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.

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Genetic mapping of tuber size distribution and marketable tuber yield under drought stress in potatoes
Aliche, Ernest B. ; Oortwijn, Marian ; Theeuwen, Tom P.J.M. ; Bachem, Christian W.B. ; Eck, Herman J. van; Visser, Richard G.F. ; Linden, Gerard van der - \ 2019
Euphytica 215 (2019)11. - ISSN 0014-2336
Association panel - Drought - Marketable tubers - Modelling - Size - Yield

Drought sensitivity of potato leads to a reduction in total tuber yield and marketable yield. An investigation of drought effects on tuber yield attributes will facilitate our understanding of how to reduce such huge yield losses. We have evaluated tuber yield, tuber size distribution and marketable yield of a set of 103 European commercial potato cultivars under irrigated and non-irrigated conditions in the field. The multi-year results from two locations, Connantre, France (2013–2015) and Nieuw-Namen in Zeeland, The Netherlands (2013–2014), were analysed. We used Normal and Gamma Distribution models to describe the tuber size distribution of tuber fresh weight and tuber number, respectively. The interactions among parameters of tuber size distribution and total/marketable tuber yield traits were analysed using correlation matrices and biplots. Finally, we used a 14K Infinium SNP marker array to find associations between the parameters or traits and genetic loci on the potato genome. Late foliage maturity facilitated a wider spread of tuber size distribution in favour of larger-sized tubers. Drought effects on total yield were representative of their impact on marketable yield, however, absolute values of total tuber number may not be indicative of marketable number of tubers. We found significant marker-trait associations between a region on chromosome 3 and the spread of tuber number distribution, size class with maximum tuber number and marketable fractions of tuber number and tuber weight. These findings will contribute to improvement and selection for drought tolerance in potato.

Assessment of spatial variability of multiple ecosystem services in grasslands of different intensities
Clec'h, Solen Le; Finger, Robert ; Buchmann, Nina ; Gosal, Arjan S. ; Hörtnagl, Lukas ; Huguenin-Elie, Olivier ; Jeanneret, Philippe ; Lüscher, Andreas ; Schneider, Manuel K. ; Huber, Robert - \ 2019
Journal of Environmental Management 251 (2019). - ISSN 0301-4797
ES provision - Land use - Management strategies - Modelling - Switzerland - Trade-offs

Grasslands provide multiple Ecosystem Services (ES) such as forage provision, carbon sequestration or habitat provision. Knowledge about the trade-offs between these ES is of great importance for grassland management. Yet, the outcome of different management strategies on ES provision is highly uncertain due to spatial variability. We aim to characterize the provision (level and spatial variability) of grassland ES under various management strategies. To do so, we combine empirical data for multiple ES with spatially explicit census data on land use intensities. We analyzed the variations of five ES (forage provision, climate regulation, pollination, biodiversity conservation and outdoor recreation) using data from biodiversity fieldwork, experimental plots for carbon as well as social network data from Flickr. These data were used to calculate the distribution of modelled individual and multiple ES values from different grassland management types in a Swiss case study region using spatial explicit information for 17,383 grassland parcels. Our results show that (1) management regime and intensity levels play an important role in ES provision but their impact depends on the ES. In general, extensive management, especially in pastures, favors all ES but forage provision, whereas intensive management favors only forage provision and outdoor recreation; (2) ES potential provision varies between parcels under the same management due to the influence of environmental drivers, related to topography and landscape structure; (3) there is a trade-offs between forage provision and other ES at the cantonal level but a synergy between forage provision and biodiversity conservation within the grassland categories, due to the negative impact of elevation on both ES. Information about multiple ES provision is key to support effective agri-environmental measures and information about the spatial variability can prevent uncertain outputs of decision-making processes.

In situ removal of four organic micropollutants in a small river determined by monitoring and modelling
Brunsch, Andrea F. ; Langenhoff, Alette A.M. ; Rijnaarts, Huub H.M. ; Ahring, Alexander ; Laak, Thomas L. ter - \ 2019
Environmental Pollution 252 (2019). - ISSN 0269-7491 - p. 758 - 766.
Micropollutants - Modelling - Monitoring - Photodegradation - Surface water

Organic micropollutants (OMPs) are widely detected in surface waters. So far, the removal processes of these compounds in situ in river systems are not yet totally revealed. In this study, a combined monitoring and modelling approach was applied to determine the behaviour of 1-H benzotriazole, carbamazepine, diclofenac and galaxolide in a small river system. Sewage treatment plant effluents and the receiving waters of the river Swist were monitored in 9 dry weather sampling campaigns (precipitation < 1 mm on the sampling day itself and <5 mm total precipitation two days before the sampling) during different seasons over a period of 3 years. With the results gained through monitoring, mass balances have been calculated to assess fate in the river. With the DWA Water Quality Model, OMP concentrations in the river were successfully simulated with OMP characteristics gained through literature studies. No removal was determined for 1-H benzotriazole and carbamazepine, whereas diclofenac showed removal that coincided with light intensity. Moreover, modelling based on light sensitivity of diclofenac also suggested relevant degradation at natural light conditions. These two approaches suggest removal by photodegradation. The highest removal in the river was detected for galaxolide, presumably due to volatilisation, sorption and biodegradation. Furthermore, short-term concentration variability in the river was determined, showing that daily concentration patterns are influenced by dynamics of sewage treatment plant effluent volumes and removal processes in the river.

Oligosaccharides fractionation cascades with 3 outlet streams
Rizki, Zulhaj ; Janssen, Anja E.M. ; Boom, Remko M. ; Padt, Albert van der - \ 2019
Separation and Purification Technology 221 (2019). - ISSN 1383-5866 - p. 183 - 194.
Membrane cascades - Modelling - Nanofiltration - Oligosaccharides

Fructooligosaccharides (FOS) were fractionated using nanofiltration cascades. Instead of creating one product and a residual stream, we report on configurations that create 3 separate product streams rich in: (1) monosaccharides (DP1), (2) DP3 and (3) DP ≥ 5. We developed a modular system allowing different operating pressures and membrane types at each stage. Two possible alternative configurations were assessed for a 3-stage cascade both experimentally and via simulation. The simulation was performed using a steady state model and was in a good agreement with the experimental data. Using the simulation model, the system was optimized towards 4 and 5 stage cascades. All designs were evaluated based on the purities and yields of 3 components of interest in the corresponding product streams. Selecting the correct set up, the cascade was able to reach maximum purity of monosaccharides to 66 wt% (from 9 wt%), DP3 to 33 wt% (from 24 wt%) and DP ≥ 5 to 54 wt% (from 34 wt%). Increasing the number of stages improved the maximum purities of the 3 fractions. However, a fifth stage did not increase the purification and the best purities were found using 4-stage rather than 5-stage cascades.

Diversity of opisthokont septin proteins reveals structural constraints and conserved motifs 06 Biological Sciences 0604 Genetics
Auxier, Benjamin ; Dee, Jaclyn ; Berbee, Mary L. ; Momany, Michelle - \ 2019
BMC Evolutionary Biology 19 (2019)1. - ISSN 1471-2148
Ancestral state reconstruction - Evolution - Gene tree-species tree reconciliation - Modelling - Opisthokont - Protein-protein interaction - Septin - Subunit

Background: Septins are cytoskeletal proteins important in cell division and in establishing and maintaining cell polarity. Although septins are found in various eukaryotes, septin genes had the richest history of duplication and diversification in the animals, fungi and protists that comprise opisthokonts. Opisthokont septin paralogs encode modular proteins that assemble into heteropolymeric higher order structures. The heteropolymers can create physical barriers to diffusion or serve as scaffolds organizing other morphogenetic proteins. How the paralogous septin modules interact to form heteropolymers is still unclear. Through comparative analyses, we hoped to clarify the evolutionary origin of septin diversity and to suggest which amino acid residues were responsible for subunit binding specificity. Results: Here we take advantage of newly sequenced genomes to reconcile septin gene trees with a species phylogeny from 22 animals, fungi and protists. Our phylogenetic analysis divided 120 septins representing the 22 taxa into seven clades (Groups) of paralogs. Suggesting that septin genes duplicated early in opisthokont evolution, animal and fungal lineages share septin Groups 1A, 4 and possibly also 1B and 2. Group 5 septins were present in fungi but not in animals and whether they were present in the opisthokont ancestor was unclear. Protein homology folding showed that previously identified conserved septin motifs were all located near interface regions between the adjacent septin monomers. We found specific interface residues associated with each septin Group that are candidates for providing subunit binding specificity. Conclusions: This work reveals that duplication of septin genes began in an ancestral opisthokont more than a billion years ago and continued through the diversification of animals and fungi. Evidence for evolutionary conservation of ~ 49 interface residues will inform mutagenesis experiments and lead to improved understanding of the rules guiding septin heteropolymer formation and from there, to improved understanding of development of form in animals and fungi.

Heat resistance of spores of 18 strains of Geobacillus stearothermophilus and impact of culturing conditions
Wells-Bennik, Marjon H.J. ; Janssen, Patrick W.M. ; Klaus, Verena ; Yang, Chi ; Zwietering, Marcel H. ; Besten, Heidy M.W. Den - \ 2019
International Journal of Food Microbiology 291 (2019). - ISSN 0168-1605 - p. 161 - 172.
Enumeration - Germination - Inactivation - Modelling - Sporulation - Variability

In this study, different methods were evaluated for enumeration of spores of G. stearothermophilus, different sporulation methods were assessed for yields and wet heat resistances of obtained spores, and subsequently, the variation in heat resistances of spores was determined. Overall, tryptone soya agar (TSA) was the most suitable medium for enumeration of spores of this thermophilic bacterium. Sporulation on different media both at 55 and at 61 °C led to considerable variation in spore heat resistance. The heat resistance of spores was highest upon sporulation on medium supplemented with free ions of calcium, potassium, magnesium and manganese (CaKMgMn). For 18 different G. stearothermophilus strains that were isolated from various sources, spores were subsequently produced on nutrient agar supplemented with CaKMgMn at 55 °C. Strain ATCC 12980T, also known as 9A20, which is commonly used in steam sterilization tests was included. The survival of spores of all strains was assessed at 125 °C and 130 °C using two independent spore batches per strain. The mean D125°C for spores of the 18 strains was 1.1 min (95% PI 0.48–2.3 min) and the mean D130°C was 0.37 min (95% PI 0.17–0.82 min). For spore inactivation of these 18 strains, a z-value of 11.1 °C was estimated, resulting in an estimated D-value of 2.4 min (95% PI 1.1–5.2) at the reference temperature 121.1 °C. Based on the data sets obtained in this study, it was found that the variability in spore heat resistance could largely be attributed to strain variability and conditions used during sporulation (especially the sporulation medium); reproduction and experimental variabilities were much smaller. The established variabilities were compared with the overall variability in spore heat resistance of G. stearothermophilus based on a meta-analysis of reported D-values. The data presented indicate that strain variability and history of sporulation each account for approximately half of the overall variability observed with respect to the heat resistance of spores of G. stearothermophilus. The findings presented in this study allow for optimal recovery of G. stearothermophilus spores from foods and a better understanding of factors that determine the heat resistance properties of spores of G. stearothermophilus. Moreover, this study once more underlines the limited effects of heat treatments used in the food industry on inactivation of spores of this bacterium.

An accurate evaluation of water availability in sub-arid Mediterranean watersheds through SWAT : Cega-Eresma-Adaja
Rivas-Tabares, David ; Tarquis, Ana M. ; Willaarts, Bárbara ; Miguel, Ángel De - \ 2019
Agricultural Water Management 212 (2019). - ISSN 0378-3774 - p. 211 - 225.
Land use - Modelling - Semi-arid regions - Streamflow - SWAT

Simulation of flow processes in hyper-regulated Mediterranean watersheds is critical when examining general water demand and established ecological flows of River Basin Management Plans. Weather dynamics in the Mediterranean zone in recent decades have been characterised by a natural variation of drought cycles. In addition, exacerbated climate change proves that water fluxes must be estimated with more exhaustive models. The aim of this study is to assess the water balance of the Cega-Eresma-Adaja (CEA) watershed, including a detailed assessment of land uses and management practices to quantify agricultural water demand for the time period 2004–2014. We used the Soil and Water Assessment Tool (SWAT), given that it is a widespread tool that involves complex processes of the water cycle on a basin scale, providing information on water dynamics related to land use as a fundamental characteristic for water balance calculation. The Nash-Sutcliffe coefficient efficiency value, the main index of calibration and validation performance, was 0.86 for the Eresma-Adaja River and 0.67 for the Cega River. This presents a good result considering the large-scale watershed studied. Analysing dry hydrological years, we found that the estimation of ecological flows for sub-arid zones needs to consider the shallow aquifer-river relationship. During spring-summer periods, with very low flow, monitoring the shallow aquifer levels ensures a good ecological status. The study reveals that aspects such as crop rotation, soil management and their associated measures in Mediterranean basins are key factors for water resource management during drought periods. These results are expected to serve stakeholders and river basin authorities in conducting better-integrated water management practices in the watershed.

Differences between low-end and high-end climate change impacts in Europe across multiple sectors
Harrison, Paula A. ; Dunford, Rob W. ; Holman, Ian P. ; Cojocaru, George ; Madsen, Marianne S. ; Chen, Pei Yuan ; Pedde, Simona ; Sandars, Daniel - \ 2019
Regional Environmental Change 19 (2019)3. - ISSN 1436-3798 - p. 695 - 709.
Cross-sectoral - High-end scenarios - Impacts - Modelling - Paris agreement

The Paris Agreement established the 1.5 and 2 °C targets based on the recognition “that this would significantly reduce the risks and impacts of climate change”. We tested this assertion by comparing impacts at the regional scale between low-end (< 2 °C; RCP2.6) and high-end (> 4 °C; RCP8.5) climate change scenarios accounting for interactions across six sectors (agriculture, forestry, biodiversity, water, coasts and urban) using an integrated assessment model. Results show that there are only minor differences in most impact indicators for the 2020s time slice, but impacts are considerably greater under high-end than low-end climate change in the 2050s and 2080s. For example, for the 2080s, mitigation consistent with the Paris Agreement would reduce aggregate Europe-wide impacts on the area of intensive agriculture by 21% (on average across climate models), on the area of managed forests by 34%, on water stress by 14%, on people flooded by 10% and on biodiversity vulnerability by 16%. Including socio-economic scenarios (SSPs 1, 3, 4, 5) results in considerably greater variation in the magnitude, range and direction of change of the majority of impact indicators than climate change alone. In particular, socio-economic factors much more strongly drive changes in land use and food production than changes in climate, sometimes overriding the differences due to low-end and high-end climate change. Such impacts pose significant challenges for adaptation and highlight the importance of searching for synergies between adaptation and mitigation and linking them to sustainable development goals.

Simulating long-term effects of bioenergy extraction on dead wood availability at a landscape scale in Sweden
Hof, Anouschka R. ; Löfroth, Therese ; Rudolphi, Jörgen ; Work, Timothy ; Hjältén, Joakim - \ 2018
Forests 9 (2018)8. - ISSN 1999-4907
Biodiversity - Biofuel - Boreal forest - Modelling - Saproxylic species

Wood bioenergy may decrease the reliance on fossil carbon and mitigate anticipated increases in temperature. However, increased use of wood bioenergy may have large impacts on forest biodiversity primarily through the loss of dead wood habitats. We evaluated both the large-scale and long-term effects of different bioenergy extraction scenarios on the availability of dead wood and the suitability of the resulting habitat for saproxylic species, using a spatially explicit forest landscape simulation framework applied in the Swedish boreal forest. We demonstrate that bioenergy extraction scenarios, differing in the level of removal of biomass, can have significant effects on dead wood volumes. Although all of the scenarios led to decreasing levels of dead wood, the scenario aimed at species conservation led to highest volumes of dead wood (about 10 m3 ha-1) and highest connectivity of dead wood patches (mean proximity index of 78), whilst the scenario aimed at reaching zero fossil fuel targets led to the lowest levels (about 8 m3 ha-1) and least connectivity (mean proximity index of 7). Our simulations stress that further exploitation of dead wood from sites where volumes are already below suggested habitat thresholds for saproxylic species will very likely have further negative effects on dead wood dependent species.

LiDAR derived topography and forest stand characteristics largely explain the spatial variability observed in MODIS land surface phenology
Misra, Gourav ; Buras, Allan ; Heurich, Marco ; Asam, Sarah ; Menzel, Annette - \ 2018
Remote Sensing of Environment 218 (2018). - ISSN 0034-4257 - p. 231 - 244.
Bavarian Forest National Park - Forest stand characteristics - Land cover - LiDAR - Modelling - Mountains - NDVI - Phenology - Spatial variability

In the past, studies have successfully identified climatic controls on the temporal variability of the land surface phenology (LSP). Yet we lack a deeper understanding of the spatial variability observed in LSP within a land cover type and the factors that control it. Here we make use of a high resolution LiDAR based dataset to study the effect of subpixel forest stand characteristics on the spatial variability of LSP metrics based on MODIS NDVI. Multiple linear regression techniques (MLR) were applied on forest stand information and topography derived from LiDAR as well as land cover information (i.e. CORINE and proprietary habitat maps for the year 2012) to predict average LSP metrics of the mountainous Bavarian Forest National Park, Germany. Six different LSP metrics, i.e. start of season (SOS), end of season (EOS), length of season (LOS), NDVI integrated over the growing season (NDVIsum), maximum NDVI value (NDVImax) and day of maximum NDVI (maxDOY) were modelled in this study. It was found that irrespective of the land cover, the mean SOS, LOS and NDVIsum were largely driven by elevation. However, inclusion of detailed forest stand information improved the models considerably. The EOS however was more complex to model, and the subpixel percentage of broadleaf forests and the slope of the terrain were found to be more strongly linked to EOS. The explained variance of the NDVImax improved from 0.45 to 0.71 when additionally considering land cover information, which further improved to 0.84 when including LiDAR based subpixelforest stand characteristics. Since completely homogenous pixels are rare in nature, our results suggest that incorporation of subpixel forest stand information along with land cover type leads to an improved performance of topography based LSP models. The novelty of this study lies in the use of topography, land cover and subpixel vegetation characteristics derived from LiDAR in a stepwise manner with increasing level of complexity, which demonstrates the importance of forest stand information on LSP at the pixel level.

Translucency in cut tomatoes
Tijskens, L.M.M. ; Schouten, R. ; Kooten, O. van; Lana, M.M. - \ 2018
In: Proceedings of the 2nd International Conference on Quality Management of Fresh Cut Produce. - International Society for Horticultural Science (Acta Horticulturae ) - ISBN 9789462612068 - p. 347 - 352.
Appearance - Fresh-cut fruit - Modelling

Translucency is one of the major problems in fresh-cut fruit. This phenomenon affects the use of tomato fruit by the fresh-cut industries. Techniques for measuring translucency are not readily available. As a consequence, the processes that are important in the development of translucency are little understood, let alone described in detail. The colour of produce depends only on the absorption of light by colouring compounds. Translucency does not change the amount of colouring agents in the product, but it does change its appearance by changing the scattering properties. As a consequence the appearance, which is the result of light absorption and scattering combined, is affected by both translucency and colour development. Consumers do buy or reject products based on total appearance. In the short life time of cut fruits, the development of colouring compounds apart from possible oxidation effects will not be very large. Understanding the development of translucency is therefore of major importance for the fresh-cut industry. The development of translucency was visually assessed in tomato slices, obtained from tomatoes at three stages of maturity (mature green, breaker stage and full red) and stored at 5°C. In a second experiment, tomato slices were stored at three temperatures (5, 9 and 13°C) to assess the effects of temperature. In both experiments, non-cut tomatoes were also assessed. The data of both experiments were analysed using a very simple exponential model based on a massive approximation of the mechanism involved. The more precursor is present, the higher the obtainable translucency will be. A model was developed based on this simplified mechanism, and used to analyse all data. The stage of development (maturity) was found to have a major effect on translucency development regulated by the amount of precursor. The rate constant, however, was the same. The temperature only had a minor effect on the rate constant with the same amount of precursor. Explained parts (R2adj) obtained for mean data were well over 97%, for the individual data the explained part was somewhat less.

A comparison of disaggregated nitrogen budgets for Danish agriculture using Europe-wide and national approaches
Kros, Johannes ; Hutchings, Nicholas J. ; Kristensen, Inge Toft ; Kristensen, Ib Sillebak ; Børgesen, Christen Duus ; Voogd, Jan Cees ; Dalgaard, Tommy ; Vries, Wim de - \ 2018
Science of the Total Environment 643 (2018). - ISSN 0048-9697 - p. 890 - 901.
Agricultural soils - Budgets - Disaggregation - Modelling - National - Nitrogen

Spatially detailed information on agricultural nitrogen (N) budgets is relevant to identify regions where there is a need for a reduction in inputs in view of various forms of N pollution. However, at the scale of the European Union, there is a lack of consistent, reliable, high spatial resolution data necessary for the calculation of regional N losses. To gain insight in the reduction in uncertainty achieved by using higher spatial resolution input data. This was done by comparing spatially disaggregated agricultural N budgets for Denmark for the period 2000–2010, generated by two versions of the European scale model Integrator, a version using high spatial resolution national data for Denmark (Integrator-DK) and a version using available data at the EU scale (Integrator-EU). Results showed that the national N fluxes in the N budgets calculated by the two versions of the model were within 1–5% for N inputs by fertilizer and manure excretion, but inputs by N fixation and N mineralisation differed by 50–100% and N uptake also differed by ca 25%, causing a difference in N leaching and runoff of nearly 50%. Comparison with an independently derived Danish national budget appeared generally to be better with Integrator-EU results in 2000 but with Integrator-DK results in 2010. However, the spatial distribution of manure distribution and N losses from Integrator-DK were closer to observed distributions than those from Integrator-EU. We conclude that close attention to local agronomic practices is needed when using a leaching fraction approach and that for effective support of environmental policymaking, Member States need to collect or submit high spatial resolution agricultural data to Eurostat.

Machine learning for ecosystem services
Willcock, Simon ; Martínez-López, Javier ; Hooftman, Danny A.P. ; Bagstad, Kenneth J. ; Balbi, Stefano ; Marzo, Alessia ; Prato, Carlo ; Sciandrello, Saverio ; Signorello, Giovanni ; Voigt, Brian ; Villa, Ferdinando ; Bullock, James M. ; Athanasiadis, Ioannis N. - \ 2018
Ecosystem Services 33 (2018)B. - ISSN 2212-0416 - p. 165 - 174.
ARIES - Artificial intelligence - Big data - Data driven modelling - Data science - Machine learning - Mapping - Modelling - Uncertainty, Weka

Recent developments in machine learning have expanded data-driven modelling (DDM) capabilities, allowing artificial intelligence to infer the behaviour of a system by computing and exploiting correlations between observed variables within it. Machine learning algorithms may enable the use of increasingly available ‘big data’ and assist applying ecosystem service models across scales, analysing and predicting the flows of these services to disaggregated beneficiaries. We use the Weka and ARIES software to produce two examples of DDM: firewood use in South Africa and biodiversity value in Sicily, respectively. Our South African example demonstrates that DDM (64–91% accuracy) can identify the areas where firewood use is within the top quartile with comparable accuracy as conventional modelling techniques (54–77% accuracy). The Sicilian example highlights how DDM can be made more accessible to decision makers, who show both capacity and willingness to engage with uncertainty information. Uncertainty estimates, produced as part of the DDM process, allow decision makers to determine what level of uncertainty is acceptable to them and to use their own expertise for potentially contentious decisions. We conclude that DDM has a clear role to play when modelling ecosystem services, helping produce interdisciplinary models and holistic solutions to complex socio-ecological issues.

Modelling the selective removal of sodium ions from greenhouse irrigation water using membrane technology
Qian, Z. ; Miedema, H. ; Smet, L.C.P.M. de; Sudhȍlter, E.J.R. - \ 2018
Chemical Engineering Research & Design 134 (2018). - ISSN 0263-8762 - p. 154 - 161.
Greenhouse - Irrigation water - Mass balance - Modelling - Na over K membrane selectivity - Sodium removal
A model is presented for the Na+ and K+ levels in the irrigation water of greenhouses, specifically those for the cultivation of tomato. The model, essentially based on mass balances, not only describes the accumulation of Na+ but includes a membrane unit for the selective removal of Na+ as well. As determined by the membrane properties, some of the K+ is removed as well. Based on real-life process parameters, the model calculates the Na+ and K+ concentration at three reference points. These process parameters include the evapotranspiration rate, the K+ uptake by the plants, the Na+ and K+ content of the fertilizer, the Na+ leaching out from the hydroponic substrate material, and the Na+ and K+ removal efficiency of the membrane unit. Using these parameters and given a constant K+ concentration of the irrigation water entering the greenhouse of 6.6 mM (resulting in the optimal K+ concentration for tomato cultivation), the composition of the solution is completely defined at all three reference points per irrigation cycle. Prime aim of this investigation is to explore the requirements for the selective membrane that currently is developed in our lab. It is found that even for a limited Na+ over K+ selectivity of 6, after a number of cycles the Na+ level reaches steady state at a level below the upper (toxic) threshold for tomato cultivation (20 mM). Economic aspects and ways of implementation of such a system are briefly discussed.
The role of nitrifier denitrification in the production of nitrous oxide revisited
Wrage-Mönnig, Nicole ; Horn, Marcus A. ; Well, Reinhard ; Müller, Christoph ; Velthof, Gerard ; Oenema, Oene - \ 2018
Soil Biology and Biochemistry 123 (2018). - ISSN 0038-0717 - p. A3 - A16.
Denitritation - Isotopomers - Modelling - Molecular methods - NO - Nitrite - Stable isotopes
Nitrifier denitrification is the reduction of nitrite (NO2 −) by ammonia-oxidizing bacteria. This process may account for up to 100% of nitrous oxide (N2O) emissions from ammonium (NH4 +) in soils and is more significant than classical denitrification under some conditions. Investigations of nitrifier denitrification have expanded in the last decade but many aspects are still not understood. In this review, we revisit our 2001 paper, present a comprehensive summary of current knowledge concerning nitrifier denitrification, and identify the many research needs. Nitrifier denitrification can be distinguished from other routes of N2O production using isotopic methods: either isotopomer techniques or a combination of 15N and 18O tracers. Our understanding of the regulation and conditions favouring nitrifier denitrification has improved over the last decade as a result of adopting molecular and modelling approaches. Environments low in oxygen, and especially those with fluctuating aerobic-anaerobic conditions, promote N2O production by nitrifier denitrification. Also, large NO2 − concentrations, which often arise following inputs of ammonium or urea, may be linked to changes in aerobicity and high pH and favour nitrifier denitrification. The effects of temperature and carbon contents on nitrifier denitrification are incompletely understood and future research needs include: the study of pathways similar to nitrifier denitrification in archaea and nitrite oxidizers; the effects of interactions among microorganisms and between microorganism and plants; and the regulation and importance of the enzymes involved. A comparison and evaluation of the methods used for differentiating the sources of N2O is urgently needed. Furthermore, results from studies of freshwater and marine environments as well as wastewater treatment, where nitrifier denitrification is also known as nitrous aerobic denitritation (up to N2O) or aerobic denitritation (up to N2), will further advance our understanding.
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.
Studying microbial functionality within the gut ecosystem by systems biology
Hornung, Bastian ; Martins dos Santos, Vitor A.P. ; Smidt, Hauke ; Schaap, Peter J. - \ 2018
Genes & Nutrition 13 (2018)1. - ISSN 1555-8932
Community interactions - Genome scale metabolic model - Gut - Metagenome - Metatranscriptome - Microbial ecology - Microbiome - Modelling - NGS - Systems biology
Humans are not autonomous entities. We are all living in a complex environment, interacting not only with our peers, but as true holobionts; we are also very much in interaction with our coexisting microbial ecosystems living on and especially within us, in the intestine. Intestinal microorganisms, often collectively referred to as intestinal microbiota, contribute significantly to our daily energy uptake by breaking down complex carbohydrates into simple sugars, which are fermented to short-chain fatty acids and subsequently absorbed by human cells. They also have an impact on our immune system, by suppressing or enhancing the growth of malevolent and beneficial microbes. Our lifestyle can have a large influence on this ecosystem. What and how much we consume can tip the ecological balance in the intestine. A "western diet" containing mainly processed food will have a different effect on our health than a balanced diet fortified with pre- and probiotics. In recent years, new technologies have emerged, which made a more detailed understanding of microbial communities and ecosystems feasible. This includes progress in the sequencing of PCR-amplified phylogenetic marker genes as well as the collective microbial metagenome and metatranscriptome, allowing us to determine with an increasing level of detail, which microbial species are in the microbiota, understand what these microorganisms do and how they respond to changes in lifestyle and diet. These new technologies also include the use of synthetic and in vitro systems, which allow us to study the impact of substrates and addition of specific microbes to microbial communities at a high level of detail, and enable us to gather quantitative data for modelling purposes. Here, we will review the current state of microbiome research, summarizing the computational methodologies in this area and highlighting possible outcomes for personalized nutrition and medicine.
Modelling the impact of future socio-economic and climate change scenarios on river microbial water quality
Islam, M.M.M. ; Iqbal, Muhammad Shahid ; Leemans, Rik ; Hofstra, Nynke - \ 2018
International Journal of Hygiene and Environmental Health 221 (2018)2. - ISSN 1438-4639 - p. 283 - 292.
Climate change - Faecal indicator bacteria - Modelling - RCPs - Socio-economic development - SSPs
Microbial surface water quality is important, as it is related to health risk when the population is exposed through drinking, recreation or consumption of irrigated vegetables. The microbial surface water quality is expected to change with socio-economic development and climate change. This study explores the combined impacts of future socio-economic and climate change scenarios on microbial water quality using a coupled hydrodynamic and water quality model (MIKE21FM-ECOLab). The model was applied to simulate the baseline (2014-2015) and future (2040s and 2090s) faecal indicator bacteria (FIB: E. coli and enterococci) concentrations in the Betna river in Bangladesh. The scenarios comprise changes in socio-economic variables (e.g. population, urbanization, land use, sanitation and sewage treatment) and climate variables (temperature, precipitation and sea-level rise). Scenarios have been developed building on the most recent Shared Socio-economic Pathways: SSP1 and SSP3 and Representative Concentration Pathways: RCP4.5 and RCP8.5 in a matrix. An uncontrolled future results in a deterioration of the microbial water quality (+75% by the 2090s) due to socio-economic changes, such as higher population growth, and changes in rainfall patterns. However, microbial water quality improves under a sustainable scenario with improved sewage treatment (-98% by the 2090s). Contaminant loads were more influenced by changes in socio-economic factors than by climatic change. To our knowledge, this is the first study that combines climate change and socio-economic development scenarios to simulate the future microbial water quality of a river. This approach can also be used to assess future consequences for health risks.
Projection of urban expansion and related changes in soil carbon stocks in the Moscow Region
Vasenev, V.I. ; Stoorvogel, J.J. ; Leemans, R. ; Valentini, R. ; Hajiaghayeva, R.A. - \ 2018
Journal of Cleaner Production 170 (2018). - ISSN 0959-6526 - p. 902 - 914.
Future carbon stocks - Logistic regression - Modelling - New Moscow - Scenarios - Urban soils

Urbanization is responsible for large environmental changes worldwide. Although traditionally urbanization was related to negative environmental impacts, recent research also highlights positive impacts like the potential of urban areas to store soil organic carbon. The net effect of urbanization on soil organic carbon is poorly understood. Negative influences of construction and soil sealing may be compensated by the establishment of green areas. Possible net effects of future urbanization on soil organic carbon stocks were explored for the Moscow Region, based on the soil survey and land conversion model. The regional urbanization was modelled as a function of environmental, socio-economic and neighbourhood factors. This yielded three alternative scenarios for urbanization: i) including neighbourhood factors; ii) excluding neighbourhood factors and focusing on environmental drivers; and iii) considering the New Moscow Project that includes the establishment of 1500 km2 of new urbanized area following governmental regulation. The three scenarios showed substantial expansion of urban areas on 30, 10 and 80%. The model, considering neighbourhood effect was the most accurate with 91% of correct predictions. Urbanization in the region mainly converted forests, fallow and arable lands. The negative effect of urbanization (i.e soil sealing and excavation of topsoil for building construction) was compensated by positive effect (e.i. urban greenery and “cultural layers”). In result an increase of soil organic carbon stocks of 4.2 ± 1.7 to 11.0 ± 2.6 Tg C was shown for all three scenarios. The highest increases in soil organic carbon stocks occurred on the less fertile Orthic Podzols and Eutric Podzoluvisols, whereas SOC stocks in Orthic Luvisols, Luvic Chernozems, Dystric Histosols and Eutric Fluvisols increased less. Subsoil C-stocks were much more affected with an extra 4 ± 1.6 to 10 ± 2.4 Tg soil organic carbon than those in the topsoils. The highest increase of both topsoil and subsoil soil organic carbon stocks occurred in the New Moscow scenario with the highest urbanization. Even when the relatively high uncertainties of the absolute C-stocks are considered, the outcomes highlight the potential of cities to enhance soil organic carbon storage. This will progressively become more important in the future following the increasing world-wide urbanization.

Development of mathematical models to predict calcium, magnesium and selenium excretion from lactating Holstein cows
Taylor, Kate ; Appuhamy, J.A.D.R.N. ; Dijkstra, J. ; Kebreab, E. - \ 2018
Animal Production Science 58 (2018)3. - ISSN 1836-0939 - p. 489 - 498.
Dairy cows - Faeces - Modelling - mineral excretion
The aim of this study was to develop and evaluate mathematical models that predict mineral excretion, particularly calcium (Ca), magnesium (Mg) and selenium (Se), from lactating dairy cows. Mineral excretion can be affected by several dietary factors. A deficiency in Ca or Mg application to pasture, among other factors, can contribute to grass tetany or wheat pasture poisoning in cows, whereas an excess can cause runoff into water supplies. Manure application with high Se concentration can also result in runoff, causing the bioaccumulation of selenium in aquatic ecosystems, wetland habitats and estuaries, leading to toxic levels in fish. A database composed of studies relating to mineral utilisation in lactating dairy cows conducted after and including the year 2000 was compiled. A meta-analysis was conducted with the aim of creating multiple empirical equations to predict Ca, Mg and Se excretion from lactating dairy cows. Calcium intake, feed Ca content, milk yield, milk protein content and acid detergent fibre content in diet were positively and linearly related to Ca excretion. Dietary crude protein content and milk fat content were negatively related to Ca excretion. Magnesium intake, feed Mg content and milk yield were positively and linearly related to Mg excretion. Selenium content of diet and dry matter intake were linearly and positively related to Se excretion. Two sets of models were developed using or excluding the intake variable and both sets of models were evaluated with independent data originating from commercial herd or individual animals. In general, intake measurements improved prediction when evaluated with independent datasets (root mean square prediction error = 8% to 19% vs 14% to 26% of the average observed value). There were substantial mean biases, particularly those evaluated with data from a commercial farm, perhaps due to inaccurate feed intake measurements. Although there was generally good agreement between predicted and observed mineral excretion, model development and evaluation would benefit from an expanded database.
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