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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
    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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  • 4
    Language: English
    In: Global Change Biology, 01 January 2010, Vol.16, 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...
    Keywords: Life Sciences ; Ecology, Environment ; Meteorology & Climatology ; Environmental Sciences ; Biology
    ISSN: 1354-1013
    E-ISSN: 1365-2486
    Source: Hyper Article en Ligne (CCSd)
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  • 5
    Language: English
    In: Science of the Total Environment, 15 November 2017, Vol.598, pp.938-948
    Description: The concentration, degree of contamination and pollution of 7 trace elements (TEs) along an urban pressure gradient were measured in 180 lawn and wood soils of the Paris region (France). Iron (Fe), a major element, was used as reference element. Copper (Cu), cadmium (Cd), lead (Pb) and zinc (Zn) were of anthropogenic origin, while arsenic (As), chromium (Cr) and nickel (Ni) were of natural origin. Road traffic was identified as the main source of anthropogenic TEs. In addition, the industrial activity of the Paris region, especially cement plants, was identified as secondary source of Cd. Soil characteristics (such as texture, organic carbon (OC) and total nitrogen (tot N) contents) tell the story of the soil origins and legacies along the urban pressure gradient and often can explain TE concentrations. The history of the land-use types was identified as a factor that allowed understanding the contamination and pollution by TEs. Urban wood soils were found to be more contaminated and polluted than urban lawns, probably because woods are much older than lawns and because of the legacy of the historical management of soils in the Paris region (Haussmann period). Lawn soils are similar to the fertile agricultural soils and relatively recently (mostly from the 1950s onwards) imported from the surrounding of Paris, so that they may be less influenced by urban conditions in terms of TE concentrations. Urban wood soils are heavily polluted by Cd, posing a high risk to the biological communities. The concentration of anthropogenic TEs increased from the rural to the urban areas, and the concentrations of most anthropogenic TEs in urban areas were equivalent to or above the regulatory reference values, raising the question of longer-term monitoring.
    Keywords: Trace Elements ; Urban-Rural Gradient ; Soils ; Green Spaces ; Lawns ; Forests ; Environmental Sciences ; Biology ; Public Health
    ISSN: 0048-9697
    E-ISSN: 1879-1026
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  • 6
    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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  • 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
    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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  • 9
    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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  • 10
    Language: English
    In: Sci Rep, 2018, Vol.8(1), pp.4057-4057
    Description: A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.
    Keywords: Biology;
    ISSN: 2045-2322
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