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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    Nieuw monitoringsmeetnet kwelders Ameland-Oost : Jaarrapportage veldwerk 2019
    Puijenbroek, Marinka E.B. van; Sonneveld, Cor - \ 2020
    Den Helder : Wageningen Marine Research (Wageningen Marine Research rapport C022/20) - 26
    Dit rapport is een update van de vorige jaarrapportage (Duin et al. 2018), waaruit de meer algemene teksten deels zijn overgenomen. Op het Waddeneiland Ameland vindt sinds 1988 bodemdaling plaats als gevolg van gaswinning. Vanaf 1993 vindt er langlopende monitoring plaats naar de mogelijke effecten van de bodemdaling op Ameland-Oost. Een van de conclusies van de laatste integrale rapportage was dat de permanent kwadraten niet geheel representatief waren voor de hele kwelder, en daarom is er in 2019 een nieuw monitoringsplan opgesteld. Onderdeel zijn 80 permanente kwadraten (PQ’s) verspreidt over Neerlands Reid en de Hon waarin in 2019 de eerste vegetatieopnames zijn gemaakt en opslibbingsmetingen met de Sedimentatie-Erosiebalk uitgevoerd. Het ‘oude’ monitoringsnetwerk is voor de laatste keer volledig opgenomen in 2018, maar een aantal PQ’s zijn wel meegenomen in het nieuwe monitoringsnetwerk in 2019. Dit is het eerste jaar dat de nieuwe PQ’s gemeten zijn en opslibbingsresultaten kunnen pas berekend worden na de volgende meting in 2020. In de voorliggende rapportage wordt het nieuwe monitoringsplan geïntroduceerd. Daarnaast worden de laatste gegevens van de opslibbing van het ‘oude’ monitoringsnetwerk voor het jaar 2018 gepresenteerd en de opslibbingsresultaten van 2019 van de ‘oude’ PQ’s die in het nieuwe monitoringsnetwerk zijn opgenomen. Gebaseerd op de metingen uitgevoerd in 2019 van het oude en nieuwe meetnet kunnen we de volgende conclusies trekken: - De opslibbing in 2018 – 2019 was binnen de range van normale waarden voor een eilandkwelder en de sedimentatie volgde het normale patroon met de hoogste waarden aan de wadrand van de kwelder en op de oeverwallen. - In het nieuwe monitoringsnetwerk is op plekken waar regressie (22 PQ’s) heeft plaatsgevonden, vooral middenkwelder veranderd in lage kwelder (14 PQ’s). Er vond meer regressie van vegetatie plaats op het Neerlands Reid (18 PQ’s) dan op de Hon (4 PQ’s). - In kwelderdelen waar tussen 1993 en 2014 regressie van de vegetatie naar lage kwelder heeft plaatsgevonden is de bedekking van kale grond hoger dan in kwelderdelen waar lage kwelder al langer stabiel voorkomt. Een toename aan kale grond slibt minder snel op of erodeert en dat kan tot verdere regressie van de vegetatie leiden.
    The pentose phosphate pathway of cellulolytic clostridia relies on 6-phosphofructokinase instead of transaldolase
    Koendjbiharie, Jeroen G. ; Hon, Shuen ; Pabst, Martin ; Hooftman, Robert ; Stevenson, David M. ; Cui, Jingxuan ; Amador-Noguez, Daniel ; Lynd, Lee R. ; Olson, Daniel G. ; Kranenburg, Richard van - \ 2020
    Journal of Biological Chemistry 295 (2020)7. - ISSN 0021-9258 - p. 1867 - 1878.

    The genomes of most cellulolytic clostridia do not contain genes annotated as transaldolase. Therefore, for assimilating pentose sugars or for generating C5 precursors (such as ribose) during growth on other (non-C5) substrates, they must possess a pathway that connects pentose metabolism with the rest of metabolism. Here we provide evidence that for this connection cellulolytic clostridia rely on the sedoheptulose 1,7-bisphosphate (SBP) pathway, using pyrophosphate-dependent phosphofructokinase (PPi-PFK) instead of transaldolase. In this reversible pathway, PFK converts sedoheptulose 7-phosphate (S7P) to SBP, after which fructose-bisphosphate aldolase cleaves SBP into dihydroxyacetone phosphate and erythrose 4-phosphate. We show that PPi-PFKs of Clostridium thermosuccinogenes and Clostridium thermocellum indeed can convert S7P to SBP, and have similar affinities for S7P and the canonical substrate fructose 6-phosphate (F6P). By contrast, (ATP-dependent) PfkA of Escherichia coli, which does rely on transaldolase, had a very poor affinity for S7P. This indicates that the PPi-PFK of cellulolytic clostridia has evolved the use of S7P. We further show that C. thermosuccinogenes contains a significant SBP pool, an unusual metabolite that is elevated during growth on xylose, demonstrating its relevance for pentose assimilation. Last, we demonstrate that a second PFK of C. thermosuccinogenes that operates with ATP and GTP exhibits unusual kinetics toward F6P, as it appears to have an extremely high degree of cooperative binding, resulting in a virtual on/off switch for substrate concentrations near its K1/2 value. In summary, our results confirm the existence of an SBP pathway for pentose assimilation in cellulolytic clostridia.

    Two Quenchers Formed During Photodamage of Phostosystem II and The Role of One Quencher in Preemptive Photoprotection
    Zavafer, Alonso ; Iermak, Ievgeniia ; Cheah, Mun Hon ; Chow, Wah Soon - \ 2019
    Scientific Reports 9 (2019). - ISSN 2045-2322

    The quenching of chlorophyll fluorescence caused by photodamage of Photosystem II (qI) is a well recognized phenomenon, where the nature and physiological role of which are still debatable. Paradoxically, photodamage to the reaction centre of Photosystem II is supposed to be alleviated by excitation quenching mechanisms which manifest as fluorescence quenchers. Here we investigated the time course of PSII photodamage in vivo and in vitro and that of picosecond time-resolved chlorophyll fluorescence (quencher formation). Two long-lived fluorescence quenching processes during photodamage were observed and were formed at different speeds. The slow-developing quenching process exhibited a time course similar to that of the accumulation of photodamaged PSII, while the fast-developing process took place faster than the light-induced PSII damage. We attribute the slow process to the accumulation of photodamaged PSII and the fast process to an independent quenching mechanism that precedes PSII photodamage and that alleviates the inactivation of the PSII reaction centre.

    Use of remote sensing techniques to optimize vegetation parameters for wave damping modelling
    Slim, P.A. ; Hon, Elbert de - \ 2019
    Selenium speciation and extractability in Dutch agricultural soils
    Supriatin, Supriatin ; Weng, Liping ; Comans, Rob N.J. - \ 2015
    Science of the Total Environment 532 (2015). - ISSN 0048-9697 - p. 368 - 382.
    Agricultural soils - Organic carbon - Selenium - Soil extraction - Speciation

    The study aimed to understand selenium (Se) speciation and extractability in Dutch agricultural soils. Top soil samples were taken from 42 grassland fields and 41 arable land fields in the Netherlands. Total Se contents measured in aqua regia were between 0.12 and 1.97mgkg-1(on average 0.58mgkg-1). Organic Se after NaOCl oxidation-extraction accounted for on average 82% of total Se, whereas inorganic selenite (selenate was not measurable) measured in ammonium oxalate extraction using HPLC-ICP-MS accounted for on average 5% of total Se. The predominance of organic Se in the soils is supported by the positive correlations between total Se (aqua regia) and total soil organic matter content, and Se and organic C content in all the other extractions performed in this study. The amount of Se extracted followed the order of aqua regia>1M NaOCl (pH8)>0.1M NaOH>ammonium oxalate (pH3)>hot water>0.43M HNO3>0.01M CaCl2. None of these extractions selectively extracts only inorganic Se, and relative to other extractions 0.43M HNO3 extraction contains the lowest fraction of organic Se, followed by ammonium oxalate extraction. In the 0.1M NaOH extraction, the hydrophobic neutral (HON) fraction of soil organic matter is richer in Se than in the hydrophilic (Hy) and humic acid (HA) fractions. The organic matter extracted in 0.01M CaCl2 and hot water is in general richer in Se compared to the organic matter extracted in 0.1M NaOH, and other extractions (HNO3, ammonium oxalate, NaOCl, and aqua regia). Although the extractability of Se follows to a large extent the extractability of soil organic carbon, there is several time variations in the Se to organic C ratios, reflecting the changes in composition of organic matter extracted.

    Effect of dissolved organic matter composition on metal speciation in soil solutions
    Ren, Zong Ling ; Tella, Marie ; Bravin, M.N. ; Comans, R.N.J. ; Dai, Jun ; Garnier, Jean Marie ; Sivry, Yann ; Doelsch, Emmanuel ; Straathof, Angela ; Benedetti, M.F. - \ 2015
    Chemical Geology 398 (2015). - ISSN 0009-2541 - p. 61 - 69.
    Composition - Dissolved organic matter - Metal speciation - NICA-Donnan modeling - SC-DMT

    Knowledge of the speciation of heavy metals and the role of dissolved organic matter (DOM) in soil solution is a key to understand metal mobility and ecotoxicity. In this study, soil column-Donnan membrane technique (SC-DMT) was used to measure metal speciation of Cd, Cu, Ni, Pb, and Zn in eighteen soil solutions, covering a wide range of metal sources and concentrations. DOM in these soil solutions was also fractionated into humic acid (HA), fulvic acid (FA), hydrophilic acid (Hy), and hydrophobic neutral organic matter (HON) by a rapid batch technique using DAX-8 resin. Our results show that in soil solution Pb and Cu are dominant in complex form, whereas Cd, Ni and Zn mainly exist as free ions; for the whole range of soil solutions, only 26.2% of DOM is humic substances and consists mainly of fulvic acid (FA). The metal speciation measured by SC-DMT was compared to the predicted ones obtained via the NICA-Donnan model using the measured FA concentrations. The free ion concentrations predicted by speciation modeling were in good agreement with the SC-DMT measurement. Moreover, we show that to make accurate modeling of metal speciation in soil solutions, the knowledge of DOM composition, especially FA fraction, is the crucial information, especially for Cu and Cd; like in previous studies the modeling of Pb speciation is not optimal and an update of Pb generic binding parameters is required to reduce model prediction uncertainties.

    Input materials and processing conditions control compost dissolved organic carbon quality
    Straathof, A.L. ; Comans, R.N.J. - \ 2015
    Bioresource Technology 179 (2015). - ISSN 0960-8524 - p. 619 - 623.
    maturity - stability - parameters - fractions - matter - waste
    Dissolved organic carbon (DOC) has been proposed as an indicator of compost maturity and stability. Further fractionation of compost DOC may be useful for determining how particular composting conditions will influence DOC quality. Eleven composts ranging in input materials and processing techniques were analyzed; concentrations of DOC ranged from 428 mg kg-1 to 7300 mg kg-1. Compost DOC was qualified by fractionation into pools of humic acids (HA), fulvic acids (FA), hydrophobic neutrals (HoN), and hydrophilic (Hi) compounds. The range in proportion of DOC pools was highly variable, even for composts with similar total DOC concentrations. Longer composting time and higher temperatures consistently corresponded with a depletion of hydrophilics, suggesting a preferential turnover of these compounds during the thermophilic composting phase. Qualification of DOC pools through fractionation may be an informative tool in predicting the effects of a processing technique on compost quality and, ultimately, soil functional processes.
    Sedimentatiemodel kwelders Ameland Fase 1: ontwerp en haalbaarheid
    Groot, A.V. de; Duin, W.E. van; Brinkman, A.G. ; Vries, P. de - \ 2014
    Den Helder : IMARES (Rapport / IMARES Wageningen UR C025/14) - 47
    kweldergronden - waterstand - bodemdaling - aardgas - overstromingen - risicoschatting - fauna - watervogels - nederlandse waddeneilanden - salt marsh soils - water level - subsidence - natural gas - floods - risk assessment - fauna - waterfowl - dutch wadden islands
    Op Ameland vindt bodemdaling plaats als gevolg van gaswinning. Dit heeft consequenties voor de opslibbingsbalans en daarmee de maaiveldhoogte van de oostelijke kwelders Neerlands Reid en De Hon, vergeleken met wanneer er geen bodemdaling zou hebben plaatsgevonden. Dit kan weer gevolgen hebben voor het broedsucces van grondbroedende vogels, dat mede afhankelijk is van het overstromingsrisico. Om de impact van gaswinning op het ecosysteem te bepalen, is het dus mede van belang om inzicht te krijgen in hoe het overstromingsrisico op de kwelders op Ameland zou zijn geweest vanaf 1986 zónder de opgetreden bodemdaling. Daarvoor is het nodig de hoogteligging zonder bodemdaling te reconstrueren.
    Dynamics of soil dissolved organic carbon pools reveal both hydrophobic and hydrophilic compounds sustain microbial respiration
    Straathof, A.L. ; Chincarini, R. ; Comans, R.N.J. ; Hoffland, E. - \ 2014
    Soil Biology and Biochemistry 79 (2014). - ISSN 0038-0717 - p. 109 - 116.
    agricultural soils - humic substances - matter fractions - biodegradation - components - absorbency
    The quality of dissolved organic carbon (DOC) released from soil organic amendments may influence soil microbial activity and the quality of the soil's DOC pools. Measurements of total DOC are often considered in relation to microbial activity levels but here we propose that quantification of DOC fractions is a more informative alternative. In a laboratory incubation, soil received DOC that was extracted from three organic matter sources: fresh compost, mature compost, and a mixture of the two. Soil microbial respiration (CO2 emission), and concentrations of hydrophobic (humic acids (HA), fulvic acids (FA) and neutrals (HoN)) and hydrophilic (Hi) DOC fractions were measured throughout the 35 d incubation. The A254 specific UV absorption of total and HA DOC were measured at the start and end of the incubation as an indicator of aromaticity. Microbial respiration rates were highest in soils amended with fresh compost DOC, which had a higher proportion of Hi compounds. Concentration of Hi was significantly and positively correlated with soil respiration, explaining 24% more variation than total DOC. Humic acid concentrations significantly decreased over 35 d, including a 33% reduction in HA from an unamended control soil. Compost treated soils' HA pools increased in aromaticity, suggesting preferential mineralization of the least aromatic HA molecules. A decrease in SUVA254 values in other HA pools may be the result of HA degradation in the absence of low-aromatic HA. Our observation of depletion of hydrophobic compounds from the HA fraction provides evidence that humic substances can be a relatively reactive pool, which can provide, together with hydrophilic compounds, a readily available C source to the microbial community.
    Advies beheeringrepen Oerderduinen Oost-Ameland
    Nijssen, M. ; Arens, B. ; Groot, A.V. de; Lammerts, E.J. ; Oost, A. - \ 2014
    Driebergen : Ontwikkeling en Beheer Natuurkwaliteit (OBN) (Report Advies-OBN-05-DK) - 20
    duinplanten - vegetatietypen - natuurtechniek - landschap - kustbeheer - hoogteligging - nederlandse waddeneilanden - friesland - duneland plants - vegetation types - ecological engineering - landscape - coastal management - altitude - dutch wadden islands - friesland
    Het gebied Oerderduinen betreft een oud, gestabiliseerd duincomplex dat ten westen en ten oosten geflankeerd wordt door de kwelders van het Nieuwlandsrijd en De Hôn. Het beheer van het gebied bestaat tot dusverre grotendeels uit “niets doen”. Dat wil zeggen dat de werking van wind en water heel lang via de natuurlijke processen verstuiving, opslibbing en afslag sturend is geweest voor de vormgeving en daarmee de huidige morfologie van het gebied. De rol van deze natuurlijke processen is in de huidige situatie sterk ingeperkt door aanleg van diverse stuifdijksystemen aan de noordzeezijde, de oeververdediging langs het Nieuwlandsrijd en de gaswinning die in dit gebied tot een aanzienlijke bodemdaling (ca. 35cm.) heeft geleid.
    How global trends may provide opportunities to enhance biodiversity and ecological networks in cities
    Snep, R.P.H. ; Vries, E.A. de; Knaap, W.G.M. van der; Kuypers, V.H.M. - \ 2010
    In: Proceedings of the 2nd International Conference of Urban Biodiversity and Design (URBIO2010), Nagoya, Japan, 18 - 22 May, 2010. - Nagoya, Japan : URBIO2010 Organizing Cmmittee - p. 63 - 63.
    Changes in agricultural land use can explain population decline in a ladybeetle species in the Czech Republic : evidence from a process-based spatially explicit model
    Bianchi, F.J.J.A. ; Hon¿k, A. ; Werf, W. van der - \ 2007
    Landscape Ecology 22 (2007)10. - ISSN 0921-2973 - p. 1541 - 1554.
    coccinella-septempunctata coleoptera - metopolophium-dirhodum - linyphiid spiders - natural enemies - landscape - aphids - biodiversity - abundance - movement - dynamics
    Changes in land use affect species interactions and population dynamics by modifying the spatial template of trophic interaction and the availability of resources in time and space. We developed a process-based spatially explicit model for evaluating the effects of land use on species viability by modelling foraging performance and energy sequestration in a stage structured, three-trophic population model. The model is parameterized with realistic parameters for a ladybeetle¿aphid¿host plant interaction, and is run in four realistic landscapes in the Czech Republic. We analysed whether changes in crop selection and fertilizer input could explain the dramatic and unexplained decline in abundance of the ladybeetle Coccinella septempunctata in the Czech Republic from 1978 to 2005. The results indicate that a major reduction in fertilizer input after the transition to a market economy, resulting in lower aphid population densities in cereal crops and negatively affecting energy sequestration, survival and reproduction of ladybeetles, provides a sufficient explanation for the observed population decline. Simulations further indicated that the population viability of C. septempunctata is highly dependent on availability of aphid prey in crops, in particular cereal, which serves as their major reproduction habitat. The results demonstrate how the abundance of naturally occurring predators, which are instrumental for biological pest control, depends upon the spatial resource template that are provided at the landscape scale.
    Kweldervegetatie op Ameland: effecten van veranderingen in de maaiveldhoogte van Nieuwlandsrijd en De Hon
    Dijkema, K.S. ; Duin, W.E. van; Dobben, H.F. van - \ 2005
    In: Monitoring effecten van bodemdaling op Ameland-Oost; evaluatie na 18 jaar gaswinning [S.l.] : Begeleidingscommissie Monitoring Bodemdaling Ameland - ISBN 9789076690063 - p. Kwelders 1 - 97.
    vegetatie - kweldergronden - monitoring - bodemdaling - mijnbouw - friesland - nederlandse waddeneilanden - vegetation - salt marsh soils - monitoring - subsidence - mining - friesland - dutch wadden islands
    Alterra bijdrage studie gaswinning Ameland, namelijk deel 5 van de studie
    Resultaten kokkelvisexperiment Ameland
    Ens, B.J. ; Jong, M.L. de; Braak, C.J.F. ter - \ 2004
    Wageningen : Alterra (Alterra-rapport 945) - 144
    schaal- en schelpdierenvisserij - kokkels - milieueffect - bodemfauna - vogels - ecologie - nederland - waddenzee - natuur - nederlandse waddeneilanden - shellfish fisheries - clams - environmental impact - soil fauna - birds - ecology - netherlands - wadden sea - nature - dutch wadden islands
    Dit rapport beschrijft de resultaten van onderzoek in de jaren 1999 t/m 2003 aan de effecten van mechanische kokkelvisserij op de bodemdieren en wadvogels. Het onderzoek is van het BACI type (Before After Control Impact), maar door omstandigheden konden slechts op één locatie waarnemingen worden gedaan: het wad onder de Hon op Ameland. Op basis van een dergelijk éénmalig experiment is het niet mogelijk onweerlegbare conclusies te trekken over het effect van bevissing. De ontwikkeling van een open gebied dat in 1999 en met name in 2000 werd bevist, werd vergeleken met de ontwikkeling van een nabijgelegen gebied dat gesloten was voor de kokkelvisserij. Bevissing leidde tot een afname van de dichtheid meerjarige Kokkels, die qua omvang goed overeenkwam met de op grond van de black box gegevens voorspelde afname. Kokkels vormden in alle jaren het hoofdvoedsel van de Scholeksters in het onderzoeksgebied en de afname van de Kokkels door bevissing leidde tot een afname van de Scholeksters. Het onderzoek leverde aanwijzingen voor een afname van de dichtheid Nonnetjes en de biomassa wormen direct na bevissing. In 2001 deed zich in zowel het open als het gesloten gebied een sterke broedval van Mosselen voor. Dit had een duidelijk effect op het voorkomen van Zilvermeeuw, Bonte Strandloper, Tureluur en Groenpootruiter. Eventueel toekomstig onderzoek naar de effecten van mechanische kokkelvisserij op het ecosysteem van de Waddenzee is alleen zinvol als wordt uitgegaan van een groot aantal onderzoekslocaties, een lange termijn en een strakke experimentele opzet.
    Jan Commelin's monograph on Cape Flora : drawings and descriptions of the plants that the Hon. Simon van der Stel, Governor at the Cape of Good Hope, found on his great journey, 1685
    Wijnands, D.O. ; Wilson, M.L. ; Toussaint van Hove, T. - \ 1996
    Stellenbosch, South Africa : University of Stellenbosch Printers - ISBN 9780620205702 - 110
    flora - identificatie - plantengeografie - planten - zuid-afrika - vaatplanten - identification - phytogeography - plants - south africa - vascular plants
    De landbouw in Achtkarspelen - Zuid
    Hon, M.J. de - \ 1990
    Den Haag : L.E.I. (Mededeling / Landbouw-Economisch Instituut no. 434) - ISBN 9789052420899 - 79
    landbouw - agrarische bedrijfsvoering - melkvee - melkveehouderij - plattelandsplanning - plattelandsontwikkeling - landgebruik - bedrijfsvoering - bedrijfsresultaten in de landbouw - rentabiliteit - nederland - friesland - agriculture - farm management - dairy cattle - dairy farming - rural planning - rural development - land use - management - farm results - profitability - netherlands - friesland
    Voedingsonderzoek bij schoolkinderen in Suriname
    Lie Hon Fong, M. ; Asmoredjo-Kirchmann, M. - \ 1979
    Voeding 40 (1979). - ISSN 0042-7926 - p. 123 - 124.
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