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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: PLoS ONE, 2014, Vol.9(1)
    Description: Despite an exceptional number of bacterial cells and species in soils, bacterial diversity seems to have little effect on soil processes, such as respiration or nitrification, that can be affected by interactions between bacterial cells. The aim of this study is to understand how bacterial cells are distributed in soil to better understand the scaling between cell-to-cell interactions and what can be measured in a few milligrams, or more, of soil. Based on the analysis of 744 images of observed bacterial distributions in soil thin sections taken at different depths, we found that the inter-cell distance was, on average 12.46 µm and that these inter-cell distances were shorter near the soil surface (10.38 µm) than at depth (〉18 µm), due to changes in cell densities. These images were also used to develop a spatial statistical model, based on Log Gaussian Cox Processes, to analyse the 2D distribution of cells and construct realistic 3D bacterial distributions. Our analyses suggest that despite the very high number of cells and species in soil, bacteria only interact with a few other individuals. For example, at bacterial densities commonly found in bulk soil (10 8 cells g −1 soil), the number of neighbours a single bacterium has within an interaction distance of ca. 20 µm is relatively limited (120 cells on average). Making conservative assumptions about the distribution of species, we show that such neighbourhoods contain less than 100 species. This value did not change appreciably as a function of the overall diversity in soil, suggesting that the diversity of soil bacterial communities may be species-saturated. All in all, this work provides precise data on bacterial distributions, a novel way to model them at the micrometer scale as well as some new insights on the degree of interactions between individual bacterial cells in soils.
    Keywords: Research Article ; Agriculture ; Biology ; Earth Sciences ; Mathematics
    E-ISSN: 1932-6203
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  • 3
    Language: English
    In: Soil Biology and Biochemistry, December 2015, Vol.91, pp.258-267
    Description: The spatial ecology of soil microbial communities and their functioning is an understudied aspect of soil microbial ecology. Much of our understanding of the spatial organisation of microbial communities has been obtained at scales that are inappropriate for identifying how microbial functioning and spatial patterns are related. In order to reveal the spatial strategies of soil microorganisms, we measured the microscale spatial distribution of 6 exoenzyme activities (EEA) and related them to the catalytic potential of three soils. The relationship between EEA profiles and microbial community structure was also measured in soil aggregates. All the EEA exhibited scale-invariant spatial clustering. The extent of spatial clustering varied significantly among EEA, suggesting that microbial communities employ different spatial strategies when foraging for different elements. The dispersed distribution of alkaline phosphatase suggests that microorganisms invest more heavily in the acquisition of P. The EEA associated with the C and N cycles, but not the P cycle, were significantly affected by management practices in the loamy soil. A significant negative relationship between the extent of spatial clustering of EEA and the overall intensity of the EEA was identified in the two loamy soils, indicating that the microscale spatial ecology of microbial activity may have a significant impact on biogeochemical cycles. No relationship was found between microbial community structure and EEA profiles in aggregates. However, a number of negative relationships between the relative abundance of certain taxa and the most dispersed EEA (alkaline phosphatase and β-glucosidase) were found, suggesting that these taxa make the EEA products available by means other than the production of exoenzymes (e.g. solubilisation of phosphate through the production of organic acids).
    Keywords: Aggregate ; Dispersion ; Exoenzyme Activity ; Management Practices ; Micro-Scale ; Spatial Distribution ; Taxonomic Microarray ; Agriculture ; Chemistry
    ISSN: 0038-0717
    E-ISSN: 1879-3428
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  • 4
    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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  • 5
    Language: English
    In: Soil Biology and Biochemistry, 2015, Vol.88, p.430(11)
    Description: To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.soilbio.2015.05.026 Byline: Runa S. Boeddinghaus, Naoise Nunan, Doreen Berner, Sven Marhan, Ellen Kandeler Abstract: In heterogeneous environments such as soil it is imperative to understand the spatial relationships between microbial communities, microbial functioning and microbial habitats in order to predict microbial services in managed grasslands. Grassland land-use intensity has been shown to affect the spatial distribution of soil microorganisms, but so far it is unknown whether this is transferable from one geographic region to another. This study evaluated the spatial distribution of soil microbial biomass and enzyme activities involved in C-, N- and P-cycling, together with physico-chemical soil properties in 18 grassland sites differing in their land-use intensity in two geographic regions: the Hainich National Park in the middle of Germany and the Swabian Alb in south-west Germany. Enzyme activities associated with the C- and N-cycles, namely [beta]-glucosidase, xylosidase and chitinase, organic carbon (C.sub.org), total nitrogen (N.sub.t), extractable organic carbon, and mineral nitrogen (N.sub.min) were higher in the Swabian Alb (Leptosols) than in the Hainich National Park (primarily Stagnosols). There was a negative relationship between bulk density and soil properties such as microbial biomass (C.sub.mic, N.sub.mic), urease, C.sub.org, and N.sub.t. The drivers (local abiotic soil properties, spatial separation) of the enzyme profiles ([beta]-glucosidase, chitinase, xylosidase, phosphatase, and urease) were determined through a spatial analysis of the within site variation of enzyme profiles and abiotic properties, using the Procrustes rotation test. The test revealed that physical and chemical properties showed more spatial pattern than the enzyme profiles. [beta]-glucosidase, chitinase, xylosidase, phosphatase, and urease activities were related to local abiotic soil properties, but showed little spatial correlation. Semivariogram modeling revealed that the ranges of spatial autocorrelation of all measured variables were site specific and not related to region or to land-use intensity. Nevertheless, land-use intensity changed the occurrence of spatial patterns measurable at the plot scale: increasing land-use intensity led to an increase in detectable spatial patterns for abiotic soil properties on Leptosols. The conclusion of this study is that microbial biomass and functions in grassland soils do not follow general spatial distribution patterns, but that the spatial distribution is site-specific and mainly related to the abiotic properties of the soils. Author Affiliation: (a) Institute of Soil Science and Land Evaluation, Soil Biology, University of Hohenheim, Stuttgart, Germany (b) CNRS, Institute of Ecology and Environmental Science, Campus AgroParisTech, 78850 Thiverval-Grignon, France Article History: Received 22 July 2014; Revised 27 May 2015; Accepted 28 May 2015
    Keywords: Soil Microbiology – Chemical Properties ; Soil Microbiology – Analysis ; Soils – Chemical Properties ; Soils – Analysis ; Hydrolases – Chemical Properties ; Hydrolases – Analysis ; Grasslands – Chemical Properties ; Grasslands – Analysis
    ISSN: 0038-0717
    Source: Cengage Learning, Inc.
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  • 6
    Language: English
    In: Soil Biology and Biochemistry, Nov, 2013, Vol.66, p.69(9)
    Description: To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.soilbio.2013.07.001 Byline: Aurore Kaisermann, Adelaide Roguet, Naoise Nunan, Pierre-Alain Maron, Nicholas Ostle, Jean-Christophe Lata Abstract: Soil microorganisms are responsible for organic matter decomposition processes that regulate soil carbon storage and mineralisation to CO.sub.2. 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 (i.e. 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 via 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. Author Affiliation: (a) Laboratoire Bioemco, CNRS/UPMC, 46 rue d'Ulm, 75230 Paris Cedex 5, France (b) Laboratoire Bioemco, CNRS/UPMC, Batiment EGER Campus AgroParisTech, F-78850 Thiverval Grignon, France (c) UMR 1347 Agroecology INRA - AgroSup Dijon - University of Burgundy, 17, rue Sully, B.V. 86510, 21065 Dijon Cedex, France (d) Platform GenoSol, UMR Agroecology INRA - AgroSup Dijon - University of Burgundy, 17, rue Sully, B.V. 86510, 21065 Dijon Cedex, France (e) Centre for Ecology and Hydrology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster LA1 4AP, UK Article History: Received 14 May 2013; Accepted 1 July 2013
    Keywords: Global Temperature Changes ; No-tillage ; Soil Carbon
    ISSN: 0038-0717
    Source: Cengage Learning, Inc.
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  • 7
    Language: English
    In: Soil Biology and Biochemistry, 2014, Vol.71, p.1(12)
    Description: To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.soilbio.2014.01.003 Byline: Hui Wei, Bertrand Guenet, Sara Vicca, Naoise Nunan, Hamada AbdElgawad, Valerie Pouteau, Weijun Shen, Ivan A. Janssens Abstract: 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 [degrees]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 [degrees]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.sub.2 efflux to global warming. Author Affiliation: (a) Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China (b) Department of Biology, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium (c) CNRS-INRA, UMR7618, BioEMCo, Batiment EGER, Campus AgroParisTech, 78850 Thiverval-Grignon, France (d) Graduate University of the Chinese Academy of Sciences, Beijing 100049, PR China Article History: Received 12 July 2013; Revised 30 December 2013; Accepted 3 January 2014
    Keywords: Enzymology – Analysis ; Forest Soils – Analysis ; Ecological Restoration – Analysis ; Enzymes – Analysis ; Bacteria – Analysis ; Global Temperature Changes – Analysis ; Ecosystems – Analysis
    ISSN: 0038-0717
    Source: Cengage Learning, Inc.
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  • 8
    Language: English
    In: Soil Biology and Biochemistry, 29 October 2010, Vol.2011(43), pp.280-286
    Keywords: Environmental Sciences ; Agriculture ; Environmental Sciences ; Chemistry
    ISSN: 0038-0717
    E-ISSN: 1879-3428
    Source: Hyper Article en Ligne (CCSd)
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  • 9
    Language: English
    In: Soil biology & biochemistry, 2011, Vol.43, 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 13C-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 CO2 and 13C–CO2, 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. ; Includes references ; p. 280-286.
    Keywords: Soil Organic Carbon ; Soil Bacteria ; Soil Pore System ; Soil Matric Potential ; Functional Diversity ; Biogeography ; Soil Ecology ; Isotope Labeling ; Stable Isotopes ; Microhabitats ; Headspace Analysis ; Soil Microorganisms ; Soil Fungi ; Carbon ; Fructose ; Mineralization ; Microbial Ecology ; Species Diversity
    ISSN: 0038-0717
    Source: AGRIS (Food and Agriculture Organization of the United Nations)
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  • 10
    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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