Wädenswil, Switzerland
Wädenswil, Switzerland

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Brankatschk K.,Agroscope Changins Wadenswil ACW | Blom J.,Bielefeld University | Goesmann A.,Bielefeld University | Smits T.H.M.,Agroscope Changins Wadenswil ACW | Duffy B.,Agroscope Changins Wadenswil ACW
Journal of Bacteriology | Year: 2011

The genome of Salmonella enterica subsp. enterica serovar Weltevreden strain 2007-60-3289-1 was sequenced. The genome sequence of this fresh-vegetable isolate from Scandinavia will be useful for the elucidation of plant host factors in comparison to other serovars of S. enterica subsp. enterica. © 2011, American Society for Microbiology.


Smits T.H.M.,Agroscope Changins Wadenswil ACW | Rezzonico F.,Agroscope Changins Wadenswil ACW | Kamber T.,Agroscope Changins Wadenswil ACW | Goesmann A.,Bielefeld University | And 4 more authors.
Journal of Bacteriology | Year: 2010

Pantoea vagans is a Gram-negative enterobacterial plant epiphyte of a broad range of plants. Here we report the 4.89-Mb genome sequence of P. vagans strain C9-1 (formerly Pantoea agglomerans), which is commercially registered for biological control of fire blight, a disease of pear and apple trees caused by Erwinia amylovora. Copyright © 2010, American Society for Microbiology. All Rights Reserved.


De Maayer P.,University of Pretoria | Venter S.N.,University of Pretoria | Kamber T.,Agroscope Changins Wadenswil ACW | Duffy B.,Agroscope Changins Wadenswil ACW | And 2 more authors.
BMC Genomics | Year: 2011

Background: The Type VI secretion apparatus is assembled by a conserved set of proteins encoded within a distinct locus. The putative effector proteins Hcp and VgrG are also encoded within these loci. We have identified numerous distinct Type VI secretion system (T6SS) loci in the genomes of several ecologically diverse Pantoea and Erwinia species and detected the presence of putative effector islands associated with the hcp and vgrG genes.Results: Between two and four T6SS loci occur among the Pantoea and Erwinia species. While two of the loci (T6SS-1 and T6SS-2) are well conserved among the various strains, the third (T6SS-3) locus is not universally distributed. Additional orthologous loci are present in Pantoea sp. aB-valens and Erwinia billingiae Eb661. Comparative analysis of the T6SS-1 and T6SS-3 loci showed non-conserved islands associated with the vgrG and hcp, and vgrG genes, respectively. These regions had a G+C content far lower than the conserved portions of the loci. Many of the proteins encoded within the hcp and vgrG islands carry conserved domains, which suggests they may serve as effector proteins for the T6SS. A number of the proteins also show homology to the C-terminal extensions of evolved VgrG proteins.Conclusions: Extensive diversity was observed in the number and content of the T6SS loci among the Pantoea and Erwinia species. Genomic islands could be observed within some of T6SS loci, which are associated with the hcp and vgrG proteins and carry putative effector domain proteins. We propose new hypotheses concerning a role for these islands in the acquisition of T6SS effectors and the development of novel evolved VgrG and Hcp proteins. © 2011 De Maayer et al; licensee BioMed Central Ltd.


Hofstetter V.,Agroscope Changins Wadenswil ACW | Buyck B.,CNRS Systematics, Biodiversity and Evolution Institute | Croll D.,ETH Zurich | Viret O.,Agroscope Changins Wadenswil ACW | And 2 more authors.
Fungal Diversity | Year: 2012

Esca disease, which attacks the wood of grapevine, has become increasingly devastating during the past three decades and represents today a major concern in all wine-producing countries. This disease is attributed to a group of systematically diverse fungi that are considered to be latent pathogens, however, this has not been conclusively established. This study presents the first in-depth comparison between the mycota of healthy and diseased plants taken from the same vineyard to determine which fungi become invasive when foliar symptoms of esca appear. An unprecedented high fungal diversity, 158 species, is here reported exclusively from grapevine wood in a single Swiss vineyard plot. An identical mycota inhabits wood of healthy and diseased adult plants and presumed esca pathogens were widespread and occurred in similar frequencies in both plant types. Pioneer esca-associated fungi are not transmitted from adult to nursery plants through the grafting process. Consequently the presumed esca-associated fungal pathogens are most likely saprobes decaying already senescent or dead wood resulting from intensive pruning, frost or other mecanical injuries as grafting. The cause of esca disease therefore remains elusive and requires well executive scientific study. These results question the assumed pathogenicity of fungi in other diseases of plants or animals where identical mycota are retrieved from both diseased and healthy individuals. © 2012 The Author(s).


Smits T.H.M.,Agroscope Changins Wadenswil ACW | Duffy B.,Agroscope Changins Wadenswil ACW
Archives of Microbiology | Year: 2011

Genomics has clarified the biosynthetic pathway for desferrioxamine E critical for iron acquisition in the enterobacterial fire blight pathogen Erwinia amylovora. Evidence for each of the individual steps and the role of desferrioxamine E biosynthesis in pathogen virulence and cell protection from host defenses is presented. Using comparative genomics, it can be concluded that desferrioxamine biosynthesis is ancestral within the genera Erwinia and Pantoea. © Springer-Verlag 2011.


Rezzonico F.,Agroscope Changins Wadenswil ACW | Smits T.H.M.,Agroscope Changins Wadenswil ACW | Duffy B.,Agroscope Changins Wadenswil ACW
Sensors (Switzerland) | Year: 2012

The LuxS enzyme, an S-ribosyl-homocysteine lyase, catalyzes the production of the signal precursor for autoinducer-2 mediated quorum sensing (QS-2) in Vibrio. Its widespread occurrence among bacteria is often considered the evidence for a universal language for interspecies communication. Presence of the luxS gene and production of the autoinducer-2 (AI-2) signal have repeatedly been the only evidences presented to assign a functional QS-2 to the most diverse species. In fact, LuxS has a primary metabolic role as part of the activated methyl cycle. In this review we have analyzed the distribution of QS-2 related genes in Enterobacteriaceae by moving the focus of the investigation from AI-2 production to the detection of potential AI-2 receptors. The latter are common in pathogens or endosymbionts of animals, but were also found in a limited number of Enterobacteriaceae of the genera Enterobacter, Klebsiella, and Pantoea that live in close association with plants or fungi. Although a precise function of QS-2 in these species has not been identified, they all show an endophytic or endosymbiontic lifestyle that suggests a role of type-2 quorum sensing in the adaptation to closed ecosystems. © 2012 by the authors; licensee MDPI, Basel, Switzerland.


Rezzonico F.,Agroscope Changins Wadenswil ACW | Vogel G.,Mabritec AG | Duffy B.,Agroscope Changins Wadenswil ACW | Tonolla M.,Instituto Cantonale Of Microbiologia
Applied and Environmental Microbiology | Year: 2010

Pantoea agglomerons is an ecologically diverse taxon that includes commercially important plant-beneficial strains and opportunistic clinical isolates. Standard biochemical identification methods in diagnostic laboratories were repeatedly shown to run into false-positive identifications of P. agglomerons, a fact which is also reflected by the high number of 16S rRNA gene sequences in public databases that are incorrectly assigned to this species. More reliable methods for rapid identification are required to ascertain the prevalence of this species in clinical samples and to evaluate the biosafety of beneficial isolates. Whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) methods and reference spectra (SuperSpectrum) were developed for accurate identification of P. agglomerons and related bacteria and used to detect differences in the protein profile within variants of the same strain, including a ribosomal point mutation conferring streptomycin resistance. MALDI-TOF MS-based clustering was shown to generally agree with classification based on gyrB sequencing, allowing rapid and reliable identification at the species level. Copyright © 2010, American Society for Microbiology. All Rights Reserved.


Kamber T.,Agroscope Changins Wadenswil ACW | Lansdell T.A.,University of Minnesota | Stockwell V.O.,Oregon State University | Ishimaru C.A.,University of Minnesota | And 2 more authors.
Applied and Environmental Microbiology | Year: 2012

Pantoea vagans C9-1 is a biocontrol strain that produces at least two antibiotics inhibiting the growth of Erwinia amylovora, the causal agent of fire blight disease of pear and apple. One antibiotic, herbicolin I, was purified from culture filtrates of P. vagans C9-1 and determined to be 2-amino-3-(oxirane-2,3-dicarboxamido)-propanoyl-valine, also known as Nß-epoxysuccinamoyl-DAP-valine. A plasposon library was screened for mutants that had lost the ability to produce herbicolin I. It was shown that mutants had reduced biocontrol efficacy in immature pear assays. The biosynthetic gene cluster in P. vagans C9-1 was identified by sequencing the flanking regions of the plasposon insertion sites. The herbicolin I biosynthetic gene cluster consists of 10 coding sequences (CDS) and is located on the 166-kb plasmid pPag2. Sequence comparisons identified orthologous gene clusters in Pantoea agglomerans CU0119 and Serratia proteamaculans 568. A low incidence of detection of the biosynthetic cluster in a collection of 45 Pantoea spp. from biocontrol, environmental, and clinical origins showed that this is a rare trait among the tested strains. © 2012, American Society for Microbiology.


Fantke P.,University of Stuttgart | Charles R.,Agroscope Changins Wadenswil ACW | Alencastro L.F.D.,Ecole Polytechnique Federale de Lausanne | Friedrich R.,University of Stuttgart | And 2 more authors.
Chemosphere | Year: 2011

Human intake of pesticide residues from consumption of processed food plays an important role for evaluating current agricultural practice. We take advantage of latest developments in crop-specific plant uptake modeling and propose an innovative dynamic model to estimate pesticide residues in the wheat-environment system, dynamiCROP. We used this model to analyze uptake and translocation of pesticides in wheat after foliar spray application and subsequent intake fractions by humans. Based on the evolution of residues in edible parts of harvested wheat we predict that between 22. mg and 2.1. g per kg applied pesticide are taken in by humans via consumption of processed wheat products. Model results were compared with experimentally derived concentrations in wheat ears and with estimated intake via inhalation and ingestion caused by indirect emissions, i.e. the amount lost to the environment during pesticide application. Modeled and measured concentrations in wheat fitted very well and deviate from less than a factor 1.5 for chlorothalonil to a maximum factor 3 for tebuconazole. Main aspects influencing pesticide fate behavior are degradation half-life in plant and time between pesticide application and crop harvest, leading to variations in harvest fraction of at least three orders of magnitude. Food processing may further reduce residues by approximately 63%. Intake fractions from residues in sprayed wheat were up to four orders of magnitude higher than intake fractions estimated from indirect emissions, thereby demonstrating the importance of exposure from consumption of food crops after direct pesticide treatment. © 2011 Elsevier Ltd.


Walsh F.,Agroscope Changins Wadenswil ACW | Ingenfeld A.,Agroscope Changins Wadenswil ACW | Zampicolli M.,Agroscope Changins Wadenswil ACW | Hilber-Bodmer M.,Agroscope Changins Wadenswil ACW | And 2 more authors.
Journal of Microbiological Methods | Year: 2011

Antibiotic application in plant agriculture is primarily used to control fire blight caused by Erwinia amylovora in pome fruit orchards. In order to facilitate environmental impact assessment for antibiotic applications, we developed and validated culture-independent quantitative real-time PCR multiplex assays for streptomycin (strA, strB, aadA and insertion sequence IS1133) and tetracycline (tetB, tetM and tetW) resistance elements in plant and soil samples. The qPCR were reproducible and consistent whether the DNA was extracted directly from bacteria, plant and soil samples inoculated with bacteria or soil samples prior to and after manure slurry treatment. The genes most frequently identified in soils pre- and post-slurry treatment were strB, aadA, tetB and tetM. All genes tested were detected in soils pre-slurry treatment, and a decrease in relative concentrations of tetB and the streptomycin resistance genes was observed in samples taken post-slurry treatment. These multiplex qPCR assays offer a cost-effective, reliable method for simultaneous quantification of antibiotic resistance genes in complex, environmental sample matrices. © 2011 Elsevier B.V.

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