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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    We will mail you new results for this query: q=Simek
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Opportunities for soil sustainability in Europe
Putten, W.H. van der; Ramirez, Kelly S. ; Poesen, Jean ; Winding, A. ; Lemanceau, Philippe ; Lisa, Lenka ; Simek, Miloslaw ; Moora, M. ; Setala, Heikki ; Zaitsev, A. ; Economou-Eliopoulos, Maria ; Hornung, E. ; Wall, David ; Angelis, P. de; Lipiec, Jerzy ; Briones, M.J.I. ; Hedlund, Katarina ; Heijden, M. ; Six, Johan ; Bardgett, Richard D. ; Powlson, D. ; Goulding, K. ; Norton, Michael - \ 2018
European Academies Science Advisory Council (EASAC) (EASAC policy report 36) - ISBN 9783804738980 - 48 p.
Marine bacterial community structure resilience to changes in protist predation under phytoplankton bloom conditions
Baltar, Federico ; Palovaara, Joakim ; Unrein, Fernando ; Catala, Philippe ; Horňák, Karel ; Šimek, Karel ; Vaqué, Dolors ; Massana, Ramon ; Gasol, Josep M. ; Pinhassi, Jarone - \ 2016
ISME Journal 10 (2016)3. - ISSN 1751-7362 - p. 568 - 581.

To test whether protist grazing selectively affects the composition of aquatic bacterial communities, we combined high-throughput sequencing to determine bacterial community composition with analyses of grazing rates, protist and bacterial abundances and bacterial cell sizes and physiological states in a mesocosm experiment in which nutrients were added to stimulate a phytoplankton bloom. A large variability was observed in the abundances of bacteria (from 0.7 to 2.4 × 10 6 cells per ml), heterotrophic nanoflagellates (from 0.063 to 2.7 × 10 4 cells per ml) and ciliates (from 100 to 3000 cells per l) during the experiment (∼3-, 45- and 30-fold, respectively), as well as in bulk grazing rates (from 1 to 13 × 10 6 bacteria per ml per day) and bacterial production (from 3 to 379 μg per C l per day) (1 and 2 orders of magnitude, respectively). However, these strong changes in predation pressure did not induce comparable responses in bacterial community composition, indicating that bacterial community structure was resilient to changes in protist predation pressure. Overall, our results indicate that peaks in protist predation (at least those associated with phytoplankton blooms) do not necessarily trigger substantial changes in the composition of coastal marine bacterioplankton communities.

Integrated approach in controlling soil-borne diseases in ornamental crop production
Boer, M. de; Os, G.J. van; Korthals, G.W. ; Raaijmakers, J.M. - \ 2011
In: Book of Abstracts International Conference Ecology of Soil Microorganisms, Prague, Czech Republic, 27 April – 1 May 2011. - - p. 250 - 250.
Regulator-based genome mining for novel bioactive compounds in soil bacteria
Bruijn, I. de; Cheng, X. ; Dekkers, E. ; Voort, M. van der; Raaijmakers, J.M. - \ 2011
In: Book of Abstracts International Conference Ecology of Soil Microorganisms, Prague, Czech Republic, 27 April – 1 May 2011. - - p. 139 - 139.
Discovery of novel microorganisms and antimicrobial traits in natural disease suppressive soils
Mendes, R. ; Voort, M. van der; Kruijt, M. ; Bruijn, I. de; Dekkers, E. ; Bakker, P.A.H.M. ; Piceno, Y.M. ; DeSantis, T.Z. ; Andersen, G.L. ; Raaijmakers, J. - \ 2011
In: International Conference Ecology of Soil Microorganisms, Microbes as Important Drivers of Soil Processes, Prague, Czech Republic, 27 April - 01 May, 2011. - - p. 288 - 288.
Soil ecosystems represent an enormous untapped resource for discovering novel microorganisms, traits and bioactive genes. Specific soils have been identified worldwide in which beneficial microorganisms guard plants against infections by soil-borne pathogens. However, the microbiological and molecular mechanisms underlying this soil immune response are largely unknown. In the present work, the microorganisms and mechanisms involved in natural suppressiveness of soils to the fungal pathogen Rhizoctonia solani were investigated by culture-dependent and independent approaches. Culture-based analyses revealed quantitative and qualitative differences in bacterial populations between Rhizoctonia suppressive and conducive soils. Subsequent genotyping and functional analyses led to the identification of novel Pseudomonas species producing yet unidentified chlorinated peptide antibiotics. The cultivationindependent approaches included PhyloChip-based community analysis and activity profiling by metagenomic analysis of rhizosphere RNA. The Phylochip analysis distinguished the bacterial communities from soils with different levels of disease suppressiveness and specifically pointed to the Proteobacteria as an important rhizosphere competent phylum and dynamic group associated with disease suppression. Although the richness observed in either suppressive or conducive soils was not significantly different, the relative abundance for some groups correlated well with the different levels of soil suppressiveness. While the cultivation-dependent approach resulted mainly in isolates of the ¿-Proteobacteria class, the Phylochip analysis revealed bacteria belonging to several phyla, including Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, Acidobacteria, Planctomycetes and Chloroflexi. In conclusio
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