Browsing by Author "Juyal, Archana"

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    Bacterial distribution in soil microhabitats at different spatial scales
    (Cranfield University, 2018-08-08 16:11) Otten, Wilfred; Eickhorst, Thilo; Juyal, Archana; Falconer, Ruth; Hapca, Simona; Schmidt, Hannes; C Baveye, Philippe
    The data underpin the results described in the Geoderma paper by Juyal et al (2018) https://doi.org/10.1016/j.geoderma.2018.07.031 entitled 'Combination of techniques to quantify the distribution of bacteria in their soil microhabitats at different spatial scales'. The data are represented in an Excel file and show counts of bacteria in individual sections of soil blocks and their corresponding pore geometry as determined by Xray CT at three different spatial scales. The data underpin the summary data described in the paper where a detailed method description is also provided.
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    Combination of techniques to quantify the distribution of bacteria in their soil microhabitats at different spatial scales
    (Elsevier, 2018-04-08) Juyal, Archana; Otten, Wilfred; Falconer, Ruth; Hapca, Simona; Schmidt, Hannes; Baveye, Philippe C.; Eickhorst, Thilo
    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.
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    Control of pore geometry in soil microcosms and its effect on the growth and spread of Pseudomonas and Bacillus sp.
    (Frontiers, 2018-07-13) Juyal, Archana; Eickhorst, Thilo; Falconer, Ruth; Baveye, Philippe C.; Spiers, Andrew; Otten, Wilfred
    Simplified experimental systems, often referred to as microcosms, have played a central role in the development of modern ecological thinking on issues ranging from competitive exclusion to examination of spatial resources and competition mechanisms, with important model-driven insights to the field. It is widely recognized that soil architecture is the key driver of biological and physical processes underpinning ecosystem services, and the role of soil architecture and soil physical conditions is receiving growing interest. The difficulty to capture the architectural heterogeneity in microcosms means that we typically disrupt physical architecture when collecting soils. We then use surrogate measures of soil architecture such as aggregate size distribution and bulk-density, in an attempt to recreate conditions encountered in the field. These bulk-measures are too crude and do not describe the heterogeneity at microscopic scales where microorganisms operate. In the current paper we therefore ask the following questions: (i) To what extent can we control the pore geometry at microscopic scales in microcosm studies through manipulation of common variables such as density and aggregate size?; (ii) What is the effect of pore geometry on the growth and spread dynamics of bacteria following introduction into soil? To answer these questions, we focus on Pseudomonas sp. and Bacillus sp. We study the growth of populations introduced in replicated microcosms packed at densities ranging from 1.2 to 1.6 g cm−3, as well as packed with different aggregate sizes at identical bulk-density. We use X-ray CT and show how pore geometrical properties at microbial scales such as connectivity and solid-pore interface area, are affected by the way we prepare microcosms. At a bulk-density of 1.6 g cm−3 the average number of Pseudomonas was 63% lower than at a bulk-density of 1.3 g cm−3. For Bacillus this reduction was 66%. Depending on the physical conditions, bacteria in half the samples took between 1.62 and 9.22 days to spread 1.5 cm. Bacillus did spread faster than Pseudomonas and both did spread faster at a lower bulk-density. Our results highlight the importance that soil physical properties be considered in greater detail in soil microbiological studies than is currently the case.
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    ItemOpen Access
    Data for spread of bacteria in soil
    (Cranfield University, 2020-04-20 14:34) Otten, Wilfred; Eickhorst, Thilo; Juyal, Archana; C Baveye, Philippe
    Data set related to the paper 'Influence of soil structure on the spread of Pseudomonas fluorescens in soil at microscale' the objective of the study was to determine the influence of soil pore characteristics on the spread of bacteria in soil. Bacteria were introduced and locally and allowed to spread through soil. Soil was resin impregnated and the location of bacteria was observed in thin sections. X-ray CT was used to determine the physical characteristics of the pore space. The data set contains the raw data published in the accompanying paper. Treatment refers to the bulk density of the soil and 2 thin sections were counted for each sample. at each micro-site in soil pore characteristics are given in the table and the number of bacterial cells found in that section through observation and counting under the microscope. Counts are converted to cell densities. The data relate to the spread of bacteria and further analysis of the data is described in the paper
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    Influence of soil structure on the spread of Pseudomonas fluorescens in soil at microscale
    (Wiley, 2020-04-24) Juyal, Archana; Otten, Wilfred; Baveye, Philippe C.; Eickhorst, Thilo
    For over a half a century, researchers have been aware of the fact that the physical and chemical characteristics of microenvironments in soils strongly influence the activity, growth, and metabolism of microorganisms. However, many aspects of the effect of soil physical characteristics, such as the pore geometry, remain poorly understood. Therefore, the objective of the present research was to determine the influence of soil pore characteristics on the spread of bacteria, observed at the scale relevant to microbes. Pseudomonas fluorescens was introduced in columns filled with 1–2 mm soil aggregates, packed at different bulk densities.. Soil microcosms were scanned at 10.87 μm voxel resolution using X‐ray computed tomography (CT) to characterize the geometry of pores. Thin sections were prepared to determine the spread and colonization of bacteria. The results showed that average bacterial cell density was 174 cells mm−2 in soil with bulk density of 1.3 g cm−3 and 99 cells mm−2 in soil with bulk density of 1.5 g cm−3. Soil porosity and solid‐pore interfaces influence the spread of bacteria and their colonization of the pore space at lower bulk density, resulting in relatively higher bacterial densities in larger pore spaces. The study also demonstrates that thin sectioning of resin impregnated soil samples can be combined with X‐ray CT to visualize bacterial colonization of a 3D pore volume. This research therefore represents a significant step towards understanding how environmental change and soil management impact bacterial diversity in soils.