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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: 2012, Vol.7(10), p.e44685
    Description: The western corn rootworm (WCR) is one of the economically most important pests of maize. A better understanding of microbial communities associated with guts and eggs of the WCR is required in order to develop new pest control strategies, and to assess the potential role of the WCR in the dissemination of microorganisms, e.g., mycotoxin-producing fungi. ; Total community (TC) DNA was extracted from maize rhizosphere, WCR eggs, and guts of larvae feeding on maize roots grown in three different soil types. Denaturing gradient gel electrophoresis (DGGE) and sequencing of 16S rRNA gene and ITS fragments, PCR-amplified from TC DNA, were used to investigate the fungal and bacterial communities, respectively. Microorganisms in the WCR gut were not influenced by the soil type. Dominant fungal populations in the gut were affiliated to spp., while was the most abundant bacterial genus. Identical ribosomal sequences from gut and egg samples confirmed a transovarial transmission of sp. Betaproteobacterial DGGE indicated a stable association of sp. with the WCR gut. Dominant egg-associated microorganisms were the bacterium sp. and the fungus ; The soil type-independent composition of the microbial communities in the WCR gut and the dominance of only a few microbial populations suggested either a highly selective environment in the gut lumen or a high abundance of intracellular microorganisms in the gut epithelium. The dominance of species in the guts indicated WCR larvae as vectors of mycotoxin-producing fungi. The stable association of sp. with WCR gut systems and the absence of corresponding sequences in WCR eggs suggested that this bacterium was postnatally acquired from the environment. The present study provided new insights into the microbial communities associated with larval guts and eggs of the WCR. However, their biological role remains to be explored.
    Keywords: Research Article ; Agriculture ; Biology ; Plant Biology ; Microbiology
    E-ISSN: 1932-6203
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  • 3
    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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  • 4
    Language: English
    In: PLoS ONE, 2011, Vol.6(3), p.e17555
    Description: Mercury-polluted environments are often contaminated with other heavy metals. Therefore, bacteria with resistance to several heavy metals may be useful for bioremediation. Cupriavidus metallidurans CH34 is a model heavy metal-resistant bacterium, but possesses a low resistance to mercury compounds. ; To improve inorganic and organic mercury resistance of strain CH34, the IncP-1β plasmid pTP6 that provides novel , genes and additional other genes was introduced into the bacterium by biparental mating. The transconjugant strain MSR33 was genetically and biochemically characterized. Strain MSR33 maintained stably the plasmid pTP6 over 70 generations under non-selective conditions. The organomercurial lyase protein MerB and the mercuric reductase MerA of strain MSR33 were synthesized in presence of Hg. The minimum inhibitory concentrations (mM) for strain MSR33 were: Hg, 0.12 and CHHg, 0.08. The addition of Hg (0.04 mM) at exponential phase had not an effect on the growth rate of strain MSR33. In contrast, after Hg addition at exponential phase the parental strain CH34 showed an immediate cessation of cell growth. During exposure to Hg no effects in the morphology of MSR33 cells were observed, whereas CH34 cells exposed to Hg showed a fuzzy outer membrane. Bioremediation with strain MSR33 of two mercury-contaminated aqueous solutions was evaluated. Hg (0.10 and 0.15 mM) was completely volatilized by strain MSR33 from the polluted waters in presence of thioglycolate (5 mM) after 2 h. ; A broad-spectrum mercury-resistant strain MSR33 was generated by incorporation of plasmid pTP6 that was directly isolated from the environment into CH34. Strain MSR33 is capable to remove mercury from polluted waters. This is the first study to use an IncP-1β plasmid directly isolated from the environment, to generate a novel and stable bacterial strain useful for mercury bioremediation.
    Keywords: Research Article ; Biology ; Microbiology ; Biotechnology
    E-ISSN: 1932-6203
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  • 5
    Language: English
    In: Applied Microbiology and Biotechnology, 2016, Vol.100(21), pp.9343-9353
    Description: Pig manures are frequently used as fertilizer or co-substrate in biogas plants (BGPs) and typically contain antibiotic residues (ARs), as well as bacteria carrying resistance genes (RGs) and mobile genetic elements (MGEs). A survey of manures from eight pig fattening and six pig breeding farms and digestates from eight BGPs in Lower Saxony, Germany was conducted to evaluate the link between antibiotic usage and ARs to RGs and MGEs present in organic fertilizers. In total, 11 different antibiotics belonging to six substance classes were applied in the farms investigated. Residue analysis revealed concentrations of tetracycline up to 300 mg kg −1 dry weight (DW) in manures and of doxycycline up to 10.1 mg kg −1 DW in digestates indicating incomplete removal during anaerobic digestion. RGs ( sul1 , sul2 , tet (A), tet (M), tet (X), qacE ∆ 1 ) were detected in total community DNA of all samples by PCR-Southern blot hybridization. Broad-host range plasmids (IncP-1, IncQ, IncN, and IncW) and integron integrase genes ( intI1 , intI2 ) were found in most manure samples with IncN and IncW plasmids being more abundant in manure from pig breeding compared to pig fattening farms. IntI1 , IncQ, and IncW plasmids were also detected in all digestates, while IncP-1, IncN, and LowGC plasmids were detected only sporadically. Our findings strongly reinforce the need for further research to identify mitigation strategies to reduce the level of contamination of organic fertilizers with ARs and transferable RGs that are applied to soil and that might influence the mobile resistome of the plant microbiome.
    Keywords: Antibiotic resistance genes ; Mobile genetic elements ; Antibiotics ; Pig husbandry ; Manures ; Digestates
    ISSN: 0175-7598
    E-ISSN: 1432-0614
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  • 6
    Language: English
    In: Applied Microbiology and Biotechnology, 2017, Vol.101(11), pp.4815-4825
    Description: On-farm biopurification systems (BPSs) represent an efficient technology for treating pesticide-contaminated wastewater. Biodegradation by genetically adapted bacteria has been suggested to perform a major contribution to the removal of pesticides in BPSs. Recently, several studies pointed to the role of IncP-1 plasmids in the degradation of pesticides in BPSs but this was never linked with catabolic markers. Therefore, a microcosm experiment was conducted in order to examine whether changes in mobile genetic element (MGE) abundances in response to the application of phenylurea herbicide linuron are linked with changes in catabolic genes. Denaturing gradient gel electrophoresis (DGGE) fingerprints of 16S ribosomal RNA gene fragments amplified from total community (TC)-DNA suggested significant shifts in the bacterial community composition. PCR-Southern blot-based detection of genes involved in linuron hydrolysis ( libA and hylA ) or degradation of its metabolite 3,4-dichloroaniline ( dcaQ I , dcaQ II , and ccdC ) in TC-DNA showed that the abundance of the hylA gene was increased faster and stronger in response to linuron application than that of the libA gene, and that the dcaQ II gene was more abundant than the isofunctional gene dcaQ I 20 and 60 days after linuron addition. Furthermore, a significant increase in the relative abundance of the IncP-1-specific korB gene in response to linuron was recorded. Our data suggest that different bacterial populations bearing isofunctional genes coding for enzymes degrading linuron seemed to be enriched in BPSs in response to linuron and that IncP-1 plasmids might be involved in their dissemination.
    Keywords: Total community DNA ; 16S rRNA genes ; Degradative genes ; PCR hybridization ; Plasmids
    ISSN: 0175-7598
    E-ISSN: 1432-0614
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  • 7
    Language: English
    In: PLoS ONE, 2012, Vol.7(5), p.e37288
    Description: Larvae of the Western Corn Rootworm (WCR) feeding on maize roots cause heavy economical losses in the US and in Europe. New or adapted pest management strategies urgently require a better understanding of the multitrophic interaction in the rhizosphere. This study aimed to investigate the effect of WCR root feeding on the microbial communities colonizing the maize rhizosphere. ; In a greenhouse experiment, maize lines KWS13, KWS14, KWS15 and MON88017 were grown in three different soil types in presence and in absence of WCR larvae. Bacterial and fungal community structures were analyzed by denaturing gradient gel electrophoresis (DGGE) of the16S rRNA gene and ITS fragments, PCR amplified from the total rhizosphere community DNA. DGGE bands with increased intensity were excised from the gel, cloned and sequenced in order to identify specific bacteria responding to WCR larval feeding. DGGE fingerprints showed that the soil type and the maize line influenced the fungal and bacterial communities inhabiting the maize rhizosphere. WCR larval feeding affected the rhiyosphere microbial populations in a soil type and maize line dependent manner. DGGE band sequencing revealed an increased abundance of in the rhizosphere of several maize lines in all soil types upon WCR larval feeding. ; The effects of both rhizosphere and WCR larval feeding seemed to be stronger on bacterial communities than on fungi. Bacterial and fungal community shifts in response to larval feeding were most likely due to changes of root exudation patterns. The increased abundance of suggested that phenolic compounds were released upon WCR wounding.
    Keywords: Research Article ; Agriculture ; Biology ; Genetics And Genomics ; Plant Biology ; Biotechnology ; Ecology
    E-ISSN: 1932-6203
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  • 8
    Language: English
    In: PLoS ONE, 2012, Vol.7(1), p.e29380
    Description: Here, we use DGGE fingerprinting and barcoded pyrosequencing data, at six cut-off levels (85–100%), of all bacteria, Alphaproteobacteria and Betaproteobacteria to assess composition in the rhizosphere of nursery plants and nursery-raised transplants, native plants and bulk sediment in a mangrove habitat. When comparing compositional data based on DGGE fingerprinting and barcoded pyrosequencing at different cut-off levels, all revealed highly significant differences in composition among microhabitats. Procrustes superimposition revealed that ordination results using cut-off levels from 85–100% and DGGE fingerprint data were highly congruent with the standard 97% cut-off level. The various approaches revealed a primary gradient in composition from nursery to mangrove samples. The affinity between the nursery and transplants was greatest when using Betaproteobacteria followed by Alphaproteobacteria data. There was a distinct secondary gradient in composition from transplants to bulk sediment with native plants intermediate, which was most prevalent using all bacteria at intermediate cut-off levels (92–97%). Our results show that PCR-DGGE provides a robust and cost effective exploratory approach and is effective in distinguishing among a priori defined groups.
    Keywords: Research Article ; Biology ; Earth Sciences ; Genetics And Genomics ; Plant Biology ; Computational Biology ; Ecology ; Marine And Aquatic Sciences
    E-ISSN: 1932-6203
    Source: PLoS
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  • 9
    Language: English
    In: Applied and environmental microbiology, July 2012, Vol.78(14), pp.4933-41
    Description: Bananas are among the most widely consumed foods in the world. In Uganda, the country with the second largest banana production in the world, bananas are the most important staple food. The objective of this study was to analyze banana-associated microorganisms and to select efficient antagonists against fungal pathogens which are responsible for substantial yield losses. We studied the structure and function of microbial communities (endosphere, rhizosphere, and soil) obtained from three different traditional farms in Uganda by cultivation-independent (PCR-SSCP fingerprints of 16S rRNA/ITS genes, pyrosequencing of enterobacterial 16S rRNA gene fragments, quantitative PCR, fluorescence in situ hybridization coupled with confocal laser scanning microscopy, and PCR-based detection of broad-host-range plasmids and sulfonamide resistance genes) and cultivation-dependent methods. The results showed microhabitat-specific microbial communities that were significant across sites and treatments. Furthermore, all microhabitats contained a high number and broad spectrum of indigenous antagonists toward identified fungal pathogens. While bacterial antagonists were found to be enriched in banana plants, fungal antagonists were less abundant and mainly found in soil. The banana stem endosphere was the habitat with the highest bacterial counts (up to 10(9) gene copy numbers g(-1)). Here, enterics were found to be enhanced in abundance and diversity; they provided one-third of the bacteria and were identified by pyrosequencing with 14 genera, including not only potential human (Escherichia, Klebsiella, Salmonella, and Yersinia spp.) and plant (Pectobacterium spp.) pathogens but also disease-suppressive bacteria (Serratia spp.). The dominant role of enterics can be explained by the permanent nature and vegetative propagation of banana and the amendments of human, as well as animal, manure in these traditional cultivations.
    Keywords: Rhizosphere ; Soil Microbiology ; Crops, Agricultural -- Microbiology ; Enterobacteriaceae -- Isolation & Purification ; Fungi -- Isolation & Purification ; Musa -- Microbiology
    ISSN: 00992240
    E-ISSN: 1098-5336
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  • 10
    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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