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Berlin Brandenburg

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  • Oxford Journals (Oxford University Press)  (8)
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  • 1
    In: FEMS Microbiology Ecology, 2013, Vol. 86(1), pp.26-35
    Description: Little is known about the factors that regulate C mineralisation at the soil pore scale or how these factors vary throughout the pore network. This study sought to understand how the decomposition of organic carbon varies within the soil pore network and to determine the relative importance of local environmental properties relative to biological properties as controlling factors. This was achieved by sterilising samples of soil and reinoculating them with axenic bacterial suspensions using the matric potential to target different locations in the pore network. Carbon mineralisation curves were described with two-compartment first-order models to distinguish CO 2 derived from the labile organic carbon released during sterilisation from CO 2 derived from organic C unaffected by sterilisation. The data indicated that the size of the labile pool of organic C, possibly of microbial origin, varied as a function of location in the pore network but that the organic carbon unaffected by sterilisation did not. The mineralisation rate of the labile C varied with the bacterial type inoculated, but the mineralisation rate of the organic C unaffected by sterilisation was insensitive to bacterial type. Taken together, the results suggest that microbial metabolism is a less significant regulator of soil organic carbon decomposition than are microbial habitat properties.
    Keywords: Pore Network ; C Mineralisation ; Microbial Habitat ; Matric Potential ; Sterilisation ; Inoculation
    ISSN: 01686496
    E-ISSN: 1574-6941
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  • 2
    In: FEMS Microbiology Ecology, 2012, Vol. 81(3), pp.673-683
    Description: The impact of the soil matric potential on the relationship between the relative abundance of degraders and their activity and on the spatial distribution of both at fine scales was determined to understand the role of environmental conditions in the degradation of organic substrates. The mineralization of 13 C-glucose and 13 C-2,4-dichlorophenoxyacetic acid (2,4-D) was measured at different matric potentials (−0.001, −0.01 and −0.316 MPa) in 6 × 6 × 6 mm 3 cubes excised from soil cores. At the end of the incubation, total bacterial and 2,4-D degrader abundances were determined by quantifying the 16S rRNA and the tfdA genes, respectively. The mineralization of 2,4-D was more sensitive to changes in matric potential than was that of glucose. The amount and spatial structure of 2,4-D mineralization decreased with matric potential, whilst the spatial variability increased. On the other hand, the spatial variation of glucose mineralization was less affected by changes in matric potential. The relationship between the relative abundance of 2,4-D degraders and 2,4-D mineralization was significantly affected by matric potential: the relative abundance of tfdA needed to be higher to reach a given level of 2,4-D mineralization in dryer than in moister conditions. The data show how microbial interactions with their microhabitat can have an impact on soil processes at larger scales.
    Keywords: 2, 4 - D ; Relative Abundance Of Degraders ; Water Content ; Glucose ; Organic Substrate Mineralization ; Spatial Variability
    ISSN: 01686496
    E-ISSN: 1574-6941
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  • 3
    In: FEMS Microbiology Letters, 2017, Vol. 364(9)
    Description: Nitrogen (N) addition is known to affect soil microbial communities, but the interactive effects of N addition with other drivers of global change remain unclear. The impacts of multiple global changes on the structure of microbial communities may be mediated by specific microbial groups with different life-history strategies. Here, we investigated the combined effects of elevated CO 2 and N addition on soil microbial communities using PLFA profiling in a short-term grassland mesocosm experiment. We also examined the linkages between the relative abundance of r- and K-strategist microorganisms and resistance of the microbial community structure to experimental treatments. N addition had a significant effect on microbial community structure, likely driven by concurrent increases in plant biomass and in soil labile C and N. In contrast, microbial community structure did not change under elevated CO 2 or show significant CO 2 × N interactions. Resistance of soil microbial community structure decreased with increasing fungal/bacterial ratio, but showed a positive relationship with the Gram-positive/Gram-negative bacterial ratio. Our findings suggest that the Gram-positive/Gram-negative bacteria ratio may be a useful indicator of microbial community resistance and that K-strategist abundance may play a role in the short-term stability of microbial communities under global change. Elevated CO 2 alone or in combination with N addition does not affect soil microbial community structure in grassland mesocosms.
    Keywords: Global Change ; Grassland ; Fungal/Bacterial Ratio ; Plfa
    E-ISSN: 1574-6968
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  • 4
    In: FEMS Microbiology Ecology, 2009, Vol. 70(1), pp.109-117
    Description: In grazed pastures, soil pH is raised in urine patches, causing dissolution of organic carbon and increased ammonium and nitrate concentrations, with potential effects on the structure and functioning of soil microbial communities. Here we examined the effects of synthetic sheep urine (SU) in a field study on dominant soil bacterial and fungal communities associated with bulk soil and plant roots (rhizoplane), using culture independent methods and a new approach to investigate the ureolytic community. A differential response of bacteria and fungal communities to SU treatment was observed. The bacterial community showed a clear shift in composition after SU treatment, which was more pronounced in bulk soil than on the rhizoplane. The fungal community did not respond to SU treatment; instead, it was more affected by the time of sampling. Redundancy analysis of data indicated that the variation in the bacterial community was related to change in soil pH, while fungal community was more responsive to dissolution of organic carbon. Like the universal bacterial community, the ureolytic community was influenced by the SU treatment. However, different taxa within the ureolytic bacterial community responded differentially to the treatment. The ureolytic community comprised of members from a range of phylogenetically different taxa and could be used to measure the effect of environmental perturbations on the functional diversity of natural ecosystems.
    Keywords: Bacterial Community ; Fungal Community ; Ureolytic Genes ; Microbial Response
    ISSN: 01686496
    E-ISSN: 1574-6941
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  • 5
    Language: English
    In: FEMS Microbiology Ecology, 2003, Vol.44(2), pp.203-215
    Description: Biological soil thin-sections and a combination of image analysis and geostatistical tools were used to conduct a detailed investigation into the distribution of bacteria in soil and their relationship with pores. The presence of spatial patterns in the distribution of bacteria was demonstrated at the microscale, with ranges of spatial autocorrelation of 1 mm and below. Bacterial density gradients were found within bacterial patches in topsoil samples and also in one subsoil sample. Bacterial density patches displayed a mosaic of high and low values in the remaining subsoil samples. Anisotropy was detected in the spatial structure of pores, but was not detected in relation to the distribution of bacteria. No marked trend as a function of distance to the nearest pore was observed in bacterial density values in the topsoil, but in the subsoil bacterial density was greatest close to pores and decreased thereafter. Bacterial aggregation was greatest in the cropped topsoil, though no consistent trends were found in the degree of bacterial aggregation as a function of distance to the nearest pore. The implications of the results presented for modelling and predicting bacterial activity in soil are discussed. ; p. 203-215.
    Keywords: Spatial Patterns ; Geostatistics ; Soil Bacteria ; Soil Thin Sections ; Soil Structure ; Image Analysis ; Environmental Sciences ; Biology
    ISSN: 0168-6496
    E-ISSN: 1574-6941
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  • 6
    Language: English
    In: FEMS Microbiology Ecology, 2005, Vol.52(1), pp.139-144
    Description: The density and spatial location of bacteria were investigated within different horizons of an upland grassland soil before and after a liming treatment to increase the numbers of large soil fauna. Bacterial cells were located by image analysis of stained thin sections and densities calculated from these data. Excrement from macro- and meso-fauna was identified using micromorphology and the densities of bacteria on specific areas of excrement measured by image analysis. There were significant differences among horizons in the density of bacterial cells, with the minimum density found in the horizon with least evidence of earthworm activity, but no difference in density between the organic H and organo-mineral Ah horizons. Soil improvement by liming significantly increased bacterial densities in all three horizons, with the greatest increase found in the horizon with the smallest density before liming. There were no differences in bacterial density between areas dominated by excrement from earthworms and excrement from enchytraeids, although densities in both areas were significantly increased by liming. Variability in bacterial density at spatial scales of less than 1 mm was linked to the occurrence of excrement. Bacterial densities within areas of both types of excrement were significantly greater than those in the surrounding soil. However, the frequency distribution of the ratios of density in excrement to that in the soil was bimodal, with a majority of occurrences having a ratio near 1 and only some 20–30% having a much larger ratio. These variations can probably be explained by variations in the age of the excrement and its suitability as a substrate.
    Keywords: Soil Micromorphology ; Soil Structure ; Biological Thin Sections ; Bacteria ; Faunal Excrement ; Temperate Grassland ; Environmental Sciences ; Biology
    ISSN: 0168-6496
    E-ISSN: 1574-6941
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  • 7
    Language: English
    In: FEMS Microbiology Ecology, 2001, Vol.37(1), pp.67-77
    Description: A method for determining the number and in situ spatial distribution of bacterial cells over spatial scales ranging from micrometres to centimetres in mineral soils is described. Biological thin sections of undisturbed cores of soil were prepared in order to preserve the spatial distribution of bacterial cells. Composite (tessellated) images in which individual bacteria can be resolved within an area of 0.282 mm2 were acquired by means of a motorised scanning microscope stage. An image processing and analysis procedure was developed to determine the numbers and locations of bacterial cells in the composite images. The image processing procedure first homogenised the background of the images and then discriminated between bacteria and non-bacterial features using the colour and morphological properties of the images of the bacterial cells. Feature edges were detected in the green channel of colour (red, green, blue) images and bacterial cell edges were confirmed in the blue channel after elimination of autofluorescent features in the red channel. No significant difference was found between the number of bacteria or associated distributions determined automatically and control values derived interactively on individual fields of view. Data relating to total bacterial counts in thin sections and in paired dispersed samples suggested that all soil bacteria were being visualised in thin sections. Significant differences between samples taken from a depth profile of a fallow arable soil were found for both cell numbers and for cell distribution as measured by an index of dispersion. ; p. 67-77.
    Keywords: Soil Biological Thin Section ; Bacterial Spatial Distribution ; Soil Structure ; Biological Dispersion ; Environmental Sciences ; Biology
    ISSN: 0168-6496
    E-ISSN: 1574-6941
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  • 8
    In: FEMS Microbiology Ecology, 2006, Vol. 56(2), pp.310-320
    Description: Soil microbial communities play an important role in nutrient cycling and nutrient availability, especially in unimproved soils. In grazed pastures, sheep urine causes local changes in nutrient concentration which may be a source of heterogeneity in microbial community structure. In the present study, we investigated the effects of synthetic urine on soil microbial community structure, using physiological (community level physiological profiling, CLPP), biochemical (phospholipid fatty acid analysis, PLFA) and molecular (denaturing gradient gel electrophoresis, DGGE) fingerprinting methods. PLFA data suggested that synthetic urine treatment had no significant effect on total microbial (total PLFA), total bacterial or fungal biomass; however, significant changes in microbial community structure were observed with both PLFA and DGGE data. PLFA data suggested that synthetic urine induced a shift towards communities with higher concentrations of branched fatty acids. DGGE banding patterns derived from control and treated soils differed, due to a higher proportion of DNA sequences migrating only to the upper regions of the gel in synthetic urine-treated samples. The shifts in community structure measured by PLFA and DGGE were significantly correlated with one another, suggesting that both datasets reflected the same changes in microbial communities. Synthetic urine treatment preferentially stimulated the use of rhizosphere-C in sole-carbon-source utilisation profiles. The changes caused by synthetic urine addition accounted for only 10–15% of the total variability in community structure, suggesting that overall microbial community structure was reasonably stable and that changes were confined to a small proportion of the communities.
    Keywords: Microbial Community Structure ; Phospholipid Fatty Acid Analysis ; Denaturing Gradient Gel Electrophoresis ; Biolog ; Soil Solution Chemistry
    ISSN: 01686496
    E-ISSN: 1574-6941
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