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  • Directory of Open Access Journals (DOAJ)  (5)
  • 1
    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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  • 2
    Language: English
    In: Scientific Reports, 01 March 2018, Vol.8(1), pp.1-1
    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: Scientific Reports
    E-ISSN: 2045-2322
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  • 3
    Language: English
    In: Frontiers in Environmental Science, 01 July 2018, Vol.6
    Description: Root surfaces are major sites of interactions between plants and associated microorganisms. Here, plants and microbes communicate via signaling molecules, compete for nutrients, and release substrates that may have beneficial or harmful effects on each other. Whilst the body of knowledge on...
    Keywords: Microbial Ecology ; Root Surface ; Bacterial Colonization ; Point Process ; Spatial Statistics ; Image Analysis ; Environmental Sciences
    E-ISSN: 2296-665X
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  • 4
    Language: English
    In: Biogeosciences, May 12, 2017, Vol.14(9), p.2429
    Description: Amazonian podzols store huge amounts of carbon and play a key role in transferring organic matter to the Amazon River. In order to better understand their C dynamics, we modelled the formation of representative Amazonian podzol profiles by constraining both total carbon and radiocarbon. We determined the relationships between total carbon and radiocarbon in organic C pools numerically by setting constant C and .sup.14 C inputs over time. The model was an effective tool for determining the order of magnitude of the carbon fluxes and the time of genesis of the main carbon-containing horizons, i.e. the topsoil and deep Bh. We performed retrocalculations to take into account the bomb carbon in the young topsoil horizons (calculated apparent .sup.14 C age from 62 to 109#xC2;#xA0;years). We modelled four profiles representative of Amazonian podzols, two profiles with an old Bh (calculated apparent .sup.14 C age 6.8 #xC3;#x97; 10.sup.3 and 8.4 #xC3;#x97; 10.sup.3 years) and two profiles with a very old Bh (calculated apparent .sup.14 C age 23.2 #xC3;#x97; 10.sup.3 and 25.1 #xC3;#x97; 10.sup.3 years). The calculated fluxes from the topsoil to the perched water table indicate that the most waterlogged zones of the podzolized areas are the main source of dissolved organic matter found in the river network. It was necessary to consider two Bh carbon pools to accurately represent the carbon fluxes leaving the Bh as observed in previous studies. We found that the genesis time of the studied soils was necessarily longer than 15 #xC3;#x97; 10.sup.3 and 130 #xC3;#x97; 10.sup.3 years for the two younger and two older Bhs, respectively, and that the genesis time calculated considering the more likely settings runs to around 15 #xC3;#x97; 10.sup.3 -25 #xC3;#x97; 10.sup.3 and 150 #xC3;#x97; 10.sup.3 -250 #xC3;#x97; 10.sup.3 years, respectively.
    Keywords: Carbon – Research ; Podzols – Models ; Podzols – Research
    ISSN: 1726-4170
    E-ISSN: 17264189
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  • 5
    Language: English
    In: Frontiers in Microbiology, 01 August 2018, Vol.9
    Description: Over the last 60 years, soil microbiologists have accumulated a wealth of experimental data showing that the bulk, macroscopic parameters (e.g., granulometry, pH, soil organic matter, and biomass contents) commonly used to characterize soils provide insufficient information to describe quantitatively...
    Keywords: Soil Microbiology ; Biodiversity ; Upscaling ; Tomography ; X-Ray Computed ; Nanosims Imaging ; Biology
    E-ISSN: 1664-302X
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