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 impact of dispersal, plant genotype and nematodes on arbuscular mycorrhizal fungal colonization
Rasmussen, Pil U. ; Chareesri, Anupol ; Neilson, Roy ; Bennett, Alison E. ; Tack, Ayco J.M. - \ 2019
Soil Biology and Biochemistry 132 (2019). - ISSN 0038-0717 - p. 28 - 35.
Arbuscular mycorrhizal fungi - Colonization ability - Dispersal - Genotype - Nematodes - Plantago lanceolata

While the majority of parasitic and mutualistic microbes have the potential for long-range dispersal, the high turnover in community composition among nearby hosts has often been interpreted to reflect dispersal constraints. To resolve this apparent contradiction, we need further insights into the relative importance of dispersal limitation, host genotype and the biotic environment on the colonization process. We focused on the important root symbionts, the arbuscular mycorrhizal (AM) fungi. We studied AM fungal colonization ability in a controlled mesocosm setting, where we placed Plantago lanceolata plants belonging to four different genotypes in sterile soil at 10, 30 and 70 cm from a central AM fungal inoculated P. lanceolata plant. In part of the mesocosms, we also inoculated the source plants with nematodes. AM fungi colonized receiver plants <1 m away over the course of ten weeks, with a strong effect of distance from source plant on AM fungal colonization. Plant genotype influenced AM fungal colonization during the early stages of colonization, while nematode inoculation had no effect on AM fungal colonization. Overall, the effect of both dispersal limitation and plant genetic variation may underlie the small-scale heterogeneity found in natural AM fungal communities.

The Transcriptomes of Xiphinema index and Longidorus elongatus Suggest Independent Acquisition of Some Plant Parasitism Genes by Horizontal Gene Transfer in Early-Branching Nematodes
Danchin, Etienne G.J. ; Perfus-Barbeoch, Laetitia ; Rancurel, Corinne ; Thorpe, Peter ; Rocha, Martine Da; Bajew, Simon ; Neilson, Roy ; Sokolova, Elena ; Silva, Corinne Da; Guy, Julie ; Labadie, Karine ; Esmenjaud, Daniel ; Helder, Hans ; Jones, John T. ; Eves-van den Akker, Sebastian - \ 2017
Genes 8 (2017)10. - ISSN 2073-4425 - 17 p.
Nematodes have evolved the ability to parasitize plants on at least four independent occasions, with plant parasites present in Clades 1, 2, 10 and 12 of the phylum. In the case of Clades 10 and 12, horizontal gene transfer of plant cell wall degrading enzymes from bacteria and fungi has been implicated in the evolution of plant parasitism. We have used ribonucleic acid sequencing (RNAseq) to generate reference transcriptomes for two economically important nematode species, Xiphinema index and Longidorus elongatus, representative of two genera within the early-branching Clade 2 of the phylum Nematoda. We used a transcriptome-wide analysis to identify putative horizontal gene transfer events. This represents the first in-depth transcriptome analysis from any plant-parasitic nematode of this clade. For each species, we assembled ~30 million Illumina reads into a reference transcriptome. We identified 62 and 104 transcripts, from X. index and L. elongatus, respectively, that were putatively acquired via horizontal gene transfer. By cross-referencing horizontal gene transfer prediction with a phylum-wide analysis of Pfam domains, we identified Clade 2-specific events. Of these, a GH12 cellulase from X. index was analysed phylogenetically and biochemically, revealing a likely bacterial origin and canonical enzymatic function. Horizontal gene transfer was previously shown to be a phenomenon that has contributed to the evolution of plant parasitism among nematodes. Our findings underline the importance and the extensiveness of this phenomenon in the evolution of plant-parasitic life styles in this speciose and widespread animal phylum.
Mapping earthworm communities in Europe
Rutgers, M. ; Orgiazzi, A. ; Gardi, C. ; Römbke, J. ; Jansch, S. ; Keith, A. ; Neilson, R. ; Boag, B. ; Schmidt, O. ; Murchie, A.K. ; Blackshaw, R.P. ; Pérès, G. ; Cluzeau, D. ; Guernion, M. ; Briones, M.J.I. ; Rodeiro, J. ; Pineiro, R. ; Diaz Cosin, D.J. ; Sousa, J.P. ; Suhadolc, M. ; Kos, I. ; Krogh, P.H. ; Faber, J.H. ; Mulder, C. ; Bogte, J.J. ; Wijnen, H.J. van; Schouten, A.J. ; Zwart, D. de - \ 2016
Applied Soil Ecology 97 (2016). - ISSN 0929-1393 - p. 98 - 111.
Existing data sets on earthworm communities in Europe were collected, harmonized, collated, modelled and depicted on a soil biodiversity map. Digital Soil Mapping was applied using multiple regressions relating relatively low density earthworm community data to soil characteristics, land use, vegetation and climate factors (covariables) with a greater spatial resolution. Statistically significant relationships were used to build habitat–response models for maps depicting earthworm abundance and species diversity. While a good number of environmental predictors were significant in multiple regressions, geographical factors alone seem to be less relevant than climatic factors. Despite differing sampling protocols across the investigated European countries, land use and geological history were the most relevant factors determining the demography and diversity of the earthworms. Case studies from country-specific data sets (France, Germany, Ireland and The Netherlands) demonstrated the importance and efficiency of large databases for the detection of large spatial patterns that could be subsequently applied at smaller (local) scales.
Mapping earthworm communities in Europe
Rutgers, Michiel ; Orgiazzi, A. ; Gardi, C. ; Rombke, J. ; Jänsch, S. ; Keith, A.M. ; Neilson, R. ; Boag, B. ; Schmidt, O. ; Murchie, A.K. ; Blackshaw, R.P. ; Rod, P. ; Pérès, G. ; Cluzeau, D. ; Guernion, M. ; Briones, M.J.I. ; Rodeiro, J. ; Pineiro, R. ; Diaz Cosin, D.J. ; Trigo, Dolores ; Sousa, Paulo J. ; Suhadolc, M. ; Kos, I. ; Krogh, Paul Henning ; Faber, J.H. ; Mulder, Christian ; Bogte, J.J. ; Wijnen, H.J. van; Schouten, A.J. ; Zwart, D. de - \ 2015
Existing data sets on earthworm communities in Europe were collected, harmonized and
modelled to illustrate our current knowledge on their European diversity and geographical
distribution. Digital Soil Mapping was applied using multiple regression techniques relating
relatively low density earthworm community data to soil characteristics, land use, vegetation
type and climate factors, that had a greater spatial resolution. Statistically significant
relationships were used to build habitat-response models to construct earthworm maps for
abundance, species richness, and diversity data. Although a number of environmental
predictors were significant in our multiple regressions, geographical factors alone were less
relevant than climatic factors. Despite differing earthworm sampling protocols, land use and
geological history were the main factors determining demography and diversity of the
earthworms across Europe. Case studies from country-specific data sets (France, Germany,
Ireland and The Netherlands) demonstrated the importance and efficiency of these large
databases for the detection of large spatial patterns that could be subsequently applied at
smaller (local) scales. Additional datasets have been later incorporated (e.g. Portugal, Italy,
England, Wales, Belgium, Finland, Austria and some countries from Eastern Europe) to
improve our predictions of earthworm geographical patterns. The improved maps will be
submitted for publication in the Global Soil Biodiversity Atlas.
Rhythms of a Transnational Marriage: Temporal Topologies of Borders in a Knowledge Migrant Family
Wagner, L.B. - \ 2014
Etnofoor : anthropological journal 26 (2014)July 2014. - ISSN 0921-5158 - p. 81 - 105.
The practices and qualities that constitute a successfully married couple are both difficult to identify, and difficult to embody. Melding two lives into one family requires synchronization of expectations and needs, of communication and understandings, of livelihoods and care. A marriage emerges from both coupled lives, of synchronous affect, and coupled livelihoods, of becoming a solvent household unit. Cross-border mobilities complicate these processes. The bureaucratic and institutional definitions of marriage, as well as its emotional and economic dimen- sions, are often difficult to reconfigure when border crossings are implicit in sustaining the marriage. Using a co-autoethnographic example of how these three rhythms of marriage – coupled life, coupled livelihood, and bureaucratic mobility – intertwine, sometimes destabilizing each other, this paper documents how the cacophony of these rhythms can create topological impediments that border (Mezzadra and Neilson 2012), in both space but especially in time, within our marriage.
Molecular Tools for Analysing Nematode Assemblages
Neilson, R. ; Donn, S. ; Griffiths, B. ; Daniell, T. ; Rybarczyk-Mydlowska, K.D. ; Elsen, S.J.J. van den; Mooijman, P.J.W. ; Helder, J. - \ 2009
In: Nematodes as Environmental Indicators / Wilson, M., Khakouli-Duarte, T., CAB International - ISBN 9781845933852 - p. 188 - 207.
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