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  • 1
    Electronic Resource
    Electronic Resource
    Viability of soil bacteria: Optimization of plate-counting technique and comparison between total counts and plate counts within different size groups (1987)
    Springer
    Microbial ecology 13 (1987), S. 59-74 
    Details
    ISSN: 1432-184X
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Viable counts of heterotropic soil bacteria were 3–5 times higher on low-nutrient agar media compared with a series of conventional agar media. Substantial amounts of monosaccharides and amino acids were present in solid media made from distilled water and agar powder, and a salt-solution agar medium (without organic substrates added) gave practically the same colony counts as the low nutrient soil extract agar medium. MPN values were comparable to or lower than plate counts. A search for slow-growing cells in the negative MPN tubes by fluorescence microscopical examination after 3 months incubation was negative. The viable counts were 2–4% of the total microscopical counts in different soils. Assuming that the colony-forming cells did not derive from the numerous “dwarf” cells present in soil, a calculated percent viability of the larger cells was about 10%. The ecological significance of the plate-counting technique is discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02014963
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  • 2
    Electronic Resource
    Electronic Resource
    The relationship between cell size and viability of soil bacteria (1987)
    Springer
    Microbial ecology 13 (1987), S. 103-114 
    Details
    ISSN: 1432-184X
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The number of bacterial cells in soil that form colonies on nutrient agar represent a small fraction of the direct microscopic counts (DMC). The colony-forming cells have larger cell dimensions than the very small (“dwarf”) cells which represent the majority of the DMC. This may indicate that the dwarf cells are species unable to form visible colonies on agar, or that they swell to normal dimensions when growing. Indigenous bacterial cells were separated from soil by density gradient centrifugation and fractionated according to diameter by filtration through polycarbonate filters. Each filtrate was studied with respect to DMC, cell dimensions, colony-forming cells (visible colonies and microcolonies), and cell dimensions during growth on the agar. The calculated average percent viability was only 0.2% for cells with diameters below 0.4μm, about 10% for cells with diameters between 0.4 and 0.6μm, and 30–40% for cells with diameters above 0.6μm. Only 10–20% of the viable cells with diameters 〈0.4μm increased their diameter to 〉0.4μm prior to growth. Thus, size change during starvation and growth cycles did not explain the high numbers of dwarf cells observed by microscopy. The results show that despite the relatively low number of colony-forming bacteria in soil, the species that form colonies may be fairly representative for the medium size and large cells, which constitute a major part of the bacterial biovolume. Thus plate counting could be a useful method to count and isolate the bacteria accounting for much of the biovolume in soil. The origin of the dwarf cells is still unclear, but the low number of small cells that increased in size seems to indicate that the majority of these bacterial cells are not small forms of ordinary sized bacteria.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02011247
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  • 3
    Electronic Resource
    Electronic Resource
    Extraction of methane-oxidizing bacteria from soil particles (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: We present a method for extraction of active methane (CH4)-oxidizing bacteria from soil samples. The method is based on physical dispersion of bacteria from the soil particles followed by separation of bacteria and soil particles by floatation in the density media Nycodenz or Percoll. Separation on Nycodenz produced very pure bacterial suspensions while separation on Percoll produced rather impure suspensions. However, more than 60% of the methane-oxidizing activity was irreversibly inhibited in the procedure using Nycodenz compared to less than 10% irreversible inhibition when Percoll was employed. The bacterial suspensions extracted from soil can be used to study the physiology and ecology of soil bacteria that oxidize methane at atmospheric concentrations. Our data indicated that these bacteria are extremely difficult to dislodge from particles compared to the majority of bacteria in soil. Tentatively, we interpret the strong attachment to long residence time (i.e. slow turnover) of the methane-oxidizing bacteria. A slow turnover/growth rate would explain why soil disturbances, like cultivation, have a long lasting effect on the oxidation of atmospheric methane in soil.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6941.1996.tb00333.x
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  • 4
    Electronic Resource
    Electronic Resource
    Evaluation of methods for extraction of bacteria from soil (1995)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 16 (1995), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Abstract Several methods for dispersion of soil were tested for possible use in procedures for extraction of bacteria. Physical cell damage on cells and efficiency in extraction of indigenous cells from soil, were investigated. Cell damage by the dispersion methods was investigated by measuring the physical cell integrity and viability of pure cultures of Escherichia coli and Bacillus subtilis, as well as soil bacteria extracted from soil, when dispersed in slurries of γ-sterilized soil. Separation of bacteria and soil particles on the basis of buoyant density was conducted with the nonionic density gradient medium Nycodenz. When slurries of γ-sterilized soil with added pure cultured cells were centrifuged (10000 × g) over cushions of Nycodenz (1.3 g ml−1), practically all the added cells were recovered in a layer on top of the cushion. This proves that a reversible attachment and cosedimentation is not an important phenomenon in this procedure. The efficiency of the different dispersion methods for the extraction of indigenous soil bacteria, was assessed after separation of dislodged and attached soil bacteria. This separation was done either on the basis of sedimentation rate by low speed centrifugation, or buoyant density by Nycodenz density gradient centrifugation. The physical dispersion by ultrasonic treatment and chemical dispersion by the use of a chelating agent together with a detergent, were inferior to physical dispersion either by Waring blender (for large volumes) or a rotating rubber pestle treatment (for smaller volumes). The physical dispersion did not appear to be destructive to the cells tested.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6941.1995.tb00277.x
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  • 5
    Electronic Resource
    Electronic Resource
    Soil bacterial DNA and biovolume profiles measured by flow-cytometry (1993)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 102 (1993), S. 0 
    Details
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Abstract Flow-cytometry was used to measure cell volumes and DNA contents of single cells in cultures of soil bacteria during exponential growth and starvation conditions. DNA was measured after staining with mitramycin/ethidium bromide. The measurement of DNA was calibrated with rifampicin-treated cells of E. coli containing even numbers of genomes per cell. Cell volumes were assessed by scatter light measurements. Constant DNA to biovolume relations over a range of cell sizes were found for each of the bacteria at exponential growth, and DNA contents per cell varied over a range equivalent to 1–4 genomes per cell. At generation times of 1.0–1.5 h, two genomes were registered as a mean. After starvation of washed cells in a salt solution (24 hrs), a fraction of the cells in each culture had DNA contents equivalent to 1 genome, but significant fractions retained DNA contents equivalent to 2–4 genomes. Attempts to create cells with even numbers of genomes per cell by treatment with rifampicin was successful on an Acinetobacter sp. In contrast, the response to rifampicin was less clear for Pseudomonas fluorescens and P. chlororaphis, and unclear for the gram positive bacteria isolated from soil. The mean decrease in biovolume upon starvation was 4.1 times (range 1.3–8.1 times) and larger than the mean decrease in DNA content of 1.8 (range 1.3–2.7 times). Cell volume determinations by measurements of scatter light was compared with volume determinations by fluorescence microscopy. The amounts of scatter light per volumes was variable, not only did we find large differences between bacterial types, but also between starving and exponentially growing cells of the same isolate. In order to use light scatter as a measure of biovolume, internal standards has to be chosen of comparable size and surface properties as to soil bacteria.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6968.1993.tb05804.x
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  • 6
    Electronic Resource
    Electronic Resource
    Comparison of Nitrosospira strains isolated from terrestrial environments (1999)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 30 (1999), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Most of our knowledge about the physiology of ammonia-oxidizing bacteria is based on experiments with Nitrosomonas europaea, which appears to be less ubiquitous than Nitrosospira. We have isolated Nitrosospiras from widely different environments and compared their specific growth rate, substrate affinity, urease activity, temperature response, pH tolerance and cell morphology. Two of the strains had a variable morphology: the spirals were less tightly coiled than the classical Nitrosospira type and a fraction of the culture had a vibrioid appearance. These vibrioid strains were also peculiar in having a much higher apparent activation energy for ammonia monooxygenase (AMO) (129 and 151 kJ mol−1) than that of the more classical Nitrosospiras (78 and 79 kJ mol−1). The differences in morphology and activation energy were congruent with the phylogeny of the genes for 16S rRNA (Utåker et al., System. Appl. Microbiol. 18) and AMO. The response to pH in the medium was investigated for four strains. The oxidation rate at the onset of the pH exposure experiment was found to obey classical steady state enzyme kinetics, assuming that NH3 (not NH4+) is the rate-limiting substrate. The calculated half saturation constants (Ks) for AMO were 6–11 μM NH3. Growth had a narrower pH range than oxidation activity and appeared to be restricted by pH-dependent factors other than NH3. All the isolated strains were urease positive, with a specific urease activity ranging from 60 to 158% of their specific AMO activity. The urease activity was unaffected by acetylene inhibition of the energy metabolism. The substrate affinity for one strain was found to be around 670 μM.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6941.1999.tb00646.x
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  • 7
    Electronic Resource
    Electronic Resource
    Temporal aspects of N-enrichment and emission of N2O to the atmosphere (1998)
    Springer
    Nutrient cycling in agroecosystems 52 (1998), S. 107-121 
    Details
    ISSN: 1573-0867
    Keywords: Global change ; model ; nitrogen cycle ; nitrogen enrichment ; nitrous oxide emission ; time scale
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Human activities result in N enrichment of the biosphere, primarily via the production of fertilizers and emission of NOx from combustion. This anthropogenic N enhance the ecosystems' primary production, hence the accumulation of organic N. As a result, affected ecosystems may take a long time to reach near-steady-state conditions, i.e. when inputs are balanced by losses through denitrification and downstream transport (terrestrial-subsoil-freshwater-sea). This implies a cumulative enhancement of N2O emission by anthropogenic N. The purpose of this paper is to explore the consequences of such cumulative effects for the future emission of N2O, assuming that the present N management does not change. Data for the total dissipation of nitrogen from the Norwegian society were used as inputs in a model of N-transformations and -transport in terrestrial ecosystems, subsoils, and freshwater. Model performance was found to be in general agreement with observed N-retention and process rates in the environment. By concomitant simulation of a pristine and a polluted scenario (i.e. with the present Norwegian N-pollution from time zero), the net impact of the N-pollution on N2O emission could be estimated. This ‘anthopogenis N2 emission’ outside the agricultural system was estimated to be 1.2, 3.7, 4.5, 5.2 and 5.7 Gg N2O–N yr-1 at time = 0, 50, 100, 200 and 300 years, respectively, after onset of the pollution. Emission estimates based on IPCC guidelines were identical with the model's prediction for emission after 50 years of N-pollution. This is a good agreement, since most of the N-pollution in Norway has taken place the last 50 years. However, this suggests that the IPCC calculation routines overestimate present emissions which are due to recent N inputs, and underestimate future emissions due to cumulative effects.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1009760623188
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  • 8
    Electronic Resource
    Electronic Resource
    Release of fossil methane from mineral soil particles, and its implication for estimation of methane oxidation in a mineral subsoil (1999)
    Springer
    Biogeochemistry 47 (1999), S. 1-14 
    Details
    ISSN: 1573-515X
    Keywords: ammonia oxidizers ; isotopic composition ; methane oxidation ; thermogenic methane
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology , Geosciences
    Notes: Abstract In a preliminary experiment we found that methane evolved from a sandy subsoil during aerobic incubation of shaken soil slurries. In the study presented here the methane was found to be released from the sand particles by mechanical weathering, caused by the grinding effect of the shaking. Large amounts of gas (about 0.5 ml gas g−1 soil) were extracted by intense grinding of the soil in gas tight serum vials. Methane was the main hydrocarbon in the emitted gas, but also a considerable amount of ethane was present, as well as minor amounts of heavier hydrocarbons (up to C6). The δ13C-values of the emitted methane and ethane were −33 ‰ and −29 ‰, respectively. Together these results demonstrate a thermogenic origin of the gas. This paper also reports the results of an incubation experiment where possible methane oxidation was looked for. If a possible release of methane is not accounted for, methane oxidation may be overlooked, as illustrated in this paper. Methane consumption was detected only in soil from 40 cm, in contrast to soil sampled at 100 cm and deeper where a slight production was measured. When methane oxidation was inhibited by dimethyl-ether, a significant release of methane was seen. The release was probably caused by chemical weathering. When this methane release was taken into account, methane oxidation was found to be present at all measured depths (40 to 200 cm). Fertilization with urea inhibited the methane oxidation at 40 cm but not at deeper layers. It is hypothesized that ammonia oxidizing bacteria were the main methane oxidizers in this mineral subsoil (deeper than 1 m), and that oxidation of methane might be a survival mechanism for ammonia oxidizers in ammonia limited environments.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00993093
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  • 9
    Electronic Resource
    Electronic Resource
    Methane oxidation potentials and fluxes in agricultural soil:Effects of fertilisation and soil compaction (2000)
    Springer
    Biogeochemistry 48 (2000), S. 323-339 
    Details
    ISSN: 1573-515X
    Keywords: ammonium-N ; cattle slurry ; NH4NO3-fertilisation ; field experiment ; incubation methane oxidation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology , Geosciences
    Notes: Abstract We have studied the inhibiting effect offertilisation and soil compaction on CH4oxidation by measuring gas fluxes and soil mineral Ndynamics in the field, and CH4 oxidation rates inlaboratory-incubated soil samples. The fertilisationand soil compaction field experiment was establishedin 1985, and the gas fluxes were measured from 1992 to1994. Methane oxidation was consistently lower infertilised than in unfertilised soil, but thereapparently was no effect of repeated fertiliseradditions on the fertilised plots. The measuredmineral N in fertilised and unfertilised soil showedlarge differences in NH4 + concentrationsjust after fertilisation, but the levels rapidlyconverged because of plant uptake and nitrification.The CH4 oxidation rate did not reflect thesecontrasting mineral N patterns, suggesting that theCH4 oxidation capacity remaining in the soil thathad been fertilised since 1985 was largely insensitiveto ammonia in the new fertiliser. Thus, competitiveinhibition by ammonia may have been involved in theearly stage of the field fertiliser experiment, butthe CH4 oxidation remaining after 7 to 9 years ofcontinued fertilisation seems not to have beenaffected by ammonia. The substrate affinity of theCH4-oxidizing microflora appeared to be the samein both the fertilised soil and the unfertilisedcontrol, as judged from the response to elevatedCH4 concentrations (52 µl l−1) inlaboratory incubations. Soil compaction resulted in apersistent reduction of CH4 influx, also seen inlaboratory incubations with sieved (4-mm mesh) soilsamples. Since the sieving presumably removesdiffusion barriers created by the soil compaction, thefact that compaction effects persisted through thesieving may indicate that soil compaction has affectedthe biological potential for CH4 oxidation in thesoil.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1006262404600
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  • 10
    Electronic Resource
    Electronic Resource
    Release of fossil methane from mineral soil particles, and its implication for estimation of methane oxidation in a mineral subsoil (1999)
    Springer
    Biogeochemistry 47 (1999), S. 1-14 
    Details
    ISSN: 1573-515X
    Keywords: ammonia oxidizers ; isotopic composition ; methane oxidation ; thermogenic methane
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology , Geosciences
    Notes: Abstract In a preliminary experiment we found that methane evolved from a sandy subsoil during aerobic incubation of shaken soil slurries. In the study presented here the methane was found to be released from the sand particles by mechanical weathering, caused by the grinding effect of the shaking. Large amounts of gas (about 0.5 ml gas g−1 soil) were extracted by intense grinding of the soil in gas tight serum vials. Methane was the main hydrocarbon in the emitted gas, but also a considerable amount of ethane was present, as well as minor amounts of heavier hydrocarbons (up to C6). The δ13C-values of the emitted methane and ethane were --33 ‰ and --29 ‰, respectively. Together these results demonstrate a thermogenic origin of the gas. This paper also reports the results of an incubation experiment where possible methane oxidation was looked for. If a possible release of methane is not accounted for, methane oxidation may be overlooked, as illustrated in this paper. Methane consumption was detected only in soil from 40 cm, in contrast to soil sampled at 100 cm and deeper where a slight production was measured. When methane oxidation was inhibited by dimethyl-ether, a significant release of methane was seen. The release was probably caused by chemical weathering. When this methane release was taken into account, methane oxidation was found to be present at all measured depths (40 to 200 cm). Fertilization with urea inhibited the methane oxidation at 40 cm but not at deeper layers. It is hypothesized that ammonia oxidizing bacteria were the main methane oxidizers in this mineral subsoil (deeper than 1 m), and that oxidation of methane might be a survival mechanism for ammonia oxidizers in ammonia limited environments.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1006120201209
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