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  • NARCIS (Royal Netherlands Academy of Arts and Sciences)  (14)
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  • 1
    In: Environmental Microbiology, September 2007, Vol.9(9), pp.2260-2273
    Description: The community structure and antagonistic potential in the rhizospheres of strawberry and oilseed rape (host plants of the fungal phytopathogen ) were assessed. The use of a new PCR‐DGGE system, designed to target ‐specific gene fragments in environmental DNA, circumvented common biases of 16S rRNA gene‐based DGGE analyses and proved to be a reliable tool to unravel the diversity of uncultured in bulk and rhizosphere soils. ‐specific fingerprints of total‐community (TC) rhizosphere DNA were surprisingly diverse, plant‐specific and differed markedly from those of the corresponding bulk soils. By combining multiple culture‐dependent and independent surveys, a group of isolates antagonistic towards was shown to be genotypically conserved, to carry the biosynthetic locus (involved in the biosynthesis of 2,4‐diacetylphloroglucinol – 2,4‐DAPG), and to correspond to a dominant and highly frequent population in the rhizosphere of field‐grown strawberries planted at three sites in Germany which have different land use histories. This population belongs to the phylogenetic lineage and showed closest relatedness to strain F113 (97% gene sequence identity in 492‐bp sequences), a biocontrol agent and 2,4‐DAPG producer. Partial gene sequences derived from isolates, clones of the strawberry rhizosphere and DGGE bands retrieved in this study represent previously undescribed gene clusters as revealed by phylogenetic analysis.
    Keywords: Ecosystem ; Anti-Infective Agents -- Metabolism ; Bacterial Proteins -- Genetics ; Plant Roots -- Microbiology ; Pseudomonas -- Genetics;
    ISSN: 1462-2912
    E-ISSN: 1462-2920
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  • 2
    Language: English
    In: PLoS ONE, 2014, Vol. 9(2)
    Description: 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.
    Keywords: Plasmid ; Incp ; Polluted Environment ; Pesticide-Contaminated ; Sediment ; Water ; Soil ; Natural Sciences ; Biological Sciences ; Microbiology ; Naturvetenskap ; Biologiska Vetenskaper ; Mikrobiologi ; Environmental Studies ; Miljövetenskapliga Studier
    ISSN: 1932-6203
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  • 3
    In: FEMS Microbiology Ecology, 2014, Vol. 87(1), pp.78-88
    Description: Difloxacin (DIF) belongs to the class of fluoroquinolone antibiotics that have been intensively used for the treatment of bacterial infections in veterinary and human medicine. The aim of this field study was to compare the effect of manure from DIF-treated pigs and untreated pigs on the bacterial community structure and resistance gene abundance in bulk soil and rhizosphere of maize. A significant effect of DIF manure on the bacterial community composition in bulk soil was revealed by denaturing gradient gel electrophoresis (DGGE) of bacterial 16S rRNA gene fragments amplified from total community DNA. In few samples, quinolone resistance genes qnrB and qnrS1/qnrS2 were detected by PCR and subsequent hybridization, while qnrA was not detected. Quantitative PCR revealed an increased abundance of the integrase gene intI1 of class I integrons and sulfonamide resistance genes sul1 and sul2 in DIF manure-treated bulk soil and rhizosphere, relative to 16S rRNA genes, while traN genes specific for LowGC-type plasmids were increased only in bulk soil. Principal component analysis of DGGE profiles suggested a manure effect in soil until day 28, but samples of days 71 and 140 were found close to untreated soil, indicating resilience of soil community compositions from disturbances by manure. 〈p〉〈fig id="fig0" position="float"〉 〈graphic alt-version="no" position="float" xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="fem12191-toc-0001" xlink:type="simple"/〉〈/fig〉 〈/p〉
    Keywords: Difloxacin ; Resistance ; Dgge ; Soil ; Manure ; Rhizosphere
    ISSN: 01686496
    E-ISSN: 1574-6941
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  • 4
    Language: English
    In: Microbial ecology, 2015, Vol.70(1), pp.141-153
    Description: The Laccaria proxima mycosphere strongly selects Variovorax paradoxus cells. Fifteen independent V. paradoxus strains, isolated from mycospheres sampled at two occasions, were investigated with respect to the occurrence of plasmids of sizes 〈60-100 kb....
    Keywords: Plasmid ; Incp-1 Beta ; Mycosphere ; Variovorax ; Iron Acquisition ; Horizontal Gene Transfer ; Horizontal Gene-Transfer ; Antibiotic-Resistance Plasmids ; Sp Strain Karsten ; Biofilm Formation ; Conjugative Plasmids ; Provides Evidence ; Bacteria ; Evolution ; Host ; Burkholderia
    ISSN: 0095-3628
    E-ISSN: 1432184X
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  • 5
    Language: English
    In: Soil Biology and Biochemistry, 2007, Vol.39(11), pp.2818-2828
    Description: A cultivation-based approach was used to determine the antagonistic potential of soil bacteria towards AG3 and f. sp. (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 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 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.
    Keywords: Suppressive Soils ; Biocontrol ; Rhizoctonia Solani ; Fusarium Oxysporum ; Siderophores ; Lytic Enzymes ; Agriculture ; Chemistry
    ISSN: 0038-0717
    E-ISSN: 1879-3428
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  • 6
    Language: English
    In: Journal of Plant Diseases and Protection, 2018, Vol.125(2), pp.121-125
    Description: In their opinion paper "The unpredictable risk imposed by microbial secondary metabolites: how safe is biological control of plant diseases?" (J. Plant Dis. Prot. 124, 413-419; https://doi.org/10.1007/s41348-017-0109-5 ), H.B. Deising, I. Gase and Y. Kubo criticize the use of microbial pesticides in plant protection. They point to the ability of microorganisms to form toxic metabolites and fear severe health problems when antagonistic microorganisms are increasingly released into agro-ecosystems. In our opinion, this view fails to reflect the reality because it largely ignores the ecology of microorganisms. In this contribution, we state reasons why biocontrol of plant diseases is a safe technology.
    Keywords: Biocontrol ; Safety ; Registration ; Metabolites
    ISSN: 1861-3829
    E-ISSN: 1861-3837
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  • 7
    Language: English
    In: 2018
    Description: The mycosphere is a hot spot for bacterial activity in soil. Bacteria must show a plethora of capacities to adapt to this habitat, and horizontal gene transfer processes like transduction may be key in the adaptation. However, studies focusing on the role of viruses in the mycosphere are currently absent. My research addressed this issue in three aspects. First, I dissects genomes of mycosphere-inhabiting Paraburkholderia strains, in order to provide a basis for bioinformatics-assisted identification of prophages. Second, I provides insight into the state-of-the-art of conceptualization of roles of (soil) viruses. Third, I contributes to the understanding of the ecological role and evolutionary trajectory of Paraburkholderia phages. To obtain a meaningful integrative perspective of the role of viromes in soil ecosystems, I advocate that hypothesis-based rather than broadly descriptive studies, based on both culture-dependent and –independent approaches are performed. By using these techniques in my research, I discovered the unexplored viral communities that interact with Paraburkholderia spp. One particular prophage, named ϕ437, was found to be spontaneously induced upon MMC induction. In the population context, such as in a biofilm, the inducibility of ϕ437 may contribute to the biofilm formation and fungal-interactivity in the mycosphere. However, this phenomenon needs further scrutiny. Furthermore, I showed complex evolutionary relationships between Paraburkholderia spp. and their phages. I propose that niche sharing over evolutionary time may have been at the basis of these genetic changes and evolutionary events. The extent of the diversity of viral communities in the mycosphere is unprecedented.
    ISBN: 978-94-034-1044-9
    ISBN: 9789403410449
    ISBN: 978-94-034-1043-2
    ISBN: 9789403410432
    Source: NARCIS (National Academic Research and Collaborations Information System)
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  • 8
    Language: English
    In: Microbial Ecology, 2007, Vol.53(3), pp.399-413
    Description: The bacterial community in soil was screened by using various molecular approaches for bacterial populations that were activated upon addition of different supplements. Plasmodiophora brassicae spores, chitin, sodium acetate, and cabbage plants were added to activate specific bacterial populations as an aid in screening for novel antagonists to plant pathogens. DNA from growing bacteria was specifically extracted from the soil by bromodeoxyuridine immunocapture. The captured DNA was fingerprinted by terminal restriction fragment length polymorphism (T-RFLP). The composition of the dominant bacterial community was also analyzed directly by T-RFLP and by denaturing gradient gel electrophoresis (DGGE). After chitin addition to the soil, some bacterial populations increased dramatically and became dominant both in the total and in the actively growing community. Some of the emerging bands on DGGE gels from chitin-amended soil were sequenced and found to be similar to known chitin-degrading genera such as Oerskovia , Kitasatospora , and Streptomyces species. Some of these sequences could be matched to specific terminal restriction fragments on the T-RFLP output. After addition of Plasmodiophora spores, an increase in specific Pseudomonads could be observed with Pseudomonas -specific primers for DGGE. These results demonstrate the utility of microbiomics, or a combination of molecular approaches, for investigating the composition of complex microbial communities in soil.
    Keywords: Microbiology -- Growth;
    ISSN: 0095-3628
    E-ISSN: 1432-184X
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  • 9
    In: FEMS Microbiology Ecology, October 2008, Vol.66(1), pp.1-2
    Description: This FEMS Microbiology Ecology Thematic Issue on Bacterial Genetics and Ecology: ‘Microbial community networks’ compiles contributions presented at the BAGECO-9 meeting held in Wernigerode, Germany (23–27 June 2007). The issue contains one MiniReview and 14 research papers. The history of the European-based BAGECO meetings dates back to the 1980s. Although there is no society associated with BAGECO meetings, their continuity is ensured by microbial ecologists who appreciate their particular atmosphere and spirit. One secret of the success of the meetings is the mix of excellent science, open and lively discussion and scientific community networking. Although the number of participants has increased continuously, the current size of the BAGECO meeting (around 300 participants in Wernigerode) allows plenary nonparallel sessions giving not only invited speakers but also Ph.D. students the chance to present their work in front of all other participants. A major reason for establishing these meetings …
    Keywords: Environmental Sciences ; Biology;
    ISSN: 0168-6496
    E-ISSN: 1574-6941
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  • 10
    Language: English
    In: 2018
    Description: There is growing understanding that the environment plays an important role both in the transmission of antibiotic resistant pathogens and in their evolution. Accordingly, researchers and stakeholders world-wide seek to further explore the mechanisms and drivers involved, quantify risks and identify suitable interventions. There is a clear value in establishing research needs and coordinating efforts within and across nations in order to best tackle this global challenge. At an international workshop in late September 2017, scientists from 14 countries with expertise on the environmental dimensions of antibiotic resistance gathered to define critical knowledge gaps. Four key areas were identified where research is urgently needed: 1) the relative contributions of different sources of antibiotics and antibiotic resistant bacteria into the environment; 2) the role of the environment, and particularly anthropogenic inputs, in the evolution of resistance; 3) the overall human and animal health impacts caused by exposure to environmental resistant bacteria; and 4) the efficacy and feasibility of different technological, social, economic and behavioral interventions to mitigate environmental antibiotic resistance.1.
    Source: NARCIS (National Academic Research and Collaborations Information System)
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