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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Long-term effects of eight soil health treatments to control plant-parasitic nematodes and Verticillium dahliae in agro-ecosystems
Korthals, G.W. ; Thoden, T.C. ; Berg, W. van den; Visser, J.H.M. - \ 2014
Applied Soil Ecology 76 (2014). - ISSN 0929-1393 - p. 112 - 123.
root-knot nematode - pratylenchus-penetrans - meloidogyne-hapla - tagetes-patula - nitrogen mineralization - biological-control - damping-off - cover crops - pyrrolizidine alkaloids - glucosinolate-profiles
There is an urgent need to test and develop sustainable methods for management of soil pathogens, such as the root-lesion nematode Pratylenchus penetrans and the soil fungus Verticillium dahliae. Ultimately this should be investigated with a multidisciplinary approach, with long-term measurements of biological and chemical parameters and their final impact on crop yield under field conditions. The present study focusses on eight soil health treatments (compost, chitin, marigold, grass–clover, biofumigation, anearobic soil disinfestation, a physical control method and a combination of marigold, compost and chitin) and two control treatments (a chemical control with 300 L/ha Metam sodium and un untreated control). These 10 treatments were studied for their effects on soil chemical quality, soil pathogens and their impact on the yield of potato, lily and carrots during 6 years. The present study did demonstrate that in comparison to chemical control, additions of chitin, anaerobic soil disinfestation and marigold are already excellent alternatives for the control of plant-parasitic nematodes and V. dahliae. We also demonstrated that grass–clover, biofumigation, Cultivit and compost are not effective alternatives for chemical control yet and further development is needed. All treatments caused a yield increase in comparison with the control. The biggest increases of more than 60% were found for the treatments with chitin. Furthermore it was demonstrated that these yield increases were probably less influenced by changes in chemical soil properties, but the consequence of changes in the soil biota, in this case especially the effective control of P. penetrans and V. dahliae. Furthermore it has been demonstrated that most of these soil health treatments could already be implemented in an arable crop rotation and probably adapted for many areas of the world where other alternatives, such as solarisation or soil flooding, are not feasible or too risky.
Calonectria diseases on ornamental plants in Europe and the Mediterranean Basion: an overview
Vitale, A. ; Crous, P.W. ; Lombard, L. ; Polizzi, G. - \ 2013
Journal of plant pathology - Formerly Rivista di patologia vegetale 95 (2013)3. - ISSN 1125-4653 - p. 463 - 476.
cylindrocladium-crotalariae microsclerotia - forest tree nurseries - 1st report - root-rot - leaf-spot - crown rot - feijoa-sellowiana - soil-temperature - mastic tree - damping-off
Species of Calonectria and their cylindrocladium-like asexual morphs are important plant pathogens of agronomic and forestry crops, especially in the tropical and subtropical regions of the world. Calonectria species have been associated with a wide range of disease symptoms on a large number of plant hosts. On horticultural crops, most records of Calonectria species come from the Northern Hemisphere, where they occur mainly in gardens and ornamental nurseries. In Europe and the Mediterranean basin, several species are widespread in nurseries and cause extensive damage to ornamental plants. In the past, identification of species was based on phenotypic characters and sexual compatibility using standardised media. More recently, morphological characteristics, phylogenetic studies (DNA sequence data of the ß-tubulin, histone H3 and translation elongation factor-1a gene regions) and mating studies have revealed the presence of several cryptic species complexes that were formerly treated as single Calonectria species. These studies resulted in the introduction of several new species. Other studies aimed at understanding environmental sustainability focused attention on soil solarisation and biological control as means for controlling these pathogens. The potential use of biological control agents (BCAs) and chemicals for controlling Calonectria-induced diseases has recently been addressed. In this review we discuss the Calonectria species detected in Europe and the Mediterranean basin, and the disease management strategies. In view of the mandatory implementation of integrated pest management (IPM) for all European countries by 2014, this paper provides basic information as a platform for the adaptation of more sustainable integrated measures to control Calonectria diseases in European nurseries.
Efficacy of four phosphate-mobilizing bacteria applied with an animal bone charcoal formulation in controlling Pythium aphanidermatum and Fusarium oxysporum f.sp. radicis lycopersici in tomato
Postma, J. ; Clematis, F. ; Nijhuis, E.H. ; Someus, E. - \ 2013
Biological Control 67 (2013)2. - ISSN 1049-9644 - p. 284 - 291.
pseudomonas-chlororaphis pa23 - rock phosphate - growth promotion - nutrient-uptake - damping-off - soil - phosphorus - biocontrol - diversity - suppressiveness
Four taxonomically different bacteria, with the ability to mobilize phosphate (P) and to colonize animal bone charcoal (ABC), were tested for their capacity to control plant pathogens. Tests were performed in the greenhouse with young tomato plants in (potting) soil and in rockwool. Plants were infested with Pythium aphanidermatum and Fusarium oxysporum f.sp. radicis-lycopersici (FORL) causing respectively damping off and crown and root rot. ABC is a porous, phosphorous containing waste product from the food industry, and was used as carrier to introduce the bacteria into the growing media. Scanning electron microscopy (SEM) pictures showed the intensive colonization of the bacteria in the interior of ABC. Of the four tested strains, Pseudomonas chlororaphis 4.4.1 was most effective in controlling the diseases. It controlled P. aphanidermatum and FORL in tomato in each of the tests. The strain appeared to be a very good root colonizer, since 1–8% of the cultural bacterial population on the tomato roots or in rhizosphere soil consisted of the introduced strain. Population densities of P. chlororaphis 4.4.1 were 0.5–5 × 107 CFU g-1 root or rhizosphere soil. Peanibacillus polymyxa 12.4.1 and Streptomyces pseudovenezuelae 13.4.2 significantly controlled P. aphanidermatum in two tests in potting soil, whereas Bacillus pumilus 4.4.2 was not effective. FORL could be controlled by B. pumilus 4.4.2 and S. pseudovenezuelae 13.4.2 in only part of the tests, whereas P. polymyxa 12.4.1 was not effective. ABC is a novel carrier for delivery of biocontrol bacteria into soil or substrate and combines biocontrol with recycling a phosphorous-rich waste product
Seed and leaf treatments with natural compounds to induce resistance against Peronospora parasitica in Brassica oleracea
Wolf, J.M. van der; Michta, A. ; Zouwen, P.S. van der; Boer, W.J. de; Davelaar, E. ; Stevens, L.H. - \ 2012
Crop Protection 35 (2012). - ISSN 0261-2194 - p. 78 - 84.
systemic acquired-resistance - induced disease resistance - defense responses - fusarium-wilt - downy mildew - damping-off - plants - protection - cucumber - growth
Seed and leaf treatments with natural compounds having a low risk profile (LRP) were evaluated for their potential to induce resistance in cabbage plants (Brassica oleracea) against Peronospora parasitica, causal organism of downy mildew. The selection of 34 LRP compounds comprised micronutrients, organic compounds such as proline, riboflavin, oligogalacturonides, aminolignosulfonates, bacterial lipopolysaccharides, and bacterial and fungal extracts. Treatments with the synthetic chemical inducers 2,6-dichloroisonicotinic acid (INA), d,l-ß-aminobutyric acid, salicylic acid, benzothiadiazole and the fungicide Previcur™ were included as controls. After seed treatment a maximum reduction of 27% diseased leaf area was found with an extract of a Lysobacter strain, compared to a reduction of 99% for INA, the most effective synthetic inducer. Seed treatments with extracts of Pectobacterium carotovorum subsp. carotovorum, Bacillus macerans, Pseudomonas syringae, Streptomyces and Xanthomonas campestris strains also reduced downy mildew infection significantly. After leaf treatment, a maximum reduction of 85% was again found with the Lysobacter extract, compared to a reduction of 99% for INA, the most effective synthetic inducer. Leaf treatments with CuSO4 (=1 mM), MnCl2 (=10 mM), K2HPO4 (100 mM), and extracts of P. syringae, P. carotovorum subsp. carotovorum, Streptomyces, X. campestris and B. macerans strains also reduced the diseased leaf area, but CuSO4 was highly phytotoxic. For seed and leaf treatments with Lysobacter extract, proline, MnCl2 and INA the effect on the induction of chitinase and glucanase activity was tested, using two pathogenesis-related proteins as markers for induced resistance. For seed treatments only INA and for leaf treatments INA, proline and MnCl2 treatments resulted in increased activity of both enzymes. The rate of enzyme activity induced by INA was dependent on the time seeds were exposed to the compound. Highlights ¿ Seed treatments with isonicotinic acid protects Brassica seedlings from Peronospora infections. ¿ Treatments of seedlings with extracts of Lysobacter protects against Peronospora infections. ¿ Effect of seed treatments is dependent on the time of incubation with the elicitor
Daily changes of infections by Pythium ultimum after a nutrient impulse in organic versus conventional soils
He, M. ; Ma, W. ; Tian, G. ; Blok, W.J. ; Khodzaeva, A. ; Zelenev, V.V. ; Semenov, A.M. ; Bruggen, A.H.C. van - \ 2010
Phytopathology 100 (2010)6. - ISSN 0031-949X - p. 593 - 600.
damping-off - bacterial-populations - root-rot - pseudomonas-fluorescens - biological indicators - microbial communities - disease suppression - plant-pathogens - wheat roots - compost
Bacterial populations (CFU) have been shown to oscillate in wavelike patterns after nutrient impulses in previous studies. The amplitudes and periods of oscillations could possibly be used as indicators of soil health analogous to the stability and resilience of biological populations widely accepted as indicators for ecosystem health. Limited plant and animal disease outbreaks can also be viewed as a manifestation of a healthy soil ecosystem. Two pot experiments were carried out to verify whether damping-off of beet seedlings by Pythium ultimum, measured as area under the disease progress curve (AUDPC), fluctuated over time after incorporation of organic materials into organic versus conventional soils, and to investigate whether daily dynamics of AUDPCs were linked to the dynamics of microbial populations and chemical parameters. AUDPCs oscillated significantly over time when Pythium bioassays were initiated daily after addition of ground grass and clover shoots (GC) into unplanted soils. Similar oscillations with significant harmonics of AUDPC were also observed in composted manure (CM)-amended soils but with smaller amplitudes than in GC-amended soils. The AUDPC harmonics in amended soils had periods similar to those of CFU of copiotrophic bacteria. Cross-correlation analysis demonstrated that periodic fluctuations of P. ultimum infections (AUDPCs) did not coincide with those of copiotrophic CFU but were shifted in phase. It appears that competition or antagonism from some fast-growing bacteria influenced pathogen infections, because these bacterial populations were growing and dying. Soil chemical variables, including pH, dissolved organic carbon, and NO(3)(-)-N, and NH(4)(+)-N contents, changed significantly in the initial 7 days after a nutrient impulse into soils. These changes were cross-correlated with copiotrophic CFU with time lags of approximately 1 to 2 days but were seldom associated with daily changes in AUDPCs. Organically managed soils always had lower AUDPC ratios of amended to nonamended treatments, indicating that organic materials showed stronger suppressive abilities to P. ultimum in organic than in conventional soils. The oscillations in AUDPCs and copiotrophic CFU in amended organic soil also had smaller amplitudes than in amended conventional soil. These results suggested that organically managed soils had a greater resistance and resilience to the disturbance of the amendments and, therefore, could be considered healthier than conventionally managed soils
Selection of phosphorus solubilizing bacteria with biocontrol potential for growth in phosphorus rich animal bone charcoal
Postma, J. ; Nijhuis, E.H. ; Sommeus, E. - \ 2010
Applied Soil Ecology 46 (2010)3. - ISSN 0929-1393 - p. 464 - 469.
pythium-aphanidermatum - rhizoctonia-solani - damping-off - plant - root - soil - management - suppressiveness - microorganisms - formulations
Bacteria with the ability to solubilize phosphorus (P) and to improve plant health were selected and tested for growth and survival in P-rich animal bone charcoal (ABC). ABC is suggested to be suitable as a carrier for biocontrol agents, offering them a protected niche as well as delivering phosphate to plants, meanwhile re-using P from waste of the food chain. Ninety-seven bacterial isolates from different soils were tested for their potential to dissolve P from ABC. Of these isolates, 60% showed positive scores; they belonged to the genera Arthrobacter, Bacillus, Burkholderia, Collimonas, Paenibacillus, Pseudomonas, Serratia, and Streptomyces. Twelve isolates from different taxonomic groups were selected for further research on growth ability and survival in ABC, and on their potential to control plant pathogens. The highest concentrations of P were dissolved by Pseudomonas chlororaphis and Bacillus pumilus, followed by Paenibacillus polymyxa, Burkholderia pyrrocinia and three Streptomyces isolates. P. chlororaphis and P. polymyxa showed strongest growth inhibition of plant pathogenic Pythium and Fusarium sp., followed by the Streptomyces spp. isolates. Research highlights Describes a stepwise selection procedure with the aim to find beneficial bacteria that can grow in animal bone charcoal (ABC). This research was part of an EU project, with the aim to recycle and upgrade waste from the food chain. The results show that several interesting beneficial bacteria could proliferate and survive in this ABC carrier. Keywords: Biological control; Phosphorus mobilization; Antagonistic bacteria; Animal bone charcoal; Pythium aphanidermatum; Fusarium oxysporum f.sp. radicis lycopersici
Effect of compost particle size on suppression of plant diseases
Lozano, J. ; Blok, W.J. ; Termorshuizen, A.J. - \ 2009
Environmental Engineering Science 26 (2009)3. - ISSN 1092-8758 - p. 601 - 607.
pythium-ultimum - damping-off - soil - mineralization - temperature - turfgrass - pathogens - biowaste - carbon - crops
Predictability of compost-induced suppression of soil-borne plant diseases is poor. Part of the variability in disease suppression could be due to the heterogeneity of a given compost. Therefore, the disease suppressive properties of different wet-sieved fractions of two composts against three soil-borne plant pathogens were studied. The ability of a green waste and a yard waste compost to suppress the soil-borne plant pathogens Fusarium oxysporum f.sp. lini (host: flax), Phytophthora cinnamomi (host: lupin), and Meloidogyne hapla (host: tomato) was determined. The following compost fractions were prepared: 2¿4 mm (40% v/v with peat-based substrate), 1¿2 mm (35 or 45% v/v; comparable number of particles and comparable organic matter content as the 2¿4 mm fraction amendment respectively), and 1¿2 mm (35% v/v) obtained from the 2¿4 mm fraction by a series of dry-sieving, crushing, and wet-sieving. The 2¿4 mm compost fraction of both composts showed significantly higher disease suppression for the three pathosystems, except for P. cinnamomi with one compost, in which there was no effect. For both composts, oxygen uptake rate showed a significant positive correlation with disease suppression of all pathogens except for P. cinnamomi. For the composts studied, substrate quality as expressed by oxygen uptake rate, seems to be of greater importance for disease suppression than compost particle size per se.
Genome-based discovery, structure prediction and functional analysis of cyclic lipopeptide antibiotics in Pseudomonas species
Bruijn, I. de; Kock, M.J.D. de; Meng, Y. ; Waard, P. de; Beek, T.A. van; Raaijmakers, J.M. - \ 2007
Molecular Microbiology 63 (2007)2. - ISSN 0950-382X - p. 417 - 428.
nonribosomal peptide synthetases - streptomyces-coelicolor genome - biofilm formation - fluorescent pseudomonads - adenylation domains - biological-control - damping-off - biosynthesis - syringae - strain
Analysis of microbial genome sequences have revealed numerous genes involved in antibiotic biosynthesis. In Pseudomonads, several gene clusters encoding non-ribosomal peptide synthetases (NRPSs) were predicted to be involved in the synthesis of cyclic lipopeptide (CLP) antibiotics. Most of these predictions, however, are untested and the association between genome sequence and biological function of the predicted metabolite is lacking. Here we report the genome-based identification of previously unknown CLP gene clusters in plant pathogenic Pseudomonas syringae strains B728a and DC3000 and in plant beneficial Pseudomonas fluorescens Pf0-1 and SBW25. For P. fluorescens SBW25, a model strain in studying bacterial evolution and adaptation, the structure of the CLP with a predicted 9-amino acid peptide moiety was confirmed by chemical analyses. Mutagenesis confirmed that the three identified NRPS genes are essential for CLP synthesis in strain SBW25. CLP production was shown to play a key role in motility, biofilm formation and in activity of SBW25 against zoospores of Phytophthora infestans. This is the first time that an antimicrobial metabolite is identified from strain SBW25. The results indicate that genome mining may enable the discovery of unknown gene clusters and traits that are highly relevant in the lifestyle of plant beneficial and plant pathogenic bacteria
Effect of agricultural management regime on Burkholderia community structure in soil
Salles, J.F. ; Elsas, J.D. van; Veen, J.A. van - \ 2006
Microbial Ecology 52 (2006)2. - ISSN 0095-3628 - p. 267 - 279.
plant-associated bacterium - land-use history - rhizoctonia-solani - biological-control - sp-nov. - cepacia complex - microbial communities - damping-off - diversity - identification
The main objective of this study was to determine the Burkholderia community structure associated with areas under different agricultural management and to evaluate to which extent this community structure is affected by changes in agricultural management. Two fields with distinct soil history (arable land and permanent grassland) were exposed to three agricultural management regimes (crop rotation, maize monoculture, and grassland). By using a culture-independent approach, based on a Burkholderia-specific polymerase chain reaction¿denaturing gradient gel electrophoresis system, it was possible to observe the conversion of Burkholderia communities typical for permanent grassland to those of arable land after four consecutive years. However, the time needed to achieve the reverse transition, i.e., converting the Burkholderia community associated with arable land to that of grassland, was beyond the duration of the field experiment. In addition, by applying principal response curves, the direction and extent of the conversion from grassland to arable land (maize monoculture and to crop rotation) were determined. Hence, the results suggested that agricultural practices, such as fertilization and tillage, were more effective in changing the Burkholderia community structure than agricultural management regime. To determine the effect of agricultural management on the Burkholderia population with biocontrol abilities, the culturable fraction of the Burkholderia community was assessed. The areas under permanent grassland and grassland converted to maize monoculture had the highest percentages of Burkholderia strains with antagonistic activity against Rhizoctonia solani AG-3, mainly Burkholderia pyrrocinia and Burkholderia sp. LMG 22929. The isolation frequency of antagonistic isolates from arable land was extremely low. Our results indicate that (changes in) agricultural management, mainly crop rotation, affect the frequency of isolation of antagonistic Burkholderia strains and that grassland represents a reservoir of Burkholderia species with great potential for agricultural applications
Suppressiveness of 18 composts against 7 pathosystems: Variability in pathogen response
Termorshuizen, A.J. ; Rijn, E. van; Gaag, D.J. van der; Alabouvette, C. ; Chen, Y. ; Lagerlöf, J. ; Malandrakis, A.A. ; Paplomatas, E.J. ; Rämert, B. ; Ryckeboer, J. ; Steinberg, C. ; Zmora-Nahum, S. - \ 2006
Soil Biology and Biochemistry 38 (2006)8. - ISSN 0038-0717 - p. 2461 - 2477.
soil microbial communities - soilborne plant-pathogens - rhizoctonia-solani - damping-off - phytophthora-cinnamomi - organic amendments - container media - pythium-ultimum - potting mixes - waste
Compost is often reported as a substrate that is able to suppress soilborne plant pathogens, but suppression varies according to the type of compost and pathosystem. Reports often deal with a single pathogen while in reality crops are attacked by multiple plant pathogens. The goal of the present study was to evaluate the disease suppression ability of a wide range of composts for a range of plant pathogens. This study was conducted by a consortium of researchers from several European countries. Composts originated from different countries and source materials including green and yard waste, straw, bark, biowaste and municipal sewage. Suppressiveness of compost-amended (20% vol./vol.) peat-based potting soil was determined against Verticillium dahliae on eggplant, Rhizoctonia solani on cauliflower, Phytophthora nicotianae on tomato, Phytophthora cinnamomi on lupin and Cylindrocladium spathiphylli on Spathiphyllum sp., and of compost-amended loamy soil (20% vol./vol.) against R. solani on Pinus sylvestris and Fusarium oxysporum f. sp. lini on flax. From the 120 bioassays involving 18 composts and 7 pathosystems, significant disease suppression was found in 54% of the cases while only 3% of the cases showed significant disease enhancement. Pathogens were affected differently by the composts. In general, prediction of disease suppression was better when parameters derived from the compost mixes were used rather than those derived from the pure composts. Regression analyses of disease suppression of the individual pathogens with parameters of compost-amended peat-based mixes revealed the following groupings: (1) competition-sensitive: F. oxysporum and R. solani/cauliflower; (2) rhizosphere-affected: V. dahliae; (3) pH-related: P. nicotianae; and (4) specific/unknown: R. solani/pine, P. cinnamomi and C. spathiphylli. It was concluded that application of compost has in general a positive or no effect on disease suppression, and only rarely a disease stimulating effect.
Relation between soil health, wave-like fluctuations in microbial populations, and soil-borne plant disease management
Bruggen, A.H.C. van; Semenov, A.M. ; Diepeningen, A.D. van; Vos, O.J. de; Blok, W.J. - \ 2006
European Journal of Plant Pathology 115 (2006)1. - ISSN 0929-1873 - p. 105 - 122.
combining biocontrol agents - organic farming systems - biological-control - bacterial-populations - damping-off - root-rot - species composition - conventional farms - mycorrhizal fungi - wheat roots
A healthy soil is often defined as a stable soil system with high levels of biological diversity and activity, internal nutrient cycling, and resilience to disturbance. This implies that microbial fluctuations after a disturbance would dampen more quickly in a healthy than in a chronically damaged and biologically impoverished soil. Soil could be disturbed by various processes, for example addition of a nutrient source, tillage, or drying-rewetting. As a result of any disturbance, the numbers of heterotrophic bacteria and of individual species start to oscillate, both in time and space. The oscillations appear as moving waves along the path of a moving nutrient source such as a root tip. The phase and period for different trophic groups and species of bacteria may be shifted indicating that succession occurs. DGGE, Biolog and FAME analysis of subsequent populations in oscillation have confirmed that there is a cyclic succession in microbial communities. Microbial diversity oscillates in opposite direction from oscillations in microbial populations. In a healthy soil, the amplitudes of these oscillations will be small, but the background levels of microbial diversity and activity are high, so that soil-borne diseases will face more competitors and antagonists. However, soil-borne pathogens and antagonists alike will fluctuate in time and space as a result of growing plant roots and other disturbances, and the periods and phases of the oscillations may vary. As a consequence, biological control by members of a single trophic group or species may never be complete, as pathogens will encounter varying populations of the biocontrol agent on the root surface. A mixture of different trophic groups may provide more complete biological control because peaks of different trophic groups occur at subsequent locations along a root. Alternatively, regular addition of soil organic matter may increase background levels of microbial activity, increase nutrient cycling, lower the concentrations of easily available nutrient sources, increase microbial diversity, and enhance natural disease suppression.
Conduciveness of different soilless growing media to Pythium root and crown rot of cucumber under near-commercial conditions
Gaag, D.J. van der; Wever, G. - \ 2005
European Journal of Plant Pathology 112 (2005)1. - ISSN 0929-1873 - p. 31 - 41.
fluorescent pseudomonads - biological-control - damping-off
Substrates made from rockwool, coir dust, pumice and perlite were compared for conduciveness to Pythium root and crown rot in cucumber under near-commercial conditions. Rockwool slabs of 7 cm height were more conducive to the Pythium disease than coir dust slabs, pumice or perlite under these conditions. Temperature, oxygen concentration and water content were determined in the substrates to explain differences in conduciveness between the inorganic substrates rockwool, pumice and perlite by differences in the physical conditions. Temperature and oxygen concentration could not explain the differences but the higher disease level on rockwool was associated with a much higher water content of this substrate as compared to coir dust, pumice and perlite. Increasing the height of the substrate from 7 to 14 cm greatly decreased the percentage of diseased plants due to the Pythium disease on rockwool but had no effect on the level of disease on perlite when the substrate had been infested 4 cm below the planting hole. This difference in response in substrate height between rockwool and perlite could be explained by a much larger decrease in water content with substrate height in the rockwool than in the perlite substrate. Temperature in the substrates were above 30 ° C for more than 6 h on sunny days in June and reached maximum values of 35 ° C or more. These temperatures are highly favourable for the pathogen P. aphanidermatum but will have adverse effects on most biocontrol strains.
Production of antifungal compounds by Lysobacter enzymogenes isolate 3.1.T8 under different conditions in relation to its efficacy as a biocontrol agent of Pythium aphanidermatum in cucumber
Folman, L.B. ; Klein, M.J.E.I.M. de; Postma, J. ; Veen, J.A. van - \ 2004
Biological Control 31 (2004)2. - ISSN 1049-9644 - p. 145 - 154.
burkholderia-cepacia ammdr1 - mediated gene-regulation - biological-control - pseudomonas-fluorescens - damping-off - root-rot - oomycete pathogens - plant-pathogens - in-vitro - bacteria
Lysobacter enzymogenes strain 3.1T8 is a potential biocontrol agent of Pythium aphanidermatum (Edson) Fitzp. in cucumber (Cucumis sativa L.). It showed in vitro antagonistic activity, hemolytic activity, and the production of a surface active compound, which decreased in media of increasing strength. One or more low molecular compounds, present in culture filtrates of 3.1T8, caused rapid immobilization of zoospores of P. aphanidermatum and inhibited cyst germination. Bioassays for suppression of root and crown rot were performed with 2-week-old cucumber plants in nutrient solution. Complete disease suppression occurred after addition of a suspension of unwashed cells grown on nutrient-poor R2A, or the filtrate of this suspension, 1 day before inoculation with zoospores. Application of washed cells caused slight suppression in one of two bioassays only. No disease suppression occurred when bacterial inoculum grown on 1/10 TSBA or in 1/10 TSB was used. In two bioassays on cucumber plants grown for 4¿5 weeks in 18-L containers, application of R2A-grown cells of 3.1T8 did not cause disease suppression. Density of 3.1T8, monitored using immunofluorescence colony staining, decreased at least 100-fold during these experiments to approximately log 3¿4 cfu ml¿1 of nutrient solution and log 5¿6 cfu g¿1 roots. Overall, the findings indicated a strong influence of nutritional resources on production of antifungal compounds by strain 3.1T8. The lack of disease suppression in hydroculture containers suggested that in situ production of the compounds was insufficient or absent, although the bacteria persisted in the nutrient solution and on the roots of cucumber
Microbial community responses to disease management soil treatments used in flower bulb cultivation
Kowalchuk, G.A. ; Os, G.J. van; Aartrijk, J. van; Veen, J.A. van - \ 2003
Biology and Fertility of Soils 37 (2003)1. - ISSN 0178-2762 - p. 55 - 63.
gradient gel-electrophoresis - 16s ribosomal-rna - pythium root-rot - ammonia-oxidizing bacteria - dna fragments - fungal communities - damping-off - class proteobacteria - beta-subdivision - 18s rdna
A number of management practices, such as soil fumigation and flooding, have been employed in efforts to control diseases and weeds in the cultivation of ornamental flower bulbs. However, such treatments may affect the suppression of Pythium root rot, a serious problem in ornamental bulb culture. To gain insight into the nature of Pythium suppression in such soils, we sought to describe the changes that these soil treatments induce in the microbial community in order to determine if particular microbial components of the system could be associated with suppression. Four polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) strategies, two targeting bacteria and two targeting fungi, were used to compare the soil-borne microbial communities of untreated, fumigated, flooded and sterilized, compost-amended soils; the dominant community members were tentatively identified by sequencing of DGGE bands. For all profiling strategies, the compost treatment of sterilized soil appeared to have the most profound effect on the dominant microbial populations in the soil. In general, different primer sets that targeted the same microbial groups, bacteria or fungi, appeared to detect the same microbial taxa, although certain sequence types were detected in only a single profiling strategy. DNA-based microbial community profiles alone were poor predictors of Pythium suppression, as the dominant microbial populations remained mostly intact, even after rigorous soil treatments such as fumigation and flooding. The restoration of suppressive activity against Pythium in compost-amended soil was associated with a different microbial community than observed in untreated, suppressive soils. Thus, although previous studies have shown the suppression of Pythium to be mediated by biological agents, effects of different microbial communities can lead to this suppression.
Characterisation of Lysobacter enzymogenes (Christensen and Cook 1978) strain 3.1T8, a powerful antagonist of fungal diseases of cucumber
Folman, L.B. ; Postma, J. ; Veen, J.A. van - \ 2003
Microbiological Research 158 (2003)2. - ISSN 0944-5013 - p. 107 - 115.
pythium root-rot - pseudomonas-fluorescens dr54 - biological-control - damping-off - bacterial communities - antifungal properties - ribosomal-rna - aphanidermatum - biocontrol - ultimum
Isolate 3.1T8 of Lysobacter enzymogenes (Christensen and Cook 1978), originating from the rhizosphere of cucumber and shown to have the potential to control Pythium aphanidermatum, is described. The strain produces extracellular proteases and lipases and shows high levels of resistance against streptomycin, kanamycin and tetracycline, but not to chloramphenicol. It shows strong in vitro antibiosis against P. aphanidermatum and several other phytopathogenic fungi. In order to identify the isolate, a carbon substrate oxidation profile (Biolog) was generated, and fatty acid methyl ester (FAME) analysis was performed. Also, the 16S rRNA gene was cloned and sequenced. With Biolog and FAME analysis, no assignment to species level was possible, because the species was not in the respective databases. BLAST analysis of the obtained sequence, followed by phylogenetic analysis, using a number of related and unrelated sequences, showed that the isolate was most closely related to Lysobacter enzymogenes (Christensen and Cook 1978).
Inability to Find Consistent Bacterial Biocontrol Agents of Pythium aphanidermatum in Cucumber Using Screens Based on Ecophysiological Traits
Folman, L.B. ; Postma, J. ; Veen, J.A. van - \ 2003
Microbial Ecology 45 (2003)1. - ISSN 0095-3628 - p. 72 - 87.
growth-promoting rhizobacteria - burkholderia-cepacia ammdr1 - biological-control - root-rot - enterobacter-cloacae - oomycete pathogens - induced resistance - damping-off - pseudomonas - soil
A collection of 821 rhizobacteria from cucumber, originating from different root locations and stages of plant development, was screened for potential biocontrol agents of Pythium aphanidermatum (Edson) Fitzp. The screening procedure exploited carbon source utilization profiles and growth rates of bacteria as indicators of a partial niche overlap with the pathogen. The bacteria were tested for growth on nine carbon sources (glucose, fucose, sucrose, maltose, asparagine, alanine, galacturonic acid, succinic acic, and linoleic acid), most of which are reported to be used by the zoospores of P. aphanidermatum in the infection process. The isolates were classified as fast- or slow-growing, depending on their growth rate in 1/10 strength TSB. By nonhierarchical cluster analysis, 20 clusters were generated of bacteria with similar profiles of carbon source utilization. Redundancy analysis showed that the type of root sample explained 47 f the variance found in the relative abundance of bacteria from the clusters. Bacteria from clusters using none or few of the carbon sources, e.g., maltose and linoleic acid, with many slow-growing isolates, showed a preference for plants in the vegetative or generative stage, or for old root regions (root base). Bacteria from clusters with fast-growing isolates, using many carbon sources, were relatively abundant in the seedling stage. A selection of 127 bacteria from the different clusters was tested for disease suppressive capabilities in bioassays on young cucumber plants in nutrient solution, inoculated with zoospores of P. aphanidermatum. Nine of these bacteria produced biosurfactants, and 27 showed antibiosis against mycelial growth in plate assays. For 31 isolates, significant positive effects on plant biomass were shown, as analyzed with a general linear regression model. For most isolates, these effects occurred only in one of two replicate assays and no reductions in the degree of root and crown rot were found. Of the isolates that used many of the tested carbon sources, only four had positive effects on plant biomass. The majority of the isolates that positively affected plant biomass used few to moderate numbers of carbon sources and did not produce antibiotics or biosurfactants. In conclusion, competition for the tested carbon sources with the zoospores did not play a decisive role in disease suppression, and no clear relation was found between ecophysiological traits and disease suppression. Only isolate 3.1T8, isolated from root tips in the generative stage of plant growth, significantly increased plant biomass and suppressed root and crown rot symptoms in five out of six bioassays. The isolate produced an antifungal substance in plate assays and showed biosurfactant production in several (cucumber-derived) media.
Polymorphisms within the prnD and pltC genes from pyrrolnitrin and pyoluteorin-producing Pseudomonas and Burkholderia spp
Souza, J.T. ; Raaijmakers, J.M. - \ 2003
FEMS Microbiology Ecology 43 (2003)1. - ISSN 0168-6496 - p. 21 - 34.
16s ribosomal-rna - biological-control - fluorescent pseudomonads - rhizoctonia-solani - maize rhizosphere - cotton seedlings - plant-growth - damping-off - cepacia - 2,4-diacetylphloroglucinol
Pyrrolnitrin (PRN) and pyoluteorin (PLT) are broad-spectrum antibiotics produced by several strains of Pseudomonas and Burkholderia species. Both antibiotics play an important role in the suppression of multiple plant pathogenic fungi. Primers were developed from conserved sequences and amplified prnD and pltC fragments from 18 Pseudomonas and four Burkholderia spp. of worldwide origin that produce either PRN or PLT or both. Subsequent RFLP (restriction fragment length polymorphisms) analysis of the 438-bp pltC fragment showed no polymorphisms among PLT-producing Pseudomonas strains. Polymorphisms within the 786-bp prnD fragment, however, allowed the assessment of the diversity among PRN-producing Pseudomonas and Burkholderia spp. to a level similar to that obtained by three 10-mer primers in random amplified polymorphic DNA analysis. Phylogenetic analysis of 16S rDNA sequences of strains representative of PRN-producing Pseudomonas and Burkholderia species correlated well with their taxonomic status. Phylogenetic relationships inferred from each of the four prn genes and from the complete sequence of the prn biosynthetic locus were similar to 16S rDNA-based phylogeny for most strains, except for Burkholderia pyrrocinia DSM 10685. Both RFLP analysis and comparison of the prn gene sequences showed that B. pyrrocinia DSM 10685 was more closely related to PRN-producing Pseudomonas strains, suggesting that lateral gene transfer may have occurred. Colony hybridization and PCR with PRN- and PLT-specific probes and primers showed that Pseudomonas and Burkholderia spp. harboring the prnD and pltC gene were not present at detectable levels on roots of wheat grown in five agricultural soils collected in The Netherlands, two of them being naturally suppressive to Gaeumannomyces graminis var. tritici. These results suggest that PRN- and PLT-producing Pseudomonas and Burkholderia sp. do not contribute to the natural suppressiveness found in these Dutch take-all decline soils.
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