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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    Microbiome dynamics of disease suppresive soils
    Gómez Expósito, Ruth - \ 2017
    Wageningen University. Promotor(en): F.P.M. Govers; J.M. Raaijmakers, co-promotor(en): J. Postma; I. de Bruijn. - Wageningen : Wageningen University - ISBN 9789463431774 - 267
    suppressive soils - soil suppressiveness - plant diseases - thanatephorus cucumeris - microbial ecology - soil microbiology - rhizosphere bacteria - soil bacteria - community ecology - soil fungi - transcriptomics - taxonomy - ziektewerende gronden - bodemweerbaarheid - plantenziekten - thanatephorus cucumeris - microbiële ecologie - bodemmicrobiologie - rizosfeerbacteriën - bodembacteriën - gemeenschapsecologie - bodemschimmels - transcriptomica - taxonomie

    Disease suppressive soils are soils in which plants do not get diseased from plant pathogens due to the presence (and activities) of the microbes present in the soil. Understanding which microbes contribute to confer suppression and through which mechanisms they can protect plants is crucial for a sustainable control of plant diseases. In the research conducted in this thesis, I first examined the role of Lysobacter species, previously associated with disease suppressive soils, in suppressing damping-off disease caused by the soil-borne fungal pathogen Rhizoctonia solani on sugar beet. The majority of the Lysobacter strains tested revealed a broad metabolic potential in producing a variety of enzymes and secondary metabolites able to suppress R. solani in vitro. However, any of these strains could consistently suppress damping-off disease when applied in soil bioassays. Their ability to promote plant growth was also tested for sugar beet, cauliflower, onion or Arabidopsis thaliana. Results indicated that any of the Lysobacter strains could consistently promote plant growth, neither via direct contact nor via volatile production. Second, I investigated whether the antagonistic activity of Lysobacter species could be triggered when applied as bacterial consortia, together with Pseudomonas and Streptomyces species. Although several bacterial combinations showed an increased antagonistic effect towards R. solani in vitro, no consistent effects were observed when these bacterial consortia were applied in vivo. Third, I investigated the dynamical changes in the bacterial community composition and functions occurring during the process of disease suppressiveness induction by performing whole community analyses using next-generation sequencing techniques. Results indicated that suppressiveness induction was most associated with changes in certain bacterial traits rather than changes in the bacteria community composition itself. Among the functions found as more active in suppressive soils were several ‘classic’ mechanisms of disease suppression, including competition for nutrients, iron and space and production of extracellular enzymes, indol-acetic-acid and hydrogen cyanide. Among the enzymes found in higher abundance in suppressive soil were these ones involved in the degradation of oxalic acid, a pathogenicity factor produced by pathogenic fungi to help infecting the host plant. Hence, I finally studied the role of bacteria able to produce enzymes able to degrade oxalic acid in suppressing R. solani disease. Enrichment of native oxalotrophic bacteria existing in soil, their isolation and further application into soil revealed that they could effectively suppress Rhizoctonia disease. Characterization of these oxalotrophic bacteria revealed that members within the Caulobacter and Nocardioides species could suppress R. solani disease by their own. Furthermore, the research done in this thesis highlights the importance of combining different techniques to unravel the mechanisms underlying disease suppression and the importance of studying function-over-phylogeny. Additionally, it also highlights the importance of organic amendments (such as oxalic acid) directly into soils in order to “engineer” the bacterial functions towards the control of diseases caused by R. solani.

    Volatile-mediated interactions in the rhizosphere
    Cordovez da Cunha, Viviane - \ 2016
    Wageningen University. Promotor(en): Francine Govers; Jos Raaijmakers, co-promotor(en): V.J. Carrion. - Wageningen : Wageningen University - ISBN 9789462579019 - 219
    rhizosphere bacteria - rhizosphere fungi - microbial interactions - volatile compounds - suppressive soils - actinobacteria - streptomyces - microbacterium - thanatephorus cucumeris - growth stimulators - biological control - defence mechanisms - genomics - transcriptomics - rizosfeerbacteriën - rizosfeerschimmels - microbiële interacties - vluchtige verbindingen - ziektewerende gronden - actinobacteria - streptomyces - microbacterium - thanatephorus cucumeris - groeistimulatoren - biologische bestrijding - verdedigingsmechanismen - genomica - transcriptomica

    Plants and microorganisms are constantly engaged in highly dynamic interactions both above- and belowground. Several of these interactions are mediated by volatile organic compounds (VOCs), small carbon-based compounds with high vapor pressure at ambient temperature. In the rhizosphere, VOCs have an advantage in intra- and interorganismal signaling since they can diffuse through soil pores over longer distances than other metabolites and are not dependent on water availability. The research described in this PhD thesis explored how beneficial and pathogenic microorganisms that live in the rhizosphere and endosphere modulate plant growth, development and resistance via the production of VOCs. In vitro and in vivo bioassays as well as different ‘omic’ approaches, such as volatomics, transcriptomics and genomics, were employed to investigate underlying mechanisms of VOC-mediated microbe-microbe and microbe-plant interactions.

    To investigate the diversity and functions of microbial VOCs, a disease-suppressive soil was used as the source of the VOC-producing microorganisms. Previous metagenomics studies reported Actinobacteria, in particular Streptomyces and Microbacterium species, as the most abundant bacterial genera found in a soil naturally suppressive to the fungal root pathogen Rhizoctonia solani. VOCs of several Streptomyces isolates inhibited hyphal growth of R. solani and in addition, promoted plant growth. Coupling the Streptomyces VOC profiles with their effects on fungal growth pinpointed methyl 2-methylpentanoate and 1,3,5-trichloro-2-methoxy benzene as antifungal VOCs. Also Microbacterium isolates showed VOC-mediated antifungal activity and plant growth promotion. VOC profiling of Microbacterium sp. EC8 revealed several sulfur-containing compounds and ketones such as dimethyl disulfide, trimethyl trisulfide and 3,3,6-trimethylhepta-1,5-dien-4-one (also known as Artemisia ketone). Genome analysis of strain EC8 revealed genes involved in sulfur metabolism. Resolving the role of the identified compounds and genes in VOC-mediated plant growth promotion and induced resistance will be subject of future studies. VOC-mediated chemical warfare underground has been proposed as a key mechanism of natural disease-suppressive soils. The results presented in this thesis indeed point in that direction. However, to more conclusively determine the role of the identified Actinobacterial VOCs in soil suppressiveness to R. solani, it will be important to demonstrate that the fungicidal VOCs are actually produced in situ at the right place and at sufficient concentrations to suppress plant infection by the pathogenic fungus.

    In agriculture, VOCs and VOC-producing microorganisms provide a potential alternative to the use of pesticides to protect plants and to improve crop production. In the past decades, several in vitro studies have described the effects of microbial VOCs on other (micro)organisms. However, little is still known on the potential of VOCs in large-scale agriculture and horticulture. The results described in this thesis show that VOCs from Microbacterium sp. EC8 stimulate the growth of Arabidopsis, lettuce and tomato, but do not control damping-off disease of lettuce caused by R. solani. Significant biomass increases were also observed for plants exposed only shortly to the bacterial VOCs prior to transplantation of the seedlings to soil. These results indicate that VOCs from strain EC8 can prime plants for growth promotion without direct contact and prolonged colonization. Furthermore, the induction of the plant growth-promoting effects appeared to be plant tissue specific. Root exposure to the bacterial VOCs led to a significant increase in plant biomass whereas shoot exposure did not result in significant biomass increase of lettuce and tomato seedlings. Genome-wide transcriptome analysis of Arabidopsis seedlings exposed to VOCs from this bacterium showed an up-regulation of genes involved in sulfur and nitrogen metabolism and in ethylene and jasmonic acid signaling. These results suggest that the blend of VOCs of strain EC8 favors, in part, the plant’s assimilation of sulfate and nitrogen, essential nutrients for plant growth, development and also resistance.

    Similar to beneficial microorganisms, plant pathogenic microorganisms have also evolved strategies to modulate growth and defense of their hosts. For instance, compounds secreted by pathogens may suppress or interfere with plant defense. In this thesis I show that R. solani produces an array of VOCs that promote growth, accelerate development, change VOC emission and reduce insect resistance of plants. Plant growth-promoting effects induced by the fungal VOCs were not transgenerational. Genome-wide transcriptome analysis of Arabidopsis seedlings revealed that exposure to fungal VOCs caused up-regulation of genes involved in auxin signaling, but down-regulation of genes involved in ethylene and jasmonic acid signaling. These findings suggest that this soil-borne pathogen uses VOCs to predispose plants for infection by stimulating lateral root formation and enhancing root biomass while suppressing defense mechanisms. Alternatively, upon perception of VOCs from soil-borne pathogens, plants may invest in root biomass while minimizing investments in defense, a trade-off that helps them to speed up growth and reproduction and to survive pathogen attack.

    In conclusion, the research presented in this thesis shows that both plants and microorganisms engage via VOCs in long-distance interactions and that beneficial and pathogenic soil microorganisms can alter plant physiology in different ways. Here, I provided a first step in identifying microbial genes involved in the regulation of biologically active VOCs as well as candidate plant genes involved in VOC perception and signal transduction. How plants sense and differentiate among VOCs from beneficial and pathogenic soil microorganisms will be an intriguing subject for future studies.

    Rhizobacterial modification of plant defenses against insect herbivores: from molecular mechanisms to tritrophic interactions
    Pangesti, N.P.D. - \ 2015
    Wageningen University. Promotor(en): Marcel Dicke; Joop van Loon. - Wageningen : Wageningen University - ISBN 9789462572836 - 224
    planten - rizosfeerbacteriën - insecten - multitrofe interacties - verdedigingsmechanismen - pseudomonas fluorescens - mamestra brassicae - pieris brassicae - plant-microbe interacties - insect-plant relaties - plant-herbivoor relaties - plants - rhizosphere bacteria - insects - multitrophic interactions - defence mechanisms - pseudomonas fluorescens - mamestra brassicae - pieris brassicae - plant-microbe interactions - insect plant relations - plant-herbivore interactions


    Plants as primary producers in terrestrial ecosystems are under constant threat from a multitude of attackers, which include insect herbivores. In addition to interactions with detrimental organisms, plants host a diversity of beneficial organisms, which include microbes in the rhizosphere. Furthermore, the interactions between plants and several groups of root-associated microbes such as mycorrhizae, plant growth promoting rhizobacteria (PGPR) and plant growth promoting fungi (PGPF) can affect plant interactions with foliar insect herbivores. The beneficial root-associated microbes are able to modify plant physiology by promoting plant growth and induced systemic resistance (ISR), in which the balance between both effects will determine the final impact on the insect herbivores. Using Arabidopsis thaliana Col-0, this thesis explores the molecular mechanisms on how plants integrate responses when simultaneously interacting with the rhizobacterium Pseudomonas fluorescens and the generalist and the specialist leaf-chewing insects Mamestra brassicae and Pieris brassicae respectively.

    A literature review on the state-of-the-art in the field of microbe-plant-insect interactions (Chapter 2) explores how root-associated microbes and insect folivores can influence each other via a shared host plant. For more than a decade, both ecological and mechanistic studies mostly focused on exploring these belowground and aboveground interactions using single microbe and single herbivore species. The importance of increasing the complexity of the study system in order to understand the interactions in more natural situations is being emphasized. Furthermore, this review discusses the role of plant hormones in regulating plant growth and defense against folivores, while simultaneously being involved in associations with root-associated microbes.

    Experimental evidence has shown patterns on the effects of mycorrhizal colonization on plant interactions with insect herbivores, and raises the question whether plant colonization by different groups of root-associated microbes has similar effects on particular categories of insect herbivores. In Chapter 3, plant-mediated effects of a non-pathogenic rhizobacterium on the performance of leaf-chewing insects, and the underlying mechanisms modulating the interactions, have been examined. Colonization of A. thaliana Col-0 roots by the bacterium P. fluorescens strain WCS417r resulted in decreased larval weight of the generalist leaf-chewing M. brassicae, and had no effect on larval weight of the specialist leaf-chewing P. brassicae. The crucial role of jasmonic acid (JA) in regulating rhizobacteria-mediated induced systemic resistance (ISR) against M. brassicae is confirmed by including plant mutants in the study. Interestingly, I also observed that rhizobacteria can induce systemic susceptibility to M. brassicae caterpillars. Comparison of M. brassicae performance and gene transcription in A. thaliana plants, grown in potting soil or a mixture of potting soil and sand in a 1:1 ratio, shows that in a mixture of potting soil and sand, rhizobacterial treatment had a consistently negative effect on M. brassicae, whereas the effect is more variable in potting soil. Rhizobacterial treatment primed plants grown in potting soil and sand for stronger expression of JA- and ethylene-regulated genes PDF1.2 and HEL, supporting stronger resistance to M. brassicae. Taken together, the results show that soil composition can be one of the factors modulating the outcome of microbe-plant-insect interactions.

    Chapter 4 further addresses the mechanisms underlying rhizobacteria-mediated ISR against the generalist leaf-chewing M. brassicae by integrating plant gene transcription, chemistry and performance of M. brassicae in wild type A. thaliana Col-0 plants and mutants defective in the JA-pathway, i.e. dde2-2 and myc2, in the ET pathway, i.e. ein2-1, and in the JA-/ET-pathway, i.e. ora59. Results of this study show that rhizobacterial colonization alone or in combination with herbivore infestation induced the expression of the defense-associated genes ORA59 and PDF1.2 at higher levels than activation by herbivore feeding alone, and the expression of both genes is suppressed in the knock-out mutant ora59. Interestingly, the colonization of plant roots by rhizobacteria alters the levels of plant defense compounds, i.e. camalexin and glucosinolates (GLS), by enhancing the synthesis of constitutive and induced levels of camalexin and aliphatic GLS while suppressing the induced levels of indole GLS. The changes are associated with modulation of the JA-/ET-signaling pathways as shown by investigating mutants. Furthermore, the herbivore performance results show that functional JA- and ET-signaling pathways are required for rhizobacteria-mediated ISR against leaf-chewing insects as observed in the knock-out mutants dde2-2 and ein2-1. The results indicate that colonization of plant roots by rhizobacteria modulates plant-insect interactions by prioritizing the ORA59-branch over the MYC2-branch, although the transcription factor ORA59 is not the only one responsible for the observed effects of rhizobacteria-mediated ISR against leaf-chewing insects.

    Taking a step further in increasing the complexity of the study system, Chapter 5 investigates how co-cultivation of P. fluorescens strains WCS417r and SS101 affects direct plant defense to the caterpillar M. brassicae. Inoculation of either P. fluorescens WCS417r or SS101 singly at root tips or simultaneously at two different positions along the roots resulted in a similar level of rhizobacterial colonization by each strain, whereas co-cultivation of both strains at either the root tips or at two different positions along the roots resulted in a higher colonization level of strain WCS417r compared to colonization by SS101. The results suggest that the site of inoculation influences the direct interactions between the two strains in the rhizosphere, as also confirmed by in vitro antagonism assays in the absence of plants. Both upon single inoculation and co-cultivation of both strains at the same or different sites along the roots, the two rhizobacterial strains induced the same strength of ISR against the caterpillar M. brassicae and the same degree of plant growth promotion. In the roots, colonization by the two strains as single or mixed culture resulted in a similar gene expression pattern of up-regulation of MYC2, down-regulation of WRKY70 and no effect on NPR1 expression, genes representing JA-signaling, SA-signaling and the node of crosstalk between the two pathways, respectively. We hypothesize that both rhizobacterial strains use negative crosstalk between JA- and SA-pathways as mechanism to suppress plant immunity and establish colonization. This study shows that competitive interactions between rhizobacterial strains known to induce plant defense in systemic tissue via different signaling pathways, may interfere with synergistic effects on ISR and plant growth promotion.

    While the effect of root-associated microbes on direct plant defense against insect herbivores has been studied previously, the effect of these microbes on indirect plant defense to herbivores is much less known. Chapter 6 explores how colonization by the rhizobacterium P. fluorescens strain WCS417r affects indirect plant defense against the generalist herbivore M. brassicae by combining behavioral, chemical and gene transcriptional approaches. The results show that rhizobacterial colonization of A. thaliana roots results in an increased attraction of the parasitoid Microplitis mediator to caterpillar-infested plants. Volatile analysis revealed that rhizobacterial colonization suppressed emission of the terpene (E)-α-bergamotene, and the aromatics methyl salicylate and lilial in response to caterpillar feeding. Rhizobacterial colonization decreased the caterpillar-induced transcription of the terpene synthase genes TPS03 and TPS04. Rhizobacteria enhanced both growth and indirect defense of plants under caterpillar attack. This study shows that rhizobacteria have a high potential to enhance the biocontrol of leaf-chewing herbivores based on enhanced attraction of parasitoids.

    Taken together, the research presented in this thesis has shown how single or combined applications of rhizobacteria affect interactions of plants with leaf-chewing insects in terms of direct and indirect resistance. Furthermore, results presented in this thesis have revealed some of the molecular mechanisms underlying plant-mediated interactions between rhizobacteria and leaf-chewing insects that can be used in developing practical approaches by applying beneficial root-associated microbes for improving plant resistance.

    Bodembacterie helpt plant tegen rupsenvraat
    Sikkema, A. ; Pangesti, N.P.D. - \ 2015
    Wageningen : St. voor Duurzame Ontwikkeling
    arabidopsis - bodembacteriën - rizosfeerbacteriën - pseudomonas - gewasbescherming - rupsen - plaagresistentie - biologische bestrijding - landbouwkundig onderzoek - arabidopsis - soil bacteria - rhizosphere bacteria - pseudomonas - plant protection - caterpillars - pest resistance - biological control - agricultural research
    Bodembacteriën die in het wortelmilieu van planten leven, verminderen de vatbaarheid van planten voor rupsenvraat. Dat blijkt uit onderzoek van Wageningse entomologen. In de modelplant Arabidopsis konden ze aantonen dat rhizobacteriën de plant in verhoogde staat van paraatheid brengen.
    Normal Operating Range of Bacterial Communities in Soil Used for Potato Cropping
    Inceoglu, O. ; Overbeek, L.S. van; Salles, J.F. ; Elsas, J.D. van - \ 2013
    Applied and Environmental Microbiology 79 (2013)4. - ISSN 0099-2240 - p. 1160 - 1170.
    16s ribosomal-rna - gradient gel-electrophoresis - microbial communities - rhizosphere bacteria - plant genotype - diversity - dynamics - ecology - growth - populations
    In this study, the impacts of six potato (Solanum tuberosum) cultivars with different tuber starch allocations (including one genetically modified [GM] line) on the bacterial communities in field soil were investigated across two growth seasons interspersed with 1 year of barley cultivation, using quantitative PCR, clone library, and PCR-denaturing gradient gel electrophoresis (DGGE) analyses. It was hypothesized that the modifications in the tuber starch contents of these plants, yielding changed root growth rates and exudation patterns, might have elicited altered bacterial communities in the soil. The data showed that bacterial abundances in the bulk soil varied over about 2 orders of magnitude across the 3 years. As expected, across all cultivars, positive potato rhizosphere effects on bacterial abundances were noted in the two potato years. The bulk soil bacterial community structures revealed progressive shifts across time, and moving-window analysis revealed a 60% change over the total experiment. Consistent with previous findings, the community structures in the potato rhizosphere compartments were mainly affected by the growth stage of the plants and, to a lesser extent, by plant cultivar type. The data from the soil under the non-GM potato lines were then taken to define the normal operating range (NOR) of the microbiota under potatoes. Interestingly, the bacterial communities under the GM potato line remained within this NOR. In regard to the bacterial community compositions, particular bacterial species in the soil appeared to be specific to (i) the plant species under investigation (barley versus potato) or, with respect to potatoes, (ii) the plant growth stage. Members of the genera Arthrobacter, Streptomyces, Rhodanobacter, and Dokdonella were consistently found only at the flowering potato plants in both seasons, whereas Rhodoplanes and Sporosarcina were observed only in the soil planted to barley
    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
    Effects of Plant Genotype and Growth Stage on the Betaproteobacterial Communities Associated with Different Potato Cultivars in Two Fields
    Inceoglu, O. ; Salles, J.F. ; Overbeek, L.S. van; Elsas, J.D. van - \ 2010
    Applied and Environmental Microbiology 76 (2010)11. - ISSN 0099-2240 - p. 3675 - 3684.
    gradient gel-electrophoresis - polymerase-chain-reaction - 16s ribosomal-rna - microbial communities - soil type - rhizosphere bacteria - promoting bacteria - substrate utilization - transgenic potatoes - medicago-truncatula
    Bacterial communities in the rhizosphere are dynamic and susceptible to changes in plant conditions. Among the bacteria, the betaproteobacteria play key roles in nutrient cycling and plant growth promotion, and hence the dynamics of their community structures in the rhizosphere should be investigated. Here, the effects of plant cultivar, growth stage, and soil type on the communities associated with potato cultivars Aveka, Aventra, Karnico, Modena, Premiere, and Desiree were assessed for two different fields containing sandy soil with either a high or low organic compound content. Thus, bacterial and betaproteobacterial PCR-denaturing gradient gel electrophoresis analyses were performed to analyze the effects of plant cultivar and growth on the rhizosphere community structure. The analyses showed that in both fields all cultivars had a rhizosphere effect on the total bacterial and betaproteobacterial communities. In addition, the plant growth stage strongly affected the betaproteobacterial communities in both fields. Moreover, the community structures were affected by cultivar, and cultivars differed in physiology, as reflected in their growth rates, root development, and estimated tuber starch contents. Analyses of betaproteobacterial clone libraries constructed for two selected cultivars (one cultivar that produced low-starch-content tubers and one cultivar that produced high-starch-content tubers), as well as bulk soil, revealed that the rhizospheres of the two cultivars selected for specific bacteria, including plant-growth-promoting bacteria, such as Variovorax and Achromobacter spp. In addition, quantitative PCR-based quantification of the Variovorax paradoxus-specific functional gene asfA (involved in desulfonation) indicated that there were clear potato rhizosphere effects on the abundance of this gene. Interestingly, both cultivar type and plant growth stage affected the community under some circumstances.
    Endophytic Colonization of Potato (Solanum tuberosum L.) by a Novel Competent Bacterial Endophyte, Pseudomonas putida Strain P9, and Its Effect on Associated Bacterial Communities
    Andreote, F.D. ; Araujo, W.L. ; Azevedo, J.L. ; Elsas, J.D. van; Rocha, U.N. da; Overbeek, L.S. van - \ 2009
    Applied and Environmental Microbiology 75 (2009)11. - ISSN 0099-2240 - p. 3396 - 3406.
    gradient gel-electrophoresis - 16s ribosomal-rna - soil microbial community - ralstonia-solanacearum - rhizosphere bacteria - systemic resistance - fluorescens strain - sequence data - plant-growth - tomato
    Pseudomonas putida strain P9 is a novel competent endophyte from potato. P9 causes cultivar-dependent suppression of Phytophthora infestans. Colonization of the rhizoplane and endosphere of potato plants by P9 and its rifampin-resistant derivative P9R was studied. The purposes of this work were to follow the fate of P9 inside growing potato plants and to establish its effect on associated microbial communities. The effects of P9 and P9R inoculation were studied in two separate experiments. The roots of transplants of three different cultivars of potato were dipped in suspensions of P9 or P9R cells, and the plants were planted in soil. The fate of both strains was followed by examining colony growth and by performing PCR-denaturing gradient gel electrophoresis (PCR-DGGE). Colonies of both strains were recovered from rhizoplane and endosphere samples of all three cultivars at two growth stages. A conspicuous band, representing P9 and P9R, was found in all Pseudomonas PCR-DGGE fingerprints for treated plants. The numbers of P9R CFU and the P9R-specific band intensities for the different replicate samples were positively correlated, as determined by linear regression analysis. The effects of plant growth stage, genotype, and the presence of P9R on associated microbial communities were examined by multivariate and unweighted-pair group method with arithmetic mean cluster analyses of PCR-DGGE fingerprints. The presence of strain P9R had an effect on bacterial groups identified as Pseudomonas azotoformans, Pseudomonas veronii, and Pseudomonas syringae. In conclusion, strain P9 is an avid colonizer of potato plants, competing with microbial populations indigenous to the potato phytosphere. Bacterization with a biocontrol agent has an important and previously unexplored effect on plant-associated communities.
    A multitrophic perspective on functioning and evolution of facilitation in plant communities
    Putten, W.H. van der - \ 2009
    Journal of Ecology 97 (2009)6. - ISSN 0022-0477 - p. 1131 - 1138.
    ammophila-arenaria - soil feedback - sand dune - ecological communities - rhizosphere bacteria - mycorrhizal fungi - insect herbivory - local adaptation - natural enemies - succession
    1. Plant facilitation has been studied mostly in the context of plant–plant interactions, whereas multitrophic interactions including those that occur below ground have not yet received much attention. Here, I will discuss how above-ground and below-ground natural enemies and their predators influence plant facilitation and its evolution. 2. Specific above-ground and below-ground plant enemies and their predators play a major role in structuring the composition and dynamics of plant communities. In successional sequences, above-ground and below-ground multitrophic level interactions may tip the balance from competitive to facilitative states and vice versa. 3. Little is known about how above-ground and below-ground multitrophic interactions develop along resource or stress gradients and how the outcomes of above-ground–below-ground interactions depend on variations in these environmental conditions. 4. Facilitated plants need to fit into the above-ground–below-ground multitrophic communities of their facilitators. 5. Little is known also about the evolution of plant facilitation. The observed distance in phylogeny between facilitators and facilitated plants suggests that host-specific enemies may very well co-determine which species become facilitated by which facilitators. 6. Further, very little attention has been given to how plant strategies (allelopathy, accumulation of enemies, monopolization of symbionts) may be the result of selection against being facilitative. 7. Synthesis. Plant facilitation cannot be understood without considering a plant's natural enemies and also its enemies' enemies. Plant enemies can turn competitive interactions into facilitative interactions, whereas the enemies' enemies can turn facilitation back into competition. Below-ground interactions will have longer-lasting effects on facilitation than those above ground, because many organisms can persist in the soil, even when the host plants have disappeared
    Effects of plant genotype and growth stage on the structure of bacterial communities associated with potato (Solanum tuberosum L.)
    Overbeek, L.S. van; Elsas, J.D. van - \ 2008
    FEMS microbiology ecology 64 (2008)2. - ISSN 0168-6496 - p. 283 - 296.
    gradient gel-electrophoresis - 16s ribosomal-rna - damping-off disease - transgenic potatoes - rhizosphere bacteria - pseudomonas-fluorescens - microbial-populations - systemic resistance - serratia-plymuthica - biological-control
    The effects of genotype, plant growth and experimental factors (soil and year) on potato-associated bacterial communities were studied. Cultivars Achirana Inta, Désirée, Merkur and transgenic Désirée line DL12 (containing T4 lysozyme gene) were assessed in two field experiments. Cross-comparisons between both experiments were made using Désirée plants. Culture-dependent and -independent approaches were used to demonstrate effects on total bacterial, actinobacterial and Pseudomonas communities in bulk and rhizosphere soils and endospheres. PCR-denaturing gradient gel electrophoresis fingerprints prepared with group-specific primers were analyzed using multivariate analyses and revealed that bacterial communities in Achirana Inta plants differed most from those of Désirée and Merkur. No significant effects were found between Désirée and DL12 lines. Plant growth stage strongly affected different plant-associated communities in both experiments. To investigate the effect of plant-associated communities on plant health, 800 isolates from rhizospheres and endospheres at the flowering stage were tested for suppression of Ralstonia solanacearum biovar 2 and/or Rhizoctonia solani AG3. A group of isolates closely resembling Lysobacter sp. dominated in young plants. Its prevalence was affected by plant growth stage and experiment rather than by plant genotype. It was concluded that plant growth stage overwhelmed any effect of plant genotype on the bacterial communities associated with potato
    Genotypic diversity and rhizosphere competence of antibiotic-producing Pseudomonas species
    Bergsma-Vlami, M. - \ 2008
    Wageningen 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 - pseudomonas - 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.
    Role of the cyclic lipopeptide massetolide A in biological control of Phytophthora infestans and in colonization of tomato plants by Pseudomonas fluorescens
    Tran, H. ; Ficke, A. ; Asiimwe, T. ; Höfte, M. ; Raaijmakers, J.M. - \ 2007
    New Phytologist 175 (2007)4. - ISSN 0028-646X - p. 731 - 742.
    induced systemic resistance - late blight - bacillus-subtilis - rhizoctonia-solani - rhizosphere bacteria - flagellin perception - local treatment - salicylic-acid - fusarium-wilt - induction
    Pseudomonas strains have shown promising results in biological control of late blight caused by Phytophthora infestans. However, the mechanism(s) and metabolites involved are in many cases poorly understood. Here, the role of the cyclic lipopeptide massetolide A of Pseudomonas fluorescens SS101 in biocontrol of tomato late blight was examined. Pseudomonas fluorescens SS101 was effective in preventing infection of tomato (Lycopersicon esculentum) leaves by P. infestans and significantly reduced the expansion of existing late blight lesions. Massetolide A was an important component of the activity of P. fluorescens SS101, since the massA-mutant was significantly less effective in biocontrol, and purified massetolide A provided significant control of P. infestans, both locally and systemically via induced resistance. Assays with nahG transgenic plants indicated that the systemic resistance response induced by SS101 or massetolide A was independent of salicylic acid signalling. Strain SS101 colonized the roots of tomato seedlings significantly better than its massA-mutant, indicating that massetolide A was an important trait in plant colonization. This study shows that the cyclic lipopeptide surfactant massetolide A is a metabolite with versatile functions in the ecology of P fluorescens SS101 and in interactions with tomato plants and the late blight pathogen P. infestans.
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