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  • 1
    Electronic Resource
    Electronic Resource
    Deep sub-seafloor prokaryotes stimulated at interfaces over geological time (2005)
    [s.l.] : Macmillian Magazines Ltd.
    Nature 436 (2005), S. 390-394 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] The sub-seafloor biosphere is the largest prokaryotic habitat on Earth but also a habitat with the lowest metabolic rates. Modelled activity rates are very low, indicating that most prokaryotes may be inactive or have extraordinarily slow metabolism. Here we present results from two Pacific ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/nature03796
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  • 2
    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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  • 3
    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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  • 4
    Electronic Resource
    Electronic Resource
    Distribution and culturability of the uncultivated ‘AGG58 cluster’ of the Bacteroidetes phylum in aquatic environments (2004)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 47 (2004), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Members of the Bacteroidetes phylum are abundant in aquatic habitats when assessed by fluorescent in situ hybridisation and in some 16S rRNA gene libraries. In this study 16S rRNA gene clone libraries were constructed with bacterial primers that amplify Bacteroidetes sequences well (27F, 1492R) from coastal seawater near Plymouth (UK) during a phytoplankton bloom. Most of the clones (66%, 106/160) affiliated with the Bacteroidetes phylum, and of these 62% (66/106; or 41% 66/160 of the entire library) clustered with marine bacterioplankton clones env.agg58, Arctic97A-17, CF17, CF96 and CF101. This phylogenetic branch of Bacteroidetes was designated the ‘AGG58 cluster’, and its presence in various aquatic environments was investigated. Two pairs of AGG58-specific 16S rRNA-gene-targeted polymerase chain reaction (PCR) primers were designed and successfully used to detect the cluster in DNA extracts from three UK coastal seawater sites, and from freshwater River Taff epilithon. In addition, 600 putative Bacteroidetes strains were isolated from these sites on relatively high-nutrient agar media. AGG58 cluster specific probes were used to screen the amplified 16S rRNA gene products from the isolates, but no members of the AGG58 cluster were discovered. The least specific probe hybridised with one River Taff water isolate (RW262 NCIMB 13979) which formed a monophyletic group with the genera Crocinitomix, Brumimicrobium and Cryomorpha of the family Cryomorphaceae in the Bacteroidetes phylum. RW262 probably represents the first isolate of a new genus within this family. This study provides new evidence that the uncultivated AGG58 group is abundant, globally distributed, and can be rapidly detected with the new PCR primers described.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1016/S0168-6496(03)00300-3
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  • 5
    Electronic Resource
    Electronic Resource
    Plasmid transfer between strains of Pseudomonas putida, and their survival, within a pilot scale percolating-filter sewage treatment system (1995)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 18 (1995), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Abstract: The ability of non-indigenous bacteria to survive and conjugate within a fully functioning pilot-scale percolating filter bed, with a substantial biofilm and a diverse invertebrate community, was investigated. Pseudomonas putida UWC8, harbouring the conjugative plasmid pQKH6, isolated from river epilithon, and P. putida UWC9 were introduced and survived in a culturable state for up to 145 days. During this time plasmid transfer, with transfer frequencies of up to 6.54 × 10−5 cfu per recipient, could be detected. The macro-invertebrate community was also investigated. The invertebrate grazers had no detectable effect upon the densities of the introduced bacteria.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6941.1995.tb00160.x
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  • 6
    Electronic Resource
    Electronic Resource
    New tools for elucidating the ecology of micro-organisms in aquatic environments (2003)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 46 (2003), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1016/S0168-6496(03)00204-6
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  • 7
    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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  • 8
    Electronic Resource
    Electronic Resource
    Diversity of mercury resistance plasmids obtained by exogenous isolation from the bacteria of sugar beet in three successive years (1996)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 20 (1996), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Abstract: Self-transmissible plasmids conferring mercury resistance were exogenously isolated from the bacterial populations of sugar beet roots (rhizoplane) and leaves (phyllosphere) into a Pseudomonas putida recipient. Fifty rhizoplane plasmids and 29 phyllosphere plasmids (60–383 kb) were purified. Numerical analysis of plasmid DNA restriction enzyme digest patterns identified five distinct groups. Three of these plasmid groups were isolated from sugar beet crops grown at the same site over three consecutive years, demonstrating their established presence. Each group of plasmids comprised individual isolates with structural additions or deletions. The frequency of exogenous isolation correlated with factors likely to influence plant growth, bacterial activity and the physiological state of donors prior to sampling. All plasmids investigated conferred narrow spectrum mercury resistance with a reductase detoxification mechanism. None of the plasmids conferred resistance to a range of antibiotics, other heavy metals, or to UV, and following transfer to recipient bacteria the range of carbon source utilisation was not altered. This is the first report of the persistence of Pseudomonas spp. plasmid structural types isolated over several years from a terrestrial habitat.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6941.1996.tb00320.x
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  • 9
    Electronic Resource
    Electronic Resource
    Retrotransfer kinetics of R300B by pQKH6, a conjugative plasmid from river epilithon (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 kinetics of conjugation, retrotransfer and mobilisation were studied at 5–15 min intervals between strains of Pseudomonas putida using plasmid pQKH6, isolated from river epilithon, and R300B. Transconjugants from the direct conjugation of pQKH6 and mobilisation of R300B by pQKH6 appeared rapidly, reaching maximum densities within 30–60 min of the start of both filter and liquid mating experiments. However, retrotransconjugants only appeared after a delay. This delay was short (approx. 45–60 min) in filter mating and much longer (2–5 h) for liquid mating experiments. Attempts at predicting the time course of retrotransconjugant development from (1) numbers of transconjugants from the conjugation and mobilisation experiments and (ii) mathematical models based on a mass action approach, both failed to reproduce the observed delay. It was concluded that retrotransfer did not proceed by either a one-step mechanism occuring early in conjugation or two separate conjugation and mobilisation steps. The clear demonstration of a delay in retrotransconjugant formation implies that a new mechanism must be sought. The likely importance of retrotransfer in the environment is discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6941.1994.tb00227.x
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  • 10
    Electronic Resource
    Electronic Resource
    Editorial (1993)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 12 (1993), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6941.1993.tb00009.x
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