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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Widespread Phytophthora infestations in European nurseries put forest, semi-natural and horticultural ecosystems at high risk of Phytophthora diseases
Jung, T. ; Orlikowski, L. ; Henricot, B. ; Abad-Campos, P. ; Aday, A.G. ; Aguín Casal, O. ; Bakonyi, J. ; Cacciola, S.O. ; Cech, T. ; Chavarriaga, D. ; Cravador, A. ; Wenneker, M. - \ 2016
Forest Pathology 46 (2016)2. - ISSN 1437-4781 - p. 134 - 163.

An analysis of incidence of Phytophthora spp. in 732 European nurseries producing forest transplants, larger specimen trees, landscape plants and ornamentals, plus 2525 areas in which trees and shrubs were planted, is presented based on work conducted by 37 research groups in 23 European countries between 1972 and 2013. Forty-nine Phytophthora taxa were recorded in 670 nurseries (91.5%); within these nurseries, 1614 of 1992 nursery stands (81.0%) were infested, although most affected plants appeared healthy. In forest and landscape plantings, 56 Phytophthora taxa were recovered from 1667 of 2525 tested sites (66.0%). Affected plants frequently showed symptoms such as crown thinning, chlorosis and dieback caused by extensive fine root losses and/or collar rot. Many well-known highly damaging host-Phytophthora combinations were frequently detected but 297 and 407 new Phytophthora-host associations were also observed in nurseries and plantings, respectively. On average, 1.3 Phytophthora species/taxa per infested nursery stand and planting site were isolated. At least 47 of the 68 Phytophthora species/taxa detected in nurseries and plantings were exotic species several of which are considered well established in both nurseries and plantings in Europe. Seven known Phytophthora species/taxa were found for the first time in Europe, while 10 taxa had not been previously recorded from nurseries or plantings; in addition, 5 taxa were first detections on woody plant species. Seven Phytophthora taxa were previously unknown to science. The reasons for these failures of plant biosecurity in Europe, implications for forest and semi-natural ecosystems and possible ways to improve biosecurity are discussed.

Effects of microelements on soil nematode assemblages seven years after contaminating an agricultural field
Nagy, P. ; Bakonyi, G. ; Bongers, A.M.T. ; Kádár, I. ; Fábián, M. ; Kiss, I. - \ 2004
Science of the Total Environment 320 (2004)2-3. - ISSN 0048-9697 - p. 131 - 143.
heavy-metals - community structure - maturity index - sewage-sludge - pollution - cadmium - copper
Long-term effects of Cd, Cr, Cu, Se and Zn were studied 7 years after artificially contaminating plots of an agricultural field on a calcareous chernozem soil. Effects of three to four different contamination levels (originally 10, 30, 90 and 270 mg kg(-1)) were studied. Nematode density was significantly reduced by 90 and 270 mg kg(-1) Se as well as by 270 mg g(-1) Cr, while 90 and 270 mg kg(-1) Se also reduced nematode generic richness. Maturity Index values (calculated for c-p 2-5 nematodes) consistently decreased with increasing Cr and Se concentration and to a lesser extent in Zn plots as well. Structure Index showed decreasing trends in increasing Cr, Se and (to a lesser extent) in Zn treatments, while in Cd it shows a moderate increase. Distribution of c-p groups was negatively affected by the increasing Cr and Se concentration, while in Zn plots, this decrease was not significant. Response of feeding groups to pollutions was similar to other parameters: Cr and Se caused significant changes toward the loss of variability. The proportion of the most sensitive omnivorous and predatory nematodes decreased clearly as a consequence of Cr and Se treatments. Zn pollution also resulted in a slight decrease in this group, while Cd caused an increase. Nematode diversity profiles showed a significant decrease in the plots of increased Cr and Se concentrations, while increased concentrations of Cu and Zn resulted in ambiguous effects. Besides providing evidence on the harmful effects of Cr and Se on a soil nematode assemblage, our results suggest that simultaneous analysis of Maturity Index, Structure Index and diversity profiles provide a promising tool in nemtological indication of soil pollution. (C) 2003 Elsevier B.V. All rights reserved.
Design and evaluation of nematode 18S rDNA primers for PCR and denaturing gradient gel electrophoresis (DGGE) of soil community DNA
Waite, I.S. ; O'Donnell, A.G. ; Harrison, A. ; Davies, J.T. ; Colvan, S.R. ; Ekschmitt, K. ; Dogan, H. ; Wolters, V. ; Bongers, A.M.T. ; Bongers, M. ; Bakonyi, G. ; Nagy, P. ; Papatheodorou, E.M. ; Stamou, G.P. ; Boström, S. - \ 2003
Soil Biology and Biochemistry 35 (2003). - ISSN 0038-0717 - p. 1165 - 1173.
16s ribosomal-rna - bacterial communities - hydrothermal vent - grassland soils - diversity - genes - biodiversity - populations - identification - quantification
Consensus nematode 185 ribosomal DNA primers were designed by aligning available 185 sequences and identifying a variable region flanked by highly conserved regions. These primers were then used to amplify nematode 18S rDNA from whole soil community DNA extracted from a range of European grassland types. Cloning of the PCR amplicons (778 bp) followed by restriction digest analysis (RFLP) resulted in the recovery of 34 unique nematode sequences from the four grasslands studied. Comparison of these data with the limited number of 18S rDNA nematode sequences currently held in on-line databases revealed that all of the sequences could be assigned to known nematode taxa albeit tentatively in some cases. Two of the sequences recovered from the site in the Netherlands (wet, hay-grassland) were recovered in a clade that included a sequence of the genus Trichodorus whilst other sequences from this site showed similarity with 185 rDNA sequences of the genus Prismatolaimus (five sequences), Xiphinema (one sequence) and Enoplus (one sequence). Of the remaining sequences, two showed some affinity with Mylonchulus (UK, upland peat), four with Steinernema (UK) and one sequence with Mesorhabditis (Hungary, east European Steppe). Three sequences from the Netherlands and one from Hungary were recovered in a clade that included a sequence of the genus Pratylenchoides whilst three further sequences from the Netherlands and two from Hungary were recovered in a clade encompassing the genus Globodera. Of the remaining nine sequences, two (NL6, NL62) formed a distinct lineage within the Adenophorea with 90% bootstrap recovery in a paraphyletic clade that included sequences of Prismatolaimus and Trichodorus. Seven sequences (three from the Netherlands, three from the UK and one from Greece) were left unassigned though the tree topology suggested some relationship (58% bootstrap recovery) with the genus Cephalobus. To assess whether primers used to amplify 185 rDNA might be used to fingerprint genetic diversity in nematode communities in soil, the environmental sequence data were used to design a second set of primers carrying a GC-clamp. These primers amplified a 469 by fragment internal to the region flanked by the primer set used to derive the nematode trees and were used to amplify 185 rDNA for subsequent analysis using denaturing gradient gel electrophoresis (DGGE). DGGE analysis of six major European grassland types revealed considerable genetic diversity between sites. However, the relationships seen with the DGGE data were inconsistent with previous studies where the same soils had been characterized with respect to functional and morphological diversity. To confine that this second set of primers was amplifying nematode sequences, selected bands on the DGGE gels were extracted, PCR amplified and sequenced. The final alignment was 337 bases. These analyses revealed the presence of sequence signatures from the genera Paratrichodorus, Plectus, Steinernema, Globodera, Cephalobus and Pratylenchoides. (C) 2003 Elsevier Ltd. All rights reserved.
Nematode community structure as indicator of soil functioning in European grassland soils
Ekschmitt, K. ; Bakonyi, G. ; Bongers, M. ; Bongers, T. ; Boström, S. ; Dogan, H. ; Harrison, A. ; Nagy, P. ; O'Donell, A.G. ; Papatheodorou, E.M. ; Sohlenius, B. ; Stamou, G.P. - \ 2001
European Journal of Soil Biology 37 (2001). - ISSN 1164-5563 - p. 263 - 268.
DEGREE - Functional role of soil nematode communities in European grassland ecosystems under climatic change
Ekschmitt, K. ; Bakonyi, G. ; Bongers, M. ; Bongers, T. ; Botröm, S. ; Dogan, H. ; Harrison, A. ; Kallimanis, A. ; Nagy, P. ; O'Donnell, A.G. ; Sohlenius, B. ; Stamou, G.P. ; Wolters, V. - \ 2000
In: DEGREE - Functional role of soil nematode communities in European grassland ecosystems under climatic change : Terrestrial Ecosystem Research in Europe: successes, challenges and policy, Egmond aan Zee, the Netherlands / Sutton, M.A., Moreno, J.M., Italy : European Communities - ISBN 9789282895702 - p. 112 - 114.
Effects of the nematofauna on microbial energy and matter transformation rates in European grassland soils
Ekschmitt, K. ; Bakonyi, G. ; Bongers, M. ; Bongers, T. ; Bostrom, S. ; Dogan, H. ; Harrison, A. ; Kallimanis, A. ; Nagy, P. ; O'Donnell, G. ; Sohlenius, B. ; Stamou, G. - \ 1999
Plant and Soil 212 (1999)1. - ISSN 0032-079X - p. 45 - 61.
The effect of the nematofauna on the microbiology and soil nitrogen status was studied in 6 major European grassland types (Northern tundra (Abisko, Sweden), Atlantic heath (Otterburn, UK), wet grassland (Wageningen, Netherlands), semi-natural temperate grassland (Linden, Germany), East European steppe (Pusztaszer, Hungary) and Mediterranean garigue (Mt. Vermion, Greece). To extend the range of temperature and humidity experienced locally during the investigation period, soil microclimates were manipulated, and at each site 14 plots were established representing selected combinations of 6 temperature and 6 moisture levels. The investigated soils divided into two groups: mineral grassland soils that were precipitation fed (garigue, wet grassland, seminatural grassland, steppe), and wet organic soils that were groundwater fed (heath, tundra). Effects of the nematofauna on the microflora were found in the mineral soils, where correlations among nematode metabolic activity as calculated from a metabolic model, and microbial activity parameters as indicated by Biolog and ergosterol measurements, were significantly positive. Correlations with bacterial activity were stronger and more consistent. Microbial parameters, in turn, were significantly correlated with the size of the soil nitrogen pools NH4, NO3, and Norganic. Furthermore, model results suggested that there were remarkable direct effects of nematodes on soil nitrogen status. Calculated monthly nematode excretion contributed temporarily up to 27% of soluble soil nitrogen, depending on the site and the microclimate. No significant correlation among nematodes and microbial parameters, or nitrogen pools, were found in the wet organic soils. The data show that the nematofauna can under favourable conditions affect soil nitrogen status in mineral grassland soils both directly by excretion of N, and indirectly by regulating microbial activity. This suggests that the differences in nitrogen availability observed in such natural grasslands partly reflect differences in the activity of their indigenous nematofauna
Effects of the nematofauna on microbial energy and matter transformation rates in European grassland soils.
Ekschmitt, K. ; Bakonyi, G. ; Bongers, T. ; Bostroem, S. ; Nagy, P. ; O'Donell, A.G. ; Sohlenius, B. ; Stamou, G.P. ; Wolters, V. - \ 1998
In: Proceedings of the 24th International Nematology Symposium, Dundee, UK - p. 30 - 30.
Effects of the nematofauna on microbial energy and matter transformation rates in European grassland soils.
Ekschmitt, K. ; Bakonyi, G. ; Bongers, T. ; Bostroem, S. ; Nagy, P. ; O'Donell, A.G. ; Sohlenius, B. ; Stamou, G.P. ; Wolters, V. - \ 1998
Nematologica 44 (1998). - ISSN 0028-2596 - p. 487 - 487.
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