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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The SEEA EEA carbon account for the Netherlands
Lof, Marjolein ; Schenau, Sjoerd ; Jong, Rixt de; Remme, Roy ; Graveland, Cor ; Hein, Lars - \ 2017
The Hague : Statistics Netherlands - 64
carbon dioxide - netherlands - carbon - economics - environment - biofuels - bioenergy - biogas - emission - kooldioxide - nederland - koolstof - economie - milieu - biobrandstoffen - bio-energie - emissie
The carbon account provides a comprehensive overview of all relevant carbon stocks and flows. The carbon account for the Netherlands was developed within the scope of the ‘System of Environmental Economic Accounts – Experimen tal Ecosystem Accounting’ (SEEA EEA) project for the Netherlands (Natuurlijk Kapitaalrekeningen Nederland: NKR_NL), which is currently c arried out jointly by Statistics Netherlands and Wageningen University. Funding and support was provided by the Ministries of Economic Affairs and Infrastructure and the Environment. Within the NKR_NL project, a number of accounts are currently under devel opment. The carbon account is described in detail in this report.
Vervolgonderzoek emissiearme Lisianthus
Raaphorst, Marcel ; Eveleens, Barbara ; Burg, Rick van der; Schuddebeurs, Lisanne - \ 2017
Bleiswijk : Wageningen UR Glastuinbouw (Rapport GTB 1440) - 30
kasgewassen - kassen - glastuinbouw - snijbloemen - emissiereductie - voedingsstoffen - gewasbescherming - kooldioxide - substraten - cultuur zonder grond - fusarium - bodemschimmels - kunstmatige verlichting - kunstlicht - greenhouse crops - greenhouses - greenhouse horticulture - cut flowers - emission reduction - nutrients - plant protection - carbon dioxide - substrates - soilless culture - soil fungi - artificial lighting - artificial light
Lisianthus growers look for methods to minimise the emission of nutrients, crop protection chemicals and CO2. In 2014 and 2015, nine crops with Lisianthus have been tested at the Delphy Improvement Centre. This report describes the four trials that have been carried out in the extended research in 2016. With this extension, a distinction was made between different substrates and intensities of assimilation lighting. In addition to knowledge about light use efficiency, water use, heat use, substrate differences and growth development, these extra crop cycles have brought to light that growing Lisianthus on substrate gives a less resilient plant against soil fungi than was experienced during the first crop cycles.
Metabolic modeling to understand and redesign microbial systems
Heck, Ruben G.A. van - \ 2017
University. Promotor(en): Vitor Martins dos Santos, co-promotor(en): Maria Suarez Diez. - Wageningen : Wageningen University - ISBN 9789463434553 - 239
micro-organismen - modelleren - kooldioxide - biotechnologie - algen - metabolisme - pseudomonas - microorganisms - modeling - carbon dioxide - biotechnology - algae - metabolism

The goals of this thesis are to increase the understanding of microbial metabolism and to functionally (re-)design microbial systems using Genome- Scale Metabolic models (GSMs). GSMs are species-specific knowledge repositories that can be used to predict metabolic activities for wildtype and genetically modified organisms. Chapter 1 describes the assumptions associated with GSMs, the GSM generation process, common GSM analysis methods, and GSM-driven strain design methods. Thereby, chapter 1 provides a background for all other chapters. In this work, there is a focus on the metabolically versatile bacterium Pseudomonas putida (chapters 2,3,4,5,6), but also other model microbes and biotechnologically or societally relevant microbes are considered (chapters 3,4,6,7,8).

GSMs are reflections of the genome annotation of the corresponding organism. For P. putida, the genome annotation that GSMs have been built on is more than ten years old. In chapter 2, this genome annotation was updated both on a structural and functional level using state-of-the-art annotation tools. A crucial part of the functional annotation relied on the most comprehensive P. putida GSM to date. This GSM was used to identify knowledge gaps in P. putida metabolism by determining the inconsistencies between its growth predictions and experimental measurements. Inconsistencies were found for 120 compounds that could be degraded by P. putida in vitro but not in silico. These compounds formed the basis for a targeted manual annotation process. Ultimately, suitable degradation pathways were identified for 86/120 as part of the functional reannotation of the P. putida genome.

For P. putida there are 3 independently generated GSMs, which is not uncommon for model organisms. These GSMs differ in generation procedure and represent different and complementary subsets of the knowledge on the metabolism of the organism. However, the differing generation procedures also makes it extremely cumbersome to compare their contents, let alone to combine them into a single consensus GSM. Chapter 3 addresses this issue through the introduction of a computational tool for COnsensus Metabolic Model GENeration (COMMGEN). COMMGEN automatically identifies inconsistencies between independently generated GSMs and semi-automatically resolves them. Thereby, it greatly facilitates a detailed comparison of independently generated GSMs as well as the construction of consensus GSMs that more comprehensively describe the knowledge on the modeled organism.

GSMs can predict whether or not the corresponding organism and derived mutants can grow in a large variety of different growth conditions. In comparison, experimental data is extremely limited. For example, BIOLOG data describes growth phenotypes for one strain in a few hundred different media, and genome-wide gene essentially data is typically limited to a single growth medium. In chapter 4 GSMs of multiple Pseudomonas species were used to predict growth phenotypes for all possible single-gene-deletion mutants in all possible minimal growth media to determine conditionally and unconditionally essential genes. This simulated data was integrated with genomic data on 432 sequenced Pseudomonas species, which revealed a clear link between the essentiality of a gene function and the persistence of the gene within the Pseudomonas genus.

Chapters 5 and 6 describe the use of GSMs to (re-)design microbial systems. P. putida is, despite its acknowledged versatile metabolism, an obligate aerobe. As the oxygen-requirement limits the potential applications of P. putida, there have been several experimental attempts to enable it to grow anaerobically, which have so far not succeeded. Chapter 5 describes an in silico effort to determine why P. putida cannot grow anaerobically using a combination of GSM analyses and comparative genomics. These analyses resulted in a shortlist of several essential and oxygen-dependent processes in P. putida. The identification of these processes has enabled the design of P. putida strains that can grow anaerobically based on the current understanding of P. putida metabolism as represented in GSMs.

Efficient microbial CO2 fixation is a requirement for the biobased community, but the natural CO2 fixation pathways are rather inefficient, while the synthetic CO2 fixation pathways have been designed without considering the metabolic context of a target organism. Chapter 6 introduces a computational tool, CO2FIX, that designs species-specific CO2 fixation pathways based on GSMs and biochemical reaction databases. The designed pathways are evaluated for their ATP efficiency, thermodynamic feasibility, and kinetic rates. CO2FIX is applied to eight different organisms, which has led to the identification of both species-specific and general CO2 fixation pathways that have promising features while requiring surprisingly few non-native reactions. Three of these pathways are described in detail.

In all previous chapters GSMs of relatively well-understood microbes have been used to gain further insight into their metabolism and to functionally (re-)design them. For complex microbial systems, such as algae (chapter 7) and gut microbial communities (chapter 8), GSMs are similarly useful, but substantially more difficult to create and analyze. Algae are widely considered as potential centerpieces of a biobased economy. Chapter 7 reviews the current challenges in algal genome annotation, modeling and synthetic biology. The gut microbiota is an incredibly complex microbial system that is crucial to our well-being. Chapter 8 reviews the ongoing developments in the modeling of both single gut microbes and gut microbial communities, and discusses how these developments will enable the move from studying correlation to causation, and ultimately the rational steering of gut microbial activity.

Chapter 9 discusses how the previous chapters contribute to the research goals of this thesis. In addition, it provides an extensive discussion on current GSM practices, the issues associated therewith, and how these issues can be tackled. In particular, the discussion focuses on issues related to: (i) The inability to distinguish between biological difference and GSM generation artifacts when using multiple GSMs, (ii) The lack of continuous GSM updates, (iii) The mismatch between what GSM predictions and experimental data represent, (iv) The need for standardization in GSM evaluation, and (v) The lack of experimental validation of GSM-driven strain design for metabolic engineering.

Paprikateelt in de hooggeïsoleerde VenLow Energy kas
Zwart, H.F. de; Gelder, A. de; Hofland-Zijlstra, J. ; Noordam, M. - \ 2017
Bleiswijk : Wageningen University & Research, BU Glastuinbouw (Rapport GTB 1435) - 34
paprika's - capsicum annuum - kassen - kasgewassen - glasgroenten - glastuinbouw - energiebesparing - energiegebruik - isolatie (insulation) - broeikasgassen - kooldioxide - sweet peppers - greenhouses - greenhouse crops - greenhouse vegetables - greenhouse horticulture - energy saving - energy consumption - insulation - greenhouse gases - carbon dioxide
In order to realise a horticultural sector that operates without the combustion of fossil fuel, the first step is to reduce the demand for heating by improving the insultation of greenhouses. This holds especially for crops that are grown at high temperatures, like sweet pepper. The Venlow Energy greenhouse with its double glass cladding and energy screen is a good example of such a highly insulated greenhouse. This report presents the results of a one year cultivation and serves as a bench mark for the state of the art in energy conserving production of Sweet Pepper in the Netherlands. It shows the greenhouse climate conditions required, and the possibilities to meet these requirements with a low energy consumption and options to realise this from sustainable sources. The application of sustainable energy sources was not tested in practice, but since the exact resources (heat and CO2) required from hour to hour were measured, it is easy to do the math on the amounts and capacities needed. The application of pure CO2 or CO2 from another sustainable source is essential when aiming at a fossil energy free horticulture. Without external CO2 the production will drop substantially, especially because an energy conserving greenhouse has typically a strongly reduced air exchange. But, for the same reason, the amount of CO2 needed to increase the CO2 concentration is quite limited, 25 kg/m² per year in this experiment. With a production of 32.5 kg class I of red Sweet Pepper per m², the experiment has shown that halving the energy consumption compared to the general practice did’nt reduced the production.
Teelt Gerbera in Balans : de invloed van lichtsom, etmaaltemperatuur en daglengte op productie, energiegebruik en plantbalans
Garcia Victoria, Nieves ; Gelder, Arie de; Kempkes, Frank ; Dings, Eugenie - \ 2017
Bleiswijk : Wageningen University & Research, BU Glastuinbouw (Rapport GTB 1417) - 102
glastuinbouw - kasgewassen - kassen - gerbera - energiegebruik - kooldioxide - kunstlicht - gewaskwaliteit - productie - greenhouse horticulture - greenhouse crops - greenhouses - energy consumption - carbon dioxide - artificial light - crop quality - production
“Gerbera: Growing in Balance” was a research project to support the reduction of energy and CO2 consumption in the cultivation of Gerbera. The varieties Pre-Semmy, Rich, Whisper and Suri were grown in three glasshouses with different treatments: “Cool Cultivation” (15°C temperature; 90 μmol light, day length 13 hour in winter); “Practice” (temperature depending on day light integral, 100 μmol/m2s light, day length 11.5 hours) and “Light Dependent” (temperature depending sharply on day light integral, 90 μmol/m2s light, day length 13 hours in winter). The day light integral was kept equal in all treatments, regardless the difference in light intensity and day length in the winter. For flower quality and energy use “Cool Cultivation” was the best treatment, but required the most kg / m² of CO2. Whisper and Suri produced more flowers / m2 in the treatment “Light Dependent” but flower weights were low. Pre-Semmy and Rich gave more flowers in the treatment “Practice”, but spalkes were weak in May and June. The 13 hour day length in winter was not detrimental to production or quality. Light sum, day length and daily temperature are the three buttons to control the plant balance for optimum production and quality. The project was Funded by the Program “Greenhouse as Energy Source” (Ministry of Economic Affairs and LTO Glaskracht) and the Knowledge Cooperative Gerbera.
CO2 uit buitenlucht
Weel, P.A. van; Vanthoor, B.H.E. - \ 2016
Wageningen UR Glastuinbouw (Rapport GTB 1423) - 32 p.
glastuinbouw - kooldioxide - ventilatie - freesia - tomaten - greenhouse horticulture - carbon dioxide - ventilation - tomatoes
The supply of additional CO2 in a greenhouse will be restricted in the future. The concentration in outside air has risen above 400 ppm. This may open the possibility to blow this air through the canopy to increase growth. In this project, the vertical CO2 concentration was measured in a vertical plane within to the canopy under different combinations of window opening, the activation of vertical fans and with or without dosing of additional CO2. For a Freesia and a tomato crop the result was that without CO2 dosing it was possible to maintain a concentration of over 350 ppm in the canopy at 5-10 cm distance from the leaf surface when the ventilation windows were open. Since, this is below outside concentration, additional supply of outside air may be an advantage. When extra CO2 was supplied, a reduction in window opening and the use of a screen increased the concentration between the canopy. The vertical distribution of CO2 within the canopy was never a problem. It can be concluded that the crop resistance to take up CO2 for a tomato and freesia crop is small and with respect to the other CO2 resistances, the crop resistance can be neglected. A positive effect of the use of vertical fans or the use of high pressure misting in the tomato greenhouse was not found, due to the strategy to keep the ventilation windows wide open. The concentration at 5-10 cm distance from the leaf is not necessarily the same concentration around the stomata because of boundary layer resistance. The effect of the boundary layer resitance on CO2 uptake is described in the report of Plant Dynamics called “Effecten van grenslaagweerstand op de fotosynthese bij tomaat en Freesia”.
Arctic climate change and decadal variability
Linden, Eveline C. van der - \ 2016
University. Promotor(en): Wilco Hazeleger, co-promotor(en): R. Bintanja. - Wageningen : Wageningen University - ISBN 9789462579453 - 197
climatic change - arctic regions - global warming - temperature - models - carbon dioxide - sea water - barents sea - klimaatverandering - arctische gebieden - opwarming van de aarde - temperatuur - modellen - kooldioxide - zeewater - barentszzee

High northern latitudes exhibit enhanced near-surface warming in a climate with increasing greenhouse gases compared to other parts of the globe, indicating an amplified climate response to external forcing. Decadal to multidecadal variability sometimes enhances and at other times reduces the long-term trends. Therefore, the influence of internal variability should be taken into account when externally forced climate signals are assessed.
This thesis contributes to our understanding of Arctic climate projections by clarifying the role of coupled ocean-sea-ice-atmosphere processes on the long-term trends and decadal variability of the Arctic climate system. Important mechanisms linked to the location of the sea ice margin and ocean heat transports into the Arctic have been identified and were shown to have a substantial effect on the Arctic's response to climate change.

Modeling the coupled exchange of water and CO2 over croplands
Combe, Marie - \ 2016
University. Promotor(en): Wouter Peters; Maarten Krol, co-promotor(en): Jordi Vila-Guerau de Arellano. - Wageningen : Wageningen University - ISBN 9789462579255 - 152
carbon cycle - carbon dioxide - modeling - water - energy exchange - crop yield - grain crops - atmosphere - koolstofcyclus - kooldioxide - modelleren - energie-uitwisseling - gewasopbrengst - graangewassen - atmosfeer

Croplands are a managed type of vegetation, with a carbon storage that is highly optimized for food production. For instance, their sowing dates are chosen by the farmers, their genetic potential is bred for high grain yields, and their on-field competition with other species is reduced to the minimum. As a result of human intervention, croplands are a major land cover type (roughly one fifth of the land area over Europe) and they experience a short growing season during which they exchange carbon and water intensively with the atmosphere. Their growth significantly affects the seasonal amplitude of CO2 mole fractions over the globe, interact with extreme weather events such as droughts and heat waves, and impact surface hydrology due to their water consumption. However, and in spite of their relevance, terrestrial biosphere models used in carbon cycle and atmospheric research often assume the phenology of croplands to be similar to the one of grasslands, and they also ignore the impact of crop management. This oversimplification is the motivation for this thesis. We focus on understanding and modeling the key surface and atmospheric processes that shape the cropland water and CO2 exchange, and the resulting impact on the CO2 mole fractions of the atmosphere overhead. We study these processes from the daily to the seasonal scale, for croplands of the mid-latitudes. In the end, we come with recommendations and a new modeling framework to represent the cropland CO2 and water exchange in the Earth System, weather and climate models.

Consultancy genereren basiskennis fotosynthese aardbei
Kaiser, E. ; Janse, J. - \ 2016
Bleiswijk : Wageningen UR Glastuinbouw (Rapport GTB 1411) - 22
aardbeien - fragaria ananassa - teelt onder bescherming - kasgewassen - glastuinbouw - fotosynthese - energiebesparing - licht - kooldioxide - strawberries - protected cultivation - greenhouse crops - greenhouse horticulture - photosynthesis - energy saving - light - carbon dioxide
To save electricity and CO2 during strawberry production, more knowledge about the photosynthesis of greenhouse-grown strawberry plants is necessary. This was tackled by measuring light- and CO2-dependent photosynthesis responses and by conducting a literature study in which several parameters of leaf-level photosynthesis were compared. From measurements conducted between middle of March and middle of May 2016 it was concluded that the rate of photosynthesis and electron transport was comparable between young and old leaves, while stomatal conductance in young leaves was always higher. Light- and CO2- saturated photosynthesis rates were higher in older leaves. Furthermore, a decrease of photosynthesis rates was visible in April, which may have been caused by acclimation of leaf biochemistry to elevated CO2 concentrations in the greenhouse. Conclusions from the literature study were that light saturation was reached at ~1000 μmol m-2 s-1 and that CO2 saturation was reached at ~1100 μmol mol-1. Average photosynthesis rates at these conditions were 18 and 35 μmol m-2 s-1, respectively. The average quantum yield of photosynthesis was ~0.06 μmol CO2 μmol-1 PAR, which is comparable to other, fast growing greenhouse crops (e.g. cucumber, tomato, sweet pepper). Large knowledge gaps about the course of photosynthesis during complete growing seasons remain.
Plantmonitoring op basis van fotosynthese sensoren : ontwikkelen en testen van sensoren
Dieleman, Anja ; Bontsema, Jan ; Jalink, Henk ; Snel, Jan ; Kempkes, Frank ; Voogt, Jan ; Pot, Sander ; Elings, Anne ; Jalink, Vincent ; Meinen, Esther - \ 2016
Bleiswijk : Wageningen UR Glastuinbouw (Rapport GTB 1405) - 86
teelt onder bescherming - glastuinbouw - kastechniek - sensors - fotosynthese - kooldioxide - energie - energiebesparing - verlichting - kunstlicht - kunstmatige verlichting - ventilatie - kunstmatige ventilatie - fluorescentie - tomaten - solanum lycopersicum - protected cultivation - greenhouse horticulture - greenhouse technology - photosynthesis - carbon dioxide - energy - energy saving - lighting - artificial light - artificial lighting - ventilation - artificial ventilation - fluorescence - tomatoes
The basic process for crop growth and production is photosynthesis. Measuring crop photosynthesis is therefore important to monitor the status of the crop and whether the greenhouse climate is set to the needs of the crop. In this project, two monitoring systems for crop photosynthesis were developed and tested. (1) The crop photosynthesis monitor is a soft sensor that can calculate the CO2 uptake of an entire crop. The basis for these calculations are the balance between CO2 supply and CO2 loss via ventilation and crop photosynthesis. By measuring the CO2 concentration and humidity inside and outside the greenhouse, the crop photosynthesis can be calculated. (2) The CropObserver is a fluorescence sensor that measures the light use efficiency of photosynthesis of a large crop area (3 x 3 m2). The crop receives light pulses from a laser in the top of the greenhouse, the sensor measures the fluorescence signal of the crop. Both sensors were tested in a tomato crop in 2014 with promising results. The sensors functioned without problems and delivered patterns of daily photosynthesis which matched the reference measurements reasonably well up to well.
Microbial electrosynthesis of biochemicals : innovations on biocatalysts, electrodes and ion-exchange for CO2 supply, chemicals production and separation
Bajracharya, S. - \ 2016
University. Promotor(en): Cees Buisman; David Strik; Deepak Pant. - Wageningen : Wageningen University - ISBN 9789462578531 - 181 p.
carbon dioxide - biofuels - chemicals - biocatalysis - ion exchange - electrodes - kooldioxide - biobrandstoffen - chemicaliën - biokatalyse - ionenuitwisseling - elektrodes

Microbial electrosynthesis (MES) is an electricity-driven production of chemicals from low-value waste using microorganisms as biocatalysts. MES from CO2 comprises conversion of CO2 to multi-carbon compounds employing microbes at the cathode which use electricity as an energy source. This thesis presents innovations on MES from CO2 using anaerobic mixed-cultures, circumventing the methane generation. Acetate was the primary product but other products including ethanol, butyrate were also produced. Establishment of active biocathode at the graphite felt cathode was achieved under long-term operation which led to the acetate accumulation up to 7-10 g L-1 at -1 V/Ag/AgCl cathode potential. CO2 reduction in MES requires continuous availability of CO2 and low cathode potential to ensure the supply of reducing equivalents/hydrogen. Use of gas diffusion biocathode doubled the CO2 mass-transfer rate which enhanced the production rates, reaching. Furthermore, a sustainable technology for manufacturing biochemicals/biofuels was demonstrated in this thesis by integrating the product separation in MES. The electricity-driven production of chemicals/biofuels from CO2/waste products and subsequent product recovery studies prospect an integration of microbial electrosynthesis with biorefineries for the up-scaling of both technologies.

Microalgae production in a biofilm photobioreactor
Blanken, Ward - \ 2016
University. Promotor(en): Rene Wijffels, co-promotor(en): Marcel Janssen. - Wageningen : Wageningen University - ISBN 9789462578425 - 234
algae - algae culture - biofilms - bioreactors - growth - production costs - biomass - artificial lighting - photosynthesis - carbon dioxide - algen - algenteelt - bioreactoren - groei - productiekosten - biomassa - kunstmatige verlichting - fotosynthese - kooldioxide

Microalgae can be used to produce high-value compounds, such as pigments or high value fatty acids, or as a feedstock for lower value products such as food and feed compounds, biochemicals, and biofuels. In order to produce these bulk products competitively, it is required to lower microalgae production cost. Production costs could be reduced by employing microalgae biofilms as a production platform. The main advantages of microalgae biofilms are a direct harvest of concentrated microalgae paste, and the uncoupling of the hydraulic retention time from the microalgal retention time. The latter allows to decrease the liquid volume or to employ dilute waste streams. To successfully employ biofilms, however, it is required that microalgal biofilms can be cultivated at high productivity and high photosynthetic efficiency. The aim of this thesis was to optimize the productivity of microalgal biofilms.

Light energy drives microalgal growth. Sunlight is free and abundant, but sunlight intensity varies over the day and the seasons. This makes it impossible to maintain optimal production conditions throughout the day. These fluctuations in irradiance can be prevented by applying artificial lighting. Although, artificial lighting will supply a constant light intensity and thus increase productivity and simplify process control, it will also increase microalgae production cost. A quantitative evaluation of lighting costs and energy requirement was still missing and this was the topic of Chapter 2. The costs related to artificial lighting were identified as 25.3 $ per kilogram of dry-weight biomass, with only 4% to 6% of the electrical energy required to power the lamps eventually stored as chemical energy in microalgal biomass. Energy loss and increased production cost may be acceptable for the production of high value products, but in general they should be avoided.

In Chapter 3, a photobioreactor design based on a rotating biological contactor (RBC) was introduced and used as a production platform for microalgal biomass cultivated in a biofilm. In the photobioreactor, referred to as the Algadisk, microalgae grow in biofilm on vertical rotating disks partially submerged in water with dissolved nutrients. The objective was to evaluate the potential of the Algadisk photobioreactor, and identify the window of operation of the process with respect to the effects of disk roughness, disk rotation speed and CO2 concentration. These parameters were evaluated in relation to biomass productivity, photosynthetic efficiency, and the long-term cultivation stability of the production process.

The mesophilic green microalga Chlorella sorokiniana was used as a model organism. In the lab-scale Algadisk reactor, a productivity of 20.1 ±0.7 gram per m2 disk surface per day and a biomass yield on light of 0.9 ±0.04 gram dry weight biomass per mol photons were obtained. This productivity could be retained over 21 weeks without re-inoculation. To obtain maximal and stable productivity it was important that the disk surface provides a structure that allows biomass retention on the disk after harvest. The retained biomass acts as inoculum for the new biofilm and is therefore essential for quick biofilm regrowth. Most important process parameters were CO2­ supply, temperature, and pH. Although deviations of these parameters from the optimal conditions resulted in productivity loss, the system quickly recovered when optimal conditions were restored. These results exhibit an apparent opportunity to employ the Algadisk photobioreactor and biofilm systems in general at large scale for microalgae biomass production provided CO2 supply is adequate.

In order to better understand the process conditions inside the biofilm a model was developed in the further chapters. These mathematical models were calibrated and validated with dedicated experiments. In Chapter 4 first a general applicable kinetic model was developed able to predict light limited microalgal growth. This model combines a mathematical description for photoautotrophic sugar production with a description for aerobic chemoheterotrophic biomass growth. The model is based on five measurable biological parameters which were obtained from literature for the purpose of this study. The model was validated on experiments described in literature for both Chlorella sorokiniana and Chlamydomonas reinhardtii. The specific growth rate was initially predicted with a low accuracy, which was most likely caused by simplifications in the light model and inaccurate parameter estimations. When optimizing the light model and input parameters the model accuracy was improved and validated. With this model a reliable engineering tool became available to predict microalgal growth in photobioreactors. This microalgal growth model was included in the biofilm growth models introduced in Chapters 5 and 6.

In Chapter 5 microalgal biofilms of Chlorella sorokiniana were grown under simulated day-night cycles at high productivity and high photosynthetic efficiency. The experimental data under day/night cycles were used to validate a microalgal biofilm growth model. For this purpose the light limited microalgal growth model from Chapter 4 was extended to include diurnal carbon-partitioning and maintenance under prolonged dark conditions. This new biofilm growth model was then calibrated and validated experimentally. Based on these experiments and model simulations no differences in the light utilization efficiency between diurnal and continuous light conditions were identified. Indirectly this shows that biomass lost overnight represents sugar consumption for synthesis of new functional biomass and maintenance related respiration. This is advantageous, as this result shows that it is possible to cultivate microalgae at high photosynthetic efficiencies on sunlight and that the night does not negatively impact overall daily productivity. Long periods of darkness resulted in reduced maintenance related respiration.

Based on simulations with the validated biofilm growth model it could be determined that the photosynthetic efficiency of biofilm growth is higher than that of suspension growth. This is related to the fact that the maintenance rate in the dark zones of the biofilm is lower compared to that in the dark zones of suspension cultures, which are continuously mixed with the photic zone.

In Chapter 3 it was identified that concentrated CO2 streams are required to obtain high productivities. However, over-supplying CO2 results into loss of CO2 to the environment and is undesirable for both environmental and economic reasons. In Chapter 6 the phototrophic biofilm growth model from Chapter 5 was extended to include CO2 and O2 consumption, production, and diffusion. The extended model was validated in growth experiments with CO2 as limiting substrate. Based on the validated model the CO2 utilization and productivity in biofilm photobioreactors were optimized by changing the gas flow rate, the number of biofilm reactors in series, and the gas composition. This resulted in a maximum CO2 utilization efficiency of 96% by employing flue gas, while the productivity only dropped 2% compared to non-CO2 limited growth. In order to achieve this 25 biofilm reactors units, or more, must be operated in series. Based on these results we conclude that concentrated CO2 streams and plug flow behaviour of the gaseous phase over the biofilm surface are essential for high CO2 utilization efficiencies and high biofilm productivity.

In Chapter 7 the implications of these studies for the further development of biofilm photobioreactors was discussed in the light of current biofilm photobioreactor designs. Design elements of state of the art biofilm photobioreactors, were combined into a new conceptual biofilm photobioreactor design. This new design combines all advantages of phototrophic biofilms minimizing the amount of material required. Further improvements by means of process control strategies were suggested that aim for maximal productivity and maximal nutrient utilization efficiency. These strategies include: control of the biofilm thickness, control of the temperature, and optimized nutrient supply strategies.

Effects of temperature and CO2 during late incubation on broiler chicken development
Maatjens, C.M. - \ 2016
University. Promotor(en): Bas Kemp, co-promotor(en): Henry van den Brand; I.A.M. van Roovert-Reijrink. - Wageningen : Wageningen University - ISBN 9789462578258 - 196 p.
broilers - embryonic development - temperature - carbon dioxide - incubation - animal physiology - broiler performance - artificial hatching - hatcheries - poultry farming - vleeskuikens - embryonale ontwikkeling - temperatuur - kooldioxide - broeden - dierfysiologie - vleeskuikenresultaten - kunstmatig bebroeden - broedinstallaties - pluimveehouderij

Incubation conditions need to be adjusted to meet embryonic requirements to obtain optimal chick quality and hatchability. Eggshell temperature (EST) can be used as a non- invasive method to determine embryo temperature. A high EST of 38.9°C during the second or third week of incubation negatively affects chicken embryo development and survival compared to a constant EST of 37.8°C during that period. These negative effects of high EST might be due to a dis-balance between metabolic rate and oxygen (O2) availability. However, effects of lowering EST, which might restore the balance between metabolic rate and O2 availability, are largely unknown. Besides EST, the carbon dioxide (CO2) concentration during late incubation also seems to affect embryo development and might even interact with EST. Based on the potential effects of (lower) EST during the last week of incubation and of CO2 during only the hatching phase, the following three aims are derived: 1, to investigate effects of EST during the last phase of the incubation process, with special attention for EST below the general accepted optimal EST of 37.8°C, 2, to examine from which day of the incubation process onward EST should be changed from 37.8°C, and 3, to investigate whether CO2 concentrations are interacting with EST during the hatcher phase.

Time until hatch was longer when an EST of 35.6°C was applied during the last week of incubation, followed by 36.7, 37.8, and 38.9°C, which is probably caused by the lower metabolic rate at an EST below 37.8°C. Hatchability of fertile eggs was not affected at low EST, and EST did not affect time between internal pipping (IP) and hatch. An EST of 35.6 and 36.7°C, resulted in a higher yolk-free body mass (YFBM) at hatch compared to 37.8 and 38.9°C, and residual yolk weight was higher at hatch at 38.9°C compared to all other EST treatments. An EST of 35.6°C resulted in higher hepatic glycogen concentration and amount at IP and hatch compared to all other EST treatments. The proposed mechanism involved is that at lower EST, metabolic rate is reduced, which prevents the embryo from O2 limitation and ensures that fatty acid oxidation from the yolk can be maintained, resulting in energy production to be invested in growth and development. At an EST of 38.9°C, metabolic rate is high, resulting in a relative O2 shortage for the embryo. Consequently, lipid oxidation is reduced, which forces the embryo to switch to alternative energy sources, such as glycogen. Because glycogen storage is very limited in the egg and embryo, alternative energy sources such as amino acids obtained from muscles might be used. A clear interaction between EST and start day of treatment was found for relative heart weight. Relative heart weight was higher at an EST of 35.6°C and decreased with increase in EST. The differences among EST became larger when the EST treatment started earlier.

Effects of CO2 on embryo physiology, embryonic organ development, and chick quality were marginal. EST interacted with CO2 mainly before IP, but effects were minor at hatch. Interactions between EST and CO2 were found at an EST of 36.7 and 37.8°C, but remained absent at an EST of 38.9°C, which might indicate that physiological systems are already challenged due to the higher metabolic rate, which limits the capacity to cope with high CO2 of the embryo.

No effect of start day of treatment was indicated for embryonic organ development and chick quality found at hatch, which suggests that EST affected these parameters only in the last phase of incubation, e.g. from E19 onward. However, first week post-hatch performance was affected by start day of treatment. The beneficial effects of a lower EST of 35.6 and 36.7°C applied during the last week of incubation found at hatch, might contribute to an enhanced development during the first week post-hatch as body weight, carcass weight, and gain to feed ratio were increased.

In conclusion, results of this thesis show that an EST below 37.8°C during late incubation is beneficial for embryo development, organ growth during incubation, and growth performance during the first week post-hatch. In addition, start day of treatment did not affect chick quality and organ growth, except heart weight, at hatch, which implies that effects of EST occur during the hatching phase, e.g. from E19 onward. Although, an effect of start day of treatment was found on first week post-hatch performance, it remains to be investigated whether an EST below 37.8°C leads to improved later life quality characteristics.

Biomassa voor de energievoorziening van tuinbouwclusters
Zwart, H.F. de; Ruijs, M.N.A. ; Visser, H.J.M. - \ 2016
Bleiswijk : Wageningen UR Glastuinbouw (Rapport GTB 1393) - 34 p.
bio-energie - glastuinbouw - haalbaarheidsstudies - economische haalbaarheid - warmte - kooldioxide - elektriciteit - biomassa - biobased economy - biochar - verbranding - opwekking van elektriciteit - warmteproductie - bioenergy - greenhouse horticulture - feasibility studies - economic viability - heat - carbon dioxide - electricity - biomass - combustion - electricity generation - heat production
Biomass combustion in combination with a cluster of greenhouses to provide heat, CO2 and electricity can provide a partly solution to the sustainability of the horticultural sector. A biomass gasification plant could also provide valuable biochar, the result of partial combustion of biocarbon. This was shown to have attractive characteristics to be used in high quality potting soil. Despite the high value of the biochar (contributing for 16% of the income from the plant), the economic feasibility of a biomass combustion plant depends heavily on governmental subsidies (SDE +). When the developed technology is used on a practical scale, a biomass plant of 8 MW thermal power and 1.4 MW of electrical power is a sound size. Such a plant fits well with a horticultural cluster of 15 hectares, consisting of 6 ha Tomato, 6 ha Pepper and 3 hectares of Chrysanthemum. The biomass plant produces over 91% of the heating and 95% of the CO2 requirement and 67% of the electricity counsumed. However during winter a lot of electricity will have to be bought, which is compensated with selling to the public grid in summer. The biomass combustion plant will mainly run on biomass is supplied from elsewhere. The biomass from the local cluster covers only 0.3% of the combusted amount. If all available biomass from Netherlands territory would be used to heat greenhouses about 20% of greenhouse industry could make use of system like described in this report.
Methodology for estimating emissions from agriculture in the Netherlands. : Calculations of CH4, NH3, N2O, NOx, PM10, PM2.5 and CO2 with the National Emission Model for Agriculture (NEMA)
Vonk, J. ; Bannink, A. ; Bruggen, C. van; Groenestein, C.M. ; Huijsmans, J.F.M. ; Kolk, J.W.H. van der; Luesink, H.H. ; Oude Voshaar, S.V. ; Sluis, S.M. ; Velthof, G.L. - \ 2016
Wageningen : Statutory Research Tasks Unit for Nature & the Environment (WOt-technical report 53) - 164 p.
air pollutants, greenhouse gases, livestock, crops, animal housing, manure storage, manure application, inorganic fertilizer, enteric fermentation, manure management, agricultural soils, liming, NIR, CRF, IIR, NFR - landbouw - gewassen - landbouwgronden - vee - huisvesting, dieren - dierlijke meststoffen - rundveemest - mestverwerking - begrazing - broeikasgassen - luchtverontreinigende stoffen - emissie - ammoniakemissie - kooldioxide - methaan - anorganische meststoffen - fermentatie - bekalking - nederland - compost - rioolslib - teelt - oogstresten - rijp worden - agriculture - crops - agricultural soils - livestock - animal housing - animal manures - cattle manure - manure treatment - grazing - greenhouse gases - air pollutants - emission - ammonia emission - carbon dioxide - methane - inorganic fertilizers - fermentation - liming - netherlands - composts - sewage sludge - cultivation - crop residues - ripening
The National Emission Model for Agriculture (NEMA) is used to calculate emissions to air from agricultural activities in the Netherlands on a national scale. Emissions of ammonia (NH3) and other N-compounds (NOx and N2O) from animal housing, manure storage, manure application and grazing are assessed using a Total Ammoniacal Nitrogen (TAN) flow model. Furthermore, emissions from application of inorganic N-fertilizer, compost and sewage sludge, cultivation of organic soils, crop residues, and ripening of crops are calculated. NEMA is also used to estimate emissions of methane (CH4) from enteric fermentation and manure management, particulate matter (PM) from manure management and agricultural soils, and carbon dioxide
(CO2) from liming. Emissions are calculated in accordance with international guidance criteria and reported in an annual Informative Inventory Report (IIR; for air pollutants) and National Inventory Report (NIR; for greenhouse gases). This methodology report describes the outline and backgrounds of the emission
calculations with NEMA
Adapting greenhouse climate for enhanced biocontrol and better performance of plant protection products
Vänninen, I. ; Meijer, R.J.M. - \ 2016
BioGreenhouse (Fact sheet BioGreenhouse 12) - 2 p.
horticulture - greenhouse horticulture - plant protection - natural enemies - pesticides - environmental temperature - humidity - lighting - carbon dioxide - plant health - organic farming - tuinbouw - glastuinbouw - gewasbescherming - natuurlijke vijanden - pesticiden - omgevingstemperatuur - vochtigheid - verlichting - kooldioxide - plantgezondheid - biologische landbouw
In greenhouse crop production, climatic parameters are often manipulated to optimize plant growth. Greenhouse climate has profound influences also on pests and their natural enemies used for biocontrol. The responses of arthropod pests, plant disease agents and natural enemies to constant temperatures and humidity are relatively well known, but many pertinent questions remain unsolved for pest and natural enemy biology and behaviour in conditions created by the newest greenhouse climate technologies and approaches. Greenhouse climate can be optimized also to benefit natural enemies and to work against pests and plant diseases, but we know less how to make this happen than we know how to manipulate plant growth through temperature, humidity, CO2 and light conditions.
Understanding photosynthesis important for CO2-dosing and lighting : CAM-plants difficult to deal with
Heuvelink, E. ; Kierkels, T. - \ 2016
In Greenhouses : the international magazine for greenhouse growers 5 (2016)1. - ISSN 2215-0633 - p. 14 - 15.
horticulture - greenhouse horticulture - carbon dioxide - dosage - cam pathway - illumination - photosynthesis - assimilation - kalanchoe - ornamental bromeliads - phalaenopsis - tuinbouw - glastuinbouw - kooldioxide - dosering - cam cyclus - belichting - fotosynthese - assimilatie - bromelia's als sierplanten
It used to be rare to come across plants that bind CO2 mainly at night: CAMplants. But it’s no longer an exception in the horticultural sector. Nowadays the best-selling pot plant in the Netherlands – phalaenopsis – belongs to this group. This then raises questions such as: When do CAM-plants behave according to the book and when don’t they? And when does it make sense to dose with CO2 and provide lighting?
Environmental and physiological control of dynamic photosynthesis
Kaiser, M.E. - \ 2016
University. Promotor(en): Leo Marcelis, co-promotor(en): Jeremy Harbinson; Ep Heuvelink. - Wageningen : Wageningen University - ISBN 9789462576346 - 248 p.
solanum lycopersicum - arabidopsis thaliana - photosynthesis - carbon dioxide - temperature - humidity - light intensity - fotosynthese - kooldioxide - temperatuur - vochtigheid - lichtsterkte

Irradiance is the main driver of photosynthesis. In natural conditions, irradiance incident on a leaf often fluctuates, due to the movement of leaves, clouds and the sun. These fluctuations force photosynthesis to respond dynamically, however with delays that are subject to rate constants of underlying processes, such as regulation of electron transport, activation states of enzymes in the Calvin cycle, and stomatal conductance (gs). For example, in leaves adapted to low irradiance that are suddenly exposed to high irradiance, photosynthesis increases slowly (within tens of minutes); this process is called photosynthetic induction. Photosynthesis in fluctuating irradiance (dynamic photosynthesis) is limited by several physiological processes, and is further modulated by environmental factors other than irradiance, such as CO2 concentration, air humidity and temperature. Studying dynamic photosynthesis and its environmental and physiological control can help to identify targets for improvements of crop growth, improve the accuracy of mathematical models of photosynthesis, and explore new, dynamic lighting strategies in greenhouses.

In this thesis, the limitations acting on dynamic photosynthesis are explored by reviewing the literature, by experimenting with a suite of environmental factors (CO2 concentration, temperature, air humidity, irradiance intensity and spectrum), genetic diversity in the form of mutants, genetic transformants and ecotypes, and by mathematical modelling. Several genotypes of tomato (Solanum lycopersicum) and the model plant Arabidopsis thaliana, all grown in climate chambers, were used in the experiments. The main findings of the thesis are that a) CO2 concentration and air humidity strongly affect the rate of change of dynamic photosynthesis through a combination of diffusional and biochemical limitations; b) Rubisco activation kinetics are pivotal in controlling rates of photosynthesis increase after a stepwise increase in irradiance, and are further affected by CO2 concentration; c) gs limits photosynthetic induction kinetics in A. thaliana but not in tomato in ambient conditions, and becomes a stronger limitation in low CO2 concentration or air humidity; and d) mesophyll conductance, non-photochemical quenching (NPQ) and sucrose synthesis do not limit dynamic photosynthesis under the conditions used.

In Chapter 1, the rationale for the research conducted is described, by introducing the concept of fluctuating irradiance and its effects on photosynthesis rates. The chapter discusses how dynamic photosynthesis is measured and described, and provides a range of possible applications of the insights gained by the research conducted in this dissertation.

In Chapter 2, the current literature is reviewed and a mechanistic framework is built to explore the effects that the environmental factors CO2 concentration, temperature and air humidity have on rates of dynamic photosynthesis. Across data from literature, higher CO2 concentration and temperature speed up photosynthetic induction and slow down its loss, thereby facilitating higher rates of dynamic photosynthesis. Major knowledge gaps exist regarding the loss of photosynthetic induction in low irradiance, dynamic changes in mesophyll conductance, and the extent of limitations imposed by gs across species and environmental conditions.

Chapter 3 is an experimental exploration of the effects of CO2 concentration, leaf temperature, air humidity and percentage of blue irradiance on rates of photosynthetic induction in dark-adapted tomato leaves. Rubisco activation, changes in stomatal and mesophyll conductance, diffusional and biochemical limitations, efficiency of electron transport through photosystem II, NPQ and transient water use efficiency, were examined to give a comprehensive overview of the environmental modulation of dynamic photosynthesis. Unlike the percentage of blue irradiance, increases in CO2 concentration, leaf temperature and air humidity all positively affected the rates of photosynthetic induction, and these effects were explained by changes in diffusional and biochemical limitations. Maximising the rates of Rubisco activation would increase CO2 assimilation by 6-10%, while maximising the rates of stomatal opening would increase assimilation by at most 1-2%, at the same time negatively affecting intrinsic water use efficiency.

In Chapter 4 it is explored whether the effects of CO2 concentration on dynamic photosynthesis are similar across various irradiance environments. Gain and loss of photosynthetic induction in several low irradiance treatments, as well as sinusoidal changes in irradiance, were studied using tomato leaves. Elevated CO2 concentration (800 ppm) enhanced the rate of photosynthetic induction by 4-12% (compared to 400 ppm) and decreased the loss of photosynthetic induction by 21-25%. Elevated CO2 concentration enhanced rates of dynamic photosynthesis regardless of initial photosynthetic induction state to a similar extent. Therefore, rising global CO2 concentration will benefit integrated assimilation throughout whole canopies, where different leaf layers experience widely differing irradiance regimes.

In Chapter 5 it is tested whether stomatal limitation exists during photosynthetic induction in tomato leaves. The abscisic acid-deficient flacca mutant and its wildtype were exposed to various CO2 concentrations to change the diffusion gradient. Despite gs being much larger in flacca, photosynthetic induction proceeded with the same speed in both genotypes in ambient CO2 concentration. This suggested that stomata did not limit photosynthetic induction in the wildtype. Using these findings, several indices of stomatal limitations were compared. Diffusional limitation, a new index, was found to be the most useful.

In Chapter 6, an exploration of some physiological limitations underlying dynamic photosynthesis is undertaken. Several mutants, transformants and ecotypes of A. thaliana, affecting rates of Rubisco activation, gs, NPQ and sucrose metabolism, were used. Next to a characterisation of their steady-state responses to CO2 concentrations and irradiance, leaves were exposed to stepwise increases and decreases in irradiance (using several intensities) and to lightflecks of several amplitudes and frequencies. Rubisco activase isoform and concentration, as well as various levels of gs, strongly affected rates of dynamic photosynthesis, while this was not the case with low NPQ or sucrose phosphate synthase concentration. This suggests Rubisco activase and gs as targets for improvement of photosynthesis in fluctuating irradiance.

Chapter 7 is a modelling exercise of dynamic photosynthesis, based on data obtained from measurements on mutants of A. thaliana (Chapter 6). This includes a goal-seeking model that allows reproducing the regulation of Rubisco by irradiance and CO2 concentration. The model also includes a full description of leaf-level NPQ, incorporates mesophyll conductance and accounts for the fundamental physics of delays introduced by open gas exchange systems on CO2 measurements. Different data sets for model calibration and validation were used. It was found that the model accurately predicted the effects of the mutants, suggesting that the assumptions of the model were sound and represented the underlying mechanisms correctly.

In Chapter 8, the findings in this thesis are synthesized. The insights gained throughout this dissertation are related to existing literature to give a comprehensive overview of the state of knowledge about the limitations of dynamic photosynthesis. The methodology of assessing transient stomatal limitations, and some aspects of using chlorophyll fluorescence measurements during photosynthetic induction, are discussed. Finally, possible applications and ideas for future research on photosynthesis in fluctuating irradiance are discussed.

Energiemonitor van de Nederlandse glastuinbouw 2014
Velden, N.J.A. van der; Smit, P.X. - \ 2015
LEI Wageningen UR (Rapport / LEI Wageningen UR 2015-122) - ISBN 9789086157211 - 58 p.
glastuinbouw - energiegebruik - energiebesparing - klimaatregeling - kastechniek - kooldioxide - emissie - greenhouse horticulture - energy consumption - energy saving - air conditioning - greenhouse technology - carbon dioxide - emission
De totale CO2-emissie nam in 2014. Ook zit de totale CO2-emissie 1,1 Mton onder het niveau van 1990 (-16%). Indien wordt gecorrigeerd voor de warme buitentemperatuur in 2014 dan is de CO2-emissie in 2014 6,0 Mton en dit ligt ook onder het doel voor 2020. In geheel Nederland ligt de CO2-emissie 2% onder het niveau van 1990. De glastuinbouw loopt daarmee voor op de landelijke ontwikkeling
Indirect calorimetry during incubation of hatching eggs
Brand, H. van den; Heetkamp, M.J.W. ; Kemp, B. - \ 2015
In: Indirect Calorimetry : Techniques, computations and applications / W.J.J., Gerrits, E., Labussière, Wageningen : Wageningen Academic Publishers - ISBN 9789086862610 - p. 231 - 246.
chickens - stable isotopes - oxygen - carbon dioxide - eggshell temperature
Indirect calorimetry can be used during incubation of avian eggs to monitor the quality of the incubation process, the development of the embryo and the utilization of nutrients. Indirect calorimetry has several benefits above direct calorimetry, particularly in hatching eggs. However, to obtain reliable measurements, some aspects of indirect calorimetry need to be taken into account. First, some attention is given to the use of respiration chambers for only one single egg or more eggs at the same time, with the advantages and disadvantages. Furthermore, attention is paid to the importance of using embryo or eggshell temperature as a tool to adjust the temperature in the respiration chamber. Since there is a strong relationship between embryo temperature and heat production (Q), the incubator temperature should be controlled depending on the desired eggshell temperature. Additionally, it is important to consider oxygen and carbon dioxide levels in the chamber, as low partial O2 pressure is related to incubation at high altitude and high CO2 levels can result from insufficient ventilation. Besides abiotic factors affecting Q, such as temperature, biotic factors, like egg weight and age of the breeder, affect Q as well. Finally, the use of stable isotopes during incubation to determine oxidation of different nutrients during the incubation process will be addressed. We conclude that indirect calorimetry during incubation of hatching eggs can give insight in the development of the embryo and the utilization of egg nutrients throughout incubation. However, to prevent misinterpretation of the results, some incubation factors (like temperature, O2 and CO2 concentration) and egg characteristics (like weight, breed and breeder age) need to be monitored and controlled.
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