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  • Ecosystem and Ecology Studies
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  • 1
    Language: English
    In: Soil Biology and Biochemistry, February 2011, Vol.43(2), pp.280-286
    Description: Microbial communities exist and are active in a complex 3-D physical framework which can cause a variety of micro-environments to develop that are more or less suitable for microbial growth, activity and survival. If there is a significant microbial biogeography at the pore scale in soil, then the relationship between microbial diversity and ecosystem function is likely to be affected by micro-environmental variations at the pore scale. In this laboratory study we show that there is a significant pore-scale microbial biogeography by labelling microbial communities in different pore size classes of undisturbed soil cores with C-labelled fructose (a soluble, labile substrate). This was achieved by adding the substrate solution to the samples at different matric potentials (−100 kPa, −3.15 kPa and −1 kPa; placing the substrate in pores with maximum diameter of 0.97, 9.7 and 97 μm, respectively) and incubating the samples for two weeks. The mineralisation of soil organic carbon and fructose was measured as CO and C–CO , respectively, in the jar headspace throughout the incubation. At the end of incubation we analysed the total microbial community structure using PLFA. The structure of microbial communities in different pore size classes was measured by PLFA stable isotope probing. Total PLFA profiles suggested that there was little effect of the incubation conditions on microbial community structure. However, labelled PLFA profiles showed that microbial community structure differed significantly among pore size classes, the differences being due primarily to variations in the abundance of mono-unsaturated lipids (Gram-biomarkers) and of the fungal biomarker (C18:2(9,12)). This is the first evidence for a significant microbial biogeography at the pore scale in undisturbed soil cores. ► Non-random variation in microbial community structure at pore scale. ► Gram-bacterial and fungal abundance change at pore scale. ► Different regions of the soil pore system can be targetted using combination of C-labelled substrate and moisture release curve.
    Keywords: Stable Isotope Probing ; Undisturbed Cores ; Matric Potential ; Plfa ; Pore Scale ; Biogeography ; Agriculture ; Chemistry
    ISSN: 0038-0717
    E-ISSN: 1879-3428
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  • 2
    Language: English
    In: Soil Biology and Biochemistry, September 2010, Vol.42(9), pp.1640-1642
    Description: A miniaturised method developed to measure the mineralisation of C-labelled organic compounds in small soil samples is presented. Soil samples (〈0.5 g) were placed in wells of microtiter plates with CO traps (NaOH-soaked glass microfiber filters) and amended with C-labelled substrate. The microtiter plate was covered with a seal and placed in a microplate clamp system to ensure that each well was airtight. After incubation, the CO traps were transferred to tightly sealed glass phials under CO -free atmosphere and the C-labelled CO was released by addition of H PO . The CO was measured by micro-GC and its isotopic signature was determined using a GC-IRMS. The qualitative and quantitative efficiency of the microplate system was demonstrated by comparison with direct measurement of CO in the headspace of phials in which similarly treated soil samples had been incubated. The two methods showed similar mineralisation rates for added C-substrates but the apparent mineralisation of soil organic matter was greater with the microtiter plate method. The microplate system presented here is suitable for studying the mineralisation of different kinds of C-labelled substrates in small soil samples and allows analysis of functional and molecular characteristics on the same micro-samples.
    Keywords: 13c-Labelling ; Co2 Trap ; Acid Release ; Mineralisation ; Microbial Scale ; Agriculture ; Chemistry
    ISSN: 0038-0717
    E-ISSN: 1879-3428
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  • 3
    Language: English
    In: Soil Biology and Biochemistry, November 2013, Vol.66, pp.69-77
    Description: Soil microorganisms are responsible for organic matter decomposition processes that regulate soil carbon storage and mineralisation to CO . Climate change is predicted to increase the frequency of drought events, with uncertain consequences for soil microbial communities. In this study we tested the hypothesis that agricultural management used to enhance soil carbon stocks would increase the stability of microbial community structure and activity in response to water-stress. Soil was sampled from a long-term field trial with three soil carbon management systems and was used in a laboratory study of the effect of a dry–wet cycle on organic C mineralisation and microbial community structure. After a drying–rewetting event, soil microcosms were maintained wet and microbial community structure and abundance as well as microbial respiration were measured for four weeks. The results showed that the NO-TILL management system, with the highest soil organic matter content and respiration rate, had a distinct bacterial community structure relative to the conventional and the TILL without fertiliser systems. In all management systems, the rewetting event clearly modified microbial community structure and activity. Both returned to their pre-drought state after 28 days. However, the magnitude of variation of C mineralisation was lower ( the resistance to stress was higher) in the NO-TILL system. The genetic structure of the NO-TILL bacterial communities was most modified by water-stress and exhibited a slower recovery rate. This suggests that land use management can increase microbial functional resistance to drought stress the establishment of bacterial communities with particular metabolic capacities. Nevertheless, the resilience rates of C mineralisation were similar among management regimes, suggesting that similar mechanisms occur, maybe due to a common soil microbial community legacy.
    Keywords: Global Change ; Bacterial Community Structure ; C Mineralisation ; Stability ; Agricultural Land Use ; Drying–Rewetting ; Agriculture ; Chemistry
    ISSN: 0038-0717
    E-ISSN: 1879-3428
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  • 4
    Language: English
    In: Soil Biology and Biochemistry, April 2014, Vol.71, pp.1-12
    Description: Thermal acclimation of soil organic matter (SOM) decomposition is frequently observed and has often been attributed to substrate depletion under warming, but other mechanisms, such as changes in microbial community structure and functioning, have received less attention. In order to determine whether shifts in microbial community structure and functioning are involved in thermal acclimation of SOM decomposition, a laboratory incubation experiment was conducted using an artificial forest soil. Samples were first subjected to different temperatures of 5, 15, and 25 °C during a 72-day pre-incubation period and then half of the microcosms from each pre-incubation temperature were incubated at 5 or 25 °C for a period of 11 days. Substantial thermal acclimation of SOM decomposition was observed, with the SOM decomposition in soils pre-incubated at higher temperatures being less sensitive to temperature. Along with the reduced temperature sensitivity in response to warming, significant changes in microbial community PLFAs, microbial biomass carbon (MBC), and the potential activities of 11 enzymes were also observed. Nevertheless, shifts in microbial community PLFAs and particular enzyme activities provided the most explanatory power for the decreased temperature sensitivity with warming, as revealed by a multivariate regression analysis. The microbial community structure shifts were mainly manifested as an increase in the relative abundance of Gram-positive bacteria and decreases in the relative abundances of Gram-negative bacteria and fungi. Microbial communities pre-incubated under lower temperatures experienced greater shifts in their structure. Substrate depletion did not occur in this short-term incubation experiment, since neither total organic carbon (TOC) nor dissolved organic carbon (DOC) decreased with increasing temperature. Our results suggest that shifts in microbial community structure and functioning may underlie the thermal acclimation of SOM decomposition and should be taken into account when predicting the response of soil CO efflux to global warming.
    Keywords: Heterotrophic Respiration ; Acclimatization ; Microbial Adaptation ; Phospholipid Fatty Acids (Plfas) ; Substrate Availability ; Carbon Cycling ; Temperate Forest ; Agriculture ; Chemistry
    ISSN: 0038-0717
    E-ISSN: 1879-3428
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  • 5
    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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  • 6
    Language: English
    In: Soil Biology and Biochemistry, November 2014, Vol.78, pp.189-194
    Description: Modelling carbon mineralisation in natural soils is a major topic in soil and climate research. Current models need to be improved to include soil structure as an influencing factor to better predict C fluxes between pedosphere and atmosphere and to estimate carbon sequestration potentials. Geometry-based mechanistic modelling approaches have recently been developed to systematically study the effect of soil structure on carbon decomposition. Such models require spatially explicit input parameters describing the architecture of the pore space and the heterogeneous distribution of microbes and organic matter as decomposable substrate. The latter is very difficult to determine , resulting in increased uncertainty in the models. To obtain more realistic input data, we have developed a novel approach to locate soil organic matter (SOM) in undisturbed aggregates of soil using a combination of synchrotron-based X-ray microtomography and osmium as a staining agent for SOM. Here, we present the first results using 5 mm sized soil aggregate samples with contrasting C-contents in which we obtained maps of organic matter distributions in relation to the pore networks at the aggregate scale.
    Keywords: Soil Organic Matter ; Soil Structure ; Carbon Sequestration ; Synchrotron Microtomography ; Staining ; Agriculture ; Chemistry
    ISSN: 0038-0717
    E-ISSN: 1879-3428
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  • 7
    Language: English
    In: Biology and Fertility of Soils, 2013, Vol.49(7), pp.939-948
    Description: Soil organisms are of fundamental importance for many soil functions, such as organic matter decomposition, nutrient cycling and energy flow. Most research suggests that soil microbial communities are functionally redundant, meaning that there is little relationship between microbial diversity and soil functions. However, the activity of biological communities is known to be affected by their physical environment. Here, the effects of changes in microbial diversity and soil structure on organic C (OC) mineralisation were investigated. Sterile soil samples that had been subjected to different physical perturbations were inoculated with microbial communities with different levels of diversity. The samples were incubated for a period of 127 days and the mineralisation of native and added ( 13 C-labelled substrates, fructose and vanillin) OC was measured. It was hypothesised that the magnitude of the effect of changes in soil structure on OC mineralisation would increase as diversity decreased. The diversity treatment had a small but significant effect on the mineralisation of SOC and of the added substrates. The soil structure treatment had a significant effect only on the mineralisation of the added substrate C. There was no interaction between diversity and soil structure treatments, indicating that the relationship between diversity and OC decomposition was not dependent on the soil physical environment.
    Keywords: Soil microbial diversity ; Soil structure ; Soil organic carbon mineralisation ; Carbon dynamics
    ISSN: 0178-2762
    E-ISSN: 1432-0789
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  • 8
    Language: English
    In: Soil Biology and Biochemistry, April 2014, Vol.71, pp.21-30
    Description: Temporal dynamics create unique and often ephemeral conditions that can influence soil microbial biogeography at different spatial scales. This study investigated the relation between decimeter to meter spatial variability of soil microbial community structure, plant diversity, and soil properties at six dates from April through November. We also explored the robustness of these interactions over time. An historically unfertilized, unplowed grassland in southwest Germany was selected to characterize how seasonal variability in the composition of plant communities and substrate quality changed the biogeography of soil microorganisms at the plot scale (10 m × 10 m). Microbial community spatial structure was positively correlated with the local environment, i.e. physical and chemical soil properties, in spring and autumn, while the density and diversity of plants had an additional effect in the summer period. Spatial relationships among plant and microbial communities were detected only in the early summer and autumn periods when aboveground biomass increase was most rapid and its influence on soil microbial communities was greatest due to increased demand by plants for nutrients. Individual properties exhibited varying degrees of spatial structure over the season. Differential responses of Gram positive and Gram negative bacterial communities to seasonal shifts in soil nutrients were detected. We concluded that spatial distribution patterns of soil microorganisms change over a season and that chemical soil properties are more important controlling factors than plant density and diversity. Finer spatial resolution, such as the mm to cm scale, as well as taxonomic resolution of microbial groups, could help determine the importance of plant species density, composition, and growth stage in shaping microbial community composition and spatial patterns.
    Keywords: Microbial Community Composition ; Spatial Patterns ; Grassland Soils ; Plfas ; Mantel Statistic ; Variogram ; Agriculture ; Chemistry
    ISSN: 0038-0717
    E-ISSN: 1879-3428
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  • 9
    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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  • 10
    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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