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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Diversity at Life Science universities
Bock, Bettina - \ 2017
diversity - Higher education - inclusion
Designing blended engineering courses
Puffelen, E.A.M. van - \ 2017
course design - online - diversity
Universities have to deal with larger differences of engagement between students and more need for outcomes-based teaching and learning that allows for differences in learning styles. In addition for engineers, the rapidly changing world brings the need to engage students in diverse learning. Wageningen University & Research is experiencing these trends. It tackles them with outcomes-based teaching and engaging students within a rich setting of blended learning. The resulting education programmes are rated as the best in the national surveys of the last twelve years. This paper describes how to design such blended learning courses based on literature. It also reflects the experience of Wageningen University & Research with its successful approach. The prerequisites for course design are a well-constructed curriculum and properly formulated Intended Learning Outcomes (ILOs). The core of course design consists of selecting and combining different types of online and on-campus Teaching and Learning Activity’s (TLAs). Generally a smart design of a combination of (many) types of TLAs is needed to create top-quality blended engineering courses. Student motivation and higher level Intended Learning Outcomes for engineering require rich on-campus TLAs that cannot be completely offered online. Conference
Fire and plant diversity at the global scale
Pausas, Juli G. ; Carvalho Ribeiro, Eloi - \ 2017
Global Ecology and Biogeography 26 (2017)8. - ISSN 1466-822X - p. 889 - 897.
diversity - fire regime - plant richness - productivity - pyrogeography

Aim: Understanding the drivers of global diversity has challenged ecologists for decades. Drivers related to the environment, productivity and heterogeneity are considered primary factors, whereas disturbance has received less attention. Given that fire is a global factor that has been affecting many regions around the world over geological time scales, we hypothesize that the fire regime should explain a significant proportion of global coarse-scale plant diversity. Location: All terrestrial ecosystems, excluding Antarctica. Time period: Data collected throughout the late 20th and early 21st century. Taxa: Seed plants (= spermatophytes = phanerogamae). Methods: We used available global plant diversity information at the ecoregion scale and compiled productivity, heterogeneity and fire information for each ecoregion using 15 years of remotely sensed data. We regressed plant diversity against environmental variables; thereafter, we tested whether fire activity still explained a significant proportion of the variance. Results: Ecoregional plant diversity was positively related to both productivity (R2 =.30) and fire activity (R2 =.38). Once productivity and other environmental variables were in the model (R2 =.50), fire regime still explained a significant proportion of the variability in plant diversity (overall model, R2 =.71). The results suggest that fire drives temporal and spatial variability in many ecosystems, providing opportunities for a diversity of plants. Main conclusions: Fire regime is a primary factor explaining plant diversity around the globe, even after accounting for productivity. Fires delay competitive exclusion, increase landscape heterogeneity and generate new niches; thus, they provide opportunities for a large variety of species. Consequently, fire regime should be considered in order to understand global ecosystem distribution and diversity.

The D3-D5 region of large subunit ribosomal DNA provides good resolution of German limnic and terrestrial nematode communities
Schenk, Janina ; Hohberg, Karin ; Helder, Hans ; Ristau, Kai ; Traunspurger, Walter - \ 2017
Nematology 19 (2017)7. - ISSN 1388-5545 - p. 821 - 837.
barcoding - diversity - German Barcode of Life - large ribosomal subunit - limno-terrestrial nematodes - molecular barcode
Reliable and well-developed DNA barcode databases are indispensable for the identification of microscopic life. However, effectiveness of molecular barcoding in identifying terrestrial specimens, and nematodes in particular, has received little attention. In this study, ca 600 ribosomal large subunit DNA fragments (D3-D5 region) were successfully amplified for 79 limnic and terrestrial nematode species sampled at 147 locations across Germany. Distinctive DNA motifs in the LSU region were identified in 80% of all species examined. For 13 supposedly single morphospecies, 2-7 LSU barcode groups were detected with a wide range of intraspecific variations (0.09-7.9%). This region seems to be more suitable for the assessment of limno-terrestrial nematode diversity than the frequently used mitochondrial gene COI, as amplification success of the latter fragment is low for several nematode species. Our reference database for nematodes may serve as a starting point for applied and fundamental studies for these ubiquitous, ecologically highly relevant, organisms.
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.

Effect of host diversity and species assemblage composition on bovine tuberculosis (bTB) risk in Ethiopian cattle
Dejene, Sintayehu ; Heitkonig, Ignas ; Prins, Herbert ; Tessema, Zewdu K. ; Boer, Fred de - \ 2017
Parasitology 144 (2017)6. - ISSN 0031-1820 - p. 783 - 792.
diversity - evenness - greater kudu - habitat use overlap - identity effect - maintenance hosts - multi-host disease ecology
Current theories on diversity–disease relationships describe host species diversity and species identity as important factors influencing disease risk, either diluting or amplifying disease prevalence in a community. Whereas the simple term ‘diversity’ embodies a set of animal community characteristics, it is not clear how different measures of species diversity are correlated with disease risk. We therefore tested the effects of species richness, Pielou's evenness and Shannon's diversity on bovine tuberculosis (bTB) risk in cattle in the Afar Region and Awash National Park between November 2013 and April 2015. We also analysed the identity effect of a particular species and the effect of host habitat use overlap on bTB risk. We used the comparative intradermal tuberculin test to assess the number of bTB-infected cattle. Our results suggested a dilution effect through species evenness. We found that the identity effect of greater kudu – a maintenance host – confounded the dilution effect of species diversity on bTB risk. bTB infection was positively correlated with habitat use overlap between greater kudu and cattle. Different diversity indices have to be considered together for assessing diversity–disease relationships, for understanding the underlying causal mechanisms. We posit that unpacking diversity metrics is also relevant for formulating disease control strategies to manage cattle in ecosystems characterized by seasonally limited resources and intense wildlife–livestock interactions.
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.

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.
Plant Species Diversity Mediates Ecosystem Stability of Natural Dune Grasslands in Response to Drought
Rooijen, Nils M. van; Keersmaecker, Wanda de; Ozinga, Wim A. ; Coppin, Pol ; Hennekens, Stephan M. ; Schaminée, Joop H.J. ; Somers, Ben ; Honnay, Olivier - \ 2015
Ecosystems 18 (2015)8. - ISSN 1432-9840 - p. 1383 - 1394.
diversity - drought - dune grasslands - ecosystem functioning - NDVI - remote sensing - stability

How plant species diversity can mediate the temporal stability of ecosystem functioning during periods of environmental stress is still a pressing question in ecology, certainly in the context of predicted increasing frequencies and intensities of climate extremes, such as drought. The vast majority of empirical research in this context is based on relatively small-scaled experiments, where plant species composition is manipulated and ecosystem functions, such as biomass production, are monitored through time. Results of these studies have generally shown that ecosystem functioning is more stable in more species-diverse communities. Yet, there is very little evidence so far that these relations also hold in naturally assembled plant communities. In this study, we combined historical vegetation and climate data with time series of remotely sensed indicators of aboveground biomass production (MODIS NDVI), to quantify how plant species diversity and plant functional diversity correlate with the temporal stability of biomass production in naturally assembled Dutch dune grasslands under the influence of fluctuating drought. We found that the negative NDVI response to drought of grasslands with a higher plant species richness and diversity was significantly lower than the response of less species rich and species-diverse grasslands, indicating a stabilizing role of plant species richness and diversity on biomass production through time. We found no relation between plant functional diversity and NDVI response to drought. This is the first study to generalize experimentally established relations between species diversity and stability of ecosystem functioning to naturally assembled grasslands across a large spatial and temporal scale.

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.
Economic performance and sustainability of a novel intercropping system on the north China plain
Huang, C. ; Liu, Q. ; Heerink, N.B.M. ; Stomph, T.J. ; Li, B. ; Liu, R. ; Zhang, H. ; Wang, C. ; Li, X. ; Zhang, C. ; Werf, W. van der; Zhang, F. - \ 2015
PLoS One 10 (2015)8. - ISSN 1932-6203 - 16 p.
reducing environmental risk - nutrient-use efficiency - food security - crop productivity - n management - resource use - agriculture - competition - fertilizer - diversity
Double cropping of wheat and maize is common on the North China Plain, but it provides limited income to rural households due to the small farm sizes in the region. Local farmers in Quzhou County have therefore innovated their production system by integration of watermelon as a companion cash crop into the system. We examine the economic performance and sustainability of this novel intercropping system using crop yield data from 2010 to 2012 and farm household survey data collected in 2012. Our results show that the gross margin of the intercropping system exceeded that of the double cropping system by more than 50% in 2012. Labor use in the intercropping system was more than three times that in double cropping. The lower returns per labor hour in intercropping, however, exceeded the average off-farm wage in the region by a significant margin. Nutrient surpluses and irrigation water use are significant larger under the intercropping system. We conclude that the novel wheat-maize/watermelon intercropping system contributes to rural poverty alleviation and household-level food security, by raising farm incomes and generating more employment, but needs further improvement to enhance its sustainability.
Seeing Central African forests through their largest trees
Bastin, J.F. ; Barbier, N. ; Réjou-Méchain, M. ; Fayolle, A. ; Gourlet-Fleury, S. ; Maniatis, D. ; Haulleville, T. De; Baya, F. ; Beeckman, H. ; Beina, D. ; Couteron, P. ; Chuyong, G. ; Dauby, G. ; Doucet, J.L. ; Droissart, V. ; Dufrêne, M. ; Ewango, C.E.N. ; Gillet, F. ; Gonmadje, C.H. ; Hart, T. ; Kavali, T. ; Kenfack, D. ; Libalah, M. ; Malhi, Y. ; Makana, J.R. ; Pélissier, R. ; Ploton, P. ; Serckx, S. ; Sonké, B. ; Stevart, T. ; Thomas, D.W. ; Cannière, C. De; Bogaert, J. - \ 2015
Scientific Reports 5 (2015). - ISSN 2045-2322 - 8 p.
tropical forest - biomass - size - distributions - diversity - dynamics
Large tropical trees and a few dominant species were recently identified as the main structuring elements of tropical forests. However, such result did not translate yet into quantitative approaches which are essential to understand, predict and monitor forest functions and composition over large, often poorly accessible territories. Here we show that the above-ground biomass (AGB) of the whole forest can be predicted from a few large trees and that the relationship is proved strikingly stable in 175 1-ha plots investigated across 8 sites spanning Central Africa. We designed a generic model predicting AGB with an error of 14% when based on only 5% of the stems, which points to universality in forest structural properties. For the first time in Africa, we identified some dominant species that disproportionally contribute to forest AGB with 1.5% of recorded species accounting for over 50% of the stock of AGB. Consequently, focusing on large trees and dominant species provides precise information on the whole forest stand. This offers new perspectives for understanding the functioning of tropical forests and opens new doors for the development of innovative monitoring strategies.
Leverages for on-farm innovation from farm typologies? An illustration for family-based dairy farms in north-west Michoacán, Mexico
Cortez Arriola, J. ; Rossing, W.A.H. ; Amendola Massiotti, R.D. ; Scholberg, J.M.S. ; Groot, J.C.J. ; Tittonell, P.A. - \ 2015
Agricultural Systems 135 (2015). - ISSN 0308-521X - p. 66 - 76.
impact assessment - management - diversity - systems - scale - indicators - households - migration
Knowledge on farm diversity provides insight into differences among farms, enables scaling from individual farm to farm population level and vice versa, and has been used in the definition of recommendation domains for introduction of novel technologies. Farm diversity can be broadly described in terms of resource endowment and resource use strategy, or in other words, in terms of scale and intensity of production. Measuring intensity of production requires much greater monitoring effort than measuring scale of production, and often only proxies of production intensity are used. Using data from a regional farm survey and from intensive on-farm monitoring the question addressed in this paper is to which extent results of farm surveys that measure primarily scale of production can inform on-farm interventions aimed at improving farm performance. The survey included a random sample of 97 out of 664 smallholder dairy farmers in a community in north-west Michoacán, Mexico. Farm types were identified by a combination of Principal Component Analysis to reduce the dimensionality of the dataset, followed by Cluster Analysis. The survey was complemented with detailed analyses of costs, revenues and productivity on 6 farms over the course of one year. Survey results revealed considerable variation among the dairy farms in land area, livestock units, amount of hired labour, and infrastructure and equipment, which led to the distinction of 4 farm types. Indicators for animal health management and feeding strategies were uniform across the 4 types. The farm types matched the distinction of family-based and semi-intensive farm types used in Mexico. The detailed analyses of the individual farms belonging to the different types, however, revealed differences in resource use strategies reflected in differences in animal productivity, labour productivity and return to labour. Differences in animal productivity and labour productivity were explained by stocking rate, albeit in different ways. Return to labour was strongly related to cost of feed. Profitability was negative for all farms and was on most farms related to high external feedstuff costs, which constituted 59–89% of the feed cost of the animal ration. The results indicate that in addition to variables reflecting resource endowment or scale of production, typologies that aim to inform on-farm interventions need to consider farm characteristics that reflect intensity of production. Which variables should be selected will need to be determined in a preliminary assessment. To enhance internal resource use efficiency as was the purpose in the current study, candidate variables expressing intensity could include the share of external feed in the ration and proxies of internal resource use, e.g. reflected in crop and milk yields. Opportunities for on-farm innovation arising from the analyses are discussed from the perspective of labour flexibility, low costs and use of internal resources.
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.

Loss of animal seed dispersal increases extinction risk in a tropical tree species due to pervasive negative density dependence across life stages
Caughlin, T.T. ; Ferguson, J.M. ; Lichstein, J.W. ; Zuidema, P.A. ; Bunyavejchewin, S. ; Levey, D.J. - \ 2015
Proceedings of the Royal Society. B: Biological Sciences 282 (2015)1798. - ISSN 0962-8452 - 9 p.
spatial-patterns - rain-forest - recruitment - consequences - neighborhood - defaunation - habitat - uncertainty - diversity - abundance
Overhunting in tropical forests reduces populations of vertebrate seed dispersers. If reduced seed dispersal has a negative impact on tree population viability, overhunting could lead to altered forest structure and dynamics, including decreased biodiversity. However, empirical data showing decreased animal-dispersed tree abundance in overhunted forests contradict demographic models which predict minimal sensitivity of tree population growth rate to early life stages. One resolution to this discrepancy is that seed dispersal determines spatial aggregation, which could have demographic consequences for all life stages. We tested the impact of dispersal loss on population viability of a tropical tree species, Miliusa horsfieldii, currently dispersed by an intact community of large mammals in a Thai forest. We evaluated the effect of spatial aggregation for all tree life stages, from seeds to adult trees, and constructed simulation models to compare population viability with and without animal-mediated seed dispersal. In simulated populations, disperser loss increased spatial aggregation by fourfold, leading to increased negative density dependence across the life cycle and a 10-fold increase in the probability of extinction. Given that the majority of tree species in tropical forests are animal-dispersed, overhunting will potentially result in forests that are fundamentally different from those existing now.
Effects of salinity on growth of plant species from terrestrializing fens
Stofberg, S.F. ; Klimkovska, A. ; Paulissen, M.P.C.P. ; Witte, J.Ph.M. ; Zee, S.E.A.T.M. van der - \ 2015
Aquatic Botany 121 (2015). - ISSN 0304-3770 - p. 83 - 90.
climate-change - water - tolerance - salt - nutrient - netherlands - macrophytes - competition - vegetation - diversity
Terrestrializing lowland fens may be temporarily exposed to elevated surface water salinity, which may have serious consequences for nature conservation. We investigated the response of five fresh water fen plant species to elevated salinity. In a controlled greenhouse experiment, these species were exposed to salt concentrations up to 3000 mg Cl- l-1. Total biomass of the five species together was significantly reduced for salinity levels from 200 mg Cl- l-1. Four individual species showed leaf death and relative growth rate reduction, with effects at 1000 mg Cl- l-1 for Succisa pratensis, Thelypteris palustris and Viola palustris, and 3000 mg Cl- l-1 for Myosotis scorpioides. Comarum palustre showed no significant (.05 level) sensitivity. Biomass distribution was investigated as well. Root-shoot ratio of four species was affected by salinity, which in at least two cases seemed to be related to leaf death. Differences in specific leaf area as a result of salinity were only observed for C. palustre. Dry matter content increased in four species as a result of salinity. Salinity tolerance did not correspond to the environmental distributions of the species, nor could species traits be related to tolerance. Surface water salinity may affect vegetation development in terrestrializing fens at low concentrations. A reduction of plant growth would cause reduced fitness of some species and may lead to reduced root mat growth. Exposure to higher concentrations could eventually lead to a decrease of species richness.
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