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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    Assessing effects of the fungicide tebuconazole to heterotrophic microbes in aquatic microcosms
    Dimitrov, M.R. ; Kosol, Sujitra ; Smidt, H. ; Brink, P.J. van den; Wijngaarden, R.P.A. van; Brock, T.C.M. ; Maltby, L. - \ 2014
    Science of the Total Environment 490 (2014). - ISSN 0048-9697 - p. 1002 - 1011.
    gradient gel-electrophoresis - leaf-litter decomposition - fresh-water microcosms - coal-mine effluent - decaying leaves - gammarus-pulex - community composition - fungal communities - primary producers - stream fungi
    Aquatic ecological risk assessment of fungicides in Europe under Regulation 1107/2009/EC does not currently assess risk to non-target bacteria and fungi. Rather, regulatory acceptable concentrations based on ecotoxicological data obtained from studies with fish, invertebrates and primary producers (including algae) are assumed to be protective to all other aquatic organisms. Here we explore the validity of this assumption by investigating the effects of a fungicide (tebuconazole) applied at its "non-microbial" HC5 concentration (the concentration that is hazardous to 5% of the tested taxa) and derived from acute single species toxicity tests on fish, invertebrates and primary producers (including algae) on the community structure and functioning of heterotrophic microbes (bacteria and aquatic fungi) in a semi-field study, using novel molecular techniques. In our study, a treatment-related effect of tebuconazole (238 µg/L) on either fungal biomass associated with leaf material or leaf decomposition or the composition of the fungal community associated with sediment could not be demonstrated. Moreover, treatment-related effects on bacterial communities associated with sediment and leaf material were not detected. However, tebuconazole exposure did significantly reduce conidia production and altered fungal community composition associated with leaf material. An effect on a higher trophic level was observed when Gammarus pulex were fed tebuconazole-exposed leaves, which caused a significant decrease in their feeding rate. Therefore, tebuconazole may affect aquatic fungi and fungally mediated processes even when applied at its "non-microbial" HC5 concentration.
    The northward shifting neophyte Tragopogon dubius is just as effective in forming mycorrhizal associations as the native T. pratensis
    Grunsven, R.H.A. van; Yuwati, T. ; Kowalchuk, G.A. ; Putten, W.H. van der; Veenendaal, E. - \ 2014
    Plant Ecology & Diversity 7 (2014)4. - ISSN 1755-0874 - p. 533 - 539.
    plant-soil feedback - functional diversity - fungal communities - ammophila-arenaria - climate-change - sand dunes - range - grass - identification - amplification
    Background: As a consequence of climate warming, many organisms are shifting their range towards higher latitudes and altitudes. As not all do so at the same speed, this may disrupt biotic interaction. Release from natural enemies through range expansion can result in invasiveness, whereas loss of mutualists can reduce plant vigour and fitness. One of the most important groups of plant symbiotic mutualists is the arbuscular mycorrhizal fungi (AMF). Aims: We used greenhouse experiments to test whether Tragopogon dubius, a species that has recently expanded its range northward and colonised the Netherlands, is able to associate with the same AMF as the native congener T. pratensis. Methods: In soils collected from four locations in the new range of T. dubius we compared the density of infective AMF propagules associating with both plant species, as well as AMF colonisation of the roots. The AMF community structure in the roots of these species was also analysed using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). Results: Tragopogon dubius and T. pratensis did not differ in any of these characteristics. Conclusions: We therefore conclude that the range-shifting T. dubius is as effective in the formation of mycorrhiza as the native congener.
    Diversity patterns of leaf-associated aquatic hyphomycetes along a broad latitudinal gradient
    Jabiol, J. ; Bruder, A. ; Gessner, M.O. ; Makkonen, M. ; McKie, B.G. ; Peeters, E.T.H.M. ; Vos, V.C.A. ; Chauvet, E. - \ 2013
    Fungal Ecology 6 (2013)5. - ISSN 1754-5048 - p. 439 - 448.
    species-diversity - community structure - fungal communities - stream - litter - biodiversity - temperature - leaves - colonization - decomposition
    Information about the global distribution of aquatic hyphomycetes is scarce, despite the primary importance of these fungi in stream ecosystem functioning. In particular, the relationship between their diversity and latitude remains unclear, due to a lack of coordinated surveys across broad latitudinal ranges. This study is a first report on latitudinal patterns of aquatic hyphomycete diversity associated with native leaf-litter species in five streams located along a gradient extending from the subarctic to the tropics. Exposure of leaf litter in mesh bags of three different mesh sizes facilitated assessing the effects of including or excluding different size-classes of litter-consuming invertebrates. Aquatic hyphomycete evenness was notably constant across all sites, whereas species richness and diversity, expressed as the Hill number, reached a maximum at mid-latitudes (Mediterranean and temperate streams). These latitudinal patterns were consistent across litter species, despite a notable influence of litter identity on fungal communities at the local scale. As a result, the bell-shaped distribution of species richness and Hill diversity deviated markedly from the latitudinal patterns of most other groups of organisms. Differences in the body-size distribution of invertebrate communities colonizing the leaves had no effect on aquatic hyphomycete species richness, Hill diversity or evenness, but invertebrates could still influence fungal communities by depleting litter, an effect that was not captured by the design of our experiment. (C) 2013 Elsevier Ltd and The British Mycological Society. All rights reserved.
    The Influence of Long-Term Copper Contaminated Agricultural Soil at Different pH Levels on Microbial Communities and Springtail Transcriptional Regulation
    Boer, T.E. de; Tas, N. ; Braster, M. ; Temminghoff, E.J.M. ; Roling, W.F.M. ; Roelofs, D. - \ 2012
    Environmental Science and Technology 46 (2012)1. - ISSN 0013-936X - p. 60 - 68.
    heavy-metal contamination - bacterial community - organic status - fungal communities - arable soil - sandy soil - diversity - toxicity - microorganisms - microarray
    Copper has long been applied for agricultural practises. Like other metals, copper is highly persistent in the environment and biologically active long after its use has ceased. Here we present a unique study on the long-term effects (27 years) of copper and pH on soil microbial communities and on the springtail Folsomia candida an important representative of the soil macrofauna, in an experiment with a full factorial, random block. design. Bacterial communities were mostly affected by pH. These effects were prominent in Acidobacteria, while Actinobacteria and Gammaroteobacteria communities were affected by original and bioavailable copper. Reproduction and survival of the collembolan F. candida was not affected by the studied copper concentrations. However, the transcriptomic responses to copper reflected a mechanism of copper transport and detoxification, while pH exerted effects on nucleotide and protein metabolism and (acute) inflammatory response. We conclude that microbial community structure reflected the history of copper contamination, while gene expression analysis of F. candida is associated with the current level of bioavailable copper. The study is a first step in the development of a molecular strategy aiming at a more comprehensive assessment of various aspects of soil quality and ecotoxicology.
    Pyrosequencing as a tool for the detection of Phytophthora species: error rate and risk of false Molecular Operational Taxonomic Units
    Vettraino, A.M. ; Bonants, P.J.M. ; Tomassini, A. ; Bruni, N. ; Vannini, A. - \ 2012
    Letters in Applied Microbiology 55 (2012)5. - ISSN 0266-8254 - p. 390 - 396.
    fungal communities - identification - phylogeny - diversity - sequences - reveals
    Aims: To evaluate the accuracy of pyrosequencing for the description of Phytophthora communities in terms of taxa identification and risk of assignment for false Molecular Operational Taxonomic Units (MOTUs). Methods and Results: Pyrosequencing of Internal Transcribed Spacer 1 (ITS1) amplicons was used to describe the structure of a DNA mixture comprising eight Phytophthora spp. and Pythium vexans. Pyrosequencing resulted in 16 965 reads, detecting all species in the template DNA mixture. Reducing the ITS1 sequence identity threshold resulted in a decrease in numbers of unmatched reads but a concomitant increase in the numbers of false MOTUs. The total error rate was 0_63% and comprised mainly mismatches (0_25%) Conclusions: Pyrosequencing of ITS1 region is an efficient and accurate technique for the detection and identification of Phytophthora spp. In environmental samples. However, the risk of allocating false MOTUs, even when demonstrated to be low, may require additional validation with alternative detection methods. Significance and Impact of the Study: Phytophthora spp. are considered among the most destructive groups of invasive plant pathogens, affecting thousands of cultivated and wild plants worldwide. Simultaneous early detection of Phytophthora complexes in environmental samples offers an unique opportunity for the interception of known and unknown species along pathways of introduction, along with the identification of these organisms in invaded environments.
    Comparing arbuscular mycorrhizal communities of individual plants in a grassland biodiversity experiment
    Voorde, T.F.J. van de; Putten, W.H. van der; Gamper, H.A. ; Hol, W.H.G. ; Bezemer, T.M. - \ 2010
    New Phytologist 186 (2010)3. - ISSN 0028-646X - p. 746 - 754.
    fungal communities - senecio-jacobaea - species-diversity - ribosomal-rna - roots - colonization - productivity - variability - ecology - soil
    Plants differ greatly in the soil organisms colonizing their roots. However, how soil organism assemblages of individual plant roots can be influenced by plant community properties remains poorly understood. We determined the composition of arbuscular mycorrhizal fungi (AMF) in Jacobaea vulgaris plants, using terminal restriction fragment length polymorphism (T-RFLP). The plants were collected from an experimental field site with sown and unsown plant communities. Natural colonization was allowed for 10 yr in sown and unsown plots. Unsown plant communities were more diverse and spatially heterogeneous than sown ones. Arbuscular mycorrhizal fungi diversity did not differ between sown and unsown plant communities, but there was higher AMF assemblage dissimilarity between individual plants in the unsown plant communities. When we grew J. vulgaris in field soil that was homogenized after collection in order to rule out spatial variation, no differences in AMF dissimilarity between sown and unsown plots were found. Our study shows that experimental manipulation of plant communities in the field, and hence plant community assembly history, can influence the AMF communities of individual plants growing in those plant communities. This awareness is important when interpreting results from field surveys and experimental ecological studies in relation to plant–symbiont interactions
    Fine roots and ectomycorrhizas as indicators of environmental change.
    Cudlin, P. ; Kieliszewska-Rokicka, B. ; Rudawska, M. ; Grebenc, T. ; Alberton, O. ; Lehto, T. ; Bakker, M.R. ; Borja, I. ; Konopka, B. ; Leski, T. ; Kraigher, H. ; Kuyper, T.W. - \ 2007
    Plant Biosystems 141 (2007)3. - ISSN 1126-3504 - p. 406 - 425.
    spruce picea-abies - pine pinus-sylvestris - experimental nitrogen addition - atmospheric carbon-dioxide - air ozone fumigation - sitchensis bong carr - norway spruce - scots pine - fagus-sylvatica - fungal communities
    Human-induced and natural stress factors can affect fine roots and ectomycorrhizas. Therefore they have potential utility as indicators of environmental change. We evaluated, through meta-analysis, the magnitude of the effects of acidic deposition, nitrogen deposition, increased ozone levels, elevated atmospheric carbon dioxide, and drought on fine roots and ectomycorrhizal (ECM) characteristics. Ectomycorrhizal colonization was an unsuitable parameter for environmental change, but fine root length and biomass could be useful. Acidic deposition had a significantly negative impact on fine roots, root length being more sensitive than root biomass. There were no significant effects of nitrogen deposition or elevated tropospheric ozone on the quantitative root parameters. Elevated CO2 had a significant positive effect. Drought had a significantly negative effect on fine root biomass. The negative effect of acidic deposition and the positive effect of elevated CO2 increased over time, indicating that effects were persistent contrary the other factors. The meta-analysis also showed that experimental conditions, including both laboratory and field experiments, were a major source of variation. In addition to quantitative changes, environmental changes affect the species composition of the ectomycorrhizal fungal community.
    Microbial community responses to disease management soil treatments used in flower bulb cultivation
    Kowalchuk, G.A. ; Os, G.J. van; Aartrijk, J. van; Veen, J.A. van - \ 2003
    Biology and Fertility of Soils 37 (2003)1. - ISSN 0178-2762 - p. 55 - 63.
    gradient gel-electrophoresis - 16s ribosomal-rna - pythium root-rot - ammonia-oxidizing bacteria - dna fragments - fungal communities - damping-off - class proteobacteria - beta-subdivision - 18s rdna
    A number of management practices, such as soil fumigation and flooding, have been employed in efforts to control diseases and weeds in the cultivation of ornamental flower bulbs. However, such treatments may affect the suppression of Pythium root rot, a serious problem in ornamental bulb culture. To gain insight into the nature of Pythium suppression in such soils, we sought to describe the changes that these soil treatments induce in the microbial community in order to determine if particular microbial components of the system could be associated with suppression. Four polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) strategies, two targeting bacteria and two targeting fungi, were used to compare the soil-borne microbial communities of untreated, fumigated, flooded and sterilized, compost-amended soils; the dominant community members were tentatively identified by sequencing of DGGE bands. For all profiling strategies, the compost treatment of sterilized soil appeared to have the most profound effect on the dominant microbial populations in the soil. In general, different primer sets that targeted the same microbial groups, bacteria or fungi, appeared to detect the same microbial taxa, although certain sequence types were detected in only a single profiling strategy. DNA-based microbial community profiles alone were poor predictors of Pythium suppression, as the dominant microbial populations remained mostly intact, even after rigorous soil treatments such as fumigation and flooding. The restoration of suppressive activity against Pythium in compost-amended soil was associated with a different microbial community than observed in untreated, suppressive soils. Thus, although previous studies have shown the suppression of Pythium to be mediated by biological agents, effects of different microbial communities can lead to this suppression.
    Molecular analysis of ectomycorrhizal basidiomycete communities in a Pinus sylvestris L. stand reveals long-term increased diversity after removal of litter and humus layers
    Smit, E. ; Veenman, C. ; Baar, J. - \ 2003
    FEMS microbiology ecology 45 (2003)1. - ISSN 0168-6496 - p. 49 - 57.
    inorganic nitrogen-sources - fungal communities - muricata forest - pure culture - scots pine - soil fungi - deposition - mycelium - identification - netherlands
    The number of fruiting bodies of ectomycorrhizal species in pine forests in The Netherlands has decreased dramatically in recent decades. This decrease has been attributed to an increase in nitrogen deposition and the accumulation of litter and humus. The effects of sod cutting and the removal of litter and humus, to restore ectomycorrhizal diversity in a Scots pine forest in Dwingeloo, The Netherlands, were investigated previously from 1990 to 1993. Removal of the litter and humus resulted in a significant increase in the numbers of species and fruiting bodies of ectomycorrhizal fungi. However, until now all data were obtained by counting fruiting bodies and the effects on mycelial development below ground were not assessed. To investigate hyphal development, DNA was extracted from bulk soil and polymerase chain reaction products were obtained by amplification using basidiomycete-specific internal transcribed spacer (ITS) primers. The differences in diversity between the control plots and the treated plots were analyzed using denaturing gradient gel electrophoresis. To assess the species composition and differences, ITS regions of the amplified fragments were cloned and sequenced. Sequences were compared with sequences from GenBank and from fruiting bodies collected from the same plots. Data indicated increased below-ground ectomycorrhizal diversity in the plots that had been subjected to removal of the litter and humus layers
    Molecular identification of ectomycorrhizal mycelium in soil horizons
    Landeweert, R. ; Leeflang, P. ; Kuyper, T.W. ; Hoffland, E. ; Rosling, A. ; Wernars, K. ; Smit, E. - \ 2003
    Applied and Environmental Microbiology 69 (2003). - ISSN 0099-2240 - p. 327 - 333.
    gradient gel-electrophoresis - environmental-samples - fungal communities - ribosomal-rna - dna extraction - forest soil - diversity - primers - growth - amplification
    Molecular identification techniques based on total DNA extraction provide a unique tool for identification of mycelium in soil. Using molecular identification techniques, the ectomycorrhizal (EM) fungal community under coniferous vegetation was analyzed. Soil samples were taken at different depths from four horizons of a podzol profile. A basidiomycete-specific primer pair (ITS1F-ITS4B) was used to amplify fungal internal transcribed spacer (ITS) sequences from total DNA extracts of the soil horizons. Amplified basidiomycete DNA was cloned and sequenced, and a selection of the obtained clones was analyzed phylogenetically. Based on sequence similarity, the fungal clone sequences were sorted into 25 different fungal groups, or operational taxonomic units (OTUs). Out of 25 basidiomycete OTUs, 7 OTUs showed high nucleotide homology (greater than or equal to99%) with known EM fungal sequences and 16 were found exclusively in the mineral soil. The taxonomic positions of six OTUs remained unclear. OTU sequences were compared to sequences from morphotyped EM root tips collected from the same sites. Of the 25 OTUs, 10 OTUs had greater than or equal to98% sequence similarity with these EM root tip sequences. The present study demonstrates the use of molecular techniques to identify EM hyphae in various soil types. This approach differs from the conventional method of EM root tip identification and provides a novel approach to examine EM fungal communities in soil.
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