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  • 1
    Electronic Resource
    Electronic Resource
    Environmentally directed mutations in the dehalogenase system of Pseudomonas putida strain PP3 (1992)
    Springer
    Archives of microbiology 158 (1992), S. 176-182 
    Details
    ISSN: 1432-072X
    Keywords: Pseudomonas putida ; Dehalogenase ; Halogenated alkanoic acid ; Resistance to halogenated alkanoic acid ; Environmentally directed mutations
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Favourable mutations involving the two dehalogenases (DehI and DehII) of Pseudomonas putida PP3 and derivative strains containing the cloned gene for DehI (dehI) occurred in response to specific environmental conditions, namely: starvation conditions; the presence of dehalogenase substrates (halogenated alkanoic acids — HAAs) which were toxic to P. putida; and/or the presence of a potential growth substrate. Fluctuation tests showed that these mutations were environmentally directed by the presence of HAAs. the mutations were associated with complex DNA rearrangements involving the movement of dehI located on a transposon DEH. Some mutations resulted in switching off the expression of either one or both of the dehalogenases, events which were effective in protecting P. putida from toxic compounds in its growth environment. Other mutations partially restored P. putida's dehalogenating capability under conditions where toxic substrates were absent. Restoration of the capability to untilize HAAs was favoured when normal growth substrates were present in the environment.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00290813
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  • 2
    Electronic Resource
    Electronic Resource
    Biofilm microbial community of a thermophilic trickling biofilter used for continuous biohydrogen production (2005)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 249 (2005), S. 0 
    Details
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Molecular methods were employed to investigate the microbial community of a biofilm obtained from a thermophilic trickling biofilter reactor (TBR) that was operated long-term to produce H2. Biomass concentration in the TBR gradually decreased as reactor bed height increased. Despite this difference in biomass concentration, samples from the bottom and middle of the TBR bed revealed similar microbial populations as determined by PCR-DGGE analysis of 16S rRNA genes. Nucleotide sequences of most DGGE bands were affiliated with the classes Clostridia and Bacilli in the phylum Firmicutes, and the most dominant bands showed a high sequence similarity to Thermoanaerobacterium thermosaccharolyticum.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1016/j.femsle.2005.05.050
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  • 3
    Electronic Resource
    Electronic Resource
    The partial purification of two dehalogenases from Pseudomonas putida PP3 (1979)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 6 (1979), S. 0 
    Details
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6968.1979.tb03710.x
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  • 4
    Electronic Resource
    Electronic Resource
    DNA extraction for 16S rRNA gene analysis to determine genetic diversity in deep sediment communities (1992)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 100 (1992), S. 0 
    Details
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Abstract A protocol was devised which permitted the extraction of DNA from deep marine sediments up to 503 m below the sea floor. These sediments have been laid down over the last 3 million years. 16S rRNA gene sequences were amplified from the DNA by the polymerase chain reaction. The details of the successful extraction and polymerase chain reaction methodology varied between samples from different depths. This emphasizes the attention to detail required to allow the diversity of bacteria in these deep sediments to be studied.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6968.1992.tb14019.x
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  • 5
    Electronic Resource
    Electronic Resource
    Molecular monitoring of culturable bacteria from deep-sea sediment of the Nankai Trough, Leg 190 Ocean Drilling Program (2004)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 48 (2004), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Culturable bacteria were detected in deep-sea sediment samples collected from the Nankai Trough site 1173 (Ocean Drilling Program, ODP, Leg 190) at 4.15 m below the seafloor with 4791 m of overlying water. In this deep ocean near surface sediment, mainly fermentative heterotrophs, autotrophic acetogens and sulfate-reducing bacteria were enriched by using two different non-selective enrichment culture media. Culturable bacterial population shifts within the deep marine sediment enrichments were monitored by using denaturating gradient gel electrophoresis (DGGE). DGGE analysis revealed a decrease in the number of 16S rRNA gene fragments from high to low carbon concentrations, and from low to high dilution of inoculum, suggesting that fast-growing bacteria were numerically dominant in enrichment culture samples. The dominant 16S rRNA fragments observed in DGGE gels were assigned to the Firmicutes, Proteobacteria (γ and δ subgroups) and Spirochaeta phyla. Continual sub-culture and purification resulted in two isolates which were phylogenetically identified as members of the genera Acetobacterium and Marinilactibacillus. Our results, which combine enrichment culturing with DGGE analysis, indicated that enrichment cultures derived from inoculum dilution and media with various concentrations of carbon could facilitate the detection and isolation of a greater number of environmentally relevant bacterial species than when using traditional enrichment techniques alone.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1016/j.femsec.2004.02.009
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  • 6
    Electronic Resource
    Electronic Resource
    Using microcosms to study gene transfer in aquatic habitats (1997)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 23 (1997), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Aquatic habitats are important potential sites for gene transfer between indigenous bacteria and released genetically engineered microorganisms (GEMs). Legislation governing GEM release, and other practical considerations, have resulted in microcosms, of varying complexity, being used to study gene transfer in aquatic environments. This article reviews these microcosms, with particular emphasis on the more complex designs and, where possible, compares gene transfer results obtained in them with in situ studies. We conclude that microcosms can give results that are consistent with those obtained in situ and thus can be relied upon to give realistic predictions of in situ behaviour.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6941.1997.tb00393.x
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  • 7
    Electronic Resource
    Electronic Resource
    Methanogen and bacterial diversity and distribution in deep gas hydrate sediments from the Cascadia Margin as revealed by 16S rRNA molecular analysis (2001)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 34 (2001), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: The microbial community of a deep (to 234 m below the sea floor) sediment gas hydrate deposit (Cascadia Margin Ocean Drilling Program Site 889/890, Leg 146) was analysed for the first time by molecular genetic techniques. Both bacterial and methanogen diversity were determined by phylogenetic analysis of ribosomal DNA sequences. High molecular mass DNA, indicative of active bacteria, was present in all of the samples. Ribosomal RNA genes were amplified from extracted DNA extracted from sediment using bacteria, and methanogen specific PCR primers, the latter designed in this study. Phylogenetic analysis of approximately 400 bacterial clones demonstrated that 96% were members of the Proteobacteria. These clones were affiliated with the α, β and γ subdivisions, with Caulobacter (Zymomonas group), Ralstonia and Pseudomonas phylotypes predominating. The methanogen clones were of low diversity and clustered in three sub-groups. Two of these sub-groups (contained 96% of the 400 clones) were closely related to Methanosarcina mazeii, while the third sub-group clustered in the Methanobacteriales. This analysis of a deep sediment gas hydrate environment shows a bacteria and methanogen community of limited diversity and confirms that the gas hydrate zone is biogeochemically active. These results are consistent with the presence of bacterial populations capable of methanogenesis throughout the core, and suggest that the methane hydrate at this site is at least partially biogenic in origin.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6941.2001.tb00773.x
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  • 8
    Electronic Resource
    Electronic Resource
    Similarity of microbial and meiofaunal community analyses for mapping ecological effects of heavy-metal contamination in soil (2002)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 40 (2002), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: The effect of long-term heavy-metal contamination on soil microbial and meiofaunal communities was assessed with a view to determining whether analysis of these communities could be used for ecological assessment of contaminated sites. Thirty soil cores were taken from an industrial site formerly used for the burning of waste from an explosives factory. The predominant contaminants in the soil were a range of heavy metals, including lead, copper and zinc. The numbers of culturable bacteria (especially those grown on Pseudomonas selective media) and the microbial community response to a suite of 95 carbon sources were suppressed in samples with high heavy-metal contamination. This corresponded to a reduction in the density and evenness of the nematode communities in the samples with high metal concentrations. Conversely the bacterial counts and responses to the 95 carbon sources were greater at sites with higher and more diverse populations of nematodes. However, epifluorescence counts of bacteria and the profiles of extracted fatty acids were not consistently altered by the heavy-metal contamination. These results suggest that culturable bacteria are effective indicators of pollution in soil, and reflect the perturbations seen in other components of the soil biota. Furthermore, this is the first study to show that both meiofaunal communities and microbial communities give similar indications of the ecological impact of heavy-metal contamination in soil.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6941.2002.tb00943.x
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  • 9
    Electronic Resource
    Electronic Resource
    Effect of sample handling on estimation of bacterial diversity in marine sediments by 16S rRNA gene sequence analysis (1994)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 15 (1994), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Abstract The diversity of bacterial communities in deep marine sediments, up to 503 metres below the sea floor of the Japan Sea, was investigated by sequence analysis of amplified 16S rRNA genes. The use of different sample handling procedures greatly affected the types and diversity of sequences obtained. DNA from sediment samples stored aerobically for up to 24 h before freezing was dominated by sequences belonging to the β- and γ-proteobacteria, many of which appeared to originate from aerobic bacteria. Sub-samples equilibrated anaerobically at 16°C, were then injected with a radiotracer and immediately frozen, to simulate the conditions of a typical control sample from a radiotracer based activity assay, contained mostly α-proteobacterial sequences. Pristine sediment samples taken anaerobically and frozen within 2 h contained the widest diversity of sequences from α-, γ-, δ-proteobacteria and Gram-positive bacteria, which appeared to have originated from predominantly anaerobic or facultative bacteria. It was clear that both samples that were not frozen immediately (within 2 h) showed signs of enrichment of specific bacterial groups. Our results strongly suggest that immediate freezing should always be employed when sediment samples are to be used to assess bacterial diversity by molecular methods.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6941.1994.tb00245.x
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  • 10
    Electronic Resource
    Electronic Resource
    Horizontal transfer of dehalogenase genes on IncP1β plasmids during bacterial adaptation to degrade α-halocarboxylic acids (2003)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 45 (2003), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: The diversity of bacterial α-halocarboxylic acid (αHA) dehalogenases from a polluted soil was investigated. Polymerase chain reaction (PCR) primers designed to amplify group I and group II dehalogenase (deh) gene sequences were used to screen bacterial isolates, nine β-Proteobacteria and one γ-Proteobacterium, from soil enrichments. Primers successfully amplified deh sequences from all 10 αHA-utilising isolates. Bacteria isolated at 15 or 30°C on chloroacetic acid or 2-chloropropionic acid from the same polluted soil were shown to contain up to four plasmids, some of these common between isolates. Analysis of deletion mutants and Southern hybridisation showed that each isolate contained an apparently identical IncP1β plasmid c. 80 kb in size, carrying group I deh genes in addition to an associated insertion sequence element. Moreover, an identical conjugative catabolic plasmid was isolated exogenously in several transconjugants independently selected from biparental matings between Ralstonia eutropha JMP222 and enrichment samples. PCR cloning and sequencing of deh genes directly from enrichment cultures inoculated with the same soil revealed that an identical deh gene was present in both primary, secondary and tertiary enrichment cultures, although this deh could not be amplified directly from soil. Two αHA-utilising bacteria isolated at lower temperature were found also to contain group II deh genes. Transfer of the deh catabolic phenotype to R. eutropha strain JMP222 occurred at high frequencies for four strains tested, a result that was consistent with assignment of the plasmids to the IncP1 incompatibility group. The promiscuous nature and broad host range of IncP plasmids make them likely to be involved in horizontal gene transfer during adaptation of bacteria to degrade organohalogens.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1016/S0168-6496(03)00158-2
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