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  • 1
    In: FEMS Microbiology Ecology, 2013, Vol. 86(1), pp.1-2
    Description: In soils, a multitude of inorganic, organic, and biological constituents build up extremely large, heterogeneous, and hierarchically organized biogeochemical interfaces (BGIs). These interfaces affect a variety of soil processes, such as the formation and the stability of soil aggregates; the movement and the spatial distribution of solutes, colloids, and gases; or the bioavailability of inorganic and organic compounds. As environmental conditions prevailing in soil frequently change over time and in space, the structural and the compositional heterogeneity of BGIs offers a multitude of microhabitats and supports growth of highly diverse microbial communities. Yet, microorganisms not only inhabit these interfaces, but they also actively participate in their formation and reorganization, as well as in their destabilization and destruction. They may thus be seen as both “architects” and “actors” …
    Keywords: Environmental Sciences ; Biology;
    ISSN: 01686496
    E-ISSN: 1574-6941
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  • 2
    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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  • 3
    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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  • 4
    In: FEMS Microbiology Ecology, 2013, Vol. 86(3), pp.415-431
    Description: Mobile genetic elements (MGEs) are considered as key players in the adaptation of bacteria to degrade organic xenobiotic recalcitrant compounds such as pesticides. We examined the prevalence and abundance of IncP-1 plasmids and IS 1071 , two MGEs that are frequently linked with organic xenobiotic degradation, in laboratory and field ecosystems with and without pesticide pollution history. The ecosystems included on-farm biopurification systems (BPS) processing pesticide-contaminated wastewater and soil. Comparison of IncP-1/IS 1071 prevalence between pesticide-treated and nontreated soil and BPS microcosms suggested that both IncP-1 and IS 1071 proliferated as a response to pesticide treatment. The increased prevalence of IncP-1 plasmids and IS 1071 -specific sequences in treated systems was accompanied by an increase in the capacity to mineralize the applied pesticides. Both elements were also encountered in high abundance in field BPS ecosystems that were in operation at farmyards and that showed the capacity to degrade/mineralize a wide range of chlorinated aromatics and pesticides. In contrast, IS 1071 and especially IncP-1, MGE were less abundant in field ecosystems without pesticide history although some of them still showed a high IS 1071 abundance. Our data suggest that MGE-containing organisms were enriched in pesticide-contaminated environments like BPS where they might contribute to spreading of catabolic genes and to pathway assembly.
    Keywords: Mobile Genetic Elements ; Biopurification System ; Incp - 1 Plasmids ; 〈Kwd〉〈Italic〉Is1071〈/Italic〉〈/Kwd〉
    ISSN: 01686496
    E-ISSN: 1574-6941
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  • 5
    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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  • 6
    In: FEMS Microbiology Ecology, 2016, Vol. 92(11)
    Keywords: Environmental Sciences ; Biology;
    E-ISSN: 1574-6941
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  • 7
    In: FEMS Microbiology Ecology, 2016, Vol. 92(11)
    Keywords: Microbiology ; Antibiotic Resistance ; Microbiology ; Antibiotics ; Antibiotic Resistance;
    ISSN: 01686496
    E-ISSN: 1574-6941
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  • 8
    Language: English
    In: FEMS Microbiology Ecology, 01/2012, Vol.79(1), pp.167-175
    Description: B urkholderia is a physiologically and ecologically diverse genus that occurs commonly in assemblages of soil and rhizosphere bacteria. Although B urkholderia is known for its heterotrophic versatility, we demonstrate that 14 distinct environmental isolates oxidized carbon monoxide (CO) and possessed the gene encoding the catalytic subunit of form I CO dehydrogenase ( coxL ). DNA from a B urkholderia isolate obtained from a passalid beetle also contained coxL as do the genomic sequences of species H160 and Ch1-1. Isolates were able to consume CO at concentrations ranging from 100 ppm (vol/vol) to sub-ambient (〈 60 ppb (vol/vol)). High concentrations of pyruvate inhibited CO uptake (〉 2.5 mM), but mixotrophic consumption of CO and pyruvate occurred when initial pyruvate concentrations were lower ( c . 400 μM). With the exception of an isolate most closely related to B urkholderia cepacia , all CO-oxidizing isolates examined were members of a nonpathogenic clade and were most closely related to B urkholderia species, B. caledonica , B. fungorum , B. oxiphila , B. mimosarum , B. nodosa , B. sacchari , B. bryophila , B. ferrariae , B. ginsengesoli , and B. unamae . However, none of these type strains oxidized CO or contained coxL based on results from PCR analyses. Collectively, these results demonstrate that the presence of CO oxidation within members of the B urkholderia genus is variable but it is most commonly found among rhizosphere inhabitants that are not closely related to B . cepacia .
    Keywords: 〈Kwd〉〈Italic〉B〈/Italic〉〈Italic〉Urkholderia〈/Italic〉〈/Kwd〉 ; Carbon Monoxide ; 〈Kwd〉〈Italic〉Coxl〈/Italic〉〈/Kwd〉;
    ISSN: FEMS Microbiology Ecology
    E-ISSN: 01686496
    E-ISSN: 15746941
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  • 9
    In: FEMS Microbiology Ecology, 2016, Vol. 92(2)
    Description: The goal of this study was to determine the fate of antibiotic resistance genes (ARGs) and class 1 integrons following the application of swine and dairy manure to soil. Soil microcosms were amended with either manure from swine fed subtherapeutic levels of antibiotics or manure from dairy cows that were given antibiotics only rarely and strictly for veterinary purposes. Microcosms were monitored for 6 months using quantitative PCR targeting 16S rRNA genes (a measure of bacterial biomass), intI1 , erm (B) , tet (A), tet (W) and tet (X). Swine manure had 10- to 100-fold higher levels of ARGs than the dairy manure, all of which decayed over time after being applied to soil. A modified Collins–Selleck model described the decay of ARGs in the soil microcosms well, particularly the characteristic in which the decay rate declined over time. By the completion of the soil microcosm experiments, ARGs in the dairy manure-amended soils returned to background levels, whereas the ARGs in swine manure remained elevated compared to control microcosms. Our research suggests that the use of subtherapeutic use of antibiotics in animal feed could lead to the accumulation of ARGs in soils to which manure is applied. The application of manure to soil from animals fed subtherapeutic levels of antibiotics can lead to the accumulation of antibiotic resistance genes. Graphical Abstract Figure. The application of manure to soil from animals fed subtherapeutic levels of antibiotics can lead to the accumulation of antibiotic resistance genes.
    Keywords: Antibiotic Resistance ; Dairy ; Manure ; Qpcr ; Subtherapeutic ; Swine
    E-ISSN: 1574-6941
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  • 10
    In: FEMS Microbiology Ecology, 2015, Vol. 91(12)
    Description: We investigated the growth of Campylobacter jejuni in biofilms with Pseudomonas aeruginosa under oxic flow conditions. We observed the growth of C. jejuni in mono-culture, deposited on pre-established P. aeruginosa biofilms, and co-inoculated with P. aeruginosa . In mono-culture, C. jejuni was unable to form biofilms. However, deposited C. jejuni continuously grew on pre-established P. aeruginosa biofilms for a period of 3 days. The growth of scattered C. jejuni clusters was strictly limited to the P. aeruginosa biofilm surface, and no intergrowth was observed. Co-culturing of C. jejuni and P. aeruginosa also enabled the growth of both organisms in biofilms, with C. jejuni clusters developing on the surface of the P. aeruginosa biofilm. Dissolved oxygen (DO) measurements in the medium showed that P. aeruginosa biofilms depleted the effluent DO from 9.0 to 0.5 mg L −1 24 hours after inoculation. The localized microaerophilic environment generated by P. aeruginosa promoted the persistence and growth of C. jejuni . Our findings show that P. aeruginosa not only prolongs the survival of C. jejuni under oxic conditions, but also enables the growth of C. jejuni on the surface of P. aeruginosa biofilms. Localized, low-oxygen environments generated by the community metabolism of P. aeruginosa biofilms enable the growth of C. jejuni biofilms under oxic flow conditions. Graphical Abstract Figure. Localized, low-oxygen environments generated by the community metabolism of P. aeruginosa biofilms enable the growth of C. jejuni biofilms under oxic flow conditions.
    Keywords: 〈Kwd〉〈Italic Toggle="Yes"〉Campylobacter Jejuni〈/Italic〉〈/Kwd〉 ; Pathogen Persistence ; Immunofluorescence ; 〈Kwd〉〈Italic Toggle="Yes"〉Pseudomonas〈/Italic〉〈/Kwd〉 ; Oligotrophic Environment ; Microaerophilic
    E-ISSN: 1574-6941
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