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  • 1
    In: Environmental Microbiology, March 2007, Vol.9(3), pp.657-666
    Description: Manuring of arable soils may stimulate the spread of resistance genes by introduction of resistant populations and antibiotics. We investigated effects of pig manure and sulfadiazine (SDZ) on bacterial communities in soil microcosms. A silt loam and a loamy sand were mixed with manure containing SDZ (10 or 100 mg per kilogram of soil), and compared with untreated soil and manured soil without SDZ over a 2‐month period. In both soils, manure and SDZ positively affected the quotients of total and SDZ‐resistant culturable bacteria [most probable number (MPN)], and transfer frequencies of plasmids conferring SDZ resistance in filter matings of soil bacteria and an recipient. Detection of sulfonamide resistance genes , and in community DNA by polymerase chain reaction (PCR) and hybridization revealed a high prevalence of in manure and manured soils, while was mainly found in the loamy sand treated with manure and high SDZ amounts, and was not detected. By PCR quantification of and bacterial genes, a transient effect of manure alone and a long‐term effect of SDZ plus manure on absolute and relative abundance in soil was shown. The dynamics in soil of class 1 integrons, which are typically associated with , was analysed by amplification of the gene cassette region. Integrons introduced by manure established in both soils. Soil type and SDZ affected the composition of integrons. The synergistic effects of manure and SDZ were still detectable after 2 months. The results suggest that manure from treated pigs enhances spread of antibiotic resistances in soil bacterial communities.
    Keywords: Microbial Drug Resistance ; Sulfadiazine;
    ISSN: 1462-2912
    E-ISSN: 1462-2920
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  • 2
    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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  • 3
    In: Environmental Microbiology, December 2006, Vol.8(12), pp.2136-2149
    Description: Despite their importance for rhizosphere functioning, rhizobacterial spp. have been mainly studied in a cultivation‐based manner. In this study a cultivation‐independent method was used to determine to what extent the factors plant species, sampling site and year‐to‐year variation influence community structure in bulk soil and in the rhizosphere of two host plants, oilseed rape and strawberry. Community DNA was extracted from bulk and rhizosphere soil samples of flowering plants collected at three different sites in Germany in two consecutive years. community structure and diversity were assessed using a polymerase chain reaction denaturing gradient gel electrophoresis (PCR‐DGGE) system to fingerprint ‐specific 16S rRNA gene fragments amplified from community DNA. Dominant and differentiating DGGE bands were excised from the gels, cloned and sequenced. The factors sampling site, plant species and year‐to‐year variation were shown to significantly influence the community structure of in rhizosphere soils. The composition of 16S rRNA gene fragments in the rhizosphere differed from that in the adjacent bulk soil and the rhizosphere effect tended to be plant‐specific. The clone sequences of most dominant bands analysed belonged to the lineage and showed closest similarity to culturable known for displaying antifungal properties. This report provides a better understanding of how different factors drive community structure and diversity in bulk and rhizosphere soils.
    Keywords: Plants (Organisms) -- Analysis;
    ISSN: 1462-2912
    E-ISSN: 1462-2920
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  • 4
    In: Environmental Microbiology, March 2009, Vol.11(3), pp.700-714
    Description: The diversity of naphthalene dioxygenase genes () in soil environments from the Maritime Antarctic was assessed, dissecting as well the influence of the two vascular plants that grow in the Antarctic and . Total community DNA was extracted from bulk and rhizosphere soil samples from Jubany station and Potter Peninsula, South Shetland Islands. genes were amplified by a nested PCR and analysed by denaturant gradient gel electrophoresis approach (PCR‐DGGE) and cloning and sequencing. The DGGE fingerprints of oil‐contaminated soil samples showed even and reproducible patterns, composed of four dominant bands. The presence of vascular plants did not change the relative abundance of genotypes compared with bulk soil. For non‐contaminated sites, amplicons were not obtained for all replicates and the variability among the fingerprints was comparatively higher, likely reflecting a lower abundance of genes. The phylogenetic analyses showed that all sequences were affiliated to the genes closely related to those described for species and related mobile genetic elements. This study revealed that a microdiversity of ‐like genes exists in microbial communities of Antarctic soils and quantitative PCR indicated that their relative abundance was increased in response to anthropogenic sources of pollution.
    Keywords: Polymerase Chain Reaction ; Genetic Research ; Soils ; Hydrocarbons ; Transposons;
    ISSN: 1462-2912
    E-ISSN: 1462-2920
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  • 5
    In: Environmental Microbiology, April 2009, Vol.11(4), pp.937-949
    Description: Bioactive amounts of antibiotics as well as resistant bacteria reach the soil through manure fertilization. We investigated plasmids that may stimulate the environmental spread and interspecies transfer of antibiotic resistance. After treatment of two soils with manure, either with or without the sulfonamide antibiotic sulfadiazine, a significant increase in copies of the sulfonamide resistance gene was detected by qPCR. All carrying plasmids, captured in from soil, belonged to a novel class of self‐transferable replicons. Manuring and sulfadiazine significantly increased the abundance of this replicon type in a chemically fertilized but not in an annually manured soil, as determined by qPCR targeting a transfer gene. Restriction patterns and antibiograms showed a considerable diversity within this novel plasmid group. Analysis of three complete plasmid sequences revealed a conserved 30 kbp backbone with only 36% G+C content, comprised of transfer and maintenance genes with moderate homology to plasmid pIPO2 and a replication module ( and ) of other descent. The plasmids differed in composition of the 27.0–28.3 kbp accessory region, each of which carried IS and several resistance genes. spp. was identified as a potential host of such LowGC‐type plasmids in manure and soil.
    Keywords: Microbial Drug Resistance -- Analysis ; Water Quality -- Analysis ; Sulfadiazine -- Analysis ; Soils -- Analysis;
    ISSN: 1462-2912
    E-ISSN: 1462-2920
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  • 6
    In: Environmental Microbiology, February 2009, Vol.11(2), pp.446-456
    Description: Crucial steps in geochemical cycles are in many cases performed by more than one group of microorganisms, but the significance of this functional redundancy with respect to ecosystem functioning is poorly understood. Ammonia‐oxidizing archaea (AOA) and their bacterial counterparts (AOB) are a perfect system to address this question: although performing the same transformation step, they belong to well‐separated phylogenetic groups. Using pig manure amended with different concentrations of sulfadiazine (SDZ), an antibiotic that is frequently used in veterinary medicine, it was possible to affect AOB and AOA to different degrees. Addition of manure stimulated growth of AOB in both soils and, interestingly, also growth of AOA was considerably stimulated in one of the soils. The antibiotic treatments decreased the manure effect notably on AOB, whereas AOA were affected to a lower extent. Model calculations concerning the respective proportions of AOA and AOB in ammonia oxidation indicate a substantial contribution of AOA in one of the soils that further increased under the influence of SDZ, hence indicating functional redundancy between AOA and AOB.
    Keywords: Geology -- Analysis ; Ammonia -- Analysis ; Soil Ecology -- Analysis ; Sulfadiazine -- Analysis ; Ecosystems -- Analysis ; Soils -- Analysis ; Universities And Colleges -- Analysis ; Geochemical Cycles -- Analysis;
    ISSN: 1462-2912
    E-ISSN: 1462-2920
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  • 7
    In: Environmental Microbiology, July 2019, Vol.21(7), pp.2426-2439
    Description: Long‐term agricultural fertilization strategies gradually change soil properties including the associated microbial communities. Cultivated crops recruit beneficial microbes from the surrounding soil environment root exudates. In this study, we aimed to investigate the effects of long‐term fertilization strategies across field sites on the rhizosphere prokaryotic ( and ) community composition and plant performance. We conducted growth chamber experiments with lettuce ( L.) cultivated in soils from two long‐term field experiments, each of which compared organic versus mineral fertilization strategies. 16S rRNA gene amplicon sequencing revealed the assemblage of a rhizosphere core microbiota shared in all lettuce plants across soils, going beyond differences in community composition depending on field site and fertilization strategies. The enhanced expression of several plant genes with roles in oxidative and biotic stress signalling pathways in lettuce grown in soils with organic indicates an induced physiological status in plants. Lettuce plants grown in soils with different fertilization histories were visibly free of stress symptoms and achieved comparable biomass. This suggests a positive aboveground plant response to belowground plant–microbe interactions in the rhizosphere. Besides effects of fertilization strategy and field site, our results demonstrate the crucial role of the plant in driving rhizosphere microbiota assemblage.
    Keywords: Soil Microbiology – Physiological Aspects ; Soil Microbiology – Analysis ; Plant Genetics – Physiological Aspects ; Plant Genetics – Analysis ; Plants (Organisms) – Physiological Aspects ; Plants (Organisms) – Analysis ; Soil Ecology – Physiological Aspects ; Soil Ecology – Analysis ; Microbiota (Symbiotic Organisms) – Physiological Aspects ; Microbiota (Symbiotic Organisms) – Analysis ; RNA – Physiological Aspects ; RNA – Analysis;
    ISSN: 1462-2912
    E-ISSN: 1462-2920
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