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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    Data from: Patterns of nitrogen-fixing tree abundance in forests across Asia and America
    Menge, Duncan N.L. ; Chisholm, Ryan A. ; Davies, Stuart J. ; Abu Salim, Kamariah ; Allen, David ; Alvarez, Mauricio ; Bourg, Norm ; Brockelman, Warren Y. ; Bunyavejchewin, Sarayudh ; Butt, Nathalie ; Ouden, Jan den; Jansen, Patrick - \ 2019
    Dryad
    Determinants of plant community diversity and structure - Forest - Smithsonian ForestGEO - legume - symbiosis - nutrient limitation - nitrogen fixation
    Symbiotic nitrogen (N)‐fixing trees can provide large quantities of new N to ecosystems, but only if they are sufficiently abundant. The overall abundance and latitudinal abundance distributions of N‐fixing trees are well characterised in the Americas, but less well outside the Americas. Here, we characterised the abundance of N‐fixing trees in a network of forest plots spanning five continents, ~5,000 tree species and ~4 million trees. The majority of the plots (86%) were in America or Asia. In addition, we examined whether the observed pattern of abundance of N‐fixing trees was correlated with mean annual temperature and precipitation. Outside the tropics, N‐fixing trees were consistently rare in the forest plots we examined. Within the tropics, N‐fixing trees were abundant in American but not Asian forest plots (~7% versus ~1% of basal area and stems). This disparity was not explained by mean annual temperature or precipitation. Our finding of low N‐fixing tree abundance in the Asian tropics casts some doubt on recent high estimates of N fixation rates in this region, which do not account for disparities in N‐fixing tree abundance between the Asian and American tropics. Synthesis. Inputs of nitrogen to forests depend on symbiotic nitrogen fixation, which is constrained by the abundance of N‐fixing trees. By analysing a large dataset of ~4 million trees, we found that N‐fixing trees were consistently rare in the Asian tropics as well as across higher latitudes in Asia, America and Europe. The rarity of N‐fixing trees in the Asian tropics compared with the American tropics might stem from lower intrinsic N limitation in Asian tropical forests, although direct support for any mechanism is lacking. The paucity of N‐fixing trees throughout Asian forests suggests that N inputs to the Asian tropics might be lower than previously thought.
    Patterns of nitrogen-fixing tree abundance in forests across Asia and America
    Menge, Duncan N.L. ; Chisholm, Ryan A. ; Davies, Stuart J. ; Abu Salim, Kamariah ; Allen, David ; Alvarez, Mauricio ; Bourg, Norm ; Brockelman, Warren Y. ; Bunyavejchewin, Sarayudh ; Butt, Nathalie ; Cao, Min ; Chanthorn, Wirong ; Chao, Wei Chun ; Clay, Keith ; Condit, Richard ; Cordell, Susan ; Silva, João Batista da; Dattaraja, H.S. ; Andrade, Ana Cristina Segalin de; Oliveira, Alexandre A. de; Ouden, Jan den; Drescher, Michael ; Fletcher, Christine ; Giardina, Christian P. ; Savitri Gunatilleke, C.V. ; Gunatilleke, I.A.U.N. ; Hau, Billy C.H. ; He, Fangliang ; Howe, Robert ; Hsieh, Chang Fu ; Hubbell, Stephen P. ; Inman-Narahari, Faith M. ; Jansen, Patrick A. ; Johnson, Daniel J. ; Kong, Lee Sing ; Král, Kamil ; Ku, Chen Chia ; Lai, Jiangshan ; Larson, Andrew J. ; Li, Xiankun ; Li, Yide ; Lin, Luxiang ; Lin, Yi Ching ; Liu, Shirong ; Lum, Shawn K.Y. ; Lutz, James A. ; Ma, Keping ; Malhi, Yadvinder ; McMahon, Sean ; McShea, William ; Mi, Xiangcheng ; Morecroft, Michael ; Myers, Jonathan A. ; Nathalang, Anuttara ; Novotny, Vojtech ; Ong, Perry ; Orwig, David A. ; Ostertag, Rebecca ; Parker, Geoffrey ; Phillips, Richard P. ; Abd. Rahman, Kassim ; Sack, Lawren ; Sang, Weiguo ; Shen, Guochun ; Shringi, Ankur ; Shue, Jessica ; Su, Sheng Hsin ; Sukumar, Raman ; Fang Sun, I. ; Suresh, H.S. ; Tan, Sylvester ; Thomas, Sean C. ; Toko, Pagi S. ; Valencia, Renato ; Vallejo, Martha I. ; Vicentini, Alberto ; Vrška, Tomáš ; Wang, Bin ; Wang, Xihua ; Weiblen, George D. ; Wolf, Amy ; Xu, Han ; Yap, Sandra ; Zhu, Li ; Fung, Tak - \ 2019
    Journal of Ecology 107 (2019)6. - ISSN 0022-0477 - p. 2598 - 2610.
    forest - legume - nitrogen fixation - nutrient limitation - Smithsonian ForestGEO - symbiosis

    Symbiotic nitrogen (N)-fixing trees can provide large quantities of new N to ecosystems, but only if they are sufficiently abundant. The overall abundance and latitudinal abundance distributions of N-fixing trees are well characterised in the Americas, but less well outside the Americas. Here, we characterised the abundance of N-fixing trees in a network of forest plots spanning five continents, ~5,000 tree species and ~4 million trees. The majority of the plots (86%) were in America or Asia. In addition, we examined whether the observed pattern of abundance of N-fixing trees was correlated with mean annual temperature and precipitation. Outside the tropics, N-fixing trees were consistently rare in the forest plots we examined. Within the tropics, N-fixing trees were abundant in American but not Asian forest plots (~7% versus ~1% of basal area and stems). This disparity was not explained by mean annual temperature or precipitation. Our finding of low N-fixing tree abundance in the Asian tropics casts some doubt on recent high estimates of N fixation rates in this region, which do not account for disparities in N-fixing tree abundance between the Asian and American tropics. Synthesis. Inputs of nitrogen to forests depend on symbiotic nitrogen fixation, which is constrained by the abundance of N-fixing trees. By analysing a large dataset of ~4 million trees, we found that N-fixing trees were consistently rare in the Asian tropics as well as across higher latitudes in Asia, America and Europe. The rarity of N-fixing trees in the Asian tropics compared with the American tropics might stem from lower intrinsic N limitation in Asian tropical forests, although direct support for any mechanism is lacking. The paucity of N-fixing trees throughout Asian forests suggests that N inputs to the Asian tropics might be lower than previously thought.

    A systematic approach for re-assembly of crop models: An example to simulate pea growth from wheat growth
    Adam, M.Y.O. ; Wery, J. ; Leffelaar, P.A. ; Ewert, F. ; Corbeels, M. ; Keulen, H. van - \ 2013
    Ecological Modelling 250 (2013). - ISSN 0304-3800 - p. 258 - 268.
    nitrogen nutrition - expert knowledge - use efficiency - water-deficit - legume - apsim - integration - parameters - frameworks - selection
    The process of crop modelling to develop operational software requires different skills, from conceptualization of the biophysical system to computer programming, involving three main scientific disciplines: agronomy, mathematics, and software engineering. Model building implies transforming a conceptual model into sets of mathematical equations and then translating these equations into a computer program. Although recent crop modelling frameworks can technically support model building, the modelling process is not always well documented and difficult to repeat. The focus of this paper is therefore on developing and documenting an approach to re-assemble crop models, i.e. develop a new model from an existing one, using a crop modelling framework and crop physiological knowledge. Modifications to an initial crop model were classified according to three categories: (i) changes in parameter values, (ii) changes in equations, and (iii) changes in overall model structure. We illustrate the approach with a case study transforming a wheat crop model into a pea crop model. We discuss the role of each actor in the process to document diverse uncertainties related to the model (i.e. contextual situation, data, structure), and the general applicability of the approach for different crop modelling frameworks. We conclude that the use of our approach to re-assemble a crop model within a modelling framework facilitates integration of different disciplines around a modelling objective, and facilitates creating transparent and reproducible models
    LysM-Type Mycorrhizal Receptor Recruited for Rhizobium Symbiosis in Nonlegume Parasponia
    Camp, R.H.M. Op den; Streng, A.J. ; Mita, S. De; Cao, Q. ; Polone, E. ; Liu, W. ; Ammiraju, J.S.S. ; Kudrna, D. ; Wing, R. ; Untergasser, A. ; Bisseling, T. ; Geurts, R. - \ 2011
    Science 331 (2011)6019. - ISSN 0036-8075 - p. 909 - 912.
    medicago-truncatula - gene family - nodulation - evolution - kinases - legume - endosymbiosis - bacteria - nodules - plants
    Rhizobium root nodule symbiosis is generally considered to be unique for legumes. However, there is one exception and that is Parasponia. In this nonlegume, the rhizobial nodule symbiosis evolved independently and is, like in legumes, induced by rhizobium Nod factors. We used Parasponia to identify genetic constrains underlying evolution of Nod factor signalling. Part of the signalling cascade, downstream of Nod factor perception, has been recruited from the more ancient arbuscular endomycorrhizal symbiosis. However, legume Nod factor receptors that activate this common signalling pathway are not essential for arbuscular endomycorrhizae. Here, we show that in Parasponia a single Nod factor-like receptor is indispensable for both symbiotic interactions. Therefore we conclude that also the Nod factor perception mechanism is recruited from the widespread endomycorrhizal symbiosis
    Transcriptome analysis of arbuscular mycorrhizal roots during development of the prepenetration apparatus
    Siciliano, V. ; Genre, A. ; Balestrini, R. ; Cappellazzo, G. ; Wit, P.J.G.M. de; Bonfante, P. - \ 2007
    Plant Physiology 144 (2007)3. - ISSN 0032-0889 - p. 1455 - 1466.
    medicago-truncatula - epidermal-cells - protein-kinase - defective mutant - genes - plant - expression - symbiosis - legume - fungi
    Information on changes in the plant transcriptome during early interaction with arbuscular mycorrhizal (AM) fungi is still limited since infections are usually not synchronized and plant markers for early stages of colonization are not yet available. A prepenetration apparatus (PPA), organized in epidermal cells during appressorium development, has been reported to be responsible for assembling a trans-cellular tunnel to accommodate the invading fungus. Here, we used PPAs as markers for cell responsiveness to fungal contact to investigate gene expression at this early stage of infection with minimal transcript dilution. PPAs were identified by confocal microscopy in transformed roots of Medicago truncatula expressing green fluorescent protein-HDEL, colonized by the AM fungus Gigaspora margarita. A PPA-targeted suppressive-subtractive cDNA library was built, the cDNAs were cloned and sequenced, and, consequently, 107 putative interaction-specific genes were identified. The expression of a subset of 15 genes, selected by reverse northern dot blot screening, and five additional genes, potentially involved in PPA formation, was analyzed by real-time reverse transcription-polymerase chain reaction and compared with an infection stage, 48 h after the onset of the PPA. Comparison of the expression profile of G. margarita-inoculated wild type and the mycorrhiza-defective dmi3-1 mutant of M. truncatula revealed that an expansin-like gene, expressed in wild-type epidermis during PPA development, can be regarded as an early host marker for successful mycorrhization. A putative Avr9/Cf-9 rapidly elicited gene, found to be up-regulated in the mutant, suggests novel regulatory roles for the DMI3 protein in the early mycorrhization process
    The Medicago truncatula lysine motif-receptor-like kinase gene family includes NFP and new nodule-expressed genes
    Arrighi, J.F. ; Barre, A. ; Amor, B. Ben; Bersoult, A. ; Campos Soriano, L. ; Mirabella, R. ; Carvalho-Niebel, F. de; Journet, E.P. ; Ghérardi, M. ; Huguet, T. ; Geurts, R. ; Dénarié, J. ; Rougé, P. ; Gough, C. - \ 2006
    Plant Physiology 142 (2006)1. - ISSN 0032-0889 - p. 265 - 279.
    nodulation factor-perception - protein-kinase - rhizobium-meliloti - genomic analysis - symbiotic genes - lysm domains - root hairs - arabidopsis - legume - infection
    Rhizobial Nod factors are key symbiotic signals responsible for starting the nodulation process in host legume plants. Of the six Medicago truncatula genes controlling a Nod factor signaling pathway, Nod Factor Perception (NFP) was reported as a candidate Nod factor receptor gene. Here, we provide further evidence for this by showing that NFP is a lysine motif (LysM)-receptor-like kinase (RLK). NFP was shown both to be expressed in association with infection thread development and to be involved in the infection process. Consistent with deviations from conserved kinase domain sequences, NFP did not show autophosphorylation activity, suggesting that NFP needs to associate with an active kinase or has unusual functional characteristics different from classical kinases. Identification of nine new M. truncatula LysM-RLK genes revealed a larger family than in the nonlegumes Arabidopsis (Arabidopsis thaliana) or rice (Oryza sativa) of at least 17 members that can be divided into three subfamilies. Three LysM domains could be structurally predicted for all M. truncatula LysM-RLK proteins, whereas one subfamily, which includes NFP, was characterized by deviations from conserved kinase sequences. Most of the newly identified genes were found to be expressed in roots and nodules, suggesting this class of receptors may be more extensively involved in nodulation than was previously known
    Seed treatments affect functional and antinutritional properties of amaranth flours
    Gamel, T.H. ; Linssen, J.P.H. ; Mesallam, A.S. ; Damir, A.A. ; Shekib, L.A. - \ 2006
    Journal of the Science of Food and Agriculture 86 (2006)7. - ISSN 0022-5142 - p. 1095 - 1102.
    africana decne seeds - chemical-composition - bean flour - in-vitro - germination - protein - legume - fractions - extrusion - cooking
    The effects of seed treatments, including cooking, popping germination and flour air classification, on the functional properties and antinutritional factors of Amaranthus caudatus and Amaranthus cruentus seeds were studied. Thermal treatments increased the water absorption with a maximum value of 5.1 and 6.3 g g-1 in flour of popped seeds of both species. Generally, fat absorption increased after the treatments. Air classification and germination followed by drying at low temperature increased the foam stability of the flours, while thermal treatment and germination followed by drying at higher temperatures reduced the foam stability. All treatments except air classification decreased the emulsion stability. Also, all treatments except germination followed by drying at 30 °C increased the flour dispersibility, whereas the soluble nitrogen index was increased in the germinated seed flours and decreased in thermal treated seeds and air-classified flours. Air classification increased the contents of phenolic compounds and phytate and decreased the contents of enzyme inhibitors, whereas the thermal treatments reduced the contents of phenolic compounds, phytate and enzyme inhibitors to a greater extent for cooking than for popping. Germination followed by drying reduced the level of phenolic compounds, phytate and enzyme inhibitors
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