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  • 1
    Electronic Resource
    Electronic Resource
    Mutational analysis of the Pseudomonas syringae pv. tomato hrpA gene encoding Hrp pilus subunit (1999)
    Oxford BSL : Blackwell Science Ltd
    Molecular microbiology 34 (1999), S. 0 
    Details
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: Plant pathogenic Pseudomonas syringae strains harbour a type III secretion pathway suggested to be involved in the delivery of effector proteins from the bacteria into plant cells. During plant interaction, the bacteria apparently produce surface appendages, termed Hrp pili, that are indispensable for the secretion process. We have created an insertion mutation library, as well as deletion mutations to hrpA, the structural gene encoding Hrp pilin. Analysis of the mutants revealed gene regions important for hrpA expression, pilus assembly and pilus-dependent autoagglutination of the bacteria. The majority of insertions in the amino-terminal half of the pilin were tolerated without bacterial interaction with plants being affected, while the carboxy-terminus appeared to be needed for pilus assembly. Insertions in the 5′ non-translated region and the first codons within the open reading frame affected mRNA production or stability and abolished protein production.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1046/j.1365-2958.1999.01635.x
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  • 2
    Electronic Resource
    Electronic Resource
    Novel organization of catechol meta-pathway genes in Sphingomonas sp. HV3 pSKY4 plasmid (1997)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 154 (1997), S. 0 
    Details
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Sphingomonas sp. strain HV3 (formerly Pseudomonas sp. HV3), which degrades aromatics and chloroaromatics, harbors a mega-plasmid, pSKY4. A sequenced 4 kb fragment of the plasmid reveals a novel gene organization for catechol meta-pathway genes. The putative meta operon starts with the cmpF gene encoding a 2-hydroxymuconic semialdehyde hydrolase. The gene has a 6 bp overlap with the previously characterized ring-cleavage gene, catechol 2,3-dioxygenase, cmpE. Downstream of cmpE is a 429 bp open reading frame of unknown function. Gene cmpC, encoding a 2-hydroxymuconic semialdehyde dehydrogenase, starts 44 bp further downstream. It has the highest homology to 2-hydroxymuconic semialdehyde dehydrogenases of dmp and xyl pathways and to XylC from the marine oligotroph Cycloclasticus oligotrophus. The gene organization is different from other known meta pathways. This is the first report of organization of plasmid-encoded meta-pathway genes in the genus Sphingomonas.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6968.1997.tb12674.x
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  • 3
    Electronic Resource
    Electronic Resource
    Activity, diversity and population size of ammonia-oxidising bacteria in oil-contaminated landfarming soil (2005)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 250 (2005), S. 0 
    Details
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Chemolithotrophic ammonia-oxidising bacteria (AOB) present in oil-contaminated landfarming soil were studied over two growing seasons in 1999 and 2000. The number of AOB (4–9 × 105 cells g−1 of dry soil) determined with the quantitative polymerase chain reaction (real-time PCR) and the rate of potential ammonium oxidation (0.05–0.28 μg NO2−–N g−1 of dry soil h−1) indicated the presence of stable AOB populations. Denaturing gradient gel electrophoresis (DGGE) profiling and sequence analysis of PCR-amplified AOB 16S rRNA genes showed dominance of Nitrosospira-like sequences in clusters 2 and 3. The present results from the chronically oil-contaminated landfarming soil support the suggested importance of Nitrosospira-like AOB in terrestrial environments.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1016/j.femsle.2005.06.057
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  • 4
    Electronic Resource
    Electronic Resource
    Effect of inoculation of a TOL plasmid containing mycorrhizosphere bacterium on development of Scots pine seedlings, their mycorrhizosphere and the microbial flora in m-toluate-amended soil (2000)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 31 (2000), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: The purpose of this study was to evaluate the influence of introduced bacteria containing a contaminant degrading plasmid on the growth and survival of pine seedlings and mycorrhizosphere microbial flora in contaminated soil. The Pseudomonas fluorescens strain OS81, originally isolated from fungal hyphae in contaminated soil, was supplied with the TOL plasmid pWW0::Km (to generate OS81(pWW0::Km)) and inoculated in humus-soil microcosms with and without pine seedlings mycorrhized with Suillus bovinus. After 3 months of regular treatment with m-toluate (mTA) solutions, the introduced catabolic plasmid was found to be disseminated in the indigenous bacterial population of both mycorrhizosphere and soil uncolonized by the fungus. Transconjugants were represented by bacteria of the genera Pseudomonas and Burkholderia and their number correlated positively with the concentration of mTA applied. Indigenous mTA degrading bacteria with low similarity to Burkholderia species were also enriched in microcosms. They were mostly associated with mycorrhizal soil or fungal structures and virtually absent in microcosms without pines. The total number of Tol+ bacteria was higher in mycorrhizospheric soil compared with bulk soil. Inoculation with P. fluorescens OS81(pWW0::Km) had a positive effect on the development of roots and fungus in contaminated soil. Both inoculation with the P. fluorescens OS81(pWW0::Km) and mTA contamination as well as the presence of mycorrhized pine roots and fungal hyphae had an effect on the microbial community structure of soil as measured by carbon source oxidation patterns. However, the impact of mTA on the microbial community was more prominent. The study indicates that an effect on plant and fungal development can be obtained by manipulating the mycorrhizosphere. Both introduction of the bacterium carrying the degradative plasmid and the plasmid itself are likely to have a positive effect not only on the organisms involved, but also on bioremediation of contaminated soil, a factor that was not directly monitored here.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6941.2000.tb00678.x
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  • 5
    Electronic Resource
    Electronic Resource
    Microbial biofilms and catabolic plasmid harbouring degradative fluorescent pseudomonads in Scots pine mycorrhizospheres developed on petroleum contaminated soil (1998)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 27 (1998), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Cellular interactions and catabolic activities of mycorrhizal root associated non-sporulating bacteria were investigated in a simplified phytoremediation simulation involving a woody plant species. Mycorrhizal Scots pine (Pinus sylvestris) seedlings pre-colonised by Suillus bovinus or Paxillus involutus were grown in forest humus containing microcosms amended with petroleum hydrocarbon (PHC) contaminated soil. Fungal hyphae of both species, emanating from mycorrhizal roots, colonised the PHC contaminated soil over a 16-week period and dense long-lived patches of S. bovinus hyphae formed on the PHC contaminated soil. Transmission electron microscopy revealed a microbial biofilm at the PHC soil-fungal interface composed of differentiated pseudoparenchymous patch hyphae supporting a morphologically diverse bacterial population. Certain non-sporulating bacterial isolates closely associated with the S. bovinus patch hyphae or P. involutus‘web’ hyphae from the PHC soil harboured similar sized mega-plasmids (approx. 150 kb). Isolates of Pseudomonas fluorescens from the ‘patch’ mycorrhizospheres represented different biovars, displayed similar REP-PCR genomic fingerprints, grew on e.g. m-toluate and m-xylene as sole carbon sources, cleaved catechol, and harboured plasmid-borne catabolic marker genes, xylE and xylMA, involved in degradation of mono-aromatics. The plasmids were transmissible in vitro, and Pseudomonas putida transconjugants retained a similar catabolic profile. The identification of microbial biofilms containing catabolic bacteria in the external mycorrhizosphere is discussed in relation to both phytoremediation mechanisms and normal efficient nutrient mobilisation from highly lignin-rich forest soils.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6941.1998.tb00529.x
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  • 6
    Electronic Resource
    Electronic Resource
    Effect of Cd-containing wood ash on the microflora of coniferous forest humus (2000)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 32 (2000), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: The use of wood ash in forestry has been questioned because the cadmium (Cd) concentration of ash, which varies between 1 and 20 mg kg−1 ash, exceeds the level allowed for fertilizers (3 mg kg−1) used in agriculture. To investigate the combined and separated effects of Cd and ash on the forest humus microflora, pumice or wood ash, spiked with a water-soluble (CdCl2) or -insoluble (CdO) form of Cd at three levels (0, 400 and 1000 mg kg−1), were applied at a fertilization level of 5000 kg ha−1 in a laboratory microcosm study. The trial consisted of 60 microcosms (five replications per treatment), which were incubated in darkness at +20°C and a constant relative air humidity of 60%. After two months the humus in the microcosms was sampled. Analyses of CO2 evolution to measure the overall microbial activity and of phospholipid fatty acid (PLFA) pattern to measure microbial community structure were performed. The substrate-use patterns of Biolog EcoPlates were analyzed as a measure of bacterial functionality. Finally the bacterial 3H-thymidine incorporation in the presence of different concentrations of Cd and the number of colony forming units (cfu) of bacteria on nutrient agar in the presence of 0, 5 and 20 mg Cd l−1 agar were applied to measure Cd tolerance. The use of pumice (pH of humus under the pumice 4.0) did not induce any changes in the above variables compared to two untreated microcosms (humus pH 3.9). Pumice was therefore used to distribute the Cd evenly over the humus surface in order to estimate the possible effect of Cd without ash (pH of humus under the ash 7.0). The application of ash increased the microbial activity, changed the PLFA and substrate-use patterns and increased cfu compared to the humus under pumice. The form and level of Cd in the ash had no further effect on this result. In the humus under pumice the level, but not the form of Cd decreased the microbial activity and changed the PLFA pattern compared to the unspiked pumice. None of the treatments induced bacterial tolerance to Cd. Ash thus protected the humus microflora from the harmful effects of Cd.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6941.2000.tb00697.x
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  • 7
    Electronic Resource
    Electronic Resource
    A putative three-dimensional targeting motif of polygalacturonase (PehA), a protein secreted through the type II (GSP) pathway in Erwinia carotovora (2002)
    Oxford, UK : Blackwell Science Ltd.
    Molecular microbiology 43 (2002), S. 0 
    Details
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: Intramolecular information specifying protein secretion through the type II (GSP) pathway of Gram-negative bacteria was investigated. Two regions of the polygalacturonase (PehA) of Erwinia carotovora containing residues proposed to be included in a targeting motif were located, one close to the C-terminus between residues 342 and 369 and another between residues 84 and 135 in the large central loops. The regions were required together to promote secretion. Further residues in the middle of the protein were required for proper positioning of the regions, suggesting that they were both involved in interaction with the GSP. To our knowledge, this is the first time that a possible three-dimensional targeting motif has been defined. At least one of the motifs comprises a cluster on the surface of the protein. The two motifs are structurally dissimilar, suggesting that there are two distinct recognition regions in the GSP apparatus. Finally, we propose that the targeting motifs are of a complex conformational nature with some variability accommodated, as illustrated by the observation that many mutations exhibited no clear phenotype individually but, in combination, severely compromised secretion.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1046/j.1365-2958.2002.02793.x
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  • 8
    Electronic Resource
    Electronic Resource
    Application of cation-exchange membranes for characterisation and imaging ammonia-oxidising bacteria in soils (2005)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 53 (2005), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: A new approach, in which ammonia-oxidizing bacteria (AOB) are entrapped from soil onto cation-exchange membranes, was applied to identify terrestrial AOB by fluorescence in situ hybridization (FISH). An experimental hot spot of ammonia oxidation was developed by establishing a gradient of ammonium substrate (200 to 〈20 mg 〈inlineGraphic alt="inline image" href="urn:x-wiley:01686496:FEM463:FEM_463_mu1" location="equation/FEM_463_mu1.gif"/〉) diffused through the cation-exchange membranes incubated in soil for 6 months. By this approach we were able to characterise and image indigenous AOB populations growing in heavily oil-polluted soil using FISH and sequence analysis of PCR-amplified 16S rRNA genes, respectively. The FISH results revealed that Nitrosospira-like AOB were dominant on the ammonium-enriched membranes incubated in the soil. Fourteen unique Nitrosospira-like 16S rRNA gene sequences belonging to clusters 2 and 3 were recovered from the soil-incubated membranes and from the soil, suggesting the importance of Nitrosospira-like AOB in the oil-polluted landfarming soil.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1016/j.femsec.2005.02.001
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  • 9
    Electronic Resource
    Electronic Resource
    Mobilisation of bacteria in soils by electro-osmosis (2004)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 49 (2004), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: A prerequisite for effective bioremediation of contaminated soil is the presence of microorganisms able to degrade the contaminants. If such microorganisms are absent initially, dissemination of bacteria and nutrients becomes necessary; this is a challenge, especially in dense soils. We studied the feasibility of disseminating bacteria by electro-osmosis in three different soil types; garden soil, fine sand, and clay. We tested migration velocities in a horizontal gel electrophoresis setup and used microcosms specially designed with electrodes in order to simulate field conditions. When an electric current is applied, the bacteria co-migrate with water to the cathode. Results were compared to those of controls without electricity, showing that electro-osmosis stimulates bacterial spreading even in low-permeability soil such as clay, although the migration velocity was lower than in the other soils tested. In fine sand, the bacteria migrated ca. 1 cm h−1, in garden soil ca. 0.6 cm h−1, and in clay ca. 0.1 cm h−1. Phenol served as a growth substrate in the microcosm tests; it appeared to improve the migration of bacteria and the number of recoverable bacteria in most tests. In clay, a moisture gradient formed, which is a factor to consider in designing field applications.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1016/j.femsec.2004.01.016
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  • 10
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    Biostimulation proved to be the most efficient method in the comparison of in situ soil remediation treatments after a simulated oil spill accident (2016)
    Springer
    Details
    Publication Date: 2016-09-27
    Print ISSN: 0944-1344
    Electronic ISSN: 1614-7499
    Topics: Energy, Environment Protection, Nuclear Power Engineering
    Published by Springer
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