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 Sphagnome Project : enabling ecological and evolutionary insights through a genus-level sequencing project
    Weston, David J. ; Turetsky, Merritt R. ; Johnson, Matthew G. ; Granath, Gustaf ; Lindo, Zoë ; Belyea, Lisa R. ; Rice, Steven K. ; Hanson, David T. ; Engelhardt, Katharina A.M. ; Schmutz, Jeremy ; Dorrepaal, Ellen ; Euskirchen, Eugénie S. ; Stenøien, Hans K. ; Szövényi, Péter ; Jackson, Michelle ; Piatkowski, Bryan T. ; Muchero, Wellington ; Norby, Richard J. ; Kostka, Joel E. ; Glass, Jennifer B. ; Rydin, Håkan ; Limpens, Juul ; Tuittila, Eeva Stiina ; Ullrich, Kristian K. ; Carrell, Alyssa ; Benscoter, Brian W. ; Chen, Jin Gui ; Oke, Tobi A. ; Nilsson, Mats B. ; Ranjan, Priya ; Jacobson, Daniel ; Lilleskov, Erik A. ; Clymo, R.S. ; Shaw, A.J. - \ 2018
    New Phytologist 217 (2018)1. - ISSN 0028-646X - p. 16 - 25.
    ecological genomics - ecosystem engineering - evolutionary genetics - genome sequencing - niche construction - peatlands - Sphagnome - Sphagnum
    Considerable progress has been made in ecological and evolutionary genetics with studies demonstrating how genes underlying plant and microbial traits can influence adaptation and even ‘extend’ to influence community structure and ecosystem level processes. Progress in this area is limited to model systems with deep genetic and genomic resources that often have negligible ecological impact or interest. Thus, important linkages between genetic adaptations and their consequences at organismal and ecological scales are often lacking. Here we introduce the Sphagnome Project, which incorporates genomics into a long-running history of Sphagnum research that has documented unparalleled contributions to peatland ecology, carbon sequestration, biogeochemistry, microbiome research, niche construction, and ecosystem engineering. The Sphagnome Project encompasses a genus-level sequencing effort that represents a new type of model system driven not only by genetic tractability, but by ecologically relevant questions and hypotheses.
    DOG1-imposed dormancy mediates germination responses to temperature cues
    Murphey, M. ; Kovach, K. ; Elnacash, T. ; He, H. ; Bentsink, L. ; Donohue, K. - \ 2015
    Environmental and Experimental Botany 112 (2015). - ISSN 0098-8472 - p. 33 - 43.
    seed-maturation environment - quantitative trait locus - recent climate-change - arabidopsis-thaliana - life-history - ectopic expression - niche construction - natural-selection - dog1-like genes - dog1
    Seed dormancy and environment-dependent germination requirements interact to determine the timing of germination in natural environments. This study tested the contribution of the dormancy gene Delay Of Germination 1 (DOG1) to primary and secondary dormancy induction in response to environmental cues, and evaluated how DOG1-mediated dormancy influenced germination responses to different temperature cues. We verified that DOG1 is involved in the induction of primary dormancy in response to cool seed-maturation temperature experienced by maternal plants, and we found that it is also involved in secondary dormancy in response to warm and prolonged cold stratification experienced by seeds during imbibition. DOG1-imposed dormancy can also mediate germination responses to environmental conditions, including cold stratification and germination temperatures experienced by imbibing seeds. Specifically, germination responsiveness to temperature cues is most apparent when seeds exhibit an intermediate degree of dormancy. However, DOG1 itself does not seem to directly regulate the response to cold stratification nor does it determine the function of temperature-dependent germination, since DOG1 mutants were capable of exhibiting increased germination after cold stratification as well as temperature-dependent germination. Instead, DOG1 has major effects on germination behavior primarily by exposing or masking underlying environmental sensitivity, and thereby strongly influences how environmentally responsive germination can be, and when during a season, it is likely to exhibit environmental sensitivity.
    Death and cannibalism in a seasonal environment facilitate bacterial coexistence
    Rozen, D.E. ; Philippe, N. ; Visser, J.A.G.M. de; Lenski, R.E. ; Schneider, D. - \ 2009
    Ecology Letters 12 (2009)1. - ISSN 1461-023X - p. 34 - 44.
    term experimental evolution - escherichia-coli mutants - general stress-response - stationary-phase - adaptive radiation - balanced polymorphism - constant environment - microbial microcosms - prolonged starvation - niche construction
    Bacterial populations can evolve and adapt to become diverse niche specialists, even in seemingly homogeneous environments. One source of this diversity arises from newly 'constructed' niches that result from the activities of the bacteria themselves. Ecotypes specialized to exploit these distinct niches can subsequently coexist via frequency-dependent interactions. Here, we describe a novel form of niche construction that is based upon differential death and cannibalism, and which evolved during 20 000 generations of experimental evolution in Escherichia coli in a seasonal environment with alternating growth and starvation. In one of 12 populations, two monophyletic ecotypes, S and L, evolved that stably coexist with one another. When grown and then starved in monoculture, the death rate of S exceeds that of L, whereas the reverse is observed in mixed cultures. As shown by experiments and numerical simulations, the competitive advantage of S cells is increased by extending the period of starvation, and this advantage results from their cannibalization of the debris of lysed L cells, which allows the S cells to increase both their growth rate and total cell density. At the molecular level, the polymorphism is associated with divergence in the activity of the alternative sigma factor RpoS, with S cells displaying no detectable activity, while L cells show increased activity relative to the ancestral genotype. Our results extend the repertoire of known cross-feeding mechanisms in microbes to include cannibalism during starvation, and confirm the central roles for niche construction and seasonality in the maintenance of microbial polymorphisms
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