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  • 1
    Language: English
    In: Applied and environmental microbiology, February 2013, Vol.79(4), pp.1410-3
    Description: To study the role of broad-host-range IncP-1 plasmids in bacterial adaptability to irregular environmental challenges, a quantitative real-time PCR assay was developed that specifically detects the korB gene, which is conserved in all IncP-1 plasmids, in environmental samples. IncP-1 plasmid dynamics in a biopurification system for pesticide wastes were analyzed.
    Keywords: Environmental Microbiology ; Bacteroidetes -- Genetics ; Plasmids -- Analysis
    ISSN: 00992240
    E-ISSN: 1098-5336
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  • 2
    Language: English
    In: Applied and environmental microbiology, July 2014, Vol.80(13), pp.4012-20
    Description: Biopurification systems (BPS) are used on farms to control pollution by treating pesticide-contaminated water. It is assumed that mobile genetic elements (MGEs) carrying genes coding for enzymes involved in degradation might contribute to the degradation of pesticides. Therefore, the composition and shifts of MGEs, in particular, of IncP-1 plasmids carried by BPS bacterial communities exposed to various pesticides, were monitored over the course of an agricultural season. PCR amplification of total community DNA using primers targeting genes specific to different plasmid groups combined with Southern blot hybridization indicated a high abundance of plasmids belonging to IncP-1, IncP-7, IncP-9, IncQ, and IncW, while IncU and IncN plasmids were less abundant or not detected. Furthermore, the integrase genes of class 1 and 2 integrons (intI1, intI2) and genes encoding resistance to sulfonamides (sul1, sul2) and streptomycin (aadA) were detected and seasonality was revealed. Amplicon pyrosequencing of the IncP-1 trfA gene coding for the replication initiation protein revealed high IncP-1 plasmid diversity and an increase in the abundance of IncP-1β and a decrease in the abundance of IncP-1ε over time. The data of the chemical analysis showed increasing concentrations of various pesticides over the course of the agricultural season. As an increase in the relative abundances of bacteria carrying IncP-1β plasmids also occurred, this might point to a role of these plasmids in the degradation of many different pesticides.
    Keywords: Interspersed Repetitive Sequences ; Bacteria -- Genetics ; Metabolic Networks and Pathways -- Genetics ; Pesticides -- Metabolism ; Water Pollutants -- Metabolism
    ISSN: 00992240
    E-ISSN: 1098-5336
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  • 3
    Language: English
    In: Plant and Soil, 2012, Vol.361(1), pp.343-357
    Description: Co-inoculation of biocontrol agents with different modes of action is assumed to improve biocontrol activity. The present study aimed to investigate the effects of single or co-inoculation of Trichoderma viride strain GB7 and Serratia plymuthica strain 3Re4-18 on microbial communities in the rhizosphere of lettuce and their ability to suppress Rhizoctonia solani AG1-IB.Growth chamber experiments with two different application modes were performed with single or co-inoculation of GB7 and 3Re4-18 in the presence or absence of R. solani. Biocontrol efficacy and plant growth parameters were assessed. Bacterial and fungal communities were analyzed by 16S rRNA gene and ITS fragments PCR-amplified from total community DNA of rhizosphere samples and analyzed by denaturing gradient gel electrophoresis.Compared to the single application, the co-inoculation of 3Re4-18 and GB7 resulted in an improved biocontrol efficacy. DGGE analysis revealed more pronounced effect on microbial community in co-inoculation treatment. The abundance of 3Re4-18 in the rhizosphere seemed to be increased in the presence of R. solani.The applied cultivation-independent methods provided insights into the complex interaction in response to the pathogen and the antagonists. Co-inoculation resulted in an improved biocontrol efficacy and an increased evenness of the microbial communities.
    Keywords: Biocontrol ; Co-inoculation ; Rhizosphere community ; 16S rRNA gene and ITS-based fingerprints
    ISSN: 0032-079X
    E-ISSN: 1573-5036
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  • 4
    Language: English
    In: Applied and environmental microbiology, August 2012, Vol.78(16), pp.5520-8
    Description: Mangroves are complex ecosystems that regulate nutrient and sediment fluxes to the open sea. The importance of bacteria and fungi in regulating nutrient cycles has led to an interest in their diversity and composition in mangroves. However, very few studies have assessed Archaea in mangroves, and virtually nothing is known about whether mangrove rhizospheres affect archaeal diversity and composition. Here, we studied the diversity and composition of Archaea in mangrove bulk sediment and the rhizospheres of two mangrove trees, Rhizophora mangle and Laguncularia racemosa, using denaturing gradient gel electrophoresis (DGGE) and pyrosequencing of archaeal 16S rRNA genes with a nested-amplification approach. DGGE profiles revealed significant structural differences between bulk sediment and rhizosphere samples, suggesting that roots of both mangrove species influence the sediment archaeal community. Nearly all of the detected sequences obtained with pyrosequencing were identified as Archaea, but most were unclassified at the level of phylum or below. Archaeal richness was, furthermore, the highest in the L. racemosa rhizosphere, intermediate in bulk sediment, and the lowest in the R. mangle rhizosphere. This study shows that rhizosphere microhabitats of R. mangle and L. racemosa, common plants in subtropical mangroves located in Rio de Janeiro, Brazil, hosted distinct archaeal assemblages.
    Keywords: Biodiversity ; DNA Barcoding, Taxonomic ; Denaturing Gradient Gel Electrophoresis ; Archaea -- Classification ; Combretaceae -- Microbiology ; Plant Roots -- Microbiology ; Rhizophoraceae -- Microbiology
    ISSN: 00992240
    E-ISSN: 1098-5336
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  • 5
    Language: English
    In: Applied and Environmental Microbiology, 2012, Vol.78(16), p.5520(9)
    Description: The diversity and composition of Archaea in mangrove bulk sediment and the rhizospheres of two mangrove trees is studied, using denaturing gradient gel electrophoresis (DGGE) and pyrosequencing. The study shows that rhizosphere microhabitats of R. mangle and L. racemosa, common plants in subtropical mangroves located in Rio de Janeiro, Brazil, host distinct archaeal assemblages.
    Keywords: Archaea – Growth ; Archaea – Distribution ; Mangroves (Plants) – Growth ; Plant Growth – Research ; Soil Microbiology – Research
    ISSN: 0099-2240
    Source: Cengage Learning, Inc.
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  • 6
    Language: English
    In: PLoS One, 2014, Vol.9(2), pp.e89922-e89922
    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.
    ISSN: 1932-6203
    Source: KU Leuven Association
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  • 7
    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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  • 8
    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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  • 9
    Language: English
    In: Frontiers in microbiology, 2013, Vol.4, pp.420
    Description: Class 1 integrons contribute to the emerging problem of antibiotic resistance in human medicine by acquisition, exchange, and expression of resistance genes embedded within gene cassettes. Besides the clinical setting they were recently reported from environmental habitats and often located on plasmids and transposons, facilitating their transfer and spread within bacterial communities. In this study we aimed to provide insights into the occurrence of genes typically associated with the class 1 integrons in previously not studied environments with or without human impact and their association with IncP-1 plasmids. Total community DNA was extracted from manure-treated and untreated soils, lettuce and potato rhizosphere, digestates, and an on-farm biopurification system and screened by PCR with subsequent Southern blot hybridization for the presence of the class 1 integrase gene intI1 as well as qacE and qacEΔ 1 resistance genes. The results revealed a widespread dissemination of class 1 integrons in the environments analyzed, mainly related to the presence of qacEΔ 1 genes. All 28 IncP-1ε plasmids carrying class 1 integrons, which were captured exogenously in a recent study from piggery manure and soils treated with manure, carried qacEΔ 1 genes. Based on the strong hybridization signals in the rhizosphere of lettuce compared to the potato rhizosphere, the abundances of intI1, qacE/qacEΔ 1, and sul1 genes were quantified relative to the 16S rRNA gene abundance by real-time PCR in the rhizosphere of lettuce planted in three different soils and in the corresponding bulk soil. A significant enrichment of intI1 and qacE/qacEΔ 1 genes was confirmed in the rhizosphere of lettuce compared to bulk soil. Additionally, the relative abundance of korB genes specific for IncP-1 plasmids was enriched in the rhizosphere and correlated to the intI1 gene abundance indicating that IncP-1 plasmids might have contributed to the spread of class 1 integrons in the analyzed soils.
    Keywords: Incp-1 Korb ; Biofilter ; Digestates ; Inti1 ; Manured Soil and Rhizosphere ; Qace ; Qaceδ1 ; Sul1
    ISSN: 1664-302X
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  • 10
    Language: English
    In: Plant and Soil, 1 January 2012, Vol.361, pp.343-357
    Description: Background and aims Co-inoculation of biocontrol agents with different modes of action is assumed to improve biocontrol activity. The present study aimed to investigate the effects of single or co-inoculation of Trichoderma viride strain GB7 and Serratia plymuthica strain 3Re4-18 on microbial communities in the rhizosphere of lettuce and their ability to suppress Rhizoctonia solani AG1-IB. Methods Growth chamber experiments with two different application modes were performed with single or co-inoculation of GB7 and 3Re4-18 in the presence or absence of R. solani. Biocontrol efficacy and plant growth parameters were assessed. Bacterial and fungal communities were analyzed by 16S rRNA gene and ITS fragments PCR-amplified from total community DNA of rhizosphere samples and analyzed by denaturing gradient gel electrophoresis. Results Compared to the single application, the co-inoculation of 3Re4-18 and GB7 resulted in an improved biocontrol efficacy. DGGE analysis revealed more pronounced effect on microbial community in co-inoculation treatment. The abundance of 3Re4-18 in the rhizosphere seemed to be increased in the presence of R. solani. Conclusions The applied cultivation-independent methods provided insights into the complex interaction in response to the pathogen and the antagonists. Co-inoculation resulted in an improved biocontrol efficacy and an increased evenness of the microbial communities.
    Keywords: Biological sciences -- Ecology -- Population ecology ; Biological sciences -- Biology -- Microbiology ; Biological sciences -- Biology -- Botany ; Health sciences -- Medical sciences -- Immunology ; Biological sciences -- Biology -- Mycology ; Biological sciences -- Biology -- Mycology ; Biological sciences -- Agriculture -- Farming ; Biological sciences -- Agriculture -- Agricultural sciences ; Biological sciences -- Biology -- Botany ; Biological sciences -- Biology -- Mycology
    ISSN: 0032079X
    E-ISSN: 15735036
    Source: Archival Journals (JSTOR)
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