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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Hatching failure and accumulation of organic pollutants through the terrestrial food web of a declining songbird in Western Europe
Oosten, H.H. van; Burg, Arnold B. van den; Arlt, Debora ; Both, Christiaan ; Brink, Nico W. van den; Chiu, Suzanne ; Crump, Doug ; Jeppsson, Tobias ; Kroon, Hans de; Traag, Wim ; Siepel, Henk - \ 2019
Science of the Total Environment 650 (2019). - ISSN 0048-9697 - p. 1547 - 1553.
Dioxin - DLC - Embryo - Inbreeding - Malformation - Passerine

Population growth in passerine birds is largely driven by fecundity. If fecundity is affected, for instance by hatching failure, populations may decline. We noted high hatching failure of up to 27% per year in relict populations of the Northern wheatear (Oenanthe oenanthe) in The Netherlands, a strongly declining, migratory passerine in Europe. This hatching failure itself can cause population decline, irrespective of other adverse factors. Additionally, we investigated the cause of hatching failure. Unhatched eggs showed egg yolk infections or embryonic malformations, part of which is associated with the actions of dioxin-like compounds (DLCs). Indeed, DLCs appear to bioaccumulate in the local foodweb, where the soil contained only background concentrations, similar to those found at many other locations. DLC concentrations in Dutch eggs were six-fold higher than those in a reference population in Sweden, where egg failure was only 6%. However, Northern wheatears appear to be only moderately sensitive to the actions of DLCs, because of their specific Ah-receptor type which may moderate the receptor mediated effects of DLCs. This indicates that the concentrations of DLCs, although elevated, may not have caused the embryo malformations or the low hatching rates. We discuss whether other toxins may be important or imbalances in the nutrition and if inbreeding may play a larger role than expected.

Plant species richness and functional groups have different effects on soil water content in a decade-long grassland experiment
Fischer, Christine ; Leimer, Sophia ; Roscher, Christiane ; Ravenek, Janneke ; Kroon, Hans de; Kreutziger, Yvonne ; Baade, Jussi ; Beßler, Holger ; Eisenhauer, Nico ; Weigelt, Alexandra ; Mommer, Liesje ; Lange, Markus ; Gleixner, Gerd ; Wilcke, Wolfgang ; Schröder, Boris ; Hildebrandt, Anke - \ 2019
Journal of Ecology 107 (2019)1. - ISSN 0022-0477 - p. 127 - 141.
biodiversity - functional groups - Jena Experiment - plant–soil–water relation - soil water content - spatial–temporal variability - species richness

The temporal and spatial dynamics of soil water are closely interlinked with terrestrial ecosystems functioning. The interaction between plant community properties such as species composition and richness and soil water mirrors fundamental ecological processes determining above-ground–below-ground feedbacks. Plant–water relations and water stress have attracted considerable attention in biodiversity experiments. Yet, although soil scientific research suggests an influence of ecosystem productivity on soil hydraulic properties, temporal changes of the soil water content and soil hydraulic properties remain largely understudied in biodiversity experiments. Thus, insights on how plant diversity—productivity relationships affect soil water are lacking. Here, we determine which factors related to plant community composition (species and functional group richness, presence of plant functional groups) and soil (organic carbon concentration) affect soil water in a long-term grassland biodiversity experiment (The Jena Experiment). Both plant species richness and the presence of particular functional groups affected soil water content, while functional group richness played no role. The effect of species richness changed from positive to negative and expanded to deeper soil with time. Shortly after establishment, increased topsoil water content was related to higher leaf area index in species-rich plots, which enhanced shading. In later years, higher species richness increased topsoil organic carbon, likely improving soil aggregation. Improved aggregation, in turn, dried topsoils in species-rich plots due to faster drainage of rainwater. Functional groups affected soil water distribution, likely due to plant traits affecting root water uptake depths, shading, or water-use efficiency. For instance, topsoils in plots containing grasses were generally drier, while plots with legumes were moister. Synthesis. Our decade-long experiment reveals that the maturation of grasslands changes the effects of plant richness from influencing soil water content through shading effects to altering soil physical characteristics in addition to modification of water uptake depth. Functional groups affected the soil water distribution by characteristic shifts of root water uptake depth, but did not enhance exploitation of the overall soil water storage. Our results reconcile previous seemingly contradictory results on the relation between grassland species diversity and soil moisture and highlight the role of vegetation composition for soil processes.

Diversiteit en krielonderzoek bij de traditionele Nederlandse hoenderrassen
Bortoluzzi, C. ; Megens, H.J.W.C. ; Crooijmans, R.P.M.A. ; Boer, Henk de; Taks, A. ; Kroon, P. ; Hoving, A.H. - \ 2018
Zeldzaam huisdier 43 (2018)3. - ISSN 0929-905X - p. 20 - 21.
Fokken van de verkrielde vorm van de grote hoenderrassen voegt genetische variatie toe aan het geheel van de Nederlandse hoender-rassen. Dat blijkt uit recent onderzoek. Maar binnen die rassen is de diversiteit laag door selectie op specifieke eigenschappen en parin-gen tussen verwante dieren.
Wolf wacht bed van regels
Jansman, Hugh - \ 2018

Provincies werken aan een herziene versie van het 'draaiboek wolf', nu het roofdier bijna 150 jaar nadat het dier in nederland was uitgeroeid terug is. In Friesland, Groningen, Overijssel, Gelderland en Limburg zijn de afgelopen maanden meerdere wolven gesignaleerd. Maar Drenthe spant de kroon. Alleen al in maart en april zijn er negen wolven gezien, waarvan zeker twee verschillende wolven schapen hebben aangevallen.

Data from: Below-ground resource partitioning alone cannot explain the biodiversity–ecosystem function relationship: a field test using multiple tracers
Jesch, Annette ; Barry, Kathryn E. ; Ravenek, Janneke M. ; Bachmann, Dörte ; Strecker, Tanja ; Weigelt, Alexandra ; Buchmann, Nina ; Kroon, Hans de; Gessler, Arthur ; Mommer, L. ; Roscher, Christiane ; Scherer-Lorenzen, Michael - \ 2018
ecosystem function and services - Jena Experiment - Levins B - resource uptake - water uptake - stable isotopes - rare element tracers - complementarity - proportional similarity
A Diurnal Rhythm in Brown Adipose Tissue Causes Rapid Clearance and Combustion of Plasma Lipids at Wakening
Berg, Rosa van den; Kooijman, Sander ; Noordam, Raymond ; Ramkisoensing, Ashna ; Abreu-Vieira, Gustavo ; Tambyrajah, Lauren L. ; Dijk, Wieneke ; Ruppert, Philip ; Mol, Isabel M. ; Kramar, Barbara ; Caputo, Rosanna ; Puig, Laura Sardón ; Ruiter, Evelien M. de; Kroon, Jan ; Hoekstra, Menno ; Sluis, Ronald J. van der; Meijer, Onno C. ; Willems van Dijk, Ko ; Kerkhof, Linda W.M. van; Christodoulides, Constantinos ; Karpe, Fredrik ; Gerhart-Hines, Zachary ; Kersten, Sander ; Meijer, Johanna H. ; Coomans, Claudia P. ; Heemst, Diana van; Biermasz, Nienke R. ; Rensen, Patrick C.N. - \ 2018
Cell Reports 22 (2018)13. - ISSN 2211-1247 - p. 3521 - 3533.
angiopoietin-like 4 - APOE3-Leiden.CETP mice - brown adipose tissue - circadian rhythm - diurnal rhythm - fatty acids - lipoprotein lipase - postprandial lipid response - triglycerides
Many favorable metabolic effects have been attributed to thermogenic activity of brown adipose tissue (BAT). Yet, time of day has rarely been considered in this field of research. Here, we show that a diurnal rhythm in BAT activity regulates plasma lipid metabolism. We observed a high-amplitude rhythm in fatty acid uptake by BAT that synchronized with the light/dark cycle. Highest uptake was found at the onset of the active period, which coincided with high lipoprotein lipase expression and low angiopoietin-like 4 expression by BAT. Diurnal rhythmicity in BAT activity determined the rate at which lipids were cleared from the circulation, thereby imposing the daily rhythm in plasma lipid concentrations. In mice as well as humans, postprandial lipid excursions were nearly absent at waking. We anticipate that diurnal BAT activity is an important factor to consider when studying the therapeutic potential of promoting BAT activity. van den Berg et al. show a strong circadian rhythm in fatty acid uptake by brown adipose tissue that peaks at wakening regardless of the light exposure period. Consequently, postprandial lipid handling by brown adipose tissue is highest at wakening, resulting in the lowest postprandial plasma lipid excursions.
Below-ground resource partitioning alone cannot explain the biodiversity-ecosystem function relationship : A field test using multiple tracers
Jesch, Annette ; Barry, Kathryn E. ; Ravenek, Janneke M. ; Bachmann, Dörte ; Strecker, Tanja ; Weigelt, Alexandra ; Buchmann, Nina ; Kroon, Hans de; Gessler, Arthur ; Mommer, Liesje ; Roscher, Christiane ; Scherer-Lorenzen, Michael - \ 2018
Journal of Ecology 106 (2018)5. - ISSN 0022-0477 - p. 2002 - 2018.
Complementarity - Ecosystem function - Jena Experiment - Levins B - Proportional similarity - Rare element tracers - Resource uptake - Stable isotopes
Below-ground resource partitioning is among the most prominent hypotheses for driving the positive biodiversity-ecosystem function relationship. However, experimental tests of this hypothesis in biodiversity experiments are scarce, and the available evidence is not consistent. We tested the hypothesis that resource partitioning in space, in time or in both space and time combined drives the positive effect of diversity on both plant productivity and total community resource uptake. At the community level, we predicted that total community resource uptake and biomass production above- and below-ground will increase with increased species richness or functional group richness. We predicted that, at the species level, resource partition breadth will become narrower, and that overlap between the resource partitions of different species will become smaller with increasing species richness or functional group richness. We applied multiple resource tracers (Li and Rb as potassium analogues, the water isotopologues-H2 18O and 2H2O, and 15N) in three seasons at two depths across a species and functional group richness gradient at a grassland biodiversity experiment. We used this multidimensional resource tracer study to test if plant species partition resources with increasing plant diversity across space, time or both simultaneously. At the community level, total community resource uptake of nitrogen and potassium and above- and below-ground biomass increased significantly with increasing species richness but not with increasing functional group richness. However, we found no evidence that resource partition breadth or resource partition overlap decreased with increasing species richness for any resource in space, time or both space and time combined. Synthesis. These findings indicate that below-ground resource partitioning may not drive the enhanced resource uptake or biomass production found here. Instead, other mechanisms such as facilitation, species-specific biotic feedback or above-ground resource partitioning are likely necessary for enhanced overall ecosystem function.
Lost in diversity: the interactions between soil-borne fungi, biodiversity and plant productivity
Mommer, L. ; Cotton, Anne ; Raaijmakers, J.M. ; Termorshuizen, A.J. ; Ruijven, J. van; Hendriks, Marloes ; Rijssel, Sophie van; Mortel, J.E. van de; Paauw, J.W.M. van der; Schijlen, E.G.W.M. ; Smit-Tiekstra, Annemiek ; Berendse, F. ; Kroon, Hans de; Dumbrell, A.J. - \ 2018
New Phytologist 218 (2018)2. - ISSN 0028-646X - p. 542 - 553.
There is consensus that plant species richness enhances plant productivity within natural grasslands, but the underlying drivers remain debated. Recently, differential accumulation of soil-borne fungal pathogens across the plant diversity gradient has been proposed as a cause of this pattern. However, the below-ground environment has generally been treated as a 'black box' in biodiversity experiments, leaving these fungi unidentified. Using next generation sequencing and pathogenicity assays, we analysed the community composition of root-associated fungi from a biodiversity experiment to examine if evidence exists for host specificity and negative density dependence in the interplay between soil-borne fungi, plant diversity and productivity. Plant species were colonised by distinct (pathogenic) fungal communities and isolated fungal species showed negative, species-specific effects on plant growth. Moreover, 57% of the pathogenic fungal operational taxonomic units (OTUs) recorded in plant monocultures were not detected in eight plant species plots, suggesting a loss of pathogenic OTUs with plant diversity. Our work provides strong evidence for host specificity and negative density-dependent effects of root-associated fungi on plant species in grasslands. Our work substantiates the hypothesis that fungal root pathogens are an important driver of biodiversity-ecosystem functioning relationships.
Depth-based differentiation in nitrogen uptake between graminoids and shrubs in an Arctic tundra plant community
Wang, Peng ; Limpens, Juul ; Nauta, Ake ; Huissteden, Corine van; Rijssel, Sophie Quirina van; Mommer, Liesje ; Kroon, Hans de; Maximov, Trofim C. ; Heijmans, Monique M.P.D. - \ 2018
Journal of Vegetation Science 29 (2018)1. - ISSN 1100-9233 - p. 34 - 41.
N - Arctic tundra - Dwarf shrubs - Graminoids - Niche differentiation - Nutrient uptake - Plant functional types - Rooting depth - Soil depth
Questions: The rapid climate warming in tundra ecosystems can increase nutrient availability in the soil, which may initiate shifts in vegetation composition. The direction in which the vegetation shifts will co-determine whether Arctic warming is mitigated or accelerated, making the understanding of successional trajectories urgent. One of the key factors influencing the competitive relationships between plant species is their access to nutrients, depending on the depth where they take up most nutrients. However, nutrient uptake at different soil depths by tundra plant species that differ in rooting depth is unclear. Location: Kytalyk Nature Reserve, northeast Siberia, Russia. Methods: We injected 15N to 5 cm, 15 cm and the thaw front of the soil in a moist tussock tundra. The absorption of 15N by grasses, sedges, deciduous shrubs and evergreen shrubs from the three depths was compared. Results: The results clearly show a vertical differentiation of N uptake by these plant functional types, corresponding to their rooting strategy. Shallow-rooting dwarf shrubs were more capable of absorbing nutrients from the upper soil than from deeper soil. Deep-rooting grasses and sedges were more capable of absorbing nutrients from deeper soil than the dwarf shrubs. The natural 15N abundances in control plants also indicate that graminoids can absorb more nutrients from the deeper soil than dwarf shrubs. Conclusions: Our results show that graminoids and shrubs in the Arctic differ in their N uptake strategies, with graminoids profiting from nutrients released at the thaw front, while shrubs mainly forage in upper soil layers. Our results suggest that tundra vegetation will become graminoid-dominated as permafrost thaw progresses and nutrient availability increases in the deep soil.
Below-ground complementarity effects in a grassland biodiversity experiment are related to deep-rooting species
Oram, Natalie J. ; Ravenek, Janneke M. ; Barry, Kathryn E. ; Weigelt, Alexandra ; Chen, Hongmei ; Gessler, Arthur ; Gockele, Annette ; Kroon, Hans de; Paauw, Jan Willem van der; Scherer-Lorenzen, Michael ; Smit-Tiekstra, Annemiek ; Ruijven, Jasper van; Mommer, Liesje - \ 2018
Journal of Ecology 106 (2018)1. - ISSN 0022-0477 - p. 265 - 277.
Additive partitioning - Diversity-productivity relationship - Jena Trait-Based Experiment - Molecular markers - Resource partitioning - Root distribution

Below-ground resource partitioning is often proposed as the underlying mechanism for the positive relationship between plant species richness and productivity. For example, if species have different root distributions, a mixture of plant species may be able to use the available resources more completely than the individual species in a monoculture. However, there is little experimental evidence for differentiation in vertical root distributions among species and its contribution to biodiversity effects. We determined species-specific root standing biomass over depth using molecular techniques (real-time qPCR) in a large grassland biodiversity experiment (one to eight plant species mixtures), in 2 years. Species-specific root biomass data were used to disentangle the effects of positive interactions between species (complementarity effects) and effects due to dominance of productive species (selection effects) on root biomass in mixtures. In a next step, these biodiversity effects were linked to the diversity of rooting depths and the averaged rooting depth of the community. Root biomass increased with species richness. This was mainly due to positive interactions (the complementarity effect), which increased with species richness below-ground. In contrast, the selection effect decreased with species richness. Although there was considerable variation in vertical root distribution between species in monocultures, the diversity of rooting strategies did not explain the complementarity effect. Rather, the abundance of deep-rooting species in mixtures (i.e. high community-weighted mean) was significantly related to the complementarity effect. Comparing the "predicted" root distribution (based on monocultures) to the actual distribution in mixtures, we found that mixtures rooted deeper than expected, but this did not better explain the complementarity effect. Synthesis. This study demonstrates that vertical root distributions of species provide only subtle evidence for resource partitioning. We found no evidence that functional diversity in vertical rooting patterns was important for the complementarity effect, in contrast to our expectation that the enhancement of productivity was due to resource partitioning. Alternatively, we found significant but weak relationships between the complementarity effect and deep-rooting communities, based on the community-weighted mean root distribution. This suggests that factors other than below-ground resource partitioning alone may drive the biodiversity-productivity relationship.

Root associated fungal communities from the Wageningen long term biodiversity-productivity experiment
Mommer, L. ; Cotton, Anne ; Raaijmakers, J.M. ; Termorshuizen, A.J. ; Ruijven, J. van; Hendriks, Marloes ; Rijssel, Sophie van; Mortel, J.E. van de; Paauw, J.W.M. van der; Schijlen, E.G.W.M. ; Smit-Tiekstra, Annemiek ; Berendse, F. ; Kroon, Hans de; Dumbrell, A.J. - \ 2017
PRJEB18545 - ERP020484
Species-rich plant communities are more productive than species-poor plant communities but the reasons behind this relationship are currently unclear. We characterised the fungal communities associated with plant roots from the Wageningen biodiversity experiment to explore the effect of plant species identity, abundance and diversity on root associated fungal communities. Briefly, the Wageningen biodiversity experiment consisted of plant communities comprised of the following plant species: Agrostis capillaris L., Anthoxanthum odoratum L., Festuca rubra L., and Holcus lanatus L., Centaurea jacea L., Leucanthemum vulgare Lamk., Plantago lanceolata L., and Rumex acetosa,.These were grown either in monocultures or 2,4 or 8 plant species mixtures. 3cm diameter soil cores were taken from this experiment in 2010 and divided into two depth increments: (0-5, 20-35 cm). Roots from each depth were washed and their fungal communities characterised using 454 GS FLX pyrosequencing of amplicon libraries of the internal transcribed spacer (ITS1) region using primers ITS1F (Gardes & Bruns 1993) and ITS2 (White et al. 1990)
Data from: Belowground complementarity effects in a grassland biodiversity experiment are related to deep-rooting species
Oram, N.J. ; Ravenek, Janneke M. ; Barry, Kathryn E. ; Weigelt, Alexandra ; Chen, Hongmei ; Gessler, Arthur ; Gockele, Annette ; Kroon, Hans de; Ruijven, J. van; Mommer, L. - \ 2017
diversity-productivity relationship - complementarity - additive partitioning - molecular markers - vertical root distributions - resource partitioning - biodiversity experiment
1. Belowground resource partitioning is often proposed as the underlying mechanism for the positive relationship between plant species richness and productivity. For example, if species have different root distributions, a mixture of plant species may be able to use the available resources more completely than the individual species in a monoculture. However, there is little experimental evidence for differentiation in vertical root distributions among species and its contribution to biodiversity effects. 2. We determined species-specific root standing biomass over depth using molecular techniques (real time-qPCR) in a large grassland biodiversity experiment (1-8 plant species mixtures), in two years. Species-specific root biomass data were used to disentangle the effects of positive interactions between species (complementarity effects) and effects due to dominance of productive species (selection effects) on root biomass in mixtures. In a next step, these biodiversity effects were linked to the diversity of rooting depths and the averaged rooting depth of the community. 3. Root biomass increased with species richness. This was mainly due to positive interactions (the complementarity effect), which increased with species richness belowground. In contrast, the selection effect decreased with species richness. Although there was considerable variation in vertical root distribution between species in monocultures, the diversity of rooting strategies did not explain the complementarity effect. Rather, the abundance of deep-rooting species in mixtures (i.e. high community weighted mean) was significantly related to the complementarity effect. Comparing the ‘predicted’ root distribution (based on monocultures) to the actual distribution in mixtures, we found that mixtures rooted deeper than expected, but this did not better explain the complementarity effect. 4. Synthesis: This study demonstrates that vertical root distributions of species provide only subtle evidence for resource partitioning. We found no evidence that functional diversity in vertical rooting patterns was important for the complementarity effect, in contrast to our expectation that the enhancement of productivity was due to resource partitioning. Alternatively, we found significant but weak relationships between the complementarity effect and deep-rooting communities, based on the community weighted mean root distribution. This suggests that factors other than belowground resource partitioning alone may drive the biodiversity-productivity relationship.
Root chemistry and soil fauna, but not soil abiotic conditions explain the effects of plant diversity on root decomposition
Chen, Hongmei ; Oram, Natalie J. ; Barry, Kathryn E. ; Mommer, Liesje ; Ruijven, Jasper van; Kroon, Hans de; Ebeling, Anne ; Eisenhauer, Nico ; Fischer, Christine ; Gleixner, Gerd ; Gessler, Arthur ; González Macé, Odette ; Hacker, Nina ; Hildebrandt, Anke ; Lange, Markus ; Scherer-lorenzen, Michael ; Scheu, Stefan ; Oelmann, Yvonne ; Wagg, Cameron ; Wilcke, Wolfgang ; Wirth, Christian ; Weigelt, Alexandra - \ 2017
Oecologia 185 (2017)3. - ISSN 0029-8549 - p. 499 - 511.
Functional groups - Jena Experiment - Root litter - SEM - Species richness
Plant diversity influences many ecosystem functions including root decomposition. However, due to the presence of multiple pathways via which plant diversity may affect root decomposition, our mechanistic understanding of their relationships is limited. In a grassland biodiversity experiment, we simultaneously assessed the effects of three pathways—root litter quality, soil biota, and soil abiotic conditions—on the relationships between plant diversity (in terms of species richness and the presence/absence of grasses and legumes) and root decomposition using structural equation modeling. Our final structural equation model explained 70% of the variation in root mass loss. However, different measures of plant diversity included in our model operated via different pathways to alter root mass loss. Plant species richness had a negative effect on root mass loss. This was partially due to increased Oribatida abundance, but was weakened by enhanced root potassium (K) concentration in more diverse mixtures. Equally, grass presence negatively affected root mass loss. This effect of grasses was mostly mediated via increased root lignin concentration and supported via increased Oribatida abundance and decreased root K concentration. In contrast, legume presence showed a net positive effect on root mass loss via decreased root lignin concentration and increased root magnesium concentration, both of which led to enhanced root mass loss. Overall, the different measures of plant diversity had contrasting effects on root decomposition. Furthermore, we found that root chemistry and soil biota but not root morphology or soil abiotic conditions mediated these effects of plant diversity on root decomposition.
Biodiversity effects on ecosystem functioning in a 15-year grassland experiment : Patterns, mechanisms, and open questions
Weisser, Wolfgang ; Roscher, Christiane ; Meyer, Sebastian T. ; Ebeling, Anne ; Luo, Guangjuan ; Allan, Eric ; Beßler, Holger ; Barnard, Romain L. ; Buchmann, Nina ; Buscot, François ; Engels, Christof ; Fischer, Christine ; Fischer, Markus ; Gessler, Arthur ; Gleixner, Gerd ; Halle, Stefan ; Hildebrandt, Anke ; Hillebrand, Helmut ; Kroon, Hans de; Lange, Markus ; Leimer, Sophia ; Roux, Xavier Le; Milcu, Alexandru ; Mommer, Liesje ; Niklaus, Pascal A. ; Oelmann, Yvonne ; Proulx, Raphael ; Roy, Jacques ; Scherber, Christoph ; Scherer-lorenzen, Michael ; Scheu, Stefan ; Tscharntke, Teja ; Wachendorf, Michael ; Wagg, Cameron ; Weigelt, Alexandra ; Wilcke, Wolfgang ; Wirth, Christian ; Schulze, Ernst Detlef ; Schmid, Bernhard ; Eisenhauer, Nico - \ 2017
Basic and Applied Ecology 23 (2017). - ISSN 1439-1791 - p. 1 - 73.
Biomass - Carbon storage - Complementarity - Multi-trophic interactions - Nutrient cycling - Selection effect
In the past two decades, a large number of studies have investigated the relationship between biodiversity and ecosystem functioning, most of which focussed on a limited set of ecosystem variables. The Jena Experiment was set up in 2002 to investigate the effects of plant diversity on element cycling and trophic interactions, using a multi-disciplinary approach. Here, we review the results of 15 years of research in the Jena Experiment, focussing on the effects of manipulating plant species richness and plant functional richness. With more than 85,000 measures taken from the plant diversity plots, the Jena Experiment has allowed answering fundamental questions important for functional biodiversity research.First, the question was how general the effect of plant species richness is, regarding the many different processes that take place in an ecosystem. About 45% of different types of ecosystem processes measured in the 'main experiment', where plant species richness ranged from 1 to 60 species, were significantly affected by plant species richness, providing strong support for the view that biodiversity is a significant driver of ecosystem functioning. Many measures were not saturating at the 60-species level, but increased linearly with the logarithm of species richness. There was, however, great variability in the strength of response among different processes. One striking pattern was that many processes, in particular belowground processes, took several years to respond to the manipulation of plant species richness, showing that biodiversity experiments have to be long-term, to distinguish trends from transitory patterns. In addition, the results from the Jena Experiment provide further evidence that diversity begets stability, for example stability against invasion of plant species, but unexpectedly some results also suggested the opposite, e.g. when plant communities experience severe perturbations or elevated resource availability. This highlights the need to revisit diversity-stability theory.Second, we explored whether individual plant species or individual plant functional groups, or biodiversity itself is more important for ecosystem functioning, in particular biomass production. We found strong effects of individual species and plant functional groups on biomass production, yet these effects mostly occurred in addition to, but not instead of, effects of plant species richness.Third, the Jena Experiment assessed the effect of diversity on multitrophic interactions. The diversity of most organisms responded positively to increases in plant species richness, and the effect was stronger for above- than for belowground organisms, and stronger for herbivores than for carnivores or detritivores. Thus, diversity begets diversity. In addition, the effect on organismic diversity was stronger than the effect on species abundances.Fourth, the Jena Experiment aimed to assess the effect of diversity on N, P and C cycling and the water balance of the plots, separating between element input into the ecosystem, element turnover, element stocks, and output from the ecosystem. While inputs were generally less affected by plant species richness, measures of element stocks, turnover and output were often positively affected by plant diversity, e.g. carbon storage strongly increased with increasing plant species richness. Variables of the N cycle responded less strongly to plant species richness than variables of the C cycle.Fifth, plant traits are often used to unravel mechanisms underlying the biodiversity-ecosystem functioning relationship. In the Jena Experiment, most investigated plant traits, both above- and belowground, were plastic and trait expression depended on plant diversity in a complex way, suggesting limitation to using database traits for linking plant traits to particular functions.Sixth, plant diversity effects on ecosystem processes are often caused by plant diversity effects on species interactions. Analyses in the Jena Experiment including structural equation modelling suggest complex interactions that changed with diversity, e.g. soil carbon storage and greenhouse gas emission were affected by changes in the composition and activity of the belowground microbial community. Manipulation experiments, in which particular organisms, e.g. belowground invertebrates, were excluded from plots in split-plot experiments, supported the important role of the biotic component for element and water fluxes.Seventh, the Jena Experiment aimed to put the results into the context of agricultural practices in managed grasslands. The effect of increasing plant species richness from 1 to 16 species on plant biomass was, in absolute terms, as strong as the effect of a more intensive grassland management, using fertiliser and increasing mowing frequency. Potential bioenergy production from high-diversity plots was similar to that of conventionally used energy crops. These results suggest that diverse 'High Nature Value Grasslands' are multifunctional and can deliver a range of ecosystem services including production-related services.A final task was to assess the importance of potential artefacts in biodiversity-ecosystem functioning relationships, caused by the weeding of the plant community to maintain plant species composition. While the effort (in hours) needed to weed a plot was often negatively related to plant species richness, species richness still affected the majority of ecosystem variables. Weeding also did not negatively affect monoculture performance; rather, monocultures deteriorated over time for a number of biological reasons, as shown in plant-soil feedback experiments.To summarize, the Jena Experiment has allowed for a comprehensive analysis of the functional role of biodiversity in an ecosystem. A main challenge for future biodiversity research is to increase our mechanistic understanding of why the magnitude of biodiversity effects differs among processes and contexts. It is likely that there will be no simple answer. For example, among the multitude of mechanisms suggested to underlie the positive plant species richness effect on biomass, some have received limited support in the Jena Experiment, such as vertical root niche partitioning. However, others could not be rejected in targeted analyses. Thus, from the current results in the Jena Experiment, it seems likely that the positive biodiversity effect results from several mechanisms acting simultaneously in more diverse communities, such as reduced pathogen attack, the presence of more plant growth promoting organisms, less seed limitation, and increased trait differences leading to complementarity in resource uptake. Distinguishing between different mechanisms requires careful testing of competing hypotheses. Biodiversity research has matured such that predictive approaches testing particular mechanisms are now possible.
Unsupervised pre-training for fully convolutional neural networks
Wiehman, Stiaan ; Kroon, Steve ; Villiers, Hendrik De - \ 2017
In: 2016 Pattern Recognition Association of South Africa and Robotics and Mechatronics International Conference, PRASA-RobMech 2016. - Institute of Electrical and Electronics Engineers Inc. - ISBN 9781509033355 - 6 p.

Unsupervised pre-Training of neural networks has been shown to act as a regularization technique, improving performance and reducing model variance. Recently, fully convolutional networks (FCNs) have shown state-of-The-Art results on various semantic segmentation tasks. Unfortunately, there is no efficient approach available for FCNs to benefit from unsupervised pre-Training. Given the unique property of FCNs to output segmentation maps, we explore a novel variation of unsupervised pre-Training specifically designed for FCNs. We extend an existing FCN, called U-net, to facilitate end-To-end unsupervised pre-Training and apply it on the ISBI 2012 EM segmentation challenge data set. We performed a battery of significance tests for both equality of means and equality of variance, and show that our results are consistent with previous work on unsupervised pre-Training obtained from much smaller networks. We conclude that end-To-end unsupervised pre-Training for FCNs adds robustness to random initialization, thus reducing model variance.

Plants are less negatively affected by flooding when growing in species-rich plant communities
Wright, Alexandra J. ; Kroon, Hans de; Visser, Eric J.W. ; Buchmann, Tina ; Ebeling, Anne ; Eisenhauer, Nico ; Fischer, Christine ; Hildebrandt, Anke ; Ravenek, Janneke ; Roscher, Christiane ; Weigelt, Alexandra ; Weisser, Wolfgang ; Voesenek, Laurentius A.C.J. ; Mommer, Liesje - \ 2017
New Phytologist 213 (2017)2. - ISSN 0028-646X - p. 645 - 656.
aerenchyma - diversity - flooding traits - grasses - legumes - plant functional groups - soil air porosity - specific leaf area (SLA)

Flooding is expected to increase in frequency and severity in the future. The ecological consequences of flooding are the combined result of species-specific plant traits and ecological context. However, the majority of past flooding research has focused on individual model species under highly controlled conditions. An early summer flooding event in a grassland biodiversity experiment in Jena, Germany, provided the opportunity to assess flooding responses of 60 grassland species in monocultures and 16-species mixtures. We examined plant biomass, species-specific traits (plant height, specific leaf area (SLA), root aerenchyma, starch content) and soil porosity. We found that, on average, plant species were less negatively affected by the flood when grown in higher-diversity plots in July 2013. By September 2013, grasses were unaffected by the flood regardless of plant diversity, and legumes were severely negatively affected regardless of plant diversity. Plants with greater SLA and more root aerenchyma performed better in September. Soil porosity was higher in higher-diversity plots and had a positive effect on plant performance. As floods become more frequent and severe in the future, growing flood-sensitive plants in higher-diversity communities and in soil with greater soil aeration may attenuate the most negative effects of flooding.

Plant species richness negatively affects root decomposition in grasslands
Chen, Hongmei ; Mommer, Liesje ; Ruijven, Jasper Van; Kroon, Hans De; Fischer, Christine ; Gessler, Arthur ; Hildebrandt, Anke ; Scherer-lorenzen, Michael ; Wirth, Christian ; Weigelt, Alexandra ; Wurzburger, Nina - \ 2017
Journal of Ecology 105 (2017)1. - ISSN 0022-0477 - p. 209 - 218.
1. Plant diversity enhances many ecosystem functions, including root biomass production, which drives soil carbon input. Although root decomposition accounts for a large proportion of carbon input for soil, little is known about plant diversity effect on this process. Plant diversity may affect root decomposition in two non-exclusive ways: by providing roots of different substrate quality (e.g. root chemistry) and/or by altering the soil environment (e.g. microclimate).
2. To disentangle these two pathways, we conducted three decomposition experiments using a litter-bag approach in a grassland biodiversity experiment. We hypothesized that: (i) plant species richness negatively affects substrate quality (indicated by increased C:N ratios), which we tested by decomposing roots collected from each experimental plot in one common plot; (ii) plant species richness positively affects soil environment (indicated by increased soil water content), which we tested by decomposing standardized roots in all experimental plots; (iii) the overall effect of plant species richness on root decomposition, due to the contrast between quality and environmental effects, is neutral, which we tested by decomposing community roots in their ‘home’ plots.
3. Plant species richness negatively affected root decomposition in all three experiments. The negative effect of plant species richness on substrate quality was largely explained by increased root C:N ratios along the diversity gradient. Functional group presence explained more variance in substrate quality than species richness. Here, the presence of grasses negatively affected substrate quality and root C:N ratios, while the presence of legumes and small herbs had positive effects. Plant species richness had a negative effect on soil environment despite its positive effect on soil water content which is known to stimulate decomposition. We argue that – instead of soil water content – a combined effect of soil temperature and seasonality might drive environmental effect of plant diversity on decomposition in our plant communities, but this remains to be tested.
4. Synthesis. Our results demonstrate that both substrate quality and soil environment contribute to the net negative effect of plant diversity on root decomposition. This study promotes our mechanistic understanding of increased soil carbon accumulation in more diverse grassland plant communities.

Data from: Plant species richness negatively affects root decomposition in grasslands
Chen, H. ; Mommer, L. ; Ruijven, J. van; Kroon, H. de; Fischer, C. ; Gessler, A. ; Hildebrandt, A. ; Scherer-Lorenzen, M. ; Wirth, C. ; Weigelt, A. - \ 2016
Biodiversity-ecosystem functioning - C:N ratio - litter bags - microenvironment - plant diversity - plant functional group - plant-soil (below-ground) interactions - root substrate quality - soil water content - the jena experiment
This data set contains mass loss of community roots decomposing in the common plot in the Jena experiment in 2014. The Metadata contains the Dataset ID in the Jena Experiment database and detailed information of column: 'plotcode' is plot ID in the Jena Experiment; 'bag_ID' is the ID for litter bags within each decomposition experiment; 'root_type' is the type of roots in the litter bags where plot coded for community roots, lolium coded for standardized roots; 'site' is the location of where decomposition happened; 'sector' is the subplots in common plot; 'mass_initial' is root mass in the litter bags before buried in the field and handling loss is seduced already; 'mass_remain' is root mass in the litter bags at each retrieval; 'date_in' is the exact dates when the litter bags were buried. In the form of DD-MM-YY; 'date_out' is the exact dates when the litter bags were retrieved. In the form of DD-MM-YY; 'actual_decomptime' is the exact days litter bags were in the field; 'massloss' is actual mass loss =100 - mass_remain/mass_initial*100; 'std_decomptime' is standardized days litter bags were in the field; 'std_massloss' is stadardized mass loss = massloss/actual_decomp.time*std_decomp.time.
Groen proceswater: zuivering brouwerijprocesafvalwater met microalgen
Dijk, W. van; Weide, R.Y. van der; Kroon, A. - \ 2016
Lelystad : ACRRES - Wageningen UR (PPO 721) - 42 p.
brouwerij-industrie - brouwerijafvalwater - afvalwater - afvalwaterbehandeling - waterzuivering - algen - biomassa - biomassa productie - afvoerwater - flotatie - algenteelt - brewing industry - brewery effluent - waste water - waste water treatment - water treatment - algae - biomass - biomass production - effluents - flotation - algae culture
In 2012 is het project Groen Proceswater gestart. Hierin worden de mogelijkheden van zuivering van brouwerijprocesafvalwater met behulp van microalgen onderzocht. Dit is gedaan in een samenwerkingsverband van Heineken Nederland BV, Algae Food & Fuel en WUR-ACRRES. De resultaten behaald in 2012 en 2013 zijn beschreven in afzonderlijke rapporten. In dit rapport zijn de resultaten van 2014 en 2015 beschreven. In 2014 is onderzocht of een voorbehandeling van het proceswater via cavitatie-flotatie het zuiveringsresultaat kan verbeteren en in 2015 of de energie-input van de LEDbelichting kan worden verminderd door te flashen (afwisselende licht-donker periodes op microseconde tijdschaal). Verder is in 2015 en 2016 via een literatuurstudie gekeken naar de verwaarding van de geproduceerde algenbiomassa en zijn de conclusies van het gehele project samengevat.
Does epicatechin contribute to the acute vascular function effects of dark chocolate? A randomized, crossover study
Dower, James I. ; Geleijnse, Marianne ; Kroon, Paul A. ; Philo, Mark ; Mensink, Marco ; Kromhout, Daan ; Hollman, Peter C.H. - \ 2016
Molecular Nutrition & Food Research 60 (2016)11. - ISSN 1613-4125 - p. 2379 - 2386.
Chocolate - Epicatechin - Flavan-3-ol - Randomized controlled trial - Vascular function

Scope: Cocoa, rich in flavan-3-ols, improves vascular function, but the contribution of specific flavan-3-ols is unknown. We compared the effects of pure epicatechin, a major cocoa flavan-3-ol, and chocolate. Methods and results: In a randomized crossover study, twenty healthy men (40-80 years) were supplemented with: (1) 70g dark chocolate (150 mg epicatechin) with placebo capsules; (2) pure epicatechin capsules (2 × 50 mg epicatechin) with 75g white chocolate; and (3) placebo capsules with 75 g white chocolate (0 mg epicatechin). Vascular function (flow-mediated dilation (FMD) and augmentation index (AIx)) were measured before and 2 hours after interventions. Epicatechin metabolites time-profiles were measured in blood to calculate the bioavailability. Pure epicatechin did not significantly improve FMD (+0.75%; p = 0.10) or AIx (-2.2%; p = 0.23) compared to placebo. Dark chocolate significantly improved FMD (+0.96%; p = 0.04) and AIx (-4.6%; p = 0.02). Differences in improvements in FMD (+ 0.21%; p = 0.65) or Aix (-2.4%; p = 0.20) between pure epicatechin and dark chocolate were not significant. The bioavailability of epicatechin did not differ between pure epicatechin and dark chocolate (p = 0.14). Conclusions: Despite differences in epicatechin dose, improvements in vascular function after pure epicatechin and chocolate were similar and the bioavailability did not differ, suggesting a role for epicatechin.

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