The Experts below are selected from a list of 324 Experts worldwide ranked by ideXlab platform

Yasumi Yagasaki - One of the best experts on this subject based on the ideXlab platform.

  • linking temperature sensitivity of soil organic matter decomposition to its molecular structure accessibility and Microbial Physiology
    Global Change Biology, 2013
    Co-Authors: Rota Wagai, Seiichiro Yonemura, Yasuhito Shirato, Syuntaro Hiradate, Ayaka W Kishimotomo, Yasumi Yagasaki
    Abstract:

    Temperature sensitivity of soil organic matter (SOM) decomposition may have a significant impact on global warming. Enzyme-kinetic hypothesis suggests that decomposition of low-quality substrate (recalcitrant molecular structure) requires higher activation energy and thus has greater temperature sensitivity than that of high-quality, labile substrate. Supporting evidence, however, relies largely on indirect indices of substrate quality. Furthermore, the enzyme-substrate reactions that drive decomposition may be regulated by Microbial Physiology and/or constrained by protective effects of soil mineral matrix. We thus tested the kinetic hypothesis by directly assessing the carbon molecular structure of low-density fraction (LF) which represents readily accessible, mineral-free SOM pool. Using five mineral soil samples of contrasting SOM concentrations, we conducted 30-days incubations (15, 25, and 35 °C) to measure Microbial respiration and quantified easily soluble C as well as Microbial biomass C pools before and after the incubations. Carbon structure of LFs (<1.6 and 1.6-1.8 g cm(-3) ) and bulk soil was measured by solid-state (13) C-NMR. Decomposition Q10 was significantly correlated with the abundance of aromatic plus alkyl-C relative to O-alkyl-C groups in LFs but not in bulk soil fraction or with the indirect C quality indices based on Microbial respiration or biomass. The warming did not significantly change the concentration of biomass C or the three types of soluble C despite two- to three-fold increase in respiration. Thus, enhanced Microbial maintenance respiration (reduced C-use efficiency) especially in the soils rich in recalcitrant LF might lead to the apparent equilibrium between SOM solubilization and Microbial C uptake. Our results showed physical fractionation coupled with direct assessment of molecular structure as an effective approach and supported the enzyme-kinetic interpretation of widely observed C quality-temperature relationship for short-term decomposition. Factors controlling long-term decomposition Q10 are more complex due to protective effect of mineral matrix and thus remain as a central question.

  • Linking temperature sensitivity of soil organic matter decomposition to its molecular structure, accessibility, and Microbial Physiology
    Global change biology, 2013
    Co-Authors: Rota Wagai, Ayaka W. Kishimoto-mo, Seiichiro Yonemura, Yasuhito Shirato, Syuntaro Hiradate, Yasumi Yagasaki
    Abstract:

    Temperature sensitivity of soil organic matter (SOM) decomposition may have a significant impact on global warming. Enzyme-kinetic hypothesis suggests that decomposition of low-quality substrate (recalcitrant molecular structure) requires higher activation energy and thus has greater temperature sensitivity than that of high-quality, labile substrate. Supporting evidence, however, relies largely on indirect indices of substrate quality. Furthermore, the enzyme-substrate reactions that drive decomposition may be regulated by Microbial Physiology and/or constrained by protective effects of soil mineral matrix. We thus tested the kinetic hypothesis by directly assessing the carbon molecular structure of low-density fraction (LF) which represents readily accessible, mineral-free SOM pool. Using five mineral soil samples of contrasting SOM concentrations, we conducted 30-days incubations (15, 25, and 35 °C) to measure Microbial respiration and quantified easily soluble C as well as Microbial biomass C pools before and after the incubations. Carbon structure of LFs (

Jens Nielsen - One of the best experts on this subject based on the ideXlab platform.

  • Use of genome-scale metabolic models for understanding Microbial Physiology.
    FEBS letters, 2010
    Co-Authors: Liming Liu, Rasmus Agren, Sergio Bordel, Jens Nielsen
    Abstract:

    The exploitation of microorganisms in industrial, medical, food and environmental biotechnology requires a comprehensive understanding of their Physiology. The availability of genome sequences and accumulation of high-throughput data allows gaining understanding of Microbial Physiology at the systems level, and genome-scale metabolic models represent a valuable framework for integrative analysis of metabolism of microorganisms. Genome-scale metabolic models are reconstructed based on a combination of genome sequence information and detailed biochemical information, and these reconstructed models can be used for analyzing and simulating the operation of metabolism in response to different stimuli. Here we discuss the requirement for having detailed physiological insight in order to exploit microorganisms for production of fuels, chemicals and pharmaceuticals. We further describe the reconstruction process of genome-scale metabolic models and different algorithms that can be used to apply these models to gain improved insight into Microbial Physiology.

  • An expanded role for Microbial Physiology in metabolic engineering and functional genomics: moving towards systems biology
    FEMS yeast research, 2002
    Co-Authors: Jens Nielsen, Lisbeth Olsson
    Abstract:

    Microbial Physiology has traditionally played a very important role in both fundamental research and in industrial applications of microorganisms. The classical approach in Microbial Physiology has been to analyze the role of individual components (genes or proteins) in the overall cell function. With the progress in molecular biology it has become possible to optimize industrial fermentations through introduction of directed genetic modification – an approach referred to as metabolic engineering. Furthermore, as a consequence of large sequencing programs the complete genomic sequence has become available for an increasing number of microorganisms. This has resulted in substantial research efforts in assigning function to all identified open reading frames – referred to as functional genomics. In both metabolic engineering and functional genomics there is a trend towards application of a macroscopic view on cell function, and this leads to an expanded role of the classical approach applied in Microbial Physiology. With the increased understanding of the molecular mechanisms it is envisaged that in the future it will be possible to describe the interaction between all the components in the system (the cell), also at the quantitative level, and this is the goal of systems biology. Clearly this will have a significant impact on Microbial Physiology as well as on metabolic engineering.

Liming Liu - One of the best experts on this subject based on the ideXlab platform.

  • IMGMD: A platform for the integration and standardisation of In silico Microbial Genome-scale Metabolic Models
    Scientific reports, 2017
    Co-Authors: Chuan Dong, Xuan Zou, Xiulai Chen, Feng-biao Guo, Liming Liu
    Abstract:

    Genome-scale metabolic models (GSMMs) constitute a platform that combines genome sequences and detailed biochemical information to quantify Microbial Physiology at the system level. To improve the unity, integrity, correctness, and format of data in published GSMMs, a consensus IMGMD database was built in the LAMP (Linux + Apache + MySQL + PHP) system by integrating and standardizing 328 GSMMs constructed for 139 microorganisms. The IMGMD database can help Microbial researchers download manually curated GSMMs, rapidly reconstruct standard GSMMs, design pathways, and identify metabolic targets for strategies on strain improvement. Moreover, the IMGMD database facilitates the integration of wet-lab and in silico data to gain an additional insight into Microbial Physiology. The IMGMD database is freely available, without any registration requirements, at http://imgmd.jiangnan.edu.cn/database.

  • Use of genome-scale metabolic models for understanding Microbial Physiology.
    FEBS letters, 2010
    Co-Authors: Liming Liu, Rasmus Agren, Sergio Bordel, Jens Nielsen
    Abstract:

    The exploitation of microorganisms in industrial, medical, food and environmental biotechnology requires a comprehensive understanding of their Physiology. The availability of genome sequences and accumulation of high-throughput data allows gaining understanding of Microbial Physiology at the systems level, and genome-scale metabolic models represent a valuable framework for integrative analysis of metabolism of microorganisms. Genome-scale metabolic models are reconstructed based on a combination of genome sequence information and detailed biochemical information, and these reconstructed models can be used for analyzing and simulating the operation of metabolism in response to different stimuli. Here we discuss the requirement for having detailed physiological insight in order to exploit microorganisms for production of fuels, chemicals and pharmaceuticals. We further describe the reconstruction process of genome-scale metabolic models and different algorithms that can be used to apply these models to gain improved insight into Microbial Physiology.

Rota Wagai - One of the best experts on this subject based on the ideXlab platform.

  • linking temperature sensitivity of soil organic matter decomposition to its molecular structure accessibility and Microbial Physiology
    Global Change Biology, 2013
    Co-Authors: Rota Wagai, Seiichiro Yonemura, Yasuhito Shirato, Syuntaro Hiradate, Ayaka W Kishimotomo, Yasumi Yagasaki
    Abstract:

    Temperature sensitivity of soil organic matter (SOM) decomposition may have a significant impact on global warming. Enzyme-kinetic hypothesis suggests that decomposition of low-quality substrate (recalcitrant molecular structure) requires higher activation energy and thus has greater temperature sensitivity than that of high-quality, labile substrate. Supporting evidence, however, relies largely on indirect indices of substrate quality. Furthermore, the enzyme-substrate reactions that drive decomposition may be regulated by Microbial Physiology and/or constrained by protective effects of soil mineral matrix. We thus tested the kinetic hypothesis by directly assessing the carbon molecular structure of low-density fraction (LF) which represents readily accessible, mineral-free SOM pool. Using five mineral soil samples of contrasting SOM concentrations, we conducted 30-days incubations (15, 25, and 35 °C) to measure Microbial respiration and quantified easily soluble C as well as Microbial biomass C pools before and after the incubations. Carbon structure of LFs (<1.6 and 1.6-1.8 g cm(-3) ) and bulk soil was measured by solid-state (13) C-NMR. Decomposition Q10 was significantly correlated with the abundance of aromatic plus alkyl-C relative to O-alkyl-C groups in LFs but not in bulk soil fraction or with the indirect C quality indices based on Microbial respiration or biomass. The warming did not significantly change the concentration of biomass C or the three types of soluble C despite two- to three-fold increase in respiration. Thus, enhanced Microbial maintenance respiration (reduced C-use efficiency) especially in the soils rich in recalcitrant LF might lead to the apparent equilibrium between SOM solubilization and Microbial C uptake. Our results showed physical fractionation coupled with direct assessment of molecular structure as an effective approach and supported the enzyme-kinetic interpretation of widely observed C quality-temperature relationship for short-term decomposition. Factors controlling long-term decomposition Q10 are more complex due to protective effect of mineral matrix and thus remain as a central question.

  • Linking temperature sensitivity of soil organic matter decomposition to its molecular structure, accessibility, and Microbial Physiology
    Global change biology, 2013
    Co-Authors: Rota Wagai, Ayaka W. Kishimoto-mo, Seiichiro Yonemura, Yasuhito Shirato, Syuntaro Hiradate, Yasumi Yagasaki
    Abstract:

    Temperature sensitivity of soil organic matter (SOM) decomposition may have a significant impact on global warming. Enzyme-kinetic hypothesis suggests that decomposition of low-quality substrate (recalcitrant molecular structure) requires higher activation energy and thus has greater temperature sensitivity than that of high-quality, labile substrate. Supporting evidence, however, relies largely on indirect indices of substrate quality. Furthermore, the enzyme-substrate reactions that drive decomposition may be regulated by Microbial Physiology and/or constrained by protective effects of soil mineral matrix. We thus tested the kinetic hypothesis by directly assessing the carbon molecular structure of low-density fraction (LF) which represents readily accessible, mineral-free SOM pool. Using five mineral soil samples of contrasting SOM concentrations, we conducted 30-days incubations (15, 25, and 35 °C) to measure Microbial respiration and quantified easily soluble C as well as Microbial biomass C pools before and after the incubations. Carbon structure of LFs (

Cynthia M. Kallenbach - One of the best experts on this subject based on the ideXlab platform.

  • Microbial Physiology and necromass regulate agricultural soil carbon accumulation
    Soil Biology and Biochemistry, 2015
    Co-Authors: Cynthia M. Kallenbach, A. S. Grandy, Serita D. Frey, Aaron F. Diefendorf
    Abstract:

    Abstract Strategies for mitigating soil organic carbon (SOC) losses in intensively managed agricultural systems typically draw from traditional concepts of soil organic matter formation, and thus emphasize increasing C inputs, especially from slowly decomposing crop residues, and reducing soil disturbance. However these approaches are often ineffective and do not adequately reflect current views of SOC cycling, which stress the important contributions of Microbial biomass (MB) inputs to SOC. We examined Microbial Physiology as an alternate mechanism of SOC accumulation under organic (ORG) compared to conventional (CT) agricultural management practices, where ORG is accumulating C despite fewer total C inputs and greater soil tillage. We hypothesized that Microbial communities in ORG have higher growth rates (MGR) and C use efficiencies (CUE) and that this relates to greater MB production and ultimately higher retention of new C inputs. We show that ORG had 50% higher CUE (±8 se) and 56% higher MGR (±22 se) relative to CT (p

  • Integrating Microbial Physiology and physio-chemical principles in soils with the Microbial-MIneral Carbon Stabilization (MIMICS) model
    Biogeosciences, 2014
    Co-Authors: W. R. Wieder, Cynthia M. Kallenbach, A. S. Grandy, G. B. Bonan
    Abstract:

    Abstract. A growing body of literature documents the pressing need to develop soil biogeochemistry models that more accurately reflect contemporary understanding of soil processes and better capture soil carbon (C) responses to environmental perturbations. Models that explicitly represent Microbial activity offer inroads to improve representations of soil biogeochemical processes, but have yet to consider relationships between litter quality, functional differences in Microbial Physiology, and the physical protection of Microbial byproducts in forming stable soil organic matter (SOM). To address these limitations, we introduce the Microbial-MIneral Carbon Stabilization (MIMICS) model, and evaluate it by comparing site-level soil C projections with observations from a long-term litter decomposition study and soil warming experiment. In MIMICS, the turnover of litter and SOM pools is governed by temperature-sensitive Michaelis–Menten kinetics and the activity of two physiologically distinct Microbial functional types. The production of Microbial residues through Microbial turnover provides inputs to SOM pools that are considered physically or chemically protected. Soil clay content determines the physical protection of SOM in different soil environments. MIMICS adequately simulates the mean rate of leaf litter decomposition observed at temperate and boreal forest sites, and captures observed effects of litter quality on decomposition rates. Moreover, MIMICS better captures the response of SOM pools to experimental warming, with rapid SOM losses but declining temperature sensitivity to long-term warming, compared with a more conventional model structure. MIMICS incorporates current Microbial theory to explore the mechanisms by which litter C is converted to stable SOM, and to improve predictions of soil C responses to environmental change.