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  • 1
    Electronic Resource
    Electronic Resource
    A mathematical model for the growth of bacterial microcolonies on marine sediment (1987)
    Springer
    Microbial ecology 13 (1987), S. 31-45 
    Details
    ISSN: 1432-184X
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Counts of bacterial microcolonies attached to deep-sea sediment particles showed 4-, 8-, 16-, and 32-celled microcolonies to be very rare. This was investigated with a mathematical model in which microcolonies grew from single cells at a constant growth rate (μ), detached from particles at constant rate (λ), and reattached as single cells. Terms for attachment of foreign bacteria (a) and death of single cells (d) were also included. The best method of fitting the model to the microcolony counts was a weighted least-squares approach by whichλ(0.83 hour−1) was estimated to be about 20 times greater thanμ(0.038 hour−1). This showed that the bacteria were very mobile between sediment particles and this mobility was explained in terms of attachment by reversible sorption. The implications of the results for the frequency of dividing cell method for estimating growth rates of sediment bacteria are discussed. The ratio ofλ andμ was found to be very robust both in terms of the errors associated with the microcolony counts and the range of microcolony sizes used to obtain the solution.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02014961
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  • 2
    Electronic Resource
    Electronic Resource
    Plasmid transfer between Pseudomonas spp. within epilithic films in a rotating disc microcosm (1989)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 62 (1989), S. 0 
    Details
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Abstract A microcosm using rotating slate discs in a chemostat was used to study bacterial population dynamics and genetic interactions in river epilithon. Populations of all introduced donor and recipient Pseudomonas spp. decreased with time but all the bacteria survived better on the slate discs than in the liquid phase. Conjugal transfer of an epilithic plasmid encoding mercury resistance (pQM1) occured with transfer frequencies of 1.4 × 10−6 to 3.6 × 10−3 per recipient, which were about 100-fold lower than in standard membrane filter mating experiments.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6968.1989.tb03665.x
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  • 3
    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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  • 4
    Electronic Resource
    Electronic Resource
    Comparison of aerobic heterotrophic taxa isolated from four root domains of mature sugar beet (Beta vulgaris) (1996)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 21 (1996), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Abstract: The distribution of bacteria in the rhizosphere, rhizoplane, interior root tissues (core) and lower root (all tissues) of mature sugar beet roots (Beta vulgaris) was compared. Of 556 isolates, 102 species from 40 genera were identified by fatty acid methyl ester gas-chromatographic (FAME-GC) analysis. The ten most common genera (Bacillus, 14%; Arthrobacter, 12%; Pseudomonas, 11%; Aureobacterium, 9%; Micrococcus, 6%; Xanthomonas, 5%; Alcaligenes, 4%; Flavobacterium, 3%; Agrobacterium, 3%; Microbacterium, 3%) accounted for 70% of isolates, and were found in each of three root domains (rhizosphere, rhizoplane and interior root tissues) on the two principal sampling occasions. Gram-positive strains were more abundant in the rhizosphere than the rhizoplane. Compared to the rhizoplane, rhizosphere bacterial communities were represented by a less diverse, more hierarchical distribution of species where twice as many isolates formed late developing colonies on isolation plates. Between October and January, the bacteria isolated from root interior tissues acquired a distinct change in taxonomic pattern, with decreased diversity and increased hierarchy. A bacterial continuum of similar taxa was observed which extended from the rhizosphere to interior root tissues.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6941.1996.tb00350.x
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  • 5
    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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  • 6
    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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  • 7
    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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  • 8
    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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  • 9
    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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  • 10
    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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