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  • 1
    In: Experimental Agriculture, 2008, Vol.44(1), pp.133-133
    Description: The increasing awareness of the value of soil ecosystem services and the need to look after soil resources in a changing climate, combined with rapid developments in techniques, make this new edition timely and of great value as a text book for soil microbiology courses.With 22 chapters authored by leading scientists in the field, the book covers the soil habitat in which the organisms live, interact and adapt, and gives a comprehensive overview of the role terrestrial organisms play in the nitrogen and carbon cycle.
    Keywords: Books ; Bioremediation;
    ISSN: 0014-4797
    E-ISSN: 1469-4441
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  • 2
    In: PLoS ONE, 2015, Vol.10(9)
    Description: There is currently a significant need to improve our understanding of the factors that control a number of critical soil processes by integrating physical, chemical and biological measurements on soils at microscopic scales to help produce 3D maps of the related properties. Because of technological limitations, most chemical and biological measurements can be carried out only on exposed soil surfaces or 2-dimensional cuts through soil samples. Methods need to be developed to produce 3D maps of soil properties based on spatial sequences of 2D maps. In this general context, the objective of the research described here was to develop a method to generate 3D maps of soil chemical properties at the microscale by combining 2D SEM-EDX data with 3D X-ray computed tomography images. A statistical approach using the regression tree method and ordinary kriging applied to the residuals was developed and applied to predict the 3D spatial distribution of carbon, silicon, iron, and oxygen at the microscale. The spatial correlation between the X-ray grayscale intensities and the chemical maps made it possible to use a regression-tree model as an initial step to predict the 3D chemical composition. For chemical elements, e.g., iron, that are sparsely distributed in a soil sample, the regression-tree model provides a good prediction, explaining as much as 90% of the variability in some of the data. However, for chemical elements that are more homogenously distributed, such as carbon, silicon, or oxygen, the additional kriging of the regression tree residuals improved significantly the prediction with an increase in the R 2 value from 0.221 to 0.324 for carbon, 0.312 to 0.423 for silicon, and 0.218 to 0.374 for oxygen, respectively. The present research develops for the first time an integrated experimental and theoretical framework, which combines geostatistical methods with imaging techniques to unveil the 3-D chemical structure of soil at very fine scales. The methodology presented in this study can be easily adapted and applied to other types of data such as bacterial or fungal population densities for the 3D characterization of microbial distribution.
    Keywords: Research Article
    E-ISSN: 1932-6203
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  • 3
    In: Ecological Applications, June 2011, Vol.21(4), pp.1202-1210
    Description: Despite the importance of fungi in soil functioning they have received comparatively little attention, and our understanding of fungal interactions and communities is lacking. This study aims to combine a physiologically based model of fungal growth with digitized images of internal pore volume of samples of undisturbed soil from contrasting management practices to determine the effect of physical structure on fungal growth dynamics. We quantified pore geometries of the undisturbed‐soil samples from two contrasting agricultural practices, conventionally plowed (chisel plow) (CT) and no till (NT), and from native‐species vegetation land use on land that was taken out of production in 1989 (NS). Then we modeled invasion of a fungal species within the soil samples and evaluated the role of soil structure on the progress of fungal colonization of the soil pore space. The size of the studied pores was ≥110 μm. The dynamics of fungal invasion was quantified through parameters of a mathematical model fitted to the fungal invasion curves. Results indicated that NT had substantially lower porosity and connectivity than CT and NS soils. For example, the largest connected pore volume occupied 79% and 88% of pore space in CT and NS treatments, respectively, while it only occupied 45% in NT. Likewise, the proportion of pore space available to fungal colonization was much greater in NS and CT than in NT treatment, and the dynamics of the fungal invasion differed among the treatments. The relative rate of fungal invasion at the onset of simulation was higher in NT samples, while the invasion followed a more sigmoidal pattern with relatively slow invasion rates at the initial time steps in NS and CT samples. Simulations allowed us to elucidate the contribution of physical structure to the rates and magnitudes of fungal invasion processes. It appeared that fragmented pore space disadvantaged fungal invasion in soils under long‐term no‐till, while large connected pores in soils under native vegetation or in tilled agriculture promoted the invasion.
    Keywords: Conventional Tillage ; Fungal Growth Model ; Fungal Invasions ; Lter Site ; Southeastern Michigan ; Usa ; Native-Succession Vegetation ; No-Till Agriculture ; Three-Dimensional Pore Space ; X-Ray Micro-Tomography
    ISSN: 1051-0761
    E-ISSN: 1939-5582
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  • 4
    Language: English
    In: PLoS ONE, 2015, Vol.10(5), p.e0123774
    Description: Soil respiration represents the second largest CO 2 flux from terrestrial ecosystems to the atmosphere , and a small rise could significantly contribute to further increase in atmospheric CO 2. Unfortunately, the extent of this effect cannot be quantified reliably, and the outcomes of experiments designed to study soil respiration remain notoriously unpredictable. In this context, the mathematical simulations described in this article suggest that assumptions of linearity and presumed irrelevance of micro-scale heterogeneity, commonly made in quantitative models of microbial growth in subsurface environments and used in carbon stock models, do not appear warranted. Results indicate that microbial growth is non-linear and, at given average nutrient concentrations, strongly dependent on the microscale distribution of both nutrients and microbes. These observations have far-reaching consequences, in terms of both experiments and theory. They indicate that traditional, macroscopic soil measurements are inadequate to predict microbial responses, in particular to rising temperature conditions, and that an explicit account is required of microscale heterogeneity. Furthermore , models should evolve beyond traditional, but overly simplistic, assumptions of lineari-ty of microbial responses to bulk nutrient concentrations. The development of a new generation of models along these lines, and in particular incorporating upscaled information about microscale processes, will undoubtedly be challenging, but appears to be key to understanding the extent to which soil carbon mineralization could further accelerate climate change.
    Keywords: Life Sciences ; Agricultural Sciences ; Soil Study ; Life Sciences ; Microbiology and Parasitology ; Sciences (General)
    ISSN: 1932-6203
    E-ISSN: 1932-6203
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  • 5
    Language: English
    In: 2012, Vol.7(9), p.e44276
    Description: Understanding of soil processes is essential for addressing the global issues of food security, disease transmission and climate change. However, techniques for observing soil biology are lacking. We present a heterogeneous, porous, transparent substrate for in situ 3D imaging of living plants and root-associated microorganisms using particles of the transparent polymer, Nafion, and a solution with matching optical properties. Minerals and fluorescent dyes were adsorbed onto the Nafion particles for nutrient supply and imaging of pore size and geometry. Plant growth in transparent soil was similar to that in soil. We imaged colonization of lettuce roots by the human bacterial pathogen Escherichia coli O157:H7 showing micro-colony development. Micro-colonies may contribute to bacterial survival in soil. Transparent soil has applications in root biology, crop genetics and soil microbiology.
    Keywords: Research Article ; Agriculture ; Biology ; Plant Biology ; Microbiology ; Biotechnology
    E-ISSN: 1932-6203
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  • 6
    Language: English
    In: Plant and Soil, 2016, Vol.408(1), pp.357-368
    Description: Background and Aims Biochar amendment to soil is a promising practice of enhancing productivity of agricultural systems. The positive effects on crop are often attributed to a promotion of beneficial soil microorganisms while suppressing pathogens e.g. This study aims to determine the influence of biochar feedstock on (i) spontaneous and fungi inoculated microbial colonisation of biochar particles and (ii) physical pore space characteristics of native and fungi colonised biochar particles which impact microbial habitat quality. Methods Pyrolytic biochars from mixed woods and Miscanthus were investigated towards spontaneous colonisation by classical microbiological isolation, phylogenetic identification of bacterial and fungal strains, and microbial respiration analysis. Physical pore space characteristics of biochar particles were determined by X-ray [mu]-CT. Subsequent 3D image analysis included porosity, surface area, connectivities, and pore size distribution. Results Microorganisms isolated from Wood biochar were more abundant and proliferated faster than those from the Miscanthus biochar. All isolated bacteria belonged to gram-positive bacteria and were feedstock specific. Respiration analysis revealed higher microbial activity for Wood biochar after water and substrate amendment while basal respiration was on the same low level for both biochars. Differences in porosity and physical surface area were detected only in interaction with biochar-specific colonisation. Miscanthus biochar was shown to have higher connectivity values in surface, volume and transmission than Wood biochars as well as larger pores as observed by pore size distribution. Differences in physical properties between colonised and non-colonised particles were larger in Miscanthus biochar than in Wood biochar. Conclusions Vigorous colonisation was found on Wood biochar compared to Miscanthus biochar. This is contrasted by our findings from physical pore space analysis which suggests better habitat quality in Miscanthus biochar than in Wood biochar. We conclude that (i) the selected feedstocks display large differences in microbial habitat quality as well as physical pore space characteristics and (ii) physical description of biochars alone does not suffice for the reliable prediction of microbial habitat quality and recommend that physical and surface chemical data should be linked for this purpose.
    Keywords: Biochar ; Microbial colonisation ; Pore geometry ; Habitat quality
    ISSN: 0032-079X
    E-ISSN: 1573-5036
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  • 7
    Language: English
    In: Journal of Hydrology, 2010, Vol.393(1), pp.1-2
    Description: Includes references ; p. 1-2.
    Keywords: Geography
    ISSN: 0022-1694
    E-ISSN: 1879-2707
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  • 8
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 18 December 2007, Vol.104(51), pp.20392-7
    Description: One of the principal challenges in epidemiological modeling is to parameterize models with realistic estimates for transmission rates in order to analyze strategies for control and to predict disease outcomes. Using a combination of replicated experiments, Bayesian statistical inference, and stochastic modeling, we introduce and illustrate a strategy to estimate transmission parameters for the spread of infection through a two-phase mosaic, comprising favorable and unfavorable hosts. We focus on epidemics with local dispersal and formulate a spatially explicit, stochastic set of transition probabilities using a percolation paradigm for a susceptible-infected (S-I) epidemiological model. The S-I percolation model is further generalized to allow for multiple sources of infection including external inoculum and host-to-host infection. We fit the model using Bayesian inference and Markov chain Monte Carlo simulation to successive snapshots of damping-off disease spreading through replicated plant populations that differ in relative proportions of favorable and unfavorable hosts and with time-varying rates of transmission. Epidemiologically plausible parametric forms for these transmission rates are compared by using the deviance information criterion. Our results show that there are four transmission rates for a two-phase system, corresponding to each combination of infected donor and susceptible recipient. Knowing the number and magnitudes of the transmission rates allows the dominant pathways for transmission in a heterogeneous population to be identified. Finally, we show how failure to allow for multiple transmission rates can overestimate or underestimate the rate of spread of epidemics in heterogeneous environments, which could lead to marked failure or inefficiency of control strategies.
    Keywords: Models, Statistical ; Population ; Communicable Diseases -- Transmission ; Disease Outbreaks -- Statistics & Numerical Data
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 9
    Language: English
    In: Geoderma, Sept 15, 2011, Vol.164(3-4), p.146(9)
    Description: To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.geoderma.2011.05.018 Byline: Simona M. Hapca, Zi X. Wang, Wilfred Otten, Clare Wilson, Philippe C. Baveye Keywords: X-ray CT; SEM-EDX; Segmentation techniques; Spatial correlation; 3D soil images; 2D chemical maps Abstract: Recent 2-dimensional measurements reveal that soils are chemically very heterogeneous at nanometric and micrometric scales. Direct measurement techniques are still lacking to extend these observations to 3 dimensions. Sequential sectioning of soils, followed by 2-dimensional mapping of chemical elements and geometric interpolation to 3D, appears to be the only available alternative. Unfortunately, sectioning of soil samples suffers from geometric distortions that are difficult to avoid in practise. In this regard, the objective of the research described in this article was to develop a procedure enabling one to locate, in a 3D X-ray microtomographic image of a soil sample, a physical surface that is obtained by sectioning and for which a number of chemical maps are available. This procedure involves three steps: (1) the reconstitution of the physical structure of the soil layer surface, (2) the alignment of the chemical maps with the reconstituted soil surface image, and (3) the 3D alignment of the 2D chemical maps with the internal structure of the soil cube. Visual comparison of the C and Si maps and of the reconstituted CT images of the layer surfaces suggests a good correspondence between them, which is supported by Pearson correlation coefficients of -0.57, -0.58, 0.45, and 0.43 for the different surfaces and elements considered. Relative to the original 3D X-ray CT image of the soil sample, the planes associated with the C and Si maps, respectively, are nearly superposed, which further confirms the validity of the alignment procedure. Article History: Received 16 November 2010; Revised 27 May 2011; Accepted 28 May 2011
    Keywords: Soil Structure -- Analysis ; Soil Structure -- Methods ; Soils -- Analysis ; Soils -- Methods
    ISSN: 0016-7061
    Source: Cengage Learning, Inc.
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  • 10
    In: The ISME Journal, 2010, Vol.5(4), p.665
    Description: The evolutionary success of the novel Wrinkly Spreader (WS) genotypes in diversifying Pseudomonas fluorescens SBW25 populations in static liquid microcosms has been attributed to the greater availability of O(2) at the air-liquid (A-L) interface where the WS produces a physically cohesive-class biofilm. However, the importance of O(2) gradients in SBW25 adaptation has never been examined. We have explicitly tested the role of O(2) in evolving populations using microsensor profiling and experiments conducted under high and low O(2) conditions. Initial colonists of static microcosms were found to establish O(2) gradients before significant population growth had occurred, converting a previously homogenous environment into one containing a resource continuum with high and low O(2) regions. These gradients were found to persist for long periods by which time significant numbers of WS had appeared colonising the high O(2) niches. Growth was O(2) limited in static microcosms, but high O(2) conditions like those found near the A-L interface supported greater growth and favoured the emergence of WS-like genotypes. A fitness advantage to biofilm formation was seen under high but not low O(2) conditions, suggesting that the cost of biofilm production could only be offset when O(2) levels above the A-L interface were high. Profiling of mature WS biofilms showed that they also contained high and low O(2) regions. Niches within these may support further diversification and succession of the developing biofilm population. O(2) availability has been found to be a major factor underlying the evolutionary success of the WS genotype in static microcosms and illustrates the importance of this resource continuum in microbial diversification and adaptation.
    Keywords: Adaptation, Physiological–Growth & Development ; Biofilms–Metabolism ; Biological Evolution–Genetics ; Environment–Growth & Development ; Genotype–Physiology ; Oxygen–Physiology ; Pseudomonas Fluorescens–Physiology ; Pseudomonas Fluorescens–Physiology ; Pseudomonas Fluorescens–Physiology ; Oxygen;
    ISSN: 1751-7362
    E-ISSN: 17517370
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