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.

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Suppression of soil-borne plant pathogens
Agtmaal, M. van - \ 2015
University. Promotor(en): Wietse de Boer; J.A. van Veen. - Wageningen : Wageningen University - ISBN 9789462572911 - 151
plantenziekteverwekkers - bodempathogenen - bodembacteriën - desinfecteren - landbouwgronden - modellen - rizosfeer - ziektewerende gronden - plant pathogens - soilborne pathogens - soil bacteria - disinfestation - agricultural soils - models - rhizosphere - suppressive soils

Soil borne plant pathogens considerably reduce crop yields worldwide and are difficult to control due to their ”masked” occurrence in the heterogeneous soil environment. This hampers the efficacy of chemical - and microbiological control agents. Outbreaks of crop diseases are not only dependent on the presence of pathogen propagules in the soil, but are also influenced by soil-related properties like physico-chemical characteristics, microbial activity and community composition. Strong competition for limited available carbon substrates restricts or prevents germination and pre-infective growth of pathogens. This competition can occur directly by rapid exploitation of substrates, so called resource competition, or indirectly via inhibitory secondary metabolites, called interference competition

The overall effect of all competition based mechanisms and the abiotic environment on disease development is known as “general disease suppression” and is the sum of all factors that reduce disease. The aim of this thesis was to study different aspects of general disease suppression, in order to get more insight into the interplay between microbial communities, pathogen dynamics, and substrate availability in different agricultural soils.

The first objective was to study the role of microbial volatile organic compounds in natural disease suppression in agricultural soils. In chapter 2 a series of simultaneous experiments were performed on a agricultural soil that received different management practises. We showed a strong correlation between root infection and -biomass production in a bioassay and the suppressive effects of microbial volatiles on the in vitro growth of the pathogen Pythium intermedium. No or weak volatile suppression coincided with significant lower root biomass and a higher disease index, whereas a strong volatile suppression related to high biomass and a low disease index. Furthermore, the composition of the original soil bacterial community showed a drastic shift due to the legacy effects of management practices, coinciding with the loss of volatile suppression. By comparing the emission profiles and the bacterial community composition of the differently managed soils, candidate inhibitory compounds and volatile producing bacterial groups could be identified. Altogether these results indicate that volatile organic compounds can have an important role in general disease suppression.

To follow up on volatile suppression chapter 3 investigates the influence of soil-related (abiotic and biotic) variables on volatile mediated in vitro growth inhibition of different plant pathogens via an extensive soil survey including 50 Dutch arable agricultural fields. The volatile mediated suppression of three phylogenetic different soil borne pathogens (Rhizoctonia solani, Fusarium oxysporum and Pythium intermedium) was linked to a wide range of soil-related variables with univariate and multivariate regression models. The overall suppression of different pathogens was linked to microbial activity and organic substrates. However, different pathogens showed different sensitivity to volatile suppression. Furthermore, the soil-related factors corresponding to volatile mediated suppression were pathogen specific. In total, the results described in this chapter show that part of volatile suppression for a particular pathogen is based on general microbial activity, but our data shows as well that the individual response is pathogen specific.

Chapter 4 explores the reservoir of potential plant pathogens harboring agricultural soils before the start of the growth season, together with the environmental drivers of this pool of pathogens. By investigating the pathogenic seedbank in relation to its environment we assessed which soil-related variables could explain differences among site pathogen community composition. Pathogens differing in phylogeny or mode of infection were related to different soil variables. For example the among-site differences in the presence of oomycetes could not be related to their environmental context. On the other hand the variation in root and shoot fungal pathogen community composition was linked to soil physico-chemical properties and non-pathogen microbial community composition, with potentially a significant role of litter saprophytes therein.

As the presence of pathogen propagules in soil is not necessarily related to disease incidence, chapter 5 investigates the dynamics of root pathogens in the presence of a root in a model rhizosphere. We developed a qPCR based assay to test the growth response of a pathogen (Pythium intermedium) to the presence of root exudates over time. This exposure to root exudates showed soil specific pathogen dynamics. This finding may indicate that in situ (microbial) processes can successfully prevent pathogen development in some of the soils but not in others. Thus this method has the potential to provide an alternative way to assess the susceptibility of a soil to certain soil-borne diseases.

The results of this thesis gave new insights into different aspects of disease suppression in agricultural soils which could serve as a fundament to develop environmentally-friendly control methods based on natural occurring ecological processes. Ideas for the implementation of this study and future research are discussed in chapter 6.

Increase of plant resistance with rhizosphere competent entomopathogenic fungi (EPF)
Tol, R.W.H.M. van - \ 2015
gewasbescherming - tuinbouw - entomopathogene schimmels - biologische bestrijding - rizosfeer - natuurlijke vijanden - bodeminsecten - insect-plant relaties - conferenties - melolontha melolontha - bodem-plant relaties - insectenplagen - plant protection - horticulture - entomogenous fungi - biological control - rhizosphere - natural enemies - soil insects - insect plant relations - conferences - soil plant relationships - insect pests
Entomopathogenic fungi are able to kill insects and are as such a potential mean for pest control. Recently it was discovered that these fungi can also colonize plant roots. Most previous work with EPF has ignored the habitat preferences and survival of the fungus outside of the host. It is possible that factors associated with fungal biology outside of the host are more important when selecting an isolate than how pathogenic it is against a particular host in a laboratory bioassay. Poster van PlantgezondheidEvent 12 maart 2015.
Chemical and biological rhizosphere interactions in low zinc soils
Duffner, A. - \ 2014
University. Promotor(en): Ellis Hoffland; Sjoerd van der Zee, co-promotor(en): Erwin Temminghoff. - Wageningen : Wageningen University - ISBN 9789462571631 - 131
bodem - zink - rizosfeer - voedingsstoffentekorten - bodemkunde - planten - voedingsstoffenopname (planten) - biologische beschikbaarheid - bodemkwaliteit - bodemvruchtbaarheid - soil - zinc - rhizosphere - nutrient deficiencies - soil science - plants - nutrient uptake - bioavailability - soil quality - soil fertility

Abstract of the PhD thesis entitled “Chemical and biological rhizosphere

interactions in low zinc soils” by Andreas Duffner

Soil provides ecosystem services critical for life. The availability of micronutrients, such as zinc (Zn), in soils is an essential factor for normal healthy growth and reproduction of plants. Zinc deficiency is, however, a global problem in crop production due to low Zn bioavailability in soils to plants. The bioavailable Zn fraction in soils is controlled by several factors and is not directly related to the total Zn content of soils. The main objective of this thesis was the determination of factors which control Zn bioavailability in soils to plants and to assess approaches to improve the prediction of Zn plant uptake.

Based on rhizobox experiments, in situ measurements in the rhizosphere as well as multisurface- and radial transport modeling approaches it was shown that the effect of root exuded citrate for increasing plant available Zn is soil specific and does not depend on a specific concentration of low molecular weight organic acids (e.g. citric acid) in the soil solution. Using various low Zn soils at the same time in an experimental setting improved the understanding of soil-responsiveness to root exuded citrate.

Another insight was that multisurface models, which are widely used to assess the potential ecotoxicological risk in metal-contaminated soils, are also accurate to predict the Zn activity in soils with low Zn levels. The predictions were validated with the soil column Donnan Membrane Technique by using various soils with low Zn levels. It was predicted that soil organic matter is the dominant Zn sorbent and controlled the Zn activity also at low soil organic matter levels. Examples were shown how this modeling approach can be used to assess management options to increase bioavailable Zn to plants.

Using soil extracted Zn fractions to directly predict the Zn plant uptake at low Zn levels was shown to be inaccurate. Using a stepwise approach where the steps of the uptake process were characterized with, respectively, Zn solid-solution distribution, adsorption of Zn to root surface, Zn uptake into root and Zn translocation to shoot made the prediction of Zn plant uptake more accurate. Root surface adsorbed Zn was shown to be a useful proxy for the bioavailable Zn.

The framework of experimental and modeling approaches which were developed and applied in this thesis can also be used to study the plant-availability of other micronutrients at low concentration levels and how that is affected by various root exuded ligands.

Biosynthesis, regulation and biological role of strigolactones in rice
Moura Luis Cardoso, C.S. De - \ 2014
University. Promotor(en): Harro Bouwmeester, co-promotor(en): Carolien Ruyter-Spira. - Wageningen : Wageningen University - ISBN 9789462570917 - 166
oryza sativa - rijst - striga - parasitaire planten - rizosfeer - lactonen - gigaspora rosea - biosynthese - rice - parasitic plants - rhizosphere - lactones - biosynthesis

In her thesis Catarina Cardoso studied strigolactone biosynthesis in rice. Strigolactones are multifunctional compounds produced by plants. They are plant hormones that regulate plant architecture, but in addition plants release strigolactones into the soil to communicate and initiate beneficial symbiosis with arbuscular mycorrhizal (AM) fungi. Parasitic plants of the genera Striga, Orobanche and Phelipanche take advantage of this communication to also recognize their hosts and infest them. These parasites infect crops and cause significant economic losses in Mediterranean regions and especially in Sub Saharan Africa where they put food security at risk. Catarina found there is large variation in strigolactone biosynthesis between the two major rice groups (indica and japonica) and located the genes responsible for this. She also showed that the different strigolactones produced by rice have a differential impact on AM fungi and seeds of parasitic plants. These findings suggest that it is possible to select crop varieties that can interact with AM fungi, without inducing parasitism. The knowledge generated in this study can contribute to the urgent need to control the worldwide parasitic weed problems. At the same time strigolactones also control plant development and the results of this study may resuylt in tools to develop better yielding and sustainable crops.

Linkages between plant traits and soil ecology in the rhizosphere and through litter decomposition
Brolsma, K.M. - \ 2014
University. Promotor(en): Ellis Hoffland, co-promotor(en): Ron de Goede. - Wageningen : Wageningen University - ISBN 9789462571068 - 112
bodemecologie - rizosfeer - ligstro - decompositie - wortels - bodembiologie - nematoda - solanum tuberosum - globodera pallida - biofumigatie - genotypen - soil ecology - rhizosphere - litter - decomposition - roots - soil biology - biofumigation - genotypes
The influence of spatiotemporal variability and adaptations to hypoxia on empirical relationships between soil acidity and vegetation
Cirkel, D.G. ; Witte, J.P.M. ; Bodegom, P.M. van; Nijp, J.J. ; Zee, S.E.A.T.M. van der - \ 2014
Ecohydrology 7 (2014)1. - ISSN 1936-0584 - p. 21 - 32.
bodemchemie - bodemaciditeit - vegetatietypen - bodem-plant relaties - soortensamenstelling - plantenfysiologie - rizosfeer - wetlands - heterogeniteit - ecohydrologie - ruimtelijke variatie - soil chemistry - soil acidity - vegetation types - soil plant relationships - species composition - plant physiology - rhizosphere - heterogeneity - ecohydrology - spatial variation - ellenberg indicator values - field-measurements - plant ecology - ph changes - iron - regression - diversity - diffusion - oxidation
Soil acidity is well known to affect the species composition of natural vegetation. The physiological adaptations of plants to soil acidity and related toxicity effects and nutrient deficiencies are, however, complex, manifold and hard to measure. Therefore, generally applicable quantifications of mechanistic plant responses to soil acidity are still not available. An alternative is the semi-quantitative and integrated response variable ‘indicator value for soil acidity’ (Rm). Although relationships between measured soil pH and Rm from various studies are usually strong, they often show systematic bias and still contain high residual variances. On the basis of a well-documented national dataset consisting of 91 vegetation plots and a dataset with detailed, within-plot, pH measurements taken at three periods during the growing season, it is shown that strong spatiotemporal variation of soil pH can be a critical source of systematic errors and statistical noise. The larger part of variation, however, could be explained by the moisture status of plots. For instance, Spearman's rho decreased from 93% for dry plots and 87% for moist plots to 59% for wet plots. The loss of relation between soil pH and Rm in the moderately acid to alkaline range at increasingly wetter plots is probably due to the establishment of aerenchyma-containing species, which are able to control their rhizosphere acidity. Adaptation to one site factor (oxygen deficit) apparently may induce indifference for other environmental factors (Fe2+, soil pH). For predictions of vegetation response to soil acidity, it is thus important to take the wetness of plots into account
Consequences of intra-specific metabolic diversity in plants for soil organisms : a baseline approach for evaluating ecological effects of genetic modifications
Kabouw, P. - \ 2012
University. Promotor(en): Wim van der Putten; N.M. van Dam, co-promotor(en): A. Biere. - S.l. : s.n. - ISBN 9789461731197 - 136
brassica oleracea var. capitata - glucosinolaten - exudaten - genetische variatie - genetische modificatie - bodemflora - bodemfauna - niet-doelorganismen - rizosfeer - transgene planten - glucosinolates - exudates - genetic variation - genetic engineering - soil flora - soil fauna - nontarget organisms - rhizosphere - transgenic plants

Plant intra-specific variation, i.e. variation within a plant species, is known to affect organisms that are directly associated to plants. These effects may be due to for example differences in nutritional quality or defensive metabolites. Plant intra-specific variation can also affect higher trophic level and organisms not directly associated to the plants, i.e. non-target organisms. These effects occur via differences in the quality of herbivores serving as host or prey, due to differences in the rates of attractiveness for higher trophic level organisms, differences in decomposition rates of litter, or differences in root exudates. Intra-specific variation occurs naturally in wild plant populations and humans have used this to select plants for agricultural use. Breeding and artificial selection for plant traits that were desirable for agricultural practices resulted in novel varieties, adding to intra-specific variation in these species.
In addition to natural variation and variation between cultivars, plant genetic modification can result in crop varieties with novel traits such as increased productivity or insect resistance. These traits may also affect non-target organisms. The question is whether these effects fall within or outside the range of non-target effects observed for conventionally bred varieties. To answer this question, one first needs to determine the range of non-target effects caused by conventional varieties, a so-called ‘baseline’.In this thesis, I examined the baseline effects that conventional white cabbage varieties have on soil organisms, the mechanisms behind these effects, and the consequences for interactions between below-and aboveground organisms. The range of effects observed in the conventionally bred varieties can then serve as a baseline for evaluating the effects of genetic modifications.
I started by examining intra-specific variation in glucosinolate concentrations and profiles in white cabbage cultivars. Glucosinolates, a group of circa 120 secondary plant compounds predominantly present in the Brassicaceae, have been shown to affect not only aboveground organisms but also belowground organisms. Glucosinolate profiles in both roots and shoots of white cabbage cultivars showed significant intra-specific variation. The root glucosinolate profiles were more diverse than in the shoots. The variation in root glucosinolate profiles between four of the cultivars was used to evaluate the effects of glucosinolates on a range of soil organisms from different trophic levels, which differ in their degree of association with plant roots. In the field I recorded that plant-parasitic nematodes were affected by the differences in the root glucosinolate profiles, whereas non-target organisms were not. The latter observation might be explained by the reduced intra-specific variation in the glucosinolate profiles of the root exudates compared to those of the roots. Even though total glucosinolate concentrations in roots and root exudates correlated positively, the number of individual glucosinolates that were recorded in the root exudates did not match those found in the roots. My experiments show that this may be due to different degradation rates of the individual glucosinolates in the soil.
By adding different soil communities to sterilized soils I examined whether belowground organisms can affect aboveground organisms via their shared host plant. For this, I used two cabbage cultivars that were highly divergent both in their effects on soil organisms and glucosinolate profiles. Microorganisms added to the soils promoted aphid population growth. The addition of nematodes tended to decrease aphid population growth. However, the effect of the soil organisms on aboveground organisms was similar for both cultivars, indicating that the outcome of below-aboveground interactions was not affected by intra-specific differences.
Genetic modification of plants could also indirectly affect plant growth, for example if the modification would affect the soil communities associated with the plants, which could subsequently affect aerial plant parts and aboveground processes. I explored this possibility by reviewing the recent literature on genetic modified plants, focusing on two case studies; rice plants modified to tolerate drought and salt stress and plants transformed to enhance their capacity to accumulate pollutants. Indeed, feedback loops between plants and the rhizosphere can result in both positive and negative feedback effects of the modified gene on aboveground plant properties. This may have unexpected consequences for the net effect of the genetic modification and eventually annihilate the positive effect of the modification on desired plant properties such as yield.
In this thesis I also showed that when evaluating genetically modified plants in greenhouse studies, effects on soil organisms are limited when compared to the field. I propose that this is due to the fact that greenhouse studies use relatively simple soils that lack the complex plant-soil interactions that can be present in the field. This is an indication that greenhouse studies have a limited predictive value for field effects on soil organisms. Greenhouse studies are nevertheless useful for selecting a suitable and manageable set of varieties that are representative for the range of variation present in the full set of available cultivars. The selection of this sub-set can be made using the appropriate statistical tools, such as multivariate statistics. The selected sub-set can then be used as a baseline for more extensive studies assessing effects on (non-target) organisms in the field. I found that for root glucosinolate profiles this was a useful approach. Whether this holds true for other traits is yet to be assessed.
Before one can evaluate whether effects of genetically modified plants fall within or outside the effects of conventional plants, a good knowledge of the range of effects that can be observed for conventional varieties is required. In this thesis, I have provided the basis for this knowledge for white cabbage, especially for belowground interactions and to some extent on belowground-aboveground interactions. Conventional varieties already differ in their effects on soil organisms and these effects can potentially result in altered below-aboveground interactions, as was simulated by the addition of specific organism groups to the soil. This range of effects can serve as a baseline to determine whether effects of genetically modified white cabbage plants fall inside or outside the range of effects that can be observed for these conventional varieties.

Climate change induced range-expanding plants : aboveground and belowground interactions
Morriën, W.E. - \ 2011
University. Promotor(en): Wim van der Putten. - [S.l.] : S.n. - ISBN 9789085859376 - 144
planten - geïntroduceerde soorten - klimaatverandering - bodemfauna - vrijlevende nematoden - bodembacteriën - rizosfeer - plaagresistentie - ziekteresistentie - herbivoren - interacties - plants - introduced species - climatic change - soil fauna - free living nematodes - soil bacteria - rhizosphere - pest resistance - disease resistance - herbivores - interactions

Burning of fossil fuels has raised the level of atmospheric carbon dioxide, which contributes to global climate warming. As a result the mean earth surface temperature has increased faster in the past decades than in the previous thousands of years before. This rapid climate warming together with habitat fragmentation and other land use changes puts a major pressure on many plants and animals. They should either adapt to the warmer climate conditions or disperse in order to keep up with their optimal climatic conditions. Range expansion brings new interactions within the ecosystem in the new range. This can lead to potential benefits, for example range shifting species that do not encounter natural enemies in the new range might become invasive. Although invasive species are a well-studied phenomenon, there is relatively little known about the general mechanisms of biological invasions under climate change. In this thesis I focus on plant species that expand range due to current climate warming. I examined how these range-expanding plants interact with aboveground herbivorous insects and - mostly - how they establish belowground interactions with components of the soil food web. I examined how these interactions in the new range may play a role in the successful establishment of climate change induced range-expanding plants in plant communities of the new range. The focus of my study was on riverine (riparian) areas along the great rivers in the Netherlands, which are well connected with southern Europe by the Rhine and Rhine-Danube canal.

In the first experiment we examined exotic plant exposure to aboveground and belowground enemies. We used plants that originated from Eurasia (intra-continental range expanders) and plants that originated from other continents (inter-continental range expanders). We compared these exotic plants with phylogenetically related natives. We grew the plants with and without non-coevolved polyphagous (generalist) herbivores, a locust Schistocerca gregaria and an aphid Myzus persicae. We also exposed all plants to a general soil community from the invaded range and compared their plant-soil feedback responses. Then I tested how individual plants responded to aboveground and belowground plant enemies and I compared this to their combined effects. I also tested whether the strength of aboveground control by generalist shoot-feeding insects was indicative of the strength of belowground control by plant-soil feedback.

In the next study I examined how the soil nematode community from the new range responds to exotic plant species compared to related native plants species. As a follow up, I determined the rhizosphere community composition of bacteria, fungi, arbuscular mycorrhizal fungi (AMF) and fusaria. All groups of microbes were analyzed qualitatively and the non-mycorrhizal fungal biomass and fusaria were also analyzed quantitatively. I tested the hypothesis that range-expanding plant species have a different rhizosphere microbial community composition than natives.

Finally, I compared the early establishment of range-expanding exotics and phylogenetically related plant species that are native in the invaded habitats. In a greenhouse I grew five range-expanding plant species and five related natives in sterilized and non-sterile inoculated soils from the new range, both alone and with a background community of plant species present in the invaded habitat. In the field, I grew the same plants species in artificially created sparse and dense plant communities. I tested whether range-expanding exotic plant species establish better under competition with native vegetation than phylogenetically related natives, because exotics may benefit from less negative interactions with the soil community compared to natives.

Biet gebaat bij juiste bacteriemix (interview met J. Raaijmakers)
Scharroo, J. ; Raaijmakers, J.M. - \ 2011
Bionieuws 21 (2011)10. - ISSN 0924-7734 - p. 5 - 5.
rizosfeerbacteriën - bodemweerbaarheid - bodembiologie - rizosfeer - suikerbieten - plantenziekten - akkerbouw - rhizosphere bacteria - soil suppressiveness - soil biology - rhizosphere - sugarbeet - plant diseases - arable farming
Aantallen bacteriën bepalen het ziektewerende vermogen van de bodem
Genoeg mycorrhiza's in bodem
Bos, J.F.F.P. - \ 2009
Boerderij 95 (2009)9. - ISSN 0006-5617 - p. 58 - 58.
uien - allium cepa - rizosfeer - mycorrhizae - mycorrhizaschimmels - opname (uptake) - onions - rhizosphere - mycorrhizas - mycorrhizal fungi - uptake
Uit onderzoek van Wageningen Universiteit blijkt dat in het verleden uienrassen onbewust al geselecteerd zijn op hun goede samenwerking met mycorrhiza's
Plants on the move: plant-soil interactions in poleward shifting plant species
Grunsven, R.H.A. van - \ 2008
University. Promotor(en): Frank Berendse; Wim van der Putten, co-promotor(en): Elmar Veenendaal. - [S.l.] : S.n. - ISBN 9789085852513 - 140
planten - plantenecologie - plantensuccessie - invasies - soorten - bodem - interacties - rizosfeer - bodemflora - bodemfauna - klimaatverandering - bodem-plant relaties - plants - plant ecology - plant succession - invasions - species - soil - interactions - rhizosphere - soil flora - soil fauna - climatic change - soil plant relationships
As a result of recent global climate change, areas that have previously been climatically unsuitable for species have now become suitable new habitats. Many plant-species are expanding their range polewards, colonizing these newly available areas. If these species are able to expand their range faster than their natural enemies they can become released from these limiting factors. A similar mechanism has been reported for invasive plant species, introduced into foreign continent, which are often found to be released from natural enemies.
An example of an invasive plant species that is introduced into a foreing contintinent is Carpobrotus edulis. This species was found to be negatively affected by the soil community collected in the native range, while the soil communities from the invaded range did not have an effect on plant performance compared to a sterilized control. I hypothesized that a similar reduction of the negative effects of the soil community can occur when plant species shift their range. This hypothesis was tested in a greenhouse experiment. I compared plant-soil feedbacks of three plant species that have recently expanded their range into The Netherlands, with three related native species. The non-native species experienced a significantly less negative effect of plant-soil feedback than the native plant species.
Concurrently with these range shifts local climate is changing and this might affect plant-soil feedback as well. In order to test this plant-soil feedbacks of six range expanding and six related native species were compared at two temperatures, 20°C and 25°C daytime temperature. While again native species showed a more negative plant-soil feedback than the non-native species, temperature did not affect the strength or direction of plant-soil feedback.
Besides pair wise comparisons between native and non-native species in the invaded range, comparisons between the native and non-native range of a range expanding plant can be used to test for effects of range shifts on plant-soil interactions. Rhizosphere soil was collected from populations of Tragopogon dubius in both the native and the recently colonized range. The soil communities from the native range had a more negative effect on plant performance than the soil communities from the invaded range as compared to sterilized controls. T. pratensis, which is native to the entire studied range, did not show this pattern.
As plant-soil interactions are the net effect of many positive and negative factors the less negative effect of plant-soil feedback can be either a result of more positive or less negative effects of the soil community. One of the mutualistic groups of organisms, the arbuscular mycorrhizal fungi (AMF) are known to be a major factor contributing to ecosystem functioning and to the maintenance of plant biodiversity and the most important soil-borne mutualists for many plants. I therefore focus on this group of soil organisms. I compared the association of T.dubius with AMF in the new part of its range with T. pratensis native to this area. Three measures for plant-fungal affinity were compared between these two plant species; the density of AMF propagules able to colonize the plant, the percentage of root length colonized by arbuscular mycorrhiza, and the composition of the resulting AMF community in the roots. This was done for four replicate soil inocula from different sites in The Netherlands. The two plant species did not differ in any of the tested factors. As there are no differences in the association with the most important mutualist the observed differences in plant-soil interaction are likely an effect of release from negative components in the soil community, e.g. soil pathogens, but further studies are needed to test this.
Alterations in biotic interactions, through climate change and range shifts, such as a release of soil-borne natural enemies, can have significant effects on the performance of plants. Predictions of future ranges and impact of range expanding plant species on invaded ecosystems can therefore not be accurately made without a thorough understanding of its biotic interactions and the way these interactions are changed by the range shifts.

Genotypic diversity and rhizosphere competence of antibiotic-producing Pseudomonas species
Bergsma-Vlami, M. - \ 2008
University. Promotor(en): Pierre de Wit, co-promotor(en): Jos Raaijmakers. - [S.l. : S.n. - ISBN 9789085049524 - 192
pseudomonas - antibiotica - rizosfeerbacteriën - rizosfeer - populatiedynamica - genetische diversiteit - biologische bestrijding - suikerbieten - antibiotics - rhizosphere bacteria - rhizosphere - population dynamics - genetic diversity - biological control - sugarbeet
The phenolic antibiotic 2,4-diacetylphloroglucinol (DAPG) has been implicated in biological control of multiple plant pathogens by fluorescent Pseudomonas species. DAPG-producing Pseudomonas strains are effective biocontrol agents, however, their ecological performance is often highly variable resulting in inconsistent disease suppression. The ecological performance is complex and determined by many bacterial traits and environmental factors, including the host plant. In this thesis, several genotypic and phenotypic characteristics underlying the ecological performance of DAPG-producing Pseudomonas were investigated.
To discriminate between genotypically different DAPG-producing Pseudomonas strains directly in rhizosphere samples without their prior isolation or enrichment on nutrient media, a simple and rapid method was developed based on polymorphisms in the polyketide synthase gene phlD. Denaturing Gradient Gel Electrophoresis (DGGE) analysis, sequencing and phylogenetic analyses of indigenous phlD+ isolates obtained from the rhizosphere of wheat, sugar beet and potato plants, resulted in the identification of seven phlD+ genotypes, designated A, B, C, D, E, F, and Z, five of which were not described previously (C, D, E, F and Z). The phlD-DGGE analysis allowed simultaneous detection of multiple phlD+ isolates in the rhizosphere and, compared to cultivation-based approaches, this technique does not have the bias toward detecting either the most dominant genotype or the genotype with higher growth rates or competitive abilities during cultivation.
Subsequent studies with representative strains of each of the Pseudomonas genotypes showed that three genotypes (A, Z and G) were superior in long-term colonization of roots of wheat, sugar beet and potato plants. These results suggest that their rhizosphere competence is not linked to a specific plant species, but is due to yet unknown characteristics that enable these strains to be competitive in different rhizosphere environments. In contrast, the rhizosphere competence of Pseudomonas genotypes E, C and F was dependent on the plant species and, therefore, these strains are considered to be specialists instead of generalists.
Results of this thesis further showed that the host plant species also have a significant effect on DAPG-production by indigenous phlD+ Pseudomonas: the wheat and potato rhizospheres supported significantly higher amounts of DAPG produced per cell basis than the rhizospheres of sugar beet and lily. In the same context, the eight Pseudomonas genotypes differed significantly in their ability to produce DAPG in the rhizosphere of sugar beet plants with in situ DAPG concentrations ranging from 1 to 144 ng per 105 cells. Based on these data, significant correlations were established between the rhizosphere competence of a genotype and in situ DAPG production levels. In general, these correlations suggest that Pseudomonas genotypes that produce high amounts of DAPG per cell basis in situ establish lower population densities in the sugar beet rhizosphere than genotypes that produce small amounts of DAPG. To our knowledge, this is the first study that shows an inverse correlation between rhizosphere competence of Pseudomonas strains and in situ antibiotic production.
Biocontrol assays showed that P. ultimum was effectively controlled by all eight Pseudomonas strains and differential effects were observed in biocontrol activity against A. cochlioides. Pseudomonas genotype G was the most effective in biocontrol of Pythium and Aphanomyces damping-off, and its biocontrol activity was due, at least in part, to DAPG production as its DAPG-deficient mutant was significantly less effective. Comparative analysis of the eight DAPG-producing Pseudomonas genotypes revealed a highly significant correlation between their rhizosphere competence and efficacy to control Aphanomyces damping-off of sugar beet. These results indicate that the more rhizosphere competent DAPG-producing Pseudomonas strains are, the higher their efficacy is to control A. cochlioides in sugar beet. The promising results obtained with genotypes A, Z and G in the sugar beet bioassays provide a strong basis for their implementation in the current integrated disease management strategies in sugar beet.
The results acquired in this thesis have shown that the identification of the genotypic diversity and rhizosphere competence of antibiotic-producing Pseudomonas species is of great value, because it may allow maximizing root colonization and disease suppression. Knowledge of genetic traits involved in host preference of these antagonistic bacteria will help to identify strains that are adequately adapted to specific host-pathogen systems. Similarly, looking into plant traits that promote the growth and activity of introduced biocontrol strains can be highly complementary and further contribute to sustainability in agriculture.
Ecology of tree roots in substrates of The Hague
Arhipova, L. ; Spijker, J.H. ; Kopinga, J. - \ 2007
Wageningen : Alterra (Alterra-rapport 1590) - 111
wortels - straatbomen - stedelijke gebieden - groeimedia - rizosfeer - substraten - bodemdegradatie - kationenuitwisselingcapaciteit - waterafstotende gronden - hydrofobiciteit - nederland - zuid-holland - roots - street trees - urban areas - growing media - rhizosphere - substrates - soil degradation - cation exchange capacity - water repellent soils - hydrophobicity - netherlands
The ecology of uniformly and non-uniformly distributed roots in layered and/or heterogeneous substrates, especially sand-peat-clay mixes, have been studied from literature and through a case study. There is a strong interaction between soil layering and/or heterogeneity and local root growth and local branching rate. In principle, the minimum area of root surface that a plant needs is very low. Real situations have much higher root surface areas for several reasons, one being the absence of synchronisation and synlocation of supply and demand of nutrients and water
Bioavailability of zinc to aerobic rice
Gao, X. - \ 2007
University. Promotor(en): Sjoerd van der Zee; F.S. Zhang, co-promotor(en): Ellis Hoffland. - [S.l.] : S.n. - ISBN 9789085046462 - 147
oryza sativa - rijst - zink - biologische beschikbaarheid - vesiculair-arbusculaire mycorrhizae - rizosfeer - bodem - voedingsstoffentekorten - rice - zinc - bioavailability - vesicular arbuscular mycorrhizas - rhizosphere - soil - nutrient deficiencies
Soil biodiversity in amazonian and other Brazilian ecosystems
Moreira, F.M.S. ; Siqueira, J.O. ; Brussaard, L. - \ 2006
Wallingford UK : CABI Publishing - ISBN 1845930320 - 280
bodembiologie - bodemflora - bodemfauna - rizosfeer - micro-organismen - biodiversiteit - amazonia - brazilië - soil biology - soil flora - soil fauna - rhizosphere - microorganisms - biodiversity - brazil
This book reviews soil biodiversity and related ecological processes in one of the key biodiversity hotspots of the world, the Amazon, and nearby regions of Brazil. It covers both the tropical savannah and rainforests. Chapters describe the biology, ecology, taxonomy, geographic distribution and sampling methods for the most important soil functional groups.
Haken en ogen aan dieper toetsen van nitraat
Elzakker, B.G. van; Gast, L. - \ 2005
Nieuwsbrief Koeien & Kansen 2005 (2005)20. - p. 4 - 4.
melkveehouderij - mestbeleid - nitraatuitspoeling - rizosfeer - grondwater - monitoring - boren - methodologie - experimenteel veldonderzoek - filters - dairy farming - manure policy - nitrate leaching - rhizosphere - groundwater - boring - methodology - field experimentation
In het Landelijk Meetnet Effecten Mestbeleid (LMM) meet het RIVM (Rijksinstituut voor Volksgezondheid en Milieu) nitraat in de bovenste meter van het grondwater. De monsters nemen we relatief eenvoudig met handboor en filterlans. We overwegen om de nitraatbelasting van grondwater tot vijf meter onder de grondwaterspiegel vast te stellen. De in het LMM toegepaste methoden lenen zich hier niet voor. Welke methode(n) wel? Om dat na te gaan onderzochten we afgelopen zomer enkele technieken op praktische bruikbaarheid. Er blijkt heel wat meer nodig dan een handboor.
Effect van factoren in het wortelmilieu op de scheutuitloop na planten bij roos : onderzoek naar effecten van pH, NH4, EC, B, mattype, fungiciden, kniphoogte en cultivar
Baas, R. ; Garcia, N. ; Kouwenhoven, D. ; Straver, N. - \ 2005
Naaldwijk : Praktijkonderzoek Plant & Omgeving B.V. (Rapporten PPO ) - 23
rosa - rozen - rizosfeer - wortelsystemen - bodembiologie - groeimedia - teelt onder bescherming - nederland - roses - rhizosphere - root systems - soil biology - growing media - protected cultivation - netherlands
Kniphoogte en ingebogen blad beïnvloeden uitloop roos
Baas, R. - \ 2005
Vakblad voor de Bloemisterij 60 (2005)33. - ISSN 0042-2223 - p. 42 - 43.
rozen - rosaceae - rizosfeer - wortelsystemen - bodembiologie - groeimedia - teelt onder bescherming - roses - rhizosphere - root systems - soil biology - growing media - protected cultivation
Verschil in uitloop van jonge scheuten bij roos wordt vooral bepaald door variatie van het uitgangsmateriaal. Dit bepaalt de snelheid van uitlopen en de grootte van de griffeltak. Hoe groter de griffel, hoe meer en zwaarder de volgende scheuten. Hoog knippen zorgt voor een snellere uitloop
Onderzoek leidt tot advies over toedienen mycorrhizaschimmels
Baar, J. ; Westerink - Petersen, J. - \ 2004
Tuin en Landschap 26 (2004)21. - ISSN 0165-3350 - p. 48 - 49.
mycorrhizae - mycorrhizaschimmels - bodemschimmels - symbiose - plantenvoeding - wortels - bomen - bepaling van groeiplaatshoedanigheden - standplaatsfactoren - inoculatie - bodeminoculatie - bodembiologie - rizosfeer - mulchen - groeiplaatsen - mycorrhizas - mycorrhizal fungi - soil fungi - symbiosis - plant nutrition - roots - trees - site class assessment - site factors - inoculation - soil inoculation - soil biology - rhizosphere - mulching - sites
Uit onderzoek van PPO-Paddestoelen en BTL Bomendienst blijkt dat toediening van mycorrhizaschimmels in combinatie met bodemverbetering in veel gevallen een oplossing is om de groei van bomen te verbeteren. Beide partijen werken samen in het ontwikkelen van een nieuw product: maatwerk in het toevoegen van mycorrhizaschimmels
Spatial and temporal fluctuations in bacteria, microfauna and mineral nitrogen in response to a nutrient impulse in soil
Zelenev, V.V. - \ 2004
University. Promotor(en): Ariena van Bruggen, co-promotor(en): A.M. Semenov. - Wageningen : s.n. - ISBN 9058089886 - 190
bodembiologie - bodemfauna - micro-organismen - bacteriën - biologische bodemactiviteit - rizosfeer - variatie - oscillatie - populatiedynamica - bevolkingsspreiding - organisch bodemmateriaal - organisch afval - voedingsstoffen - wiskundige modellen - simulatiemodellen - soil biology - soil fauna - microorganisms - bacteria - biological activity in soil - rhizosphere - variation - oscillation - population dynamics - population distribution - soil organic matter - organic wastes - nutrients - mathematical models - simulation models
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