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1

Electronic Resource

Molecular analysis of methanogenic archaeal communities in managed and natural upland pasture soils (2003)

Nicol, Graeme W. ; Glover, L. Anne ; Prosser, James I.

Oxford, UK : Blackwell Science Ltd

Global change biology 9 (2003), S. 0

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ISSN: 1365-2486

Source: Blackwell Publishing Journal Backfiles 1879-2005

Topics: Biology , Energy, Environment Protection, Nuclear Power Engineering , Geography

Notes: Grassland management influences soil archaeal communities, which appear to be dominated by nonthermophilic crenarchaeotes. To determine whether methanogenic Archaea associated with the Euryarchaeota lineage are also present in grassland soils, anaerobic microcosms containing both managed (improved) and natural (unimproved) grassland rhizosphere soils were incubated for 28 days to encourage the growth of anaerobic Archaea. The contribution of potential methanogenic organisms to the archaeal community was assessed by the molecular analysis of RNA extracted from soil, using primers targeting all Archaea and Euryarchaeota. Archaeal RT-PCR products were obtained from all anaerobic microcosms. However, euryarchaeal RT-PCR products (of putative methanogen origin) were obtained only from anaerobic microcosms of improved soil, their presence coinciding with detectable methane production. Sequence analysis of excised denaturing gradient gel electrophoresis (DGGE) bands revealed the presence of euryarchaeal organisms that could not be detected before anaerobic enrichment. These data indicate that nonmethanogenic Crenarchaeota dominate archaeal communities in grassland soil and suggest that management practices encourage euryarchaeal methanogenic activity.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1046/j.1365-2486.2003.00673.x

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2

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Potential luminescence as an indicator of activation of genetically-modified Pseudomonas fluorescens in liquid culture and in soil

Meikle, A. ; Glover, L. ; Killham, K. ; [et al.]

Amsterdam : Elsevier

Soil Biology and Biochemistry 26 (1994), S. 747-755

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ISSN: 0038-0717

Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002

Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1016/0038-0717(94)90268-2

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3

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Effect of temperature and plasmid carriage on nonculturability in organisms targeted for release (1995)

Oliver, James D. ; McDougald, Diane ; Barrett, Tanya ; [et al.]

Oxford, UK : Blackwell Publishing Ltd

FEMS microbiology ecology 17 (1995), S. 0

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ISSN: 1574-6941

Source: Blackwell Publishing Journal Backfiles 1879-2005

Topics: Biology

Notes: Abstract: The ability to track genetically modified bacteria released into the environment is essential for assessing their persistence and dispersal. Some bacteria can enter a ‘viable but nonculturable’ (VBNC) state in which the cells remain viable while losing the ability to grow on routine culture media. Thus, VBNC cells are not detectable by standard plating methods. In order to determine what conditions, if any, induce this state in Pseudomonas fluorescens, Pseudomonas syringae, and Escherichia coli, cells were ‘marked’ with lux genes, either chromosomally or on one of two different plasmids. Variations in temperature, but not nutrient or NaCl concentrations, affected culturability of these strains and induced the VBNC state. The temperature which induced the VBNC state in the two pseudomonads depended on whether or not the cell carried one of the two lux-marked plasmids. This effect was shown not to be due to the presence of the lux genes, as their removal from the plasmid had no effect on entry into the VBNC state. Instead, the effect appeared to depend on the location of the plasmid DNA, as a strain of P. fluorescens with the same plasmid integrated into the chromosome behaved identically to the parent strain. The fact that plasmids may have such a dramatic effect on culturability has significant implications for the monitoring of genetically modified bacteria intended for environmental release.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1111/j.1574-6941.1995.tb00147.x

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4

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The role of the earthworm Lumbricus terrestris in the transport of bacterial inocula through soil (1996)

Thorpe, Ian S. ; Prosser, James I. ; Glover, L. Anne ; [et al.]

Springer

Biology and fertility of soils 23 (1996), S. 132-139

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ISSN: 1432-0789

Keywords: Key words Bacterial inocula lux modified ; Pseudomonas fluorescens ; Repacked soil microcosms ; Earthworms ; Lumbricus terrestris ; Leaching patterns

Source: Springer Online Journal Archives 1860-2000

Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition

Notes: Abstract Two laboratory experiments were used to investigate the effect of the earthworm Lumbricus terrestris on transport of genetically marked Pseudomonas fluorescens inocula through soil microcosms. The microcosms comprised cylindrical cores of repacked soil with or without earthworms. Late log-phase cells of P. fluorescens, chromosomally marked with lux genes encoding bioluminescence, were applied to the surface of soil cores as inoculated filter paper discs. In one experiment, 5 and 10 days after inoculation, cores were destructively harvested to determine concentrations of marked pseudomonads with depth relative to the initial inoculum applied. Transport of the bacteria occurred only in the presence of earthworms. In a second experiment cores were subjected to simulated rainfall events 18 h after inoculation with lux-marked bacteria at 3-day intervals over a 24-day period. Resulting leachates were analysed for the appearance of the marked bacteria, and after 28 days cores were destructively harvested. Although some marked cells (less than 0.1% of the inoculum applied) were leached through soil in percolating water, particularly in the presence of earthworms, the most important effect of earthworms on cell transport was through burial of inoculated litter rather than an increase in bypass flow due to earthworm channels.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/BF00336053

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5

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The role of the earthworm Lumbricus terrestris in the transport of bacterial inocula through soil (1996)

Thorpe, Ian S. ; Killham, Ken ; Prosser, James I. ; [et al.]

Springer

Biology and fertility of soils 23 (1996), S. 132-139

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ISSN: 1432-0789

Keywords: Bacterial inocula lux modified ; Pseudomonas fluorescens ; Repacked soil microcosms ; Earthworms ; Lumbricus terrestris ; Leaching patterns

Source: Springer Online Journal Archives 1860-2000

Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition

Notes: Abstract Two laboratory experiments were used to investigate the effect of the earthworm Lumbricus terrestris on transport of genetically marked Pseudomonas fluorescens inocula through soil microcosms. The microcosms comprised cylindrical cores of repacked soil with or without earthworms. Late log-phase cells of P. fluorescens, chromosomally marked with lux genes encoding bioluminescence, were applied to the surface of soil cores as inoculated filter paper discs. In one experiment, 5 and 10 days after inoculation, cores were destructively harvested to determine concentrations of marked pseudomonads with depth relative to the initial inoculum applied. Transport of the bacteria occurred only in the presence of earthworms. In a second experiment cores were subjected to simulated rainfall events 18 h after inoculation with lux-marked bacteria at 3-day intervals over a 24-day period. Resulting leachates were analysed for the appearance of the marked bacteria, and after 28 days cores were destructively harvested. Although some marked cells (less than 0.1% of the inoculum applied) were leached through soil in percolating water, particularly in the presence of earthworms, the most important effect of earthworms on cell transport was through burial of inoculated litter rather than an increase in bypass flow due to earthworm channels.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/BF00336053

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6

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Transient expression of a chloramphenicol acetyltransferase gene following transfection of Physarum polycephalum myxamoebae (1988)

McCurrach, Karen ; Glover, L. Anne ; Hardman, Norman

Springer

Current genetics 13 (1988), S. 71-74

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ISSN: 1432-0983

Keywords: Promoter ; Repetitive DNA ; Electroporation ; DNA transfection (Physarum polycephalum)

Source: Springer Online Journal Archives 1860-2000

Topics: Biology

Notes: Summary A plasmid was constructed containing a replication origin sequence from the Physarum ribosomal DNA molecule, and a bacterial chloramphenicol acetyltransferase (CAT) gene linked to a putative promoter of the long terminal repeat (LTR) of the Physarum “HpaII-repeat” element. The plasmid was transfected into Physarum myxamoebae either by electroporation or CaCl2 treatment. In both cases significant transient levels of CAT gene expression were detected. Results were compared with those obtained with plasmids in which CAT gene expression was driven by eukaryotic virus promoters.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/BF00365759

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7

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Identification of a second retrotransposon-related element in the genome of Physarum polycephalum (1990)

McCurrach, K. J. ; Rothnie, H. M. ; Hardman, N. ; [et al.]

Springer

Current genetics 17 (1990), S. 403-408

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ISSN: 1432-0983

Keywords: Physarum polycephalum ; Retrotransposon ; Tp1 ; Tp2

Source: Springer Online Journal Archives 1860-2000

Topics: Biology

Notes: Summary The repetitive fraction of the genome of the eukaryotic slime mould Physarum polycephalum is dominated by Tp1, a family of retrotransposon-like sequences. Tp1 elements are arranged in scrambled clusters probably arising from integration of the element into copies of its own sequence. The present report describes a second sequence family, Tp2, which has been identified within cloned DNA segments of scrambled Tp1 sequences. Like Tp1, the Tp2 element is structurally related to retrotransposons, having long terminal direct repeats and being flanked by an apparent target site duplication, but its relatively short length (1.68 kb) indicates that it is probably incapable of encoding all the functions necessary for its own mobilisation. analysis of the coding potential of the Tp2 element supports this view, although a striking homology to a nucleic acid binding domain common to many retrotransposons was identified. As with Tp1, putative regulatory signals can be identified in the LTRs of Tp2. Identical arrangements of Tp2 with respect to Tp1 in more than one independently derived clone indicate that non-functional copies of Tp2 may be mobilised as part of a Tp1 transcriptional unit.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/BF00334518

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8

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Novel method for the study of the population dynamics of a genetically modified microorganism in the gut of the earthworm Lumbricus terrestris (1993)

Thorpe, Ian S. ; Killham, Ken ; Prosser, James I. ; [et al.]

Springer

Biology and fertility of soils 15 (1993), S. 55-59

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ISSN: 1432-0789

Keywords: Genetically modified microorganisms ; Population dynamics ; Earthworm gut ; Pseudomonas fluorescens ; Lumbricus terrestris

Source: Springer Online Journal Archives 1860-2000

Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition

Notes: Summary A laboratory microcosm study was used to investigate the survival and population dynamics of genetically modified microorganisms (GMM) in the gut of Lumbricus terrestris. Three methods of axenic earthworm production were investigated. An antibiotic mixture of streptomycin and cycloheximide was introduced either passively, mixed with sterile soil or cellulose, or actively, by teflon catheter. Worms treated by all methods lost weight but this was least for the catheter method which was also the only method to produce axenic earthworms. Axenic earthworms were used to determine the effect of competition with indigenous gut bacteria on ingested GMM. The GMM used was Pseudomonas fluorescens, strain 10586/FAC510, with chromosomally inserted Lux genes for bioluminescence, and chromosomal resistance to rifampicin. The bacteria were grown up to the mid-exponential phase before inoculation into earthworms. Bacteria in faecal material were enumerated by dilution plate counting using selective agar. The GMM were re-isolated from the casts of both antibiotic-treated and untreated earthworms. Lower concentrations of GMM and higher concentrations of indigenous bacteria in the casts of untreated compared to antibiotic-treated earthworms suggested that competition is a fundamental control on population dynamics of the introduced bacterial inocula ingested by earthworms. The catheter method, developed in this study, is proposed as a technique to contribute to the risk assessment of environmental release of GMM.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/BF00336289

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9

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Broad-scale approaches to the determination of soil microbial community structure: Application of the community DNA hybridization technique (1996)

Griffiths, B. S. ; Ritz, K. ; Glover, L. A.

Springer

Microbial ecology 31 (1996), S. 269-280

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ISSN: 1432-184X

Source: Springer Online Journal Archives 1860-2000

Topics: Biology

Notes: Abstract Broad-scale approaches seek to integrate information on whole microbial communities. It is widely recognized that culture techniques are too selective and unrepresentative to allow a realistic assessment of the overall structure of microbial communities. Techniques based on fatty acid or metabolic profiles determine the phenotypic composition of the community. Complementary information about the genotypic structure of soil microbial communities necessitates analysis of community DNA. To determine broad-scale differences in soil microbial community structure (i.e., differences at the whole community level, rather than specific differences in species composition), we have applied a community hybridization technique to determine the similarity and relative diversity of two samples by cross hybridization. In previous studies this assay failed with whole-soil community DNA. Usable hybridization signals were obtained using whole-soil DNA, in this study, by digesting the DNA with restriction enzymes before the labeling with a random-primer reaction. The community hybridization technique was tested using a graded series of microbial fractions, increasing in complexity, all isolated from the same soil sample. This demonstrated that single bacterial species and a mixture of cultivable bacteria were less complex and only 5% similar to whole-community DNA or bacteria directly extracted from the soil. Extracted bacterial and whole-community DNA were 75% similar to each other and equally complex. When DNA was extracted from four different agricultural soils, their similarities ranged from 35 to 75%. The potential usefulness of community hybridization applied to soil microbial communities is discussed.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/BF00171571

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