische sectoren. Ook wordt inzicht gegeven in opgetreden ontwikkelingen in de laatste decennia, en wordt een vergelijk gemaakt met de nationale ontwikkeling.
    Varkenshouderij: Barometer Duurzame landbouw Noord-Brabant
    Venema, G.S. ; Dolman, M.A. ; Smit, A.B. ; Jukema, G.D. ; Wisman, J.H. ; Jager, J.H. - \ 2019
    Wageningen Economic Research - 33 p.
    VarkenshouderijBarometer Duurzame landbouw Noord-Brabant | Wageningen Economic ResearchDe factsheet Varkenshouderij maakt onderdeel uit van de Barometer Duurzame landbouw Noord-Brabant. In opdracht van de provincie Noord-Brabant wordt op basis van feiten over een breed terrein een zo actueel mogelijk beeld gegeven van de primaire agrarische sectoren. Ook wordt inzicht gegeven in opgetreden ontwikkelingen in de laatste decennia, en wordt een vergelijk gemaakt met de nationale ontwikkeling.
    Boomkwekerij: Barometer Duurzame landbouw Noord-Brabant
    Venema, G.S. ; Dolman, M.A. ; Smit, A.B. ; Jukema, G.D. ; Wisman, J.H. ; Jager, J.H. - \ 2019
    Wageningen Economic Research - 24 p.
    De factsheet Boomkwekerij maakt onderdeel uit van de Barometer Duurzame landbouw Noord-Brabant. In opdracht van de provincie Noord-Brabant wordt op basis van feiten over een breed terrein een zo actueel mogelijk beeld gegeven van de primaire agrarische sectoren. Ook wordt inzicht gegeven in opgetreden ontwikkelingen in de laatste decennia, en wordt een vergelijk gemaakt met de nationale ontwikkeling.
    Innovatieproject Hondsbossche Duinen : Eindrapportage, definitief 01
    Bodde, Willem ; Huiskes, H.P.J. ; IJff, S. ; Kramer, H. ; Kuiters, A.T. ; Lagendijk, Georgette ; Leenders, Jakolien ; Ouwerkerk, S.J. ; Scholl, M.M. ; Smit, Marije ; Smits, N.A.C. ; Stuurman, Roelof ; Valk, Bert van der; Verheijen, Anne ; Vries, Daisy de; Wegman, Carolien - \ 2019
    Ecoshape (Wageningen Marine Research Rapport C002/19) - 145 p.
    Effect of Feeding Zero- or High-Tannin Faba Bean Cultivars and Dehulling on Growth Performance, Carcass Traits and Yield of Saleable Cuts of Broiler Chickens
    Cho, M. ; Smit, M.N. ; He, L. ; Kopmels, F.C. ; Beltranena, E. - \ 2019
    Journal of Applied Poultry Research 28 (2019)4. - ISSN 1056-6171 - p. 1305 - 1323.
    broiler chicken - carcass trait - convicine - dehulling - faba bean cultivars - growth performance - vicine

    Color-flowered, high-tannin faba bean (FB; Vicia faba) cultivars are more tolerant to frost around harvest time than white-flowered, zero-tannin cultivars. Tannins concentrated on the seed hull reduce both starch and protein digestibility. We therefore evaluated feeding 2 zero-tannin (Snowbird, Snowdrop) or 2 high-tannin (Fabelle, Malik) FB cultivars and the effect of dehulling to reduce tannin content on broiler growth performance, carcass traits, and yield of saleable cuts. Male Ross 708 chicks (n = 585) were fed 1 of 4 FB cultivars either non-dehulled or dehulled in starter (12%, 0–12 d), grower (24%, 13–25 d), and finisher (36%, 26–41 d) mash diets replacing soybean meal (SBM) and wheat grain (control diet). Overall, daily feed intake was greatest for Snowbird and Fabelle, and lowest for Malik; Snowdrop was intermediate. Daily weight gain was greater for Fabelle than other cultivars, and greater for control than FB cultivars. Gain-to-feed ratio (G:F) was greatest for Fabelle but lowest for Snowbird; Snowdrop was not different from Fabelle or Malik, and Malik was not different from Snowbird. Broiler G:F and chilled carcass weight were greater for controls than FB cultivars. Breast meat yield (BMY) was greater for Snowbird, and lower for Fabelle; Malik was not different from Snowbird or Snowdrop; Snowdrop was not different from Fabelle. Dehulling FB lowered BMY. Feeding broilers low-vicine/convicine high-tannin Fabelle resulted in slightly better growth performance but lower BMY than feeding zero-tannin cultivars or high-tannin Malik. Dehulling FB did not improve broiler growth performance or carcass dressing to the level of controls fed SBM-wheat only.

    The new tanning solutions come from sugar beet pulps
    Broek, Ben van den - \ 2019
    Beter Bodembeheer Magazine : Kennis en inspiratie voor beter bodembeheer in de landbouw
    Smit, Elsbeth ; Nienhuis, Ciska - \ 2019
    Wageningen : Beter Bodembeheer - 8 p.
    In Groesbeek groeit de vegaburger van morgen
    Goot, Atze Jan van der - \ 2019
    Changes in the waterbird community of the Parc National du Banc d’Arguin, Mauritania, 1980–2017
    Oudman, Thomas ; Schekkerman, Hans ; Kidee, Amadou ; Roomen, Marc Van; Camara, Mohamed ; Smit, Cor ; Horn, Job Ten; Piersma, Theunis ; El-Hacen, El-Hacen Mohamed - \ 2019
    Bird Conservation International (2019). - ISSN 0959-2709 - p. 1 - 16.
    banc-darguin - bird census - global change - east atlantic flyways - NMDS - population decline - shorebirds - waterbird community
    The Parc National du Banc d’Arguin in Mauritania hosts the largest concentrations of coastal waterbirds along the East Atlantic Flyway. In spite of this importance, a review of the changes in the numbers of waterbirds in the area is lacking since the first complete count in 1980. Here we analysed the seven complete waterbird counts made since then, and the additional yearly counts made in one subunit (Iwik region) since 2003.We present evidence for changes in the community composition of waterbirds over the past four decades. Total waterbird numbers showed a decrease between 1980 and 2017, with only Great White Pelican Pelecanus onocrotalus showing a significant
    increase in numbers. Five species showed significant declines: Long-tailed Cormorant Phalacrocorax africanus, Red Knot Calidris canutus, Bar-tailed Godwit Limosa lapponica, Eurasian Curlew Numenius arquata, and Western Marsh Harrier Circus aeruginosus. In the remaining species, the variation in numbers between counts was too large, and the number of complete counts too small, for trends to be detected. The yearly counts at Iwik region also showed sharp decreases in the numbers of Red Knot, Bar-tailed Godwit, and Marsh Harrier, but not of Long-tailed Cormorant and Eurasian Curlew. A multivariate analysis revealed a significant effect of year on species composition, which was caused mainly by changes in the species depending on the intertidal mudflats for feeding (generally in decline) vs. the species depending on fish and crustaceans in the sublittoral and offshore zones (often showing increases).
    Derde Wereld : Speciaal nummer: Reünie van de redactie
    Arts, B.J.M. ; Boekrand, Edith ; Hees, Ted van; Hebinck, Paul ; Hoebink, Paul ; Kesteren, Johan van; Lindert, Paul van; Maasen van den Brink, Monica ; Meeuws, René ; Naerssen, Ton van; Nijpels, Maarten ; Ploeg, Jan Douwe van der; Scheffer, Rudolf ; Toor, Toon van; Velden, Fons van der; Vossen, Jan ; Wesemael-Smit, Lillian van - \ 2019
    Derde Wereld, Een eenmalige uitgave 2019 (2019). - 138 p.
    Toegankelijk toerism : Op weg naar een 'inclusieve' reisindustrie
    Duim, V.R. van der; Smit, B. ; Ormond, M.E. ; Papp, B. ; Fricke, J. ; Schmitz, Paulina ; Heiningen, Joost van - \ 2019
    Wageningen : Wageningen University and Research Center - 31 p.
    Inkomensraming land- en tuinbouw 2019 - Bert Smit licht de akkerbouw sector toe
    Smit, A.B. - \ 2019
    Wageningen : Wageningen Economic Research
    Naar een inclusieve toeristische sector
    Duim, V.R. van der; Smit, Bert ; Ormond, M.E. - \ 2019
    In: Trendrapport toerisme recreatie en vrije tjid 2019 / Vermeulen, et al, T, Elst : CELTH, CBS, PleisureWorld NRIT - ISBN 9789491625091 - p. 124 - 127.
    Balans tussen boer en natuur is centenkwestie
    Oenema, Oene - \ 2019
    GeneNoteBook, a collaborative notebook for comparative genomics
    Holmer, Rens ; Velzen, Robin van; Geurts, Rene ; Bisseling, Ton ; Ridder, Dick de; Smit, Sandra - \ 2019
    Bioinformatics 35 (2019)22. - ISSN 1367-4803 - p. 4779 - 4781.

    SUMMARY: Analysis and comparison of genomic and transcriptomic datasets have become standard procedures in biological research. However, for non-model organisms no efficient tools exist to visually work with multiple genomes and their metadata, and to annotate such data in a collaborative way. Here we present GeneNoteBook: a web based collaborative notebook for comparative genomics. GeneNoteBook allows experimental and computational researchers to query, browse, visualize and curate bioinformatic analysis results for multiple genomes. GeneNoteBook is particularly suitable for the analysis of non-model organisms, as it allows for comparing newly sequenced genomes to those of model organisms. AVAILABILITY AND IMPLEMENTATION: GeneNoteBook is implemented as a node.js web application and depends on MongoDB and NCBI BLAST. Source code is available at https://github.com/genenotebook/genenotebook. Additionally, GeneNoteBook can be installed through Bioconda and as a Docker image. Full installation instructions and online documentation are available at https://genenotebook.github.io. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

    Integrative pangenome analysis of the Pectobacterium genus
    Jonkheer, Eef ; Brankovics, Balázs ; Houwers, I.M. ; Wolf, J.M. van der; Bonants, P.J.M. ; Vreeburg, R.A.M. ; Sheikhizadeh Anari, S. ; Ridder, D. de; Smit, S. ; Lee, T.A.J. van der - \ 2019
    Protocol Energiemonitor Glastuinbouw : vernieuwde versie tot en met 2018
    Velden, N.J.A. van der; Smit, P.X. - \ 2019
    Wageningen : Wageningen Economic Research (Wageningen Economic Research nota 2019-111a) - ISBN 9789463952057 - 41
    Energiemonitor van de Nederlandse glastuinbouw 2018
    Velden, Nico van der; Smit, Pepijn - \ 2019
    Wageningen : Wageningen Economic Research (Wageningen Economic Research rapport 2019-111) - ISBN 9789463952040 - 61
    The greenhouse horticulture sector and the Dutch government have agreed on a target of 4.6 Mtonnes of total CO2 emissions in 2020. In 2018, CO2 emissions from the sector remained at the same level as the previous year (5.7 Mtonnes), which exceeded the target level. CO2 emissions were also stable over the entire 2014-2018 period. Although CO2 emissions were reduced during this period due to a smaller production area, more use of sustainable energy and more purchasing of electricity, they also rose due to more sale of electricity from CHP and increased energy consumption per m2. In 2018, the proportion of sustainable energy in total energy consumption increased to 7.3%. Geothermal heat was the most important sustainable source, with the largest growths in geothermal heat and purchase of sustainable heat. Energy efficiency also remained the same in 2018. Between 2010 and 2018, the share of natural gas in the total energy supply for the sector has decreased from 88% to 81%.
    Hecaton: Reliably detecting copy number variation in plant genomes using short read sequencing data
    Wijfjes, Raúl Y. ; Smit, Sandra ; Ridder, Dick De - \ 2019
    BMC Genomics 20 (2019)1. - ISSN 1471-2164
    Copy number variation - Machine learning - Plant adaptation - Structural variation

    Background: Copy number variation (CNV) is thought to actively contribute to adaptive evolution of plant species. While many computational algorithms are available to detect copy number variation from whole genome sequencing datasets, the typical complexity of plant data likely introduces false positive calls. Results: To enable reliable and comprehensive detection of CNV in plant genomes, we developed Hecaton, a novel computational workflow tailored to plants, that integrates calls from multiple state-of-the-art algorithms through a machine-learning approach. In this paper, we demonstrate that Hecaton outperforms current methods when applied to short read sequencing data of Arabidopsis thaliana, rice, maize, and tomato. Moreover, it correctly detects dispersed duplications, a type of CNV commonly found in plant species, in contrast to several state-of-the-art tools that erroneously represent this type of CNV as overlapping deletions and tandem duplications. Finally, Hecaton scales well in terms of memory usage and running time when applied to short read datasets of domesticated and wild tomato accessions. Conclusions: Hecaton provides a robust method to detect CNV in plants. We expect it to be of immediate interest to both applied and fundamental research on the relationship between genotype and phenotype in plants.

    Inkomenseffecten van de GLB-aanpassingen per 2020 : een quick scan
    Berkhout, Petra ; Jager, Jacob ; Smit, Bert - \ 2019
    Wageningen : Wageningen Economic Research (Wageningen Economic Research rapport 2019-114) - ISBN 9789463951944 - 41
    Minister Schouten heeft in mei 2019 vier scenario’s geschetst voor de nationale invulling van het Gemeenschappelijke Landbouwbeleid (GLB) na 2020. Kamerlid Bisschop heeft gevraagd om een vijfde scenario op te stellen, en de gevolgen van de verschillende scenario’s voor het inkomen uit bedrijf en de economische vitaliteit van landbouwbedrijven in kaart te laten brengen. Dit rapport geeft een doorrekening op hoofdlijnen van de scenario’s voor het inkomen uit bedrijf en een analyse van de gevolgen voor de economische vitaliteit van landbouwbedrijven. De laatste is mede gebaseerd op een analyse van de wijze waarop bedrijven in de huidige implementatieperiode van het GLB (2014-2020) zijn omgegaan met veranderingen in de toeslagen.
    Plantaardige ketens in beeld
    Bremmer, Johan ; Janssens, Bas ; Ruijs, Marc ; Benninga, Jan ; Stokkers, Robert ; Splinter, Gerben ; Smit, Pepijn ; Puister-Jansen, Linda ; Lakner, Dóra - \ 2019
    Wageningen : Wageningen Economic Research (Wageningen Economic Research 2019-069) - 148
    N-valerate formation from methanol based propionate chain elongation in mixed cultures
    Smit, Sanne de; Leeuw, Kasper de; Buisman, Cees ; Strik, David - \ 2019
    Wageningen University & Research
    PRJEB32281 - ERP114940
    Objective depended successes for pea-wheat strip intercropping
    Dümmer, Ruben ; Smit, Elsbeth ; Apeldoorn, D.F. van; Cuperus, Fogelina ; Sukkel, W. - \ 2019
    In: First European Conference on Crop Diversification. - INRA - p. 176 - 177.
    Development of a conceptual framework to evaluate organic fertilisers : assessment on soil quality and agronomic, environmental and economics aspects
    Schoumans, Oscar ; Ehlert, P.A.I. ; Hanegraaf, M.C. ; Römkens, P.F.A.M. ; Pustjens, A.M. ; Koeijer, T.J. de; Boer, H.C. de; Nienhuis, C. ; Kortstee, H. ; Smit, A.B. - \ 2019
    Wageningen : Wageningen Environmental Research (Wageningen Environmental Research report report 2964) - ISBN 9789463951630 - 95
    Risk of pneumonia among residents living near goat and poultry farms during 2014-2016
    Post, Pim M. ; Hogerwerf, Lenny ; Huss, Anke ; Petie, Ronald ; Boender, Gert Jan ; Baliatsas, Christos ; Lebret, Erik ; Heederik, Dick ; Hagenaars, Thomas J. ; IJzermans, Joris C. ; Smit, Lidwien A.M. - \ 2019
    PLoS ONE 14 (2019)10. - ISSN 1932-6203

    In the Netherlands, an association was found between the prevalence of pneumonia and living near goat and poultry farms in 2007-2013. This association then led to regulatory decisions to restrict the building of new goat farms and to reduce emissions of poultry farms. Confirmation of these results, however, is required because the period of previous analyses overlapped a Q-fever epidemic in 2007-2010. To confirm the association, we performed a population-based study during 2014-2016 based on general practitioner (GP) data. Electronic medical records of 90,183 persons were used to analyze the association between pneumonia and the population living in the proximity (within 500-2000 m distance) of goat and poultry farms. Data were analyzed with three types of logistic regression (with and without GP practice as a random intercept and with stratified analyses per GP practice) and a kernel model to discern the influence of different statistical methods on the outcomes. In all regression analyses involving adults, a statistically significant association between pneumonia and residence within 500 meters of goat farms was found (odds ratio [OR] range over all analyses types: 1.33-1.60), with a decreasing OR for increasing distances. In kernel analyses (including all ages), a population-attributable risk between 6.0 and 7.8% was found for a distance of 2000 meters in 2014-2016. The associations were consistent across all years and robust for mutual adjustment for proximity to other animals and for several other sensitivity analyses. However, associations with proximity to poultry farms are not supported by the present study. As the causes of the elevated pneumonia incidence in persons living close to goat farms remain unknown, further research into potential mechanisms is required for adequate prevention.

    50 years of nutrition research. What next?
    Feskens, Edith ; Kersten, Sander ; Brouwer, Inge - \ 2019
    Broeders mijden de publiciteit
    Jong, I.C. de - \ 2019
    Stikstof moet ruim gehalveerd, saneren van boeren rond kwetsbare natuur niet genoeg
    Gies, T.J.A. ; Kros, J. ; Voogd, J.C.H. - \ 2019
    Hoe arm en zielig is de boer?
    Peet, G.F.V. van der - \ 2019
    Typologie van boeren in Flevoland : Een verkenning van typen boeren die het anders willen
    Smit, A.B. ; Schoorlemmer, H.A.B. ; Balen, D.J.M. van; Janssens, S.R.M. ; Wolf, P.L. de - \ 2019
    Wageningen : Wageningen Economic Research (Wageningen Economic Research rapport 2019-106) - ISBN 9789463951395 - 25
    Agriculture in the province of Flevoland is very diverse in identity and presentation. The sector contains different ‘types’ of entrepreneurship besides different subsectors (field and vegetable farming, dairy farming, greenhouse horticulture, flower bulb growing, etc.). These types not only hold conventional, organic and biodynamic agriculture. There is also much variation within these three main stream types as to the motivation of farmers ‘to change’ and the direction in which they are moving. This report contains an inventory of such types and of the innovations that take place within those types.
    The FAIR Funder pilot programme to make it easy for funders to require and for grantees to produce FAIR Data
    Wittenburg, Peter ; Sustkova, Hana Pergl ; Montesanti, Annalisa ; Bloemers, Margreet ; Waard, S.H. de; Musen, Mark A. ; Graybeal, John ; Hettne, Kristina M. ; Jacobsen, Annika ; Pergl, Robert ; Hooft, Rob W.W. ; Staiger, Christine ; Gelder, Celia W.G. van; Knijnenburg, Sebastiaan L. ; Arkel, A.C. van; Meerman, Bert ; Wilkinson, Mark D. ; Sansone, S.A. ; Rocca-Serra, Philippe ; McQuilton, Peter ; Gonzalez-Beltran, Alejandra N. ; Aben, G.J.C. ; Henning, P. ; Menezes Alencar, Maria Simone de; Ribeiro, C. ; Silva, C.R.L. ; Sayao, Luis ; Sales, Luana ; Veiga, Viviane ; Lima, Jefferson ; Dib, Simone ; Xavier dos Santos, Paula dos; Murtinho, R. ; Tendel, Jakob ; Schaap, B.F. ; Brouwer, P.M. ; Gavai, A.K. ; Bouzembrak, Yamine ; Marvin, Hans J.P. ; Mons, Albert ; Kuhn, Tobias ; Gambardella, A.A. ; Miranda Azevedo, Ricardo de; Muhonen, Vesa ; Naald, Mira van der; Smit, N.W. ; Buys, M.J. ; Bruin, Taco F. de; Schoots, Fieke ; Goodson, H.J.E. ; Rzepa, Henry S. ; Jeffery, Keith G. ; Shanahan, Hugh P. ; Axton, M. ; Tkachenko, Veniamin ; Deslattes Maya, Anne ; Meyers, Natalie ; Conlon, Michael ; Haak, Laurel L. ; Schultes, Erik - \ 2019
    arXiv - 13 p.
    There is a growing acknowledgement in the scientific community of the importance of making experimental data machine findable, accessible, interoperable, and reusable (FAIR). Recognizing that high quality metadata are essential to make datasets FAIR, members of the GO FAIR Initiative and the Research Data Alliance (RDA) have initiated a series of workshops to encourage the creation of Metadata for Machines (M4M), enabling any self-identified stakeholder to define and promote the reuse of standardized, comprehensive machine-actionable metadata. The funders of scientific research recognize that they have an important role to play in ensuring that experimental results are FAIR, and that high quality metadata and careful planning for FAIR data stewardship are central to these goals. We describe the outcome of a recent M4M workshop that has led to a pilot programme involving two national science funders, the Health Research Board of Ireland (HRB) and the Netherlands Organisation for Health Research and Development (ZonMW). These funding organizations will explore new technologies to define at the time that a request for proposals is issued the minimal set of machine-actionable metadata that they would like investigators to use to annotate their datasets, to enable investigators to create such metadata to help make their data FAIR, and to develop data-stewardship plans that ensure that experimental data will be managed appropriately abiding by the FAIR principles. The FAIR Funders design envisions a data-management workflow having seven essential stages, where solution providers are openly invited to participate. The initial pilot programme will launch using existing computer-based tools of those who attended the M4M Workshop.
    Verkenning kennisbehoeftes van agrariërs t.a.v. natuurinclusieve landbouw en het reeds bestaande aanbod van deze kennis : waar is de match, de mismatch en hoe die te overbruggen
    Cuperus, Fogelina ; Smit, Elsbeth ; Faber, Jelle ; Casu, Flavia ; Schütt, Jeroen ; Rooij, Sabine van; Doorn, Anne van; Hondebrink, Merel ; Wagenaar, Jan Paul ; Sloot, Peter - \ 2019
    Lelystad : Stichting Wageningen Research, Wageningen Plant Research, Business unit Open Teelten (Rapport / Stichting Wageningen Research, Wageningen Plant Research, Business unit Open Teelten WPR-797) - 44
    Bodemtop snijdt hete hangijzers aan
    Brussaard, L. - \ 2019
    Verdienmodellen natuurinclusieve landbouw
    Polman, Nico ; Dijkshoorn, Marijke ; Doorneweert, Bart ; Rijk, Piet ; Vogelzang, Theo ; Reinhard, Stijn ; Smit, Bert ; Splinter, Gerben ; Heideveld, Antoine ; Geerts, Rob ; Grin, John ; Korevaar, Hein ; Setten, Bert van; Vrolijk, Maarten - \ 2019
    Wageningen : Wageningen Economic Research - 64
    Associations between antimicrobial use and the faecal resistome on broiler farms from nine European countries
    Luiken, Roosmarijn E.C. ; Gompel, Liese Van; Munk, Patrick ; Sarrazin, Steven ; Joosten, Philip ; Dorado-García, Alejandro ; Borup Hansen, Rasmus ; Knudsen, Berith E. ; Bossers, Alex ; Wagenaar, Jaap A. ; Aarestrup, Frank M. ; Dewulf, Jeroen ; Mevius, Dik J. ; Heederik, Dick J.J. ; Smit, Lidwien A.M. ; Schmitt, Heike - \ 2019
    Journal of Antimicrobial Chemotherapy 74 (2019)9. - ISSN 0305-7453 - p. 2596 - 2604.

    OBJECTIVES: To determine associations between farm- and flock-level antimicrobial usage (AMU), farm biosecurity status and the abundance of faecal antimicrobial resistance genes (ARGs) on broiler farms. METHODS: In the cross-sectional pan-European EFFORT study, conventional broiler farms were visited and faeces, AMU information and biosecurity records were collected. The resistomes of pooled faecal samples were determined by metagenomic analysis for 176 farms. A meta-analysis approach was used to relate total and class-specific ARGs (expressed as fragments per kb reference per million bacterial fragments, FPKM) to AMU (treatment incidence per DDD, TIDDDvet) per country and subsequently across all countries. In a similar way, the association between biosecurity status (Biocheck.UGent) and the resistome was explored. RESULTS: Sixty-six (38%) flocks did not report group treatments but showed a similar resistome composition and roughly similar ARG levels to antimicrobial-treated flocks. Nevertheless, we found significant positive associations between β-lactam, tetracycline, macrolide and lincosamide, trimethoprim and aminoglycoside antimicrobial flock treatments and ARG clusters conferring resistance to the same class. Similar associations were found with purchased products. In gene-level analysis for β-lactams and macrolides, lincosamides and streptogramins, a significant positive association was found with the most abundant gene clusters blaTEM and erm(B). Little evidence was found for associations with biosecurity. CONCLUSIONS: The faecal microbiome in European broilers contains a high diversity of ARGs, even in the absence of current antimicrobial selection pressure. Despite this, the relative abundance of genes and the composition of the resistome is positively related to AMU in European broiler farms for several antimicrobial classes.

    Anaerobic Degradation of Non-Methane Alkanes by "Candidatus Methanoliparia" in Hydrocarbon Seeps of the Gulf of Mexico
    Laso-Pérez, Rafael ; Hahn, Cedric ; Vliet, Daan M. van; Tegetmeyer, Halina E. ; Schubotz, Florence ; Smit, Nadine T. ; Pape, Thomas ; Sahling, Heiko ; Bohrmann, Gerhard ; Boetius, Antje ; Knittel, Katrin ; Wegener, Gunter - \ 2019
    mBio 10 (2019)4. - ISSN 2150-7511
    alkane degradation - archaea - methanogenesis - methyl-coenzyme M reductase - oil seeps

    Crude oil and gases in the seabed provide an important energy source for subsurface microorganisms. We investigated the role of archaea in the anaerobic degradation of non-methane alkanes in deep-sea oil seeps from the Gulf of Mexico. We identified microscopically the ethane and short-chain alkane oxidizers "Candidatus Argoarchaeum" and "Candidatus Syntrophoarchaeum" forming consortia with bacteria. Moreover, we found that the sediments contain large numbers of cells from the archaeal clade "Candidatus Methanoliparia," which was previously proposed to perform methanogenic alkane degradation. "Ca. Methanoliparia" occurred abundantly as single cells attached to oil droplets in sediments without apparent bacterial or archaeal partners. Metagenome-assembled genomes of "Ca. Methanoliparia" encode a complete methanogenesis pathway including a canonical methyl-coenzyme M reductase (MCR) but also a highly divergent MCR related to those of alkane-degrading archaea and pathways for the oxidation of long-chain alkyl units. Its metabolic genomic potential and its global detection in hydrocarbon reservoirs suggest that "Ca. Methanoliparia" is an important methanogenic alkane degrader in subsurface environments, producing methane by alkane disproportionation as a single organism.IMPORTANCE Oil-rich sediments from the Gulf of Mexico were found to contain diverse alkane-degrading groups of archaea. The symbiotic, consortium-forming "Candidatus Argoarchaeum" and "Candidatus Syntrophoarchaeum" are likely responsible for the degradation of ethane and short-chain alkanes, with the help of sulfate-reducing bacteria. "Ca. Methanoliparia" occurs as single cells associated with oil droplets. These archaea encode two phylogenetically different methyl-coenzyme M reductases that may allow this organism to thrive as a methanogen on a substrate of long-chain alkanes. Based on a library survey, we show that "Ca. Methanoliparia" is frequently detected in oil reservoirs and may be a key agent in the transformation of long-chain alkanes to methane. Our findings provide evidence for the important and diverse roles of archaea in alkane-rich marine habitats and support the notion of a significant functional versatility of the methyl coenzyme M reductase.

    ‘Nedersoja’ groeit gestaag, maar kan (nog lang) niet op tegen overvloed aan import uit de Amerika's
    Timmer, R.D. - \ 2019
    Gaat het mes in de ‘stikstofhouderij’? D66 wil het aantal kippen en varkens in Nederland halveren
    Hoste, Robert - \ 2019
    Effects of extreme rainfall events are independent of plant species richness in an experimental grassland community
    Padilla, Francisco M. ; Mommer, Liesje ; Caluwe, Hannie de; Smit-Tiekstra, Annemiek E. ; Visser, Eric J.W. ; Kroon, Hans de - \ 2019
    Oecologia 191 (2019)1. - ISSN 0029-8549 - p. 177 - 190.
    Biodiversity - Climate change - Drought - Overyielding - Resistance - Roots - Stability

    Global climate models predict more frequent periods of drought stress alternated by heavier, but fewer rainfall events in the future. Biodiversity studies have shown that such changed drought stress may be mitigated by plant species richness. Here, we investigate if grassland communities, differing in species richness, respond differently to climatic extremes within the growing season. In a 3-year outdoor mesocosm experiment, four grassland species in both monoculture and mixture were subjected to a rainfall distribution regime with two levels: periods of severe drought in the summer intermitted by extreme rainfall events versus regular rainfall over time. Both treatments received the same amount of water over the season. Extreme rainfall combined with drought periods resulted in a 15% decrease in aboveground biomass in the second and third year, compared to the regular rainfall regime. Root biomass was also reduced in the extreme rainfall treatment, particularly in the top soil layer (− 40%). All species developed higher water use efficiencies (less negative leaf δ13C) in extreme rainfall than in regular rainfall. These responses to the rainfall/drought treatment were independent of species richness, although the mixtures were on an average more productive in terms of biomass than the monocultures. Our experimental results suggest that mixtures are similarly able to buffer these within-season rainfall extremes than monocultures, which contrasts with findings in the studies on natural droughts. Our work demonstrates the importance of investigating the interactions between rainfall distribution and drought periods for understanding effects of climate change on plant community performance.

    Endotoxin and particulate matter emitted by livestock farms and respiratory health effects in neighboring residents
    Rooij, Myrna M.T. de; Smit, Lidwien A.M. ; Erbrink, Hans J. ; Hagenaars, Thomas J. ; Hoek, Gerard ; Ogink, Nico W.M. ; Winkel, Albert ; Heederik, Dick J.J. ; Wouters, Inge M. - \ 2019
    Environment International 132 (2019). - ISSN 0160-4120
    Air pollution - Emissions - Endotoxin - Livestock farming - Public health - Spatial modelling

    Background: Living in livestock-dense areas has been associated with health effects, suggesting airborne exposures to livestock farm emissions to be relevant for public health. Livestock farm emissions involve complex mixtures of various gases and particles. Endotoxin, a pro-inflammatory agent of microbial origin, is a constituent of livestock farm emitted particulate matter (PM) that is potentially related to the observed health effects. Quantification of livestock associated endotoxin exposure at residential addresses in relation to health outcomes has not been performed earlier. Objectives: We aimed to assess exposure-response relations for a range of respiratory endpoints and atopic sensitization in relation to livestock farm associated PM10 and endotoxin levels. Methods: Self-reported respiratory symptoms of 12,117 persons participating in a population-based cross-sectional study were analyzed. For 2494 persons, data on lung function (spirometry) and serologically assessed atopic sensitization was additionally available. Annual-average PM10 and endotoxin concentrations at home addresses were predicted by dispersion modelling and land-use regression (LUR) modelling. Exposure-response relations were analyzed with generalized additive models. Results: Health outcomes were generally more strongly associated with exposure to livestock farm emitted endotoxin compared to PM10. An inverse association was observed for dispersion modelled exposure with atopic sensitization (endotoxin: p =.004, PM10: p =.07) and asthma (endotoxin: p =.029, PM10: p =.022). Prevalence of respiratory symptoms decreased with increasing endotoxin concentration at the lower range, while at the higher range prevalence increased with increasing concentration (p <.05). Associations between lung function parameters with exposure to PM10 and endotoxin were not statistically significant (p >.05). Conclusions: Exposure to livestock farm emitted particulate matter is associated with respiratory health effects and atopic sensitization in non-farming residents. Results indicate endotoxin to be a potentially plausible etiologic agent, suggesting non-infectious aspects of microbial emissions from livestock farms to be important with respect to public health.

    Oostlandse glastuinbouw zet koers naar 2030 : Verduurzamingsrichtingen energievoorziening van de Oostlandse glastuinbouw
    Smit, Pepijn ; Velden, N.J.A. van der - \ 2019
    Wageningen : Wageningen Economic Research (Rapport / Wageningen Economic Research 2019-066) - ISBN 9789463950176 - 52
    For greenhouse horticulture in the region of Oostland far-reaching changes are foreseen in three scenarios for 2030 when looking at energy use. The scenarios consist of pessimistic, moderate and optimistic development routes of greenhouse horticulture in the Oostland region. The changes have the most impact on energy supply sources, which will rely less on natural gas and more on sustainable sources and purchase of energy from third parties, and are a result of changes in energy demand and mutations of sector structure, sustainability efforts of the greenhouse enterprises with their partners and government policy. The changes have a positive effect on the reduction of CO2 emissions and the share of renewable energy. It has emerged that energy sustainability is related to the modernisation of greenhouses, that cooperation between companies, their partners and governments is essential and that expansion of energy-networks are of great importance. The glasshouse horticulture in Oostland distinguishes itself with its own characteristics in terms of sector structure, energy demand and energy supply from national greenhouse horticulture.
    CO2-behoefte glastuinbouw 2030
    Velden, N.J.A. van der; Smit, P.X. - \ 2019
    Wageningen : Wageningen Economic Research (Wageningen Economic Research rapport 2019-074) - ISBN 9789463950091 - 43
    Greenhouse horticulture is actively working on reducing the use of fossil fuels and CO2 emission. At present greenhouse horticulture uses CO2 as a fertiliser for crops and this CO2 is mainly obtained from the smoke gasses of gas-fired CHP units and heating boilers used in this sector. A limited amount of the CO2 required is purchased externally. In the future, without CO2 emission or natural gas consumption, the sector will lose its internal supply of CO2 and a larger external CO2 supply will be needed. The projected external CO2 requirement in 2030 varies from 1.8 Mton in the pessimistic scenario to 3.0 Mton in the optimistic scenario. In the optimistic scenario there is more economic growth, a larger greenhouse acreage and a higher CO2 dosage per m2 greenhouse. The opposite is the case in the pessimistic scenario. To achieve a reduction in CO2 a tariff structure is required for CO2 supply that is based less on fixed costs and more on variable costs.
    Methanol based elongation of propionate and propionate and acetate in continuous and batch mixed culture systems
    Smit, Sanne de; Leeuw, K.D. de; Buisman, C.J.N. ; Strik, D.P.B.T.B. - \ 2019
    chain elongation - selective pressure - open-culture fermentation - mixed culture fermentation - biobased chemicals - methanol - butyrate - n-valerate
    Continuous methanol based chain elongation of propionate to n-valerate was performed in a mixed culture reactor. Additionally, the study shows simultaneous methanol based elongation of propionate and acetate to respectively n-valerate and iso/n-butyrate in a continuous mixed culture reactor. A range of mixed culture batch experiments was performed with methanol and propionate and the initial pH ranging from 5 to 7.5 (steps of 0.5)
    Kosten van zwarte braak voor aaltjesbestrijding : Saldoverliezen en bewerkingskosten van zwarte braak bij sanering van Melodogyne soorten
    Smit, A.B. ; Jager, J.H. - \ 2019
    Wageningen : Wageningen Economic Research - 2 p.
    Unraveling the regulation of plant vascular identity
    Smit, Margot Evelien - \ 2019
    Wageningen University. Promotor(en): D. Weijers. - Wageningen : Wageningen University - ISBN 9789463439572 - 206

    During plant embryogenesis, the future body plan of the plant is laid down. Part of this development is the specification of cell identities: the outer epidermis, the middle ground tissue and the inner vascular cells. In this thesis we have looked at the genetic components that control plant vascular identity. We have traced back the first vascular cells to the 16-cell embryo and discovered that the development of vascular identity is not a single step but rather a multi-step process. Upstream of this multi-step process we discovered a large set of candidate regulators that control vascular identity. After focusing one of these candidates we now hypothesize that the protein GBF2 can regulate vascular gene expression. Together with proteins that act downstream of the plant hormone auxin, GBF2 interacts with specific DNA sequences to regulate the initiation of vascular development.

    Risicomodellering veehouderij en gezondheid (RVG) : modellering van regionale endotoxineconcentraties en relaties met gezondheidseffecten
    Heederik, Dick ; Erbrink, Hans ; Farokhi, Azadeh ; Hagenaars, Thomas ; Hoek, Gerard ; Ogink, Nico ; Rooij, Myrna de; Smit, Lidwien ; Winkel, Albert ; Wouters, Inge - \ 2019
    Wageningen : Wageningen University & Research (IRAS UU 2019-01) - 133
    Continuous n-valerate formation from propionate and methanol in an anaerobic chain elongation open-culture bioreactor
    Smit, Sanne M. De; Leeuw, Kasper D. de; Buisman, Cees J.N. ; Strik, David P.B.T.B. - \ 2019
    Biotechnology for Biofuels 12 (2019)1. - ISSN 1754-6834 - 16 p.
    Biobased chemicals - Butyrate - Chain elongation - Methanol - Mixed-culture fermentation - n-Valerate - Open-culture fermentation - Selective pressure

    Background: Chain elongation forms a new platform technology for the circular production of biobased chemicals from renewable carbon and energy sources. This study aimed to develop a continuous methanol-based chain elongation process for the open-culture production of a new-generation biofuel precursor and potential platform chemical: n-valerate. Propionate was used as a substrate for chain elongation to n-valerate in an anaerobic open-culture bioreactor. In addition, the co-production of n- and iso-butyrate in addition to n-valerate via, respectively, acetate and propionate elongation was investigated. Results: n-Valerate was produced during batch and continuous experiments with a pH in the range 5.5-5.8 and a hydraulic retention time of 95 h. Decreasing the pH from 5.8 to 5.5 caused an increase of the selectivity for n-valerate formation (from 58 up to 70 wt%) during methanol-based propionate elongation. n-Valerate and both n- and iso-butyrate were produced during simultaneous methanol-based elongation of propionate and acetate. Propionate was within the open-culture preferred over acetate as a substrate with 10-30% more consumption. Increasing the methanol concentration in the influent (from 250 to 400 mM) resulted in a higher productivity (from 45 to 58 mmol C/L/day), but a lower relative product selectivity (from 49 to 43 wt%) of n-valerate. The addition of acetate as a substrate did not change the average n-valerate productivities. Within the continuous bioreactor experiments, 6 to 17 wt% of formed products was methane. The microbial community during all steady-states in both methanol-based elongation bioreactors was dominated by species related to Clostridium luticellarii and Candidatus Methanogranum. C. luticellarii is the main candidate for n-valerate formation from methanol and propionate. Conclusions: n-Valerate was for the first time proven to be produced from propionate and methanol by an open-culture bioreactor. Methanogenic activity can be inhibited by decreasing the pH, and the n-valerate productivity can be improved by increasing the methanol concentration. The developed process can be integrated with various biorefinery processes from thermochemical, (bio)electrochemical, photovoltaic and microbial technologies. The findings from this study form a useful tool to steer the process of biological production of chemicals from biomass and other carbon and energy sources.

    Nulmeting Regionale Energiemonitor Glastuinbouw Greenport West-Holland
    Velden, Nico van der; Smit, Pepijn - \ 2019
    Wageningen : Wageningen Economic Research (Wageningen Economic Research nota 2019-060) - 15
    Glastuinbouw en reductie CO2-emissie. In Nederland wordt door vele partijen gewerkt aan reductie van de CO2-emisisie, zo ook de glastuinbouw. Hiervoor wordt door het ministerie van Landbouw, Natuur en Voedselkwaliteit (LNV) en Glastuinbouw Nederland samengewerkt binnen het Programma Kas als Energiebron (KaE). De CO2-emissie kan worden gereduceerd langs twee hoofdlijnen: energiebesparing (vraagreductie) en energievoorziening zonder CO2-emissie. Dit laatste betreft de inzet van duurzame energiebronnen en de inkoop warmte en elektriciteit in combinatie met de benodigde externe CO2-voorziening. Door het bedrijfsoverstijgende karakter is de tweede hoofdlijn afhankelijk van activiteiten op regionaal niveau. Regionale organisaties zoals de Greenport West-Holland (GPWH) zijn ook actief om tot reductie van de CO2-emissie te komen. In 2017 hebben 35 partijen binnen de GPWH een energieakkoord getekend met sectordoelen voor 2030 in de GPWH-gemeenten. GPWH heeft Wageningen Economic Research gevraagd een nulmeting uit te voeren voor de GPWH-regio. Hiernaast heeft KaE gevraagd om een conceptueel raamwerk te ontwikkelen voor een Regionale Energiemonitor Glastuinbouw.Voor het raamwerk voor de Regionale Energiemonitor Glastuinbouw is voortgebouwd op de Nationale Energiemonitor Glastuinbouw die door Wageningen Economic Research jaarlijks wordt uitgevoerd voor KaE. De nulmeting voor GPWH is gemaakt op basis van dit conceptueel raamwerk (Van der Velden en Smit, 2019). Binnen GPWH zijn de deelregio’s West, Oost en Zuid in beschouwing genomen.
    Conceptueel ontwerp Regionale Energiemonitor Glastuinbouw
    Velden, Nico van der; Smit, Pepijn - \ 2019
    Wageningen : Wageningen Economic Research (Wageningen Economic Research nota 2019-061) - 19
    Phosphorus recovery from co-digested pig slurry : development of the RePeat process
    Regelink, Inge ; Ehlert, Phillip ; Smit, Geo ; Everlo, Sjoerd ; Prinsen, Arjan ; Schoumans, Oscar - \ 2019
    Wageningen : Wageningen Environmental Research (Wageningen Environmental Research report 2949) - 65
    In the Netherlands, the agricultural sector produces more manure than can be applied on agricultural land within the P application standards. The excess amount of manure should be exportedto other regions with a demand for P fertilisers. An alternative for current manure export is manure processing in which manure is processed into valuable fertiliser products. This reports describes a process in which the solid fraction of co-digested manure is processed into a concentrated P fertiliser and a nutrient-poor organic soil improver. The recovered P fertiliser can be used as a secondary raw material for fertiliser production or for export whereas the soil improver can be used on arable soils in the nearby region of the manure treatment plant. The separation process, called RePeat, consists of a acidification and dilution step to extract P from the solid fraction followed by a base addition step to recovery P. The proof of principle was given in a previous report (Schoumans et al., 2017). This reports describes additional laboratory and pilot tests (Chapter 2-4). Attention was given to the reuse of water within the process, the dewatering of calcium phosphate versus struvite and the selection of separation equipment for a demonstration plant. Chapter 5 gives the process mass balances calculated using a mass balance model. Chapter 6 assesses the quality of the organic soil improver in terms of its carbon- and nitrogen mineralisation rate. An example of a business case for the process is included in Chapter 7. The results were used to design a demonstration plant for the RePeat process to be built at Groot Zevert Vergisting B.V. in Beltrum.
    Voor succesvolle kringlooplandbouw moet de veestapel fors kleiner (maar veganisme is niet de oplossing)
    Boer, Imke de; Ittersum, Martin van - \ 2019

    Als Nederland de overgang wil maken naar een circulaire landbouw, zal de veestapel misschien wel gehalveerd moeten worden, zeggen twee Wageningse hoogleraren. Maar veganisme is ook niet de oplossing.

    Gebruik onkruidbestrijdingsmiddelen en glyfosaat in de land- en tuinbouw
    Smit, A.B. ; Jager, J.H. ; Everdingen, W.H. van; Meulen, H.A.B. van der - \ 2019
    Wageningen Economic Research (Factsheet Wageningen Economic Research 2019-015) - 7 p.
    Het ministerie van Landbouw, Natuur en Voedselveiligheid heeft aan Wageningen
    Economic Research de vraag gesteld om vanuit beschikbare gegevens verzameld
    in het Bedrijveninformatienet inzage te geven in het gebruik van
    onkruidbestrijdingsmiddelen en in het bijzonder van glyfosaat in de land- en
    tuinbouw. Aanleiding voor deze vraag is de motie Grashoff c.s. over het
    verminderen van het gebruik van glyfosaat in de landbouw (Kamerstuk 27858, nr.
    384). In deze publicatie is voor zeven gespecialiseerde bedrijfstypes vanaf 2011
    tot en met 2016 een overzicht gegeven van het totaal gebruik en het gebruik per
    ha uitgedrukt in hoeveelheid kg werkzame stof per jaar. Dit betreft zowel
    onkruidbestrijdingsmiddelen in het algemeen als glyfosaat in het bijzonder.
    The antimicrobial resistome in relation to antimicrobial use and biosecurity in pig farming, a metagenome-wide association study in nine European countries
    Gompel, Liese Van; Luiken, Roosmarijn E.C. ; Sarrazin, Steven ; Munk, Patrick ; Knudsen, Berith E. ; Hansen, Rasmus B. ; Bossers, Alex ; Aarestrup, Frank M. ; Dewulf, Jeroen ; Wagenaar, Jaap A. ; Mevius, Dik J. ; Schmitt, Heike ; Heederik, Dick J.J. ; Dorado-García, Alejandro ; Smit, Lidwien A.M. - \ 2019
    Journal of Antimicrobial Chemotherapy 74 (2019)4. - ISSN 0305-7453 - p. 865 - 876.

    OBJECTIVES: Previous studies in food-producing animals have shown associations between antimicrobial use (AMU) and resistance (AMR) in specifically isolated bacterial species. Multi-country data are scarce and only describe between-country differences. Here we investigate associations between the pig faecal mobile resistome and characteristics at the farm-level across Europe. METHODS: A cross-sectional study was conducted among 176 conventional pig farms from nine European countries. Twenty-five faecal samples from fattening pigs were pooled per farm and acquired resistomes were determined using shotgun metagenomics and the Resfinder reference database, i.e. the full collection of horizontally acquired AMR genes (ARGs). Normalized fragments resistance genes per kilobase reference per million bacterial fragments (FPKM) were calculated. Specific farm-level data (AMU, biosecurity) were collected. Random-effects meta-analyses were performed by country, relating farm-level data to relative ARG abundances (FPKM). RESULTS: Total AMU during fattening was positively associated with total ARG (total FPKM). Positive associations were particularly observed between widely used macrolides and tetracyclines, and ARGs corresponding to the respective antimicrobial classes. Significant AMU-ARG associations were not found for β-lactams and only few colistin ARGs were found, despite high use of these antimicrobial classes in younger pigs. Increased internal biosecurity was directly related to higher abundances of ARGs mainly encoding macrolide resistance. These effects of biosecurity were independent of AMU in mutually adjusted models. CONCLUSIONS: Using resistome data in association studies is unprecedented and adds accuracy and new insights to previously observed AMU-AMR associations. Major components of the pig resistome are positively and independently associated with on-farm AMU and biosecurity conditions.

    WUR-onderzoek legt belangrijkste uitdagingen bloot in bedrijfsvoering boeren en tuinders - Regelgeving zit veerkracht boer in de weg
    Meuwissen, M.P.M. ; Slijper, H.T. - \ 2019
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