Please use this identifier to cite or link to this item: http://hdl.handle.net/1893/30276
Appears in Collections:Computing Science and Mathematics Journal Articles
Peer Review Status: Refereed
Title: Combination of techniques to quantify the distribution of bacteria in their soil microhabitats at different spatial scales
Author(s): Juyal, Archana
Otten, Wilfred
Falconer, Ruth
Hapca, Simona
Schmidt, Hannes
Baveye, Philippe C
Eickhorst, Thilo
Keywords: X-ray CT
Fluorescence microscopy
Soil bacteria
Pore geometry
Soil sections
Spatial distribution
Issue Date: 15-Jan-2019
Citation: Juyal A, Otten W, Falconer R, Hapca S, Schmidt H, Baveye PC & Eickhorst T (2019) Combination of techniques to quantify the distribution of bacteria in their soil microhabitats at different spatial scales. Geoderma, 334, pp. 165-174. https://doi.org/10.1016/j.geoderma.2018.07.031
Abstract: To address a number of issues of great societal concern at the moment, like the sequestration of carbon, information is direly needed about interactions between soil architecture and microbial dynamics. Unfortunately, soils are extremely complex, heterogeneous systems comprising highly variable and dynamic micro-habitats that have significant impacts on the growth and activity of inhabiting microbiota. Data remain scarce on the influence of soil physical parameters characterizing the pore space on the distribution and diversity of bacteria. In this context, the objective of the research described in this article was to develop a method where X-ray microtomography, to characterize the soil architecture, is combined with fluorescence microscopy to visualize and quantify bacterial distributions in resin-impregnated soil sections. The influence of pore geometry (at a resolution of 13.4 μm) on the distribution of Pseudomonas fluorescens was analysed at macro- (5.2 mm × 5.2 mm), meso- (1 mm × 1 mm) and microscales (0.2 mm × 0.2 mm) based on an experimental setup simulating different soil architectures. The cell density of P. fluorescens was 5.59 x 107(SE 2.6 x 106) cells g−1 soil in 1–2 mm and 5.84 x 107(SE 2.4 x 106) cells g−1 in 2–4 mm size aggregates soil. Solid-pore interfaces influenced bacterial distribution at micro- and macroscale, whereas the effect of soil porosity on bacterial distribution varied according to three observation scales in different soil architectures. The influence of soil porosity on the distribution of bacteria in different soil architectures was observed mainly at the macroscale, relative to micro- and mesoscales. Experimental data suggest that the effect of pore geometry on the distribution of bacteria varied with the spatial scale, thus highlighting the need to consider an “appropriate spatial scale” to understand the factors that regulate the distribution of microbial communities in soils. The results obtained to date also indicate that the proposed method is a significant step towards a full mechanistic understanding of microbial dynamics in structured soils. © 2018 Elsevier B.V.
DOI Link: 10.1016/j.geoderma.2018.07.031
Rights: This is the accepted refereed manuscript of: Juyal A, Otten W, Falconer R, Hapca S, Schmidt H, Baveye PC & Eickhorst T (2019) Combination of techniques to quantify the distribution of bacteria in their soil microhabitats at different spatial scales. Geoderma, 334, pp. 165-174. https://doi.org/10.1016/j.geoderma.2018.07.031 © 2018, Elsevier Licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International: http://creativecommons.org/licenses/by-nc-nd/4.0/
Licence URL(s): http://creativecommons.org/licenses/by-nc-nd/4.0/

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