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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Biotic interactions and trait-based ecosystem functioning in soil
Sechi, Valentina - \ 2017
University. Promotor(en): Lijbert Brussaard, co-promotor(en): Ron de Goede; C. Mulder; M. Rutgers. - Wageningen : Wageningen University - ISBN 9789463431316 - 176
soil - ecosystems - plant-animal interactions - interactions - soil biology - soil quality - grasslands - collembola - diversity - bodem - ecosystemen - plant-dier interacties - interacties - bodembiologie - bodemkwaliteit - graslanden - diversiteit

Recent emphasis on ecosystem services as a framework to evaluate ecosystems and to promote their sustainable use has drawn attention to how organisms contribute to the delivery of services. Soil attributes and biotic interactions play important roles in ecological processes (e.g. soil formation, nutrient turnover, carbon sequestration and transformation) and, consequently, in the related delivery of ecosystem services.

Therefore, understanding how soil organisms interact and how they respond to environmental conditions is fundamental to preserve soil functioning and provide a meaningful assessment of ecosystem services. Functional traits determine individual responses to pressures and their effects on ecosystem functioning hence, investigating soil ecosystems from a trait-based perspective offers an interesting opportunity to link the functional responses of the organisms to environmental pressures and to give insight into how the entire community influences ecological processes.

The main objective of this thesis is to develop and to test concepts for a trait-driven quantification of ecosystem services through the assessment of the effects of land management on soil processes. In particular, it focuses on exploring the potential of a trait-based approach in identifying and better understanding the response of the soil biota to environmental pressures and analyses the responses of soil organisms in terms of changes in functional trait distribution and trophic interactions.

This work shows that approaches taking the whole soil community into consideration are more suitable to give insight into the effect of anthropogenic pressure on ecosystem functioning than approaches based on single taxonomic groups. Moreover, performing combined analysis (e.g. analysing body-mass distribution and trophic grouping) helps to better identify community response to environmental pressure.

A clear methodology for the next step, i.e. quantification of ecosystem services, is still lacking due to the current difficulties to link and quantify the effect of anthropogenic pressure to ecosystem functioning in soil. For this reason, it is essential that methods analysed in this thesis will be further explored under different environmental pressures to enable the development of tools to be used at the interface of science and society for sustainable development.

Concealed diversity : taxonomical, phytogeographical and phytosociological notes on brambles (Rubus L. subgen. Rubus) in north-west Europe
Haveman, Rense - \ 2017
University. Promotor(en): Joop Schaminee, co-promotor(en): Rienk Jan Bijlsma. - Wageningen : Wageningen University - ISBN 9789463431019 - 200
rubus - diversity - taxonomy - phytogeography - geographical distribution - biogeography - apomixis - northwestern europe - diversiteit - taxonomie - plantengeografie - geografische verdeling - biogeografie - noordwest-europa

Rubus subgen. Rubus (bramble) is one of the large plant genera in Europe, consisting of only a few sexual biological species and at least 700 apomictic lineages. In this thesis, it is argued that the stabilised apomict lineages should best be regarded species, even if their distribution area doesn’t meet the requirements of a regional species as defined in several publications by Weber. Included is a checklist of Dutch bramble species, comprising 191 species belonging to Rubus subgen. Rubus. In the Netherlands, 97 of the 191 species are classified as regional species, with a distribution area diameter under 500 km. On the basis of distribution data of bramble species in Ireland, the UK, Denmark, Germany, and the Netherlands, 12 phytogeographical bramble-regions are distinguished. Although ecological factors play a role in the realisation of these regions, it is argued that the found patterns are primarily the result of evolutionary processes. The density and species composition of Rubus scrubs in the Netherlands is studied using landscape transects. At landscape scale, the bramble species in the scrubs are not randomly distributed, causing a spatial clustering of floristically similar bramble scrubs. It was concluded that only a part of the diversity of Rubus scrubs was accounted for in the Dutch national vegetation classification, and a new scrub type (the Rubetum taxandriae) was described on the basis of these findings. Rubus scrubs are an important biotope for rare shrub species and endemic Rubus species. Additionally, scrubs rich in bramble species are important because they provide foraging and nesting habitats for numerous vertebrates and invertebrates. It is recommended to include the apomict Rubus species in biodiversity accounts, for instance in the national standard list of plant species, as well as the Red List.

Werken aan diversiteit in tarwe en groenten : voor meer variatie op het veld, in het winkelschap en op het bord
Nuijten, Edwin ; Lammerts van Bueren, Edith - \ 2016
Driebergen : Louis Bolk Instituut (Publicatie / Louis Bolk Instituut 2016-030 LbP) - 20
kwekers - biologische landbouw - rassen (planten) - tarwe - zaden - plantenveredeling - groenten - genetische diversiteit - diversiteit - biologische plantenveredeling - growers - organic farming - varieties - wheat - seeds - plant breeding - vegetables - genetic diversity - diversity - organic plant breeding
Van 2014 tot 2016 heeft het Louis Bolk Instituut onderzoek gedaan naar de mogelijkheden van een breder assortiment in gewassen voor de teler (op het veld) en voor de consument (op het bord). Aanleiding voor het onderzoek is dat het aantal rassen dat aangepast is aan biologische teeltomstandigheden (rassen die dus zonder gebruik van kunstmest en bestrijdingsmiddelen kunnen) beperkt is en blijft. Veel veredelingsbedrijven kunnen vanwege de ontwikkelingskosten geen aparte rassen ontwikkelen voor een kleine markt. Meestal worden rassen uit het bestaande (gangbare) assortiment geselecteerd voor biologische vermeerdering. Bovendien zijn biologische telers en handelaren meegegaan in de huidige eisen voor hoge opbrengst en uniforme eindproducten. Het aanbieden van zaadvaste rassen in plaats van bijvoorbeeld hybride rassen is daarmee commercieel niet meteen vanzelfsprekend. Divers en Dichtbij Van 2014 tot 2016 heeft het Louis Bolk Instituut onderzoek gedaan naar de mogelijkheden van een breder assortiment in gewassen voor de teler (op het veld) en voor de consument (op het bord). Dit onderzoek is samen met Estafette Odin BV en de biologische dynamische telers GAOS in Swifterbant, De Groenen Hof in Esbeek en de Maatschap Dames en Heren Vos in Kraggenburg uitgevoerd. Het doel van dit project Divers en Dichtbij was de diversiteit op het veld en op het bord te vergroten. Daarmee bedoelen we niet alleen meer verschillende rassen, maar vooral andere type rassen of populaties die zelf meer genetische variatie bezitten. Dat kan door te kiezen voor zaadvaste rassen bij groentegewassen en populaties bij granen. Tot nu toe is populatieveredeling alleen toegepast bij granen en nog niet of nauwelijks bij groentegewassen (zie voor definities Box 1 op pagina 7). Dit betekent ook een keuze voor andere manieren van veredelen en selecteren. Aanleiding voor het onderzoek is dat het aantal rassen dat aangepast is aan biologische teeltomstandigheden (rassen die dus zonder gebruik van kunstmest en bestrijdingsmiddelen kunnen) beperkt is en blijft. Veel veredelingsbedrijven kunnen vanwege de ontwikkelingskosten geen aparte rassen ontwikkelen voor een kleine markt. Meestal worden rassen uit het bestaande (gangbare) assortiment geselecteerd voor biologische vermeerdering. Bovendien zijn biologische telers en handelaren meegegaan in de huidige eisen voor hoge opbrengst en uniforme eindproducten. Het aanbieden van zaadvaste rassen in plaats van bijvoorbeeld hybride rassen is daarmee commercieel niet meteen vanzelfsprekend. En toch heeft ons brede speurwerk in dit project wel degelijk een aantal interessante zaadvaste rassen opgeleverd! Want gelukkig zijn er in Europa en Amerika diverse biologische veredelaars actief in het veredelen van zaadvaste rassen en populaties. De informatie in deze brochure is bedoeld voor telers en andere ketenpartijen om meer te leren over de mogelijkheden van zaadvaste rassen bij groenten en populaties bij tarwe.
Mixed culture engineering for steering starter functionality
Spuś, Maciej - \ 2016
University. Promotor(en): Eddy Smid; Tjakko Abee. - Wageningen : Wageningen University - ISBN 9789462578333 - 170
bacteriophages - predation - microorganisms - starters - genetics - diversity - bacteriofagen - predatie - micro-organismen - zuursels - genetica - diversiteit

Undefined mixed complex starter cultures are broadly used in Gouda-type cheese production due to their robustness to phage predation, resilience for changes in environmental conditions and aroma compounds production ability during ripening. These microbial communities of lactic acid bacteria prior their isolation and deposition in starter culture collections were continuously used at the farm-level production facilities. Thus, one can consider undefined mixed complex starters as domesticated microbial communities. The process of domestication was facilitated by humans who have been continuously repeating successful fermentations using part of previous batch as inoculum (i.e. back-slopping). Therefore, a term ‘community breeding’ can describe this human-driven domestication of microbial communities. Community breeding of a model complex starter Ur led to establishment of a simple two-species composition of Lactococcus lactis and Leuconostoc mesenteroides represented by, in total, 8 genetic lineages. At the same time, this simple microbial community displays a high degree of intraspecies diversity, presumably caused by evolutionary processes of horizontal gene transfer, genome decay and mutations. Such diversity at strain level is particularly interesting in the context of continuous bacteriophage predation pressure present in this microbial community. It is thought that constant-diversity (CD) dynamics, based on the ‘kill-the-winner’ principles, is operational in Ur starter at the strain level. According to CD model, the fittest strain(s), which feed on the most abundant substrate, will be selected against due to density-dependent phage predation. The control of the fittest strain abundance by bacteriophages opens space for differentiation of strains via eco-evolutionary feedbacks. In particular, strains of complex starter culture not only adapted to quickly acidify milk (via efficient consumption of lactose and protein to peptides degradation), but concurrently, to consume other substrates present in milk. In addition, throughout the process of community breeding microbe-microbe interactions between community members have evolved. These interactions have led to division of metabolic labor among strains present in the culture, and eventually to better starter microbial community functioning.

The aim of this thesis was to investigate the factors impacting the formation of compositionally and functionally stable undefined mixed complex starter cultures to further use this knowledge in steering its functionality, and potentially in developing new strategies for robust starter culture design. To facilitate this study, well-characterized Ur culture strain isolates were used to systematically reconstitute the starter culture into multi-strain blends with increasing level of strain and genetic lineage diversity. The investigation of factors such as phage predation, level of strain and genetic lineage diversity as well as environmental conditions, was performed during experimental evolution studies in milk. The functionality of the (evolved) starter cultures was tested in an adapted lab-scale MicroCheese model system. The specific approach used in each of the research chapters is described below in more detail.

Strains isolated from Ur starter culture were characterized in terms of their resistance against bacteriophages isolated from the same starter (Chapter 2). This test confirmed high diversity in phage resistance among strains belonging to different genetic lineages as well as among strains of the same lineage. Next, selected strains, which represented different levels of bacteriophage predation: resistant, moderately resistant, sensitive and no detectable sensitivity, were mixed in simple blends containing 4 strains representing 3 genetic lineages of Ur starter (3 such blends were designed). These blends were exposed to phage predation (one phage per blend) at the onset of prolonged sequential propagation experiment or propagated without phage addition (control). Throughout the serial propagation the genetic lineage composition was monitored. During the propagation of control blends we detected quick domination of a single lineage. This dominating lineage contained strains sensitive to phages. Genetic lineage level composition of the phage-challenged blends was much more dynamic suggesting the impact of phage predation. The relatively low strain diversity introduced in these blends was not high enough to sustain maximal diversity at the level of lineages.

Chapter 3 describes a study using defined blends with higher complexity by extending the number of strains used. In total, 24 strains representing all 8 Ur starter lineages were exposed in sequential propagation experiment to a cocktail of 3 phages isolated from Ur starter. The propagation in milk of this multi-strain blend was executed for more than 500 generations and the abundance of genetic lineages was monitored throughout. Similarly as in the simple blends experiment, control blends were not exposed to bacteriophages. In control blends we observed a domination of one genetic lineage upon serial propagation, which resembles a periodic-selection-like (PS) behavior, where the fittest strains are dominating the microbial community and in result genetic-lineage diversity is being substantially reduced. In contrast, the composition of phage-challenged blends was again more dynamic than in control blends. In one of the phage-challenged blends behavior characteristic for a constant-diversity dynamics model was observed; throughout the serial transfer experiment, genetic lineage diversity was maintained by the presence of phage predation at relatively high level. In case of the second phage-challenged blend, due to a stochastic event, which likely caused a reduction in phage pressure, we observed a gradual recovery of the fittest strains, which again resembled a periodic-selection behavior. Therefore, phage predation, among other factors, can lead to shifts in microbial community population dynamics resulting in alternative stable states.

The experimental evolution approach, resembling traditional process of back-slopping, was used in a Long-term experimental evolution of Undefined Mixed Starter Culture (LUMSC) study described in Chapter 4. The aim of this study was to investigate the compositional and functional stability ascribed to the undefined mixed Ur starter during enclosed prolonged propagation without any possible external influx of bacterial or phage material. Surprisingly, during this 1000-generation long experiment the enforced conditions of specific incubation temperature and propagation regime resulted in enrichment of previously not detected strain of Lactococcus laudensis. This strain was found to consume a by-product of metabolism of another strain present in the community, in particular, D-mannitol produced by Le. mesenteroides. Thus, a new putative interaction in the microbial community of the complex starter culture was found. This new interaction and the possible ability of L. laudensis to efficiently use peptides released by caseinolytic L. lactis ssp. cremoris resulted in a relatively high abundance of L. laudensis in all evolved LUMSC cultures. The high abundance of L. laudensis had a certain effect on the functionality of the cultures. The aroma profiles of model lab-scale milli-cheeses manufactured with LUMSC cultures, showed significant differences in formation of esters and alcohols when compared to cheeses produced with the original Ur starter. Moreover, L. laudensis strain was not only under the radar of previously used culture-dependent and culture-independent methods, but as well, under the radar of phage predation continuously present throughout the LUMSC experiment. This observation sheds new light on the possibility of how a strain can emerge to relatively high abundance in an enclosed serially propagated microbial community operating in accordance with CD dynamics model.

Finally, the aspect of adaptation to environmental conditions was addressed by the study of an adjunct strain of Lactobacillus helveticus DSM 20075 described in Chapter 5. The aim was to develop a strain with increased autolytic capacity in conditions resembling the cheese matrix to possibly improve cheese ripening. The approach used here was based on a previously reported study, where the incubation of Lactococcus lactis MG1363 at high temperature resulted in spontaneous mutations causing stable heat-resistant and, in some cases, salt-hypersensitive phenotypes. In present study, after incubation of the Lb. helveticus DSM 20075 adjunct at different high temperatures (45-50 °C), heat-sensitive variants were recovered from plates. These variants were further characterized in terms of their growth rates at elevated temperatures (42-45 °C) and their autolytic capacity in low pH buffer with addition of NaCl. One of the variants (V50) showed substantially increased intracellular lactate dehydrogenase enzyme activity in the buffer suggesting its increased autolytic capacity. Next, both wild type and variant V50 were tested as adjuncts in lab-scale model milli-cheeses to determine their possible impact on the cheese aroma profiles. Indeed, adjunct strains, both WT and the variant, impacted the aroma profiles by producing benzaldehyde. In case of the variant strain the relative abundance of this compound was 3-fold higher. The applied strategy of incubating Lb. helveticus DSM20075 at high temperature resulted in specific, but different than in case of L. lactis MG1363, mutations suggesting another, yet to be elucidated, mechanisms for increasing the autolytic capacity of industrially-relevant strains. The approach of high-temperature incubation can be applied in dairy industry for the selection of (adjunct) cultures targeted at accelerated cheese ripening and aroma formation.

In conclusion, the work presented in this thesis highlights the importance of co-evolution of strains in compositional and functional stability of the complex undefined mixed starter culture. In particular, the factors such as heterogeneity of bacteriophage resistance among highly related strains, microbe-microbe interactions and division of metabolic labor are crucial for optimal functioning of a complex starter microbial community. Further investigation of the factors impacting the composition of starter cultures is crucial to steer the functionality in a desired direction. With straightforward methods, such as changing the incubation temperature or the propagation regime it is possible to induce shifts in strain composition and thereby obtain cultures with new characteristics. Moreover, experimental evolution studies with microbial communities used in food fermentation can lead to the discovery of new strains with potentially new characteristics. Additionally, the study of microbial communities of starter cultures not only delivers industrially applicable knowledge but also reveals the action of basic principles in microbial ecology and evolution.

Using genetic resources : Rules for international exchange
Crisson, L.J.R. ; Visser, L. - \ 2016
genetische bronnen van diersoorten - genetische bronnen van plantensoorten - genetische bronnen - internationale verdragen - internationale samenwerking - eu regelingen - diversiteit - animal genetic resources - plant genetic resources - genetic resources - international agreements - international cooperation - eu regulations - diversity
International rules for the exchange and use of genetic resources have been agreed upon, and providers and users are obliged to follow these rules. This folder provides background information on the relevant international agreements, explains various terms that are often used, and provides basic guidance for users seeking access to genetic resources. This folder is relevant for all Dutch public institutes, companies and individuals using genetic resources for research and development.
Kleurrijk Groen
Kloek, M.E. ; Buijs, A.E. ; Boersema, J. ; Schouten, M.G.C. - \ 2015
Vakblad Natuur Bos Landschap 12 (2015)117. - ISSN 1572-7610 - p. 3 - 5.
recreatie - openbaar groen - etnische groepen - immigranten - natuur - natuurbeheer - diversiteit - recreation - public green areas - ethnic groups - immigrants - nature - nature management - diversity
Natuurorganisaties vermoeden dat allochtone Nederlanders minder in de natuur komen dan autochtone Nederlanders. Er waren tot nu toe echter weinig harde cijfers over het natuurbezoek van allochtonen. Is een wandeling in de natuur inderdaad een ‘witte’ aangelegenheid, en hoe kunnen natuurorganisaties ervoor zorgen dat hun vrijwilligersbestand meer kleur krijgt? In het onderzoek ‘Colourful green’ van Marjolein Kloek, waarop zij op 28 augustus promoveerde aan Wageningen Universiteit (vakgroep Natuurbeheer en Plantecologie), laat zij zien dat het belangrijk is om allochtonen niet over één kam te scheren.
On the biology and evolution of fungi from soda soils
Grum-Grzhimaylo, A. - \ 2015
University. Promotor(en): Bas Zwaan, co-promotor(en): Fons Debets. - Wageningen : Wageningen University - ISBN 9789462574281 - 232
bodemschimmels - zoute gronden - diversiteit - bodembiologie - evolutie - soil fungi - saline soils - diversity - soil biology - evolution

Summary to the thesis “On the biology and evolution of fungi from soda soils”

Alexey Grum-Grzhimaylo

The presented thesis addresses aspects of biology and evolution of fungi that were recovered from saline soda soils. The work highlights the fact that saline soda soils are populated by a large diversity of fungi capable of withstanding high salts content and high pH. Some of these fungi have been shown to require exceptionally high pH and salts to grow optimally and therefore are called alkaliphiles.

Introductory CHAPTER 1 provides examples of seemingly inhabitable environments and some of its most prominent tenants, with the emphasis on soda lakes ecosystem and alkaliphilic organisms. Aspects of physiology and major adaptive strategies to high pH and salts found in bacteria are portrayed. To our knowledge, there are no studies devoted to the fungi inhabiting saline soda lakes making this work a starting point towards further explorations in the field.

In CHAPTER 2, I show that fungi are actually present in saline soils and focus closely on the fungus that dominated across all our soda soils samples. This fungus displayed a rare obligate alkaliphilic phenotype – it was capable of growing at pH 11.4 on agar plates, with the optimum of around 9–10 and no ability to grow at pH 5.2. Using a combination of morphological and phylogenetic approaches, I describe it as a new name Sodiomyces alkalinus (previously known as Heleococcum alkalinum). We looked at the morphological details of its life cycle and tested for the capacity of utilizing various carbon sources. Given its unique extreme physiology, dominance across the soil samples, and partly for historical reasons, S. alkalinus has become our model organism that found considerable attention across this thesis.

Inspired by the fact that saline soda soils harbour new fungi, I moved on to the investigation of another set of isolates we obtained from soda soils, which belong to the Emericellopsis group (Hypocreales). CHAPTER 3 presents an investigation of the Emericellopsis isolates that showed a much broader pH preference tagging them as facultative alkaliphiles. Here again, combined morphological, phylogenetic, and physiological data allowed us to set this group apart from the rest and described it as a new species – Emericellopsis alkalina. This species is genetically unrelated to S. alkalinus, which provides evidence for the alkaliphilic trait to be polyphyletic, i.e. arisen several times throughout evolutionary history. I showed E. alkalina to be genetically closer to marine-bourne isolates than typical terrestrial species. Such a result provides evidence for the origin of alkaliphilic trait in this group from the marine-bourne fungi, as sea and soda soils environmental factors coincide.

CHAPTER 4 is devoted to a systematic study of our whole collection of fungi recovered from saline soda soils across the world. I investigate over a hundred isolates morphologically, phylogenetically, and test them for growth pH preference. These data confirms the notion that alkaliphily is polyphyletic and has emerged in several lineages of the fungal phylogenetic tree. Detailed morphological descriptions and phylogenetic reconstructions gave me confidence in describing several more new species. A prominent finding is the discovery of two additional Sodiomyces species that also show the obligate alkaliphilic adaptation. Systematic approaches let me to link certain morphological characters of the species to the alkaliphilic phenotype they possess. Although a substantial part of fungi from soda soils indeed displayed alkaliphilic capabilities, we detected typical neutrophilic species that presumably are transient or reside in a dormant state as spores or survival structures.

The next chapters of the thesis are focused on S. alkalinus, chosen as a model organism for studying alkaliphily that we sequenced in collaboration with Joint Genome Institute (Walnut Creek, USA). CHAPTER 5 looks into the aspects of the hydrolytic capabilities of S. alkalinus. The genome and transcriptome provide immense body of data that gave insight on the enzyme sets encoded in the genome involved in the degradation of carbohydrate compounds (so-called CAZymes). Such in silico analysis was backed-up by the enzyme bioassays carried out at various pH and substrates. In S. alkalinus, I found cellulolytic and hemicellulolytic enzymes that act at high pH, as opposed to neutrophilic A. oryzae enzymes that were active mostly at pH 6. Another prominent finding was the detection of strong proteolytic enzymes acting optimally at pH 8. Based on the genome data and bioassays patterns, I speculate on the ecological role of S. alkalinus in soda soils.

CHAPTER 6 addresses the aspects of the PacC transcription factor, a key player in mediating the gene expression under different ambient pH. I sought to find differences in the primary structure of PacC or detecting the multicopiness of the pacC gene, given its function under extreme alkaline conditions. It turned out that the primary structure of the PacC was the same as in other fungi and the pacC gene is presented in a single copy in S. alkalinus genome. However, I noted a shifted expression and proteolytic activation pattern of PacC if compared to neutrophilic fungi. This results provides evidence for the re-tuned pH-sensors on the plasma membrane, however we could not convincingly detect signs of positive selection affecting the PalH sensors that would change its threshold to trigger the downstream molecular cascade.

CHAPTER 7 gives insights into a quite unexpected finding – the presence of viruses in several of the S. alkalinus isolates. I show their effective vertical but not horizontal transmission. Possession of dsRNA as genetic material, icosahedral shapes, and symptomless phenotypes are common characters for a mycovirus. The virus I studied in S. alkalinus exhibits these exact same features. Curiously, no other alkaliphiles from our collection nor known sister species harboured mycoviruses, making this the first instance of mycoviruses detected in an alkaliphilic filamentous fungus.

CHAPTER 8 focuses on another peculiar finding – a bacterial gene in the genome of S. alkalinus. Presumably introduced by a horizontal gene transfer event, this gene encodes for a DD-peptidase homologue commonly found in bacteria, but only in very few eukaryotes. I found only three fungi that possess this gene; two are alkaliphilic – S. alkalinus and its sister species Acremonium alcalophilum. This suggests the importance of this gene for alkaliphily in those species. The DD-peptidase gene appears to be functional and its peak expression was observed at pH 8. Comparative analysis showed this fungal DD-peptidase to be closely related to the homologues derived from halophilic and alkaliphilic bacteria, rather than from neutrophilic ones. I speculate on the putative function of this unusual gene, including the role in the build-up of exo-cellular matrix or defense against dense communities of prokaryotes in soda soils.

The discussion in CHAPTER 9 contemplates on the results obtained throughout the thesis and provides future perspectives on the topic.

Evaluation of dietary diversity scores to assess nutrient adequacy among rural Kenyan women
Ngala, S.A. - \ 2015
University. Promotor(en): Frans Kok, co-promotor(en): Inge Brouwer; A.M. Mwangi. - Wageningen : Wageningen University - ISBN 9789462574236 - 149
kenya - gezondheid van vrouwen - voedingsstoffen - sporenelementen - voedingsgeschiktheid - diversiteit - plattelandsbevolking - kwantitatieve methoden - kwalitatieve methoden - women's health - nutrients - trace elements - nutritional adequacy - diversity - rural population - quantitative methods - qualitative methods

Evaluation of dietary diversity scores to assess nutrient adequacy among rural Kenya women

S. A. Ngala

Abstract

Background:The major cause of micronutrient deficiencies are low intake due to monotonous diets, especially among women of child bearing age. Dietary diversity score has been found to be a good proxy indicator for micronutrient adequacy. However, there are still outstanding methodological questions related to seasonal effects, food intake methods, selection of foods and the cut-off for estimating the prevalence of acceptable nutrient adequacy. This thesis evaluated the performance of a simple dietary diversity score for assessing nutrient adequacy in the diets of rural women in Kenya.

Methods: The study was conducted in Mbooni Division, Makueni District, Kenya among non-pregnant, non-lactating women of reproductive age having a child between 2-5 years. Food consumption data was collected by 3 non-consecutive 24hour-recalls and a qualitative 24hour-recall in pre-harvest (period 1, October 2007, n=73) and post-harvest (period 2, April 2008, n=203) seasons. Dietary diversity scores (DDS) were derived based on 10 and 13 food groups with minimum intake threshold per food group of 0 and 15 g respectively. Mean probability of adequacy (MPA) was calculated based on intake of 11 micronutrients.

Results: The dietary diversity score (DDS) and mean probability of adequacy (MPA) were significantly but moderately associated in both seasons (r=0.40 and r=0.38 period 1 and 2) and the association was independent of season (p=0.45). The DDS from a qualitative 24 hour recall (DDSql) showed little agreement with quantitative 24 hour recall (DDSqn) with a mean difference (DDSqn-DDSql) of -0.51±1.46 (Period 1) and -0.58±1.43 (period 2), with lower correlation between MPA and DDS for DDSql (r=0.14 and 0.19 in period 1 and 2, p>0.05) compared to DDSqn (r=0.40 and 0.54 in period 1 and 2, p<0.01). The Informative food-based scores and the food group-based scores were moderately associated with mean probability of adequacy (r=0.54-0.59 in period 1; r=0.37- 0.45 in period 2) with higher values for informative food based scores. The Minimum Dietary Diversity of Women (MDD-W) and mean probability of adequacy were significantly but moderately associated in both seasons (r=0.43-0.58 in period 1; r=0.24-0.50 in period 2) with but the use of a cutoff of consuming 5 or more food groups as indication of nutrient adequacy resulted in high total misclassification in both periods.

Conclusion: A dietary diversity score can be used as a simple proxy for micronutrient adequacy, independent of season. The dietary diversity score derived from qualitative free-listing 24-hour recall formed a poor indicator, needing further refinement to improve its performance. The informative food-based score performs moderately better in predicting nutrient adequacy, but its advantages do not outway those of the food group-based scores, and the latter is therefore preferred. The Minimum Dietary Diversity score for Women, formed a good indicator to predict nutrient adequacy, but using the cutoff of 5 or more food groups resulted in an overestimation of prevalence of adequate intake in our resource poor population.

People, soil and manioc interactions in the upper Amazon region
Peña Venegas, C.P. - \ 2015
University. Promotor(en): Paul Struik, co-promotor(en): Tjeerd-Jan Stomph; Gerard Verschoor. - Wageningen : Wageningen University - ISBN 9789462573222 - 210
bodem - landbouw - inheemse kennis - bodemtypen (antropogeen) - inheemse volkeren - ecosystemen - cassave - manihot - diversiteit - menselijke invloed - amazonia - soil - agriculture - indigenous knowledge - soil types (anthropogenic) - indigenous people - ecosystems - cassava - diversity - human impact

Abstract

Clara Patricia Peña Venegas (2015). People, soil and manioc interactions in the upper Amazon region. PhD thesis, Wageningen University, The Netherlands, with summaries in English and Dutch, 210 pp.

The presence of anthropogenic soils, or Amazonian Dark Earths (ADE), fuels the debate about how pristine the Amazon ecosystem actually is, and about the degree to which humans affected Amazonian diversity in the past. Most upland soils of the Amazon region are very acid, highly weathered, and have a limited nutrient holding capacity; together, these characteristics limit permanent or intensive agriculture. Várzeas or floodplains that are periodically enriched with Andean sediments carried and deposited by rivers that cross the Amazon Basin, are moderately fertile but experience periodic floods that limit agriculture to crops able to produce in a short time. ADE patches in uplands usually are more fertile than non-anthropogenic uplands, providing a better environment for agriculture. Most studies about how people manage a broad portfolio of natural and anthropogenic soils come from non-indigenous farmers of Brazil. There is limited information about how indigenous people use a broad soil portfolio, and how this affects the diversity of their staple crop, manioc. With the aim to contribute to the understanding of the role of ADE in indigenous food production, as compared with other soils, and in order to provide information about how indigenous people use and create diversity in Amazonia, research was carried out among five different ethnic groups living in two locations of the Colombian Amazon.

Several social and natural science methods were used during the study. These included ethnography, participant observation, structured and un-structured interviews, sampling of soil and manioc landraces, standardized protocols for the quantification of soil physical and chemical variables, and molecular techniques to assess genetic diversity of manioc and arbuscular mycorrhizal fungi.

Results indicate that ADE patches from the Middle Caquetá region of Colombia are not contrastingly more fertile than surrounding, non-anthropogenic upland soils, except for higher levels of available phosphorus in ADE. Indigenous farmers from the Middle Caquetá region do not use ADE more frequently or more intensively than non-ADE uplands. The swidden agriculture practiced on ADE and on non-ADE uplands is similar. Although ADE patches were not specifically important for swiddens and therefore relatively unimportant for the production of manioc. They were important as sites for indigenous settlements and for maintaining agroforestry systems with native and exotic species that do not grow in soils with low available phosphorus. Várzeas were also used for agriculture, whether farmers had access to ADE or not. Differences occurred between locations in the type of floodplains selected and the way they were cultivated. Those differences were not related to differences in soil conditions but were associated with the cultural traditions of the different ethnic groups who cultivate low floodplains, as well as labor availability when organizing collective work (mingas) to harvest floodplains.

Manioc diversity among indigenous communities was not predominantly related with differences in soil types. Complete manioc stocks were cultivated equally on ADE, non-ADE uplands or várzeas. One issue that could be related with this non-specificity in manioc-soil combinations was the similar arbuscular mycorrhizal fungi diversity of soils and the high number of arbuscular mycorrhizal symbionts associated to manioc roots; these were shown to be independent from the physicochemical composition of the soil or the manioc landrace. Differences in the diversity of manioc stocks among ethnic groups were predominantly related to cultural values attached to different manioc landraces.

This study of indigenous agriculture in environments with natural and anthropogenic soils indicates that people have had an important role in transforming the Amazonian ecosystem through agriculture, with consequences on forest composition and forest dynamics. Pre-Columbian people contributed to this by creating an additional soil- the Amazonian Dark Earths. Although ADE are not presently considered to play a major role in indigenous food production, indigenous people believe that ADE have had an important role in the management of the first maniocs cultivated by their ancestors. The domestication of manioc and the creation and maintenance of hundreds of different landraces by indigenous people contributed, and still contributes, to the region’s plant diversity.

Uniformer mondiaal dieet heeft gevolgen voor voedselzekerheid
Struik, P. ; Khoury, C.K. - \ 2014
Bionieuws 24 (2014)5. - ISSN 0924-7734 - p. 10 - 11.
landbouwproductie - voedselgewassen - diversiteit - agricultural production - food crops - diversity
De afgelopen vijftig jaar vonden in het wereldwijde eetpatroon drastische veranderingen plaats, waaronder grotere hoeveelheden oliehoudende gewassen en minder stapelgewassen van regionaal belang. Een wereldwijde studie toont aan dat eetpatronen de afgelopen vijftig jaar op elkaar zijn gaan lijken.
Increasing homogeneity in global food supplies and the implications for food security
Khoury, C.K. ; Bjorkman, A.D. ; Dempewolf, H. ; Ramirez-Villegas, J. ; Guarino, L. ; Jarvis, A. ; Rieseberg, L.H. ; Struik, P.C. - \ 2014
Proceedings of the National Academy of Sciences of the United States of America 111 (2014)11. - ISSN 0027-8424 - p. 4001 - 4006.
voedselzekerheid - soortendiversiteit - diversiteit - voedselvoorziening - gewassen - basisproducten - genetische bronnen van plantensoorten - food security - species diversity - diversity - food supply - crops - commodities - plant genetic resources - plant genetic-resources - climate-change - ecosystem services - farming systems - biodiversity - productivity - nutrition - policy - world
The narrowing of diversity in crop species contributing to the world’s food supplies has been considered a potential threat to food security. However, changes in this diversity have not been quantified globally. We assess trends over the past 50 y in the richness, abundance, and composition of crop species in national food supplies worldwide. Over this period, national per capita food supplies expanded in total quantities of food calories, protein, fat, and weight, with increased proportions of those quantities sourcing from energy-dense foods. At the same time the number of measured crop commodities contributing to national food supplies increased, the relative contribution of these commodities within these supplies became more even, and the dominance of the most significant commodities decreased. As a consequence, national food supplies worldwide became more similar in composition, correlated particularly with an increased supply of a number of globally important cereal and oil crops, and a decline of other cereal, oil, and starchy root species. The increase in homogeneity worldwide portends the establishment of a global standard food supply, which is relatively species-rich in regard to measured crops at the national level, but species-poor globally. These changes in food supplies heighten interdependence among countries in regard to availability and access to these food sources and the genetic resources supporting their production, and give further urgency to nutrition development priorities aimed at bolstering food security.
Samen op zoek naar nieuwe kansen
Wijsman, J.W.M. - \ 2014
Vlissingen : Delta Academy van Hogeschool Zeeland; University of Applied Sciences - 10
aquacultuur - delta's - samenwerking - diversiteit - natuurgebieden - transport over water - openbare redes - waterbeheer - natuurbeheer - aquacultuur en milieu - waterkwaliteit - afvalwater - waterzuivering - aquaculture - deltas - cooperation - diversity - natural areas - water transport - public speeches - water management - nature management - aquaculture and environment - water quality - waste water - water treatment
Dit lectoraat richt zich specifiek op aquacultuur in deltagebieden. Een delta kenmerkt zich door een grote dynamiek als gevolg van de getijdenwerking vanuit zee, door de menging van zout- met zoetwater en de slib- en nutriëntenaanvoer vanuit de rivier. Veel verschillende functies komen er samen. De veelheid aan functies leidt vaak tot conflicten, maar soms kunnen verschillende functies elkaar juist versterken. Dit maakt aquacultuur in deltagebieden een zeer interessant onderzoeksthema waar verschillende belangen en disciplines samenkomen. Zo vindt in Nederland de extensieve schelpdierkweek plaats in Natura-2000 gebieden. Enerzijds is de kweek afhankelijk van natuurwaarden zoals productiviteit en waterkwaliteit. Anderzijds kan het de natuurwaarden ook positief of negatief beïnvloeden. De uitdaging zit hem in het zoeken naar kansen waarbij aquacultuur en andere gebruiksfuncties zoals natuur, veiligheid en recreatie elkaar versterken om daar waar conflicten optreden samen te zoeken naar oplossingen.
Elke teler kan voor zijn gewas het juiste diffuse glas vinden (interview met Silke Hemming en Tom Dueck)
Bezemer, J. ; Dueck, T.A. ; Hemming, S. - \ 2013
Onder Glas 10 (2013)6/7. - p. 7 - 9.
glastuinbouw - teelt onder bescherming - diffuus glas - diffusiecoëfficiënt - coating - lichtdoorlating - besluitvorming - kwaliteit - diversiteit - kastechniek - greenhouse horticulture - protected cultivation - diffused glass - diffusivity - light transmission - decision making - quality - diversity - greenhouse technology
Het gebruik van diffuus glas heeft een positief effect op de teeltresultaten. Maar de teler die voor de investering wil kiezen, ziet verschillende vragen op zich afkomen. Want het ene diffuse glas is het andere niet. De teler moet de verschillen kennen en de effecten van diffuus glas op zijn gewas begrijpen. Daarna kan hij op zoek naar het glas van zijn keuze.
Naar gekleurde recreatie in het groen
Kloek, M.E. - \ 2013
Wageningen UR
recreatie - stadsomgeving - stedelijke samenleving - natuur - diversiteit - cultuur - recreation - urban environment - urban society - nature - diversity - culture
In de Nederlandse multiculturele samenleving wonen, werken en recreëren mensen met verschillende culturele achtergronden. Deze diversiteit aan culturen zie je echter minder goed terug wanneer je de Nederlandse natuur in gaat. Daar kom je Nederlanders van allochtone afkomst nauwelijks tegen. Vinden zij de Nederlandse natuur te saai, te wild, of niet interessant? In een artikel in Trouw en tijdens het symposium van de Heimans en Thijsse Stichting over 'De relatie tussen mens en natuur in een verstedelijkte omgeving', laat onderzoeker Marjolein Kloek zien welke ideeën over recreatie en natuur leven onder Chinese, Turkse en Nederlandse jongeren.
A historical analysis of diversity trends in French and Dutch lettuce cultivars
Wouw, M.J. van de; Treuren, R. van; Hintum, T.J.L. van - \ 2013
Euphytica 190 (2013)2. - ISSN 0014-2336 - p. 229 - 239.
genetische erosie - genetische diversiteit - lactuca sativa - slasoorten - rassen (planten) - oude plantenrassen - diversiteit - frankrijk - nederland - bladgroenten - groenten - genetic erosion - genetic diversity - lettuces - varieties - old varieties - diversity - france - netherlands - leafy vegetables - vegetables - genebank collection - erosion
Using historical seed catalogues in combination with molecular fingerprinting data, diversity trends of lettuce, representing an important vegetable with active breeding programmes, were studied. Seed catalogues originating from France and the Netherlands from five different decades, the earliest dating from the 1840s, were checked for the occurence of lettuce cultivars. A total of 225 catalogues, with 7,311 records of lettuce, representing 878 different cultivars were found. The number of unique cultivars on offer by French and Dutch companies showed a small continuous increase until the 1960s, after which the number of cultivars on offer more than doubled to a total of 534 in the 1990s. Only a relatively small overlap between France and the Netherlands in the range of cultivars offered was observed. The 1960s appeared to be a period with many changes: the lowest genetic diversity in lettuce cultivars was found for this decade, whereas after the 1960s the number of companies supplying lettuce seeds reduced dramatically. The percentage of companies in a decade offering an identical cultivar decreased over time, and in the 1990s almost all cultivars were unique to only a single company. The possible relations of the observed trends with the developments in plant variety protection and in the plant breeding industry are discussed.
An ecogeographic analysis of Oryza series Sativae in Asia and the Pacific
Banaticla-Hilario, M.C.N. - \ 2012
University. Promotor(en): Marc Sosef, co-promotor(en): Ronald van den Berg; K.L. McNally. - S.l. : s.n. - ISBN 9789461733788 - 237
oryza - oryza sativa - oryza nivara - genetische bronnen van plantensoorten - plantengeografie - plantenecologie - diversiteit - in-situ conservering - plantenmorfologie - taxonomie - genetica - genenbanken - azië - plant genetic resources - phytogeography - plant ecology - diversity - in situ conservation - plant morphology - taxonomy - genetics - gene banks - asia

The non-cultivated speciesof the genus Oryza can provide a genetic arsenal of useful traits for improving the widely cultivated and consumed Asian rice (O. sativa). The diversity of these valuable plant resources must be well understood to ensure their effective in- and ex-situ conservation. In this thesis, we examined the ecogeographic variations within and between the three species of Oryza series Sativae in Asia and the Pacific. We looked at species differentiation from different spatial scales by analysing sympatric accession pairs of O. meridionalis and O. rufipogon and of O. nivara and O. rufipogon.

We conducted phenotypic analyses in Chapter 2. The strong influence of ecology on species morphology was demonstrated in the ordination and cluster analyses results where O. meridionalis and O. nivara grouped together and were separated from O. rufipogon. We detected greater differentiation of O. nivara and O. rufipogon in South Asia and positive correlations between spatial and intraspecific (interpopulation) morphological distances in continental Asia. We found significant correlations between geoclimatic factors and certain character measurements within species and observed that seedling height, culm number and diameter, leaf size, and anther length exhibit contrasting responses for O. nivara and O. rufipogon. We confirmed significant morphological differences between the three species, between the South and Southeast Asian populations of O. nivara, and between the Australasian and the non-Australasian populations of O. rufipogon and provided botanical descriptions to delineate O. meridionalis, O. nivara and O. rufipogon morphologically.

In Chapter 3, we genotyped the same set of accessions with 29 SSR markers and applied a variety of methods for genetic diversity analysis. Based on ordination and phylogenetic results, we verified that O. meridionalis is a genetically distinct species and that O. nivara and O. rufipogon overlap genetically across their geographic distribution. However, Bayesian clustering analysis recognized local-scale species separation of O. nivara and O. rufipogon implying stronger interspecific gene flow barriers in smaller spatial units. Concurrently, AMOVA indicated that the bulk (64%) of genetic variation in Asia Pacific series Sativae can be found among accessions and the lesser portions within accessions (26%) and among species (10%). We captured contrasting intraspecific variation patterns for O. nivara and O. rufipogon where the former exhibited low diversity, high population differentiation and isolation by distance mainly in South Asia while the latter displayed high diversity, low population differentiation and isolation by distance primarily in continental Southeast Asia. We established that altitude is correlated negatively to accession diversity and positively to local-scale species differentiation. Using Bayesian inference, we identified eight genetically distinct population groups: C1) Indian and Bangladeshi O. nivara; C2) Cambodian O. nivara; C3) Southeast Asian O. rufipogon; C4) O. meridionalis; C5) Nepalese O. nivara; C6) non-Cambodian Southeast Asian O. nivara; C7) Australasian O. rufipogon; and C8) South Asian O. rufipogon. Cluster analysis grouped the aromatic and japonica cultivar groups of O. sativa with O. rufipogon in South Asia and the indica and aus groups with O. nivara from Thailand and Cambodia, respectively. O. nivara from Nepal seemed genetically isolated from the other population groups. We also detected variation patterns that agreed with the results in Chapter 1 such as the South and Southeast Asian divisions of O. nivara, the divergence of Australasian populations from the rest of O. rufipogon and the greater differentiation of O. nivara and O. rufipogon in South Asia.

In Chapter 4, we conducted artificial crossing experiments to 15 selected parental accessions of O. meridionalis, O. nivara, and O. rufipogon and assessed the extent of several post-pollination isolating mechanisms in Oryza series Sativae. We observed reproductive incompatibility within and between the inbreeding species O. meridionalis and O. nivara and high intraspecific crossability of the outcrossing O. rufipogon where viable and non-sterile F1 hybrids were produced only by combinations with a parental distance that ranged from 1062 to 3813 kilometers. Insular Southeast Asian and/or Australasian accessions of O. rufipogon were the most reproductively successful parents. O. rufipogon exhibited significant pre-zygotic species isolation (in terms of seed set) and reduced post-zygotic isolation, and seemed symmetrically compatible with O. nivara and asymmetrically compatible with O. meridionalis. We obtained few annual hybrids with relatively high fertilities from crosses between O. rufipogon and O. nivara and numerous perennial hybrids with low fertilities from crosses between O. rufipogon and O. meridionalis. Crossability estimates did not show significant correlations with geographic distance between parents. However, we discerned reduced seed set and F1 fertility in interspecific combinations with sympatric parents compared to crosses with non-sympatric parents, indicative of reinforced species isolation in sympatry. We evaluated the F1 offspring of different cross combinations and found a mixture of intermediate and parental character traits in interspecific hybrids.

We discussed the taxonomic implications of the research results in Chapter 5 where we specifically dealt with the opposing views of lumping or splitting of O. nivara and O. rufipogon. We concluded that these two taxadeserve to be treated as separate species based on the following biosystematic evidence obtained from the thesis: 1) ecological distinction; 2) considerable prezygotic barriers; 3) opposing patterns of gene flow and genetic variation; 4) local-scale genetic divergence and 5) enhanced reproductive barriers under sympatric conditions. We identified ecogeography as a major driving force in the diversification of Oryza series Sativae in Asia and the Pacific and suggested that ecological speciation gave rise to O. nivara and O. rufipogon. We also presented recognizable geographic races within species.

Ultimately in Chapter 6, we emphasized the importance of our study in several aspects of rice science and identified results that agreed with prior Oryza diversity studies. At the same time, we presented previously unreported morphological and genetic variation patterns that were established in this thesis. We discussed the possible applications of the research results to wild rice conservation, covering in situ strategies as well as gene bank practices. We also highlighted the potential role of O. nivara in Asian rice domestication where it could have either directly given rise to the indica cultivar group or hybridized/introgressed with migrated japonica cultivars in India, eventually leading to the development of indica.

Home garden: a potential strategy for food and nutrition security in HIV households : a case study in rural Ghana
Akrofi, S. - \ 2012
University. Promotor(en): Paul Struik, co-promotor(en): Lisa Price. - [S.l. : S.n. - ISBN 9789461732743 - 239
gezinstuinen - voedselzekerheid - diversiteit - agrobiodiversiteit - hiv-infecties - voedingstoestandbepaling - ghana - home gardens - food security - diversity - agro-biodiversity - hiv infections - nutritional assessment
Lichtminnende gewassen verlangen 50% haze en een hoge transmissie
Staalduinen, J. van; Hemming, S. - \ 2012
Onder Glas 9 (2012)6. - p. 11 - 13.
glastuinbouw - teelt onder bescherming - kasgewassen - beglazing - afdeklagen - diversiteit - rentabiliteit - kosten-batenanalyse - besluitvorming - greenhouse horticulture - protected cultivation - greenhouse crops - glazing - coatings - diversity - profitability - cost benefit analysis - decision making
Het aanbod van diffuse kasdekmaterialen en coatings werd in het recente verleden steeds breder, maar wordt geleidelijk opgeschoond. Dat maakt het op termijn mogelijk om een beperkt aantal soorten in grotere hoeveelheden, dus goedkoper te produceren. De meerwaarde van diffuus licht is afdoende bewezen, maar onderzoek naar de precieze effecten van glasstructuren en coatings op specifieke gewassen blijft wenselijk. Waar staan we nu, wat kunnen we ermee en waar spitst het onderzoek zich de komende jaren op toe?
Veel substraten geschikt mits je watergift en bemesting aanpast : rekening houden met specifieke eisen van de plant
Heuvelink, E. ; Kierkels, T. - \ 2012
Onder Glas 9 (2012)1. - p. 5 - 7.
sierteelt - substraten - materialen - diversiteit - mestgiften - irrigatie - eigenschappen - besluitvorming - glastuinbouw - ornamental horticulture - substrates - materials - diversity - dressings - irrigation - properties - decision making - greenhouse horticulture
De diversiteit in substraten neemt nog steeds toe. Je kunt vaak niet zeggen dat de ene beter is dan de andere. Als je maar rekening houdt met hun karakteristieke eigenschappen en de water- en meststoffengift aanpast. En rekening houdt met de specifieke eisen van de plant. Die laatste behandelen we in dit artikel.
Grenzeloze natuur
Schaminee, J.H.J. - \ 2011
Groen : vakblad voor groen in stad en landschap 67 (2011)1. - ISSN 0166-3534 - p. 36 - 40.
deltagronden - natuurbescherming - diversiteit - versnipperen - menselijke activiteit - natuur - landschapselementen - delta soils - nature conservation - diversity - chipping - human activity - nature - landscape elements
Wanneer de betekenis van de natuur van Nederland in internationaal verband ter sprake wordt gebracht, dan is de eerste reactie vaak een smalende, die van een meewarige glimlach. Zo'n klein landje, overbevolkt, zo zeer onder de voet gelopen, daar kan die toch niets voorstellen? We hebben in ons land toch geen wolven, elanden of beren? Denk eens aan het hooggebergte, aan de eindeloze steppen in Rusland en Oekraïne of aan de toendra's in het hoge noorden. 'Een stukje bosje ter grootte van een krant' schreef Bloem in zijn beroemde gedicht De Dapperstraat.
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