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  • Baveye, Philippe C  (9)
  • Microorganisms
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  • 1
    Language: English
    In: Journal of Soil and Water Conservation, Nov-Dec, 2007, Vol.62(6), p.139A(5)
    Description: Role of soil in causing global warming is discussed. Soils are major players in the carbon cycle. Soils contain the equivalent of about 300 times the amount of carbon now released annually through the burning of fossil fuels. In many soils, carbon stocks contain large amounts of nitrogen, whose metabolism by microorganisms can also contribute to greenhouse gas emissions. It is shown that small changes of the amount of carbon contained in soils may lead to sources or sinks of greenhouse gases. Increased release of carbon by world soils can drastically exacerbate atmospheric carbon dioxide (CO sub(2)) levels, leading to accelerated global warming and to a positive feedback mechanism that may cause climate change to get completely out of hand.
    Keywords: Air Pollution -- Social Aspects ; Air Pollution -- Control ; Global Warming -- Influence ; Soil Ecology -- Research ; Soil Chemistry -- Research
    ISSN: 0022-4561
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  • 2
    Language: English
    In: Ecological Modelling, 2011, Vol.222(12), pp.1998-2010
    Description: ► The individual-based INDISIM-SOM model is far more sensitive to some parameters than to others. ► Key parameters for the evolution of C and N are microbial maintenance, energy, and death probability. ► The nitrification rate, in particular, appears highly affected by the death probability. ► The sensitivity analysis indicates what simplification of the model is possible. ► It also shows which parameters need to be evaluated with more accuracy than is currently achievable. The fate of soil carbon and nitrogen compounds in soils in response to climate change is currently the object of significant research. In particular, there is much interest in the development of a new generation of micro-scale models of soil ecosystems processes. Crucial to the elaboration of such models is the ability to describe the growth and metabolism of small numbers of individual microorganisms, distributed in a highly heterogeneous environment. In this context, the key objective of the research described in this article was to further develop an individual-based soil organic matter model, INDISIM-SOM, first proposed a few years ago, and to assess its performance with a broader experimental data set than previously considered. INDISIM-SOM models the dynamics and evolution of carbon and nitrogen associated with organic matter in soils. The model involves a number of state variables and parameters related to soil organic matter and microbial activity, including growth and decay of microbial biomass, temporal evolutions of easily hydrolysable N, mineral N in ammonium and nitrate, CO and O . The present article concentrates on the biotic components of the model. Simulation results demonstrate that the model can be calibrated to provide good fit to experimental data from laboratory incubation experiments performed on three different types of Mediterranean soils. In addition, analysis of the sensitivity toward its biotic parameters shows that the model is far more sensitive to some parameters, i.e., the microbial maintenance energy and the probability of random microbial death, than to others. These results suggest that, in the future, research should focus on securing better measurements of these parameters, on environmental determinants of the switch from active to dormant states, and on the causes of random cell death in soil ecosystems.
    Keywords: Individual-Based Model ; Soil Microbial Activity ; Soil Organic Matter ; C and N Mineralization ; Microbial Parameters ; Environmental Sciences ; Ecology
    ISSN: 0304-3800
    E-ISSN: 1872-7026
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  • 3
    Language: English
    In: Frontiers in Environmental Science, 01 February 2015, Vol.3
    Description: Current estimates of global soil C are slightly over 4000 Pg C, which is more than five and a half times the amount of carbon currently in the atmosphere or, put differently, is equivalent to about 400 times the amount of C released yearly to the atmosphere by fossil fuel consumption or cement manufacture...
    Keywords: Food Security ; Global Climate Change ; Microorganisms ; Soil Structure ; Soil Organic Matter ; Soil Science Research ; Environmental Sciences
    E-ISSN: 2296-665X
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  • 4
    In: Soil Science, 2010, Vol.175(8), pp.363-374
    Description: The need to predict with reasonable accuracy the fate of soil C and N compounds in soils in response to climate change is stimulating interest in a new generation of microscale models of soil ecosystem processes. Essential to the development of such models is the ability to describe the growth and metabolism of small numbers of individual microorganisms. In this context, the key objective of the research described in this article was to further develop an individual-based soil organic matter (SOM) model, INDISIM-SOM, first proposed a few years ago, and to assess its performance with a broader data set than previously considered. The INDISIM-SOM models the dynamics and evolution of C and N associated with organic matter in soils. The model involves a number of state variables and parameters related to SOM and microbial activity, including growth and decay of microbial biomass, temporal evolution of mineralized intermediate C and N, mineral N in ammonium and nitrate, carbon dioxide, and O2. Simulation results demonstrate good fit of the model to experimental data from laboratory incubation experiments performed on three different types of Mediterranean soils. A second objective was to determine the sensitivity of the model toward its various parameters. Sensitivity was small for several of the parameters, suggesting possible simplifications of the model for specific uses, but was significant particularly for the parameter associated with the fraction of the soil C present in the biomass. These results suggest that research should be focused on improving the measurement of this latter parameter.
    Keywords: Microorganisms ; Metabolism ; Climate Change ; Soil Microorganisms ; Soil Testing ; Evolution ; Simulation ; Biomass ; Carbon ; Nitrogen;
    ISSN: 0038-075X
    E-ISSN: 15389243
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  • 5
    Language: English
    In: Frontiers in Environmental Science, 01 June 2017, Vol.5
    Description: Groundwater contamination by oocysts of the waterborne pathogen Cryptosporidium parvum is a significant cause of animal and human disease worldwide. Although research has been undertaken in the past to determine how specific physical and chemical properties of soils affect the risk of groundwater contamination by C. parvum, there is as yet no clear conclusion concerning the range of mobility of C. parvum that one should expect in field soils. In this context, the key objective of this research was to determine the magnitude of C. parvum transport in a number of soils, under conditions in which fast and preferential transport has been successfully prevented. C. parvum oocysts were applied at the surface of different soils and subjected to artificial rainfall. Apparently for the first time, quantitative PCR was used to detect and enumerate oocysts in the soil columns and in the leachates. The transport of oocysts by infiltrating water, and the considerable retention of oocysts in soil was demonstrated for all soils, although differences in the degree of transport were observed with soils of different types. More oocysts were found in leachates from sandy loam soils than in leachates from loamy sand soils and the retention of oocysts in different soils did not significantly differ. The interaction of various processes of the hydrologic system and biogeochemical mechanisms contributed to the transport of oocysts through the soil matrix. Results suggest that the interplay of clay, organic matter, and Ca2+ facilitates and mediates the transfer of organic matter from mineral surfaces to oocysts surface, resulting in the enhanced breakthrough of oocysts through matrices of sandy loam soils compared to those of loamy sand soils. Although the number of occysts that penetrate the soil matrix account for only a small percentage of initial inputs, they still pose a significant threat to human health, especially in groundwater systems with a water table not too distant from the soil surface. The results of the research demonstrate a critical need for the simultaneous study of the interaction of various processes affecting oocysts transport in the subsurface, and for its expansion into complex systems, in order to obtain a coherent picture of the behavior of C. parvum oocysts in soils.
    Keywords: Cryptosporidium ; Microorganisms ; Groundwater ; Soil Transport ; Qpcr ; Environmental Sciences
    E-ISSN: 2296-665X
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  • 6
    Language: English
    In: Frontiers in Environmental Science, 01 June 2019, Vol.7
    Description: Quigley et al. try to characterize the spatial heterogeneity of the soil matrix in macroaggregates obtained from soils associated with three contrasting long-term managements (conventionally-managed and biologically-based row-crop agricultural systems, along with a primary successional unmanaged system),...
    Keywords: Microbial Ecology ; Carbon Sequestration ; Soil Organic Matter ; Greenhouse Gas Production ; Dynamics ; Modeling ; Environmental Sciences
    E-ISSN: 2296-665X
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  • 7
    Language: English
    In: Environmental Science & Technology, 09/2007, Vol.41(18), pp.6343-6349
    Description: The response of microorganisms to metal contamination of soils varies significantly from one investigation to another. One explanation is that metals are heterogeneously distributed at spatial scales relevant to microbes and that microoorganisms are able to avoid zones of intense contamination. This article aims to assess the microscale distribution of Cu in a vineyard soil. The spatial distribution of Cu was measured at two resolutions (0.3 mm and 20 mm) in thin sections of the surface 4 cm of undisturbed soil by electron microprobe and synchrotron X-ray microfluorescence spectroscopy. Bulk physicochemical analyses of Cu, pH, organic matter, texture, and mineralogy were performed. The results indicate that the Cu distribution is strongly heterogeneous at both scales of observation. Entire regions of the thin sections are virtually devoid of Cu, whereas highly localized "hotspots" have Cu signal intensities thousands of times higher than background. The distribution of Rb, or Al and Si, indicators of clay minerals, or Fe (iron (hydr)oxides), show that Cu is not preferentially associated with these mineral phases. Instead, Cu hotspots are associated with particulate organic matter. These observations suggest modification of current sampling protocols, and design of ecotoxicological experiments involving microorganisms, for contaminated soils.
    Keywords: Vineyards ; Fluorescence ; Spatial Distribution ; Contamination ; Heavy Metals ; Hot Spots ; Organic Matter ; Electron Microprobe ; Retinoblastoma Protein ; Copper ; Spectroscopy ; Clays ; Soil Microorganisms ; Soil ; Soil Pollution ; Particulate Organic Matter ; Ionizing Radiation ; Microorganisms ; Mapping ; Sampling ; Ph Effects ; Iron ; Minerals ; Hot Spots ; Metals ; Clay ; Fluorescence ; Organic Matter ; Soil Contamination ; Particulates ; Mineralogy ; Spatial Distribution ; Vineyards ; Microorganisms ; Minerals ; Iron ; Land Pollution ; Antibiotics & Antimicrobials;
    ISSN: 0013-936X
    E-ISSN: 1520-5851
    Source: American Chemical Society (via CrossRef)
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  • 8
    Language: English
    In: Computers and Geosciences, February 2019, Vol.123, pp.20-37
    Description: In recent years, technological advances have stimulated researchers to try to unravel the extremely complex microscale processes that control the activity of microorganisms in soils. In particular, significant work has been carried out on the development of models able to accurately predict the microscale distribution of water, and the location of air–water interfaces in pores. A comparison, by Pot et al. (2015), of two different modeling approaches with actual synchrotron-based tomography data, shows that a two-phase lattice Boltzmann model (LBM) is able to predict remarkably well the location of air–water interfaces but is extremely slow, whereas a morphological model (MOSAIC), representing the pore space as a collection of spherical balls, provides a reasonable approximation of the observed air–water interfaces when each ball is allowed to drain independently, but does so blazingly fast. Interfaces predicted by MOSAIC, however, tend to have nonphysical shapes. In that general context, the key objective of the research described in the present article, based on the same tomography data as Pot et al. (2015), was to find out to what extent the use of ellipsoids instead of spherical balls in MOSAIC could not appreciably speed up computations, or at least, at equal computational time, provide a quantitatively better approximation of water-air interfaces. As far as we know, this is the first time an ellipsoids-based approximation of the soil pore space is proposed. A secondary objective was to assess whether ellipsoids might yield smoother, more physical, interfaces. Simulation results indicate that the use of ellipsoids provides a sizeable increase in accuracy in the prediction of air-water interfaces, an approximately 6-fold drop in computation time, and much more realistic-looking interfaces, compared to what is obtained with spherical balls. These observations are encouraging for the use of models based on geometric primitives to describe a range of microscale processes, and to address the still daunting issue of upscaling to the macroscopic scale.
    Keywords: Pore Scale ; Synchroton X-Ray Micro Computed Tomography ; Soil Air-Water Interfaces ; Computational Geometry ; 3d Volume Segmentation ; Morphological Modeling ; Geology
    ISSN: 0098-3004
    E-ISSN: 1873-7803
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  • 9
    Language: English
    In: Frontiers in Environmental Science, 01 February 2018, Vol.6
    Description: (1991) proposed the first quantitative assessment of the potential for a “feedback effect” whereby the additional carbon dioxide released from decomposition of organic matter in soils in a warmer world could accelerate climate change. Aside from this historically-minded introduction, the book contains...
    Keywords: Environmental Sciences
    E-ISSN: 2296-665X
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