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  • Elsevier (CrossRef)  (39)
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  • 1
    Language: English
    In: Current Opinion in Microbiology, June 2014, Vol.19, pp.v-vii
    Description: To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.mib.2014.06.011 Byline: Kornelia Smalla Author Affiliation: Julius KAaAaAeA hn-Institut, Federal Research Centre for Cultivated Plan (JKI), Institute for Epidemiology and Pathogen Diagnostics (EP), Messeweg 11-12, 38104 Braunschweig, Germany
    Keywords: Biology
    ISSN: 1369-5274
    E-ISSN: 1879-0364
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  • 2
    Language: English
    In: Journal of Hazardous Materials, 2010, Vol.184(1), pp.523-532
    Description: Twenty-six different plant species were analyzed regarding their performance in soil contaminated with petroleum oil. Two well-performing species, Italian ryegrass ( var. Taurus), Birdsfoot trefoil ( var. Leo) and the combination of these two plants were selected to study the ecology of plant-associated, culturable alkane-degrading bacteria. Hydrocarbon degrading bacteria were isolated from the rhizosphere, root interior and shoot interior and subjected to the analysis of 16S rRNA gene, the 16S and 23S rRNA intergenic spacer region and alkane hydroxylase genes. Furthermore, we investigated whether alkane hydroxylase genes are plasmid located. Higher numbers of culturable, alkane-degrading bacteria were associated with Italian ryegrass, which were also characterized by a higher diversity, particularly in the plant interior. Only half of the isolated bacteria hosted known alkane hydroxylase genes ( and cytochrome P153-like). Degradation genes were found both on plasmids as well as in the chromosome. In regard to application of plants for rhizodegradation, where support of numerous degrading bacteria is essential for efficient break-down of pollutants, Italian ryegrass seems to be more appropriate than Birdsfoot trefoil.
    Keywords: Alkane Hydroxylase ; 16s Rrna Gene ; Rhizosphere ; Endophytes ; Italian Ryegrass ; Birdsfoot Trefoil ; Engineering ; Law
    ISSN: 0304-3894
    E-ISSN: 1873-3336
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  • 3
    Language: English
    In: Soil Biology and Biochemistry, December 2014, Vol.79, pp.57-67
    Description: The study of interactions between minerals, organic matter (OM) and microorganisms is essential for the understanding of soil functions such as OM turnover. Here, we present an interdisciplinary approach using artificial soils to study the establishment of the microbial community and the formation of macro-aggregates as a function of the mineral composition by using artificial soils. The defined composition of a model system enables to directly relate the development of microbial communities and soil structure to the presence of specific constituents. Five different artificial soil compositions were produced with two types of clay minerals (illite, montmorillonite), metal oxides (ferrihydrite, boehmite) and charcoal incubated with sterile manure and a microbial community derived from a natural soil. We used the artificial soils to analyse the response of these model soil systems to additional sterile manure supply (after 562 days). The artificial soils were subjected to a prolonged incubation period of more than two years (842 days) in order to take temporally dynamic processes into account. In our model systems with varying mineralogy, we expected a changing microbial community composition and an effect on macro-aggregation after OM addition, as the input of fresh substrate will re-activate the artificial soils. The abundance and structure of 16S rRNA gene and internal transcribed spacer (ITS) fragments amplified from total community DNA were studied by quantitative real-time PCR (qPCR) and denaturing gradient gel electrophoresis (DGGE), respectively. The formation of macro-aggregates (〉2 mm), the total organic carbon (OC) and nitrogen (N) contents, the OC and N contents in particle size fractions and the CO respiration were determined. The second manure input resulted in higher CO respiration rates, 16S rRNA gene and ITS copy numbers, indicating a stronger response of the microbial community in the matured soil-like system. The type of clay minerals was identified as the most important factor determining the composition of the bacterial communities established. The additional OM and longer incubation time led to a re-formation of macro-aggregates which was significantly higher when montmorillonite was present. Thus, the type of clay mineral was decisive for both microbial community composition as well as macro-aggregation, whereas the addition of other components had a minor effect. Even though different bacterial communities were established depending on the artificial soil composition, the amount and quality of the OM did not show significant differences supporting the concept of functional redundancy.
    Keywords: Dgge ; Illite ; Montmorillonite ; Decomposition ; Respiration ; Soil Formation ; 16s Rrna Gene ; Its Fragment ; Agriculture ; Chemistry
    ISSN: 0038-0717
    E-ISSN: 1879-3428
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  • 4
    Language: English
    In: Science of the Total Environment, 15 April 2018, Vol.621, pp.725-733
    Description: Metal resistance has been associated with antibiotic resistance due to co- or cross-resistance mechanisms. Here, metal contaminated mine soil treated with organic wastes was screened for the presence of mobile genetic elements (MGEs). The occurrence of conjugative IncP-1 and mobilizable IncQ plasmids, as well as of class 1 integrons, was confirmed by PCR and Southern blot hybridization, suggesting that bacteria from these soils have gene-mobilizing capacity with implications for the dissemination of resistance factors. Moreover, exogenous isolation of MGEs from the soil bacterial community was attempted under antibiotic selection pressure by using as recipient. Seventeen putative transconjugants were identified based on increased antibiotic resistance. Metabolic traits and metal resistance of putative transconjugants were investigated, and whole genome sequencing was carried out for two of them. Most putative transconjugants displayed a multi-resistant phenotype for a broad spectrum of antibiotics. They also displayed changes regarding the ability to metabolise different carbon sources, RNA: DNA ratio, growth rate and biofilm formation. Genome sequencing of putative transconjugants failed to detect genes acquired by horizontal gene transfer, but instead revealed a number of nonsense mutations, including in , whose inactivation was linked to the observed resistance to aminoglycosides. Our results confirm that mine soils contain MGEs encoding antibiotic resistance. Moreover, they point out the role of spontaneous mutations in achieving low-level antibiotic resistance in a short time, which was associated with a trade-off in the capability to metabolise specific carbon sources.
    Keywords: Antibiotic Resistance ; Competitive Fitness ; Conjugative Plasmids ; Imipenem ; Integrons ; Environmental Sciences ; Biology ; Public Health
    ISSN: 0048-9697
    E-ISSN: 1879-1026
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  • 5
    Language: English
    In: Environmental Pollution, October 2017, Vol.229, pp.854-862
    Description: A biopurification system (BPS) is used on-farm to clean pesticide-contaminated wastewater. Due to high pesticide loads, a BPS represents a hot spot for the proliferation and selection as well as the genetic adaptation of discrete pesticide degrading microorganisms. However, while considerable knowledge exists on the biodegradation of specific pesticides in BPSs, the bacterial community composition of these systems has hardly been explored. In this work, the Shannon diversity, the richness and the composition of the bacterial community within an operational BPS receiving wastewater contaminated with various pesticides was, for the first time, elucidated over the course of an agricultural season, using DGGE profiling and pyrosequencing of 16S rRNA gene fragments amplified from total community DNA. During the agricultural season, an increase in the concentration of pesticides in the BPS was observed along with the detection of significant community changes including a decrease in microbial diversity. Additionally, a significant increase in the relative abundance of , mainly the , was found, and OTUs (operational taxonomic units) affiliated to responded positively during the course of the season. Furthermore, a banding-pattern analysis of 16S rRNA gene-based DGGE fingerprinting, targeting the - and as well as the , indicated that the might play an important role. Interestingly, a decrease of and was observed, indicating their selective disadvantage in a BPS, to which pesticides have been introduced. A decrease in microbial diversity was seen along with significant changes in bacterial community structure in a BPS receiving pesticides during the course of an agricultural season. OTUs affiliated to responded positively.
    Keywords: Bacterial Communities ; Shannon Diversity ; 16s Rrna Gene Sequencing ; Dgge Profiling ; Biopurification System ; Pesticide Degradation ; Engineering ; Environmental Sciences ; Anatomy & Physiology
    ISSN: 0269-7491
    E-ISSN: 1873-6424
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  • 6
    Language: English
    In: Current Opinion in Microbiology, June 2011, Vol.14(3), pp.236-243
    Description: The usage of antibiotics in animal husbandry has promoted the development and abundance of antibiotic resistance in farm environments. Manure has become a reservoir of resistant bacteria and antibiotic compounds, and its application to agricultural soils is assumed to significantly increase antibiotic resistance genes and selection of resistant bacterial populations in soil. The genome location of resistance genes is likely to shift towards mobile genetic elements such as broad-host-range plasmids, integrons, and transposable elements. Horizontal transfer of these elements to bacteria adapted to soil or other habitats supports their environmental transmission independent of the original host. The human exposure to soil-borne resistance has yet to be determined, but is likely to be severely underestimated.
    Keywords: Biology
    ISSN: 1369-5274
    E-ISSN: 1879-0364
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  • 7
    Language: English
    In: Systematic and Applied Microbiology, May 2018, Vol.41(3), pp.191-197
    Description: The plant tumorigenic strain NCPPB 1650 isolated from , and four nonpathogenic strains isolated from tumors on grapevine (strain 384), raspberry (strain 839) and blueberry (strains B20.3 and B25.3) were characterized by using polyphasic taxonomic methods. Based on 16S rRNA gene phylogeny, strains were clustered within the genus . Furthermore, multilocus sequence analysis (MLSA) based on the partial sequences of , and housekeeping genes indicated that five strains studied form a novel species. Their closest relatives were sp. R89-1, and . Authenticity of the novel species was confirmed by average nucleotide identity (ANI) and DNA–DNA hybridization (DDH) comparisons between strains NCPPB 1650 and B20.3, and their closest relatives, since obtained values were considerably below the proposed thresholds for the species delineation. Whole-genome-based phylogeny further supported distinctiveness of the novel species, that forms together with , and sp. R89-1 a well-delineated sub-clade of spp. named “rubi”. As for other species of the genus , the major fatty acid of the strains studied was 18:1 w7c (73.42–78.12%). The five strains studied were phenotypically distinguishable from other species of the genus . Overall, polyphasic characterization showed that the five strains studied represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain of is NCPPB 1650 (=DSM 30203 = LMG 230 = CFBP 4470 = IAM 13558 = JCM 20915 ).
    Keywords: Crown Gall ; Mlsa ; Ani ; in Silico Ddh ; Whole-Genome-Based Phylogeny ; Sub-Clade “rubi” ; Biology
    ISSN: 0723-2020
    E-ISSN: 1618-0984
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  • 8
    Language: English
    In: Trends in Microbiology, September 2014, Vol.22(9), pp.536-545
    Description: Large amounts of veterinary antibiotics are applied worldwide to farm animals and reach agricultural fields by manure fertilization, where they might lead to an increased abundance and transferability of antibiotic-resistance determinants. In this review we discuss recent advances, limitations, and research needs in determining the fate of veterinary antibiotics and resistant bacteria applied with manure to soil, and their effects on the structure and function of soil microbial communities in bulk soils and the rhizosphere. The increased abundance and mobilization of antibiotic-resistance genes (ARGs) might contribute to the emergence of multi-resistant human pathogens that increasingly threaten the successful antibiotic treatment of bacterial infections.
    Keywords: Antibiotic-Resistance Genes ; Horizontal Gene Transfer ; Rhizosphere ; Biology
    ISSN: 0966-842X
    E-ISSN: 1878-4380
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  • 9
    Language: English
    In: Journal of Microbiological Methods, 2010, Vol.80(1), pp.63-69
    Description: and its teleomorphic stage play a key role for ecosystem functioning in terrestrial habitats. However, little is known about the ecology of the fungus. In this study we developed a novel -specific primer pair for diversity analysis. Based on a broad range master alignment, specific primers (ITS F/ITS R) were designed that comprise an approximate 650 bp fragment of the internal transcribed spacer region from all taxonomic clades of the genus This amplicon is suitable for identification with Key and BLAST. Moreover, this primer system was successfully applied to study the communities in the rhizosphere of different potato genotypes grown at two field sites in Germany. Cloning and sequencing confirmed the specificity of the primer and revealed a site-dependent composition. Based on the new primer system a semi-nested approach was used to generate amplicons suitable for denaturing gradient gel electrophoresis (DGGE) analysis and applied to analyse communities in the rhizosphere of potatoes. High field heterogeneity of communities was revealed by both DGGE. Furthermore, qPCR showed significantly different copy numbers between the sites
    Keywords: Trichoderma ; Its Region ; Diversity ; Rhizosphere ; Biology
    ISSN: 0167-7012
    E-ISSN: 1872-8359
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  • 10
    Language: English
    In: Plasmid, July 2013, Vol.70(1), pp.110-119
    Description: In spite of the contribution of plasmids to the spread of antibiotic resistance in human pathogens, little is known about the transferability of various drug resistance plasmids in bacterial biofilms. The goal of this study was to compare the efficiency of transfer of 19 multidrug resistance plasmids into recipient biofilms and determine the effects of biofilm age, biofilm-donor exposure time, and donor-to-biofilm attachment on this process. An recipient biofilm was exposed separately to 19 donors, each with a different plasmid, and transconjugants were determined by plate counting. With few exceptions, plasmids that transferred well in a liquid environment also showed the highest transferability in biofilms. The difference in transfer frequency between the most and least transferable plasmid was almost a million-fold. The ‘invasibility’ of the biofilm by plasmids, or the proportion of biofilm cells that acquired plasmids within a few hours, depended not only on the type of plasmid, but also on the time of biofilm exposure to the donor and on the ability of the plasmid donor to attach to the biofilm, yet not on biofilm age. The efficiency of donor strain attachment to the biofilm was not affected by the presence of plasmids. The most invasive plasmid was pHH2-227, which based on genome sequence analysis is a hybrid between IncU-like and IncW plasmids. The wide range in transferability in an biofilm among plasmids needs to be taken into account in our fight against the spread of drug resistance.
    Keywords: Conjugation ; Multidrug Resistance Plasmids ; Gene Transfer ; Attachment ; Pili ; Batch Culture Biofilm ; Biology
    ISSN: 0147-619X
    E-ISSN: 1095-9890
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