Records 1 - 20 / 371
Plant communities on nitrogen-rich soil are less sensitive to soil moisture than plant communities on nitrogen-poor soil
Shovon, Tanvir Ahmed ; Rozendaal, Danaë M.A. ; Gagnon, Daniel ; Gendron, Fidji ; Vetter, Mary ; Vanderwel, Mark C. - \ 2020
Journal of Ecology 108 (2020)1. - ISSN 0022-0477 - p. 133 - 144.
community assembly - environmental filtering - light - multiple resource limitation - nitrogen - plant strategies - soil moisture - trait-based ecology
Plant species composition and diversity are known to change across local gradients of light, moisture and nutrients, but ecologists still have a relatively limited understanding of how communities respond to multiple limiting resources. We used a trait-based approach to investigate how the functional composition and diversity of forest understorey plant communities change along gradients in light, soil moisture and nitrogen availability. We used a total of seven leaf, root and whole-plant traits for 55–78 species, and estimated the effects of the three resources on the mean and dispersion of these traits in understorey plant communities across 50 forest sites. Soil moisture and nitrogen availability (C/N ratio) both influenced plant community traits, but light availability (canopy openness) did not. Generally, increases in moisture and nitrogen both resulted in shifts towards more acquisitive resource use strategies, including greater leaf area, specific leaf area and maximum plant height, and lower leaf dry matter content, root dry matter content and rooting depth. Functional diversity of most traits also increased with increasing soil moisture and nitrogen. Although most traits varied with soil moisture on nitrogen-poor sites, moisture did not influence of the distribution of any traits on nitrogen-rich sites. Synthesis. Independent co-limitation of soil moisture and nitrogen appeared to influence the functional composition and diversity of understorey vegetation in our study area. The co-occurrence of species with resource acquisitive and conservative strategies on nitrogen-rich sites may make plant communities relatively resistant to changes to soil moisture. These results suggest that altered precipitation regimes under climate change could lead to greater changes in the composition and diversity of plant communities on nutrient-poor soils than on nutrient-rich soils.
Ultraviolet radiation enhances salicylic acid-mediated defense signaling and resistance to Pseudomonas syringae DC3000 in a jasmonic acid-deficient tomato mutant
Escobar Bravo, Rocío ; Chen, Gang ; Grosser, Katharina ; Dam, Nicole M. Van; Leiss, Kirsten A. ; Klinkhamer, Peter G.L. - \ 2019
Plant Signaling & Behavior 14 (2019)4. - ISSN 1559-2316 - p. e1581560 - e1581560.
Abscisic acid - auxin - jasmonates - light - salicylic acid - ultraviolet radiation - western flower thrips
Ultraviolet radiation (UV) is an important modulator of plant defenses against biotic stresses. We have recently described that different supplemental UV exposure times and irradiance intensities enhanced tomato (Solanum lycopersicum) resistance to Western flower thrips (Frankliniella occidentalis). UV increased jasmonic acid-isoleucine (JA-Ile) and salicylic acid (SA) levels, as well as the expression of JA- and SA-responsive genes, before thrips herbivory. Here we report how UV affects tomato defense responses upon thrips infestation, and resistance to pathogens that are susceptible to the activation of SA-associated defenses. Our experiments reveal that, at 7 days after thrips infestation, UV did not enhance the levels of jasmonates, auxin or abscisic acid. UV also did not affect the expression of JA-responsive genes in the cultivar Moneymaker, the jasmonate deficient mutant def-1, the type-VI trichome deficient mutant od-2, or their wild-type Castlemart. However, UV strongly activated SA-associated defense responses in def-1 after thrips infestation. Further bioassays showed that UV increased def-1 resistance to the hemi-biotrophic bacterial pathogen Pseudomonas syringae pv. tomato DC3000, which is susceptible to SA-mediated defenses. Our results suggest that UV might enhance tomato resistance to this pathogen in the JA deficient genotype through the activation of SA defenses.
Phenotypic plasticity as a clue for invasion success of the submerged aquatic plant Elodea nuttallii
Szabó, S. ; Peeters, E.T.H.M. ; Várbíró, G. ; Borics, G. ; Lukács, B.A. - \ 2019
Plant Biology 21 (2019)1. - ISSN 1435-8603 - p. 54 - 63.
Alien - aquatic plant - competition - light - macrophyte - nitrogen
Two closely related alien submerged aquatic plants were introduced into Europe. The new invader (Elodea nuttallii) gradually displaced E. canadensis even at sites where the latter was well established. The aim of the study was to evaluate the combined effects of environmental factors on several phenotypic characteristics of the two Elodea species, and to relate these phenotypic characteristics to the invasion success of E. nuttallii over E. canadensis. In a factorial design, Elodea plants were grown in aquaria containing five different nitrogen concentrations and incubated at five different light intensities. We used six functional traits (apical shoot RGR), total shoot RGR, relative elongation, root length, lateral spread, branching degree) to measure the environmental response of the species. We calculated plasticity indices to express the phenotypic differences between species. Light and nitrogen jointly triggered the development of phenotypic characteristics that make E. nuttallii a more successful invader in eutrophic waters than E. canadensis. The stronger invader showed a wider range of phenotypic plasticity. The apical elongation was the main difference between the two species, with E. nuttallii being more than two times longer than E. canadensis. E. canadensis formed dense side shoots even under high shade and low nitrogen levels, whereas E. nuttallii required higher light and nitrogen levels. We found that under more eutrophic conditions, E. nuttallii reach the water surface sooner than E. canadensis and through intensive branching outcompetes all other plants including E. canadensis. Our findings support the theory that more successful invaders have wider phenotypic plasticity.
Photosynthetic efficiency in microalgal lipid production
Remmers, Ilse M. - \ 2017
Wageningen University. Promotor(en): R.H. Wijffels, co-promotor(en): P.P. Lamers. - Wageningen : Wageningen University - ISBN 9789463434607 - 200
algae - biofuels - light - triacylglycerols - lipids - metabolism - algae culture - cultural methods - algen - biobrandstoffen - licht - triacylglycerolen - lipiden - metabolisme - algenteelt - cultuurmethoden
Microalgae can contain large amounts of lipids which make them a promising feedstock for sustainable production of food, feed, fuels and chemicals. Various studies, including pilot-scale, have been performed and the knowledge on microalgal processes has advanced quickly. Unfortunately, current production costs for cultivation are still too high for bulk lipid production from microalgae.
One of the major causes for the high costs of bulk lipid production is the reduced solar-to-lipid conversion efficiency. Current research, however, does not provide sufficient insight to identify optimization targets. Therefore, in this thesis we have studied the lipid production in microalgae in depth.
Different TAG-accumulation strategies were investigated from a process engineering and metabolic point of view. The combination of all findings were used in the general discussion to thoroughly evaluate the microalgal lipid accumulation strategies. Current phototrophic microalgal lipid yields are still 10 times lower than the theoretical maximum. There is, however, still an enormous potential for further improvements. Future research should focus on (genetically) improved strains and advanced cultivation strategies, including adaptation to fluctuating outdoor weather conditions.
This thesis was performed within the EU FP7 FUEL4ME project under grand agreement No 308938. Objective of this program is to develop a sustainable and scalable process for biofuels from microalgae and to valorize the by-products.
Species mixing effects on forest productivity in the Netherlands
Lu, Huicui - \ 2017
Wageningen University. Promotor(en): G.M.J. Mohren, co-promotor(en): F.J. Sterck. - Wageningen : Wageningen University - ISBN 9789463436397 - 134
mixed forests - temperate zones - deciduous forests - soil fertility - light - yields - netherlands - gemengde bossen - gematigde klimaatzones - loofverliezende bossen - bodemvruchtbaarheid - licht - opbrengsten - nederland
Many monoculture forests (dominated by a single tree species) have been converted to mixed-species forests (dominated by more than one tree species) in Europe over the last decades. The main reason for this conversion was to increase productivity, including timber production, and enhance other ecosystem services, such as conservation of biodiversity and other nature values. In addition, it has been suggested that mixed-species forests are more resistant, resilient and stable to disturbances.
In line with the niche complementarity hypothesis, inter-specific differences in crown architecture, leaf phenology, shade tolerance and root distribution may allow tree species to partition resources in mixed forests. Such mechanisms may lead to a higher productivity of mixed forests versus monoculture forests, a phenomenon often referred to as overyielding. Interestingly, the stress-gradient hypothesis and the resource-ratio hypothesis suggests that such inter-specific interactions vary along a soil fertility gradient, but in different ways. The stress-gradient hypothesis emphasizes that more efficient partitioning increases overyielding at low fertility soils, whereas the resource ratio hypothesis considers that the denser packing of crowns on fertile soils allows for partitioning of light and overyielding on high fertility soils. Several studies have been carried out about species mixing effects on forest productivity, but so far their findings are ambiguous. Probably, this ambiguity comes from the sites that they studied, which differ in species, age, management history, and/or environmental conditions.
This thesis analyses the mixing effect on productivity in relation to the combination of species, stand age and soil fertility, and discusses possible consequences of forest management, for five two-species mixtures in the Netherlands: Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco)–beech (Fagus sylvatica L.), pine (Pinus sylvestris L.)–oak (Quercus robur L.), oak–beech, oak–birch (Betula pendula Roth) and pine–birch. These mixtures and their corresponding monoculture stands were studied using long-term permanent forest plots over multiple decades, but also using two inventories (around 2003 and 2013) across the entire Netherlands. These forest plots data were used together with empirical models at total stand level (chapter 2), species level (chapter 3) and tree level (chapter 4) to evaluate the mixing effect on forest productivity.
In chapter 2, four two-species mixtures and their corresponding monospecific stands were compared for productivity (volume stem wood in m3 ha-1 year-1). It was explored whether mixing species differing in leaf phenology and shade tolerance would lead to overyielding of mixed forest stands, and whether overyielding changes with stand development. In line with the niche complementarity hypothesis, the two evergreen–deciduous species mixtures (Douglas-fir–beech and pine–oak) showed overyielding whereas deciduous–deciduous species mixtures (oak–beech and oak–birch) did not. The overyielding was strongest for the Douglas-fir–beech mixture than the pine–oak mixture, which can be attributed to the greater difference in shade tolerance in the former mixture. Overyielding did not significantly change with stand development. It is argued that the regular thinning maintained the ability of species to partition resources, i.e. the complementary resource use in those mixed stands over all stand ages.
In chapter 3, it was analysed which of the two species in these four mixtures contributed to overyielding, and whether this overyielding changed along a soil fertility gradient. It was discovered that both the fast-growing and the slow-growing species could contribute to overyielding. Yet, it was mainly the fast-growing Douglas-fir that contributed to higher productivity in the Douglas-fir–beech mixtures, and the slow-growing oak that did so in the pine–oak mixtures. For both mixtures, the greatest relative productivity gain was achieved by mixtures on the poorer soils. At first sight, these results seem in line with the stress-gradient hypothesis and not the resource-ratio hypothesis. Yet, it was argued that not only complementary use of soil resources, but also use of light, may contribute to the higher productivity of mixed stands on the poorer soils.
In chapter 4, it was assessed how the growth of individual trees in mixtures was influenced by inter- and intra-specific competition, and whether this competition was mainly size-symmetric for soil resources or size-asymmetric for light on soils differing in fertility. This chapter focussed on three mixtures, i.e. oak–birch, pine–oak and pine–birch, which were available at sufficient numbers in the Dutch national forest inventory data. It was concluded that intra-specific competition was not necessarily stronger than inter-specific competition and this competitive reduction was less seen at lower soil fertility and dependent on species mixtures, which is not in line with the stress-gradient hypothesis. Moreover, size-asymmetric competition for light was more associated with tree basal area growth than size-symmetric competition for soil resources, suggesting that light is the most limiting resource. Competition for light was generally much stronger at high fertility soils, supporting the resource-ratio hypothesis. These results suggest that light is the most limiting resource for tree basal area growth and that reduced competition for light can be explained to some degree by complementarity in light use to increase tree growth in mixed forests.
This thesis thus described the productivity patterns when mixing tree species and explored possible mechanisms of higher productivity in mixed stands compared with monoculture stands in the Netherlands. Complementary use of aboveground and belowground resources probably contributes to the higher productivity in mixed stands, but other factors including pathogens, nutrient cycling and litter decomposition were not addressed but cannot be excluded. Overyielding in Douglas-fir–beech and pine–oak mixtures was maintained over time, probably owing to the intensive thinning in Dutch forests. The results shed new light on the stress-gradient and resource-ratio hypotheses. For mixtures in Dutch forest, the greatest productivity gain in Douglas-fir–beech and pine–oak mixtures was achieved on the poorer soils, and it was argued that this is at least partially driven by complementary use of light, while the role of complementarity in use of soil resources is more obscure. Overall, this thesis suggest a substantial potential of species mixing for increasing productivity, which may run in parallel with enhancing other ecosystem services such as conservation of diversity and other nature values. Yet, more experimental studies on productivity in mixed stands are required to better unravel alternative mechanisms. Such understanding is required to manage the forests effectively in a century of unpreceded human driven changes in environmental conditions.
How virtual shade sheds light on plant plasticity
Bongers, Franca J. - \ 2017
Wageningen University. Promotor(en): N.P.R. Anten, co-promotor(en): R. Pierik; J.B. Evers. - Wageningen : Wageningen University - ISBN 9789463432047 - 140
planten - fenotypen - fenotypische variatie - modellen - arabidopsis - natuurlijke selectie - schaduw - reacties - concurrentie tussen planten - licht - plants - phenotypes - phenotypic variation - models - arabidopsis - natural selection - shade - responses - plant competition - light
Phenotypic plasticity is the ability of a genotype to express multiple phenotypes in accordance with different environments. Although variation in plasticity has been observed, there is limited knowledge on how this variation results from natural selection. This thesis analyses how variation in the level of plasticity influences light competition between plants and how this variation could result from selection, driven by light competition, in various environments. As an exemplary case of phenotypic plasticity, this thesis focusses on phenotypic responses of the annual rosette plant Arabidopsis thaliana (Brassicaceae) in response to the proximity of neighbour plants, as signalled through the red : far—red (R:FR) ratio, which are responses associated with the shade avoidance syndrome (SAS).
Plant experiments were conducted to measure variation in these plastic responses and a functional-structural plant (FSP) model was created that simulates plant structures in 3D and includes these organ-level plastic responses while simulating explicitly a heterogeneous light environment. Simulating individual plants that explicitly compete for light, while their phenotype changes through plasticity, gave insights in the role of the level of phenotypic plasticity and site of signal perception on plant competitiveness. In addition, an analysis on how natural selection in different environments acts on the level of plasticity was performed by combining FSP simulations and evolutionary game theoretical (EGT) principles.
Open normen licht bij het bedrijfsmatig houden van gezelschapsdieren : praktische handvatten voor de controle op het voldoen aan ethologische en fysiologische behoeften van honden en konijnen
Ruis, Marko A.W. ; Borg, Joanne A.M. van der - \ 2017
Wageningen : Wageningen Livestock Research (Wageningen Livestock Research rapport 981) - 42
honden - konijnen - licht - kunstlicht - dierenwelzijn - dierhouderij - gezelschapsdieren - diergedrag - huisvesting, dieren - diergezondheid - dogs - rabbits - light - artificial light - animal welfare - animal husbandry - pets - animal behaviour - animal housing - animal health
This report describes the development of practical tools for inspectors to monitor compliance with the target welfare regulations with regard to provison of light for dogs and rabbits that are kept and sold commercially. On the basis of a literature study on the influence of light on the welfare and functioning of dogs and rabbits, and in the context of the situation in practice, tools were developed to supervise and advice in a systematic way. By this the inspector can make an informed assessment about whether or not enforcing rules on the provision of light.
Dynamic photosynthesis under a fluctuating environment: a modelling-based analysis
Morales Sierra, Alejandro - \ 2017
Wageningen University. Promotor(en): Paul Struik; Jaap Molenaar, co-promotor(en): Xinyou Yin; Jeremy Harbinson. - Wageningen : Wageningen University - ISBN 9789463430456 - 282
photosynthesis - modeling - analysis - environmental factors - light - canopy - leaves - crop physiology - metabolism - fotosynthese - modelleren - analyse - milieufactoren - licht - kroondak - bladeren - gewasfysiologie - metabolisme
In their natural environment, leaves are exposed to rapid fluctuations of irradiance. Research on CO2 assimilation under fluctuating irradiance often relies on measurements of gas exchange during transients where irradiance is rapidly increased or decreased, after the leaf has adapted to a particular set of environmental conditions. In the field, such increases and decreases occur mostly because of sunflecks (rapid increases in irradiance on a low irradiance background) created by gaps in the canopy and plant movement by wind, and cloudflecks (rapid decreases in irradiance on a high irradiance background) generated by clouds that transiently block the sun.
In this dissertation, the metabolic regulation of photosynthesis and how this may limit dynamic CO2 assimilation is studied in silico with the development and application of simulation models. In order to support the development of the models, a review of the literature was performed as well as an experiment designed to generate data on dynamic CO2 assimilation for different photosynthetic mutants of Arabidopsis thaliana. In addition to providing these models to the research community, this dissertation also identifies multiple targets that may be used for improving dynamic CO2 assimilation in plants. It further demonstrates that the dynamic responses of CO2 assimilation to changes in irradiance has a significant effect on canopy CO2 assimilation, even for dense canopies exposed to open skies, resembling the conditions of commercial crops.
In Chapter 1, the context of this dissertation is presented. The societal relevance of this research is argued, making reference to the role that photosynthesis could play in addressing global problems such as food and energy security. The necessary background on the physiology of photosynthesis is provided, with special emphasis on the terminology and concepts required to understand the rest of the dissertation, with the aim of making the contents more accessible to a wider audience. Then, prior literature on the specific topics of this dissertation (i.e., photosynthesis in a dynamic environment and its mathematical modelling) is presented, with a chronological approach that analyses the evolution of ideas and methodologies up to the present.
In Chapter 2, the current literature on dynamic CO2 assimilation is reviewed, with an emphasis on the effects of environmental conditions ([CO2], temperature, and air humidity) on the rates of photosynthetic induction and loss of induction. This review reveals major knowledge gaps, especially on the loss of induction. The little data available indicates that rates of photosynthetic induction increase with [CO2], which could be explained by a weak effect on Rubisco activation and a strong effect on stomatal opening. Increases in temperature also increase the rates of photosynthetic induction, up to an optimum, beyond which a strong negative effect can be observed, which could be attributed to deactivation of Rubisco activase.
In Chapter 3, an experiment is presented that makes use of several photosynthetic mutants of A. thaliana. Downregulating non-photochemical quenching and sucrose synthesis did not have any significant effect on dynamic CO2 assimilation, whereas CO2 diffusion and Rubisco activation exerted stronger limitations. Further analysis reveals that whether stomatal opening limits CO2 assimilation after an increase in irradiance depends on the stomatal conductance prior to the change in irradiance. A threshold value of 0.12 mol m−2 s−1 (defined for fluxes of water vapour) could be defined, above which stomata did not affect the rates of photosynthetic induction. The comparison of measurements across irradiance levels also indicated that the apparent rate constant of Rubisco activation is irradiance-dependent, at least for irradiance levels below 150 μmol m−2 s−1.
In Chapter 4, a phenomenological model of leaf-level CO2 assimilation is presented. The model is described in detail and all the parameters are first estimated with published data, and later refined by fitting the model to the data from Chapter 3. Additional data from the experiment in Chapter 3 is used to validate predictions of CO2 assimilation under lightflecks for the different photosynthetic mutants. The model predicts accurately dynamic CO2 assimilation for the different photosynthetic mutants by only modifying those parameters that are affected by the mutation. This demonstrates that the model has a high predictive power and that the equations, although phenomenological in nature, have a solid physiological basis.
The model is further used to analyse, in silico, the limitations imposed by different photosynthetic processes on dynamic CO2 assimilation at the leaf and canopy level, allowing a more in depth analysis than in Chapter 3. The analysis demonstrates that results obtained at the leaf level should not be extrapolated directly to the canopy level, as the spatial and temporal distribution of irradiance within a canopy is more complex than what is achieved in experimental protocols. Both at the leaf and canopy level, CO2 diffusion is strongly limiting, followed by photoinhibition, chloroplast movements and Rubisco activation.
In Chapter 5, a mechanistic model of the dynamic, metabolic regulation of the electron transport chain is presented. The model is described in detail and all the parameters are estimated from published literature, using measurements on A. thaliana when available. Predictions of the model are tested with steady-state and dynamic measurements of gas exchange, chlorophyll fluorescence and absorbance spectroscopy on A. thaliana, with success.
The analysis in silico indicates that a significant amount of alternative electron transport is required to couple ATP and NADPH production and demand, and most of it is associated with nitrogen assimilation and export of redox power through the malate shuttle. The analysis also reveals that the relationship between ATP synthesis and the proton motive force is highly regulated by the concentrations of substrates (ADP, ATP and inorganic phosphate), and this regulation facilitates an increase in non-photochemical quenching under conditions of low metabolic activity in the stroma.
In Chapter 6, the findings of Chapters 2–5 are summarised and employed to answer in detail the four research questions formulated in Chapter 1. Of great interest is the identification of six potential targets that may be used to improve dynamic CO2 assimilation. These targets are: (i) regulation of Rubisco activity through changes in the amount or regulation of Rubisco activase, (ii) acceleration of stomatal opening and closure, (iii) a lower /ATP for ATP synthesis, (iv) faster relaxation of non-photochemical quenching, (v) reduced chloroplast movements, and (vi) reduced photoinhibition by increased rates of repair of Photosystem II.
Tuning for light and more : engineering phototrophy and membrane proteins in Escherichia coli
Claassens, Nicolaas J.H.P. - \ 2017
Wageningen University. Promotor(en): John van der Oost; Willem de Vos, co-promotor(en): Vitor Martins dos Santos. - Wageningen : Wageningen University - ISBN 9789463430920 - 328
escherichia coli - phototropism - membranes - proteins - light - photosystem i - gene expression - escherichia coli - fototropie - membranen - eiwitten - licht - fotosysteem i - genexpressie
The application of microbial and plant photosynthesis for biobased production on the one hand has a huge potential but on the other hand photosynthesis has serious limitations regarding its efficiency. Hence, studying both fundamental features of photosynthetic processes and engineering of photosystems is of paramount interest, exploring the engineering of photosystems is the overarching aim of this thesis. As described in Chapter 1, natural photosystems may be modified or transplanted to allow for more efficient conversion of solar light energy into biochemical energy. Hereto ambitious proposals to engineer photosystems have been made, and to realize those endeavors the disciplines of synthetic and systems biology are required. To explore how to apply and improve those disciplines hereto, the work described in this thesis has focused on the transplantation of simple photosystems (proton-pumping rhodopsins; PPRs) into the cell membrane of the heterotrophic model bacterium Escherichia coli. Both in silico analyses, including metabolic and thermodynamic modeling (Chapter 3) and a series of experimental studies on transplanting PPR photosystems (Chapters 4,6 and 7) were performed, which identified several challenges, limitations and most importantly opportunities. This thesis also describes the application of novel tools to substantially improve the functional production of PPRs and a variety of other membrane proteins in E. coli.
Chapter 2 provides more details on previously reported examples of heterologous expression of PPRs in several hosts, and on the physiological impact of these transplanted photosystems. Based on this evaluation, some suggestions are made to improve and further exploit the transplantation of these photosystems.
In Chapter 3 a systematic, integrated in silico analysis is made of anaerobic, photo-electro-autotrophic synthetic metabolism in E. coli, consisting of (i) a PPR photosystem for ATP regeneration, (ii) an electron uptake pathway, and (iii) a natural or synthetic carbon fixation pathway. Constraint-based metabolic modelling of E. coli central metabolism is used, in combination with kinetic and thermodynamic pathway analyses. The photo-electro-autotrophic designs are predicted to have a limited potential for anaerobic, autotrophic growth of E. coli, given the relatively low ATP regenerating capacity of the PPR photosystems, and the relatively high ATP consumption due to maintenance. In general these analyses illustrate the potential of in silico analyses to identify potential bottlenecks and solutions in complex designs for autotrophic and photosynthetic metabolism, as a basis for subsequent experimental implementation.
To tackle a main bottleneck of PPR systems: their functional membrane-embedded production level, the heterologous production in E. coli of the proton-pumping rhodopsins from Gloeobacter violaceus (GR) and from Thermus thermophilus JL18 (TR) is quantified and experimentally optimized in Chapter 4. High constitutive production of both rhodopsin proteins is achieved by fine-tuning transcription and translation. Besides the canonical retinal pigment, the GR system has the ability to bind a light-harvesting antennae pigment, echinenone. After optimization of the heterologous pigment biosynthesis pathways for either retinal or echinenone production, appropriate quantities of retinal or echinenone for PPR reconstitution were detected in E. coli. Association of echinenone with GR broadens its absorption spectrum in E. coli, broadening the potential for light-harvesting also to blue light. Optimization of the branched pathway for simultaneous biosynthesis of both retinal and echinenone has been attempted by using a smart library of variable Ribosome Binding Sites (RBSs) with varying strengths (RedLibs). In general, the here described approaches towards improved functional production of rhodopsin photosystems in E. coli and their pigments may prove more widely applicable for heterologous production of more complex photosystems and other systems.
In Chapter 5 an up-to-date overview is provided on how codon usage can influence functional protein production. The fact that all known organisms have an incomplete set of tRNAs, indicates that biased codon usage could act as a general mechanism that allows for fine-tuning the translation speed. Although translation initiation is the key control step in protein production, it is broadly accepted that codon bias, especially in regions further downstream of the start codon, can contribute to the translation efficiency by tuning the translation elongation rate. Modulation of the translation speed depends on a combination of factors, including the secondary structure of the transcript (more or less RNA hairpins), the codon usage landscape (frequent and more rare codons) and for bacteria also RBS-like sequences at which ribosomes can pause. The complex combination of interdependent factors related to codon usage that can influence translation initiation and elongation. This complexity makes that the design of synthetic genes for heterologous expression is still in its infancy, and despite the availability of some codon usage algorithms, it is often as well a matter of trial and error.
In Chapter 6 the effect of different codon usage algorithms (optimization and harmonization) has been experimentally tested for heterologous production of membrane proteins. Apart from the codon usage algorithms also the combined effect of transcriptional fine-tuning in E. coli LEMO21(DE3) was assessed. The overproduction of 6 different membrane-embedded proteins, including 4 PPR variants (from bacteria, archaea and eukaryotes), was tested. For production of tested PPR variants, the different codon usage algorithms hardly influenced production, while transcriptional tuning had a large impact on production levels. Interestingly, for the other two tested non-PPR membrane proteins, some codon usage variants significantly improved production on top of transcriptional tuning. For both these proteins the codon-optimization algorithm reduced functional production below that of the wild-type codon variant, while the harmonization algorithm gave significantly higher production, equal or even higher than for the wild-type variant.
In Chapter 7 it is demonstrated that a translational-tuning system can be used to successfully optimize the expression of several membrane proteins, based on initial findings presented in Chapter 4. The employed, recently developed Bicistronic Design (BCD) system is based on translational coupling of a gene encoding a short leader peptide and the gene of interest that is under control of a variable ribosome binding site. A standardized library of 22 RBSs allows for precise, gene context-independent, fine-tuning of expression of this second gene, here encoding a membrane protein. For all four membrane proteins tested in this study the BCD approach resulted in 3 to 7-fold higher protein levels than those obtained by two other recently developed methods for optimizing membrane protein production. The presented approach allows for inducer-free, constitutive, high-level production of membrane proteins in E. coli, which can be widely applicable for both membrane protein purification studies as well as for synthetic biology projects involving membrane proteins.
In Chapter 8 a broad review and perspectives are provided on the potential of microbial autotrophs for the production of value-added compounds from CO2. Both photoautotrophic and chemolithoautotrophic production platforms are discussed, and recent progress in improving their efficiency and production potential is highlighted. Transplantation efforts for photosystems, but also for CO2 fixation pathways and electron uptake systems are discussed. An overview is provided on novel in silico and experimental approaches to engineer components related to autotrophy in heterotrophic and autotrophic model hosts, including approaches applied in this thesis. Future avenues are discussed for realizing more efficient autotrophic production platforms.
Finally, in Chapter 9 and 10 the work in this thesis is summarized and a general discussion is provided on future avenues for engineering of PPR photosystems, photosystems in general and on the optimization of membrane protein production.
LED’s zijn geschikt om snel dips en pieken in natuurlijk licht op te vangen
Gelder, Arie de - \ 2016
led lamps - roses - heat exchangers - heat - thermal radiation - light - artificial light - greenhouse horticulture
Recente trends in de vogelstand nabij de Eerste Bathpolder en mogelijke effecten van verlengde assimilatiebelichting
Tamis, J.E. ; Jongbloed, R.H. ; Ysebaert, T. - \ 2016
Den Helder : Wageningen Marine Research (Wageningen Marine Research rapport C128/16) - 59
vogels - lichtregiem - licht - glastuinbouw - natura 2000 - zeeland - birds - light regime - light - greenhouse horticulture - natura 2000 - zeeland
In de Eerste Bathpolder in de provincie Zeeland (gemeente Reimerswaal, nabij Rilland en grenzend aan het Natura 2000-gebied Oosterschelde) is sinds 2000 een aantal kassen gevestigd in een glastuinbouwgebied. Voor elk Natura 2000-gebied gelden instandhoudingsdoelen, die aangeven welke leefgebieden en welke soorten (plant en dier) behouden of hersteld moeten worden. Eén van de mogelijke effecten van de glastuinbouwbedrijven op de nabije omgeving is effecten van zogenaamd groeilicht (assimilatiebelichting) op de buitendijkse natuur van de Oosterschelde (met name op vogels). In 2009 heeft IMARES een deskstudie, veldonderzoek en analyse van vogeltellingen uitgevoerd, op basis waarvan geen duidelijke effecten van assimilatiebelichting op de beschermde vogelsoorten zijn aangetoond (Ysebaert et al., 2009). Onlangs hebben de glastuinbouwbedrijven nieuwe belichtingsstrategieën ontwikkeld wat een reductie van de lichtuitstoot bewerkstelligt van maximaal 34% t.o.v. de bestaande situatie, gebaseerd op de totale lichtbelasting gedurende een jaar. Het voorgestelde lichtregime veroorzaakt echter in de avond (van zonsondergang tot 20.00 uur) wel een tijdelijke verhoging van de lichtbelasting, vooral in de wintermaanden. Daarom is aan Wageningen Marine Research (voorheen IMARES) gevraagd opnieuw onderzoek te doen naar de recente trends in de vogelstand en de mogelijke effecten van langer belichten op de kwalificerende (Natura 2000-) natuurwaarden nabij de Eerste Bathpolder. Dit rapport beschrijft de resultaten van dit onderzoek.
Prima opbrengst winterlichtgewas komkommer in innovatieve kas : zowel energiebesparing als productieverhoging haalbaar
Janse, Jan - \ 2016
greenhouses - greenhouse horticulture - cucumis - innovations - winter - light - light transmission - cultivation - energy consumption
Eerste proef met dynamisch lichtrecept in tomaat geeft 8% meerproductie
Dieleman, Anja ; Weerheim, Kees - \ 2016
led lamps - colour - cultivation - light - tomatoes - plants - greenhouse horticulture - lamps
Het Nieuwe Gewas : sturen van de plantvorm voor verhoogde lichtbenutting
Gelder, Arie de; Janse, Jan ; Warmenhoven, Mary - \ 2016
Bleiswijk : Wageningen UR Glastuinbouw (Rapport GTB 1407) - 62
tomaten - solanum lycopersicum - kasgewassen - glasgroenten - glastuinbouw - energiebesparing - plantenontwikkeling - gewasteelt - licht - tomatoes - solanum lycopersicum - greenhouse crops - greenhouse vegetables - greenhouse horticulture - energy saving - plant development - crop management - light
Wageningen UR Greenhouse horticulture searched in the “The New Crop” project for the crop structure that best contributes to the goal of energy-efficient production and therefore energy saving, by removing 33, 44 or 55% of the leaves at a young stage. On October 10th 2014 the experiment started with topped plants of the tomato variety Brioso grafted on Maxifort. Dry matter production was lowest in the very open crop, however partitioning to the fruits was highest in that treatment. Therefore, this crop produced in the winter under assimilation lighting most. In summer, the standard treatment was the best and the production in this treatment was highest. The plants in the very open treatment were shorter and had smaller leaves than the plants of the standard treatment. This is might be due to a different red: far red ratio of light in the crop. Leaf picking at a young stage contributes to better distribution of assimilates to the fruits. This can be used as a crop management measure as the plant in winter develops too much leaves. The project was funded by the Dutch energy transition program “Kas als Energiebron”.
Energiebesparing met LED belichting in gerbera : resultaten van 1ste jaar LED onderzoek
García, Nieves ; Weerheim, Kees ; Helm, Frank van der; Kempkes, Frank ; Visser, Pieter de; Groot, Marco - \ 2016
Bleiswijk : Wageningen UR Glastuinbouw (Report GTB 1389) - 66
gerbera - glastuinbouw - kasgewassen - kassen - kastechniek - teelt onder bescherming - energiebesparing - led lampen - kunstlicht - kunstmatige verlichting - licht - verlichting - gerbera - greenhouse horticulture - greenhouse crops - greenhouses - greenhouse technology - protected cultivation - energy saving - led lamps - artificial light - artificial lighting - light - lighting
In the winter 2013-2014 Wageningen UR Greenhouse Horticulture conducted studies on energy saving opportunities in the cultivation of gerbera, CV Kimsey. The research was funded by the program Greenhouse as Energy Source from the Ministry of Economic Affairs and LTO Glaskracht. The contribution of LED lighting, LED interlighting, a lower intensity of the light installation, and light integration was investigated. An electricity savings of 45% was the target. By using LED lighting a 20% electricity savings are possible in exchange for a small production loss (2.3%) and some additional heat demand (9%). By installing 80 instead of 100 μmol light gerbera growers can save another 20% energy costing only 3.9% production without sacrificing quality. The targeted PAR sum for light integration was too high to contribute to electricity savings. The use of 20 μmol LED interlighting in combination with 60 μmol top light (LED or SON-T) resulted in significantly less production (9%) and lower flower quality: shorter and lighter, smaller diameter and a lower % of dry matter) than 80 μmol top light.
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 - fragaria ananassa - 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.
Light on phloem transport (an MRI approach)
Prusova, Alena - \ 2016
Wageningen University. Promotor(en): Herbert van Amerongen, co-promotor(en): Henk van As. - Wageningen : Wageningen University - ISBN 9789462579156 - 130
solanum lycopersicum - phloem - light - flow - photoperiod - nuclear magnetic resonance - biophysics - magnetic resonance imaging - solanum lycopersicum - floëem - licht - stroming - fotoperiode - kernmagnetische resonantie - biofysica - kernspintomografie
This thesis (Light on phloem transport – an MRI approach) aims to answer the question whether phloem transport can be a limiting factor for photosynthesis efficiency (and ultimately causing a bottleneck towards achieving higher yields). To answer this key question, we manipulated the source: sink ratio within tomato (Solanum lycopersicum L.) while measuring phloem transport with magnetic resonance imaging (MRI) flowmetry. Additionally we compared phloem flow characteristics of two potato plants (Solanum tuberosum L.) which differed in source : sink ratio. In Chapter 2, the source strength was manipulated by varying the light intensity. An increase in phloem sap volume flow under higher light intensities was observed. However, under all light intensities applied, the phloem flow velocity was found to be constant (as has previously been suggested in other studies) although a clear diurnal pattern was observed. This finding does not fit in current models to describe the mechanism of phloem transport and a different mechanism must be at play. The results of this chapter demonstrate that increased levels of photo-assimilates are transported in sieve tubes, which are activated when needed by the plant. This is the first study which shows that plants activate individual sieve tubes when more photo-assimilates are available, yet maintain constant velocity. Those observations were in a tomato plant with pruned fruit trusses (i.e., in a simplified system). In Chapter 3, we investigated whether tomato plants still exhibit constant phloem flow velocity (with a diurnal pattern) under normal conditions, i.e., with strong sinks (tomato fruits) still attached. This was tested for both a long and short photoperiod by measuring flow characteristics with MRI flowmetry. We simultaneously monitored other plant processes like xylem flow rates with a heat balance sensor, net photosynthesis with gas exchange and stem diameter changes with a linear motion potentiometer. With this integrated approach, we revealed a correlation between night phloem volume flow, dark respiration and stem growth. We also conclusively showed that phloem volume flow performs a diurnal pattern under a variety of source-sink ratios which appears to be a normal behaviour for tomato plants growing under moderately-high light conditions. In chapters 2 and 3 we learned that under higher source strength a greater amount of phloem sap is transported, but the changes in flow were not accompanied by changes in velocity. To further our understanding of the mechanisms driving phloem transport, it is of interest to know how the sucrose concentration in phloem sap relates to phloem flow. In Chapter 4 we used an average T2 relaxation time in the phloem vascular tissue region to reveal the plant’s phloem carbon status under source manipulation. In this chapter we demonstrated that T2 relaxation time, when measured in parallel with phloem flow, can provide additional information about phloem region carbon status, i.e., changes in the T2 relaxation time are correlated with changes in sucrose concentration in the whole phloem region.
When studying phloem transport in plants with magnetic resonance imaging (MRI) flowmetry, plants which are relatively easy to manipulate (e.g. fruit pruning) like tomato have so far been used. However, tomato plants (used in all three previous chapters) have relatively low sink strength beneath the MRI measurement site. A potentially preferable approach is to work with plants with strong sinks beneath the measurement site. In Chapter 5 we studied potato as a potentially better test subject for MRI flowmetry as it possesses strong sink below the MRI measurement site (i.e., developing tubers). For that purpose we used two potato plants (cv. Desiree) both with several developing tubers. One of the plants overexpressed the StSWEET gene (35S:StSWEET) which appears to have altered its source : sink ratio. As a result, the 35S:StSWEET plant transported 60% more phloem sap than Desiree WT. Strikingly, the average phloem flow velocity in both plants was the same and the greater amount of transported phloem sap in the 35S:StSWEET plant was accommodated by more sieve tubes than in Desiree WT. This finding agrees with the hypothesis about the conserved nature of phloem flow velocity, where volume flow is regulated by the number of active sieve tubes (Chapter 2 and 3). In this chapter we also demonstrate that a potato plant with developing tubers represents a good subject to study phloem transport with MRI flowmetry. We concluded that under optimal conditions (which are commonly met in greenhouses) phloem transport is likely to reach its maximum capacity and therefore photosynthesis could be limited by the export and transport of photo-assimilates because of the finite number of sieve tubes and constant flow velocity.
Antenna size reduction in microalgae mass culture
Mooij, T. de - \ 2016
Wageningen University. Promotor(en): Rene Wijffels, co-promotor(en): Marcel Janssen. - Wageningen : Wageningen University - ISBN 9789462578890 - 196
algae culture - algae - light - photobioreactors - photosynthesis - mutants - algenteelt - algen - licht - fotobioreactoren - fotosynthese - mutanten
The thesis describes the potential of microalgae with a reduced light harvesting antenna for biomass production under mass culture conditions (high biomass density, high light intensity). Theoretically, the lower chlorophyll content reduces the light harvesting capacity and with that the amount of photosaturation. The result would be an increase of the biomass yield on light energy, which is especially favorable at high light intensities. In practice, it was found that the productivity of several antenna size mutants strains was equal, or even lower than that of wild type microalgae. The genetically modified algae suffered from a reduced fitness, possibly because the antenna alterations led to impaired photoprotection mechanisms. In an alternative approach, it was found that by spectral tuning (applying different light colours) oversaturation was decreased and the productivity of wild type microalgae was increased. Special attention was paid to photoacclimation behavior of wild type microalgae. It was investigated whether ‘natural acclimation’ can be exploited to maximize productivity. In the last chapter, the competition between antenna size mutants and wild type cells is investigated by means of a modeling approach. It became clear that a wild type infection of an antenna size mutant culture should be prevented at all costs, as the mutants have a reduced competitive strength.
Plant ‘voelt’ zwaartekracht vooral met speciale zetmeelkorrels : altijd interactie tussen geotropie en fototropie
Heuvelink, E. ; Kierkels, T. - \ 2016
Onder Glas 13 (2016)4. - p. 50 - 51.
tuinbouw - plantkunde - zwaartekracht - zetmeelkorrels - groeianalyse - gravitropie - fototropie - celmembranen - licht - auxinen - horticulture - botany - gravity - starch granules - growth analysis - gravitropism - phototropism - cell membranes - light - auxins
Charles Darwin is niet alleen bekend door de evolutietheorie. De negentiende eeuwse wetenschapper was namelijk de eerste die rond 1880 aantoonde dat planten reageren op de zwaartekracht. Daarna was het nog 125 jaar wachten voordat duidelijk werd dat planten de zwaartekracht ook echt nodig hebben voor een normale groei.
Natural genetic variation for regulation of photosynthesis response to light in Arabidopsis thaliana
Rooijen, R. van - \ 2016
Wageningen University. Promotor(en): Maarten Koornneef, co-promotor(en): Mark Aarts; Jeremy Harbinson. - Wageningen : Wageningen University - ISBN 9789462578203 - 235
arabidopsis thaliana - photosynthesis - genetic variation - light - efficiency - arabidopsis thaliana - fotosynthese - genetische variatie - licht - efficiëntie
The efficiency of photosynthesis results from the composition and organization of the plant’s internal structural components as well as the capability of response to environmental fluctuations. This thesis aims at identifying the genetic loci that are regulating the (sub-) processes in photosynthetic acclimation to increased irradiance levels, in order to obtain the genetic information useful to breed for photosynthetic performance. It uses genome wide association studies (GWAS) to reveal which genetic loci are being exploited in nature for keeping good photosynthetic performances in natural conditions. Phenotypic variation among natural accessions in photosynthetic light use efficiency response to increased growth irradiance is related to its variation in genetics in order to identify the associated genetic loci. In Chapter 2 is described which light environment reveals most natural variation in photosynthetic performance and for which photosynthetic parameter this is. It shows different Arabidopsis accessions display different photosynthetic responses to various light environments, well relatable to genetic differences. A candidate gene list for the direct response to increased growth irradiance was revealed after performing genome wide association analysis. Chapter 3 elaborates on the genome wide association results by visualizing the dynamics of the associated genetic loci over the time course of the photosynthetic response to increased irradiance. It shows it is possible to simplify the complexity of photosynthetic physiology as well as the genetic analysis in such way to confirm the causal genes underlying the associated loci, by confirming this for the YELLOW SEEDLING 1 (YS1) gene, a gene encoding a Pentatrico-Peptide-Repeat (PPR) protein involved in RNA editing of plastid-encoded genes essential for photosystems I and II. Genetic variation for any trait can be on the transcriptional level or on the functional level. In Chapter 4, the gene regulation in three Arabidopsis accessions with contrasting photosynthesis efficiency responses to increased irradiance is studied. These differences in photosynthesis efficiency are associated to differences in activation extents of heat responsive genes as well as to differences in the presence of a gene activation pathway acting on membrane lipid remodelling, suggested to maintain balanced cellular phosphate concentrations. Chapter 5 confirms the significance of maintaining balanced cellular phosphate concentrations for photosynthesis efficiency responses to increased irradiance. It describes how genome wide association mapping and linkage mapping combine to reveal genetic epistatic interactions between PHOSPHATIDIC ACID PHOPSPHOHYDROLASE 2 (PAH2, phosphate metabolism gene) and ASPARAGINE SYNTHETASE 2 (ASN2, nitrogen metabolism gene), both acting in the delivery of orthophosphate in the chloroplast. In conclusion this thesis contributes new insights into the physiological and molecular pathways underlying photosynthesis responses to increased growth irradiances.