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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    Metabolic modeling to understand and redesign microbial systems
    Heck, Ruben G.A. van - \ 2017
    Wageningen University. Promotor(en): V.A.P. Martins dos Santos, co-promotor(en): M. Suárez Diez. - Wageningen : Wageningen University - ISBN 9789463434553 - 239
    micro-organismen - modelleren - kooldioxide - biotechnologie - algen - metabolisme - pseudomonas - microorganisms - modeling - carbon dioxide - biotechnology - algae - metabolism - pseudomonas

    The goals of this thesis are to increase the understanding of microbial metabolism and to functionally (re-)design microbial systems using Genome- Scale Metabolic models (GSMs). GSMs are species-specific knowledge repositories that can be used to predict metabolic activities for wildtype and genetically modified organisms. Chapter 1 describes the assumptions associated with GSMs, the GSM generation process, common GSM analysis methods, and GSM-driven strain design methods. Thereby, chapter 1 provides a background for all other chapters. In this work, there is a focus on the metabolically versatile bacterium Pseudomonas putida (chapters 2,3,4,5,6), but also other model microbes and biotechnologically or societally relevant microbes are considered (chapters 3,4,6,7,8).

    GSMs are reflections of the genome annotation of the corresponding organism. For P. putida, the genome annotation that GSMs have been built on is more than ten years old. In chapter 2, this genome annotation was updated both on a structural and functional level using state-of-the-art annotation tools. A crucial part of the functional annotation relied on the most comprehensive P. putida GSM to date. This GSM was used to identify knowledge gaps in P. putida metabolism by determining the inconsistencies between its growth predictions and experimental measurements. Inconsistencies were found for 120 compounds that could be degraded by P. putida in vitro but not in silico. These compounds formed the basis for a targeted manual annotation process. Ultimately, suitable degradation pathways were identified for 86/120 as part of the functional reannotation of the P. putida genome.

    For P. putida there are 3 independently generated GSMs, which is not uncommon for model organisms. These GSMs differ in generation procedure and represent different and complementary subsets of the knowledge on the metabolism of the organism. However, the differing generation procedures also makes it extremely cumbersome to compare their contents, let alone to combine them into a single consensus GSM. Chapter 3 addresses this issue through the introduction of a computational tool for COnsensus Metabolic Model GENeration (COMMGEN). COMMGEN automatically identifies inconsistencies between independently generated GSMs and semi-automatically resolves them. Thereby, it greatly facilitates a detailed comparison of independently generated GSMs as well as the construction of consensus GSMs that more comprehensively describe the knowledge on the modeled organism.

    GSMs can predict whether or not the corresponding organism and derived mutants can grow in a large variety of different growth conditions. In comparison, experimental data is extremely limited. For example, BIOLOG data describes growth phenotypes for one strain in a few hundred different media, and genome-wide gene essentially data is typically limited to a single growth medium. In chapter 4 GSMs of multiple Pseudomonas species were used to predict growth phenotypes for all possible single-gene-deletion mutants in all possible minimal growth media to determine conditionally and unconditionally essential genes. This simulated data was integrated with genomic data on 432 sequenced Pseudomonas species, which revealed a clear link between the essentiality of a gene function and the persistence of the gene within the Pseudomonas genus.

    Chapters 5 and 6 describe the use of GSMs to (re-)design microbial systems. P. putida is, despite its acknowledged versatile metabolism, an obligate aerobe. As the oxygen-requirement limits the potential applications of P. putida, there have been several experimental attempts to enable it to grow anaerobically, which have so far not succeeded. Chapter 5 describes an in silico effort to determine why P. putida cannot grow anaerobically using a combination of GSM analyses and comparative genomics. These analyses resulted in a shortlist of several essential and oxygen-dependent processes in P. putida. The identification of these processes has enabled the design of P. putida strains that can grow anaerobically based on the current understanding of P. putida metabolism as represented in GSMs.

    Efficient microbial CO2 fixation is a requirement for the biobased community, but the natural CO2 fixation pathways are rather inefficient, while the synthetic CO2 fixation pathways have been designed without considering the metabolic context of a target organism. Chapter 6 introduces a computational tool, CO2FIX, that designs species-specific CO2 fixation pathways based on GSMs and biochemical reaction databases. The designed pathways are evaluated for their ATP efficiency, thermodynamic feasibility, and kinetic rates. CO2FIX is applied to eight different organisms, which has led to the identification of both species-specific and general CO2 fixation pathways that have promising features while requiring surprisingly few non-native reactions. Three of these pathways are described in detail.

    In all previous chapters GSMs of relatively well-understood microbes have been used to gain further insight into their metabolism and to functionally (re-)design them. For complex microbial systems, such as algae (chapter 7) and gut microbial communities (chapter 8), GSMs are similarly useful, but substantially more difficult to create and analyze. Algae are widely considered as potential centerpieces of a biobased economy. Chapter 7 reviews the current challenges in algal genome annotation, modeling and synthetic biology. The gut microbiota is an incredibly complex microbial system that is crucial to our well-being. Chapter 8 reviews the ongoing developments in the modeling of both single gut microbes and gut microbial communities, and discusses how these developments will enable the move from studying correlation to causation, and ultimately the rational steering of gut microbial activity.

    Chapter 9 discusses how the previous chapters contribute to the research goals of this thesis. In addition, it provides an extensive discussion on current GSM practices, the issues associated therewith, and how these issues can be tackled. In particular, the discussion focuses on issues related to: (i) The inability to distinguish between biological difference and GSM generation artifacts when using multiple GSMs, (ii) The lack of continuous GSM updates, (iii) The mismatch between what GSM predictions and experimental data represent, (iv) The need for standardization in GSM evaluation, and (v) The lack of experimental validation of GSM-driven strain design for metabolic engineering.

    Zieke bomen krijgen een jas aan (onderzoek van André van Lammeren en Fons van Kuik)
    Lammeren, Andre van - \ 2015
    arboriculture - street trees - chestnuts - aesculus - plant protection - plant pathogenic bacteria - pseudomonas - tree surgery - heat treatment - cultural control - educational resources
    Investment appraisal of technology innovations on dairy farm electricity consumption
    Upton, J. ; Murphy, M. ; Boer, I.J.M. de; Groot Koerkamp, P.W.G. ; Berentsen, P.B.M. ; Shalloo, L. - \ 2015
    Journal of Dairy Science 98 (2015)2. - ISSN 0022-0302 - p. 898 - 909.
    lactation curve - milk-yield - raw-milk - cows - pseudomonas - water
    The aim of this study was to conduct an investment appraisal for milk-cooling, water-heating, and milk-harvesting technologies on a range of farm sizes in 2 different electricity-pricing environments. This was achieved by using a model for electricity consumption on dairy farms. The model simulated the effect of 6 technology investment scenarios on the electricity consumption and electricity costs of the 3 largest electricity-consuming systems within the dairy farm (i.e., milk-cooling, water-heating, and milking machine systems). The technology investment scenarios were direct expansion milk-cooling, ice bank milk-cooling, milk precooling, solar water-heating, and variable speed drive vacuum pump-milking systems. A dairy farm profitability calculator was combined with the electricity consumption model to assess the effect of each investment scenario on the total discounted net income over a 10-yr period subsequent to the investment taking place. Included in the calculation were the initial investments, which were depreciated to zero over the 10-yr period. The return on additional investment for 5 investment scenarios compared with a base scenario was computed as the investment appraisal metric. The results of this study showed that the highest return on investment figures were realized by using a direct expansion milk-cooling system with precooling of milk to 15°C with water before milk entry to the storage tank, heating water with an electrical water-heating system, and using standard vacuum pump control on the milking system. Return on investment figures did not exceed the suggested hurdle rate of 10% for any of the ice bank scenarios, making the ice bank system reliant on a grant aid framework to reduce the initial capital investment and improve the return on investment
    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.
    Cultivation-Independent Screening Revealed Hot Spots of IncP-1, IncP-7 and IncP-9 Plasmid Occurrence in Different Environmental Habitats
    Dealtry, S. ; Ding, G.C. ; Weichelt, V. ; Dunon, V. ; Schluter, A. ; Martini, M.C. ; Papa, M.F. Del; Lagares, A. ; Amos, G.C.A. ; Wellington, E.M.H. ; Gaze, W.H. ; Sipkema, D. ; Sjoling, S. ; Springael, D. ; Heuer, H. ; Elsas, J.D. ; Thomas, C. ; Smalla, K. - \ 2014
    PLoS ONE 9 (2014)2. - ISSN 1932-6203
    resistance genes - naphthalene - pseudomonas - adaptation - prevalence - transposon - diversity - sediment - biobeds
    IncP-1, IncP-7 and IncP-9 plasmids often carry genes encoding enzymes involved in the degradation of man-made and natural contaminants, thus contributing to bacterial survival in polluted environments. However, the lack of suitable molecular tools often limits the detection of these plasmids in the environment. In this study, PCR followed by Southern blot hybridization detected the presence of plasmid-specific sequences in total community (TC-) DNA or fosmid DNA from samples originating from different environments and geographic regions. A novel primer system targeting IncP-9 plasmids was developed and applied along with established primers for IncP-1 and IncP-7. Screening TC- DNA from biopurification systems (BPS) which are used on farms for the purification of pesticide-contaminated water revealed high abundances of IncP-1 plasmids belonging to different subgroups as well as IncP-7 and IncP-9. The novel IncP-9 primer-system targeting the rep gene of nine IncP-9 subgroups allowed the detection of a high diversity of IncP-9 plasmid specific sequences in environments with different sources of pollution. Thus polluted sites are "hot spots'' of plasmids potentially carrying catabolic genes.
    Bacterieziekten in Prunus
    Dalfsen, Pieter van - \ 2013
    prunus - woody plants - bacterial diseases - detection - pseudomonas syringae pv. morsprunorum - xanthomonas - pseudomonas - monitoring - tests - cultural methods - phytosanitary measures
    Geïntegreerde beheersstrategie Pythium in bolgewassen
    Boer, M. de; Vreeburg, P.J.M. ; Breeuwsma, S.J. ; Bent, J. van der; Roelofs, P.F.M.M. - \ 2013
    Lisse : Praktijkonderzoek Plant en Omgeving BBF - 32
    pythium - plantenziekteverwekkende schimmels - gewasbescherming - bloembollen - wortelrot - bestrijdingsmethoden - fungiciden - pseudomonas - groenbemesters - veldproeven - modules - pythium - plant pathogenic fungi - plant protection - ornamental bulbs - root rots - control methods - fungicides - pseudomonas - green manures - field tests - modules
    Pythium is een grondgebonden schimmel die in diverse bolgewassen, maar vooral bij hyacint en krokus, veel schade veroorzaakt door wortelrot. Dit wortelrot leidt tot slechte groei van de bol en dus tot opbrengstderving. Er is momenteel één fungicide (Ridomil Gold) toegelaten om Pythium te bestrijden. Echter, de toepassing van dit fungicide resulteert niet altijd in een Pythium vrij gewas. Uit eerder onderzoek is bekend dat wortelrot in hyacint ook bestreden wordt door toepassing van een bacterie, Pseudomonas SS101, en door het onderwerken van een groenbemester zoals bladrammenas. Maar, net als bij Ridomil Gold, geldt ook voor deze maatregelen dat wanneer deze maatregel alleen wordt toegepast dit vaak niet resulteert in een betrouwbare en voldoende bestrijding. Daarom is in een meerdere jaren durend project onderzocht of het toepassen van (combinaties van) deze maatregelen gedurende een aantal jaren achter elkaar in verschillende samenstellingen wel effectief Pythium wortelrot kan bestrijden. De verwachting is dat op deze manier Pythium gedurende een aantal jaren met behulp van verschillende mechanismen wordt bestreden zodat de bestrijding veel effectiever is en langdurig.
    Minder lage RV biedt mogelijkheden tot energiebesparing: Bij Phalaenopsis is 75% RV laag genoeg om Pseudomonas te voorkomen
    Arkesteijn, M. ; Ludeking, D.J.W. - \ 2011
    Onder Glas 8 (2011)8. - p. 50 - 51.
    phalaenopsis - plantenplagen - pseudomonas - preventie - gewasbescherming - relatieve vochtigheid - energiebesparing - landbouwkundig onderzoek - glastuinbouw - groenten - potplanten - phalaenopsis - plant pests - pseudomonas - prevention - plant protection - relative humidity - energy saving - agricultural research - greenhouse horticulture - vegetables - pot plants
    Pseudomonas catteyea is al een oud probleem in de teelt van phalaenopsis. Bij een relatieve luchtvochtigheid van 90% kan de bacterie zich snel verspreiden door de kas. Uit recent onderzoek blijkt dat dit probleem minder optreedt bij een RV van 75% of lager. De RV verlagen tot 60% zoals nu gebeurt, hoeft dus niet. Dit biedt mogelijkheden tot energiebesparing.
    Detectie en beheersing van bacterierot veroorzaakt door Pseudomonas cattleyae in Phalaenopsis
    Ludeking, D.J.W. ; Hamelink, R. ; Kromwijk, J.A.M. ; Schenk, M.F. ; Vermunt, A. ; Woets, F. - \ 2011
    Bleiswijk : Wageningen UR Glastuinbouw (Rapporten GTB 1096) - 31
    phalaenopsis - bacterieziekten - infectie - pseudomonas - bladvlekkenziekte - black spot - moleculaire technieken - relatieve vochtigheid - waterzuivering - invloeden - phalaenopsis - bacterial diseases - infection - pseudomonas - leaf spotting - black spot - molecular techniques - relative humidity - water treatment - influences
    Phalaenopsis growers suffer from mayor losses up to 20% due to bacterial spot. This bacterial infection in caused by the Acidovorax avenae subsp. cattleyae. In practice this bacterial disease is also known as Pseudomonas. This bacterium is causing black leaf spots with a yellow border. Pseudomonas cattleyae is very contagious and is promoted by high temperatures en moist conditions. In this project Groen Agro Control laboratory (Delfgauw) has developed a molecular analysis method to detect Pseudomonas cattleyae in different matrices. The influence of the relative humidity on the development of Pseudomonas cattleyae is investigated during this research. The results show that a relative humidity of 90% strongly promotes infection of the bacteria. A relative humidity of 75% shows no extra dispersion of Pseudomonas cattleyae compared to a greenhouse compartment with a continuous relative humidity of 60%. This knowledge offers the opportunity to safe energy in the cultivation of Phalaenopsis. During this research the effects of water treatments on the dispersion of Pseudomonas cattleyae have been investigated. The results show that a treatment with hydrogen peroxide (20 ppm) offers the best reduction of dispersion. This treatment turns out to be better than the control and all other treatments. This research has led to new insights about the dispersal and optimal growing conditions of this bacteria, but leads to new questions. Questions, about other different dosages and the effects of other water treatments, but also about the optimal level to promote plant growth and reduce bacterial infections, have to be investigated in new research.
    Detection of Xanthomonas axonopodis pv. phaseoli in bean seeds by flow cytometry, immunostaining and direct viable counting
    Tebaldi, N.D. ; Peters, J. ; Chitarra, L.G. ; Souza, R.M. ; Zouwen, P.S. van der; Bergervoet, J.H.W. ; Wolf, J.M. van der - \ 2010
    Tropical Plant Pathology 35 (2010)4. - ISSN 1982-5676 - p. 213 - 222.
    carboxyfluorescein diacetate - monoclonal-antibodies - dairy-products - total bacteria - campestris - viability - identification - enumeration - pseudomonas - microscopy
    Flow cytometric analysis of immuno-stained cells (immuno-FCM) was compared to immunofluorescence microscopy (IF) and dilution plating on a semi-selective medium, for quantitative detection of Xanthomonas axonopodis pv. phaseoli (Xap) in bean seed extracts. Cell concentrations of Xap between 103-107 CFU/mL were added to healthy bean seed extracts. A flow cytometry sorting procedure was developed to separate immuno-stained Xap cells from crude seed extracts and confirming by PCR. FCM was evaluated for direct viable counting (DVC) of Xap using combinations of propidium iodide (PI) and carboxy fluorescein diacetate (cFDA) or PI and SYTO 9 and also the combination of immuno-FCM and PI. Dilution plating and IF allowed detection of Xap in bean seed extracts in a range of 103-106 CFU/mL and immuno-FCM from 104-106 CFU/mL. Sorted cells could be detected in crude seed extracts by PCR without further extraction. FCM also allowed quantification of viable cells of Xap after DVC procedures; the red fluorescent dye propidium iodide was used to identify dead cells in combination with the green fluorescent dyes cFDA or SYTO 9, these identifying live cells. The combination of immuno-FCM and PI could be more promising and reliable to detect this pathogen in seeds. Key words: seed pathology, flow sorting, PCR-amplification, viability probes, immunofluorescence, bacteria.
    Kasproef detectie en beheersing van Pseudomonas cattleyae in Phalaenopsis
    Kromwijk, J.A.M. ; Ludeking, D.J.W. ; Woets, F. ; Vermunt, A. ; Schenk, M.F. - \ 2010
    gewasbescherming - bacteriën - infecties - verspreide infecties - preventie - pseudomonas - phalaenopsis - glastuinbouw - plant protection - bacteria - infections - disseminated infections - prevention - pseudomonas - phalaenopsis - greenhouse horticulture
    Samenvatting van een kasproef getiteld "detectie en beheersing van Pseudomonas cattleyae in Phalaenopsis"
    Slijmstelen bij Zantedeschia
    Leeuwen, P.J. van; Pham, K.T.K. ; Dees, R.H.L. ; Doorn, J. van - \ 2009
    Lisse : PPO Bloembollen en Bomen (PPO Rapport 32 340357 00) - 49
    erwinia - pseudomonas - afwijkingen, planten - zantedeschia - vaasleven - houdbaarheid (kwaliteit) - landbouwkundig onderzoek - nederland - erwinia - pseudomonas - plant disorders - zantedeschia - vase life - keeping quality - agricultural research - netherlands
    Slijmstelen zijn bloemstengels van Zantedeschia die op de vaas vooral aan de onderkant verslijmen als gevolg van bacterieaantasting. Deze afwijking vormt een van de grootste problemen in de afzet van de bloemen. Hoewel vermoed werd dat Erwinia (carotovora subsp. carotovora) de veroorzaker is, blijken ook Pseudomonas-soorten die pectinasen (celwandafbrekende enzymen) produceren, slijmstelen te kunnen veroorzaken. Op grond van de DNA-sequentie van deze pectinase (pel-) genen zijn in PCR deze bacteriën te identificeren; het pel-gen blijkt noodzakelijk om slijmstelen te kunnen veroorzaken. Bij lokalisatie-experimenten bleek soms bij de oogst ook hoog in de steel veel bacteriën aanwezig te zijn; het trekken van de stelen lijkt geen knikstelen te kunnen veroorzaken. Injectie van stelen met Erwinia of Pseudomonas veroorzaakte slijmstelen. Ook kunnen bacteriën overleven op (veiling-) fust, rekjes en in water. Het is aannemelijk, dat er gezonde en zieke partijen stelen zijn; in sommige partijen zit al een percentage pseudomonaden, mogelijk latent. Als beheersingsmaatregelen kan dienen het afsnijden van de onderste 2-5 cm van de steel; dit levert significant minder slijmstelen op. Middelen zoals de chloorpil en Florissant werken goed mits er niet te hoge aantallen bacteriën in het vaaswater zitten; deze middelen kunnen echter niet via passieve diffusie hoog in de stelen komen. Er bleek geen goede correlatie tussen aantallen bacteriën in de bloemstelen enerzijds en het ontstaan van slijmstelen; niet alle bacteriën die hierin groeien geven namelijk slijmstelen. © Praktijkonderzoek
    Methoden voor residuafbraak op fruit
    Jong, P.F. de; Balkhoven-Baart, J.M.T. - \ 2009
    De Fruitteelt 99 (2009)37. - ISSN 0016-2302 - p. 10 - 11.
    fruitteelt - pruimen - onderstammen - pseudomonas - groot-brittannië - fruit growing - plums - rootstocks - great britain
    De ervaringen met de pruimonderstam VVA-1 zijn divers. Sommige percelen hebben te maken met veel uitval door Pseudomonas- al dan niet weg te schrijven aan de onderstam - aan andere percelen is geen zieke boom te ontdekken. Een reden voor de Productcommissie Steenfruit om eens een kijkje te nemen naar ervaringen in Groot-Brittanië
    Genotypische diversiteit en rhizosfeerkolonisatie van DAPG-producerende Pseudomonas spp.
    Bergsma-Vlami, M. - \ 2009
    Gewasbescherming 40 (2009)3. - ISSN 0166-6495 - p. 117 - 118.
    genotypische variatie - pseudomonas - soorten - antibiotica - biologische bestrijding - gewasbescherming - genetic variance - pseudomonas - species - antibiotics - biological control - plant protection
    Het antibioticum 2,4-diacetylphloroglucinol (DAPG) speelt een belangrijke rol in biologische bestrijding van verschillende plantenpathogenen door fluorescerende Pseudomonas-soorten. DAPG-producerende Pseudomonas-stammen zijn effectief in biologische bestrijding, maar hun saprofytisch vermogen is vaak variabel met als gevolg dat ook de mate van ziekteonderdrukking niet altijd consistent is
    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.
    Tijdbom pseudomonas nog niet onklaar gemaakt
    Kruistum, G. van; Overbeek, L.S. van - \ 2008
    Groenten & Fruit 18 (2008)4. - ISSN 0925-9708 - p. 48 - 49.
    tuinbouw - allium porrum - preien - pseudomonas - bacterieziekten - gewasverliezen - plantenziektebestrijding - onderzoek - plantenziekteverwekkende bacteriën - horticulture - leeks - bacterial diseases - crop losses - plant disease control - research - plant pathogenic bacteria
    Vooral in Limburg en Noord-Brabant zijn de productieverliezen door Pseudomonas in prei groot. De bacterie blijkt latent aanwezig te zijn op meer dan 60 procent van de bemonsterde percelen voor de opkweek en teelt van prei
    Screening of bacterial isolates from various European soils for in vitro antagonistic activity towards Rhizoctonia solani and Fusarium oxysporum: Site-dependent composition and diversity revealed
    Adesina, M.F. ; Lembke, A. ; Costa, R. ; Speksnijder, A.G.C.L. ; Smalla, K. - \ 2007
    Soil Biology and Biochemistry 39 (2007)11. - ISSN 0038-0717 - p. 2818 - 2828.
    microbial community structure - biological-control - suppressive soils - plant-pathogens - pseudomonas - wilt - microorganisms - rhizosphere - mechanisms - diseases
    A cultivation-based approach was used to determine the in vitro antagonistic potential of soil bacteria towards Rhizoctonia solani AG3 and Fusarium oxysporum f. sp. lini (Foln3). Four composite soil samples were collected from four agricultural sites with previous documentation of disease suppression, located in France (FR), the Netherlands (NL), Sweden (SE) and the United Kingdom (UK). Similarly, two sites from Germany (Berlin, G-BR; and Braunschweig, G-BS) without documentation of disease suppression were sampled. Total bacterial counts were determined by plating serial dilutions from the composite soil samples onto R2A, AGS and King's B media. A total of 1,788 isolates (approximately 100 isolates per medium and site) was screened for antifungal activity, and in vitro antagonists (327 isolates) were found amongst the dominant culturable bacteria isolated from all six soils. The overall proportion of antagonists and the number of isolates with inhibitory activity against F. oxysporum were highest in three of the suppressive soils (FR, NL and SE). Characterization of antagonistic bacteria revealed a high phenotypic and genotypic diversity. Siderophore and protease activity were the most prominent phenotypic traits amongst the antagonists. The composition and diversity of antagonists in each soil was site-specific. Nevertheless, none of the antimicrobial traits of bacteria potentially contributing to soil suppressiveness analyzed in this study could be regarded as specific to a given site.
    Onderdrukking van ziekten en plagen in prei
    Overbeek, L.S. van; Kruistum, G. van; Visser, J.H.M. - \ 2007
    pseudomonas - preien - allium porrum - plantenziekteverwekkende bacteriën - gewasbescherming - vollegrondsteelt - pseudomonas - leeks - allium porrum - plant pathogenic bacteria - plant protection - outdoor cropping
    Onderzoek naar het onderdrukken van Pseudomonas (bacterievlekkenziekte) in prei
    Interactions between biosurfactant-producing Pseudomonas and Phytophthora species
    Tran, H. - \ 2007
    Wageningen University. Promotor(en): Pierre de Wit, co-promotor(en): Jos Raaijmakers. - [S.l.] : S.n. - ISBN 9789085047445 - 136
    plantenziekteverwekkende schimmels - phytophthora - biologische bestrijding - pseudomonas - oppervlaktespanningsverlagende stoffen - gastheer parasiet relaties - oömycota - plant pathogenic fungi - phytophthora - biological control - pseudomonas - surfactants - host parasite relationships - oomycota
    Fluorescent Pseudomonas bacteria produce a wide variety of antimicrobial metabolites, including soap-like compounds referred to as biosurfactants. The results of this thesis showed that biosurfactant-producing Pseudomonas bacteria are effective in controlling Phytophthora foot rot disease of black pepper in Vietnam and promote root and shoot development of the ‘King of Spices’. Biosurfactant-producing P. fluorescens strain SS101 was also effective in controlling tomato late blight caused by Phytophthora infestans. Current and future studies focus on how to implement these biocontrol agents in an integrated management practice to control Phytophthora diseases. The broad-spectrum activity of these antagonistic Pseudomonas bacteria and their biosurfactants also provide new opportunities to apply these agents for the protection and growth promotion of other crops.
    Effect van tussengewassen, Ridomil Gold en Pseudomonaden op Pythium beheersing in crocus en hyacint
    Bijman, V.P. ; Breeuwsma, S.J. ; Boer, M. de; Koster, A.T.J. ; Bent, J. van der - \ 2005
    Gewasbescherming 36 (2005)1. - ISSN 0166-6495 - p. 21 - 23.
    tussengewassen (intercrops) - pseudomonas - fungiciden - crocus - hyacinthus - intercrops - pseudomonas - fungicides - crocus - hyacinthus
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