Assessment of Dickeya and Pectobacterium spp. on vegetables and ornamentals (Soft rot)
Wolf, J.M. van der; Bergsma-Vlami, M. ; Saddler, G. ; Hélias, V. ; Tsror, L. ; Yedida, Iris ; Pirhonen, M. ; Degefu, Yeshtila ; Tuomisto, J.T. ; Lojkowska, Ewa ; Li, Sean - \ 2020
Zenodo - 109 p.
Euphresco - Plant health - Dickeya - Pectobacterium - soft rot - vegetables - ornamentals - diagnostics - surveys - epidemiology - management
Dickeya and Pectobacterium belonging to the group of soft rot Pectobacteriaceae (SRP) are causing emerging problems in a wide range of vegetable and ornamental crops in Europe, including potato, carrot, cabbage, Chinese cabbage, celery, leek, pepper, parsley, Zantedeschia, hyacinth, Dahlia, Chrysanthemum, Philodendron, Freesia, Saintpaulia, Iris, Aglaonema, Crocus, Campanula and Phalaenopsis. The phytopathogens in both genera are genetically and phenotypically highly diverse. Disease problems in the different hosts are associated with the introduction of new variants or by spread of groups already present in Europe. Within this Euphresco project we aimed to identify and assess the risks of these new variants, and to develop management strategies, including reliable diagnostic methods to prevent introductions and further spread of SRP. To reach our goals, meetings were organized and collaborations were established with specialists worldwide. All information on meetings, protocols and activities of the Euphresco group are published on the Dickeya/Pectobacterium website, conveyed by the James Hutton Institute in Invergowrie (Scotland) (https://engage.hutton.ac.uk, contact person Dr I. Toth/Dr J. Fairly).
During the project, 1.5 days meetings were held in 2015 in Gdansk (Poland), in 2016 in Helsinki (Finland), in 2017 in Edinburgh (Scotland) and in 2018 in Emmeloord (The Netherlands). Meetings were attended by an average of 30 participants from organizations in EU member states, North- and Latin America, Africa, Asia and Australia.
One project’s objective was to develop methods for the detection and identification of Pectobacterium and Dickeya species in different matrices. For this, a panel of reference strains has been compiled for Dickeya and Pectobacterium species. Most strains have been deposited in international collections. For most strains also whole genome sequence data are available. During the course of this project, several diagnostic tests were developed and evaluated, often based on the TaqMan technology.
In several countries, surveys in potato and ornamental crops were conducted, but also in other matrices of the potato ecosystem, including water used for irrigation. In addition, new taxonomic groups that have been identified, are now new species including: P. versatile, P. aquaticum, P. fontis and P. polonicum. In potato, P. brasiliense became dominant as blackleg causing organism and has largely outcompeted D. solani in the last five years. In surface water in Europe, D. zeae was found to be the dominant SRP. In other continents, serious outbreaks of potato blackleg with other SRP has been reported, such as D. dianthicola in the USA and Australia. Various new SRP have been described, namely P. punjabense, P. peruviense, P. polaris, D. lacustris and D. zantedeschia. For the first time, D. fangzhongdai was described in Phalaenopsis. Not all species can cause potato blackleg.
Studies on various virulence factors were conducted for SRP, such as on chemoreceptors, small phenolic plant compounds interacting with signal molecules of Pectobacterium involved in the quorum sensing mechanism of the pathogen. A Tn-seq approach was developed and used to identify new virulence factors.
Information was exchanged on disease management strategies which include cultivation practices, resistance breeding, hygiene and the use of (bio-) control agents. A strict hygiene and an intensive monitoring of seed lots was found to be associated with a significant reduction of infections with blackleg causing SRP. A phage therapy has been developed to protect (seed) potato tubers against soft rot during storage. Various bacteriophages and bacterial antagonists were characterized and some evaluated for control of potato soft rot and/or blackleg. Steam treatments for seed tubers were found to decrease the blackleg incidence. Cold plasma treatment was found to kill SRP grown in vitro. Similarly, stabilized silver nanostructures killed SRP. It was found that seed potato lots can differ in suppressiveness against D. solani. Indications were found that the microbiome in tuber tissue plays a role in this.
Xylella-onderzoek toont nieuwste ontwikkelingen
Bonants, P.J.M. ; Bakker, Daniel ; Bergsma-Vlami, M. ; Schenk, M. - \ 2018
De Boomkwekerij (2018)8. - ISSN 0923-2443 - p. 16 - 17.
Eind 2017 kwamen meer dan 250 onderzoekers uit de hele wereld bij elkaar in het Spaanse Palma de Mallorca om de voortgang van het onderzoek aan Xylella fasridiosa te bespreken. Experts presenteerde de nieuwste wetenschappelijke ontwikkelingen.
The Perfect Match: Simultaneous Strawberry Pollination and Bio-Sampling of the Plant Pathogenic Bacterium Erwinia pyrifoliae by Honey Bees Apis mellifera
Steen, Sjef van der; Bergsma-Vlami, M. ; Wenneker, M. - \ 2018
Sustainable Agriculture Research 7 (2018)1. - ISSN 1927-050X - p. 25 - 32.
In this study we show that honey bee colonies placed in a greenhouse for pollination of strawberry can simultaneously be used to indicate the presence of the plant pathogenic bacterium Erwinia pyrifoliae. This was demonstrated by using two methods of qualitative sacrificial and non-sacrificial bio sampling of the honey bee colony. A novel method for non-sacrificial subsampling, named the Beehold device, was applied. Applying the Beehold device did not disturb or affect negatively the honey bee colony. The study demonstrated that the integration of pollination service and bio-sampling functioned. In the sacrificially derived honey bee subsamples, E. pyrifoliae was detected prior to any visible infection in the plant; however, E. pyrifoliae was detected via non-sacrificial sampling at the same time as plant infection was first observed. The Beehold device is a practical tool for monitoring plant pathogens via forager bees during flowering until fruit onset, but is not as sensitive as directly sampling honey bees.
Epidemiology of Erwinia pyrifoliae, a new pathogen on strawberry in the Netherlands
Wenneker, M. ; Bergsma-Vlami, M. ; Steen, J.J.M. van der - \ 2017
In: 8th International Strawberry Symposium. - International Society for Horticultural Science (Acta Horticulturae ) - ISBN 9789462611528 - p. 721 - 726.
Bacterial disease - Fire blight - Honeybees
During the late spring of 2013 strawberry plants (Fragaria × ananassa Duch. 'Elsanta') were showing an intense blackening of their immature fruits, their fruit calyxes and the peduncule were found at several locations (greenhouses) in The Netherlands. Symptoms include brown petals, green young fruits turning brown, malformed fruits and bacterium slime (ooze) formation on the surface of the young fruits. Fruits did not develop or were in many cases heavily malformed. In certain cases 40% of the crop was lost. Isolations from these symptomatic immature strawberry fruits yielded Erwinia-like colonies on YPG (yeast peptone glucose) agar. The isolates differed biochemically from E. amylovora and they were closely related to biochemical profiles of the Erwinia pyrifoliae reference strain LMG 25888. The isolates were further identified as E. pyrifoliae based on the real time PCR assay. Pathogenicity of several isolates was tested and confirmed on potted strawberry plants ('Elsanta' and 'Selva'). Honeybees from pollinating colonies were tested to detect E. pyrifoliae in a flowering strawberry greenhouse cultivation. Host range, mechanisms of survival and spread of this new Erwinia species on strawberry will be discussed.
|Epidemiology of Erwinia pyrifoliae, a new pathogen on strawberry in the Netherlands
Wenneker, M. ; Bergsma-Vlami, M. ; Steen, J.J.M. van der - \ 2016
In: Book of abstracts, 8th International Strawberry Symposium International Society for Horticultural Science - p. 73 - 73.
|Honeybee colonies for crop pollination and bio-sampling of plant pathogens : Early detection of Erwinia pyrifoliae in strawberry with the honeybee colony
Steen, Sjef van der; Bergsma-Vlami, M. ; Kogel, W.J. de; Wenneker, M. - \ 2016
|A new bacterial disease of strawberry in the Netherlands caused by Erwinia pyrifoliae.
Wenneker, M. ; Bergsma-Vlami, M. - \ 2015
IOBC/WPRS Bulletin 110 (2015). - ISSN 0253-1100 - p. 3 - 7.
During the late spring in 2013 strawberry plants (Fragaria x ananassa cv. Elsanta) showing an intense blackening of their immature fruits, their fruit calyxes and the attached stems were found at several locations (greenhouses) in the Netherlands. The isolates differed biochemically from E. amylovora and they were closely related to biochemical profiles of the Erwinia pyrifoliae reference strain LMG 25888. The isolates were further identified as E. pyrifoliae based on the real time PCR assay. Pathogenicity of several isolates was tested and confirmed on potted strawberry plants (cv. Elsanta).
Erwinia pyrifoliae, a new pathogen on strawberry in the Netherlands
Wenneker, M. ; Bergsma-Vlami, M.M. - \ 2015
Journal of Berry Research 5 (2015)1. - ISSN 1878-5093 - p. 17 - 22.
BACKGROUND: During the late spring of 2013 strawberry plants grown under protection (Fragaria x ananassa cv. Elsanta) were found at several locations in the Netherlands showing an intense brown to black discoloration of their immature fruits, their fruit calyx and the attached stems. OBJECTIVE: Identification of a new bacterial disease on strawberry. METHOD: Identification and characterization was based on the requirements of EPPO (European and Mediterranean Plant Protection Organization), followed by a pathogenicity test on strawberry plants for verification of the virulence. RESULTS: The isolates exhibited biochemical profiles closely related to Erwinia pyrifoliae reference strain LMG 25888. The isolates were further identified as E. pyrifoliae based on the real time PCR assay. Pathogenicity of several isolates was tested and confirmed on potted strawberry plants (cvs. Elsanta and Selva). CONCLUSION: Erwinia pyrifoliae is a pathogen on strawberry. Thus far occurrence of this pathogen on strawberry has not been reported nor its presence outside Asia.
|Erwinia pyrifoliae as a new pathogen on strawberry in the Netherlands
Wenneker, M. ; Bergsma-Vlami, M.M. - \ 2014
In: Book of abstracts VIII Workshop on Integrated Soft Fruit Production. - Vigalzano di Pergine Valsugana (TN) : Fondazione Edmund Mach - p. 3 - 4.
During the late spring in 2013 strawberry plants (Fragaria x ananassa cv. Elsanta) were found at several locations in the Netherlands showing an intense blackening of their immature fruits, their fruit calyx and the attached stems. There were no symptoms observed on the leaves. The discoloration was also observed inside the young fruits, which presented an intense darkening or blackening of the fruit tissue at the edges and an intense shining of the fruit tissue in the middle. Fruits did not develop or were in many cases heavily malformed. In certain cases 40% of the crop was lost. The release of bacterial slime was additionally observed on the surface of the young fruits and their stems. Isolations from these symptomatic immature strawberry fruits yielded Erwinia-like colonies on YPG (Yeast Peptone Glucose) agar. Characterization of the isolates revealed Gram negative bacterial cells, giving a negative reaction on Levan, and on media containing pectin. Bacteria have the following biochemical features: positive for sorbitol, but negative for gelatine, esculin and D-raffinose. The isolates differed biochemically from E. amylovora and they were closely related to biochemical profiles of the Erwinia pyrifoliae reference strain LMG 25888. The isolates were further identified as E. pyrifoliae based on the real time PCR assay (Wensing et al., 2012). Pathogenicity of several isolates was tested and confirmed on potted strawberry plants (cv. Elsanta). Inoculation by injecting a thick bacterial suspension (108 cfu/ml) in the epicalyx of three immature strawberry fruits per plant quickly resulted in oily necrosis with abundant formation of exudate on the epicalyx and on the sepals. A few inoculated fruitlets with the isolates and E. pyrifoliae reference strain LMG 25888 developed similar symptoms to the ones observed in the original samples in three to four weeks. The bacterium was re-isolated from the affected symptomatic fruitlets and identity of the re-isolates was confirmed by PCR, indicating that E. pyrifoliae had caused the disease. Spray inoculation of strawberry flowers resulted in necrosis without ooze formation. Erwinia pyrifoliae is closely related to the main fire blight pathogen E. amylovora. The pathogen E. pyrifoliae was described for the first time in 1999 in Korea (Kim et al., 1999; 2001). E. pyrifoliae is primarily a pathogen of Asian or Nashi pear (Pyrus pyrifolia) causing fire blight on Nashi pear and is considered to have a restricted geographic distribution in East Asia (Korea and Japan). Thus far occurrence of this pathogen on strawberry has not been reported nor its presence outside Asia.
|Nieuwe bacterieziekte in aardbei
Wenneker, M. ; Laarhoven, A. van; Bergsma-Vlami, M. - \ 2014
Groenten en Fruit Magazine 40 (2014)6. - ISSN 1879-7318 - p. 40 - 41.
Molecular typing of Dutch isolates of Xanthomonas arboricola pathovar pruni isolated from ornamental cherry laurel
Bergsma-Vlami, M. ; Martin, W. ; Koenraadt, H. ; Teunissen, H. ; Pothier, J.F. ; Duffy, B. ; Doorn, J. van - \ 2012
Journal of Plant Pathology: rivista di patologia vegetale 94 (2012)Supp.1. - ISSN 1125-4653 - p. S29 - S35.
pectate lyase secretion - acutatum-sensu-lato - colletotrichum-acutatum - c-gloeosporioides - sp-nov - fruit - diversity - infection - susceptibility - pathogenicity
Xanthomonas arboricola pv. pruni (Xap) has been found in several cherry laurel (Prunus laurocerasus) nurseries in the Netherlands, causing leaf spot. As no information is available yet about the epidemiology of this quarantine bacterium in cherry laurel, molecular typing of Xap isolates can considerably improve our understanding of pathogen spread between various cherry laurel production systems in different regions of the Netherlands and pathogen relatedness among different disease outbreaks. In this study, the genotypic diversity within a population of 25 Xap isolates isolated from different cherry laurel cultivars grown in different locations in the Netherlands between 2008-2010, was assessed using Multiple-locus variable-number analysis (MLVA). The identity of these Xap isolates was initially determined based on the EPPO standard PM 7/64. Confirmation of the identity of these Xap isolates was additionally achieved with diverse methodologies, including gyrase subunit B (gyrB) sequence typing, BOXand ERIC-PCR, AFLP, and Xap-specific PCR’s: one based on the previously described Pagani primers (2004) (conventional-PCR and its TaqMan-PCR variant) and one based on the recently described Pothier primers (2011c). Based on the results of the MLVA analysis, the Dutch population of Xap isolates could be divided into two groups; however no correlation with the geographical origin or any other character of these isolates could be established. Additionally, based on colony morphology, a panel of 5 look-a-likes were isolated from symptomatic leaves of P. laurocerasus which reacted in the Xap-specific PCR described by Pagani (2004) but that did not react in the Xap-specific PCR described by Pothier et al. (2011c). Further characterisation of these look-a-like isolates with AFLP, BOXand ERIC-PCR, and gyrB sequencing showed that the Xap-specific PCR described by Pagani does not discriminate between Xap and the look-a-like isolates. Similarly to Pagani PCR, the performance of a pathogenicity test with a pure culture of the isolate was not always discriminative between Xap and the look-a-like isolates, unraveling a complexity in Xanthomonas pathogenicity. Therefore, in routine screening based on the EPPO standard PM 7/64, complementary techniques such as BOX- ERIC-PCR, gyrB sequencing, Xap-specific PCR described by Pothier (2011c), MLVA and AFLP should be used to obtain a reliable diagnosis of Xap and avoid false positive results.
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
Bruinrot bij aardappel
Janse, J.D. ; Bergsma-Vlami, M.M. ; Wenneker, M. - \ 2009
Gewasbescherming 40 (2009)4. - ISSN 0166-6495 - p. 176 - 187.
ralstonia solanacearum - plantenziekteverwekkende bacteriën - aardappelen - vermeerderingsmateriaal - verwelkingsziekten - besmetting - bestrijdingsmethoden - symptomen - ziektedistributie - wetenschappelijk onderzoek - maatregelen - diagnostiek - moleculaire diagnostiek - ralstonia solanacearum - plant pathogenic bacteria - potatoes - propagation materials - wilts - contamination - control methods - symptoms - disease distribution - scientific research - measures - diagnostics - molecular diagnostics
De quarantaineziekte bruinrot van aardappel, veroorzaakt door de bacterie Ralstonia (voorheen : Pseudomonas solanacearum) werd in Nederland voor het eerst met zekerheid aangetroffen in 1992. Het betrof een geïsoleerd geval in Zuid-Limburg, dat later verbonden bleek te zijn met een eerder opgetreden besmetting in België. Sindsdien is door een grote inspanning van de Plantenziektenkundige Dienst (PD), de Nederlandse Algemene Keuringsdienst (NAK), het bedrijfsleven en het onderzoek (Plant Research International (PRI - voorheen IPO) en Wageningen Universiteit veel bereikt. Dit artikel geeft een overzicht van de aanpak en het onderzoek sinds de uitbraak van bruinrot in 1995 en werpt een blik vooruit naar toekomstige ontwikkelingen
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.
Influence of plant species on population dynamics, genotypic diversity and antibiotic production by indigenous Pseudomonas spp
Bergsma-Vlami, M. ; Prins, M.E. ; Raaijmakers, J.M. - \ 2005
FEMS microbiology ecology 52 (2005)1. - ISSN 0168-6496 - p. 59 - 69.
all decline soils - fluorescent pseudomonas - 2,4-diacetylphloroglucinol-producing pseudomonas - microbial communities - maize rhizosphere - steroid saponins - in-vitro - biocontrol - wheat - frequency
The population dynamics, genotypic diversity and activity of naturally-occurring 2,4-diacetylphloroglucinol (DAPG)-producing Pseudomonas spp. was investigated for four plant species (wheat, sugar beet, potato, lily) grown in two different soils. All four plant species tested, except lily and in some cases wheat, supported relatively high rhizosphere populations (5 × 104 to 1 × 106 CFU/g root) of indigenous DAPG-producing Pseudomonas spp. during successive cultivation in both a take-all suppressive and a take-all conducive soil. Although lily supported on average the highest population densities of fluorescent Pseudomonas spp., it was the least supportive of DAPG-producing Pseudomonas spp. of all four plant species. The genotypic diversity of 492 DAPG-producing Pseudomonas isolates, assessed by Denaturing Gradient Gel Electrophoresis (DGGE) analysis of the phlD gene, revealed a total of 7 genotypes. Some of the genotypes were found only in the rhizosphere of a specific plant, whereas the predominant genotypes were found at significantly higher frequencies in the rhizosphere of three plant species (wheat, sugar beet and potato). Statistical analysis of the phlD+ genotype frequencies showed that the diversity of the phlD+ isolates from lily was significantly lower than the diversity of phlD+ isolates found on wheat, sugar beet or potato. Additionally, soil type had a significant effect on both the phlD+ population density and the phlD+ genotype frequencies, with the take-all suppressive soil being the most supportive. HPLC analysis further showed that the plant species had a significant effect on DAPG-production by the indigenous phlD+ population: the wheat and potato rhizospheres supported significantly higher amounts of DAPG produced per cell basis than the rhizospheres of sugar beet and lily. Collectively, the results of this study showed that the host plant species has a significant influence on the dynamics, composition and activity of specific indigenous antagonistic Pseudomonas spp.
Assessment of the genotypic diversity of antibiotic-producing Pseudomonas species in the rhizosphere by denaturing gradient gel electrophoresis
Bergsma-Vlami, M. ; Prins, M.E. ; Staats, M. ; Raaijmakers, J.M. - \ 2005
Applied and Environmental Microbiology 71 (2005)2. - ISSN 0099-2240 - p. 993 - 1003.
16s ribosomal-rna - 2,4-diacetylphloroglucinol-producing fluorescent pseudomonas - black root-rot - genetic diversity - environmental-samples - bacterial communities - microbial-populations - natural environments - maize rhizosphere - pcr-dgge
The genotypic diversity of antibiotic-producing Pseudomonas spp. provides an enormous resource for identifying strains that are highly rhizosphere competent and superior for biological control of plant diseases. In this study, a simple and rapid method was developed to determine the presence and genotypic diversity of 2,4-diacetylphloroglucinol (DAPG)-producing Pseudomonas strains in rhizosphere samples. Denaturing gradient gel electrophoresis (DGGE) of 350-bp fragments of phlD, a key gene involved in DAPG biosynthesis, allowed discrimination between genotypically different phlD+ reference strains and indigenous isolates. DGGE analysis of the phlD fragments provided a level of discrimination between phlD+ genotypes that was higher than the level obtained by currently used techniques and enabled detection of specific phlD+ genotypes directly in rhizosphere samples with a detection limit of approximately 5 x 103 CFU/g of root. DGGE also allowed simultaneous detection of multiple phlD+ genotypes present in mixtures in rhizosphere samples. DGGE analysis of 184 indigenous phlD+ isolates obtained from the rhizospheres of wheat, sugar beet, and potato plants resulted in the identification of seven phlD+ genotypes, five of which were not described previously based on sequence and phylogenetic analyses. Subsequent bioassays demonstrated that eight genotypically different phlD+ genotypes differed substantially in the ability to colonize the rhizosphere of sugar beet seedlings. Collectively, these results demonstrated that DGGE analysis of the phlD gene allows identification of new genotypic groups of specific antibiotic-producing Pseudomonas with different abilities to colonize the rhizosphere of sugar beet seedlings
|Influence of plant species on population dynamics, genotypic diversity and in situ antibiotic production by indigenous Pseudomonas spp
Bergsma-Vlami, M. ; Prins, M.E. ; Raaijmakers, J.M. - \ 2004
In: Book of Abstracts International Congress Rhizosphere 2004, Munich, Germany, 12-17 September 2004 - p. 34 - 34.
|Using biosynthetic gene phlD to assess diversity of DAPG-producing Pseudomonas spp. by DGGE
Bergsma-Vlami, M. ; Prins, M. ; Raaijmakers, J.M. - \ 2003
In: Book of Abstracts of Offered Papers 8th International Congress of Plant Pathology, Christchurch, New Zealand, 2-7 February 2003 [S.l.] : S.n. - ISBN 9780864761514 - p. 45 - 45.
|Genotypic diversity and colonization preference of Pseudomonas spp. producing the antibiotic DAPG
Bergsma-Vlami, M. ; Prins, M. ; Raaijmakers, J.M. - \ 2003
In: Book of Abstracts of Offered Papers 8th International Congress of Plant Pathology, Christchurch, New Zealand, 2-7 February 2003 [S.l.] : S.n. - ISBN 9780864761514 - p. 45 - 45.
|Diversity and host specificity of Pseudomonas spp. producing the antibiotic 2,4-diacetylphloroglucinol (DAPG)
Bergsma-Vlami, M. ; Prins, M.E. ; Staats, M. ; Raaijmakers, J.M. - \ 2002
In: Influence of a-biotic and biotic factors on biocontrol agents - p. 45 - 48.