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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    Wheat-derived arabinoxylans reduced M2-macrophage functional activity, but enhanced monocyte-recruitment capacity
    Govers, Coen ; Tang, Yongfu ; Stolte, Ellen H. ; Wichers, Harry J. ; Mes, Jurriaan J. - \ 2020
    Food & Function 11 (2020)8. - ISSN 2042-6496 - p. 7073 - 7083.

    The immunomodulatory properties of non-digestible polysaccharides (NDPs) have been recognized in in vitro and in vivo studies. The latter mostly demonstrated altered frequencies and inflammatory status of immune cells as clinical parameters. Most of the NDP activity will be exerted in the intestine where they can directly interact with macrophages. The predominant macrophage phenotype in the intestine is M2-like, with M1-like macrophages arising during inflammation. Here, we investigated transcriptional and functional impact on these macrophage phenotypes by NDP-treatment (i.e. yeast-derived soluble β-glucan (yeast-βG), apple-derived RG-I (apple-RGI), shiitake-derived β-glucan (shiitake-βG) or wheat-derived arabinoxylan (wheat-AX)). Wheat-AX, and to a lesser extent shiitake-βG and apple-RGI but not yeast-βG, reduced endocytosis and antigen processing capacity of M1- and M2-like macrophages. Moreover, the NDPs, and most notably wheat-AX, strongly induced transcription and secretion of a unique set of cytokines and chemokines. Conditioned medium from wheat-AX-treated M2-like macrophages subsequently demonstrated strongly increased monocyte recruitment capacity. These findings are in line with clinically observed immunomodulatory aspects of NDPs making it tempting to speculate that clinical activity of some NDPs is mediated through enhanced chemoattraction and modifying activity of intestinal immune cells.

    Compositional profiling of porcine tonsillar microbiota around weaning in relation to abundance of Streptococcus suis
    Gaiser, Rogier ; Kranenbarg-Stolte, Ellen ; Boekhorst, Jos ; Timmerman, Harro ; Kleerebezem, Michiel ; Wells, Jerry ; Baarlen, Peter van - \ 2020
    Wageningen University & Research
    16S profiling - infectious disease - microbial antagonism - microbial co-occurrence
    Some Streptococcus suis strains are associated with post-weaning disease in piglets and are emerging zoonotic pathogens of humans. The piglet microbiota may positively or negatively influence colonisation of S. suis and invasive disease risk. To identify bacterial taxa correlated with S. suis abundance, samples from the tonsil and small intestine of piglets were collected around weaning for compositional microbiota profiling.
    Immune regulation by human colonic bacteria and short-chain fatty acids
    Winaris, Nuning - \ 2020
    Wageningen University. Promotor(en): J.M. Wells, co-promotor(en): E. Kranenbarg-Stolte. - Wageningen : Wageningen University - ISBN 9789463952446 - 211

    The intestinal microbiota plays a crucial role in the homeostasis of the human gastrointestinal tract by maintaining an anti-inflammatory status. Microbial imbalance in the gut, which is often referred to as ‘dysbiosis’, is known to be one of the major contributors to many human diseases, including inflammatory bowel disease (IBD). IBD is characterized by a chronic inflammation, but the current available treatment with anti-inflammatory drugs is often not effective. Therefore, the overarching aim of this thesis was to try to find bacterial strains or bacterial metabolites that have an immunomodulatory (i.e. an anti-inflammatory) function and may therefore be used as a therapy or treatment of IBD. In collaboration with the Rowett Institute, University of Aberdeen in Scotland, UK and the Department of Medical Microbiology, at the University Medical Centre Groningen, The Netherlands, a large number of colonic anaerobic bacteria were isolated from healthy patients. In our lab, we cultured more than 100 of these different strains of bacteria under strictly anaerobic conditions. We observed their growth characteristics and investigated their immunomodulatory properties. A high ratio between secreted anti-and pro-inflammatory cytokines (IL-10/IL-12 ratio) has been reported to be an indicator of positive correlation between in vitro trials and the attenuation of clinical symptoms in in vivo mouse models of colitis. Our initial screening therefore started with stimulation of peripheral mononuclear blood lymphocytes (PBMCs) with standardized concentrations of the bacteria or their culture supernatant. We determined the cytokine secretion of these PBMC after bacterial stimulation and determined the IL-10/IL-12 ratio. Additionally we checked if the viability of the PBMC was not affected by the bacterial strains or their metabolites which were secreted in the supernatant. As IBD is characterized by periods of remission and occasional flare-ups (periods of higher inflammation), we investigated both healthy and disease situations. To achieve this, we added heat inactivated bacteria (HIB) to our PBMC culture. These HIB triggered a strong induction of both pro-and anti- inflammatory cytokines, which is reminiscent of actual inflammation. Co-stimulation with both HIB and our bacterial strains enabled us to investigate the effect of the bacterial strains ‘during inflammation’. Additionally, we checked whether the bacterial strains were able to trigger NF-κB signalling via Toll like receptor (TLR) activation, which is one of the most known mechanisms to modulate immune response of the host. Finally, to assess oxidative stress, which is known to occur during flare-ups and damages the epithelial cells, we investigated whether the different bacterial strains were able to modulate nitric oxide (NO) secretion by a mouse macrophage (RAW 264.7) cell line. Again we were able to mimic an inflammatory situation by addition of bacterial lipopolysaccharides (LPS) to these cells and could thereby also investigate the effect of bacteria in an already inflamed gut.

    In Chapter 2 we summarize the characterisation of 68 different colonic anaerobic bacteria tested. Most importantly, we found that there is a large variation among the tested strains in their immunomodulatory properties. The variation in induction of cytokine and NO secretion as well as in the ability to trigger NF-κB signalling between strains was significant. Interestingly, the bacterially induced immune profiles were highly strain dependent and not characteristic for a specific bacterial species. We must therefore conclude that generalizations cannot be made easily and any newly discovered strain needs to be individually investigated to determine its immunomodulatory properties. However, we could identify three different immune profiles, resulting from bacterial stimulation. The first ‘immunostimulatory’ profile was characterized by strongly inducing cytokine secretion in PBMCs. Most of these strains also elicited relatively high concentrations of NO secretion and strong NF-κB signalling after TLR activation. The second ‘immunomodulatory’ profile was characterized by induction of only moderate amounts of cytokine secretion. However, when an inflammatory status was mimicked (addition of HIB), these strains were able to attenuate the secretion of pro- inflammatory cytokines. The final ‘immuno suppressive’ or ‘silent’ profile was characterized by a low capacity to induce cytokine or NO secretion. More importantly, when HIB was added as an inflammatory stimulus, these strains attenuated the resulting pro-inflammatory cytokine response.

    Several studies showed that there is a negative correlation between the relative abundance of F. prausnitzii and the disease severity of IBD, therefore a causal connection has been suggested. Indeed, several in vivo studies have shown that addition of certain strains of F. prausnitzii could attenuate clincal symptoms of colitis in mice. We therefore focused on another 28 bacterial strains that all belonged to the species of F. prausnitzii in Chapter 3. After thorough in vitro investigation we have to conclude that the immunomodulatory properties are really strain specific, as the tested properties of the strains (cytokine, NO secretion and NF-κB signaling via TLR activation) do not correlate with genomic phylogenetic clusters. Among the different strains tested, we found all three different immune profiles that were observed in Chapter 2. Moreover, the general assumption that all F. prausnitzii strains induce strong IL-10 secretion was found to not be universally true, as there were some ‘silent’ strains that hardly induced any IL-10 secretion. Interestingly, one of the strains that was the strongest activator of NF-κB signaling, hardly induced any cytokine secretion, which suggest some specific mechanism to prevent downstream effects. Indeed this strain manifested a ‘silent’ profile and as such was considered to be of interest for further in vivo trials.

    During the in vitro screening procedures described above we observed that the culture supernatant of all strains tested was able to attenuate HIB induced cytokine secretion. Further investigations showed that the original growth medium (without any bacteria present), and especially the short chain fatty acids (SCFA) in the medium also triggered this attenuation effect. SCFA were reported to have immunomodulatory effects, but the studies were not  all consistent. Most studies showed that butyrate induced  IL-10  secretion  by  immune cells and thereby triggered regulatory T cell differentiation. In Chapter 4 we compared the effects of acetate and butyrate on different immune cell mechanisms. We found that butyrate decreased cell viability when administered at higher concentrations, whereas similar, or even higher concentrations of acetate did not affect cell viability. Interestingly, although both acetate and butyrate were able to attenuate HIB induced secretion of pro- inflammatory cytokines, only acetate was able to increase the anti-inflammatory cytokine IL-10. More importantly, butyrate actually decreased the secretion of the anti-inflammatory IL-10 in vitro in both PBMC as well as CD14+ monocytes. This decreased IL-10 secretion could result in an overall more inflammatory response (lower IL-10/IL-12 ratio) compared to the response triggered by acetate. To investigate how butyrate and acetate elicited their effects, we tried to determine the mechanism by which they affected cytokine secretion. As G protein-coupled receptors (GPCR) are known to mediate the effect of SCFA, we blocked the expression of GPCR in monocyte-derived dendritic cells (MDDC) with specific inhibitors. The attenuating effects of SCFA on HIB induced cytokine secretion were still observed, suggesting that modulation of cytokine secretion used an GPCR-independent mechanism. Butyrate (and to a lesser extent acetate) are also known to affect histone acetylation and could thereby modulate gene transcription. We found that butyrate indeed increased histone acetylation, which may point to a mechanism used in modulation of cytokines secretion. Interestingly, NF- κB activation was also found to be differentially modulated by acetate compared to butyrate, although the underlying mechanism has not yet been elucidated.

    As we found clear effects of both acetate and butyrate on cytokine secretion by PBMC and CD14+   monocyte, we wondered if other biological pathways would be affected as well. We therefore stimulated CD14+ monocytes with acetate and butyrate (with or without co- stimulation with HIB) and investigated the resulting transcription profile in Chapter 5. Our monocytes showed the same attenuation of pro-inflammatory cytokine secretion in HIB induced samples as was seen in the PBMC and CD14+ monocyte. Acetate did not cause major effects in the number of regulated genes, but butyrate significantly affected the regulation of many different (immune) pathways and genes therein.

    To compare the effects that SCFA might have on epithelial cells with the effects we found on immune cells, we investigated the effect of SCFA on an ex vivo 3D porcine ileum organoid model in Chapter 6. We exposed the organoid cells to acetate and butyrate and performed a transcriptomic analysis. Similar to the results of the transcriptomic analysis of CD14+ monocyte, butyrate proved to elicit greater changes in gene expression compared to acetate and substantially affected apoptosis and cell-cycle related pathways. In contrast, acetate mainly affected cellular metabolism process- related pathways, suggesting a less damaging effect on gut epithelial function compared to butyrate.

    To conclude our studies, we tested several bacterial strains that appeared promising in the in vitro trials, in an in vivo mouse DSS-induced colitis model in Chapter 7. We observed attenuation of the clinical symptoms after addition of these ‘silent’ strains, which confirm our hypothesis that the bacterial strains that induced an ‘silent’ profile would be able to reduce colonic inflammation.

    In the last chapter, Chapter 8, we summarize and discuss the combined results from this thesis in the context of other studies regarding host- microbe interactions, probiotics and the effects of SCFA. We explain how these findings contribute to a better understanding of the immunomodulatory properties of colonic anaerobic bacterial strains and their metabolites and provide suggestions for future research, and reflect on the overall aim of this thesis.

    Ecologisch onderzoek Getij Grevelingen : Onderzoek naar de historische ontwikkeling van het watersysteem en inschatting van de autonome ontwikkeling vergeleken met getijscenario’s en effecten op Natura 2000-soorten en habitats bij gedempt getij
    Tangelder, Marijn ; Ysebaert, Tom ; Wijsman, Jeroen ; Janssen, John ; Mulder, Ingeborg ; Nolte, Arno ; Stolte, Willem ; Rooijen, Nils van; Boogaart, Lisanne van den; Arts, Floor ; Hoekstein, Mark ; Sluijter, Maarten ; Jagt, Helga van der; Kaardinaal, Edwin - \ 2019
    Yerseke : Wageningen Marine Research (Wageningen Marine Research rapport C089/19) - 230
    Quantifying the dynamics of microtopography during a snowmelt event
    Barneveld, Robert J. ; Zee, Sjoerd E.A.T.M. van der; Stolte, Jannes - \ 2019
    Earth Surface Processes and Landforms 44 (2019)13. - ISSN 0197-9337 - p. 2544 - 2556.
    frost heave - microtopography - snowmelt - soil roughness - terrestrial laser scanner

    Knowledge of soil microtopography and its changes in space and over time is important to the understanding of how tillage influences infiltration, runoff generation and erosion. In this study, the use of a terrestrial laser scanner (TLS) is assessed for its ability to quantify small changes in the soil surface at high spatial resolutions for a relatively large surface area (100 m2). Changes in soil surface morphology during snow cover and melt are driven by frost heave, slaking, pressure exertion by the snowpack and overland flow (erosion and deposition). An attempt is undertaken to link these processes to observed changes at the soil surface. A new algorithm for soil surface roughness is introduced to make optimal use of the raw point cloud. This algorithm is less scale dependent than several commonly used roughness calculations. The results of this study show that TLSs can be used for multitemporal scanning of large surfaces and that small changes in surface elevation and roughness can be detected. Statistical analysis of the observed changes against terrain indices did not yield significant evidence for process differentiation.

    Lactobacillus mucosae DPC 6426 as a bile-modifying and immunomodulatory microbe
    Ryan, Paul M. ; Stolte, Ellen H. ; London, Lis E.E. ; Wells, Jerry M. ; Long, Sarah L. ; Joyce, Susan A. ; Gahan, Cormac G.M. ; Fitzgerald, Gerald F. ; Ross, R.P. ; Caplice, Noel M. ; Stanton, Catherine - \ 2019
    BMC Microbiology 19 (2019)1. - ISSN 1471-2180
    Bile acid - Bile salt hydrolase (BSH) - CVD - Exopolysaccharide - Hypercholesterolaemia

    Background: Lactobacillus mucosae DPC 6426 has previously demonstrated potentially cardio-protective properties, in the form of dyslipidaemia and hypercholesterolemia correction in an apolipoprotein-E deficient mouse model. This study aims to characterise the manner in which this microbe may modulate host bile pool composition and immune response, in the context of cardiovascular disease. Lactobacillus mucosae DPC 6426 was assessed for bile salt hydrolase activity and specificity. The microbe was compared against several other enteric strains of the same species, as well as a confirmed bile salt hydrolase-active strain, Lactobacillus reuteri APC 2587. Results: Quantitative bile salt hydrolase assays revealed that enzymatic extracts from Lactobacillus reuteri APC 2587 and Lactobacillus mucosae DPC 6426 demonstrate the greatest activity in vitro. Bile acid profiling of porcine and murine bile following incubation with Lactobacillus mucosae DPC 6426 confirmed a preference for hydrolysis of glyco-conjugated bile acids. In addition, the purified exopolysaccharide and secretome of Lactobacillus mucosae DPC 6426 were investigated for immunomodulatory capabilities using RAW264.7 macrophages. Gene expression data revealed that both fractions stimulated increases in interleukin-6 and interleukin-10 gene transcription in the murine macrophages, while the entire secretome was necessary to increase CD206 transcription. Moreover, the exopolysaccharide elicited a dose-dependent increase in nitric oxide and interleukin-10 production from RAW264.7 macrophages, concurrent with increased tumour necrosis factor-α secretion at all doses. Conclusions: This study indicates that Lactobacillus mucosae DPC 6426 modulates both bile pool composition and immune system tone in a manner which may contribute significantly to the previously identified cardio-protective phenotype.

    Prioritising areas for soil conservation measures in small agricultural catchments in Norway, using a connectivity index
    Barneveld, R.J. ; Zee, S.E.A.T.M. van der; Greipsland, I. ; Kværnø, S.H. ; Stolte, J. - \ 2019
    Geoderma 340 (2019). - ISSN 0016-7061 - p. 325 - 336.

    Measures designed to control erosion serve two purposes: on site (reduce soil loss) and off site (reduce sediment delivery to streams and lakes). While these objectives often coincide or at least are complementary, they could result in different priority areas when spatial planning is concerned. Prioritising for soil loss reduction at the field level will single out areas with high erosion risk. When sediment flux at the catchment scale is concerned, sediment pathways need to be identified in ex ante analyses of soil conservation plans. In Norway, different subsidy schemes are in place to reduce the influx of solutes and sediments to the freshwater system. Financial support is given to agronomic measures, the most important of which is reduced autumn tillage where areas with higher erosion risk receive higher subsidies. The objectives of this study are (1) to assess the use of an index of connectivity to estimate specific sediment yields, and (2) to test whether conservation measures taken in critical source areas are more effective than those taken at where erosion risk levels are the highest. Different modelling approaches are combined to assess soil loss at catchment level from sheet and gully erosion and soil losses through the drainage system. A calibration on two parameters gave reasonable results for annual soil loss. This model calibration was then used to quantify the effectiveness of three strategies for spatial prioritisation: according to hydrological connectivity, sheet erosion risk level and estimated specific sediment yield. The latter two strategies resulted in a maximum reduction in total soil loss due to reduced autumn tillage of 10%. Both model performance and the effectiveness of the different prioritisation strategies varied between the study catchments.

    Integrated, spatial distributed modelling of surface runoff and soil erosion during winter and spring
    Starkloff, Torsten ; Stolte, Jannes ; Hessel, Rudi ; Ritsema, Coen ; Jetten, Victor - \ 2018
    Catena 166 (2018). - ISSN 0341-8162 - p. 147 - 157.
    Freezing and thawing - LISEM - Modelling - Snowmelt - Soil erosion - UEBGrid
    In cold climate regions a significant fraction of annual soil erosion in agricultural land occurs during snowmelt and rain on partially frozen soils. Physically based and spatially distributed soil erosion models have proved to be good tools for understanding the processes occurring at catchment scale during rainfall erosion. However, most existing erosion models do not account for snow in a suitable way. A combination of the UEBGrid snow pack model and the LISEM erosion model was therefore used in this study. The aim was to test and validate this model combination and to assess its utility in relation to quantification and process understanding. Applying this model combination to simulate surface runoff and soil erosion showed that, in principle, it is possible to satisfactorily simulate surface runoff and observed soil erosion patterns during winter. The values for the calibration parameters were similar for the two chosen winter periods when the rainfall and snowmelt episodes occurred. However, the calibration procedure showed that the utility of this combination had several limitations. It is hoped that this study can help to improve existing models and trigger new developments in including snow pack dynamics and soil freezing and thawing in soil erosion models.
    Investigating the development of shallow snowpacks on arable land, using comprehensive field observations and spatially distributed snow modelling
    Starkloff, Torsten ; Stolte, Jannes ; Hessel, Rudi ; Ritsema, Coen - \ 2018
    Hydrology Research 49 (2018)1. - ISSN 1998-9563 - p. 41 - 59.
    Catchment scale - Snow dynamic modelling - Snow hydrology - Snow water equivalent - Spatiotemporal variability - UEBGrid
    Shallow (<1 m deep) snowpacks on agricultural areas are an important hydrological component in many countries, which determines how much meltwater is potentially available for overland flow, causing soil erosion and flooding at the end of winter. Therefore, it is important to understand the development of shallow snowpacks in a spatially distributed manner. This study combined field observations with spatially distributed snow modelling using the UEBGrid model, for three consecutive winters (2013-2015) in southern Norway. Model performance was evaluated by comparing the spatially distributed snow water equivalent (SWE) measurements over time with the simulated SWE. UEBGrid replicated SWE development at catchment scale with satisfactory accuracy for the three winters. The different calibration approaches which were necessary for winters 2013 and 2015 showed the delicacy of modelling the change in shallow snowpacks. Especially the refreezing of meltwater and prevention of runoff and infiltration of meltwater by frozen soils and ice layers can make simulations of shallow snowpacks challenging.
    Catchment hydrology during winter and spring and the link to soil erosion: A case study in Norway
    Starkloff, Torsten ; Hessel, Rudi ; Stolte, Jannes ; Ritsema, Coen - \ 2017
    Nordic Hydrology 4 (2017)1. - ISSN 0029-1277
    Infiltration - Modelling - SHAW - Snow - Soil erosion - Soil freezing

    In the Nordic countries, soil erosion rates in winter and early spring can exceed those at other times of the year. In particular, snowmelt, combined with rain and soil frost, leads to severe soil erosion, even, e.g., in low risk areas in Norway. In southern Norway, previous attempts to predict soil erosion during winter and spring have not been very accurate owing to a lack of catchment-based data, resulting in a poor understanding of hydrological processes during winter. Therefore, a field study was carried out over three consecutive winters (2013, 2014 and 2015) to gather relevant data. In parallel, the development of the snow cover, soil temperature and ice content during these three winters was simulated with the Simultaneous Heat and Water (SHAW) model for two different soils (sand, clay). The field observations carried out in winter revealed high complexity and diversity in the hydrological processes occurring in the catchment. Major soil erosion was caused by a small rain event on frozen ground before snow cover was established, while snowmelt played no significant role in terms of soil erosion in the study period. Four factors that determine the extent of runoff and erosion were of particular importance: (1) soil water content at freezing; (2) whether soil is frozen or unfrozen at a particular moment; (3) the state of the snow pack; and (4) tillage practices prior to winter. SHAW performed well in this application and proved that it is a valuable tool for investigating and simulating snow cover development, soil temperature and extent of freezing in soil profiles.

    Dietary protein sources differentially affect microbiota, mTOR activity and transcription of mTOR signaling pathways in the small intestine
    Kar, Soumya K. ; Jansman, Alfons J.M. ; Benis, Nirupama ; Ramiro-Garcia, Javier ; Schokker, Dirkjan ; Kruijt, Leo ; Stolte, Ellen H. ; Taverne-Thiele, Johanna J. ; Smits, Mari A. ; Wells, Jerry M. - \ 2017
    PLoS ONE 12 (2017)11. - ISSN 1932-6203
    Dietary protein sources can have profound effects on host-microbe interactions in the gut that are critically important for immune resilience. However more knowledge is needed to assess the impact of different protein sources on gut and animal health. Thirty-six wildtype male C57BL/6J mice of 35 d age (n = 6/group; mean ± SEM body weight 21.9 ± 0.25 g) were randomly assigned to groups fed for four weeks with semi synthetic diets prepared with one of the following protein sources containing (300 g/kg as fed basis): soybean meal (SBM), casein, partially delactosed whey powder, spray dried plasma protein, wheat gluten meal and yellow meal worm. At the end of the experiment, mice were sacrificed to collect ileal tissue to acquire gene expression data, and mammalian (mechanistic) target of rapamycin (mTOR) activity, ileal digesta to study changes in microbiota and serum to measure cytokines and chemokines. By genome-wide transcriptome analysis, we identified fourteen high level regulatory genes that are strongly affected in SBM-fed mice compared to the other experimental groups. They mostly related to the mTOR pathway. In addition, an increased (P < 0.05) concentration of granulocyte colony-stimulating factor was observed in serum of SBM-fed mice compared to other dietary groups. Moreover, by 16S rRNA sequencing, we observed that SBM-fed mice had higher (P < 0.05) abundances of Bacteroidales family S24-7, compared to the other dietary groups. We showed that measurements of genome-wide expression and microbiota composition in the mouse ileum reveal divergent responses to diets containing different protein sources, in particular for a diet based on SBM.
    Winter hydrology and soil erosion processes in an agricultural catchment in Norway
    Starkloff, Torsten - \ 2017
    Wageningen University. Promotor(en): C.J. Ritsema, co-promotor(en): J. Stolte; R. Hessel. - Wageningen : Wageningen University - ISBN 9789463432207 - 154
    catchment hydrology - erosion - winter - snow - norway - hydrologie van stroomgebieden - erosie - winter - sneeuw - noorwegen

    In regions with a Nordic climate, soil erosion rates in winter and early spring can exceed those occurring during other seasons of the year. In this context, this study was initiated to improve our understanding of the interaction between agricultural soils and occurring winter conditions. The main objective was to better understand how hydrological processes in a catchment are influenced by snow, ice, and freeze-thaw cycles of soils, leading to runoff and soil erosion in winter and spring conditions.

    For this purpose, detailed spatially and temporally distributed measurements and observations in a small catchment in Norway were executed during three consecutive winter/spring periods. During the winter/spring periods of 2013-2014, 2014-2015 and 2015-2016, soil water content, soil temperature, and snow cover properties were measured. In addition, numerous soil samples were taken to determine the soil hydraulic characteristics of the investigated soils and to quantify the changes in their macropore networks due to freeze-thaw events, using X-ray imaging.

    With the collected data and deduced process understanding, it was possible to model and quantify the spatial and temporal development of snow packs. Furthermore, the field observations revealed how the interaction of tillage, state of the soils and snow cover at a certain time can lead to none or extensive surface runoff and soil erosion.

    Integrating acquired data, observations and process knowledge facilitated advances in simulating and quantifying surface runoff and soil erosion rates across the catchment under investigation. The models applied and the maps and output derived are crucial elements for presenting current state and problems in the catchment to stakeholders (such as farmers), providing a starting point for discussing ways to prevent and reduce further runoff and erosion. For model calibration and validation, including interpretation of modelling results, good knowledge of the area and availability of detailed data are essential, especially when processes such as freezing-thawing of soils and ice layer and snow-pack dynamics have to be considered also.

    In order to reduce runoff and soil erosion during winter and snowmelt conditions in the future, more targeted research is required in order to address the full range of existing knowledge gaps in this field, as identified in this particular study also.

    Quantifying the impact of a succession of freezing-thawing cycles on the pore network of a silty clay loam and a loamy sand topsoil using X-ray tomography
    Starkloff, Torsten ; Larsbo, Mats ; Stolte, Jannes ; Hessel, Rudi ; Ritsema, Coen - \ 2017
    Catena 156 (2017). - ISSN 0341-8162 - p. 365 - 374.
    Freezing and thawing - Porosity analysis - Soil macropore structure - X-ray tomography

    In the Nordic countries, changes in pore structure during winter can affect e.g. water transport capacity in soils after winter. A reduction in pore space can cause an increase in runoff volume due to snowmelt and rain, resulting in flooding and soil erosion. This study quantified the effect of freezing-thawing cycles (FTCs) on the macropore structure of a silt and a sandy soil. Six consecutive FTCs were applied to intact soil samples, which were scanned after 0, 1, 2, 4 and 6 FTCs with an industrial X-ray scanner. Using state-of-the-art image processing and analysis techniques, changes in soil macropore network characteristics were quantified. The results showed that freezing-thawing affected the looser sandy soil more than the silt with its more cohesive structure. However, in both soils freezing-thawing had a negative effect on properties of macropore networks (e.g. reduction in macroporosity, thickness and specific surface area of macropores). These findings can help improve understanding of how undisturbed soils react to different winter conditions, which can be beneficial in the development of models for predicting flooding and soil erosion.

    Broadening the antibacterial spectrum of histidine kinase autophosphorylation inhibitors via the use of ε-poly-L-lysine capped mesoporous silica-based nanoparticles
    Velikova, Nadya ; Mas, Nuria ; Miguel-Romero, Laura ; Polo, Lorena ; Stolte, Ellen ; Zaccaria, Edoardo ; Cao, Rui ; Taverne, Nico ; Murguía, José Ramón ; Martinez-Manez, Ramon ; Marina, Alberto ; Wells, Jerry - \ 2017
    Nanomedicine: Nanotechnology, Biology, and Medicine 13 (2017)2. - ISSN 1549-9634 - p. 569 - 581.
    Drug delivery - Gram negative - Multi-drug resistance - Nanotechnology - Two-component systems
    Two-component systems (TCS) regulate diverse processes such as virulence, stress responses, metabolism and antibiotic resistance in bacteria but are absent in humans, making them promising targets for novel antibacterials. By incorporating recently described TCS histidine kinase autophosphorylation inhibitors (HKAIs) into ε-poly-L-lysine capped nanoparticles (NPs) we could overcome the Gram negative (Gr−) permeability barrier for the HKAIs. The observed bactericidal activity against Gr− bacteria was shown to be due to the enhanced delivery and internalization of the HKAIs and not an inhibitory or synergistic effect of the NPs. The NPs had no adverse effects on mammalian cell viability or the immune function of macrophages in vitro and showed no signs of toxicity to zebrafish larvae in vivo. These results show that HKAIs are promising antibacterials for both Gr− and Gr + pathogens and that NPs are a safe drug delivery technology that can enhance the selectivity and efficacy of HKAIs against bacteria.
    Soil threats in Europe: status, methods, drivers and effects on ecosystem services : deliverable 2.1 RECARE project
    Stolte, Jannes ; Tesfai, Mehreteab ; Oygarden, Lilian ; Kvaerno, Sigrun ; Keizer, Jacob ; Verheijen, Frank ; Panagos, Pano ; Ballabio, Cristiana ; Hessel, R. - \ 2016
    European Commission DG Joint Research Centre (JRC Technical reports ) - ISBN 9789279540189 - 207 p.
    Solutions for ecosystem-level protection of ocean systems under climate change
    Queirós, Ana M. ; Huebert, Klaus B. ; Keyl, Friedemann ; Fernandes, Jose A. ; Stolte, Willem ; Maar, Marie ; Kay, Susan ; Jones, Miranda C. ; Hamon, Katell G. ; Hendriksen, Gerrit ; Vermard, Youen ; Marchal, Paul ; Teal, Lorna R. ; Somerfield, Paul J. ; Austen, Melanie C. ; Barange, Manuel ; Sell, Anne F. ; Allen, Icarus ; Peck, Myron A. - \ 2016
    Global Change Biology 22 (2016)12. - ISSN 1354-1013 - p. 3927 - 3936.
    climate change - conservation - COP21 - ecosystem model - habitat - marine spatial planning - ocean - ocean acidification - species distribution - warming
    The Paris Conference of Parties (COP21) agreement renewed momentum for action against climate change, creating the space for solutions for conservation of the ocean addressing two of its largest threats: climate change and ocean
    acidification (CCOA). Recent arguments that ocean policies disregard a mature conservation research field and that protected areas cannot address climate change may be oversimplistic at this time when dynamic solutions for the
    management of changing oceans are needed. We propose a novel approach, based on spatial meta-analysis of climate impact models, to improve the positioning of marine protected areas to limit CCOA impacts. We do this by estimating the vulnerability of ocean ecosystems to CCOA in a spatially explicit manner and then co-mapping human activities such as the placement of renewable energy developments and the distribution of marine protected areas. We test this approach in the NE Atlantic considering also how CCOA impacts the base of the food web which supports protected species, an aspect often neglected in conservation studies. We found that, in this case, current regional conservation plans protect areas with low ecosystem-level vulnerability to CCOA, but disregard how species may redistribute to new, suitable and productive habitats. Under current plans, these areas remain open to commercial
    extraction and other uses. Here, and worldwide, ocean conservation strategies under CCOA must recognize the longterm importance of these habitat refuges, and studies such as this one are needed to identify them. Protecting these
    areas creates adaptive, climate-ready and ecosystem-level policy options for conservation, suitable for changing oceans.
    Operationalizing ecosystem services for the mitigation of soil threats : A proposed framework
    Schwilch, Gudrun ; Bernet, Lea ; Fleskens, Luuk ; Giannakis, Elias ; Leventon, Julia ; Marañón, Teodoro ; Mills, Jane ; Short, Chris ; Stolte, Jannes ; Delden, Hedwig Van; Verzandvoort, Simone - \ 2016
    Ecological Indicators 67 (2016). - ISSN 1470-160X - p. 568 - 597.
    Decision support - Ecosystem services - Europe - Land management - Soil functions - Soil threats

    Despite numerous research efforts over the last decades, integrating the concept of ecosystem services into land management decision-making continues to pose considerable challenges. Researchers have developed many different frameworks to operationalize the concept, but these are often specific to a certain issue and each has their own definitions and understandings of particular terms. Based on a comprehensive review of the current scientific debate, the EU FP7 project RECARE proposes an adapted framework for soil-related ecosystem services that is suited for practical application in the prevention and remediation of soil degradation across Europe. We have adapted existing frameworks by integrating components from soil science while attempting to introduce a consistent terminology that is understandable to a variety of stakeholders. RECARE aims to assess how soil threats and prevention and remediation measures affect ecosystem services. Changes in the natural capital's properties influence soil processes, which support the provision of ecosystem services. The benefits produced by these ecosystem services are explicitly or implicitly valued by individuals and society. This can influence decision- and policymaking at different scales, potentially leading to a societal response, such as improved land management. The proposed ecosystem services framework will be applied by the RECARE project in a transdisciplinary process. It will assist in singling out the most beneficial land management measures and in identifying trade-offs and win-win situations resulting from and impacted by European policies. The framework thus reflects the specific contributions soils make to ecosystem services and helps reveal changes in ecosystem services caused by soil management and policies impacting on soil. At the same time, the framework is simple and robust enough for practical application in assessing soil threats and their management with stakeholders at various levels.

    Identification of commensal species positively correlated with early stress responses to a compromised mucus barrier
    Sovran, Bruno ; Lu, Peng ; Loonen, Linda M.P. ; Hugenholtz, Floor ; Belzer, Clara ; Stolte, Ellen H. ; Boekschoten, Mark V. ; Baarlen, Peter Van; Smidt, Hauke ; Kleerebezem, Michiel ; Vos, Paul De; Renes, Ingrid B. ; Wells, Jerry M. ; Dekker, Jan - \ 2016
    Inflammatory Bowel Diseases 22 (2016)4. - ISSN 1078-0998 - p. 826 - 840.
    Bacteroidetes - colitis - Muc2 deficiency - stress markers

    Background: Our aims were (1) to correlate changes in the microbiota to intestinal gene expression before and during the development of colitis in Muc2 -/- mice and (2) to investigate whether the heterozygote Muc2 +/- mouse would reveal host markers of gut barrier stress. Methods: Colon histology, transcriptomics, and microbiota profiling of faecal samples was performed on wild type, Muc2 +/-, and Muc2 -/- mice at 2, 4, and 8 weeks of age. Results: Muc2 -/- mice develop colitis in proximal colon after weaning, resulting in inflammatory and adaptive immune responses, and expression of genes associated with human inflammatory bowel disease. Muc2 +/- mice do not develop colitis, but produce a thinner mucus layer. The transcriptome of Muc2 +/- mice revealed differential expression of genes participating in mucosal stress responses and exacerbation of a transient inflammatory state around the time of weaning. Young wild type and Muc2 +/- mice have a more constrained group of bacteria as compared with the Muc2 -/- mice, but at 8 weeks the microbiota composition is more similar in all mice. At all ages, microbiota composition discriminated the groups of mice according to their genotype. Specific bacterial clusters correlated with altered gene expression responses to stress and bacteria, before colitis development, including colitogenic members of the genus Bacteroides. Conclusions: The abundance of Bacteroides pathobionts increased before histological signs of pathology suggesting they may play a role in triggering the development of colitis. The Muc2 +/- mouse produces a thinner mucus layer and can be used to study mucus barrier stress in the absence of colitis.

    Soil surface roughness: Comparing old and new measuring methods and application in a soil erosion model
    Thomsen, L.M. ; Baartman, J.E.M. ; Barneveld, R.J. ; Starkloff, T. ; Stolte, J. - \ 2015
    SOIL 1 (2015)1. - ISSN 2199-3971 - p. 399 - 410.

    Quantification of soil roughness, i.e. the irregularities of the soil surface due to soil texture, aggregates, rock fragments and land management, is important as it affects surface storage, infiltration, overland flow, and ultimately sediment detachment and erosion. Roughness has been measured in the field using both contact methods (such as roller chain and pinboard) and sensor methods (such as stereophotogrammetry and terrestrial laser scanning (TLS)). A novel depth-sensing technique, originating in the gaming industry, has recently become available for earth sciences: the Xtion Pro method. Roughness data obtained using various methods are assumed to be similar; this assumption is tested in this study by comparing five different methods to measure roughness in the field on 1 m2 agricultural plots with different management (ploughing, harrowing, forest and direct seeding on stubble) in southern Norway. Subsequently, the values were used as input for the LISEM soil erosion model to test their effect on the simulated hydrograph at catchment scale. Results show that statistically significant differences between the methods were obtained only for the fields with direct seeding on stubble; for the other land management types the methods were in agreement. The spatial resolution of the contact methods was much lower than for the sensor methods (10 000 versus at least 57 000 points per square metre). In terms of costs and ease of use in the field, the Xtion Pro method is promising. Results from the LISEM model indicate that especially the roller chain overestimated the random roughness (RR) values and the model subsequently calculated less surface runoff than measured. In conclusion, the choice of measurement method for roughness data matters and depends on the required accuracy, resolution, mobility in the field and available budget. It is recommended to use only one method within one study.

    Development and application of a web-based geographical tool for WR&R technologies : Technologies for Water Recycling and Reuse in Latin American Context: Assessment, Decision Tools and Implementable Strategies under an Uncertain Future
    Verzandvoort, S.J.E. ; Oertlé, Emmanuel ; Gross, T. ; Breitenmoser, L. ; Engbretsen, A. ; Stolte, J. ; Gonzalez Martin, Gerardo ; Heesmans, H.I.M. ; Heidema, A.H. ; Assinck, F.B.T. ; Elsen, H.G.M. van den; Walvoort, D.J.J. ; Beek, R. van - \ 2015
    - 110 p.
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