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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Soil networks become more connected and take up more carbon as nature restoration progresses
Morriën, W.E. ; Hannula, S.E. ; Snoek, L.B. ; Helmsing, N.R. ; Zweers, Hans ; Hollander, M. de; Soto, Raquel Luján ; Bouffaud, Marie Lara ; Buée, M. ; Dimmers, W.J. ; Duyts, Henk ; Geisen, Stefan ; Girlanda, Mariangela ; Griffiths, R.I. ; Jorgensen, H.B. ; Jensen, J. ; Plassart, P. ; Redecker, Dirk ; Schmelz, R.M. ; Schmidt, Olaf ; Thomson, Bruce C. ; Tisserant, Emilie ; Uroz, Stephane ; Winding, Anne ; Bailey, M.J. ; Bonkowski, M. ; Faber, J.H. ; Martin, F. ; Lemanceau, Philippe ; Boer, W. de; Veen, J.A. van; Putten, W.H. van der - \ 2017
Nature Communications 8 (2017). - ISSN 2041-1723 - 10 p.
Soil organisms have an important role in aboveground community dynamics and ecosystem functioning in terrestrial ecosystems. However, most studies have considered soil biota as a black box or focussed on specific groups, whereas little is known about entire soil networks. Here we show that during the course of nature restoration on abandoned arable land a compositional shift in soil biota, preceded by tightening of the belowground networks, corresponds with enhanced efficiency of carbon uptake. In mid- and long-term abandoned field soil, carbon uptake by fungi increases without an increase in fungal biomass or shift in bacterial-to-fungal ratio. The implication of our findings is that during nature restoration the efficiency of nutrient cycling and carbon uptake can increase by a shift in fungal composition and/or fungal activity. Therefore, we propose that relationships between soil food web structure and carbon cycling in soils need to be reconsidered.
Ecological network analysis reveals the inter-connection between soil biodiversity and ecosystem function as affected by land use across Europe
Creamer, R.C. ; Hannula, S.E. ; Leeuwen, J.P. van; Stone, D. ; Rutgers, M. ; Schmelz, R.M. ; Ruiter, P.C. de; Bohse Hendriksen, N. ; Bolger, T. ; Bouffaud, M.L. ; Buee, M. ; Calvalho, F. ; Costa, D. ; Dirilgen, T. ; Francisco, R. ; Griffiths, B.S. ; Griffiths, R. ; Martin, F. ; Martins da Silva, P. ; Mendes, S. ; Morais, P.V. ; Pereira, C. ; Philippot, L. ; Plassart, P. ; Redecker, D. ; Römbke, J. ; Sousa, J.P. ; Wouterse, M. ; Lemanceau, P. - \ 2016
Applied Soil Ecology 97 (2016). - ISSN 0929-1393 - p. 112 - 124.
Soil organisms are considered drivers of soil ecosystem services (primary productivity, nutrient cycling, carbon cycling, water regulation) associated with sustainable agricultural production. Soil biodiversity was highlighted in the soil thematic strategy as a key component of soil quality. The lack of quantitative standardised data at a large scale has resulted in poor understanding of how soil biodiversity could be incorporated into legislation for the protection of soil quality. In 2011, the EcoFINDERS (FP7) project sampled 76 sites across 11 European countries, covering five biogeographical zones (Alpine, Atlantic, Boreal, Continental and Mediterranean) and three land-uses (arable, grass, forestry). Samples collected from across these sites ranged in soil properties; soil organic carbon (SOC), pH and texture. To assess the range in biodiversity and ecosystem function across the sites, fourteen biological methods were applied as proxy indicators for these functions. These methods measured the following: microbial diversity: DNA yields (molecular biomass), archaea, bacteria, total fungi and arbuscular mycorrhizal fungi; micro fauna diversity: nematode trophic groups; meso fauna diversity: enchytraeids and Collembola species; microbial function: nitrification, extracellular enzymes, multiple substrate induced respiration, community level physiological profiling and ammonia oxidiser/nitrification functional genes. Network analysis was used to identify the key connections between organisms under the different land use scenarios. Highest network density was found in forest soils and lowest density occurred in arable soils. Key taxomonic units (TUs) were identified in each land-use type and in relation to SOC and pH categorisations. Top-connected taxonomic units (i.e. displaying the most co-occurrence to other TUs) were identified for each land use type. In arable sites this was dominated by bacteria and fungi, while in grassland sites bacteria and fungi were most connected. In forest soils archaeal, enchytraeid and fungal TUs displayed the largest number of neighbours, reflecting the greatest connectivity. Multiple regression models were applied to assess the potential contribution of soil organisms to carbon cycling and storage and nutrient cycling of specifically nitrogen and phosphorus. Key drivers of carbon cycling were microbial biomass, basal respiration and fungal richness; these three measures have often been associated with carbon cycling in soils. Regression models of nutrient cycling were dependent on the model applied, showing variation in biological indicators.
Pairwise Transcriptomic Analysis of the Interactions Between the Ectomycorrhizal Fungus Laccaria bicolor S238N and Three Beneficial, Neutral and Antagonistic Soil Bacteria
Deveau, A. ; Barret, M. ; Diedhiou, A.G. ; Leveau, J. ; Boer, W. de; Martin, F. ; Frey-Klett, P. - \ 2015
Microbial Ecology 69 (2015)1. - ISSN 0095-3628 - p. 146 - 159.
Ectomycorrhizal fungi are surrounded by bacterial communities with which they interact physically and metabolically during their life cycle. These bacteria can have positive or negative effects on the formation and the functioning of ectomycorrhizae. However, relatively little is known about the mechanisms by which ectomycorrhizal fungi and associated bacteria interact. To understand how ectomycorrhizal fungi perceive their biotic environment and the mechanisms supporting interactions between ectomycorrhizal fungi and soil bacteria, we analysed the pairwise transcriptomic responses of the ectomycorrhizal fungus Laccaria bicolor (Basidiomycota: Agaricales) when confronted with beneficial, neutral or detrimental soil bacteria. Comparative analyses of the three transcriptomes indicated that the fungus reacted differently to each bacterial strain. Similarly, each bacterial strain produced a specific and distinct response to the presence of the fungus. Despite these differences in responses observed at the gene level, we found common classes of genes linked to cell–cell interaction, stress response and metabolic processes to be involved in the interaction of the four microorganisms.
Meeting Report: Fungal Genomics Meets Social Media: Highlights of the 28th Fungal Genetics Conference at Asilomar
Momany, M. ; Pietro, A. Di; Alexander, W.G. ; Barker, B.M. ; Harb, O.S. ; Kamoun, S. ; Martin, F. ; Pires, J.C. ; Stajich, J.E. ; Thomma, B.P.H.J. ; Unruh, S. - \ 2015
G3 : Genes Genomes Genetics 5 (2015)12. - ISSN 2160-1836 - p. 2523 - 2525.
Balanced Harvest in the Real World. Scientific, Policy and Operational Issues in an Ecosystem Approach to Fisheries
Garcia, S.M. ; Bianchi, G. ; Charles, A. ; Kolding, J. ; Rice, J. ; Rochet, M.J. ; Zhou, S. ; Delius, G. ; Reid, D. ; Zwieten, P.A.M. van; Atcheson, M. ; Bartley, D. ; Borges, L. ; Bundy, A. ; Dagorn, L. ; Dunn, D. ; Hall, M. ; Heino, M. ; Jacobsen, B. ; Jacobsen, N.S. ; Law, R. ; Makino, M. ; Martin, F. ; Skern-Mauritzen, M. ; Suuronen, P. ; Symons, D. - \ 2015
Gland, Switzerland : IUCN - 94 p.
The concept of the Ecosystem Approach has entered the fishery harvesting discussions both from fishery perspectives (Reykjavik Declaration; FAO 2003 Annex to the Code of Conduct and from the principles of the Ecosystem Approach adopted by the CBD in 1995. Both perspectives establish the need to maintain ecosystem structure and functioning, whether for sustainable use of biodiversity (CBD) or simply to keep exploited ecosystems healthy and productive (fisheries). In response, the “Balanced Harvest” (BH) concept was suggested by a group of scientists brought together by the IUCN Fisheries Experts Group during the CBD CoP 10 in 2010. The meeting and the BH concept as consolidated there highlighted some of the collateral ecological effects of current fishing patterns and unbalanced removals of particular components of the food web, stimulating a critical rethinking of current approaches to fisheries management. The meeting on “Balanced Harvest in the real world - Scientific, policy and operational issues in an ecosystem approach to fisheries” (Rome, September 29-October 2, 2014) examined the progress made since 2010 on a number of fronts. It considered questions related to the scientific underpinning of the BH concept, including theory, modelling, and empirical observations. It began to explore the economic, policy and management implications of harvesting in a more balanced way.
Carbohydrate utilization and metabolism is highly differentiated in Agaricus bisporus
Patyshakuliyeva, A. ; Jurak, E. ; Kohler, A. ; Baker, A. ; Battaglia, E. ; Bruijn, W. de; Burton, K.S. ; Challen, M.P. ; Cuotinho, P.M. ; Eastwood, D.C. ; Gruben, B.S. ; Makela, M.R. ; Martin, F. ; Nadal, M. ; Brink, J. van den; Wiebenga, A. ; Zhou, M. ; Henrissat, B. ; Kabel, M.A. ; Gruppen, H. ; Vries, R.P. de - \ 2013
BMC Genomics 14 (2013). - ISSN 1471-2164 - 14 p.
cell-wall polysaccharides - aspergillus-niger - wheat-straw - d-galactose - trehalose phosphorylase - mannitol dehydrogenase - sporophore development - enzyme-activities - button mushroom - fruit bodies
Background - Agaricus bisporus is commercially grown on compost, in which the available carbon sources consist mainly of plant-derived polysaccharides that are built out of various different constituent monosaccharides. The major constituent monosaccharides of these polysaccharides are glucose, xylose, and arabinose, while smaller amounts of galactose, glucuronic acid, rhamnose and mannose are also present. Results - In this study, genes encoding putative enzymes from carbon metabolism were identified and their expression was studied in different growth stages of A. bisporus. We correlated the expression of genes encoding plant and fungal polysaccharide modifying enzymes identified in the A. bisporus genome to the soluble carbohydrates and the composition of mycelium grown compost, casing layer and fruiting bodies. Conclusions - The compost grown vegetative mycelium of A. bisporus consumes a wide variety of monosaccharides. However, in fruiting bodies only hexose catabolism occurs, and no accumulation of other sugars was observed. This suggests that only hexoses or their conversion products are transported from the vegetative mycelium to the fruiting body, while the other sugars likely provide energy for growth and maintenance of the vegetative mycelium. Clear correlations were found between expression of the genes and composition of carbohydrates. Genes encoding plant cell wall polysaccharide degrading enzymes were mainly expressed in compost-grown mycelium, and largely absent in fruiting bodies. In contrast, genes encoding fungal cell wall polysaccharide modifying enzymes were expressed in both fruiting bodies and vegetative mycelium, but different gene sets were expressed in these samples
Community genetics in the time of next-generation molecular technologies
Gugerli, F. ; Brandl, R. ; Castagneyrol, B. ; Franc, A. ; Jactel, H. ; Koelewijn, H.P. ; Martin, F. ; Peter, M. ; Pritsch, K. ; Schröder, H. ; Smulders, M.J.M. ; Kremer, A. ; Ziegenhagen, B. - \ 2013
Molecular Ecology 22 (2013)12. - ISSN 0962-1083 - p. 3198 - 3207.
linkage disequilibrium - nucleotide diversity - arthropod community - herbivore community - demographic history - ecosystem genetics - emerging synthesis - fungal diversity - laccaria-bicolor - plant genotype
Understanding the interactions of co-occurring species within and across trophic levels provides key information needed for understanding the ecological and evolutionary processes that underlie biological diversity. As genetics has only recently been integrated into the study of community-level interactions, the time is right for a critical evaluation of potential new, gene-based approaches to studying communities. Next-generation molecular techniques, used in parallel with field-based observations and manipulative experiments across spatio-temporal gradients, are key to expanding our understanding of community-level processes. Here, we introduce a variety of ‘-omics’ tools, with recent studies of plant–insect herbivores and of ectomycorrhizal systems providing detailed examples of how next-generation approaches can revolutionize our understanding of interspecific interactions. We suggest ways that novel technologies may convert community genetics from a field that relies on correlative inference to one that reveals causal mechanisms of genetic co-variation and adaptations within communities.
Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire
Lévesque, C.A. ; Brouwer, H. ; Cano, L. ; Hamilton, J.P. ; Holt, C. ; Huitema, E. ; Raffaele, S. ; Robideau, G.P. ; Thines, M. ; Win, J. ; Zerillo, M.M. ; Beakes, G.W. ; Boore, J.L. ; Busam, D. ; Dumas, B. ; Ferriera, S. ; Fuerstenberg, S.I. ; Gachon, C.M.M. ; Gaulin, E. ; Govers, F. ; Grenville-Briggs, L. ; Horner, N. ; Hostetler, J. ; Jiang, R.H.Y. ; Johnson, J. ; Krajaejun, T. ; Lin, H. ; Meijer, H.J.G. ; Moore, B. ; Morris, P. ; Phuntmart, V. ; Puiu, D. ; Shetty, J. ; Stajich, J.E. ; Tripathy, S. ; Wawra, S. ; West, P. van; Whitty, B.R. ; Coutinho, P.M. ; Henrissat, B. ; Martin, F. ; Thomas, P.D. ; Tyler, B.M. ; Vries, R.P. de; Kamoun, S. ; Yandell, M. ; Tisserat, N. ; Buell, C.R. - \ 2010
Genome Biology 11 (2010)7. - ISSN 1474-7596 - 22 p.
oomycete phytophthora-infestans - potato famine pathogen - protein families - mitochondrial genome - pleiotropic drug - gene family - arabidopsis-thaliana - cadherin superfamily - microbe interactions - molecular evolution
Background - Pythium ultimum is a ubiquitous oomycete plant pathogen responsible for a variety of diseases on a broad range of crop and ornamental species. Results -The P. ultimum genome (42.8 Mb) encodes 15,290 genes and has extensive sequence similarity and synteny with related Phytophthora species, including the potato blight pathogen Phytophthora infestans. Whole transcriptome sequencing revealed expression of 86% of genes, with detectable differential expression of suites of genes under abiotic stress and in the presence of a host. The predicted proteome includes a large repertoire of proteins involved in plant pathogen interactions, although, surprisingly, the P. ultimum genome does not encode any classical RXLR effectors and relatively few Crinkler genes in comparison to related phytopathogenic oomycetes. A lower number of enzymes involved in carbohydrate metabolism were present compared to Phytophthora species, with the notable absence of cutinases, suggesting a significant difference in virulence mechanisms between P. ultimum and more host-specific oomycete species. Although we observed a high degree of orthology with Phytophthora genomes, there were novel features of the P. ultimum proteome, including an expansion of genes involved in proteolysis and genes unique to Pythium. We identified a small gene family of cadherins, proteins involved in cell adhesion, the first report of these in a genome outside the metazoans. Conclusions - Access to the P. ultimum genome has revealed not only core pathogenic mechanisms within the oomycetes but also lineage-specific genes associated with the alternative virulence and lifestyles found within the pythiaceous lineages compared to the Peronosporaceae.
The rhizosphere zoo: An overview of plant-associated communities of microorganisms, including phages, bacteria, archaea, and fungi, and some of their structuring factors
Buée, M. ; Boer, W. de; Martin, F. ; Overbeek, L.S. van; Jurkevitch, E. - \ 2009
Plant and Soil 321 (2009)1-2. - ISSN 0032-079X - p. 189 - 212.
burkholderia-cepacia complex - gradient gel-electrophoresis - disease-suppressive soils - fine-scale distribution - field-grown wheat - real-time pcr - ectomycorrhizal fungi - microbial diversity - mycorrhizal fungi - ribosomal-rna
Rhizosphere microorganisms have two faces, like Janus the Roman god of gates and doors who symbolizes changes and transitions, from one condition to another. One face looks at the plant root, the other sees the soil. The ears and the nose sense the other gods around and the mouths are wide open, swallowing as much as they can, and as described in Chapter 11, they also are busy talking. These faces may as well represent Hygieia (the Greek god of Health and Hygiene, the prevention of sickness and the continuation of good health) and Morta (the Roman god of death) for rhizosphere microbes can be beneficial, and promote plant growth and well being (Chapter 12) or detrimental, causing plant sickness and death (Chapter 13). It can be argued that many rhizosphere microbes are “neutral”, faceless saprophytes that decompose organic materials, perform mineralization and turnover processes. While most may not directly interact with the plant, their effects on soil biotic and abiotic parameters certainly have an impact on plant growth. Maybe they are Janus’ feet, the unsung heroes of the rhizosphere. This chapter addresses some aspects of the taxonomical and functional microbial diversity of the rhizosphere. Bacteria, Archea, viruses and Fungi will be at the heart of our discussion, while other rootassociated eukaryotes are the subjects of other chapters
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