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 relationship between leaf area growth and biomass accumulation in Arabidopsis thaliana
    Weraduwage, S.M. ; Chen, J. ; Anozie, F.C. ; Morales Sierra, A. ; Weise, S.E. ; Sharkey, T.D. - \ 2015
    Frontiers in Plant Science 6 (2015). - ISSN 1664-462X - 21 p.
    plant-growth - photosynthetic acclimation - nighttime transpiration - phaseolus-vulgaris - starch turnover - root-growth - model - respiration - light - maintenance
    Leaf area growth determines the light interception capacity of a crop and is often used as a surrogate for plant growth in high-throughput phenotyping systems. The relationship between leaf area growth and growth in terms of mass will depend on how carbon is partitioned among new leaf area, leaf mass, root mass, reproduction, and respiration. A model of leaf area growth in terms of photosynthetic rate and carbon partitioning to different plant organs was developed and tested with Arabidopsis thaliana L. Heynh. ecotype Columbia (Col-0) and a mutant line, gigantea-2 (gi-2), which develops very large rosettes. Data obtained from growth analysis and gas exchange measurements was used to train a genetic programming algorithm to parameterize and test the above model. The relationship between leaf area and plant biomass was found to be non-linear and variable depending on carbon partitioning. The model output was sensitive to the rate of photosynthesis but more sensitive to the amount of carbon partitioned to growing thicker leaves. The large rosette size of gi-2 relative to that of Col-0 resulted from relatively small differences in partitioning to new leaf area vs. leaf thickness.
    Quantifying the source-sink balance and carbohydrate content in three tomato cultivars
    Li, T. ; Heuvelink, E. ; Marcelis, L.F.M. - \ 2015
    Frontiers in Plant Science 6 (2015). - ISSN 1664-462X
    dry-matter production - leaf photosynthesis - plant-growth - leaves - strength - yield - metabolism - simulation - storage - light
    Supplementary lighting is frequently applied in the winter season for crop production in greenhouses. The effect of supplementary lighting on plant growth depends on the balance between assimilate production in source leaves and the overall capacity of the plants to use assimilates. This study aims at quantifying the source-sink balance and carbohydrate content of three tomato cultivars differing in fruit size, and to investigate to what extent the source/sink ratio correlates with the potential fruit size. Cultivars Komeet (large size), Capricia (medium size), and Sunstream (small size, cherry tomato) were grown from 16 August to 21 November, at similar crop management as in commercial practice. Supplementary lighting (High Pressure Sodium lamps, photosynthetic active radiation at 1 m below lamps was 162 mu mol photons m(-2) s(-1); maximum 10 h per day depending on solar irradiance level) was applied from 19 September onward. Source strength was estimated from total plant growth rate using periodic destructive plant harvests in combination with the crop growth model TOMSIM. Sink strength was estimated from potential fruit growth rate which was determined from non-destructively measuring the fruit growth rate at non-limiting assimilate supply, growing only one fruit on each truss. Carbohydrate content in leaves and stems were periodically determined. During the early growth stage, Komeet' and Capricia' showed sink limitation and 'Sunstream' was close to sink limitation. During this stage reproductive organs had hardly formed or were still small and natural irradiance was high (early September) compared to winter months. Subsequently, during the fully fruiting stage all three cultivars were strongly source-limited as indicated by the low source/sink ratio (average source/sink ratio from 50 days after planting onward was 0.17, 0.22, and 0.33 for 'Komeet, 'Capricia,' and 'Sunstream,' respectively). This was further confirmed by the fact that pruning half of the fruits hardly influenced net leaf photosynthesis rates. Carbohydrate content in leaves and stems increased linearly with the source/sink ratio. We conclude that during the early growth stage under high irradiance, tomato plants are sink-limited and that the level of sink limitation differs between cultivars but it is not correlated with their potential fruit size. During the fully fruiting stage tomato plants are source-limited and the extent of source limitation of a cultivar is positively correlated with its potential fruit size.
    Growth dynamics of tree nursery seedlings: The case of oil palm
    Akpo, E. ; Stomph, T.J. ; Kossou, D. ; Struik, P.C. - \ 2014
    Scientia Horticulturae 175 (2014). - ISSN 0304-4238 - p. 251 - 257.
    plant-growth - field performance - feeding damage - pot size - leaf - fertilization - plantations - populations - attributes - management
    Tree seedling survival in the field partly depends on management during seedling production. Insight into how nursery practices affect seedling growth dynamics would generate understanding in how to optimise tree seedling production. The objective of this study was to analyse the growth dynamics of oil palm seedlings to evaluate the effects of bag size, substrate type, and fertiliser supply, and their interactions. An experiment was run in 2011 (March to November 2011) and repeated in 2012 (April to October 2012) using three bag sizes, four substrates, and three levels of fertiliser supply (3 × 4 × 3 factorial design). Seedling height, collar diameter and number of leaves were measured over time. Seedling growth was analysed by comparing treatment effects at monthly intervals. Data were also fitted to growth curves to analyse treatment effects on absolute and relative rates of increase in seedling height, collar diameter and number of leaves. While substrate and fertiliser supply effects were fairly constant over time, bag size effects increased with larger variance explained over time. We observed that bag size effects overtook substrate, fertiliser and interaction effects from about two months onwards. Seedling height and collar diameter followed an exponential growth while number of leaves increased linearly over time. Analysis of generated data with the different growth models indicated that seedling growth rates were mainly under the influence of bag size, followed by substrate. Interactions between nursery practices, although significant sometimes, did not account for a large part of experimental error. Implications for tree seedling management are further discussed.
    Arbuscular mycorrhizal impacts on competitive interactions between Acacia etbaica and Boswellia papyrifera seedlings under drought stress
    Birhane, E. ; Sterck, F.J. ; Bongers, F. ; Kuyper, T.W. - \ 2014
    Journal of Plant Ecology 7 (2014)3. - ISSN 1752-9921 - p. 298 - 308.
    interspecific competition - plant-growth - trade-offs - fungi - frankincense - infection - traits - associations - populations - coexistence
    Aims Arbuscular mycorrhizal fungi can have a substantial effect on the water and nutrient uptake by plants and the competition between plants in harsh environments where resource availability comes in pulses. In this study we focus on interspecific competition between Acaia etbaica and Boswellia papyrifera that have distinctive resource acquisition strategies. We compared the extent of interspecific competition with that of intraspecific competition. Methods In a greenhouse study we examined the influence of Arbuscular Mycorrhiza (AM) and pulsed water availability on competitive interactions between seedlings of the rapidly growing species A. etbaica and the slowly growing species B. papyrifera. A factorial experimental design was used. The factors were AM, two water levels and five species combinations Important Findings Seedlings of both species benefitted from AM when grown alone, and the positive growth response to pulsed water availability in B. papyrifera seedlings was in contrast with the negative growth response for A. etbaica seedlings. AM also affected the competitive performance of both species. B. papyrifera was not affected by intraspecific competition, whereas A. etbaica was negatively affected compared to the seedlings grown alone. This effect was stronger in the presence of AM. In interspecific competition, A. etbaica outcompeted B. papyrifera. Mycorrhiza and pulsed water availability did not affect the outcome of interspecific competition, and the aggressivity index of A. etbaica remained unchanged. The extent to which AM influences plant competition in a drought-stressed environment may depend on belowground functional traits of the species. AM and pulsed water availability could modify the balance between intraspecific and interspecific competition. By affecting the balance between intraspecific and interspecific competition, both factors could impact the establishment and survival of seedlings.
    Nitrogen cycling in summer active perennial grass systems in South Australia: Non-symbiotic nitrogen fixation
    Gupta, V.V.S.R. ; Kroker, S.J. ; Hicks, M. ; Davoren, W. ; Descheemaeker, K.K.E. ; Llewellyn, R. - \ 2014
    Crop and Pasture Science 65 (2014)10. - ISSN 1836-0947 - p. 1044 - 1056.
    microbial community structure - nifh gene diversity - fixing bacteria - functional-significance - diazotrophic bacteria - plant-growth - n-2 fixation - soil - rhizosphere - carbon
    Non-symbiotic nitrogen (N2) fixation by diazotrophic bacteria is a potential source for biological N inputs in non-leguminous crops and pastures. Perennial grasses generally add larger quantities of above- and belowground plant residues to soil, and so can support higher levels of soil biological activity than annual crops. In this study, the hypothesis is tested that summer-active perennial grasses can provide suitable microsites with the required carbon supply for N2 fixation by diazotrophs, in particular during summer, through their rhizosphere contribution. In a field experiment on a Calcarosol at Karoonda, South Australia, during summer 2011, we measured populations of N2-fixing bacteria by nifH-PCR quantification and the amount of 15N2 fixed in the rhizosphere and roots of summer-active perennial grasses. Diazotrophic N2 fixation estimates for the grass roots ranged between 0.92 and 2.35 mg 15N kg–1 root day–1. Potential rates of N2 fixation for the rhizosphere soils were 0.84–1.4 mg 15N kg–1 soil day–1 whereas the amount of N2 fixation in the bulk soil was 0.1–0.58 mg 15N kg–1 soil day–1. Populations of diazotrophic bacteria in the grass rhizosphere soils (2.45 × 106 nifH gene copies g–1 soil) were similar to populations in the roots (2.20 × 106 nifH gene copies g–1 roots) but the diversity of diazotrophic bacteria was significantly higher in the rhizosphere than the roots. Different grass species promoted the abundance of specific members of the nifH community, suggesting a plant-based selection from the rhizosphere microbial community. The results show that rhizosphere and root environments of summer-active perennial grasses support significant amounts of non-symbiotic N2 fixation during summer compared with cropping soils, thus contributing to biological N inputs into the soil N cycle. Some pasture species also maintained N2 fixation in October (spring), when the grasses were dormant, similar to that found in soils under a cereal crop. Surface soils in the rainfed cropping regions of southern Australia are generally low in soil organic matter and thus have lower N-supply capacity. The greater volume of rhizosphere soil under perennial grasses and carbon inputs belowground can potentially change the balance between N immobilisation and mineralisation processes in the surface soils in favour of immobilisation, which in turn contributes to reduced N losses from leaching.
    Do earthworms affect phosphorus availability to grass? A pot experiment.
    Vos, M.J. ; Ros, M.B.H. ; Koopmans, G.F. ; Groenigen, J.W. van - \ 2014
    Soil Biology and Biochemistry 79 (2014). - ISSN 0038-0717 - p. 34 - 42.
    pontoscolex-corethrurus glossoscolecidae - organic-matter - phosphate adsorption - colloidal phosphorus - lumbricus-terrestris - geophagous earthworm - soil-phosphorus - tropical soil - plant-growth - casts
    The largest part of phosphorus (P) in soil is bound by the soil solid phase; its release to the soil solution therefore often does not meet the demand of plants. Since global P fertilizer reserves are declining, it becomes increasingly important to better utilize soil P. We tested whether earthworm activity can increase P availability to grass (Lolium perenne L.) in a 75-day greenhouse pot experiment in a soil with low P availability. The full factorial design included two factors: P fertilization (control without P; phytate; and inorganic P) and earthworm population (control without earthworms; Lumbricus rubellus Hoffmeister, Lr; Aporrectodea caliginosa Savigny, Ac; and Lumbricus terrestris L., Lt). At four times during the experiment, aboveground plant growth and P uptake were determined. In a separate incubation experiment, earthworm casts and bulk soil were analyzed for inorganic and organic P in water extracts. We observed higher levels of dissolved P pools (p <0.001) in the water extracts of earthworm casts compared to those of the bulk soil. The magnitude of the difference differed between earthworm species, with the largest levels for Lr: from
    Phenological development of East African highland banana involves trade-offs between physiological age and chronological age
    Taulya, G. ; Asten, P.J.A. van; Leffelaar, P.A. ; Giller, K.E. - \ 2014
    European Journal of Agronomy 60 (2014). - ISSN 1161-0301 - p. 41 - 53.
    relative growth-rate - musa-spp. - plant-growth - life-history - soil-water - leaf-area - photosynthesis - acclimation - temperature - yield
    The phenology of East African highland banana (Musa acuminata AAA-EA, hereafter referred to as ‘highland banana’) is poorly understood. We tested three hypotheses: (1) the physiological age at flowering is independent of site effects, (2) there is no difference in threshold size at flowering between sites with different growth potential, and (3) morphological and physiological components of highland banana relative growth rate (RGR) contribute equally to mitigate growth reduction in response to limiting supply of water, K or N. The physiological age of highland banana plants from field trials at Kawanda (central Uganda) and Ntungamo (south-western Uganda) was computed from daily temperature records. Growth analysis was conducted using RGR, net assimilation rate (NAR), specific leaf area (SLA) and leaf mass ratio (LMR) estimated from allometry. Growth response coefficients were used for quantifying the relative contribution of NAR, SLA and LMR to RGR. Physiological age at flowering was delayed by 739 °C d at Kawanda compared with that at Ntungamo whose chronological age at flowering was in turn 51 d older. At both sites a threshold total dry mass of 1.5 kg per plant was required for flowering. Faster absolute growth rate and NAR fostered by wet conditions, K input and cooler temperatures enabled plants at Ntungamo to attain the threshold total dry mass sooner than those at Kawanda, hence the phenotypic plasticity in age at flowering. Net assimilation rate contributed at least 90% to RGR increase due to wet conditions at both sites. The contribution of NAR to RGR increase in response to K at Kawanda reduced to 38% while that for SLA increased to 49%. Net assimilation rate contributes more to highland banana RGR modulation than SLA except when warmer conditions reduce NAR. Differences in crop growth rate cause phenotypic plasticity in highland banana rate of phenological development.
    Biochar application rate affects biological nitrogen fixation in red clover conditional on potassium availability
    Mia, S. ; Groenigen, J.W. van; Voorde, T.F.J. van de; Oram, N.J. ; Bezemer, T.M. ; Mommer, L. ; Jeffery, S.L. - \ 2014
    Agriculture, Ecosystems and Environment 191 (2014). - ISSN 0167-8809 - p. 83 - 91.
    fast-pyrolysis biochar - natural-abundance - plant-growth - soil - carbon - n-15 - consequences - hydrochar - australia - nutrition
    Increased biological nitrogen fixation (BNF) by legumes has been reported following biochar application to soils, but the mechanisms behind this phenomenon remain poorly elucidated. We investigated the effects of different biochar application rates on BNF in red clover (Trifolium pratense L.). Red clover was grown in mono or mixed cultures with red fescue grass (Festuca rubra L.) and plantain (Plantago lanceolata L.) at a range of different biochar application rates (0, 10, 50 and 120 t ha-1). In a separate experiment, nutrient effects of biochar on BNF were investigated using nitrogen, phosphorous and potassium (N, P and K) and micronutrient fertilization using the same plant species. Biochar addition increased BNF and biochar applied at a rate of 10 t ha-1 led to the highest rate of BNF. Total biomass also showed the greatest increase at this application rate. An application rate of 120 t ha-1 significantly decreased biomass production in both single and mixed cultures when compared to the control, with the greatest reduction occurring in red clover. Furthermore, BNF was significantly higher in pots in which red clover was grown in mixed cultures compared to monocultures. In the absence of biochar, K fertilization caused a significant increase in BNF. For N, P, and micronutrient fertilization, BNF did not significantly differ between treatments with and without biochar addition. We conclude that different biochar application rates lead to different effects in terms of BNF and biomass production. However, due to the high variety of biochar properties, different application rates should be investigated on a case specific basis to determine the optimum biochar application strategies.
    Identification, cloning and characterization of the tomato TCP transcription factor family
    Parapunova, V.A. ; Busscher, M. ; Busscher-Lange, J. ; Lammers, M. ; Karlova, R.B. ; Bovy, A.G. ; Angenent, G.C. ; Maagd, R.A. de - \ 2014
    BMC Plant Biology 14 (2014). - ISSN 1471-2229
    mads-box gene - arabidopsis-thaliana - fruit-development - leaf development - high-throughput - plant-growth - dna-binding - expression - time - interference
    Background: TCP proteins are plant-specific transcription factors, which are known to have a wide range of functions in different plant species such as in leaf development, flower symmetry, shoot branching, and senescence. Only a small number of TCP genes has been characterised from tomato (Solanum lycopersicum). Here we report several functional features of the members of the entire family present in the tomato genome. Results: We have identified 30 Solanum lycopersicum SlTCP genes, most of which have not been described before. Phylogenetic analysis clearly distinguishes two homology classes of the SlTCP transcription factor family - class I and class II. Class II differentiates in two subclasses, the CIN-TCP subclass and the CYC/TB1 subclass, involved in leaf development and axillary shoots formation, respectively. The expression patterns of all members were determined by quantitative PCR. Several SlTCP genes, like SlTCP12, SlTCP15 and SlTCP18 are preferentially expressed in the tomato fruit, suggesting a role during fruit development or ripening. These genes are regulated by RIN (RIPENING INHIBITOR), CNR (COLORLESS NON-RIPENING) and SlAP2a (APETALA2a) proteins, which are transcription factors with key roles in ripening. With a yeast one-hybrid assay we demonstrated that RIN binds the promoter fragments of SlTCP12, SlTCP15 and SlTCP18, and that CNR binds the SlTCP18 promoter. This data strongly suggests that these class I SlTCP proteins are involved in ripening. Furthermore, we demonstrate that SlTCPs bind the promoter fragments of members of their own family, indicating that they regulate each other. Additional yeast one-hybrid studies performed with Arabidopsis transcription factors revealed binding of the promoter fragments by proteins involved in the ethylene signal transduction pathway, contributing to the idea that these SlTCP genes are involved in the ripening process. Yeast two-hybrid data shows that SlTCP proteins can form homo and heterodimers, suggesting that they act together in order to form functional protein complexes and together regulate developmental processes in tomato.
    Transcriptional coordination between leaf cell differentiation and chloroplast development established by TCP20 and theand chloroplast development established by TCP20 and theand chloroplast development established by TCP20 and the subgroup Ib bHLH transcription factors
    Andriankaja, M.E. ; Danisman, S.D. ; Mignolet-Spruyt, L.F. ; Claeys, H. ; Kochanke, I. ; Vermeersch, M. ; Milde, L. De; Bodt, S. De; Storme, V. ; Skirycz, A. ; Maurer, F. ; Bauer, P. ; Mühlenbock, P. ; Breusegem, F. Van; Angenent, G.C. ; Immink, R.G.H. ; Inzé, D. - \ 2014
    Plant Molecular Biology 85 (2014)3. - ISSN 0167-4412 - p. 233 - 245.
    iron-deficiency responses - arabidopsis-thaliana - plant-growth - gene-expression - chromatin immunoprecipitation - metal transporter - oxidative stress - circadian clock - pale cress - in-vivo
    The establishment of the photosynthetic apparatus during chloroplast development creates a high demand for iron as a redox metal. However, iron in too high quantities becomes toxic to the plant, thus plants have evolved a complex network of iron uptake and regulation mechanisms. Here, we examined whether four of the subgroup Ib basic helix-loop-helix transcription factors (bHLH38, bHLH39, bHLH100, bHLH101), previously implicated in iron homeostasis in roots, also play a role in regulating iron metabolism in developing leaves. These transcription factor genes were strongly up-regulated during the transition from cell proliferation to expansion, and thus sink-source transition, in young developing leaves of Arabidopsis thaliana. The four subgroup Ib bHLH genes also showed reduced expression levels in developing leaves of plants treated with norflurazon, indicating their expression was tightly linked to the onset of photosynthetic activity in young leaves. In addition, we provide evidence for a mechanism whereby the transcriptional regulators SAC51 and TCP20 antagonistically regulate the expression of these four subgroup Ib bHLH genes. A loss-offunction mutant analysis also revealed that single mutants of bHLH38, bHLH39, bHLH100, and bHLH101 developed smaller rosettes than wild-type plants in soil. When grown in agar plates with reduced iron concentration, triple bhlh39 bhlh100 bhlh101 mutant plants were smaller than wildtype plants. However, measurements of the iron content in single and multiple subgroup Ib bHLH genes, as well as transcript profiling of iron response genes during early leaf development, do not support a role for bHLH38, bHLH39, bHLH100, and bHLH101 in iron homeostasis during early leaf development.
    Responses of supplemental blue light on flowering and stem extension growth of cut chrysanthemum
    Jeong, S.W. ; Hogewoning, S.W. ; Ieperen, W. van - \ 2014
    Scientia Horticulturae 165 (2014). - ISSN 0304-4238 - p. 69 - 74.
    plant-growth - spectral filters - red - morifolium - photosynthesis - gibberellins - phytochrome - end - photoperiod - inhibition
    To determine the effects of blue (B) spectrum supplemental lighting on flower bud formation and stem elongation growth of cut chrysanthemum, plants of ‘Zembla’ cultivar were grown for 42 days under 4 different light treatments. Treatments comprised: RB (11 h of mixed red and blue [RB] light), RB + B (11 h of mixed RB light and then 4 h of supplemental B light), LRB + B (15 h of mixed RB light and then 4 h of supplemental B light) and RB + LB (11 h of mixed RB light and then 13 h of B light) by using light-emitting diodes. Diurnal patterns in the net assimilation rate were observed, depending on light-quality combinations. Under mixed RB light, the net assimilation rate increased rapidly, then slightly decreased under B light, and finally dropped to negative values during darkness. Final stem length was the highest in plants grown under RB + LB, followed by LRB + B, RB + B and then RB treatment. The stem lengths under RB + B, LRB + B and RB + LB were 1.3, 1.5 and 1.7 times longer than that of RB treatment, respectively. However, fully developed flower buds were formed under RB and RB + B treatments only. The extended final stem length of RB + B plants was determined by internode extension. Overall, our results indicate that supplemental B light, at least in part, may promote stem and internode elongation growth without any inhibitory effect on flower bud formation. The results of this study present a useful practical technique for optimizing cut chrysanthemum production in greenhouse horticulture.
    Can exploiting natural genetic variation in leaf photosynthesis contribute to increasing rice productivity? A simulation analysis
    Gu, J. ; Yin, X. ; Stomph, T.J. ; Struik, P.C. - \ 2014
    Plant, Cell & Environment 37 (2014)1. - ISSN 0140-7791 - p. 22 - 34.
    oryza-sativa l. - introgression lines - physiological traits - critical-appraisal - co2 assimilation - plant-growth - crop yields - leaves - model - rubisco
    Rice productivity can be limited by available photosynthetic assimilates from leaves. However, the lack of significant correlation between crop yield and leaf photosynthetic rate (A) is noted frequently. Engineering for improved leaf photosynthesis has been argued to yield little increase in crop productivity because of complicated constraints and feedback mechanisms whenmoving up from leaf to crop level.Herewe examined the extent to which natural genetic variation in A can contribute to increasing rice productivity. Using the mechanistic model GECROS,we analysed the impact of genetic variation inAon crop biomass production, based on the quantitative trait loci for various photosynthetic components within a rice introgression line population.We showed that genetic variation in A of 25% can be scaled up equally to crop level, resulting in an increase in biomass of 22–29% across different locations and years. This was probably because the genetic variation in A resulted not only from Rubisco (ribulose 1,5-bisphosphate carboxylase/oxygenase)-limited photosynthesis but also from electron transport-limited photosynthesis; as a result, photosynthetic rates could be improved for both light-saturated and light-limited leaves in the canopy. Rice productivity could be significantly improved by mining the natural variation in existing germ-plasm, especially the variation in parameters determining light-limited photosynthesis.
    A review of earthworm impact on soil function and ecosystem services
    Blouin, M. ; Hodson, M.E. ; Delgado, E.A. ; Baker, G. ; Brussaard, L. ; Butt, K.R. ; Dai, J. ; Dendooven, L. ; Peres, G. ; Tondoh, J.E. ; Cluzeau, D. ; Brun, J.J. - \ 2013
    European Journal of Soil Science 64 (2013)2. - ISSN 1351-0754 - p. 161 - 182.
    polycyclic aromatic-hydrocarbons - northern hardwood forests - south-eastern australia - ray computed-tomography - organic-matter dynamics - oil-contaminated soil - pb/zn mine tailings - nitrous-oxide n2o - lumbricus-terrestris - plant-growth
    Biodiversity is responsible for the provision of many ecosystem services; human well-being is based on these services, and consequently on biodiversity. In soil, earthworms represent the largest component of the animal biomass and are commonly termed ecosystem engineers'. This review considers the contribution of earthworms to ecosystem services through pedogenesis, development of soil structure, water regulation, nutrient cycling, primary production, climate regulation, pollution remediation and cultural services. Although there has been much research into the role of earthworms in soil ecology, this review demonstrates substantial gaps in our knowledge related in particular to difficulties in identifying the effects of species, land use and climate. The review aims to assist people involved in all aspects of land management, including conservation, agriculture, mining or other industries, to obtain a broad knowledge of earthworms and ecosystem services.
    Computational modeling of the BRI1-receptor system
    Esse, G.W. van; Harter, K. ; Vries, S.C. de - \ 2013
    Plant, Cell & Environment 36 (2013)9. - ISSN 0140-7791 - p. 1728 - 1737.
    brassinosteroid signal-transduction - plasma-membrane - plant-growth - arabidopsis-thaliana - auxin transport - root-growth - fluorescence microscopy - gsk3-like kinases - egf receptors - protein
    Computational models are useful tools to help understand signalling pathways in plant cells. A systems biology approach where models and experimental data are combined can provide experimentally verifiable predictions and novel insights. The brassinosteroid insensitive 1 (BRI1) receptor is one of the best-understood receptor systems in Arabidopsis with clearly described ligands, mutants and associated phenotypes. Therefore, BRI1-mediated signalling is attractive for mathematical modelling approaches to understand and interpret the spatial and temporal dynamics of signal transduction cascades in planta. To establish such a model, quantitative data sets incorporating local protein concentration, binding affinity and phosphorylation state of the different pathway components are essential. Computational modelling is increasingly employed in studies of plant growth and development. In this section, we have focused on the use of quantitative imaging of fluorescently labelled proteins as an entry point in modelling studies
    A mathematical model for the co-receptors SERK1 and SERK3 in BRI1 mediated signaling
    Esse, G.W. van; Mourik, S. van; Albrecht, C. ; Leeuwen, J. ; Vries, S.C. de - \ 2013
    Plant Physiology 163 (2013)3. - ISSN 0032-0889 - p. 1472 - 1481.
    innate immunity - arabidopsis-thaliana - tyrosine kinases - plant-growth - bri1 - bak1 - pathways - autophosphorylation - transduction - endocytosis
    Brassinosteroids (BRs) are key regulators in plant growth and development. The main BR perceiving receptor in Arabidopsis is Brassinosteroid Insensitive 1 (BRI1). Seedling root growth and hypocotyl elongation can be accurately predicted using a model for BRI1 receptor activity. Genetic evidence shows that non ligand-binding co-receptors of the Somatic Embryogenesis Receptor-like Kinase (SERK) family are essential for BRI1 signal transduction. A relatively simple biochemical model based on the properties of SERK loss-of-function alleles explains complex physiological responses of the BRI1 mediated BR pathway. The model uses BRI1-BR occupancy as the central estimated parameter and includes BRI1-SERK interaction based on mass action kinetics and accurately describes wild type root growth and hypocotyl elongation. Simulation studies suggest that the SERK co-receptors primarily act to increase the magnitude of the BRI1 signal. The model predicts that only a small number of active BRI1-SERK complexes are required to carry out BR signaling at physiological ligand concentration. Finally, when calibrated with single mutants, the model predicts that roots of the serk1serk3 double mutant are almost completely BL-insensitive, while the double mutant hypocotyls remain sensitive. This points to residual BRI1 signaling or to a different co-receptor requirement in shoots.
    A dynamic model of tomato fruit growth integrating cell division, cell growth and endoreduplication
    Fanwoua, J. ; Visser, P.H.B. de; Heuvelink, E. ; Yin, X. ; Struik, P.C. ; Marcelis, L.F.M. - \ 2013
    Functional Plant Biology 40 (2013)11. - ISSN 1445-4408 - p. 1098 - 1114.
    individual cucumber fruits - cycle regulation - dna endoreduplication - simulation-model - plant-growth - dry-matter - mesocarp cells - size control - temperature - carbon
    In this study, we developed a model of tomato (Solanum lycopersicum L.) fruit growth integrating cell division, cell growth and endoreduplication. The fruit was considered as a population of cells grouped in cell classes differing in their initial cell age and cell mass. The model describes fruit growth from anthesis until maturation and covers the stages of cell division, endoreduplication and cell growth. The transition from one stage to the next was determined by predefined cell ages expressed in thermal time. Cell growth is the consequence of sugar import from acommon pool of assimilates according to the source–sink concept. During most parts of fruit growth, potential cell growth rate increases with increasing cell ploidy and follows the Richards growth function. Cell division or endoreduplication occurs when cells exceed a critical threshold cell mass : ploidy ratio. The model was parameterised and calibrated for low fruit load conditions and was validated for high fruit load and various temperature conditions. Model sensitivity analysis showed that variations in final fruit size are associated with variations in parameters involved in the dynamics of cell growth and cell division. The model was able to accurately predict final cell number, cell mass and pericarp mass under various contrasting fruit load and most of the temperature conditions. The framework developed in this model opens the perspective to integrate information on molecular control of fruit cellular processes into the fruit model and to analyse gene-by-environment interaction effects on fruit growth.
    Visualization of BRI1 and BAK1(SERK3) membrane receptor heterooligomers during brassinosteroid signaling.
    Bücherl, C.A. ; Esse, G.W. van; Kruis, A. ; Luchtenberg, J. ; Westphal, A.H. ; Aker, J.C.M. ; Hoek, A. van; Albrecht, C. ; Borst, J.W. ; Vries, S.C. de - \ 2013
    Plant Physiology 162 (2013)2. - ISSN 0032-0889 - p. 1911 - 1925.
    agrobacterium-mediated transformation - growth-factor receptors - gsk3-like kinase bin2 - transcription factors - plant-growth - arabidopsis-thaliana - extracellular domain - chemokine receptors - plasma-membrane - gene-expression
    The leucine-rich repeat receptor-like kinase BRASSINOSTEROID-INSENSITIVE1 (BRI1) is the main ligand-perceiving receptor for brassinosteroids (BRs) in Arabidopsis (Arabidopsis thaliana). Binding of BRs to the ectodomain of plasma membrane (PM)-located BRI1 receptors initiates an intracellular signal transduction cascade that influences various aspects of plant growth and development. Even though the major components of BR signaling have been revealed and the PM was identified as the main site of BRI1 signaling activity, the very first steps of signal transmission are still elusive. Recently, it was shown that the initiation of BR signal transduction requires the interaction of BRI1 with its SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE (SERK) coreceptors. In addition, the resolved structure of the BRI1 ectodomain suggested that BRI1-ASSOCIATED KINASE1 [BAK1](SERK3) may constitute a component of the ligand-perceiving receptor complex. Therefore, we investigated the spatial correlation between BRI1 and BAK1(SERK3) in the natural habitat of both leucine-rich repeat receptor-like kinases using comparative colocalization analysis and fluorescence lifetime imaging microscopy. We show that activation of BR signaling by exogenous ligand application resulted in both elevated colocalization between BRI1 and BAK1(SERK3) and an about 50% increase of receptor heterooligomerization in the PM of live Arabidopsis root epidermal cells. However, large populations of BRI1 and BAK1(SERK3) colocalized independently of BRs. Moreover, we could visualize that approximately 7% of the BRI1 PM pool constitutively heterooligomerizes with BAK1(SERK3) in live root cells. We propose that only small populations of PM-located BRI1 and BAK1(SERK3) receptors participate in active BR signaling and that the initiation of downstream signal transduction involves preassembled BRI1-BAK1(SERK3) heterooligomers.
    East African highland bananas (Musa spp. AAA-EA) 'worry' more about potassium deficiency than drought stress
    Taulya, G. - \ 2013
    Field Crops Research 151 (2013). - ISSN 0378-4290 - p. 45 - 55.
    foliar nutrient status - biomass allocation - osmotic adjustment - plant-growth - root ratio - soil-water - nitrogen - shoot - fertilizer - weevil
    Drought stress, potassium (K) and nitrogen (N) deficiencies are major constraints to rain-fed East African highland banana (EAHB) production in Uganda. It was hypothesised that the reduction in fresh bunch mass and increase in dry matter (DM) allocation to corms with drought stress, K and N deficiency is additive. Individual plant measurements at harvest from two field trials in central and south western Uganda were analyzed to evaluate effects of cumulative rainfall (CRF) received 365 days from sucker emergence, mineral K and N inputs on EAHB bunch yields. Dry matter content in aerial shoot (leaves and pseudostems) relative to that in the subterranean corm was also analyzed to evaluate DM allocation plasticity due to drought stress, K and N deficiency. This was verified with allometric analysis using pre-harvest stage plants from farms of known K and N nutritional status and plants from a screen house drought stress pot trial in Uganda. Dry matter production and yields were mainly driven by K interacting with CRF. Within 12 months, K input (250-600 kg K ha(-1) yr(-1)) increased bunch yield from 8 to 15 Mg ha(-1) yr(-1) irrespective of whether dry (CRF <1100 mm) or wet (CRF >= 1100 mm) conditions prevailed, possibly due to K-mediated osmotic adjustment under dry conditions. Without K input, wet conditions increased bunch yield from 6 to 8 Mg ha(-1) yr(-1) while dry conditions decreased it from 6 to 4 Mg ha(-1) yr(-1) within 12 months. Total DM and its distribution between the biomass structures followed similar trends. Nitrogen input (150-400 kg N ha(-1) yr(-1)) neither affected bunch yield nor DM allocation at harvest stage. At pre-harvest stage, reduction in DM allocation to the corm per unit increase in total DM was 14-22% significantly lower with N and/or K deficiency compared with that under sufficient K and N. Drought stress per se had no effect on DM allocation but enhanced DM allocation shifts due to K deficiency. Drought-stressed EAHB thus increase DM allocation to subterranean structures only if K-deficient, unlike responses reported for other plant species. Potassium nutrition is perhaps a more viable entry point for mitigation of drought stress in EAHB cropping systems than irrigation but this requires further agronomic and economic evaluation. It may be important to account for carbon allocated to osmotic adjustment for realistic simulation of water- and K-limited growth in EAHB. (c) 2013 Elsevier B.V. All rights reserved.
    Co-Variation between Seed dormancy, growth rate and flowering time changes with latitude in Arabidopsis thaliana
    Debieu, M. ; Tang, C. ; Stich, B. ; Sikosek, T. ; Effgen, S. ; Josephs, E. ; Schmitt, J. ; Nordborg, M. ; Koornneef, M. ; Meaux, J. De - \ 2013
    PLoS ONE 8 (2013)5. - ISSN 1932-6203
    natural allelic variation - genome-wide association - quantitative-trait loci - life-history - genetic-variation - clinal variation - plant-growth - native range - germination - adaptation
    Life-history traits controlling the duration and timing of developmental phases in the life cycle jointly determine fitness. Therefore, life-history traits studied in isolation provide an incomplete view on the relevance of life-cycle variation for adaptation. In this study, we examine genetic variation in traits covering the major life history events of the annual species Arabidopsis thaliana: seed dormancy, vegetative growth rate and flowering time. In a sample of 112 genotypes collected throughout the European range of the species, both seed dormancy and flowering time follow a latitudinal gradient independent of the major population structure gradient. This finding confirms previous studies reporting the adaptive evolution of these two traits. Here, however, we further analyze patterns of co-variation among traits. We observe that co-variation between primary dormancy, vegetative growth rate and flowering time also follows a latitudinal cline. At higher latitudes, vegetative growth rate is positively correlated with primary dormancy and negatively with flowering time. In the South, this trend disappears. Patterns of trait co-variation change, presumably because major environmental gradients shift with latitude. This pattern appears unrelated to population structure, suggesting that changes in the coordinated evolution of major life history traits is adaptive. Our data suggest that A. thaliana provides a good model for the evolution of trade-offs and their genetic basis
    A mathematical model for BRI1 mediated signaling in root growth and hypocotyl elongation
    Esse, G.W. van; Mourik, S. van; Stigter, J.D. ; Hove, C.C.A. ten; Molenaar, J. ; Vries, S.C. de - \ 2012
    Plant Physiology 160 (2012). - ISSN 0032-0889 - p. 523 - 532.
    receptor kinase bri1 - single-molecule analysis - arabidopsis-thaliana - plasma-membrane - gene-expression - plant-growth - negative cooperativity - biosynthesis inhibitor - structural basis - auxin transport
    Brassinosteroid (BR) signaling is essential for plant growth and development. In Arabidopsis (Arabidopsis thaliana), BRs are perceived by the BRASSINOSTEROID INSENSITIVE1 (BRI1) receptor. Root growth and hypocotyl elongation are convenient downstream physiological outputs of BR signaling. A computational approach was employed to predict root growth solely on the basis of BRI1 receptor activity. The developed mathematical model predicts that during normal root growth, few receptors are occupied with ligand. The model faithfully predicts root growth, as observed in bri1 loss-of-function mutants. For roots, it incorporates one stimulatory and two inhibitory modules, while for hypocotyls, a single inhibitory module is sufficient. Root growth as observed when BRI1 is overexpressed can only be predicted assuming that a decrease occurred in the BRI1 half-maximum response values. Root growth appears highly sensitive to variation in BR concentration and much less to reduction in BRI1 receptor level, suggesting that regulation occurs primarily by ligand availability and biochemical activity.
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