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  • Wiley Online Library  (54)
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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
    In: Molecular Ecology, March 2014, Vol.23(6), pp.1392-1404
    Description: Salt marsh sediments are sinks for various anthropogenic contaminants, giving rise to significant environmental concern. The process of salt marsh plant survival in such environment is very intriguing and at the same time poorly understood. The plant–microbe interactions may play a key role in the process of environment and detoxification. In this study, a combination of culture‐dependent and culture‐independent molecular approaches [enrichment cultures, polymerase chain reaction (), denaturing gradient gel electrophoresis (), sequencing] were used to investigate the effect of petroleum hydrocarbons () contamination on the structure and function [polycyclic aromatic hydrocarbon () dioxygenase genes] of endophytic bacterial communities of salt marsh plant species ( and ) in the estuarine system Ria de Aveiro (Portugal). Pseudomonads dominated the cultivable fraction of the endophytic communities in the enrichment cultures. In a set of fifty isolates tested, nine were positive for genes encoding for dioxygenases () and four were positive for plasmid carrying genes encoding degradation enzymes (c). Interestingly, these plasmids were only detected in isolates from most severely ‐polluted sites. The results revealed site‐specific effects on endophytic communities, related to the level of contamination in the sediment, and plant‐species‐specific ‘imprints’ in community structure and in genes encoding for dioxygenases. These results suggest a potential ecological role of bacterial plant symbiosis in the process of plant colonization in urban estuarine areas exposed to contamination.
    Keywords: Endophytic ; ‐Degrading Genes ; Polycyclic Aromatic Hydrocarbon ; Salt Marsh Plants
    ISSN: 0962-1083
    E-ISSN: 1365-294X
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  • 3
    In: FEMS Microbiology Letters, 2013, Vol. 348(2), pp.127-132
    Description: LowGC-type plasmids conferring resistance to sulfonamides have been frequently isolated from manure and manured soil. However, knowledge on the dynamics of plasmid-carrying populations in soil and their response to the presence of sulfonamides is scarce. Here, we investigated effects of the sulfonamide resistance conferring plasmid pHHV216 on the fitness of Acinetobacter baylyi BD413 in soil after application of manure with or without the sulfonamide antibiotic sulfadiazine (SDZ). The persistence of A. baylyi BD413 pHHV216 in competition to its plasmid-free variant was followed in soil microcosms. CFU counts showed a decrease in A. baylyi BD413 in manured soils over the experimental period of 32 days by about 0.5 log units. The proportion of the plasmid-carrying populations decreased from 50 to 〈 40% in the absence of SDZ, while the proportion of plasmid-carrying BD413 increased from 50 to about 65% with SDZ added. The data suggest that SDZ introduced via manure into soil was bioaccessible, providing a fitness advantage for the plasmid-carrying population of BD413 in soil, while the plasmid conferred a fitness disadvantage when selective pressure by SDZ was absent. In future, this method may be used as a tool for the assessment of bioavailability of antibiotics in soil.
    Keywords: Plasmid ; Sulfadiazine ; Antibiotic Resistance ; Soil ; Antibiotic Selection ; Host Fitness
    ISSN: 0378-1097
    E-ISSN: 1574-6968
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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
    Language: English
    In: Biometrical Journal, January 2012, Vol.54(1), pp.94-107
    Description: A modification of the principal component test is presented. It uses a weighted combination of the sums of squares for different principal components and is thus more powerful in high‐dimensional settings with small sample sizes. Under usual normality assumptions, a rotation test is proposed which enables an exact conditional parametric test. The procedure is demonstrated with microarray data for the bacterial composition in the rhizosphere of different potato cultivars. In simulation studies, the power of the proposed statistic is compared with the competing multivariate parametric tests.
    Keywords: High‐Dimensional Data ; Phylochip ; Principal Component Test ; Rotation Test
    ISSN: 0323-3847
    E-ISSN: 1521-4036
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  • 7
    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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  • 8
    In: FEMS Microbiology Ecology, 2010, Vol. 73(1), pp.190-196
    Description: Phytopathogenic populations need genetic flexibility to adapt to continually improving plant defences. The gene pool transferred by broad-host-range plasmids provides genetic variation for the population. However, a population has to balance this benefit with the risk of acquiring deleterious foreign DNA. This could be achieved by modulating the ratio of individuals with high or low permissiveness to broad-host-range plasmids. We investigated whether plasmid uptake varied among genetically indistinguishable isolates of Dickeya sp. from a 400 m 2 field plot. The transfer frequencies of broad-host-range IncP-1 plasmids from Escherichia coli to Dickeya differed significantly among isolates. The transfer frequencies for plasmids pTH10 and pB10 of the divergent α- and β-subgroups of IncP-1, respectively, correlated well. Strains that differed in permissiveness for these plasmids by orders of magnitude were not distinguishable by other phenotypic traits analysed, by genomic fingerprints or hrpN gene sequences. Such strains were isolated in close vicinity and from different plots of the field, indicating a reasonably fast genetic mechanism of switching between low and high permissiveness.
    Keywords: Bacterial Population Heterogeneity ; Plasmid Ecology ; Broad - Host - Range Plasmids ; Evolvability ; Adaptability ; 〈Kwd〉〈Italic〉Erwinia Chrysanthemi〈/Italic〉〈/Kwd〉
    ISSN: 01686496
    E-ISSN: 1574-6941
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  • 9
    In: FEMS Microbiology Letters, 2013, Vol. 342(2), pp.168-178
    Description: Plant protection via disease-suppressive bacteria in desert farming requires specific biological control agents (BCAs) adapted to the unique arid conditions. We performed an ecological study of below-ground communities in desert farm soil and untreated desert soil, and based on these findings, selected antagonists were hierarchically evaluated. In contrast to the highly specific 16S rRNA fingerprints of bacterial communities in soil and cultivated medicinal plants, internal transcribed spacer profiles of fungal communities were less discriminative and mainly characterised by potential pathogens. Therefore, we focused on in vitro bacterial antagonists against pathogenic fungi. Based on the antifungal potential and genomic diversity, 45 unique strains were selected and characterised in detail. Bacillus/Paenibacillus were most frequently identified from agricultural soil, but antagonists from the surrounding desert soil mainly belonged to Streptomyces . All strains produced antibiotics against the nematode Meloidogyne incognita , and one-third showed additional activity against the bacterial pathogen Ralstonia solanacearum . Altogether, 13 broad-spectrum antagonists with antibacterial, antifungal and nematicidal activity were found. They belong to seven different bacterial species of the genera Bacillus and Streptomyces . These Gram-positive, spore-forming bacteria are promising drought-resistant BCAs and a potential source for antibiotics. Their rhizosphere competence was shown by fluorescence in situ hybridisation combined with laser scanning microscopy.
    Keywords: Biological Control Agents ; Microbial Communities ; Medicinal Plants ; Soilborne Pathogens
    ISSN: 0378-1097
    E-ISSN: 1574-6968
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  • 10
    In: FEMS Microbiology Ecology, 2013, Vol. 86(1), pp.15-25
    Description: To study the influence of the clay minerals montmorillonite (M) and illite (I), the metal oxides ferrihydrite (F) and aluminum hydroxide (A), and charcoal (C) on soil bacterial communities, seven artificial soils with identical texture provided by quartz (Q) were mixed with sterilized manure as organic carbon source before adding a microbial inoculant derived from a Cambisol. Bacterial communities established in artificial soils after 90 days of incubation were compared by DGGE analysis of bacterial and taxon-specific 16S rRNA gene amplicons. The bacterial community structure of charcoal-containing soils highly differed from the other soils at all taxonomic levels studied. Effects of montmorillonite and illite were observed for Bacteria and Betaproteobacteria , but not for Actinobacteria or Alphaproteobacteria . A weak influence of metal oxides on Betaproteobacteria was found. Barcoded pyrosequencing of 16S rRNA gene amplicons done for QM, QI, QIF, and QMC revealed a high bacterial diversity in the artificial soils. The composition of the artificial soils was different from the inoculant, and the structure of the bacterial communities established in QMC soil was most different from the other soils, suggesting that charcoal provided distinct microenvironments and biogeochemical interfaces formed. Several populations with discriminative relative abundance between artificial soils were identified.
    Keywords: Clay Minerals ; Charcoal ; Bacterial Communities ; 16s Rrna Gene ; Dgge ; Pyrosequencing
    ISSN: 01686496
    E-ISSN: 1574-6941
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