Staff Publications

Staff Publications

  • external user (warningwarning)
  • Log in as
  • language uk
  • About

    '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.

    We have a manual that explains all the features 

    Current refinement(s):

    Records 1 - 20 / 60

    • help
    • print

      Print search results

    • export

      Export search results

    Check title to add to marked list
    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.

    Mining into interspecific bacterial interactions
    Tyc, Olaf - \ 2016
    Wageningen University. Promotor(en): Wietse de Boer, co-promotor(en): Paolina Garbeva. - Wageningen : Wageningen University - ISBN 9789462578340 - 234
    soil bacteria - secondary metabolites - microbial interactions - antibiotics - nutrients - bodembacteriën - secundaire metabolieten - microbiële interacties - antibiotica - voedingsstoffen

    In terrestrial ecosystems bacteria live in close proximity with many different microbial species and form complex multi-species networks. Within those networks bacteria are constantly interacting with each other and produce a plethora of secondary metabolites like antibiotics, enzymes, volatiles and other compounds from diverse chemical classes. Several independent studies revealed that the production of secondary metabolites by soil bacteria can be influenced by the interaction with other microorganisms in their vicinity.

    In this thesis we show how interspecific interactions between soil bacteria influence the production of soluble and volatile secondary metabolites, gene expression and fitness. To elucidate the effect of interspecific interactions on antimicrobial activity in soil bacteria a high-through-put screening method was developed and applied on a collection of 146 rhizobacterial isolates obtained from similar habitats. In addition we examined if the production of volatile organic compounds is influenced by interspecific interactions. Thus, the identity and antimicrobial activity of volatiles produced by bacteria cultivated in monoculture as well in interaction were examined. Furthermore a sand microcosm approach was applied to investigate how Pseudomonas fluorescens strain Pf0-1 responded to the presence of monocultures and mixtures of a Gram-negative (Pedobacter sp. V48) and a Gram-positive (Bacillus sp. V102) bacterial strain under two nutritional conditions.

    The interaction between a gram-negative Burkholderia and a gram-positive Paenibacillus isolate was subjected to detailed metabolome, volatolome and transcriptome analysis. One distinct volatile and one non-volatile compound produced only during interspecific interaction but not in the monoculture were identified. The activity of the interacting bacteria and the compounds produced during interaction were tested against a range of human and plant pathogens.

    In summary, this thesis extends the knowledge about the effect of interspecific bacterial interactions on secondary metabolites production (soluble and volatiles), gene expression and fitness in bacteria. The exploitation of such bacterial interspecific interactions can be an important “tool” for the discovery of novel antimicrobial and agro-chemical compounds. The obtained knowledge can help in selecting the right players in synthetic communities that fulfil important ecosystem services like disease suppression in agricultural crop systems.

    Plant growth promotion by Pseudomonas fluorescens : mechanisms, genes and regulation
    Cheng, X. - \ 2016
    Wageningen University. Promotor(en): Francine Govers; J.M. Raaijmakers, co-promotor(en): M. van der Voort. - Wageningen : Wageningen University - ISBN 9789462578753 - 192
    soil bacteria - pseudomonas fluorescens - plants - growth stimulators - soil suppressiveness - plant diseases - induced resistance - biochemistry - biosynthesis - plant-microbe interactions - transcriptomics - bodembacteriën - pseudomonas fluorescens - planten - groeistimulatoren - bodemweerbaarheid - plantenziekten - geïnduceerde resistentie - biochemie - biosynthese - plant-microbe interacties - transcriptomica

    Pseudomonas fluorescens is a Gram-negative rod shaped bacterium that has a versatile metabolism and is widely spread in soil and water. P. fluorescens strain SBW25 (Pf.SBW25) is a well-known model strain to study bacterial evolution, plant colonization and biocontrol of plant diseases. It produces the biosurfactant viscosin, a lipopeptide that plays a key role in motility, biofilm formation and activity against zoospores of Phytophthora infestans and other oomycete pathogens. In addition to viscosin, Pf.SBW25 produces other metabolites with activity against plant pathogens. The production of these yet unknown metabolites appeared to be regulated by the GacS/GacA two-component regulatory system (the Gac-system). The second P. fluorescens strain SS101 (Pf.SS101) studied in this thesis is known for its plant growth-promoting activities but the underlying mechanisms and genes are largely unknown. Therefore, in this study, we aimed to identify novel metabolites and biosynthetic genes in Pf.SBW25 and Pf.SS101, and to investigate their role in plant growth promotion and biocontrol. To this end, a multidisciplinary approach involving bioinformatic analysis of the genome sequences of strains Pf.SBW25 and Pf.SS101, microarray-based expression profiling, screening of genomic libraries, bioactivity assays, mass spectrometric image analysis (MALDI-IMS) and GC/MSMS analysis was adopted. In conclusion, we showed that the GacS/GacA two-component system as a global regulator of the expression of genes play important roles in antagonism of Pseudomonas fluorescens toward plant pathogenic microbes as well as in plant growth promotion and ISR. Growth promotion by P. fluorescens is associated with alterations in auxin biosynthesis and transport, steroid biosynthesis, carbohydrate metabolism and sulfur assimilation. Moreover, advanced chemical profiling allowed us to compare the metabolite profiles of free-living P. fluorescens and P. fluorescens living in association with plant roots. A better understanding of yet unknown mechanisms exploited by the various Pseudomonas fluorescens strains will lead to new opportunities for the discovery and application of natural bioactive compounds for both industrial and agricultural purposes.

    Intracellular accommodation of rhizobia in legume host cell: the fine-tuning of the endomembrane system
    Gavrin, A.Y. - \ 2015
    Wageningen University. Promotor(en): Ton Bisseling, co-promotor(en): E. Federova. - Wageningen : Wageningen University - ISBN 9789462574182 - 160
    peulgewassen - rhizobium - bodembacteriën - endosymbiose - wortelknolletjes - membranen - waardplanten - legumes - rhizobium - soil bacteria - endosymbiosis - root nodules - membranes - host plants

    The symbiosis of legumes with rhizobia leads to the formation of root nodules. Rhizobia which are hosted inside specialized infected cells are surrounded by hostderived membranes, forming symbiosomes. Although it is known that symbiosome formation involves proliferation of membranes and changing of host cell architecture the mechanisms involved in these processes remain largely uncovered.

    In this thesis, I studied in more detail the adaptation of the endomembrane system of infected cells to intracellular rhizobia. I have shown that in the first cell layer of the nitrogen-fixing zone, the vacuole of the infected cells shrinks, creating space for the expanding symbiosomes. Here the expression of homotypic fusion and vacuole protein sorting complex (HOPS) genes VPS11 and VPS39 are switched off, whereas tonoplast proteins, like the vacuolar aquaporin TIP1g, are targeted to the symbiosome membrane. These observations suggest that tonoplast-targeted traffic in infected cells is altered. This retargeting is essential for the maturation of symbiosomes.

    Accommodation of intracellular rhizobia requires also the reorganization of the actin cytoskeleton. I have shown that during symbiosome development the symbiosomes become surrounded by a dense actin network and in this way, the actin configuration in infected cells is changed markedly. The actin nucleating factor ARP3 is operational in the rearrangement of actin around the symbiosome.

    It is known that the plasma membrane is inelastic; its capacity to stretch is only around 1-3%. Exocytosis of new membrane material is therefore involved in changes in the size of the membrane surface and in repair of damaged membrane loci. Membrane tension may create a vector for the fusion of membrane vesicles. To test this, the localization of proteins from the group of synaptotamin calcium sensors involved in membrane fusion, was studied. I have shown that the Medicago synaptotamins, MtSyt2 and MtSyt3, are localised on protrusions of the host plasma membrane created by expanding rhizobia (infection threads, cell wall-free unwalled droplets). Hence, at these sites of contact between symbionts membrane tension may create a vector for exocytosis.

    It is known that the host cell wall is modified during the development of infected cells. This process is mediated by the exocytotic pathway employing vesicle-associated membrane proteins (VAMPs) from the VAMP721 family. Previously it was shown in Medicago nodules, that cell-wall free interface membrane formation during bacterial release is dependent on these proteins. I have shown that the pectin modifying enzyme pectate lyase is delivered to the site of bacterial release in soybean nodules by VAMP721-positive vesicles.

    My study uncovered new mechanisms involved in the adaptation of host cells to intracellular rhizobia: defunctionalization of the vacuole, actin cytoskeleton rearrangement and the retargeting of host cell proteins to the interface membrane.

    Suppression of soil-borne plant pathogens
    Agtmaal, M. van - \ 2015
    Wageningen 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.

    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.
    Mycophagous soil bacteria
    Rudnick, M.B. - \ 2015
    Wageningen University. Promotor(en): Wietse de Boer, co-promotor(en): H. van Veen. - Wageningen : Wageningen University - ISBN 9789462572539 - 160
    bodembacteriën - bodemflora - bodembiologie - collimonas - bodemschimmels - bodemecologie - soil bacteria - soil flora - soil biology - collimonas - soil fungi - soil ecology
    Abstract

    Soil microorganisms evolved several strategies to compete for limited nutrients in soil. Bacteria of the genus Collimonas developed a way to exploit fungi as a source of organic nutrients. This strategy has been termed “mycophagy”. In this thesis, research is presented with a focus on two aspects of bacterial mycophagy: 1) Investigation of strategies and traits that are important for Collimonas bacteria to enable a mycophagous lifestyle, 2) Investigation of occurrence of mycophagy among other soil bacteria.

    Focusing on Collimonas bacteria, we find that several traits related to the mycophagous interaction with the fungal hosts, such as production of fungal inhibitors, are phylogenetically conserved. This implies that differentiation in lifestyles of Collimonas strains, is corresponding with phylogenetic distance. Furthermore, we show that collimonads are very motile in a soil-like matrix, especially when being confronted with low nutrient concentrations. This high motility can be used in order to effectively move towards oxalic acid (a metabolite exuded by a range of fungi for different purposes) in a concentration depended manner. Our results suggest that directed motility is an important trait, characterizing the mycophagous lifestyle of collimonads.

    In order to screen for other mycophagous bacteria besides collimonads, two baiting approaches (long- and short-term) were developed. With both approaches, we find fungal hyphae to be commonly colonized by specific communities of rhizosphere mycophagous bacteria. Furthermore, mycophagous colonizers show clear feeding preferences for fungal hosts. Interestingly, a surprisingly high amount of mycophagous bacteria belong to genera well known to harbor plant pathogenic strains. Considering the importance of mycophagous bacteria in the rhizosphere, we finally propose the “Sapro-Rhizosphere” concept. This concept states that a substantial amount of plant derived carbon that is channeled through rhizosphere fungi (primary consumers) might be finally consumed by mycophagous bacteria (secondary consumers).

    Taken together, by using molecular biological as well as microbiological methods, this thesis further extends our knowledge on the ecology of mycophagous Collimonas bacteria and highlights the importance of mycophagous bacteria in the rhizosphere.

    Oligotrophic bacteria and root disease suppression in organically managed soils
    Senechkin, I.V. - \ 2013
    Wageningen University. Promotor(en): Ariena van Bruggen, co-promotor(en): Leo van Overbeek. - Wageningen : Wageningen University - ISBN 9789461738035 - 141
    bodempathogenen - plantenziekteverwekkers - thanatephorus cucumeris - fusarium oxysporum - bodembacteriën - bodembeheer - biologische landbouw - linum usitatissimum - vlas - modellen - bodemweerbaarheid - soilborne pathogens - plant pathogens - thanatephorus cucumeris - fusarium oxysporum - soil bacteria - soil management - organic farming - linum usitatissimum - flax - models - soil suppressiveness

    The objective of this thesis was to obtain a better understanding of soil health in terms of microbial and chemical characteristics as well as suppression of soil borne plant pathogens. Organic soils were chosen as an appropriate model for studying soil health. Four different organic amendments were applied on two experimental fields with different crop history, providing a diverse range of soil quality levels. Many soil microbial variables were measured, including copiotrophic and oligotrophic bacterial populations, the abundance and diversity of Eubacteria, Alphaproteobacteria, Pseudomonas and fungal communities, as well as several microbial genes involved in nitrogen cycling. Plant disease suppressiveness was used as a quantitative integrative parameter reflecting the health status of soils. Rhizoctonia solani on beet and Fusarium oxysporum on flax were selected as pathosystems; areas under disease progress curves were measured in bioassays with differentially amended field soils and were related to soil parameters. Combined rather than single amendments enhanced Fusarium suppression, but Rhizoctonia suppression was more related to crop history than organic amendments. No universal correlations were found between disease suppression and microbial and chemical parameters, although pH and organic matter affected microbial communities and Fusarium wilt. A significant relation between ammonia oxidizing bacteria and disease suppression was observed for both pathogens; this relation was likely indirect via nitrogen availability and pH. No direct relationship was found between quantities of N cycling genes and disease suppression. A specific emphasis was put on the potential role of oligotrophic bacteria in soil health and disease suppression. Bacteria isolated on low carbon medium (10 mg C/L) were repeatedly transferred onto this medium to select true oligotrophic bacteria. Most isolates could grow on both low carbon and higher carbon (1000 mg C/L) media and belonged to Streptomyces, Rhizobium, Bradyrhizobium and Mesorhizobium. A new oligotrophic isolate was identified as Collimonas sp. IS343 and its interaction with R. solani was studied. This strain was better adapted to oligotrophic conditions than a copiotrophic Collimonas reference strain and was more effective in controlling R. solani. This thesis provided a better understanding of some aspects of soil health and emphasized the role of oligotrophic bacteria, a poorly understood but very important group of soil inhabitants.

    Weerbaarheid, ook tegen plantenvirussen
    Kock, M.J.D. de; Stijger, I. - \ 2013
    Vakblad voor de Bloemisterij 68 (2013)10. - ISSN 0042-2223 - p. 30 - 31.
    plantenvirussen - plantenziekten - teeltsystemen - diagnostische technieken - bodembacteriën - bodemschimmels - plantengenetica - landbouwkundig onderzoek - vermeerderingsmateriaal - plant viruses - plant diseases - cropping systems - diagnostic techniques - soil bacteria - soil fungi - plant genetics - agricultural research - propagation materials
    Virus afbreken, symptomen onderdrukken en infectie voorkomen. Dit zijn de drie strategieën die de weerbaarheid van de plant en het teeltsysteem tegen virussen kunnen verhogen. Soms is het al direct toepasbaar.
    Searching for branched glycerol dialkyl glycerol tetraether membrane lipid producing bacteria in soil
    Aydin, R. - \ 2012
    Wageningen University. Promotor(en): Fons Stams; Hauke Smidt. - S.l. : s.n. - ISBN 9789461733795 - 166
    bodembacteriën - bodemmicrobiologie - vertakte vetzuren - acidobacteria - soil bacteria - soil microbiology - branched chain fatty acids - acidobacteria

    KEYWORDS:Branched GDGTs, proxy, pH, temperature, Acidobacteria, methylotrophy, high-throughput techniques

    Bacteria present in soil and peat bog environments were previously found to produce branched glycerol dialkyl glycerol tetraether membrane lipids (GDGTs) that are used as a paleoenvironmental proxy to estimate historic soil temperature and pH. Based on the composition and abundance of branched GDGTs, two indices were previously defined, of which the degree of Cyclisation of Branched Tetraethers (CBT) is related to soil pH and the degree of Methylation of Branched Tetraethers (MBT) is related to both soil pH and mean annual air temperature (MAT) . It was hypothesized that bacteria produce branched GDGTs as a response to changes in pH and temperature. Members of the phylum Acidobacteria were proposed to produce branched GDGTs based on their abundance in peat environments, rich in GDGTs. Recently, it was shown that two representatives from subdivision 1 and 3, Edaphobacter aggregans Wbg-1T and Acidobacteriaceae strain A2-4c, are able to produce these membrane lipids. However, environmental distribution of branched GDGTs is diverse indicating that members of additional subdivisions of Acidobacteria or yet other phyla might also be able to produce branched GDGTs.

    TheAcidobacteria constitute a diverse and ubiquitous phylum and its members play an important role especially in terrestrial environments. Information about the Acidobacteria was collected, including their phylogeny and taxonomy, their role in nature, genomic traits and methods applied for their isolation.

    Soil is a very dynamic and complex ecosystem and soil organisms are major components of the soil. They are crucial for both soil structure and soil processes. The biological activity in the soil mainly occurs in the topsoil, which contains soil organisms and plant roots. Soil microorganisms including bacteria, archaea and fungi are responsible for nutrient cycling and decomposition of organic residues. Microbial activities are strongly influenced by a range of abiotic and biotic factors and by the interaction between different microorganisms. To get insight into the influence of environmental parameters on the bacterial diversity in relation to production of branched GDGTs, soil samples containing variable amounts of these lipids were taken from different locations, namely from two different hot springs (Surprise Valley, California, USA) and along the watershed of the Têt river (France). Bacterial community composition was characterized by using high-throughput cultivation independent techniques as well as selective cultivation. It was shown that both pH and temperature strongly affected microbial community composition. Data presented in this thesis furthermore suggest that besides Acidobacteria, members of additional phyla might also responsible for the observed production of branched GDGTs. Notably, occurrence and relative abundance of members of the Alpha- and Deltaproteobacteria and Bacteroidetes were related to the abundance of branched GDGTs. Furthermore, enrichment studies at different pH, temperature and with different substrates suggested that methanol might be a good carbon source to enrich for producers of branched GDGTs. Unfortunately, attempts towards the isolation of branched GDGTs producing bacteria were unsuccessful. However, a novel methylotrophic Azospirillum species, Azospirillum methanolicus, was isolated.In addition to that, novel methylotrophic candidate genera including Acidobacteria subdivision 1 and Pedobacter were identified from initial enrichment studies.

    In conclusion, data presented in this thesis showed that temperature and pH have a strong effect on the microbial community composition in all soil studied here. Although branched GDGTs producing bacteria were not isolated, the data described in this thesis may help to design new strategies to isolate and identify target bacteria in the future.

    De rol van Collimonas sp. 343 in de onderdrukking van Rhizotonia solani AG2 onder nutriëntenlimitering in de bodem
    Overbeek, L.S. van; Senechkin, I.V. ; Er, H.L. ; Vos, O.J. de; Bruggen, A.H.C. van - \ 2012
    Gewasbescherming 43 (2012)4. - ISSN 0166-6495 - p. 128 - 128.
    bodempathogenen - thanatephorus cucumeris - bodemweerbaarheid - bodembiologie - bodembacteriën - wetenschappelijk onderzoek - gewasbescherming - soilborne pathogens - thanatephorus cucumeris - soil suppressiveness - soil biology - soil bacteria - scientific research - plant protection
    Onder bepaalde omstandigheden, zoals behandelingen met verschillende soorten organische stof, zijn bodems weerbaarder tegen Rhizoctonia solani. De vraag is wat het mechanisme achter deze verhoogde weerbaarheid is en de hypothese van de onderzoekers is dat de levende fractie van de bodem hier voor verantwoordelijk is.
    Microbial community structure elucidates performance of Glyceria maxima plant microbial fuel cell
    Timmers, R.A. ; Rothballer, M. ; Strik, D.P.B.T.B. ; Engel, M. ; Schulz, M. ; Hartmann, A. ; Hamelers, H.V.M. ; Buisman, C.J.N. - \ 2012
    Applied Microbiology and Biotechnology 94 (2012)2. - ISSN 0175-7598 - p. 537 - 548.
    targeted oligonucleotide probes - iron-reducing bacteria - in-situ hybridization - electricity-generation - fe(iii)-reducing bacterium - shewanella-putrefaciens - activated-sludge - soil bacteria - rice plants - human feces
    The plant microbial fuel cell (PMFC) is a technology in which living plant roots provide electron donor, via rhizodeposition, to a mixed microbial community to generate electricity in a microbial fuel cell. Analysis and localisation of the microbial community is necessary for gaining insight into the competition for electron donor in a PMFC. This paper characterises the anode-rhizosphere bacterial community of a Glyceria maxima (reed mannagrass) PMFC. Electrochemically active bacteria (EAB) were located on the root surfaces, but they were more abundant colonising the graphite granular electrode. Anaerobic cellulolytic bacteria dominated the area where most of the EAB were found, indicating that the current was probably generated via the hydrolysis of cellulose. Due to the presence of oxygen and nitrate, short-chain fatty acid-utilising denitrifiers were the major competitors for the electron donor. Acetate-utilising methanogens played a minor role in the competition for electron donor, probably due to the availability of graphite granules as electron acceptors.
    Multiple approaches to enhance the cultivability of bacteria associated with the marine sponge Haliclona (gellius) sp
    Sipkema, D. ; Schippers, K.J. ; Maalcke, W.J. ; Yang, Y. ; Salim, S. ; Blanch, H.W. - \ 2011
    Applied and Environmental Microbiology 77 (2011)6. - ISSN 0099-2240 - p. 2130 - 2140.
    soil bacteria - rhopaloeides odorabile - microbial community - aplysina-aerophoba - growth-medium - microorganisms - cultivation - diversity - culturability - populations
    Three methods were examined to cultivate bacteria associated with the marine sponge Haliclona (gellius) sp.: agar plate cultures, liquid cultures, and floating filter cultures. A variety of oligotrophic media were employed, including media with aqueous and organic sponge extracts, bacterial signal molecules, and siderophores. More than 3,900 isolates were analyzed, and 205 operational taxonomic units (OTUs) were identified. Media containing low concentrations of mucin or a mixture of peptone and starch were most successful for the isolation of diversity, while the commonly used marine broth did not result in a high diversity among isolates. The addition of antibiotics generally led to a reduced diversity on plates but yielded different bacteria than other media. In addition, diversity patterns of isolates from agar plates, liquid cultures, and floating filters were significantly different. Almost 89% of all isolates were Alphaproteobacteria; however, members of phyla that are less commonly encountered in cultivation studies, such as Planctomycetes, Verrucomicrobia, and Deltaproteobacteria, were isolated as well. The sponge-associated bacteria were categorized into three different groups. The first group represented OTUs that were also obtained in a clone library from previously analyzed sponge tissue (group 1). Furthermore, we distinguished OTUs that were obtained from sponge tissue (in a previous study) but not from sponge isolates (group 2), and there were also OTUs that were not obtained from sponge tissue but were obtained from sponge isolates (group 3). The 17 OTUs categorized into group 1 represented 10 to 14% of all bacterial OTUs that were present in a large clone library previously generated from Haliclona (gellius) sp. sponge tissue, which is higher than previously reported cultivability scores for sponge-associated bacteria. Six of these 17 OTUs were not obtained from agar plates, which underlines that the use of multiple cultivation methods is worthwhile to increase the diversity of the cultivable microorganisms from sponges.
    Climate change induced range-expanding plants : aboveground and belowground interactions
    Morriën, W.E. - \ 2011
    Wageningen 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.

    Transcriptional and antagonistic responses of Pseudomonas fluorescens Pf0-1 to phylogenetically different bacterial competitors
    Garbeva, P. ; Silby, M.W. ; Raaijmakers, J.M. ; Levy, S.B. ; Boer, W. de - \ 2011
    ISME Journal 5 (2011)6. - ISSN 1751-7362 - p. 973 - 985.
    microbial community composition - gene-expression - corynebacterium-glutamicum - chemical communication - natural environments - microarray analyses - soil bacteria - growth - aeruginosa - biosynthesis
    The ability of soil bacteria to successfully compete with a range of other microbial species is crucial for their growth and survival in the nutrient-limited soil environment. In the present work, we studied the behavior and transcriptional responses of soil-inhabiting Pseudomonas fluorescens strain Pf0-1 on nutrient-poor agar to confrontation with strains of three phylogenetically different bacterial genera, that is, Bacillus, Brevundimonas and Pedobacter. Competition for nutrients was apparent as all three bacterial genera had a negative effect on the density of P. fluorescens Pf0-1; this effect was most strong during the interaction with Bacillus. Microarray-based analyses indicated strong differences in the transcriptional responses of Pf0-1 to the different competitors. There was higher similarity in the gene expression response of P. fluorescens Pf0-1 to the Gram-negative bacteria as compared with the Gram-positive strain. The Gram-negative strains did also trigger the production of an unknown broad-spectrum antibiotic in Pf0-1. More detailed analysis indicated that expression of specific Pf0-1 genes involved in signal transduction and secondary metabolite production was strongly affected by the competitors’ identity, suggesting that Pf0-1 can distinguish among different competitors and fine-tune its competitive strategies. The results presented here demonstrate that P. fluorescens Pf0-1 shows a species-specific transcriptional and metabolic response to bacterial competitors and provide new leads in the identification of specific cues in bacteria–bacteria interactions and of novel competitive strategies, antimicrobial traits and genes.
    Stimulering van ziektewerend vermogen van de bodem, Thema: Functionele biodiversiteit BO-12.03-004-002
    Postma, J. ; Schilder, M.T. ; Scholten, O.E. ; Burger-Meijer, K. - \ 2011
    S.n.
    gewasbescherming - plantenziektebestrijding - antagonisten - bodembacteriën - bodemkwaliteit - ziektebestrijdende teeltmaatregelen - rhizoctonia - fusarium oxysporum - bodemweerbaarheid - ziektewerende gronden - plant protection - plant disease control - antagonists - soil bacteria - soil quality - cultural control - rhizoctonia - fusarium oxysporum - soil suppressiveness - suppressive soils
    In eerder onderzoek is aangetoond dat de aanwezigheid van antagonistische Lysobacter-soorten correleert met ziektewering tegen Rhizoctonia solani. Daarnaast zijn er aanwijzingen dat mycorrhiza-schimmels de aantasting door Fusarium oxysporum in ui kunnen onderdrukken. Onderzoek naar welke teeltmaatregelen deze ziektewerende micro-organismen zodanig kunnen stimuleren dat een hogere bodemweerbaarheid ontstaat tegen deze plantenziektes.
    Cultivation of hitherto-uncultured bacteria belonging to the Verrucomicrobia subdivision 1 from the potato (Solanum tuberosum L.) rhizosphere
    Rocha, U.N. da; Andreote, F.D. ; Azevedo, J.L. ; Elsas, J.D. van; Overbeek, L.S. van - \ 2010
    Journal of Soils and Sediments 10 (2010)2. - ISSN 1439-0108 - p. 326 - 339.
    16s ribosomal-rna - soil bacteria - community structure - sequence data - pure culture - diversity - culturability - growth - genes - electrophoresis
    The role of dominant bacterial groups in the plant rhizosphere, e.g., those belonging to the phyla Acidobacteria and Verrucomicrobia, has, so far, not been elucidated, and this is mainly due to the lack of culturable representatives. This study aimed to isolate hitherto-uncultured bacteria from the potato rhizosphere by a combination of cultivation approaches. An agar medium low in carbon availability (oligotrophic agar medium) and either amended with potato root exudates or catalase or left unamended was used with the aim to improve the culturability of bacteria from the potato rhizosphere. The colony forming unit numbers based on colonies and microcolonies were compared with microscopically determined fluorescence-stained cell numbers. Taxonomical diversity of the colonies was compared with that of library clones made from rhizosphere DNA, on the basis of 16S rRNA gene comparisons. The oligotrophic media amended or not with catalase or rhizosphere extract recovered up to 33.6% of the total bacterial numbers, at least seven times more than the recovery observed on R2A. Four hitherto-uncultured Verrucomicrobia subdivision 1 representatives were recovered on agar, but representatives of this group were not found in the clone library. The use of oligotrophic medium and its modifications enabled the growth of colony numbers, exceeding those on classical agar media. Also, it led to the isolation of hitherto-uncultured bacteria from the potato rhizosphere. Further improvement in cultivation will certainly result in the recovery of other as-yet-unexplored bacteria from the rhizosphere, making these groups accessible for further investigation, e.g., with respect to their possible interactions with plants.
    Organisch stof en bodemweerbaarheid
    Os, G.J. van; Bent, J. van der - \ 2010
    bodemfauna - bodembacteriën - bodemschimmels - organische stof - gewasbescherming - bodemweerbaarheid - soil fauna - soil bacteria - soil fungi - organic matter - plant protection - soil suppressiveness
    Bacteriën en schimmels in de grond kunnen ziekten en plagen onderdrukken, zgn. bodemweerbaarheid of ziektewering. Organische stof is voedsel voor dit bodemleven. Vraag van het samengevatte onderzoek was of een hoger organische stof gehalte leidt tot een beter bodemleven en betere bodemweerbaarheid.
    Exploration of hitherto-uncultured bacteria from the rhizosphere
    Rocha, U.N. da; Overbeek, L.S. van; Elsas, J.D. van - \ 2009
    FEMS microbiology ecology 69 (2009)3. - ISSN 0168-6496 - p. 313 - 328.
    microbial community structure - soil bacteria - plant-growth - 16s rdna - marine bacterioplankton - phylum acidobacteria - chemical-processes - wheat rhizosphere - field conditions - analysis reveals
    The rhizosphere environment selects a particular microbial community that arises from the one present in bulk soil due to the release of particular compounds in exudates and different opportunities for microbial colonization. During plant-microorganism coevolution, microbial functions supporting plant health and productivity have developed, of which most are described in cultured plant-associated bacteria. This review discusses the state of the art concerning the ecology of the hitherto-uncultured bacteria of the rhizosphere environment, focusing on Acidobacteria, Verrucomicrobia and Planctomycetes. Furthermore, a strategy is proposed to recover bacterial isolates from these taxa from the rhizosphere environment.
    Resistentie in de bodem. Deelrapport project Antibiotica in de bodem
    Schmitt, H. ; Lahr, J. ; Bhumibhamon, G. - \ 2009
    Gouda : Stiching Kennisontwikkeling en kennisoverdracht Bodem (SKB) (Projectnr: PP8348 ) - 20
    dierlijke meststoffen - bodemverontreiniging - antibiotica - bodembacteriën - antibioticaresistentie - monitoring - animal manures - soil pollution - antibiotics - soil bacteria - antibiotic resistance - monitoring
    Terwijl antibioticum-resistentie in ziekenhuizen en landbouwhuisdieren relatief goed onderzocht is, is veel minder bekend over het optreden van resistentie in het milieu. Een mogelijk belangrijke bron van resistentie in het milieu is het uitrijden van mest van intensief gehouden landbouwhuisdieren op landbouwgronden. In deze studie werd een pilot-onderzoek verricht naar de rol van bemesting met varkensdrijfmest voor resistentie in zandige landbouwgronden. Er werd gekozen voor een veld-benadering, waarbij drie bedrijven tijdens de periode van bemesting regelmatig werden bemonstert (vlak voor, en een dag, een week en vier weken na de bemesting). Op elk bedrijf werd in de nabijheid van de veldlocatie ook een referentielocatie gekozen, om de lange termijn effecten van bemesting te kunnen vergelijken met een soortgelijke, maar niet bemestte grond.
    Check title to add to marked list
    << previous | next >>

    Show 20 50 100 records per page

     
    Please log in to use this service. Login as Wageningen University & Research user or guest user in upper right hand corner of this page.