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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    Models for assessing engineered nanomaterial fate and behaviour in the aquatic environment
    Williams, Richard J. ; Harrison, Samuel ; Keller, Virginie ; Kuenen, Jeroen ; Lofts, Stephen ; Praetorius, Antonia ; Svendsen, Claus ; Vermeulen, Lucie C. ; Wijnen, Jikke van - \ 2019
    Current Opinion in Environmental Sustainability 36 (2019). - ISSN 1877-3435 - p. 105 - 115.

    Engineered nanomaterials (ENMs, material containing particles with at least one dimension less than 100 nm) are present in a range of consumer products and could be released into the environment from these products during their production, use or end-of-life. The high surface to volume ratio of nanomaterials imparts a high reactivity, which is of interest for novel applications but may raise concern for the environment. In the absence of measurement methods, there is a need for modelling to assess likely concentrations and fate arising from current and future releases. To assess the capability that exists to do such modelling, progress in modelling ENM fate since 2011 is reviewed. ENM-specific processes represented in models are mainly limited to aggregation and, in some instances, dissolution. Transformation processes (e.g. sulphidation), the role of the manufactured coatings, particle size distribution and particle form and state are still usually excluded. Progress is also being made in modelling ENMs at larger scales. Currently, models can give a reasonable assessment of the fate of ENMs in the environment, but a full understanding will likely require fuller inclusion of these ENM-specific processes.

    Niet direct kappen en snoeien bij essentaksterfte
    Hiemstra, Jelle - \ 2017
    Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification
    Dejonghe, Wim ; Kuenen, Sabine ; Mylle, Evelien ; Vasileva, Mina ; Keech, Olivier ; Viotti, Corrado ; Swerts, Jef ; Fendrych, Matyáš ; Ortiz-Morea, Fausto Andres ; Mishev, Kiril ; Delang, Simon ; Scholl, Stefan ; Zarza, Xavier ; Heilmann, Mareike ; Kourelis, Jiorgos ; Kasprowicz, Jaroslaw ; Nguyen, Le Son Long ; Drozdzecki, Andrzej ; Houtte, Isabelle Van; Szatmári, Anna Mária ; Majda, Mateusz ; Baisa, Gary ; Bednarek, Sebastian York ; Robert, Stéphanie ; Audenaert, Dominique ; Testerink, Christa ; Munnik, Teun ; Damme, Daniël Van; Heilmann, Ingo ; Schumacher, Karin ; Winne, Johan ; Friml, Jií ; Verstreken, Patrik ; Russinova, Eugenia - \ 2016
    Nature Communications 7 (2016). - ISSN 2041-1723

    ATP production requires the establishment of an electrochemical proton gradient across the inner mitochondrial membrane. Mitochondrial uncouplers dissipate this proton gradient and disrupt numerous cellular processes, including vesicular trafficking, mainly through energy depletion. Here we show that Endosidin9 (ES9), a novel mitochondrial uncoupler, is a potent inhibitor of clathrin-mediated endocytosis (CME) in different systems and that ES9 induces inhibition of CME not because of its effect on cellular ATP, but rather due to its protonophore activity that leads to cytoplasm acidification. We show that the known tyrosine kinase inhibitor tyrphostinA23, which is routinely used to block CME, displays similar properties, thus questioning its use as a specific inhibitor of cargo recognition by the AP-2 adaptor complex via tyrosine motif-based endocytosis signals. Furthermore, we show that cytoplasm acidification dramatically affects the dynamics and recruitment of clathrin and associated adaptors, and leads to reduction of phosphatidylinositol 4,5-biphosphate from the plasma membrane.

    Wandelende maaiers en bemesters in Purmerend : 180 lammeren moeten veldkwaliteit Purmersteijn verbeteren
    Schoot, Jan Rinze van der - \ 2016
    sports grounds - grazing - lambs - sheep - sward renovation

    Al enige tijd liep fieldmanager Jan Butter ermee rond, het idee om de velden te laten begrazen door lammeren. Dit jaar werd die wens werkelijkheid. Op 3 juli werden onder toeziend oog van diverse belangstellenden 180 lammeren losgelaten op complex Purmersteijn. Daar begrazen en bepoepen de beestjes, afkomstig van een plaatselijke boer, zo’n drie weken lang de natuurgrasvelden, in de hoop dat zij de veldkwaliteit helpen verbeteren nog voordat het voetbalseizoen begint

    Xylella fastidiosa: de stand van zaken : hebben zich voor de markt belangrijke ontwikkelingen voorgedaan?
    Hiemstra, Jelle - \ 2016

    In nummer 6-2015 besteedde Boom in Business uitgebreid aandacht aan Xylella fastidiosa (Xf). Onder de kop ‘Xylella fastidiosa aan de wandel’ werd verslag gedaan over de opmars van de bacterie in Europa. Waar iedereen bang voor was, gebeurde: al snel maakte de bacterie de oversteek naar het vasteland. Hoe staat het er nu voor? Boom in Business brengt de stand van zaken in kaart.

    Can differences in soil community composition after peat meadow restoration lead to different decomposition and mineralization rates?
    Dijk, J. van; Didden, W.A.M. ; Kuenen, F. ; Bodegom, P.M. van; Verhoef, H.A. ; Aerts, R. - \ 2009
    Soil Biology and Biochemistry 41 (2009)8. - ISSN 0038-0717 - p. 1717 - 1725.
    fresh-water wetlands - scots pine forest - nitrogen mineralization - microbial communities - northern wetlands - nutrient dynamics - food webs - carbon - diversity - protozoa
    Reducing decomposition and mineralization of organic matter by increasing groundwater levels is a common approach to reduce plant nutrient availability in many peat meadow restoration projects. The soil community is the main driver of these processes, but how community composition is affected by peat meadow restoration is largely unknown. Furthermore, it is unclear whether restoration induced changes could lead to altered decomposition and mineralization rates. We determined soil community composition in restored peat meadows with different groundwater levels and soil pH. This composition was subsequently used in food web model calculations of C and N mineralization rates to assess whether differences in soil community composition may have contributed to differences in decomposition and mineralization rates observed between these meadows. Community composition of micro-organisms, Collembola and Enchytraeidae differed considerably between meadows and were correlated with differences in groundwater levels and soil pH. Collembolan and enchytraeid species from wet and neutral environments were more abundant at meadows with higher groundwater levels. Lower fungal to bacterial PLFA ratios and higher numbers of protozoa indicated an increased importance of the bacterial part of the food web at meadows with higher groundwater levels. Food web model calculations suggested that the observed changes in community composition would lead to higher rates of C and N mineralization at meadows with high groundwater levels. Results from modeling were consistent with field measurements of C mineralization, but not with measurements of N mineralization
    Competition and coexistence of sulfate-reducing bacteria, acetogens and methanogens in a lab-scale anaerobic bioreactor as affected by changing substrate to sulfate ratio
    Dar, S. ; Kleerebezem, R. ; Stams, A.J.M. ; Kuenen, J.G. ; Muyzer, G. - \ 2008
    Applied Microbiology and Biotechnology 78 (2008)6. - ISSN 0175-7598 - p. 1045 - 1055.
    16s ribosomal-rna - gradient gel-electrophoresis - oligonucleotide probes - metabolic interactions - microbial-populations - reduction - identification - communities - diversity - reducers
    The microbial population structure and function of natural anaerobic communities maintained in lab-scale continuously stirred tank reactors at different lactate to sulfate ratios and in the absence of sulfate were analyzed using an integrated approach of molecular techniques and chemical analysis. The population structure, determined by denaturing gradient gel electrophoresis and by the use of oligonucleotide probes, was linked to the functional changes in the reactors. At the influent lactate to sulfate molar ratio of 0.35 mol mol(-1), i.e., electron donor limitation, lactate oxidation was mainly carried out by incompletely oxidizing sulfate-reducing bacteria, which formed 80-85% of the total bacterial population. Desulfomicrobium- and Desulfovibrio-like species were the most abundant sulfate-reducing bacteria. Acetogens and methanogenic Archaea were mostly outcompeted, although less than 2% of an acetogenic population could still be observed at this limiting concentration of lactate. In the near absence of sulfate (i.e., at very high lactate/sulfate ratio), acetogens and methanogenic Archaea were the dominant microbial communities. Acetogenic bacteria represented by Dendrosporobacter quercicolus-like species formed more than 70% of the population, while methanogenic bacteria related to uncultured Archaea comprising about 10-15% of the microbial community. At an influent lactate to sulfate molar ratio of 2 mol mol(-1), i.e., under sulfate-limiting conditions, a different metabolic route was followed by the mixed anaerobic community. Apparently, lactate was fermented to acetate and propionate, while the majority of sulfidogenesis and methanogenesis were dependent on these fermentation products. This was consistent with the presence of significant levels (40-45% of total bacteria) of D. quercicolus-like heteroacetogens and a corresponding increase of propionate-oxidizing Desulfobulbus-like sulfate-reducing bacteria (20% of the total bacteria). Methanogenic Archaea accounted for 10% of the total microbial community
    Stress responses investigated; application of zinc and heat to Terrestrial Model Ecosystems from heavy metal polluted grassland
    Kools, S.A.E. ; Berg, M.P. ; Boivin, M.E.Y. ; Wurff, A.W.G. van der; Gestel, C.A.M. van; Straalen, N.M. van; Kuenen, F.J.A. - \ 2008
    Science of the Total Environment 406 (2008)3. - ISSN 0048-9697 - p. 462 - 468.
    potentially harmful substances - field-validation - stability - biodiversity - instrument - complexity - soils - tme
    This study tested the hypothesis that soils with a deprived biodiversity due to metal pollution are less stable than non-polluted soils, containing a more diverse community. For this, soils were sampled from specific grasslands in the Netherlands that contain elevated heavy metal concentrations (Cu, Pb and Zn). Soils that showed the largest differences in metal concentrations were incubated in the laboratory using Terrestrial Model Ecosystems (TMEs). This approach enabled simultaneous measurement of structural (bacteria, nematodes, enchytraeids, earthworms) and functional parameters (nitrogen leaching, feeding activity, CO2 production, plant growth). The highest polluted soils showed a lower bacterial growth, and decreased enchytraeid and nematode biomass and diversity, hence a deprived community. More nitrate leached from high polluted soils, while all other functional endpoints did not differ. Additional stress application of zinc and heat was used to test the stability. Zinc treatment caused effects only in the higher polluted soils, observed at several moments in time for enchytraeids, CO2 fluxes and plant growth. Heat stress caused a large reduction in enchytraeid and earthworm biomass. Ammonium leaching was decreased by heat treatments in the most polluted soils, while CO2 was increased by heat in less polluted soils. Most effects were seen in the most polluted systems and it was concluded that they seem less stable.
    Exposure and ecological effects of toxic mixtures at field-relevant concentrations : model validation and integration of the SSEO programme
    Posthuma, L. ; Vijver, M.G. ; Eijsackers, H.J.P. ; Hendrikx, A.J. ; Klok, T.C. ; Koelmans, A.A. ; Kuenen, F. ; Mulder, C. ; Rutgers, M. ; Brink, P.J. van den; Gestel, C.A.M. van; Veltman, K. ; Wijnhoven, S. - \ 2007
    Bilthoven : RIVM (RIVM report 860706002/2007) - 199
    bodemverontreiniging - veengronden - ecotoxicologie - uiterwaarden - biesbosch - soil pollution - peat soils - ecotoxicology - river forelands - biesbosch
    Effects of diffuse pollution on the environment were studied at three contaminated areas in the Netherlands: the flood plains of a large lowland river (Waal), a tidal area (Biesbosch) and a peat soil area (near Vinkeveen)
    Coexistence of physiologically similar sulfate reducing bacteria in a full-scale sulfidogenic bioreactor fed with a single organic electron donor
    Dar, S. ; Stams, A.J.M. ; Kuenen, J.G. ; Muyzer, G. - \ 2007
    Applied Microbiology and Biotechnology 75 (2007)6. - ISSN 0175-7598 - p. 1463 - 1472.
    16s ribosomal-rna - gradient gel-electrophoresis - carbinolicus sp-nov - microbial communities - waste-water - oligonucleotide probes - oxidizing bacteria - diversity - identification - reactor
    A combination of culture-dependent and independent methods was used to study the co-existence of different sulfate-reducing bacteria (SRB) in an upflow anaerobic sludge bed reactor treating sulfate-rich wastewater. The wastewater was fed with ethanol as an external electron donor. Twenty six strains of SRB were randomly picked and isolated from the highest serial dilution that showed growth (i.e. 108). Repetitive enterobacterial palindromic polymerase chain reaction and whole cell protein profiling revealed a low genetic diversity, with only two genotypes among the 26 strains obtained in the pure culture. The low genetic diversity suggests the absence of micro-niches within the reactor, which might be due to a low spatial and temporal micro-heterogeneity. The total 16S rDNA sequencing of two representative strains L3 and L7 indicated a close relatedness to the genus Desulfovibrio. The two strains differed in as many as five physiological traits, which might allow them to occupy distinct niches and thus co-exist within the same habitat. Whole cell hybridisation with fluorescently labeled oligonucleotide probes was performed to characterise the SRB community in the reactor. The isolated strains Desulfovibrio L3 and Desulfovibrio L7 were the most dominant SRB, representing 30¿35% and 25¿35%, respectively, of the total SRB community. Desulfobulbus-like bacteria contributed for 20¿25%, and the Desulfobacca acetoxidans-specific probe targeted approximately 15¿20% of the total SRB. The whole cell hybridisation results thus revealed a consortium of four different species of SRB that can be enriched and maintained on a single energy source in a full-scale sulfidogenic reactor.
    Diversity, activity, and abundance of sulfate-reducing bacteria in saline nad hypersaline soda lakes
    Foti, M. ; Sorokin, D.Y. ; Lomans, B.P. ; Mussman, M. ; Zacharova, E.E. ; Pimenov, N.V. ; Kuenen, J.G. ; Muyzer, G. - \ 2007
    Applied and Environmental Microbiology 73 (2007)7. - ISSN 0099-2240 - p. 2093 - 2100.
    sulfur-oxidizing bacteria - fresh-water sediment - 16s ribosomal-rna - sp-nov. - mono lake - gen. nov. - environment - reduction - community - microorganisms
    Soda lakes are naturally occurring highly alkaline and saline environments. Although the sulfur cycle is one of the most active element cycles in these lakes, little is known about the sulfate-reducing bacteria (SRB). In this study we investigated the diversity, activity, and abundance of SRB in sediment samples and enrichment cultures from a range of (hyper)saline soda lakes of the Kulunda Steppe in southeastern Siberia in Russia. For this purpose, a polyphasic approach was used, including denaturing gradient gel electrophoresis of dsr gene fragments, sulfate reduction rate measurements, serial dilutions, and quantitative real-time PCR (qPCR). Comparative sequence analysis revealed the presence of several novel clusters of SRB, mostly affiliated with members of the order Desulfovibrionales and family Desulfobacteraceae. We detected sulfate reducers and observed substantial sulfate reducing rates (between 12 and 423 µmol/dm3 day¿1) for most lakes, even at a salinity of 475 g/liter. Enrichments were obtained at salt saturating conditions (4 M Na+), using H2 or volatile fatty acids as electron donors, and an extremely halophilic SRB, strain ASO3-1, was isolated. Furthermore, a high dsr gene copy number of 108 cells per ml was detected in a hypersaline lake by qPCR. Our results indicate the presence of diverse and active SRB communities in these extreme ecosystems.
    Evaluation of information indices as indicators of environmental stress in terrestrial soils
    Tobor-Kaplon, M.A. ; Holtkamp, R. ; Scharler, U.M. ; Doroszuk, A. ; Kuenen, F.J.A. ; Bloem, J. ; Ruiter, P.C. de - \ 2007
    Ecological Modelling 208 (2007)1. - ISSN 0304-3800 - p. 80 - 90.
    ecological network analysis - fresh-water inflow - microbial communities - ecosystem attributes - functional stability - tolerant grass - river estuary - copper - zinc - food
    Information indices from Ecosystem Network Analysis (ENA) can be used to quantify the development of an ecosystem in terms of its size and organization. There are two types of indices, i.e. absolute indices that describe both the size and organization of ecosystem (Total System Throughput (TST)¿system size, Ascendancy (A)¿size of organized flows and Development Capacity (C)¿upper limit for A, Overhead (L)¿size of unorganized flows) and relative indices that describe only the organization (Average Mutual Information (AMI = A:TST), Flow Diversity (H = C:TST), Relative Overhead (RL = L:TST)). It is theorized that environmental stress impair the ecosystem development and that the effect of stress can be quantified with the ENA information indices. Here we applied ENA on a case of environmental stress in a terrestrial ecosystem, i.e. soils that have endured long-term exposure to elevated copper concentration and altered pH. The absolute indices showed an unexpected pattern of response to pollution, suggesting that ecosystems in polluted soils are more active and better organized than these in unpolluted soils. The relative indices, alternatively, responded to pollution as predicted by theory, i.e. with decrease of stress (pollution level) the level of specialization increased (increase of AMI) and losses of energy, e.g. due to respiration, decreased (decrease of Overhead). The diversity and evenness of flows showed hump-backed relationship with stress. Less polluted soils appeared to be less vulnerable to external disturbances and more efficient in processing energy (higher Relative Ascendancy (RA = A:C)) than polluted soils. The relative information indices were rigid to changes in values of assumed parameters. The relative indices, opposite to absolute indices, appeared to be useful as indicators of environmental stress on the ecosystem level.
    Quantifying the impact of stress on soil ecosystem development using Information Indices (Ecosystem Network Analysis)
    Tobor-Kaplon, M.A. ; Holtkamp, R. ; Scharler, U.M. ; Doroszuk, A. ; Kuenen, F.J.A. ; Bloem, J. ; Ruiter, P.C. de - \ 2006
    In: Controversies and solutions in environmental sciences; abstract book SETAC Europe 16th annual meeting. - Brussels (Belgium) : SETAC - p. 91 - 91.
    Editorial: Fast, simple, and low cost testing for drug resistance of pathogens: the way ahead
    Pas, M.F.W. te; Kuenen-Claes, J.M.H. ; Büscher, P. - \ 2005
    The Lancet 366 (2005)9484. - ISSN 0140-6736 - p. 437 - 438.
    trypanosoma-brucei - african trypanosomes
    Evaluation of ecosystem stability in metal polluted soils by stress-on-stress experiments
    Kools, S.A.E. ; Boivin, M.E.Y. ; Wurff, A.W.G. van der; Kuenen, F. ; Gestel, C.A.M. van; Straalen, N.M. van - \ 2004
    In: Netherlands Scientific Symposium Soil and water, Woudschoten, 2-3 June 2004 Woudschoten, Zeist : - p. 6 - 6.
    The biological sulfur cycle: novel opportunities for environmental biotechnology
    Lens, P.N.L. ; Kuenen, J.G. - \ 2001
    In: Anaerobic digestion for sustainable development. - Wageningen : WUR, Environmental Technology, 2001 - p. 61 - 70.
    The biological sulfur cycle: novel opportunities for environmental biotechnology
    Lens, P.N.L. ; Kuenen, J.G. - \ 2001
    Water Science and Technology 44 (2001)8. - ISSN 0273-1223 - p. 57 - 66.
    Biological treatment of spent caustics.
    Janssen, A.J.H. ; Buisman, C. ; Lettinga, G. ; Straten, G. van; Bontsema, J. ; Kuenen, J.G. ; Zwart, J.M.M. de - \ 1996
    Octrooinummer: WO9804503, gepubliceerd: 1996-07-29.
    A process for the biological treatment of a spent caustic solution containing sulphides is disclosed, wherein the solution is introduced into an aerobic reactor containing sulphide-oxidising bacteria, and the sulphides are partly converted to elemental sulphur and partly to sulphate by controlling the redox potential in the reactor at a value below -300 mV (against an Ag/AgCl reference electrode), or below -97 (against a H2 reference electrode). Also disclosed is process for the biological treatment of an aqueous solution containing sulphides and/or mercaptans in an aerobic reactor, wherein the solution is treated in the presence of bacteria of the new species Methylophaga sulfidovorans
    Heterotrophic nitrification and aerobic denitrification in Alcaligenes faecalis strain TUD.
    Niel, E.W.J. van; Braber, K.J. ; Robertson, L.A. ; Kuenen, J.G. - \ 1992
    Antonie van Leeuwenhoek: : Nederlandsch tijdschrift voor hygiëne, microbiologie en serologie 62 (1992). - ISSN 0003-6072 - p. 231 - 237.
    Role of quinoproteen glucose-dehydrogenase in gluconic acid production by Acinetobacter calcoaceticus
    Bont, J.A.M. de; Dokter, P. ; Schie, B.J. van; Dijken, J.P. van; Frank Jzn, J. ; Duine, J.A. ; Kuenen, J.G. - \ 1984
    Antonie van Leeuwenhoek: : Nederlandsch tijdschrift voor hygiëne, microbiologie en serologie 50 (1984). - ISSN 0003-6072 - p. 76 - 77.
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