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  • 1
    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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  • 2
    Language: English
    In: Soil Biology and Biochemistry, December 2014, Vol.79, pp.57-67
    Description: The study of interactions between minerals, organic matter (OM) and microorganisms is essential for the understanding of soil functions such as OM turnover. Here, we present an interdisciplinary approach using artificial soils to study the establishment of the microbial community and the formation of macro-aggregates as a function of the mineral composition by using artificial soils. The defined composition of a model system enables to directly relate the development of microbial communities and soil structure to the presence of specific constituents. Five different artificial soil compositions were produced with two types of clay minerals (illite, montmorillonite), metal oxides (ferrihydrite, boehmite) and charcoal incubated with sterile manure and a microbial community derived from a natural soil. We used the artificial soils to analyse the response of these model soil systems to additional sterile manure supply (after 562 days). The artificial soils were subjected to a prolonged incubation period of more than two years (842 days) in order to take temporally dynamic processes into account. In our model systems with varying mineralogy, we expected a changing microbial community composition and an effect on macro-aggregation after OM addition, as the input of fresh substrate will re-activate the artificial soils. The abundance and structure of 16S rRNA gene and internal transcribed spacer (ITS) fragments amplified from total community DNA were studied by quantitative real-time PCR (qPCR) and denaturing gradient gel electrophoresis (DGGE), respectively. The formation of macro-aggregates (〉2 mm), the total organic carbon (OC) and nitrogen (N) contents, the OC and N contents in particle size fractions and the CO respiration were determined. The second manure input resulted in higher CO respiration rates, 16S rRNA gene and ITS copy numbers, indicating a stronger response of the microbial community in the matured soil-like system. The type of clay minerals was identified as the most important factor determining the composition of the bacterial communities established. The additional OM and longer incubation time led to a re-formation of macro-aggregates which was significantly higher when montmorillonite was present. Thus, the type of clay mineral was decisive for both microbial community composition as well as macro-aggregation, whereas the addition of other components had a minor effect. Even though different bacterial communities were established depending on the artificial soil composition, the amount and quality of the OM did not show significant differences supporting the concept of functional redundancy.
    Keywords: Dgge ; Illite ; Montmorillonite ; Decomposition ; Respiration ; Soil Formation ; 16s Rrna Gene ; Its Fragment ; Agriculture ; Chemistry
    ISSN: 0038-0717
    E-ISSN: 1879-3428
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  • 3
    Language: English
    In: Applied Microbiology and Biotechnology, 2013, Vol.97(3), pp.1361-1371
    Description: Bacterial wilt caused by Ralstonia solanacearum is a serious threat for agricultural production in China. Eight soil bacterial isolates with activity against R. solanacearum TM15 (biovar 3) were tested in this study for their in vitro activity towards ten genetically diverse R. solanacearum isolates from China. The results indicated that each antagonist showed remarkable differences in its ability to in vitro antagonize the ten different R. solanacearum strains. Strain XY21 (based on 16S rRNA gene sequencing affiliated to Serratia ) was selected for further studies based on its in vitro antagonistic activity and its excellent rhizocompetence on tomato plants. Under greenhouse conditions XY21 mediated biocontrol of tomato wilt caused by seven different R. solanacearum strains ranged from 19 to 70 %. The establishment of XY21 and its effects on the bacterial community in the tomato rhizosphere were monitored by denaturing gradient gel electrophoresis of 16S rRNA gene fragments PCR-amplified from total community DNA. A positive correlation of the in vitro antagonistic activities of XY21 and the actual biocontrol efficacies towards seven genetically different R. solanacearum strains was found and further confirmed by the efficacy of XY21 in controlling bacterial wilt under field conditions.
    Keywords: Ralstonia solanacearum ; Biocontrol ; sp. ; Rhizocompetence ; Pathogen diversity ; DGGE
    ISSN: 0175-7598
    E-ISSN: 1432-0614
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  • 4
    Language: English
    In: Plant and Soil, 2016, Vol.406(1), pp.389-408
    Description: Aims The effects of biofumigation with Brassica juncea 'Terra Plus' and Raphanus sativus 'Defender' in comparison to Basamid on apple plant growth and on soil microbial communities were studied at three sites affected by replant disease under field conditions. Methods Apple rootstocks were planted on differently treated plots to evaluate the effect of the treatments on plant growth under field and greenhouse conditions. The glucosinolates in biofumigant plant organs and their breakdown products in soils were determined. Denaturing gradient gel electrophoresis fingerprints were performed with 16S rRNA gene and ITS fragments amplified from total community DNA extracted from different soils. Results The highest glucosinolate concentrations were found in inflorescences of both biofumigant plant species with no differences between sites. The most abundant degradation product in soil biofumigated with B. juncea was 2-propenyl isothiocyanate, while in soil treated with R. sativus only 4-(methylthio)-3-butenyl isothiocyanate was detected. Effects of biofumigation were recorded to be stronger on fungi than on bacteria. Growth of apple rootstocks was positively affected by the treatments in a site-dependent manner. Conclusions The effects of biofumigation evaluated by the apple plant growth were site-dependent and might result from suppression of soil-borne pests and pathogens, changes in soil microbial community compositions, and additional nutrients from the incorporated biomass.
    Keywords: Apple replant disease ; Bacterial community composition ; Biofumigation ; DGGE ; Fungal community composition ; Glucosinolate ; Indicator plant ; Isothiocyanate ; Malus domestica
    ISSN: 0032-079X
    E-ISSN: 1573-5036
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  • 5
    Language: English
    In: Frontiers in microbiology, 2012, Vol.3, pp.290
    Description: Considering their key role for ecosystem processes, it is important to understand the response of microbial communities in unpolluted soils to pollution with polycyclic aromatic hydrocarbons (PAH). Phenanthrene, a model compound for PAH, was spiked to a Cambisol and a Luvisol soil. Total community DNA from phenanthrene-spiked and control soils collected on days 0, 21, and 63 were analyzed based on PCR-amplified 16S rRNA gene fragments. Denaturing gradient gel electrophoresis (DGGE) fingerprints of bacterial communities increasingly deviated with time between spiked and control soils. In taxon specific DGGE, significant responses of Alphaproteobacteria and Actinobacteria became only detectable after 63 days, while significant effects on Betaproteobacteria were detectable in both soils after 21 days. Comparison of the taxonomic distribution of bacteria in spiked and control soils on day 63 as revealed by pyrosequencing indicated soil type specific negative effects of phenanthrene on several taxa, many of them belonging to the Gamma-, Beta-, or Deltaproteobacteria. Bacterial richness and evenness decreased in spiked soils. Despite the significant differences in the bacterial community structure between both soils on day 0, similar genera increased in relative abundance after PAH spiking, especially Sphingomonas and Polaromonas. However, this did not result in an increased overall similarity of the bacterial communities in both soils.
    Keywords: Dgge ; Bacterial Communities ; Phenanthrene ; Pyrosequencing ; Unpolluted Soil
    E-ISSN: 1664-302X
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  • 6
    Language: English
    In: Frontiers in Microbiology, 01 February 2018, Vol.9
    Description: Biocontrol inoculants often show inconsistency in their efficacy at field scale and the reason for this remains often unclear. A high rhizosphere competence of inoculant strains is assumed to be a key factor for successful biocontrol effects as the biocontrol strain has to compete with the...
    Keywords: Rhizoctonia Solani ; Plant Health ; Biocontrol ; Plant Disease ; Bacterial Community ; Dgge ; Biology
    E-ISSN: 1664-302X
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  • 7
    Language: English
    In: Frontiers in Microbiology, Nov 6, 2015
    Description: Replant disease (RD) severely affects apple production in propagation tree nurseries and in fruit orchards worldwide. This study aimed to investigate the effects of soil disinfection treatments on plant growth and health in a biotest in two different RD soil types under greenhouse conditions and to link the plant growth status with the bacterial community composition at the time of plant sampling. In the biotest performed we observed that the aboveground growth of apple rootstock M26 plants after 8 weeks was improved in the two RD soils either treated at 50°C or with gamma irradiation compared to the untreated RD soils. Total community DNA was extracted from soil loosely adhering to the roots and quantitative real-time PCR revealed no pronounced differences in 16S rRNA gene copy numbers. 16S rRNA gene-based bacterial community analysis by denaturing gradient gel electrophoresis (DGGE) and 454-pyrosequencing revealed significant differences in the bacterial community composition even after 8 weeks of plant growth. In both soils, the treatments affected different phyla but only the relative abundance of Acidobacteria was reduced by both treatments. The genera Streptomyces, Bacillus, Paenibacillus, and Sphingomonas had a higher relative abundance in both heat treated soils, whereas the relative abundance of Mucilaginibacter, Devosia, and Rhodanobacter was increased in the gamma-irradiated soils and only the genus Phenylobacterium was increased in both treatments. The increased abundance of genera with potentially beneficial bacteria, i.e., potential degraders of phenolic compounds might have contributed to the improved plant growth in both treatments.
    Keywords: Genetic Research – Analysis ; Genetic Research – Growth ; Apples – Analysis ; Apples – Growth ; Soils – Analysis ; Horticultural Industry – Analysis ; Horticultural Industry – Growth ; RNA – Analysis ; RNA – Growth ; Environmental Management – Analysis ; Environmental Management – Growth
    ISSN: 1664-302X
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  • 8
    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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  • 9
    In: FEMS Microbiology Ecology, 2013, Vol. 86(1), pp.3-14
    Description: Microbial communities in soil reside in a highly heterogeneous habitat where diverse mineral surfaces, complex organic matter and microorganisms interact with each other. This study aimed to elucidate the long-term effect of the soil mineral composition and charcoal on the microbial community composition established in matured artificial soils and their response to phenanthrene. One year after adding sterile manure to different artificial soils and inoculating microorganisms from a Cambisol, the matured soils were spiked with phenanthrene or not and incubated for another 70 days. 16S rRNA gene and internal transcribed spacer fragments amplified from total community DNA were analyzed by denaturing gradient gel electrophoresis. Metal oxides and clay minerals and to a lesser extent charcoal influenced the microbial community composition. Changes in the bacterial community composition in response to phenanthrene differed depending on the mineral composition and presence of charcoal, while no shifts in the fungal community composition were observed. The abundance of ring-hydroxylating dioxygenase genes was increased in phenanthrene-spiked soils except for charcoal-containing soils. Here we show that the formation of biogeochemical interfaces in soil is an ongoing process and that different properties present in artificial soils influenced the bacterial response to the phenanthrene spike.
    Keywords: Artificial Soils ; Rhdα Genes ; 16s Rrna Genes ; Its ; Dgge
    ISSN: 01686496
    E-ISSN: 1574-6941
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  • 10
    In: FEMS Microbiology Ecology, 2015, Vol. 91(10)
    Description: Aconcagua River basin (Central Chile) harbors diverse economic activities such as agriculture, mining and a crude oil refinery. The aim of this study was to assess environmental drivers of microbial communities in Aconcagua River estuarine soils, which may be influenced by anthropogenic activities taking place upstream and by natural processes such as tides and flood runoffs. Physicochemical parameters were measured in floodplain soils along the estuary. Bacteria , Actinobacteria, Alphaproteobacteria , Betaproteobacteria , Pseudomonas , Bacillus and Fungi were studied by DGGE fingerprinting of 16S rRNA gene and ribosomal ITS-1 amplified from community DNA. Correlations between environment and communities were assessed by distance-based redundancy analysis. Mainly hydrocarbons, pH and the composed variable copper/arsenic/calcium but in less extent nitrogen and organic matter/phosphorous/magnesium correlated with community structures at different taxonomic levels. Aromatic hydrocarbons degradation potential by bacterial community was studied. Polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenases genes were detected only at upstream sites. Naphthalene dioxygenase ndo genes were heterogeneously distributed along estuary, and related to Pseudomonas, Delftia, Comamonas and Ralstonia . IncP-1 plasmids were mainly present at downstream sites, whereas IncP-7 and IncP-9 plasmids showed a heterogeneous distribution. This study strongly suggests that pH, copper, arsenic and hydrocarbons are main drivers of microbial communities in Aconcagua River estuarine soils. Microbial communities from Aconcagua River estuarine soils are mainly influenced by environmental factors such as pH, copper, arsenic and hydrocarbons, indicating inputs from mining and a crude oil refinery. Graphical Abstract Figure. Microbial communities from Aconcagua River estuarine soils are mainly influenced by environmental factors such as pH, copper, arsenic and hydrocarbons, indicating inputs from mining and a crude oil refinery.
    Keywords: Microbial Community ; Aconcagua River ; Dgge ; 16s Rrna Gene ; Pah - Rhd Gene ; Incp Plasmid
    E-ISSN: 1574-6941
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