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Berlin Brandenburg

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  • Wiley (CrossRef)  (13)
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  • 1
    Language: English
    In: Journal of Plant Nutrition and Soil Science, August 2017, Vol.180(4), pp.425-429
    Description: The microbial habitat is rarely studied in soil microbial ecology even though microbial cells are exposed and adapt to their local environmental conditions. The physical environment also constrains interactions among organisms. The nature of microbial communities and their functioning can only be fully understood if their habitat is accounted for. Here, I describe the soil microbial habitat and show how our understanding of microbial functioning has been shaped by this line of investigation.
    Keywords: Diffusion ; Functional Redundancy ; Microbial Communities ; Micro‐Habitat ; Microscale
    ISSN: 1436-8730
    E-ISSN: 1522-2624
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  • 2
    In: Global Change Biology, January 2010, Vol.16(1), pp.416-426
    Description: It is estimated that in excess of 50% of the soil carbon stock is found in the subsoil (below 20–30 cm). Despite this very few studies have paid attention to the subsoil. Although surface and subsurface horizons differ in pedological, environmental and physicochemical features, which are all likely to affect the mechanisms and biological actors involved, models of carbon dynamics tend to assume that the underlying processes are identical in all horizons, but with lower gross fluxes in the subsurface. The aim of this study was to test this assumption by analysing factors governing organic matter decomposition in topsoil (from depths of 5–10 cm) and subsoil (from depths of 80–100 cm). To this end, we established incubations that lasted 51 days, in which factors that were thought to control organic matter mineralization were altered: oxygen concentration, soil structure and the energetic and nutritional status. At the end of the incubation period, the microbial biomass was measured and the community level physiological profiles established. The mineralization per unit organic carbon proved to be as important in the subsoil as it was in surface samples, in spite of lower carbon contents and different catabolic profiles. Differences in the treatment effects indicated that the controls on C dynamics were different in topsoil and subsoil: disrupting the structure of the subsoil caused a 75% increase in mineralization while the surface samples remained unaffected. On the other hand, a significant priming affect was found in the topsoil but not in the subsoil samples. Spatial heterogeneity in carbon content, respiration and microbial communities was greater in subsoil than in topsoil at the field scale. These data suggest greater attention should be paid to the subsoil if global C dynamics is to be fully understood.
    Keywords: C ; C Dynamics ; Microbial Community Structure ; Stable Isotopes ; Subsoil
    ISSN: 1354-1013
    E-ISSN: 1365-2486
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  • 3
    Language: English
    In: African Journal of Ecology, May 2011, Vol.99(3), pp.828-837
    Description: 1. Declines in availability of plant resources to pollinators are a major cause of pollinator loss. The management of plant communities to enhance floral resources is often proposed as a way to sustain pollinator populations. Nectar, the main energetic resource for pollinators, plays a...
    Keywords: Environmental Sciences ; Life Sciences ; Plant-Soil Inter-Actions ; Above-Ground-Below-Ground Interactions ; Attractiveness ; Competition ; Diversity ; Floral Display ; Nectar ; Plant-Plant Interactions ; Plant-Pollinator Interactions ; Environmental Sciences ; Biology ; Zoology ; Ecology
    ISSN: 0141-6707
    ISSN: 00220477
    E-ISSN: 1365-2028
    E-ISSN: 13652745
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  • 4
    In: Functional Ecology, December 2014, Vol.28(6), pp.1523-1533
    Description: A major question in ecology is to know how ecosystem function is affected by the number of species. After two decades of research, the nature, shape, and causes of the relationships between biodiversity and ecosystem functioning remain unresolved. Huston ([Huston, M.A., 1997]) suggested that a statistical ‘sampling effect’ for a few dominant species produced the patterns observed in experiments, while Tilman et al. ([Tilman, D., 1997a]) argued that the observed responses were due to the number of species rather than the properties of a few. Here, we present a general, theoretical and parsimonious model using combinatorial probabilities to describe the assembly effect as a probabilistic process. Our basic assumption is that community function is determined by random drawing from a fixed species pool composed of three classes of species. The species classes differ in their effect on community function and are ordered in a simple dominance hierarchy (subordinate, dominant and super‐dominant species). Community function is determined by prevalent dominance rules: the dominance by the majority of species mimics the effect of dominant species, i.e. the function is determined by the dominant or super‐dominant species class the most numerous within the community; the dominance by the presence of species mimics the effect of keystone species, i.e. the function is determined by the species that is ranked highest in the dominance hierarchy. The model produces significant fits to four experimental data sets obtained for plant and microbial communities, including monotonic and hump‐shaped curves. The results indicate that the model gave good fits under both the dominance rules in any data set, suggesting that the random sampling effect provides a parsimonious explanation for the various relationships observed in diversity‐ecosystem functioning experiments. The model describes a random assembly process that produces variation in ecosystem functioning in response to number of species selected from a regional species pool composed of several classes of species differing in their ecosystem effects and relative dominance. This simple model reproduces all shapes of diversity‐ecosystem functioning relationships reported in the experimental literature. The results suggest that the multi‐faceted response of ecosystems to biodiversity may be nothing more than manifestations of random assembly effects and variation in species properties. Lay
    Keywords: Assembly Process ; Biological Interactions ; Dominance ; Keystone ; Modelling ; Probability ; Sampling Effect ; Theoretical Ecology
    ISSN: 0269-8463
    E-ISSN: 1365-2435
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  • 5
    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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  • 6
    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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  • 7
    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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  • 8
    Language: English
    In: Rapid Communications in Mass Spectrometry, 15 January 2007, Vol.21(1), pp.29-34
    Description: The spatial location of microorganisms and their activity within the soil matrix have major impacts on biological processes such as nutrient cycling. However, characterizing the biophysical interface in soils is hampered by a lack of techniques at relevant scales. A novel method for studying the distribution of microorganisms that have incorporated isotopically labelled substrate (‘active’ microorganisms) in relation to the soil microbial habitat is provided by nano‐scale secondary ion mass spectrometry (NanoSIMS). are ubiquitous in soil and were therefore used as a model for ‘active’ microorganisms in soil. Batch cultures (NCTC 10038) were grown in a minimal salt medium containing N‐ammonium sulphate (N ratio of 1.174), added to quartz‐based white sand or soil (coarse textured sand), embedded in Araldite 502 resin and sectioned for NanoSIMS analysis. The N‐enriched could be identified within the soil structure, demonstrating that the NanoSIMS technique enables the study of spatial location of microbial activity in relation to the heterogeneous soil matrix. This technique is complementary to the existing techniques of digital imaging analysis of soil thin sections and scanning electron microscopy. Together with advanced computer‐aided tomography of soils and mathematical modelling of soil heterogeneity, NanoSIMS may be a powerful tool for studying physical and biological interactions, thereby furthering our understanding of the biophysical interface in soils. Copyright © 2006 John Wiley & Sons, Ltd.
    Keywords: Soil Microbiology ; Soil -- Analysis;
    ISSN: 0951-4198
    E-ISSN: 1097-0231
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  • 9
    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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  • 10
    In: Environmental Microbiology, February 2008, Vol.10(2), pp.534-541
    Description: Soils support an enormous microbial diversity, but the ecological drivers of this diversity are poorly understood. Interactions between the roots of individual grass species and the arbuscular mycorrhizal (AM) fungi and bacteria in their rhizoplane were studied in a grazed, unimproved upland pasture. Individual root fragments were isolated from soil cores, DNA extracted and used to identify plant species and assess rhizoplane bacterial and AM fungal assemblages, by amplifying part of the small‐subunit ribosomal RNA gene, followed by terminal restriction fragment length polymorphism analysis. For the first time we showed that AM fungal and bacterial assemblages are related and that this relationship occurred at the community level. Principal coordinate analyses of the data show that the AM fungi were a major factor determining the bacterial assemblage on grass roots. We also report a strong influence of the composition of the plant community on AM fungal assemblage. The bacterial assemblage was also influenced by soil pH and was spatially structured, whereas AM fungi were influenced neither by the bacteria nor by soil pH. Our study shows that linkages between plant roots and their microbial communities exist in a complex web of interactions that act at individual and at community levels, with AM fungi influencing the bacterial assemblage, but not the other way round.
    Keywords: Ribosomal Rna -- Analysis;
    ISSN: 1462-2912
    E-ISSN: 1462-2920
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