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Sample records for situ microbial metabolism

  1. Diagnosis of In Situ Metabolic State and Rates of Microbial Metabolism During In Situ Uranium Bioremediation with Molecular Techniques

    Energy Technology Data Exchange (ETDEWEB)

    Lovley, Derek R. [University of Massachusetts, Amherst

    2012-11-28

    The goal of these projects was to develop molecule tools to tract the metabolic activity and physiological status of microorganisms during in situ uranium bioremediation. Such information is important in able to design improved bioremediation strategies. As summarized below, the research was highly successful with new strategies developed for estimating in situ rates of metabolism and diagnosing the physiological status of the predominant subsurface microorganisms. This is a first not only for groundwater bioremediation studies, but also for subsurface microbiology in general. The tools and approaches developed in these studies should be applicable to the study of microbial communities in a diversity of soils and sediments.

  2. In situ metabolism in halite endolithic microbial communities of the hyperarid Atacama Desert

    Directory of Open Access Journals (Sweden)

    Alfonso F Davila

    2015-10-01

    Full Text Available The Atacama Desert of northern Chile is one of the driest regions on Earth, with areas that exclude plants and where soils have extremely low microbial biomass. However, in the driest parts of the desert there are microorganisms that colonize the interior of halite nodules in fossil continental evaporites, where they are sustained by condensation of atmospheric water triggered by the salt substrate. Using a combination of in situ observations of variable chlorophyll fluorescence and controlled laboratory experiments, we show that this endolithic community is capable of carbon fixation both through oxygenic photosynthesis and potentially ammonia oxidation. We also present evidence that photosynthetic activity is finely tuned to moisture availability and solar insolation and can be sustained for days, and perhaps longer, after a wetting event. This is the first demonstration of in situ active metabolism in the hyperarid core of the Atacama Desert, and it provides the basis for proposing a self-contained, endolithic community that relies exclusively on non-rainfall sources of water. Our results contribute to an increasing body of evidence that even in hyperarid environments active metabolism, adaptation and growth can occur in highly specialized microhabitats.

  3. Imaging microbial metal metabolism in situ under conditions of the deep-sea hydrothermal vents

    Science.gov (United States)

    Oger, P. M.; Daniel, I.; Simionovici, A.; Picard, A.

    2006-12-01

    High-pressure biotopes are the most widely spread biotopes on Earth. They represent one possible location for the origin of life. They also share striking similarities with extraterrestrial biotopes such as those postulated for Europe or Mars. In absence of light, dissimilatory reduction of metals (DMR) is fueling the ecosystem. Monitoring the metabolism of the deep-sea hydrothermal vent microbial fauna under P, T and chemical conditions relevant to their isolation environment can be difficult because of the confinement and because most spectroscopic probes do not sense metallic ions in solution. We demonstrated the possibility to use Xray spectroscopy to monitor the speciation of metallic species in solution. Experiments were performed at The ESRF using Selenium (Se) detoxification by Agrobacterium tumefaciens as an analog of DMR. The reduction of Se from selenite to the metal was monitored by a combiantion of two Xray spectroscopic techniques (XANES and μXRF). Cells were incubated in the low pressure DAC in growth medium supplemented with 5mM Selenite and incubated under pressures up to 60 Mpa at 30°C for 24h. The evolution of the speciation can be easily monitored and the concentration of each Se species determined from the Xray spectra by linear combinations of standard spectra. Selenite is transformed by the bacterium into a mixture of metal Se and methylated Se after 24 hours. Se detoxification is observed in situ up to at least 25 MPa. The technique, developped for Se can be adapted to monitor other elements more relevant to DMR such as As, Fe or S, which should allow to monitor in situ under controlled pressure and temperature the metabolism of vent organisms. It is also amenable to the monitoring of toxic metals. Xray spectroscopy and the lpDAC are compatible with other spectroscopic techniques, such as Raman, UV or IR spectroscopies, allowing to probe other metabolic activities. Hence, enlarging the range of metabolic information that can be obtained in

  4. Quantitative Raman Spectroscopy to monitor microbial metabolism in situ under pressure

    Science.gov (United States)

    Picard, A.; Daniel, I.; Oger, P.

    2006-12-01

    at least 65 MPa. No ethanol was detected at 100 MPa. From these data, the pressure at which ethanol fermentation stops in yeast was calculated to be 87±7 MPa. These results indicate that the activity of one or several enzymes of the glycolytic pathway is enhanced at low pressure. At higher pressure, they become progressively repressed, and are completely inhibited above 87 MPa. Our in situ monitoring constitutes a direct demonstration of yeast metabolism in situ under pressure up to 100 MPa. Our data agree with previous ex-situ data by Abe and Horikoshi (4). However, we observed that ethanol production is not completely inhibited around 50 MPa as predicted, but could be detected at significantly higher pressures (up to 87 MPa). QSR is a powerful method to monitor microbial activities, since almost any organic molecule with a carbon chain ranging from 1 to 6 carbon can be detected and quantified. The only limitation of QSR is that the Raman spectrum of the molecule exhibits at least one peak not masked by the spectrum of the growth medium. 1 Pelletier M J Appl Spectr 57:20A-42A, 2003 2 Daniel I, Oger P, Picard A, Cardon H and Chervin J-C (submitted to Rev Sci Instr) 3 Picard A, Daniel I, Montagnac G and Oger P (submitted to Extremophiles) 4 Abe F and Horikoshi K Extremophiles 1: 89-93, 1997

  5. Microbial Metabolism in Serpentinite Fluids

    Science.gov (United States)

    Crespo-Medina, M.; Brazelton, W. J.; Twing, K. I.; Kubo, M.; Hoehler, T. M.; Schrenk, M. O.

    2013-12-01

    Serpentinization is the process in which ultramafic rocks, characteristic of the upper mantle, react with water liberating mantle carbon and reducing power to potenially support chemosynthetic microbial communities. These communities may be important mediators of carbon and energy exchange between the deep Earth and the surface biosphere. Our work focuses on the Coast Range Ophiolite Microbial Observatory (CROMO) in Northern California where subsurface fluids are accessible through a series of wells. Preliminary analyses indicate that the highly basic fluids (pH 9-12) have low microbial diversity, but there is limited knowledge about the metabolic capabilities of these communties. Metagenomic data from similar serpentine environments [1] have identified Betaproteobacteria belonging to the order Burkholderiales and Gram-positive bacteria from the order Clostridiales as key components of the serpentine microbiome. In an effort to better characterize the microbial community, metabolism, and geochemistry at CROMO, fluids from two representative wells (N08B and CSWold) were sampled during recent field campaigns. Geochemical characterization of the fluids includes measurements of dissolved gases (H2, CO, CH4), dissolved inorganic and organic carbon, volatile fatty acids, and nutrients. The wells selected can be differentiated in that N08B had higher pH (10-11), lower dissolved oxygen, and cell counts ranging from 105-106 cells mL-1 of fluid, with an abundance of the betaproteobacterium Hydrogenophaga. In contrast, fluids from CSWold have slightly lower pH (9-9.5), DO, and conductivity, as well as higher TDN and TDP. CSWold fluid is also characterized for having lower cell counts (~103 cells mL-1) and an abundance of Dethiobacter, a taxon within the phylum Clostridiales. Microcosm experiments were conducted with the purpose of monitoring carbon fixation, methanotrophy and metabolism of small organic compounds, such as acetate and formate, while tracing changes in fluid

  6. Assessment of microbial in situ activity in contaminated aquifers

    Energy Technology Data Exchange (ETDEWEB)

    Kaestner, M. [UFZ-Umweltforschungszentrum Leipzig-Halle GmbH, Department Bioremediation, Permoserstrasse 15, 04318 Leipzig (Germany); Fischer, A.; Nijenhuis, I.; Stelzer, N.; Bombach, P.; Richnow, H.H. [UFZ-Umweltforschungszentrum Leipzig-Halle GmbH, Department Isotopenbiogeochemie, Permoserstrasse 15, 04318 Leipzig (Germany); Geyer, R. [UFZ-Umweltforschungszentrum Leipzig-Halle GmbH, Department Umweltmikrobiologie, Permoserstrasse 15, 04318 Leipzig (Germany); Tebbe, C.C. [Institut fuer Agraroekologie, Bundesforschungsanstalt fuer Landwirtschaft (FAL), D-38116 Braunschweig (Germany)

    2006-06-15

    Microbial ecologists and environmental engineers share the interest in identifying the key microorganisms responsible for compound turnover in the environment and in estimating the respective transformation rates. For the successful application of Natural Attenuation processes, a reliable assessment of the in situ turnover of a contaminant in an aquifer is essential. Here, we review and present new details of two recently developed approaches concerning the assessment of in situ biodegradation: (i) determination of biodegradation caused by microbial metabolism in a contamination plume by stable isotope fractionation analysis (SIFA) and (ii) determination of the actual degradation under the respective environmental conditions in the aquifer by using in situ microcosms (BACTRAPS registered) amended with {sup 13}C-labeled substrates as tracer compounds. Based on stable isotope fractionation analysis, the degradation occurring under anoxic biogeochemical conditions at a respective site can be calculated for the entire plume. This has been shown for benzene and toluene at the Zeitz site and partly for chlorobenzene at the Bitterfeld site. By use of the in situ microcosm approach with {sup 13}C-labeled compounds, the microbial in situ degradation under strictly anaerobic conditions could be proven for benzene and toluene in Zeitz and for chlorobenzene in Bitterfeld. The transformation of {sup 13}C-carbon of the labeled substrate into microbial fatty acids confirmed the assimilation of the pollutant resulting in the formation of biomass. In addition, metabolites such as benzylsuccinic acid were found in the toluene-amended microcosms indicating anaerobic degradation of toluene. This result corresponds to the geochemical conditions found at the field site and therefore, the microcosm approach with {sup 13}C-labeled compounds can be used to assign the predominant in situ degradation pathways in a contaminated aquifer. Since fatty acids profiles alone are often too

  7. In situ uranium stabilization by microbial metabolites

    International Nuclear Information System (INIS)

    Turick, Charles E.; Knox, Anna S.; Leverette, Chad L.; Kritzas, Yianne G.

    2008-01-01

    Microbial melanin production by autochthonous bacteria was explored in this study as a means to increase U immobilization in U contaminated soil. This article demonstrates the application of bacterial physiology and soil ecology for enhanced U immobilization in order to develop an in situ, U bio-immobilization technology. We have demonstrated microbial production of a metal chelating biopolymer, pyomelanin, in U contaminated soil from the Tims Branch area of the Department of Energy (DOE), Savannah River Site (SRS), South Carolina, as a result of tyrosine amendments. Bacterial densities of pyomelanin producers were >10 6 cells per g wet soil. Pyomelanin demonstrated U complexing and mineral binding capacities at pH 4 and 7. In laboratory studies, in the presence of goethite or illite, pyomelanin enhanced U sequestration by these minerals. Tyrosine amended soils in a field test demonstrated increased U sequestration capacity following pyomelanin production up to 13 months after tyrosine treatments

  8. IN SITU URANIUM STABILIZATION BY MICROBIAL METABOLITES

    Energy Technology Data Exchange (ETDEWEB)

    Turick, C; Anna Knox, A; Chad L Leverette,C; Yianne Kritzas, Y

    2006-11-29

    Soil contaminated with U was the focus of this study in order to develop in-situ, U bio-immobilization technology. We have demonstrated microbial production of a metal chelating biopolymer, pyomelanin, in U contaminated soil from the Tims Branch area of the Department of Energy (DOE) Savannah River Site (SRS) as a result of tyrosine amendments. Bacterial densities of pyomelanin producers were >106 cells/g wet soil. Pyomelanin demonstrated U chelating and mineral binding capacities at pH 4 and 7. In laboratory studies, in the presence of goethite or illite, pyomelanin enhanced U sequestration by these minerals. Tyrosine amended soils in field tests demonstrated increased U sequestration capacity following pyomelanin production up to 13 months after tyrosine treatments.

  9. Metabolic heterogeneity in clonal microbial populations.

    Science.gov (United States)

    Takhaveev, Vakil; Heinemann, Matthias

    2018-02-21

    In the past decades, numerous instances of phenotypic diversity were observed in clonal microbial populations, particularly, on the gene expression level. Much less is, however, known about phenotypic differences that occur on the level of metabolism. This is likely explained by the fact that experimental tools probing metabolism of single cells are still at an early stage of development. Here, we review recent exciting discoveries that point out different causes for metabolic heterogeneity within clonal microbial populations. These causes range from ecological factors and cell-inherent dynamics in constant environments to molecular noise in gene expression that propagates into metabolism. Furthermore, we provide an overview of current methods to quantify the levels of metabolites and biomass components in single cells. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

  10. Microbial Metabolism and Inhibition Studies of Phenobarbital

    African Journals Online (AJOL)

    Erah

    techniques, high performance liquid chromatography (HPLC), mass spectrometry (MS) ... Keywords: Microbial metabolism, Phenobarbital, Inhibition studies, Rhizopus stolonifer, CYP 2C9, .... 24 h of incubation 0.5 ml of drug solution was ... mode, positive: spray voltage, 3.5 KV: ... Rhizopus stolonifer showed an extra peak at.

  11. Enhancing microbial production of biofuels by expanding microbial metabolic pathways.

    Science.gov (United States)

    Yu, Ping; Chen, Xingge; Li, Peng

    2017-09-01

    Fatty acid, isoprenoid, and alcohol pathways have been successfully engineered to produce biofuels. By introducing three genes, atfA, adhE, and pdc, into Escherichia coli to expand fatty acid pathway, up to 1.28 g/L of fatty acid ethyl esters can be achieved. The isoprenoid pathway can be expanded to produce bisabolene with a high titer of 900 mg/L in Saccharomyces cerevisiae. Short- and long-chain alcohols can also be effectively biosynthesized by extending the carbon chain of ketoacids with an engineered "+1" alcohol pathway. Thus, it can be concluded that expanding microbial metabolic pathways has enormous potential for enhancing microbial production of biofuels for future industrial applications. However, some major challenges for microbial production of biofuels should be overcome to compete with traditional fossil fuels: lowering production costs, reducing the time required to construct genetic elements and to increase their predictability and reliability, and creating reusable parts with useful and predictable behavior. To address these challenges, several aspects should be further considered in future: mining and transformation of genetic elements related to metabolic pathways, assembling biofuel elements and coordinating their functions, enhancing the tolerance of host cells to biofuels, and creating modular subpathways that can be easily interconnected. © 2016 International Union of Biochemistry and Molecular Biology, Inc.

  12. In-Situ Microbial Conversion of Sequestered Greenhouse Gases

    Energy Technology Data Exchange (ETDEWEB)

    Scott, A R; Mukhopadhyay, M; Balin, D F

    2012-09-06

    The objectives of the project are to use microbiological in situ bioconversion technology to convert sequestered or naturally-occurring greenhouse gases, including carbon dioxide and carbon monoxide, into methane and other useful organic compounds. The key factors affecting coal bioconversion identified in this research include (1) coal properties, (2) thermal maturation and coalification process, (3) microbial population dynamics, (4) hydrodynamics (5) reservoir conditions, and (6) the methodology of getting the nutrients into the coal seams. While nearly all cultures produced methane, we were unable to confirm sustained methane production from the enrichments. We believe that the methane generation may have been derived from readily metabolized organic matter in the coal samples and/or biosoluble organic material in the coal formation water. This raises the intriguing possibility that pretreatment of the coal in the subsurface to bioactivate the coal prior to the injection of microbes and nutrients might be possible. We determined that it would be more cost effective to inject nutrients into coal seams to stimulate indigenous microbes in the coal seams, than to grow microbes in fermentation vats and transport them to the well site. If the coal bioconversion process can be developed on a larger scale, then the cost to generate methane could be less than $1 per Mcf

  13. Engineering microbial fatty acid metabolism for biofuels and biochemicals

    DEFF Research Database (Denmark)

    Marella, Eko Roy; Holkenbrink, Carina; Siewers, Verena

    2017-01-01

    microbial catalysis. This review summarizes the recent advances in the engineering of microbial metabolism for production of fatty acid-derived products. We highlight the efforts in engineering the central carbon metabolism, redox metabolism, controlling the chain length of the products, and obtaining...

  14. Metabolic network modeling of microbial interactions in natural and engineered environmental systems

    Directory of Open Access Journals (Sweden)

    Octavio ePerez-Garcia

    2016-05-01

    interactions can be used to analyze complex ‘omics’ data and to infer and optimize metabolic processes. Thereby SMN models are suitable to capitalize on advances in high-throughput molecular and metabolic data generation. SMN models are starting to be applied to describe microbial interactions during wastewater treatment, in-situ bioremediation, methanogenic fermentation and bioplastic production. Despite their current challenges, we envisage that SMN models have future potential for the design and development of novel growth media, biochemical pathways and synthetic microbial associations.

  15. Microbially Mediated Immobilization of Contaminants Through In Situ Biostimulation

    International Nuclear Information System (INIS)

    Scott Fendorf

    2003-01-01

    In most natural environments, a multitude of metabolic substrates are resent simultaneously. Organisms that can utilize uranium as a metabolic substrate for respiration also may have the ability to use a variety of other oxidized substrates as electron acceptors. Thus, these substrates are, in effect, competing for electrons that are being passed through the electron transport chain during respiration. To assess the feasibility of in situ immobilization of uranium in subsurface environments and to understand the cycling of uranium, it is necessary to discern the chemical and/or biological conditions dictating which terminal electron acceptor(s) will be utilized

  16. Microbially Mediated Immobilization of Contaminants Through In Situ Biostimulation

    Energy Technology Data Exchange (ETDEWEB)

    Scott Fendorf

    2003-07-31

    In most natural environments, a multitude of metabolic substrates are resent simultaneously. Organisms that can utilize uranium as a metabolic substrate for respiration also may have the ability to use a variety of other oxidized substrates as electron acceptors. Thus, these substrates are, in effect, competing for electrons that are being passed through the electron transport chain during respiration. To assess the feasibility of in situ immobilization of uranium in subsurface environments and to understand the cycling of uranium, it is necessary to discern the chemical and/or biological conditions dictating which terminal electron acceptor(s) will be utilized.

  17. In situ hydrogen consumption kinetics as an indicator of subsurface microbial activity

    Science.gov (United States)

    Harris, S.H.; Smith, R.L.; Suflita, J.M.

    2007-01-01

    There are few methods available for broadly assessing microbial community metabolism directly within a groundwater environment. In this study, hydrogen consumption rates were estimated from in situ injection/withdrawal tests conducted in two geochemically varying, contaminated aquifers as an approach towards developing such a method. The hydrogen consumption first-order rates varied from 0.002 nM h-1 for an uncontaminated, aerobic site to 2.5 nM h-1 for a contaminated site where sulfate reduction was a predominant process. The method could accommodate the over three orders of magnitude range in rates that existed between subsurface sites. In a denitrifying zone, the hydrogen consumption rate (0.02 nM h-1) was immediately abolished in the presence of air or an antibiotic mixture, suggesting that such measurements may also be sensitive to the effects of environmental perturbations on field microbial activities. Comparable laboratory determinations with sediment slurries exhibited hydrogen consumption kinetics that differed substantially from the field estimates. Because anaerobic degradation of organic matter relies on the rapid consumption of hydrogen and subsequent maintenance at low levels, such in situ measures of hydrogen turnover can serve as a key indicator of the functioning of microbial food webs and may be more reliable than laboratory determinations. ?? 2007 Federation of European Microbiological Societies.

  18. In Situ Correlated Molecular Imaging of Chemically Communicating Microbial Communities

    Energy Technology Data Exchange (ETDEWEB)

    Bohn, Paul W. [Univ. of Notre Dame, IN (United States); Shrout, J. D. [Univ. of Notre Dame, IN (United States); Sweedler, J. V. [Univ. of Illinois, Urbana-Champaign, IL (United States); Farrand, S. [Univ. of Illinois, Urbana-Champaign, IL (United States)

    2016-01-25

    This document constitutes the final technical report for DE-SC0006642, In Situ Correlated Molecular Imaging of Chemically Communicating Microbial Communities, a project carried out collaboratively by investigators at Notre Dame and UIUC. The work carried out under DOE support in this project produced advances in two areas: development of new highly sophisticated correlated imaging approaches and the application of these new tools to the growth and differentiation of microbial communities under a variety of environmental conditions. A significant effort involved the creation of technical enhancements and sampling approaches to allow us to advance heterocorrelated mass spectrometry imaging (MSI) and correlated Raman microscopy (CRM) from bacterial cultures and biofilms. We then exploited these measurement advances in heterocorrelated MS/CRM imaging to determine relationship of signaling molecules and excreted signaling molecules produced by P. aeruginosa to conditions relevant to the rhizosphere. In particular, we: (1) developed a laboratory testbed mimic for the rhizosphere to enable microbial growth on slides under controlled conditions; (2) integrated specific measurements of (a) rhamnolipids, (b) quinolone/quinolones, and (c) phenazines specific to P. aeruginosa; and (3) utilized the imaging tools to probe how messenger secretion, quorum sensing and swarming behavior are correlated with behavior.

  19. [Improving industrial microbial stress resistance by metabolic engineering: a review].

    Science.gov (United States)

    Fu, Ruiyan; Li, Yin

    2010-09-01

    Metabolic engineering is a technologic platform for industrial strain improvement and aims not only at modifying microbial metabolic fluxes, but also improving the physiological performance of industrial microbes. Microbes will meet multiple stresses in industrial processes. Consequently, elicited gene responses might result in a decrease in overall cell fitness and the efficiency of biotransformation. Thus, it is crucial to develop robust and productive microbial strains that can be integrated into industrial-scale bioprocesses. In this review, we focus on the progress of these novel methods and strategies for engineering stress-tolerance phenotypes referring to rational metabolic engineering and inverse metabolic engineering in recent years. In addition, we also address problems existing in this area and future research needs of microbial physiological functionality engineering.

  20. Preliminary feasibility and cost analysis of the in-situ microbial filter concept

    International Nuclear Information System (INIS)

    Wijensinghe, A.M.; Knapp, R.B.; Taylor, R.T.; Carman, L.M.

    1992-01-01

    In this report the cost of installing and operating an in-situ microbial filter to remediate a site at which the groundwater is contaminated by TCE is estimated and compared against the cost of remediation by a standard pump and treat method. In this microbial filter method, relatively thin vertical filters are installed in the subsurface to intercept contaminant plumes that are being transported by the flowing groundwater. The filters are created by injecting into the subsurface methanotrophic microbes grown in surface bioreactors and allowing them to become attached to the soil. The microbes produce an enzyme (MMO) that fortuitously catalyzes the degradation of TCE into carbon dioxide, water and chloride ions. Because no external energy or carbon source is provided, the microbes remain metabolically active only for a limited time so that the filter needs to be periodically replenished with fresh microbes. Two methods of establishing and maintaining the microbial filter using either vertical or horizontal wells were studied. In the pump and treat method considered for comparison, the groundwater pumped to the surface is first subjected to air-stripping of the liquid-phase volatile organic compound (i.e., VOC) from the groundwater followed by adsorption of the heated vapor-phase VOC by granular activated carbon (i.e., GAC) within a packed-bed filter

  1. Microbial heterotrophic metabolic rates constrain the microbial carbon pump

    Digital Repository Service at National Institute of Oceanography (India)

    Robinson, C.; Ramaiah, N.

    (2008). 10. P.A. del Giorgio, J. J. Cole, in MicrobialEcologyoftheOceans D. L. Kirchman Ed. (JohnWiley & Sons, Inc. NewYork ed. 1. 2000),pp. 289–325. 11. A. B. Burd etal., DeepSeaRes.II 57, 1557 (2010). 12. S. Martinez-García, E. Fernández, M.... R.A. Straza, D. L. Kirchman, Aquat.Microb.Ecol. 62, 267(2011). 16. O. Hoegh-Guldberg, J. F. Bruno, Science 328,1523 (2010). 17. J. Piontek, M. Lunau, N. Handel, C. Borchard, M.Wurst,A. Engel, Biogeosciences 7, 1615 (2010). 18. J. K.Apple, P.A. del...

  2. Gut Microbial Glycerol Metabolism as an Endogenous Acrolein Source

    OpenAIRE

    Zhang, Jianbo; Sturla, Shana; Lacroix, Christophe; Schwab, Clarissa

    2018-01-01

    ABSTRACT Acrolein is a highly reactive electrophile causing toxic effects, such as DNA and protein adduction, oxidative stress, endoplasmic reticulum stress, immune dysfunction, and membrane damage. This Opinion/Hypothesis provides an overview of endogenous and exogenous acrolein sources, acrolein’s mode of action, and its metabolic fate. Recent reports underpin the finding that gut microbial glycerol metabolism leading to the formation of reuterin is an additional source of endogenous acrole...

  3. Microbial Development and Metabolic Engineering | Bioenergy | NREL

    Science.gov (United States)

    Diversity Our genetically engineered microbes utilize a variety of feedstock including cellulose, xylan , syngas, simple sugars, organic acids, and carbon dioxide (CO2). We have modified the metabolic pathways

  4. Microbial diversity and metabolic networks in acid mine drainage habitats

    Directory of Open Access Journals (Sweden)

    Celia eMendez-Garcia

    2015-05-01

    Full Text Available Acid mine drainage (AMD emplacements are low-complexity natural systems. Low-pH conditions appear to be the main factor underlying the limited diversity of the microbial populations thriving in these environments, although temperature, ionic composition, total organic carbon and dissolved oxygen are also considered to significantly influence their microbial life. This natural reduction in diversity driven by extreme conditions was reflected in several studies on the microbial populations inhabiting the various micro-environments present in such ecosystems. Early studies based on the physiology of the autochthonous microbiota and the growing success of omics technologies have enabled a better understanding of microbial ecology and function in low-pH mine outflows; however, complementary omics-derived data should be included to completely describe their microbial ecology. Furthermore, recent updates on the distribution of eukaryotes and ultra-micro-archaea demand their inclusion in the microbial characterisation of AMD systems. In this review, we present a complete overview of the bacterial, archaeal (including ultra-micro-archaeal and eukaryotic diversity in these ecosystems and include a thorough depiction of the metabolism and element cycling in AMD habitats. We also review different metabolic network structures at the organismal level, which is necessary to disentangle the role of each member of the AMD communities described thus far.

  5. Detection of denitrification genes by in situ rolling circle amplification - fluorescence in situ hybridization (in situ RCA-FISH) to link metabolic potential with identity inside bacterial cells

    DEFF Research Database (Denmark)

    Hoshino, Tatsuhiko; Schramm, Andreas

    2010-01-01

    target site. Finally, the RCA product inside the cells was detected by standard fluorescence in situ hybridization (FISH). The optimized protocol showed high specificity and signal-to-noise ratio but low detection frequency (up to 15% for single-copy genes and up to 43% for the multi-copy 16S rRNA gene...... as Candidatus Accumulibacter phosphatis by combining in situ RCA-FISH with 16S rRNA-targeted FISH. While not suitable for quantification because of its low detection frequency, in situ RCA-FISH will allow to link metabolic potential with 16S rRNA (gene)-based identification of single microbial cells.......). Nevertheless, multiple genes (nirS and nosZ; nirS and the 16S rRNA gene) could be detected simultaneously in P. stutzeri. Environmental application of in situ RCA-FISH was demonstrated on activated sludge by the differential detection of two types of nirS-defined denitrifiers; one of them was identified...

  6. Microbial Regulation of Glucose Metabolism and Insulin Resistance

    Directory of Open Access Journals (Sweden)

    Silke Crommen

    2017-12-01

    Full Text Available Type 2 diabetes is a combined disease, resulting from a hyperglycemia and peripheral and hepatic insulin resistance. Recent data suggest that the gut microbiota is involved in diabetes development, altering metabolic processes including glucose and fatty acid metabolism. Thus, type 2 diabetes patients show a microbial dysbiosis, with reduced butyrate-producing bacteria and elevated potential pathogens compared to metabolically healthy individuals. Furthermore, probiotics are a known tool to modulate the microbiota, having a therapeutic potential. Current literature will be discussed to elucidate the complex interaction of gut microbiota, intestinal permeability and inflammation leading to peripheral and hepatic insulin resistance. Therefore, this review aims to generate a deeper understanding of the underlying mechanism of potential microbial strains, which can be used as probiotics.

  7. Microbial Metabolism and Inhibition Studies of Phenobarbital ...

    African Journals Online (AJOL)

    Purpose: Screening scale studies were performed with eight cultures for their ability to metabolize phenobarbital, an antiepileptic, sedative, hypnotic and substrate for CYP 2C9 and 2C19. Methods: The transformation of phenobarbital was confirmed and characterized by fermentation techniques, high performance liquid ...

  8. Arsenic and selenium in microbial metabolism

    Science.gov (United States)

    Stolz, John F.; Basu, Partha; Santini, Joanne M.; Oremland, Ronald S.

    2006-01-01

    Arsenic and selenium are readily metabolized by prokaryotes, participating in a full range of metabolic functions including assimilation, methylation, detoxification, and anaerobic respiration. Arsenic speciation and mobility is affected by microbes through oxidation/reduction reactions as part of resistance and respiratory processes. A robust arsenic cycle has been demonstrated in diverse environments. Respiratory arsenate reductases, arsenic methyltransferases, and new components in arsenic resistance have been recently described. The requirement for selenium stems primarily from its incorporation into selenocysteine and its function in selenoenzymes. Selenium oxyanions can serve as an electron acceptor in anaerobic respiration, forming distinct nanoparticles of elemental selenium that may be enriched in (76)Se. The biogenesis of selenoproteins has been elucidated, and selenium methyltransferases and a respiratory selenate reductase have also been described. This review highlights recent advances in ecology, biochemistry, and molecular biology and provides a prelude to the impact of genomics studies.

  9. Microbial community assembly and metabolic function during mammalian corpse decomposition

    Energy Technology Data Exchange (ETDEWEB)

    Metcalf, J. L.; Xu, Z. Z.; Weiss, S.; Lax, S.; Van Treuren, W.; Hyde, E. R.; Song, S. J.; Amir, A.; Larsen, P.; Sangwan, N.; Haarmann, D.; Humphrey, G. C.; Ackermann, G.; Thompson, L. R.; Lauber, C.; Bibat, A.; Nicholas, C.; Gebert, M. J.; Petrosino, J. F.; Reed, S. C.; Gilbert, J. A.; Lynne, A. M.; Bucheli, S. R.; Carter, D. O.; Knight, R.

    2015-12-10

    Vertebrate corpse decomposition provides an important stage in nutrient cycling in most terrestrial habitats, yet microbially mediated processes are poorly understood. Here we combine deep microbial community characterization, community-level metabolic reconstruction, and soil biogeochemical assessment to understand the principles governing microbial community assembly during decomposition of mouse and human corpses on different soil substrates. We find a suite of bacterial and fungal groups that contribute to nitrogen cycling and a reproducible network of decomposers that emerge on predictable time scales. Our results show that this decomposer community is derived primarily from bulk soil, but key decomposers are ubiquitous in low abundance. Soil type was not a dominant factor driving community development, and the process of decomposition is sufficiently reproducible to offer new opportunities for forensic investigations.

  10. Microbial community assembly and metabolic function during mammalian corpse decomposition

    Science.gov (United States)

    Metcalf, Jessica L; Xu, Zhenjiang Zech; Weiss, Sophie; Lax, Simon; Van Treuren, Will; Hyde, Embriette R.; Song, Se Jin; Amir, Amnon; Larsen, Peter; Sangwan, Naseer; Haarmann, Daniel; Humphrey, Greg C; Ackermann, Gail; Thompson, Luke R; Lauber, Christian; Bibat, Alexander; Nicholas, Catherine; Gebert, Matthew J; Petrosino, Joseph F; Reed, Sasha C.; Gilbert, Jack A; Lynne, Aaron M; Bucheli, Sibyl R; Carter, David O; Knight, Rob

    2016-01-01

    Vertebrate corpse decomposition provides an important stage in nutrient cycling in most terrestrial habitats, yet microbially mediated processes are poorly understood. Here we combine deep microbial community characterization, community-level metabolic reconstruction, and soil biogeochemical assessment to understand the principles governing microbial community assembly during decomposition of mouse and human corpses on different soil substrates. We find a suite of bacterial and fungal groups that contribute to nitrogen cycling and a reproducible network of decomposers that emerge on predictable time scales. Our results show that this decomposer community is derived primarily from bulk soil, but key decomposers are ubiquitous in low abundance. Soil type was not a dominant factor driving community development, and the process of decomposition is sufficiently reproducible to offer new opportunities for forensic investigations.

  11. Using Deep UV Raman Spectroscopy to Identify In Situ Microbial Activity

    Science.gov (United States)

    Sapers, H. M.; Wanger, G.; Amend, J.; Orphan, V. J.; Bhartia, R.

    2017-12-01

    labels will allow in situ detection of metabolically-targeted active community members on complex natural substrates providing a crucial link between microbial activity and environmental context.

  12. The Role of Microbial Amino Acid Metabolism in Host Metabolism

    Directory of Open Access Journals (Sweden)

    Evelien P. J. G. Neis

    2015-04-01

    Full Text Available Disruptions in gut microbiota composition and function are increasingly implicated in the pathogenesis of obesity, insulin resistance, and type 2 diabetes mellitus. The functional output of the gut microbiota, including short-chain fatty acids and amino acids, are thought to be important modulators underlying the development of these disorders. Gut bacteria can alter the bioavailability of amino acids by utilization of several amino acids originating from both alimentary and endogenous proteins. In turn, gut bacteria also provide amino acids to the host. This could have significant implications in the context of insulin resistance and type 2 diabetes mellitus, conditions associated with elevated systemic concentrations of certain amino acids, in particular the aromatic and branched-chain amino acids. Moreover, several amino acids released by gut bacteria can serve as precursors for the synthesis of short-chain fatty acids, which also play a role in the development of obesity. In this review, we aim to compile the available evidence on the contribution of microbial amino acids to host amino acid homeostasis, and to assess the role of the gut microbiota as a determinant of amino acid and short-chain fatty acid perturbations in human obesity and type 2 diabetes mellitus.

  13. Effects of introducing heterologous pathways on microbial metabolism with respect to metabolic optimality

    DEFF Research Database (Denmark)

    Kim, Hyun Uk; Kim, Byoungjin; Seung, Do Young

    2014-01-01

    reactions are more frequently introduced into various microbial hosts. The genome-scale metabolic simulations of Escherichia coli strains engineered to produce 1,4-butanediol, 1,3-propanediol, and amorphadiene suggest that microbial metabolism shows much different responses to the introduced heterologous...... reactions in a strain-specific manner than typical gene knockouts in terms of the energetic status (e.g., ATP and biomass generation) and chemical production capacity. The 1,4-butanediol and 1,3-propanediol producers showed greater metabolic optimality than the wild-type strains and gene knockout mutants...... for the energetic status, while the amorphadiene producer was metabolically less optimal. For the optimal chemical production capacity, additional gene knockouts were most effective for the strain producing 1,3-propanediol, but not for the one producing 1,4-butanediol. These observations suggest that strains having...

  14. Structural and metabolic responses of microbial community to sewage-borne chlorpyrifos in constructed wetlands.

    Science.gov (United States)

    Zhang, Dan; Wang, Chuan; Zhang, Liping; Xu, Dong; Liu, Biyun; Zhou, Qiaohong; Wu, Zhenbin

    2016-06-01

    Long-term use of chlorpyrifos poses a potential threat to the environment that cannot be ignored, yet little is known about the succession of substrate microbial communities in constructed wetlands (CWs) under chlorpyrifos stress. Six pilot-scale CW systems receiving artificial wastewater containing 1mg/L chlorpyrifos were established to investigate the effects of chlorpyrifos and wetland vegetation on the microbial metabolism pattern of carbon sources and community structure, using BIOLOG and denaturing gradient gel electrophoresis (DGGE) approaches. Based on our samples, BIOLOG showed that Shannon diversity (H') and richness (S) values distinctly increased after 30days when chlorpyrifos was added. At the same time, differences between the vegetated and the non-vegetated systems disappeared. DGGE profiles indicated that H' and S had no significant differences among four different treatments. The effect of chlorpyrifos on the microbial community was mainly reflected at the physiological level. Principal component analysis (PCA) of both BIOLOG and DGGE showed that added chlorpyrifos made a difference on test results. Meanwhile, there was no difference between the vegetation and no-vegetation treatments after addition of chlorpyrifos at the physiological level. Moreover, the vegetation had no significant effect on the microbial community at the genetic level. Comparisons were made between bacteria in this experiment and other known chlorpyrifos-degrading bacteria. The potential chlorpyrifos-degrading ability of bacteria in situ may be considerable. Copyright © 2016. Published by Elsevier B.V.

  15. Gut Microbial Glycerol Metabolism as an Endogenous Acrolein Source

    Directory of Open Access Journals (Sweden)

    Jianbo Zhang

    2018-01-01

    Full Text Available Acrolein is a highly reactive electrophile causing toxic effects, such as DNA and protein adduction, oxidative stress, endoplasmic reticulum stress, immune dysfunction, and membrane damage. This Opinion/Hypothesis provides an overview of endogenous and exogenous acrolein sources, acrolein’s mode of action, and its metabolic fate. Recent reports underpin the finding that gut microbial glycerol metabolism leading to the formation of reuterin is an additional source of endogenous acrolein. Reuterin is an antimicrobial multicomponent system consisting of 3-hydroxypropionaldehyde, its dimer and hydrate, and also acrolein. The major conclusion is that gut microbes can metabolize glycerol to reuterin and that this transformation occurs in vivo. Given the known toxicity of acrolein, the observation that acrolein is formed in the gut necessitates further investigations on functional relevance for gut microbiota and the host.

  16. Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism.

    Science.gov (United States)

    Broman, Elias; Sjöstedt, Johanna; Pinhassi, Jarone; Dopson, Mark

    2017-08-09

    A key characteristic of eutrophication in coastal seas is the expansion of hypoxic bottom waters, often referred to as 'dead zones'. One proposed remediation strategy for coastal dead zones in the Baltic Sea is to mix the water column using pump stations, circulating oxygenated water to the sea bottom. Although microbial metabolism in the sediment surface is recognized as key in regulating bulk chemical fluxes, it remains unknown how the microbial community and its metabolic processes are influenced by shifts in oxygen availability. Here, coastal Baltic Sea sediments sampled from oxic and anoxic sites, plus an intermediate area subjected to episodic oxygenation, were experimentally exposed to oxygen shifts. Chemical, 16S rRNA gene, metagenomic, and metatranscriptomic analyses were conducted to investigate changes in chemistry fluxes, microbial community structure, and metabolic functions in the sediment surface. Compared to anoxic controls, oxygenation of anoxic sediment resulted in a proliferation of bacterial populations in the facultative anaerobic genus Sulfurovum that are capable of oxidizing toxic sulfide. Furthermore, the oxygenated sediment had higher amounts of RNA transcripts annotated as sqr, fccB, and dsrA involved in sulfide oxidation. In addition, the importance of cryptic sulfur cycling was highlighted by the oxidative genes listed above as well as dsvA, ttrB, dmsA, and ddhAB that encode reductive processes being identified in anoxic and intermediate sediments turned oxic. In particular, the intermediate site sediments responded differently upon oxygenation compared to the anoxic and oxic site sediments. This included a microbial community composition with more habitat generalists, lower amounts of RNA transcripts attributed to methane oxidation, and a reduced rate of organic matter degradation. These novel data emphasize that genetic expression analyses has the power to identify key molecular mechanisms that regulate microbial community responses

  17. Coupling Spatiotemporal Community Assembly Processes to Changes in Microbial Metabolism

    Energy Technology Data Exchange (ETDEWEB)

    Graham, Emily B.; Crump, Alex R.; Resch, Charles T.; Fansler, Sarah; Arntzen, Evan; Kennedy, David W.; Fredrickson, Jim K.; Stegen, James C.

    2016-12-16

    Community assembly processes govern shifts in species abundances in response to environmental change, yet our understanding of assembly remains largely decoupled from ecosystem function. Here, we test hypotheses regarding assembly and function across space and time using hyporheic microbial communities as a model system. We pair sampling of two habitat types through hydrologic fluctuation with null modeling and multivariate statistics. We demonstrate that dual selective pressures assimilate to generate compositional changes at distinct timescales among habitat types, resulting in contrasting associations of Betaproteobacteria and Thaumarchaeota with selection and with seasonal changes in aerobic metabolism. Our results culminate in a conceptual model in which selection from contrasting environments regulates taxon abundance and ecosystem function through time, with increases in function when oscillating selection opposes stable selective pressures. Our model is applicable within both macrobial and microbial ecology and presents an avenue for assimilating community assembly processes into predictions of ecosystem function.

  18. Soil Microbial Community Contribution to Small Headwater Stream Metabolism.

    Science.gov (United States)

    Clapcott, J. E.; Gooderham, J. P.; Barmuta, L. A.; Davies, P. E.

    2005-05-01

    The temporal dynamics of sediment respiration were examined in seven small headwater streams in forested catchments in 2004. A strong seasonal response was observed with higher respiration rates in depositional zones than in gravel runs. The data were also examined in the context of proportional habitat distributions that highlighted the importance of high flow events in shaping whole stream metabolic budgets. This study specifically examines the question of terrestrial soil respiration contribution to whole stream metabolism by the controlled inundation of terrestrial soils. The experiment included six experimentally inundated terrestrial zones, six terrestrial controls, and six in-stream depositional zones. Sediment bacterial respiration was measured using 14C leucine incorporation and cotton strip bioassays were also employed to provide an indicative measure of sediment microbial activity. Despite high variability and exhibiting significantly lower bacterial activity than in-stream sediments, modelling using flow data and habitat mapping illustrated the important contribution of terrestrial soil respiration to the whole stream metabolic budgets of small headwater streams. In addition, microbial community composition examined using phospholipid fatty acid analysis clearly differentiated between terrestrial and aquatic communities. Freshly inundated terrestrial communities remained similar to un-inundated controls after 28 days.

  19. Mechanistic links between gut microbial community dynamics, microbial functions and metabolic health

    Science.gov (United States)

    Ha, Connie WY; Lam, Yan Y; Holmes, Andrew J

    2014-01-01

    Gut microbes comprise a high density, biologically active community that lies at the interface of an animal with its nutritional environment. Consequently their activity profoundly influences many aspects of the physiology and metabolism of the host animal. A range of microbial structural components and metabolites directly interact with host intestinal cells and tissues to influence nutrient uptake and epithelial health. Endocrine, neuronal and lymphoid cells in the gut also integrate signals from these microbial factors to influence systemic responses. Dysregulation of these host-microbe interactions is now recognised as a major risk factor in the development of metabolic dysfunction. This is a two-way process and understanding the factors that tip host-microbiome homeostasis over to dysbiosis requires greater appreciation of the host feedbacks that contribute to regulation of microbial community composition. To date, numerous studies have employed taxonomic profiling approaches to explore the links between microbial composition and host outcomes (especially obesity and its comorbidities), but inconsistent host-microbe associations have been reported. Available data indicates multiple factors have contributed to discrepancies between studies. These include the high level of functional redundancy in host-microbiome interactions combined with individual variation in microbiome composition; differences in study design, diet composition and host system between studies; and inherent limitations to the resolution of rRNA-based community profiling. Accounting for these factors allows for recognition of the common microbial and host factors driving community composition and development of dysbiosis on high fat diets. New therapeutic intervention options are now emerging. PMID:25469018

  20. Genome-enabled Modeling of Microbial Biogeochemistry using a Trait-based Approach. Does Increasing Metabolic Complexity Increase Predictive Capabilities?

    Science.gov (United States)

    King, E.; Karaoz, U.; Molins, S.; Bouskill, N.; Anantharaman, K.; Beller, H. R.; Banfield, J. F.; Steefel, C. I.; Brodie, E.

    2015-12-01

    The biogeochemical functioning of ecosystems is shaped in part by genomic information stored in the subsurface microbiome. Cultivation-independent approaches allow us to extract this information through reconstruction of thousands of genomes from a microbial community. Analysis of these genomes, in turn, gives an indication of the organisms present and their functional roles. However, metagenomic analyses can currently deliver thousands of different genomes that range in abundance/importance, requiring the identification and assimilation of key physiologies and metabolisms to be represented as traits for successful simulation of subsurface processes. Here we focus on incorporating -omics information into BioCrunch, a genome-informed trait-based model that represents the diversity of microbial functional processes within a reactive transport framework. This approach models the rate of nutrient uptake and the thermodynamics of coupled electron donors and acceptors for a range of microbial metabolisms including heterotrophs and chemolithotrophs. Metabolism of exogenous substrates fuels catabolic and anabolic processes, with the proportion of energy used for cellular maintenance, respiration, biomass development, and enzyme production based upon dynamic intracellular and environmental conditions. This internal resource partitioning represents a trade-off against biomass formation and results in microbial community emergence across a fitness landscape. Biocrunch was used here in simulations that included organisms and metabolic pathways derived from a dataset of ~1200 non-redundant genomes reflecting a microbial community in a floodplain aquifer. Metagenomic data was directly used to parameterize trait values related to growth and to identify trait linkages associated with respiration, fermentation, and key enzymatic functions such as plant polymer degradation. Simulations spanned a range of metabolic complexities and highlight benefits originating from simulations

  1. Metabolic modelling of polyhydroxyalkanoate copolymers production by mixed microbial cultures

    Directory of Open Access Journals (Sweden)

    Reis Maria AM

    2008-07-01

    Full Text Available Abstract Background This paper presents a metabolic model describing the production of polyhydroxyalkanoate (PHA copolymers in mixed microbial cultures, using mixtures of acetic and propionic acid as carbon source material. Material and energetic balances were established on the basis of previously elucidated metabolic pathways. Equations were derived for the theoretical yields for cell growth and PHA production on mixtures of acetic and propionic acid as functions of the oxidative phosphorylation efficiency, P/O ratio. The oxidative phosphorylation efficiency was estimated from rate measurements, which in turn allowed the estimation of the theoretical yield coefficients. Results The model was validated with experimental data collected in a sequencing batch reactor (SBR operated under varying feeding conditions: feeding of acetic and propionic acid separately (control experiments, and the feeding of acetic and propionic acid simultaneously. Two different feast and famine culture enrichment strategies were studied: (i either with acetate or (ii with propionate as carbon source material. Metabolic flux analysis (MFA was performed for the different feeding conditions and culture enrichment strategies. Flux balance analysis (FBA was used to calculate optimal feeding scenarios for high quality PHA polymers production, where it was found that a suitable polymer would be obtained when acetate is fed in excess and the feeding rate of propionate is limited to ~0.17 C-mol/(C-mol.h. The results were compared with published pure culture metabolic studies. Conclusion Acetate was more conducive toward the enrichment of a microbial culture with higher PHA storage fluxes and yields as compared to propionate. The P/O ratio was not only influenced by the selected microbial culture, but also by the carbon substrate fed to each culture, where higher P/O ratio values were consistently observed for acetate than propionate. MFA studies suggest that when mixtures of

  2. Microbial production of antioxidant food ingredients via metabolic engineering.

    Science.gov (United States)

    Lin, Yuheng; Jain, Rachit; Yan, Yajun

    2014-04-01

    Antioxidants are biological molecules with the ability to protect vital metabolites from harmful oxidation. Due to this fascinating role, their beneficial effects on human health are of paramount importance. Traditional approaches using solvent-based extraction from food/non-food sources and chemical synthesis are often expensive, exhaustive, and detrimental to the environment. With the advent of metabolic engineering tools, the successful reconstitution of heterologous pathways in Escherichia coli and other microorganisms provides a more exciting and amenable alternative to meet the increasing demand of natural antioxidants. In this review, we elucidate the recent progress in metabolic engineering efforts for the microbial production of antioxidant food ingredients - polyphenols, carotenoids, and antioxidant vitamins. Copyright © 2013 Elsevier Ltd. All rights reserved.

  3. In situ acetate separation in microbial electrosynthesis from CO

    NARCIS (Netherlands)

    Bajracharya, Suman; Burg, van den Bart; Vanbroekhoven, Karolien; Wever, De Heleen; Buisman, Cees J.N.; Pant, Deepak; Strik, David P.B.T.B.

    2017-01-01

    Bioelectrochemical reduction of carbon dioxide (CO2) to multi-carbon organic compounds particularly acetate has been achieved in microbial electrosynthesis (MES) using the reducing equivalents produced at the electrically polarized cathode. MES based on CO2 reduction

  4. Shifts in the Microbial Population in Relation to in situ Caries Progression

    NARCIS (Netherlands)

    Thomas, R. Z.; Zijnge, V.; Cicek, A.; de Soet, J. J.; Harmsen, H. J. M.; Huysmans, M. C. D. N. J. M.

    2012-01-01

    The shift in microbial diversity from young to mature plaque, related to caries activity on sound and restored surfaces, was studied using denaturing gradient gel electrophoresis. During a 20-week in situ study on caries progression 8 subjects wearing restored and unrestored dentin and enamel

  5. Shifts in the microbial population in relation to in situ caries progression

    NARCIS (Netherlands)

    Thomas, R.Z.; Zijnge, V.; Ciçek, A.; de Soet, J.J.; Harmsen, H.J.M.; Huysmans, M.C.D.N.J.M.

    2012-01-01

    The shift in microbial diversity from young to mature plaque, related to caries activity on sound and restored surfaces, was studied using denaturing gradient gel electrophoresis. During a 20-week in situ study on caries progression 8 subjects wearing restored and unrestored dentin and enamel

  6. In situ microbial systems for the enhancement of oil recovery

    International Nuclear Information System (INIS)

    Moses, V.

    1991-01-01

    Microbial Enhancement of Oil Recovery (MEOR) offers important new opportunities in the quest for increased oil production. It refers not to a single technique but rather to a collection of methodologies, analogous to parallel non-microbiological methods. MEOR has relevance for many type of production and reservoir problems detailed protocols: may be tailored specifically to a range of individual reservoir conditions. Microorganisms downhole can generate a wide variety of chemical products from inexpensive feed stocks: where these are more cost-effective than oil field chemicals injected from the surface, microbial methods may win widespread acceptance. MEOR methods must be defined precisely; in any particular reservoir procedure their proposed mechanism of action must be clearly understood and criteria established for evaluating their success. The most important applications for MEOR are 1) the production f insoluble or highly viscous polymer to control coning or to plug selectively high permeability thief zones and fractures, 2) the continuous generation of the active agents for polymer-and/or surfactant floods, 3) matrix acidisation and acid fracturing in carbonate rocks stimulate flows into production wells. All these approaches are currently actively been explored; several programmes for field-testing microbial EOR methods already exist, or are being readied, and rapid progress is likely within the next few years. (author)

  7. In-situ detection of microbial life in the deep biosphere in igneous ocean crust

    Directory of Open Access Journals (Sweden)

    Everett Cosio Salas

    2015-11-01

    Full Text Available The deep biosphere is a major frontier to science. Recent studies have shown the presence and activity of cells in deep marine sediments and in the continental deep biosphere. Volcanic lavas in the deep ocean subsurface, through which substantial fluid flow occurs, present another potentially massive deep biosphere. We present results from the deployment of a novel in-situ logging tool designed to detect microbial life harbored in a deep, native, borehole environment within igneous oceanic crust, using deep ultraviolet native fluorescence spectroscopy. Results demonstrate the predominance of microbial-like signatures within the borehole environment, with densities in the range of 105 cells/mL. Based on transport and flux models, we estimate that such a concentration of microbial cells could not be supported by transport through the crust, suggesting in situ growth of these communities.

  8. In situ Detection of Microbial Life in the Deep Biosphere in Igneous Ocean Crust.

    Science.gov (United States)

    Salas, Everett C; Bhartia, Rohit; Anderson, Louise; Hug, William F; Reid, Ray D; Iturrino, Gerardo; Edwards, Katrina J

    2015-01-01

    The deep biosphere is a major frontier to science. Recent studies have shown the presence and activity of cells in deep marine sediments and in the continental deep biosphere. Volcanic lavas in the deep ocean subsurface, through which substantial fluid flow occurs, present another potentially massive deep biosphere. We present results from the deployment of a novel in situ logging tool designed to detect microbial life harbored in a deep, native, borehole environment within igneous oceanic crust, using deep ultraviolet native fluorescence spectroscopy. Results demonstrate the predominance of microbial-like signatures within the borehole environment, with densities in the range of 10(5) cells/mL. Based on transport and flux models, we estimate that such a concentration of microbial cells could not be supported by transport through the crust, suggesting in situ growth of these communities.

  9. Balancing cellular redox metabolism in microbial electrosynthesis and electro fermentation - A chance for metabolic engineering.

    Science.gov (United States)

    Kracke, Frauke; Lai, Bin; Yu, Shiqin; Krömer, Jens O

    2018-01-01

    More and more microbes are discovered that are capable of extracellular electron transfer, a process in which they use external electrodes as electron donors or acceptors for metabolic reactions. This feature can be used to overcome cellular redox limitations and thus optimizing microbial production. The technologies, termed microbial electrosynthesis and electro-fermentation, have the potential to open novel bio-electro production platforms from sustainable energy and carbon sources. However, the performance of reported systems is currently limited by low electron transport rates between microbes and electrodes and our limited ability for targeted engineering of these systems due to remaining knowledge gaps about the underlying fundamental processes. Metabolic engineering offers many opportunities to optimize these processes, for instance by genetic engineering of pathways for electron transfer on the one hand and target product synthesis on the other hand. With this review, we summarize the status quo of knowledge and engineering attempts around chemical production in bio-electrochemical systems from a microbe perspective. Challenges associated with the introduction or enhancement of extracellular electron transfer capabilities into production hosts versus the engineering of target compound synthesis pathways in natural exoelectrogens are discussed. Recent advances of the research community in both directions are examined critically. Further, systems biology approaches, for instance using metabolic modelling, are examined for their potential to provide insight into fundamental processes and to identify targets for metabolic engineering. Copyright © 2017 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

  10. In Situ Ecophysiology of Microbial Biofilm Communities Analyzed by CMEIAS Computer-Assisted Microscopy at Single-Cell Resolution

    Directory of Open Access Journals (Sweden)

    Youssef G. Yanni

    2013-06-01

    Full Text Available This paper describes the utility of CMEIAS (Center for Microbial Ecology Image Analysis System computer-assisted microscopy to extract data from accurately segmented images that provide 63 different insights into the ecophysiology of microbial populations and communities within biofilms and other habitats. Topics include quantitative assessments of: (i morphological diversity as an indicator of impacts that substratum physicochemistries have on biofilm community structure and dominance-rarity relationships among populations; (ii morphotype-specific distributions of biovolume body size that relate microbial allometric scaling, metabolic activity and growth physiology; (iii fractal geometry of optimal cellular positioning for efficient utilization of allocated nutrient resources; (iv morphotype-specific stress responses to starvation, environmental disturbance and bacteriovory predation; (v patterns of spatial distribution indicating positive and negative cell–cell interactions affecting their colonization behavior; and (vi significant methodological improvements to increase the accuracy of color-discriminated ecophysiology, e.g., differentiation of cell viability based on cell membrane integrity, cellular respiratory activity, phylogenetically differentiated substrate utilization, and N-acyl homoserine lactone-mediated cell–cell communication by bacteria while colonizing plant roots. The intensity of these ecophysiological attributes commonly varies at the individual cell level, emphasizing the importance of analyzing them at single-cell resolution and the proper spatial scale at which they occur in situ.

  11. Variation in antibiotic-induced microbial recolonization impacts on the host metabolic phenotypes of rats.

    Science.gov (United States)

    Swann, Jonathan R; Tuohy, Kieran M; Lindfors, Peter; Brown, Duncan T; Gibson, Glenn R; Wilson, Ian D; Sidaway, James; Nicholson, Jeremy K; Holmes, Elaine

    2011-08-05

    The interaction between the gut microbiota and their mammalian host is known to have far-reaching consequences with respect to metabolism and health. We investigated the effects of eight days of oral antibiotic exposure (penicillin and streptomycin sulfate) on gut microbial composition and host metabolic phenotype in male Han-Wistar rats (n = 6) compared to matched controls. Early recolonization was assessed in a third group exposed to antibiotics for four days followed by four days recovery (n = 6). Fluorescence in situ hybridization analysis of the intestinal contents collected at eight days showed a significant reduction in all bacterial groups measured (control, 10(10.7) cells/g feces; antibiotic-treated, 10(8.4)). Bacterial suppression reduced the excretion of mammalian-microbial urinary cometabolites including hippurate, phenylpropionic acid, phenylacetylglycine and indoxyl-sulfate whereas taurine, glycine, citrate, 2-oxoglutarate, and fumarate excretion was elevated. While total bacterial counts remained notably lower in the recolonized animals (10(9.1) cells/g faeces) compared to the controls, two cage-dependent subgroups emerged with Lactobacillus/Enterococcus probe counts dominant in one subgroup. This dichotomous profile manifested in the metabolic phenotypes with subgroup differences in tricarboxylic acid cycle metabolites and indoxyl-sulfate excretion. Fecal short chain fatty acids were diminished in all treated animals. Antibiotic treatment induced a profound effect on the microbiome structure, which was reflected in the metabotype. Moreover, the recolonization process was sensitive to the microenvironment, which may impact on understanding downstream consequences of antibiotic consumption in human populations.

  12. In situ coral reef oxygen metabolism: an eddy correlation study.

    Directory of Open Access Journals (Sweden)

    Matthew H Long

    Full Text Available Quantitative studies of coral reefs are challenged by the three-dimensional hard structure of reefs and the high spatial variability and temporal dynamics of their metabolism. We used the non-invasive eddy correlation technique to examine respiration and photosynthesis rates, through O2 fluxes, from reef crests and reef slopes in the Florida Keys, USA. We assessed how the photosynthesis and respiration of different reef habitats is controlled by light and hydrodynamics. Numerous fluxes (over a 0.25 h period were as high as 4500 mmol O2 m(-2 d(-1, which can only be explained by efficient light utilization by the phototrophic community and the complex canopy structure of the reef, having a many-fold larger surface area than its horizontal projection. Over diel cycles, the reef crest was net autotrophic, whereas on the reef slope oxygen production and respiration were balanced. The autotrophic nature of the shallow reef crests implies that the export of organics is an important source of primary production for the larger area. Net oxygen production on the reef crest was proportional to the light intensity, up to 1750 µmol photons m(-2 s(-1 and decreased thereafter as respiration was stimulated by high current velocities coincident with peak light levels. Nighttime respiration rates were also stimulated by the current velocity, through enhanced ventilation of the porous framework of the reef. Respiration rates were the highest directly after sunset, and then decreased during the night suggesting that highly labile photosynthates produced during the day fueled early-night respiration. The reef framework was also important to the acquisition of nutrients as the ambient nitrogen stock in the water had sufficient capacity to support these high production rates across the entire reef width. These direct measurements of complex reefs systems yielded high metabolic rates and dynamics that can only be determined through in situ, high temporal resolution

  13. Colonization Habitat Controls Biomass, Composition, and Metabolic Activity of Attached Microbial Communities in the Columbia River Hyporheic Corridor

    Energy Technology Data Exchange (ETDEWEB)

    Stern, Noah; Ginder-Vogel, Matthew; Stegen, James C.; Arntzen, Evan; Kennedy, David W.; Larget, Bret R.; Roden, Eric E.; Kostka, Joel E.

    2017-06-09

    Hydrologic exchange plays a critical role in biogeochemical cycling within the hyporheic zone (the interface between river water and groundwater) of riverine ecosystems. Such exchange may set limits on the rates of microbial metabolism and impose deterministic selection on microbial communities that adapt to dynamically changing dissolved organic carbon (DOC) sources. This study examined the response of attached microbial communities (in situcolonized sand packs) from groundwater, hyporheic, and riverbed habitats within the Columbia River hyporheic corridor to “cross-feeding” with either groundwater, river water, or DOC-free artificial fluids. Our working hypothesis was that deterministic selection duringin situcolonization would dictate the response to cross-feeding, with communities displaying maximal biomass and respiration when supplied with their native fluid source. In contrast to expectations, the major observation was that the riverbed colonized sand had much higher biomass and respiratory activity, as well as a distinct community structure, compared with those of the hyporheic and groundwater colonized sands. 16S rRNA gene amplicon sequencing revealed a much higher proportion of certain heterotrophic taxa as well as significant numbers of eukaryotic algal chloroplasts in the riverbed colonized sand. Significant quantities of DOC were released from riverbed sediment and colonized sand, and separate experiments showed that the released DOC stimulated respiration in the groundwater and piezometer colonized sand. These results suggest that the accumulation and degradation of labile particulate organic carbon (POC) within the riverbed are likely to release DOC, which may enter the hyporheic corridor during hydrologic exchange, thereby stimulating microbial activity and imposing deterministic selective pressure on the microbial community composition.

    IMPORTANCEThe influence of river water

  14. Responses of microbial community functional structures to pilot-scale uranium in situ bioremediation

    Energy Technology Data Exchange (ETDEWEB)

    Xu, M.; Wu, W.-M.; Wu, L.; He, Z.; Van Nostrand, J.D.; Deng, Y.; Luo, J.; Carley, J.; Ginder-Vogel, M.; Gentry, T.J.; Gu, B.; Watson, D.; Jardine, P.M.; Marsh, T.L.; Tiedje, J.M.; Hazen, T.C.; Criddle, C.S.; Zhou, J.

    2010-02-15

    A pilot-scale field test system with an inner loop nested within an outer loop was constructed for in situ U(VI) bioremediation at a US Department of Energy site, Oak Ridge, TN. The outer loop was used for hydrological protection of the inner loop where ethanol was injected for biostimulation of microorganisms for U(VI) reduction/immobilization. After 2 years of biostimulation with ethanol, U(VI) levels were reduced to below drinking water standard (<30 {micro}gl{sup -1}) in the inner loop monitoring wells. To elucidate the microbial community structure and functions under in situ uranium bioremediation conditions, we used a comprehensive functional gene array (GeoChip) to examine the microbial functional gene composition of the sediment samples collected from both inner and outer loop wells. Our study results showed that distinct microbial communities were established in the inner loop wells. Also, higher microbial functional gene number, diversity and abundance were observed in the inner loop wells than the outer loop wells. In addition, metal-reducing bacteria, such as Desulfovibrio, Geobacter, Anaeromyxobacter and Shewanella, and other bacteria, for example, Rhodopseudomonas and Pseudomonas, are highly abundant in the inner loop wells. Finally, the richness and abundance of microbial functional genes were highly correlated with the mean travel time of groundwater from the inner loop injection well, pH and sulfate concentration in groundwater. These results suggest that the indigenous microbial communities can be successfully stimulated for U bioremediation in the groundwater ecosystem, and their structure and performance can be manipulated or optimized by adjusting geochemical and hydrological conditions.

  15. Quantitative comparison of the in situ microbial communities in different biomes

    Energy Technology Data Exchange (ETDEWEB)

    White, D.C. [Tennessee Univ., Knoxville, TN (United States)]|[Oak Ridge National Lab., TN (United States); Ringelberg, D.B.; Palmer, R.J. [Tennessee Univ., Knoxville, TN (United States). Center for Environmental Biotechnology

    1995-12-31

    A system to define microbial communities in different biomes requires the application of non-traditional methodology. Classical microbiological methods have severe limitations for the analysis of environmental samples. Pure-culture isolation, biochemical testing, and/or enumeration by direct microscopic counting are not well suited for the estimation of total biomass or the assessment of community composition within environmental samples. Such methods provide little insight into the in situ phenotypic activity of the extant microbiota since these techniques are dependent on microbial growth and thus select against many environmental microorganisms which are non- culturable under a wide range of conditions. It has been repeatedly documented in the literature that viable counts or direct counts of bacteria attached to sediment grains are difficult to quantitative and may grossly underestimate the extent of the existing community. The traditional tests provide little indication of the in situ nutritional status or for evidence of toxicity within the microbial community. A more recent development (MIDI Microbial Identification System), measure free and ester-linked fatty acids from isolated microorganisms. Bacterial isolates are identified by comparing their fatty acid profiles to the MIKI database which contains over 8000 entries. The application of the MIKI system to the analysis of environmental samples however, has significant drawbacks. The MIDI system was developed to identify clinical microorganisms and requires their isolation and culture on trypticase soy agar at 27{degrees}C. Since many isolates are unable to grow at these restrictive growth conditions, the system does not lend itself to identification of some environmental organisms. A more applicable methodology for environmental microbial analysis is based on the liquid extrication and separation of microbial lipids from environmental samples, followed by quantitative analysis using gas chromatography/

  16. Microbial Metabolic Roles in Bedrock Degradation and the Genesis of Biomineral and Biopattern Biosignatures in Caves and Mines

    Science.gov (United States)

    Boston, P. J.

    2016-12-01

    In subsurface environments like natural or anthropogenic caves (aka mines), microorganisms facilitate considerable bedrock degradation under a variety of circumstances. Mobilization of materials from these processes frequently produces distinctive biominerals, identifiable biotextures, and unique biopatterns. Microbial activities can even determine the form of speleothems (secondary mineral cave decorations), thus providing highly conspicuous macroscopic biosignatures. It is critical to understand microbial-mineral interactions, recognizing that while the lithology controls important aspects of the environment, in turn, the geochemistry is greatly affected by the biology. Microbial communities can contribute to the actual formation of cavities (speleogenesis), and subsequent enlargement of caves and vugs and the mineral deposits that enrich many subterranean spaces. A major challenge is to quantify such influences. Genetic analysis is revealing a vast but highly partitioned biodiversity in the overall rock fracture habitat of Earth's crust especially in caves and mines where the three phases of matter (solid rock, fluids, and gases) typically interact producing high niche richness. Lessons learned from the microbial/geochemical systems that we have studied include: 1) significant similarities in metabolic functions between different geochemical systems, 2) ubiquity of metal oxidation for energy, 3) ubiquity of biofilms, some highly mineralized, 4) highly interdependent, multi-species communities that can only transform materials in consortia, 5) complex ecological succession including characteristic pioneer species, 6) often very slow growth rates in culture, 7) prevalence of very small cell sizes, ( 100 - 500 nm diam.), 8) mineral reprecipitation of mobilized materials, often dependent on the presence of live microbial communities to produce initial amorphous compounds followed by gradual crystallization, and 9) resultant in situ self-fossilization. Microbial

  17. In situ microbial fuel cell-based biosensor for organic carbon

    DEFF Research Database (Denmark)

    de Jesus dos Santos Peixoto, Luciana; Min, Booki; Martins, Gilberto

    2011-01-01

    The biological oxygen demand (BOD) may be the most used test to assess the amount of pollutant organic matter in water; however, it is time and labor consuming, and is done ex-situ. A BOD biosensor based on the microbial fuel cell principle was tested for online and in situ monitoring of biodegra......The biological oxygen demand (BOD) may be the most used test to assess the amount of pollutant organic matter in water; however, it is time and labor consuming, and is done ex-situ. A BOD biosensor based on the microbial fuel cell principle was tested for online and in situ monitoring...... of biodegradable organic content of domestic wastewater. A stable current density of 282±23mA/m2 was obtained with domestic wastewater containing a BOD5 of 317±15mg O2/L at 22±2°C, 1.53±0.04mS/cm and pH 6.9±0.1. The current density showed a linear relationship with BOD5 concentration ranging from 17±0.5mg O2/L...

  18. Rumen microbial communities influence metabolic phenotypes in lambs

    Directory of Open Access Journals (Sweden)

    Diego P. Morgavi

    2015-10-01

    Full Text Available The rumen microbiota is an essential part of ruminants forging their nutrition and health. Despite its importance, it is not fully understood how various groups of rumen microbes affect host-microbe relationships and functions. The aim of the study was to simultaneously explore the rumen microbiota and the metabolic phenotype of lambs for identifying host-microbe associations and potential biomarkers of digestive functions. Twin lambs, separated in two groups after birth were exposed to practices (isolation and gavage with rumen fluid with protozoa or protozoa-depleted that differentially restricted the acquisition of microbes. Rumen microbiota, fermentation parameters, digestibility and growth were monitored for up to 31 weeks of age. Microbiota assembled in isolation from other ruminants lacked protozoa and had low bacterial and archaeal diversity whereas digestibility was not affected. Exposure to adult sheep microbiota increased bacterial and archaeal diversity independently of protozoa presence. For archaea, Methanomassiliicoccales displaced Methanosphaera. Notwithstanding, protozoa induced differences in functional traits such as digestibility and significantly shaped bacterial community structure, notably Ruminococcaceae and Lachnospiraceae lower up to 6 folds, Prevotellaceae lower by ~40%, and Clostridiaceae and Veillonellaceae higher up to 10 folds compared to microbiota without protozoa. An orthogonal partial least squares-discriminant analysis of urinary metabolome matched differences in microbiota structure. Discriminant metabolites were mainly involved in amino acids and protein metabolic pathways while a negative interaction was observed between methylotrophic methanogens Methanomassiliicoccales and trimethylamine N-oxide. These results stress the influence of gut microbes on animal phenotype and show the potential of metabolomics for monitoring rumen microbial functions.

  19. Compartmentalized metabolic network reconstruction of microbial communities to determine the effect of agricultural intervention on soils

    Science.gov (United States)

    Álvarez-Yela, Astrid Catalina; Gómez-Cano, Fabio; Zambrano, María Mercedes; Husserl, Johana; Danies, Giovanna; Restrepo, Silvia; González-Barrios, Andrés Fernando

    2017-01-01

    Soil microbial communities are responsible for a wide range of ecological processes and have an important economic impact in agriculture. Determining the metabolic processes performed by microbial communities is crucial for understanding and managing ecosystem properties. Metagenomic approaches allow the elucidation of the main metabolic processes that determine the performance of microbial communities under different environmental conditions and perturbations. Here we present the first compartmentalized metabolic reconstruction at a metagenomics scale of a microbial ecosystem. This systematic approach conceives a meta-organism without boundaries between individual organisms and allows the in silico evaluation of the effect of agricultural intervention on soils at a metagenomics level. To characterize the microbial ecosystems, topological properties, taxonomic and metabolic profiles, as well as a Flux Balance Analysis (FBA) were considered. Furthermore, topological and optimization algorithms were implemented to carry out the curation of the models, to ensure the continuity of the fluxes between the metabolic pathways, and to confirm the metabolite exchange between subcellular compartments. The proposed models provide specific information about ecosystems that are generally overlooked in non-compartmentalized or non-curated networks, like the influence of transport reactions in the metabolic processes, especially the important effect on mitochondrial processes, as well as provide more accurate results of the fluxes used to optimize the metabolic processes within the microbial community. PMID:28767679

  20. Compartmentalized metabolic network reconstruction of microbial communities to determine the effect of agricultural intervention on soils.

    Directory of Open Access Journals (Sweden)

    María Camila Alvarez-Silva

    Full Text Available Soil microbial communities are responsible for a wide range of ecological processes and have an important economic impact in agriculture. Determining the metabolic processes performed by microbial communities is crucial for understanding and managing ecosystem properties. Metagenomic approaches allow the elucidation of the main metabolic processes that determine the performance of microbial communities under different environmental conditions and perturbations. Here we present the first compartmentalized metabolic reconstruction at a metagenomics scale of a microbial ecosystem. This systematic approach conceives a meta-organism without boundaries between individual organisms and allows the in silico evaluation of the effect of agricultural intervention on soils at a metagenomics level. To characterize the microbial ecosystems, topological properties, taxonomic and metabolic profiles, as well as a Flux Balance Analysis (FBA were considered. Furthermore, topological and optimization algorithms were implemented to carry out the curation of the models, to ensure the continuity of the fluxes between the metabolic pathways, and to confirm the metabolite exchange between subcellular compartments. The proposed models provide specific information about ecosystems that are generally overlooked in non-compartmentalized or non-curated networks, like the influence of transport reactions in the metabolic processes, especially the important effect on mitochondrial processes, as well as provide more accurate results of the fluxes used to optimize the metabolic processes within the microbial community.

  1. Unravelling core microbial metabolisms in the hypersaline microbial mats of Shark Bay using high-throughput metagenomics

    Energy Technology Data Exchange (ETDEWEB)

    Ruvindy, Rendy; White III, Richard Allen; Neilan, Brett Anthony; Burns, Brendan Paul

    2015-05-29

    Modern microbial mats are potential analogues of some of Earth’s earliest ecosystems. Excellent examples can be found in Shark Bay, Australia, with mats of various morphologies. To further our understanding of the functional genetic potential of these complex microbial ecosystems, we conducted for the first time shotgun metagenomic analyses. We assembled metagenomic nextgeneration sequencing data to classify the taxonomic and metabolic potential across diverse morphologies of marine mats in Shark Bay. The microbial community across taxonomic classifications using protein-coding and small subunit rRNA genes directly extracted from the metagenomes suggests that three phyla Proteobacteria, Cyanobacteria and Bacteriodetes dominate all marine mats. However, the microbial community structure between Shark Bay and Highbourne Cay (Bahamas) marine systems appears to be distinct from each other. The metabolic potential (based on SEED subsystem classifications) of the Shark Bay and Highbourne Cay microbial communities were also distinct. Shark Bay metagenomes have a metabolic pathway profile consisting of both heterotrophic and photosynthetic pathways, whereas Highbourne Cay appears to be dominated almost exclusively by photosynthetic pathways. Alternative non-rubisco-based carbon metabolism including reductive TCA cycle and 3-hydroxypropionate/4-hydroxybutyrate pathways is highly represented in Shark Bay metagenomes while not represented in Highbourne Cay microbial mats or any other mat forming ecosystems investigated to date. Potentially novel aspects of nitrogen cycling were also observed, as well as putative heavy metal cycling (arsenic, mercury, copper and cadmium). Finally, archaea are highly represented in Shark Bay and may have critical roles in overall ecosystem function in these modern microbial mats.

  2. Nitrification-driven forms of nitrogen metabolism in microbial mat communities thriving along an ammonium-enriched subsurface geothermal stream

    Science.gov (United States)

    Nishizawa, Manabu; Koba, Keisuke; Makabe, Akiko; Yoshida, Naohiro; Kaneko, Masanori; Hirao, Shingo; Ishibashi, Jun-ichiro; Yamanaka, Toshiro; Shibuya, Takazo; Kikuchi, Tohru; Hirai, Miho; Miyazaki, Junichi; Nunoura, Takuro; Takai, Ken

    2013-07-01

    We report here the concurrence and interaction among forms of nitrogen metabolism in thermophilic microbial mat communities that developed in an ammonium-abundant subsurface geothermal stream. First, the physical and chemical conditions of the stream water at several representative microbial mat habitats (including upper, middle and downstream sites) were characterized. A thermodynamic calculation using these physical and chemical conditions predicted that nitrification consisting of ammonia and nitrite oxidations would provide one of the largest energy yields of chemolithotrophic metabolisms. Second, near-complete prokaryotic 16S rRNA gene clone analysis was conducted for representative microbial mat communities at the upper, middle and downstream sites. The results indicated a dynamic shift in the 16S rRNA gene phylotype composition through physical and chemical variations of the stream water. The predominant prokaryotic components varied from phylotypes related to hydrogeno (H2)- and thio (S)-trophic Aquificales, thermophilic methanotrophs and putative ammonia-oxidizing Archaea (AOA) located upstream (72 °C) to the phylotypes affiliated with putative AOA and nitrite-oxidizing bacteria (NOB) located at the middle and downstream sites (65 and 57 °C, respectively). In addition, the potential in situ metabolic activities of different forms of nitrogen metabolism were estimated through laboratory experiments using bulk microbial mat communities. Finally, the compositional and isotopic variation in nitrogen compounds was investigated in the stream water flowing over the microbial mats and in the interstitial water inside the mats. Although the stream water was characterized by a gradual decrease in the total ammonia concentration (ΣNH3: the sum of ammonia and ammonium concentrations) and a gradual increase in the total concentration of nitrite and nitrate (NO2- + NO3-), the total inorganic nitrogen concentration (TIN: the sum of ΣNH3, NO2- and NO3- concentrations

  3. Metaproteomics: extracting and mining proteome information to characterize metabolic activities in microbial communities.

    Science.gov (United States)

    Abraham, Paul E; Giannone, Richard J; Xiong, Weili; Hettich, Robert L

    2014-06-17

    Contemporary microbial ecology studies usually employ one or more "omics" approaches to investigate the structure and function of microbial communities. Among these, metaproteomics aims to characterize the metabolic activities of the microbial membership, providing a direct link between the genetic potential and functional metabolism. The successful deployment of metaproteomics research depends on the integration of high-quality experimental and bioinformatic techniques for uncovering the metabolic activities of a microbial community in a way that is complementary to other "meta-omic" approaches. The essential, quality-defining informatics steps in metaproteomics investigations are: (1) construction of the metagenome, (2) functional annotation of predicted protein-coding genes, (3) protein database searching, (4) protein inference, and (5) extraction of metabolic information. In this article, we provide an overview of current bioinformatic approaches and software implementations in metaproteome studies in order to highlight the key considerations needed for successful implementation of this powerful community-biology tool. Copyright © 2014 John Wiley & Sons, Inc.

  4. Does canine inflammatory bowel disease influence gut microbial profile and host metabolism?

    OpenAIRE

    Xu, Jia; Verbrugghe, Adronie; Louren?o, Marta; Janssens, Geert P. J.; Liu, Daisy J. X.; Van de Wiele, Tom; Eeckhaut, Venessa; Van Immerseel, Filip; Van de Maele, Isabel; Niu, Yufeng; Bosch, Guido; Junius, Greet; Wuyts, Brigitte; Hesta, Myriam

    2016-01-01

    Background Inflammatory bowel disease (IBD) refers to a diverse group of chronic gastrointestinal diseases, and gut microbial dysbiosis has been proposed as a modulating factor in its pathogenesis. Several studies have investigated the gut microbial ecology of dogs with IBD but it is yet unclear if this microbial profile can alter the nutrient metabolism of the host. The aim of the present study was to characterize the faecal bacterial profile and functionality as well as to determine host me...

  5. Monitoring of the microbial community composition of the saline aquifers during CO2 storage by fluorescence in situ hybridisation

    OpenAIRE

    Daria Morozova; M. Wandrey; Mashal Alawi; Martin Zimmer; Andrea Vieth-Hillebrand [Vieth; M. Zettlitzer; Hilke Würdemann

    2010-01-01

    This study reveals the first analyses of the composition and activity of the microbial community of a saline CO2 storage aquifer. Microbial monitoring during CO2 injection has been reported. By using fluorescence in situ hybridisation (FISH), we have shown that the microbial community was strongly influenced by the CO2 injection. Before CO2 arrival, up to 6 × 106 cells ml−1 were detected by DAPI staining at a depth of 647 m below the surface. The microbial community was dominated by the dom...

  6. Olive Ridley Sea Turtle Hatching Success as a Function of Microbial Abundance and the Microenvironment of In Situ Nest Sand at Ostional, Costa Rica

    Directory of Open Access Journals (Sweden)

    Vanessa S. Bézy

    2014-01-01

    Full Text Available Sea turtle hatching success at mass nesting beaches is typically lower than at solitary nesting beaches, presumably due in part to high rates of microbial metabolism resulting from the large input of organic matter from turtle eggs. Therefore, we tested the hypothesis that hatching success varies across areas of the beach in conjunction with differences in the physical nest environment and microbial abundance of in situ olive ridley sea turtle nests at Ostional, Costa Rica. We marked natural nests in high-density, low-density, and tidal-wash nesting areas of the beach and monitored clutch pO2 and temperature throughout the incubation period. We quantified hatching success and collected samples of nest sand during nest excavations. We quantified microbial abundance (bacteria and fungi with a quantitative polymerase chain reaction (qPCR analysis. Hatching success was lower in nests with lower pO2, higher temperatures, higher organic matter content, and higher microbial abundance. Our results suggest that the lower oxygen within the nest environment is likely a result of the high microbial abundance and rates of decomposition in the nest sand and that these factors, along with increased temperature of clutches in the high-density nesting area, are collectively responsible for the low hatching success at Ostional.

  7. Understanding aquatic microbial processes using EEM's and in-situ fluorescence sensors

    Science.gov (United States)

    Fox, Bethany; Attridge, John; Rushworth, Cathy; Cox, Tim; Anesio, Alexandre; Reynolds, Darren

    2015-04-01

    The diverse origin of dissolved organic matter (DOM) in aquatic systems is well documented within the literature. Previous literature indicates that coloured dissolved organic matter (CDOM) is, in part, transformed by aquatic microbial processes, and that dissolved organic material derived from a microbial origin exhibits tryptophan-like fluorescence. However, this phenomenon is not fully understood and very little data is available within the current literature. The overall aim of our work is to reveal the microbial-CDOM interactions that give rise to the observed tryptophan-like fluorescence. The work reported here investigates the microbial processes that occur within freshwater aquatic samples, as defined by the biochemical oxygen demand (BOD) test, as a function of the T1 peak (λex/em 280/330-370 nm). A series of standard water samples were prepared using glucose, glutamic acid, BOD dilution water and a bacterial seed (Cole-Parmer BOD microbe capsules). Samples were spiked with CDOM (derived from an environmental water body) and subjected to time resolved BOD analysis and as excitation-emission fluorescence spectroscopy. All EEM spectral data was interrogated using parallel factor analysis (PARAFAC) in an attempt to determine the presence and dominance (relative intensities) of the CDOM-related and T1-related fluorophores within the samples. In-situ fluorescence sensors (Chelsea Technologies Group Ltd.) were also used to monitor the T1 fluorescence peak (UviLux Tryptophan) and the CDOM fluorescence peak (UviLux CDOM) during experiments. Tryptophan-like fluorescence was observed (albeit transient) in both spiked and un-spiked standard water samples. By furthering our understanding of aquatic organic matter fluorescence, its origin, transformation, fate and interaction with aquatic microbiological processes, we aim to inform the design of a new generation in-situ fluorescence sensor for the monitoring of aquatic ecosystem health.

  8. Laboratory treatability studies preparatory to field testing a resting-cell in situ microbial filter bioremediation strategy

    International Nuclear Information System (INIS)

    Taylor, R.T.; Hanna, M.L.

    1995-04-01

    Prior to a down-hole-column treatability test of a Methylosinus trichosporium OB3b attached-resting-cell in situ biofilter strategy, a set of three sequential laboratory experiments were carried out to define several key operational parameters and to evaluate the likely degree of success at a NASA Kennedy Space Center site. They involved the cell attachment to site-specific sediments, the intrinsic resting-cell biotransformation capacities for the contaminants of interest plus their time-dependent extents of biodegradative removal at the concentrations of concern, and a scaled in situ mini-flow-through-column system that closely mimics the subsurface conditions during a field-treatability or pilot test of an emplaced resting-cell filter. These experiments established the conditions required for the complete metabolic removal of a vinyl chloride (VC), cis-dichlororthylene (cis-DCE) and trichloroethylene (TCE) mixture. However, the gas chromatographic (GC) procedures that we utilized and the mini-flow-through column data demonstrated that, at most, only about 50--70% of the site-water VC, cis-DCE, and TCE would be biodegraded. This occurred because of a limiting level of dissolved oxygen, which was exacerbated by the simultaneous presence of several additional previously unrecognized groundwater components, especially methane, that are also competing substrates for the whole-cell soluble methane monooxygenase (sMMO) enzyme complex. Irrespective, collectively the simplicity of the methods that we have developed and the results obtainable with them appear to provide relevant laboratory-based test-criteria before taking our microbial filter strategy to an in situ field treatability or pilot demonstration stage at other sites in the future

  9. Microbial population heterogeneity versus bioreactor heterogeneity: evaluation of Redox Sensor Green as an exogenous metabolic biosensor

    DEFF Research Database (Denmark)

    Baert, Jonathan; Delepierre, Anissa; Telek, Samuel

    2016-01-01

    Microbial heterogeneity in metabolic performances has attracted a lot of attention, considering its potential impact on industrial bioprocesses. However, little is known about the impact of extracellular perturbations (i.e. bioreactor heterogeneity) on cell-to-cell variability in metabolic...

  10. Ultrasonication aided in-situ transesterification of microbial lipids to biodiesel.

    Science.gov (United States)

    Zhang, Xiaolei; Yan, Song; Tyagi, Rajeshwar Dayal; Surampalli, Rao Y; Valéro, Jose R

    2014-10-01

    In-situ transesterification of microbial lipid to biodiesel has been paid substantial attention due to the fact that the lipid extraction and transesterification can be conducted in one-stage process. To improve the feasibility of in-situ transesterification, ultrasonication was employed to reduce methanol requirement and reaction time. The results showed that the use of ultrasonication could achieve high conversion of lipid to FAMEs (92.1% w lipid conversion/w total lipids) with methanol to lipid molar ratio 60:1 and NaOH addition 1% w/w lipid in 20 min, while methanol to lipid molar ratio 360:1, NaOH addition 1% w/w lipid, and reaction time 12h was required to obtain similar yield in in-situ transesterification without ultrasonication. The compositions of FAMEs obtained in case of ultrasonication aided in-situ transesterification were similar as that of two-stage extraction followed by transesterification processes. Copyright © 2014. Published by Elsevier Ltd.

  11. GENOME-BASED MODELING AND DESIGN OF METABOLIC INTERACTIONS IN MICROBIAL COMMUNITIES

    Directory of Open Access Journals (Sweden)

    Radhakrishnan Mahadevan

    2012-10-01

    With the advent of genome sequencing, omics technologies, bioinformatics and genome-scale modeling, researchers now have unprecedented capabilities to analyze and engineer the metabolism of microbial communities. The goal of this review is to summarize recent applications of genome-scale metabolic modeling to microbial communities. A brief introduction to lumped community models is used to motivate the need for genome-level descriptions of individual species and their metabolic interactions. The review of genome-scale models begins with static modeling approaches, which are appropriate for communities where the extracellular environment can be assumed to be time invariant or slowly varying. Dynamic extensions of the static modeling approach are described, and then applications of genome-scale models for design of synthetic microbial communities are reviewed. The review concludes with a summary of metagenomic tools for analyzing community metabolism and an outlook for future research.

  12. Microbial metabolism and community structure in response to bioelectrochemically enhanced remediation of petroleum hydrocarbon-contaminated soil.

    Science.gov (United States)

    Lu, Lu; Huggins, Tyler; Jin, Song; Zuo, Yi; Ren, Zhiyong Jason

    2014-04-01

    This study demonstrates that electrodes in a bioelectrochemical system (BES) can potentially serve as a nonexhaustible electron acceptor for in situ bioremediation of hydrocarbon contaminated soil. The deployment of BES not only eliminates aeration or supplement of electron acceptors as in contemporary bioremediation but also significantly shortens the remediation period and produces sustainable electricity. More interestingly, the study reveals that microbial metabolism and community structure distinctively respond to the bioelectrochemically enhanced remediation. Tubular BESs with carbon cloth anode (CCA) or biochar anode (BCA) were inserted into raw water saturated soils containing petroleum hydrocarbons for enhancing in situ remediation. Results show that total petroleum hydrocarbon (TPH) removal rate almost doubled in soils close to the anode (63.5-78.7%) than that in the open circuit positive controls (37.6-43.4%) during a period of 64 days. The maximum current density from the BESs ranged from 73 to 86 mA/m(2). Comprehensive microbial and chemical characterizations and statistical analyses show that the residual TPH has a strongly positive correlation with hydrocarbon-degrading microorganisms (HDM) numbers, dehydrogenase activity, and lipase activity and a negative correlation with soil pH, conductivity, and catalase activity. Distinctive microbial communities were identified at the anode, in soil with electrodes, and soil without electrodes. Uncommon electrochemically active bacteria capable of hydrocarbon degradation such as Comamonas testosteroni, Pseudomonas putida, and Ochrobactrum anthropi were selectively enriched on the anode, while hydrocarbon oxidizing bacteria were dominant in soil samples. Results from genus or phylum level characterizations well agree with the data from cluster analysis. Data from this study suggests that a unique constitution of microbial communities may play a key role in BES enhancement of petroleum hydrocarbons

  13. Unique Microbial Diversity and Metabolic Pathway Features of Fermented Vegetables From Hainan, China

    Science.gov (United States)

    Peng, Qiannan; Jiang, Shuaiming; Chen, Jieling; Ma, Chenchen; Huo, Dongxue; Shao, Yuyu; Zhang, Jiachao

    2018-01-01

    Fermented vegetables are typically traditional foods made of fresh vegetables and their juices, which are fermented by beneficial microorganisms. Herein, we applied high-throughput sequencing and culture-dependent technology to describe the diversities of microbiota and identify core microbiota in fermented vegetables from different areas of Hainan Province, and abundant metabolic pathways in the fermented vegetables were simultaneously predicted. At the genus level, Lactobacillus bacteria were the most abundant. Lactobacillus plantarum was the most abundant species, followed by Lactobacillus fermentum, Lactobacillus pentosaceus, and Weissella cibaria. These species were present in each sample with average absolute content values greater than 1% and were thus defined as core microbiota. Analysis results based on the alpha and beta diversities of the microbial communities showed that the microbial profiles of the fermented vegetables differed significantly based on the regions and raw materials used, and the species of the vegetables had a greater effect on the microbial community structure than the region from where they were harvested. Regarding microbial functional metabolism, we observed an enrichment of metabolic pathways, including membrane transport, replication and repair and translation, which implied that the microbial metabolism in the fermented vegetables tended to be vigorous. In addition, Lactobacillus plantarum and Lactobacillus fermentum were calculated to be major metabolic pathway contributors. Finally, we constructed a network to better explain correlations among the core microbiota and metabolic pathways. This study facilitates an understanding of the differences in microbial profiles and fermentation pathways involved in the production of fermented vegetables, establishes a basis for optimally selecting microorganisms to manufacture high-quality fermented vegetable products, and lays the foundation for better utilizing tropical microbial

  14. Unique Microbial Diversity and Metabolic Pathway Features of Fermented Vegetables From Hainan, China

    Directory of Open Access Journals (Sweden)

    Qiannan Peng

    2018-03-01

    Full Text Available Fermented vegetables are typically traditional foods made of fresh vegetables and their juices, which are fermented by beneficial microorganisms. Herein, we applied high-throughput sequencing and culture-dependent technology to describe the diversities of microbiota and identify core microbiota in fermented vegetables from different areas of Hainan Province, and abundant metabolic pathways in the fermented vegetables were simultaneously predicted. At the genus level, Lactobacillus bacteria were the most abundant. Lactobacillus plantarum was the most abundant species, followed by Lactobacillus fermentum, Lactobacillus pentosaceus, and Weissella cibaria. These species were present in each sample with average absolute content values greater than 1% and were thus defined as core microbiota. Analysis results based on the alpha and beta diversities of the microbial communities showed that the microbial profiles of the fermented vegetables differed significantly based on the regions and raw materials used, and the species of the vegetables had a greater effect on the microbial community structure than the region from where they were harvested. Regarding microbial functional metabolism, we observed an enrichment of metabolic pathways, including membrane transport, replication and repair and translation, which implied that the microbial metabolism in the fermented vegetables tended to be vigorous. In addition, Lactobacillus plantarum and Lactobacillus fermentum were calculated to be major metabolic pathway contributors. Finally, we constructed a network to better explain correlations among the core microbiota and metabolic pathways. This study facilitates an understanding of the differences in microbial profiles and fermentation pathways involved in the production of fermented vegetables, establishes a basis for optimally selecting microorganisms to manufacture high-quality fermented vegetable products, and lays the foundation for better utilizing

  15. Microbial methane from in situ biodegradation of coal and shale: A review and reevaluation of hydrogen and carbon isotope signatures

    Science.gov (United States)

    Vinson, David S.; Blair, Neal E.; Martini, Anna M.; Larter, Steve; Orem, William H.; McIntosh, Jennifer C.

    2017-01-01

    Stable carbon and hydrogen isotope signatures of methane, water, and inorganic carbon are widely utilized in natural gas systems for distinguishing microbial and thermogenic methane and for delineating methanogenic pathways (acetoclastic, hydrogenotrophic, and/or methylotrophic methanogenesis). Recent studies of coal and shale gas systems have characterized in situ microbial communities and provided stable isotope data (δD-CH4, δD-H2O, δ13C-CH4, and δ13C-CO2) from a wider range of environments than available previously. Here we review the principal biogenic methane-yielding pathways in coal beds and shales and the isotope effects imparted on methane, document the uncertainties and inconsistencies in established isotopic fingerprinting techniques, and identify the knowledge gaps in understanding the subsurface processes that govern H and C isotope signatures of biogenic methane. We also compare established isotopic interpretations with recent microbial community characterization techniques, which reveal additional inconsistencies in the interpretation of microbial metabolic pathways in coal beds and shales. Collectively, the re-assessed data show that widely-utilized isotopic fingerprinting techniques neglect important complications in coal beds and shales.Isotopic fingerprinting techniques that combine δ13C-CH4 with δD-CH4 and/or δ13C-CO2have significant limitations: (1) The consistent ~ 160‰ offset between δD-H2O and δD-CH4 could imply that hydrogenotrophic methanogenesis is the dominant metabolic pathway in microbial gas systems. However, hydrogen isotopes can equilibrate between methane precursors and coexisting water, yielding a similar apparent H isotope signal as hydrogenotrophic methanogenesis, regardless of the actual methane formation pathway. (2) Non-methanogenic processes such as sulfate reduction, Fe oxide reduction, inputs of thermogenic methane, anaerobic methane oxidation, and/or formation water interaction can cause the apparent carbon

  16. In situ bioremediation of trichloroethylene-contaminated water by a resting-cell methanotrophic microbial filter

    International Nuclear Information System (INIS)

    Taylor, R.T.; Duba, A.G.; Durham, W.B.; Hanna, M.L.; Jackson, K.J.; Jovanovich, M.C.; Knapp, R.B.; Knezovich, J.P.; Shah, N.N.; Shonnard, D.R.; Wijesinghe, A.M.

    1992-10-01

    The Lawrence Livermore National Laboratory is testing and developing an in situ microbial filter technology for remediating migrating subsurface plumes contaminated with low concentrations of trichloroethylene (TCE). Their current focus is the establishment of a replenishable bioactive zone (catalytic filter) along expanding plume boundaries by the Injection of a representative methanotrophic bacterium, Methylosinus trichosporium OB3b. We have successfully demonstrated this microbial filter strategy using emplaced, attached resting cells (no methane additions) in a 1.1-m flow-through test bed loaded with water-saturated sand. Two separate 24 h pulses of TCE (109 ppb and 85 ppb), one week apart, were pumped through the system at a flow velocity of 1.5 cm/h; no TCE (<0.5 ppb) was detected on the downstream side of the microbial filter. Subsequent excavation of the wet sand confirmed the existence of a TCE-bioactive zone 19 days after it had been created. An enhanced longevity of the cellular, soluble-form methane monooxygenase produced by this methanotroph Is a result of our laboratory bioreactor culturing conditions. Additional experiments with cells in sealed vials and emplaced in the 1.1-m test bed yielded a high resting-cell finite TCE biotransformation capacity of ∼ 0.25 mg per mg of bacteria; this is suitable for a planned sand-filled trench field demonstration at a Lawrence Livermore National Laboratory site

  17. Application of microbial biomass and activity measures to assess in situ bioremediation of chlorinated solvents

    International Nuclear Information System (INIS)

    Phelps, T.J.; Herbes, S.E.; Palumbo, A.V.; Pfiffner, S.M.; Mackowski, R.; Ringelberg, D.; White, D.C.; Tennessee Univ., Knoxville, TN

    1993-01-01

    Evaluating the effectiveness of chlorinated solvent remediation in the subsurface can be a significant problem given uncertainties in estimating the total mass of contaminants present. If the remediation technique is a biological activity, information on the progress and success of the remediation may be gained by monitoring changes in the mass and activities of microbial populations. The in situ bioremediation demonstration at the US Department of Energy (DOE) Savannah River Site (SRS) is designed to test the effectiveness of methane injection for the stimulation of in sediments. Past studies have shown the potential for degradation by native microbial populations. The design and implementation of the SRS Integrated Demonstration is described in this volume. A control phase without treatment was followed by a phase withdrawing air. The next phase included vacuum extraction plus air injection into the lower horizontal well located below the water table. The next period included the injection of 1% methane in air followed by injection of 4% methane in air. Based on the literature, it was hypothesized that the injection of methane would stimulate methanotrophic populations and thus accelerate biological degradation of TCE. Measuring the success of bioremediation is a complex effort that includes monitoring of changes in microbial populations associated with TCE degradation. These monitoring efforts are described in this paper and in related papers in this volume

  18. Towards the understanding of microbial metabolism in relation to microbial enhanced oil recovery

    DEFF Research Database (Denmark)

    Halim, Amalia Yunita; Nielsen, Sidsel Marie; Nielsen, Kristian Fog

    2017-01-01

    In this study, Bacillus licheniformis 421 was used as a model organism to understand the effects of microbial cell growth and metabolite production under anaerobic conditions in relation to microbial enhanced oil recovery. The bacterium was able to grow anaerobically on different carbon compounds...

  19. Deep-Sea Hydrothermal Vent Viruses Compensate for Microbial Metabolism in Virus-Host Interactions.

    Science.gov (United States)

    He, Tianliang; Li, Hongyun; Zhang, Xiaobo

    2017-07-11

    Viruses are believed to be responsible for the mortality of host organisms. However, some recent investigations reveal that viruses may be essential for host survival. To date, it remains unclear whether viruses are beneficial or harmful to their hosts. To reveal the roles of viruses in the virus-host interactions, viromes and microbiomes of sediment samples from three deep-sea hydrothermal vents were explored in this study. To exclude the influence of exogenous DNAs on viromes, the virus particles were purified with nuclease (DNase I and RNase A) treatments and cesium chloride density gradient centrifugation. The metagenomic analysis of viromes without exogenous DNA contamination and microbiomes of vent samples indicated that viruses had compensation effects on the metabolisms of their host microorganisms. Viral genes not only participated in most of the microbial metabolic pathways but also formed branched pathways in microbial metabolisms, including pyrimidine metabolism; alanine, aspartate, and glutamate metabolism; nitrogen metabolism and assimilation pathways of the two-component system; selenocompound metabolism; aminoacyl-tRNA biosynthesis; and amino sugar and nucleotide sugar metabolism. As is well known, deep-sea hydrothermal vent ecosystems exist in relatively isolated environments which are barely influenced by other ecosystems. The metabolic compensation of hosts mediated by viruses might represent a very important aspect of virus-host interactions. IMPORTANCE Viruses are the most abundant biological entities in the oceans and have very important roles in regulating microbial community structure and biogeochemical cycles. The relationship between virus and host microbes is broadly thought to be that of predator and prey. Viruses can lyse host cells to control microbial population sizes and affect community structures of hosts by killing specific microbes. However, viruses also influence their hosts through manipulation of bacterial metabolism. We found

  20. Evidence for the microbial in situ conversion of oil to methane in the Dagang oilfield

    Energy Technology Data Exchange (ETDEWEB)

    Jimenez, N.; Richnow, H.H. [Helmholtz-Zentrum fuer Umweltforschung (UFZ), Leipzig (Germany). Abt. Isotopenbiogeochemie; Cai, M. [Helmholtz-Zentrum fuer Umweltforschung (UFZ), Leipzig (Germany). Abt. Isotopenbiogeochemie; University of Science and Technology, Beijing (China). School of Civil and Environment Engineering; Straaten, N.; Krueger, M. [Bundesanstalt fuer Geowissenschaften und Rohstoffe BGR Geozentrum (BGR), Hannover (Germany). Fachbereich Geochemie der Rohstoffe; Yao, Jun [University of Science and Technology, Beijing (China). School of Civil and Environment Engineering

    2013-08-01

    In situ biotransformation of oil to methane was investigated in a reservoir in Dagang, China using chemical fingerprinting, isotopic analyses, and molecular and biological methods. The reservoir is highly methanogenic despite chemical indications of advanced oil degradation, such as depletion of n-alkanes, alkylbenzenes, and light polycyclic aromatic hydrocarbon (PAHs) fractions or changes in the distribution of several alkylated polycyclic aromatic hydrocarbons. The degree of degradation strongly varied between different parts of the reservoir, ranging from severely degraded to nearly undegraded oil compositions. Geochemical data from oil, water and gas samples taken from the reservoir are consistent with in situ biogenic methane production linked to aliphatic and aromatic hydrocarbon degradation. Microcosms were inoculated with production and injection waters in order to characterize these processes in vitro. Subsequent degradation experiments revealed that autochthonous microbiota are capable of producing methane from {sup 13}C-labelled n-hexadecane or 2-methylnaphthalene, and suggest that further methanogenesis may occur from the aromatic and polyaromatic fractions of Dagang reservoir fluids. The microbial communities from produced oil-water samples were composed of high numbers of microorganisms (on the order to 10{sup 7}), including methane-producing Archaea within the same order of magnitude. In summary, the investigated sections of the Dagang reservoir may have significant potential for testing the viability of in situ conversion of oil to methane as an enhanced recovery method, and biodegradation of the aromatic fractions of the oil may be an important methane source. (orig.)

  1. Metabolic engineering for the microbial production of isoprenoids: Carotenoids and isoprenoid-based biofuels

    Directory of Open Access Journals (Sweden)

    Fu-Xing Niu

    2017-09-01

    Full Text Available Isoprenoids are the most abundant and highly diverse group of natural products. Many isoprenoids have been used for pharmaceuticals, nutraceuticals, flavors, cosmetics, food additives and biofuels. Carotenoids and isoprenoid-based biofuels are two classes of important isoprenoids. These isoprenoids have been produced microbially through metabolic engineering and synthetic biology efforts. Herein, we briefly review the engineered biosynthetic pathways in well-characterized microbial systems for the production of carotenoids and several isoprenoid-based biofuels.

  2. An integrated study to analyze soil microbial community structure and metabolic potential in two forest types.

    Science.gov (United States)

    Zhang, Yuguang; Cong, Jing; Lu, Hui; Yang, Caiyun; Yang, Yunfeng; Zhou, Jizhong; Li, Diqiang

    2014-01-01

    Soil microbial metabolic potential and ecosystem function have received little attention owing to difficulties in methodology. In this study, we selected natural mature forest and natural secondary forest and analyzed the soil microbial community and metabolic potential combing the high-throughput sequencing and GeoChip technologies. Phylogenetic analysis based on 16S rRNA sequencing showed that one known archaeal phylum and 15 known bacterial phyla as well as unclassified phylotypes were presented in these forest soils, and Acidobacteria, Protecobacteria, and Actinobacteria were three of most abundant phyla. The detected microbial functional gene groups were related to different biogeochemical processes, including carbon degradation, carbon fixation, methane metabolism, nitrogen cycling, phosphorus utilization, sulfur cycling, etc. The Shannon index for detected functional gene probes was significantly higher (PThe regression analysis showed that a strong positive (Pthe soil microbial functional gene diversity and phylogenetic diversity. Mantel test showed that soil oxidizable organic carbon, soil total nitrogen and cellulose, glucanase, and amylase activities were significantly linked (Pthe relative abundance of corresponded functional gene groups. Variance partitioning analysis showed that a total of 81.58% of the variation in community structure was explained by soil chemical factors, soil temperature, and plant diversity. Therefore, the positive link of soil microbial structure and composition to functional activity related to ecosystem functioning was existed, and the natural secondary forest soil may occur the high microbial metabolic potential. Although the results can't directly reflect the actual microbial populations and functional activities, this study provides insight into the potential activity of the microbial community and associated feedback responses of the terrestrial ecosystem to environmental changes.

  3. Kinetic modeling of microbially-driven redox chemistry of radionuclides in subsurface environments: Coupling transport, microbial metabolism and geochemistry

    Energy Technology Data Exchange (ETDEWEB)

    WANG,YIFENG; PAPENGUTH,HANS W.

    2000-05-04

    Microbial degradation of organic matter is a driving force in many subsurface geochemical systems, and therefore may have significant impacts on the fate of radionuclides released into subsurface environments. In this paper, the authors present a general reaction-transport model for microbial metabolism, redox chemistry, and radionuclide migration in subsurface systems. The model explicitly accounts for biomass accumulation and the coupling of radionuclide redox reactions with major biogeochemical processes. Based on the consideration that the biomass accumulation in subsurface environments is likely to achieve a quasi-steady state, they have accordingly modified the traditional microbial growth kinetic equation. They justified the use of the biogeochemical models without the explicit representation of biomass accumulation, if the interest of modeling is in the net impact of microbial reactions on geochemical processes. They then applied their model to a scenario in which an oxic water flow containing both uranium and completing organic ligands is recharged into an oxic aquifer in a carbonate formation. The model simulation shows that uranium can be reduced and therefore immobilized in the anoxic zone created by microbial degradation.

  4. Kinetic modeling of microbially-driven redox chemistry of radionuclides in subsurface environments: Coupling transport, microbial metabolism and geochemistry

    International Nuclear Information System (INIS)

    Wang, Yifeng; Papenguth, Hans W.

    2000-01-01

    Microbial degradation of organic matter is a driving force in many subsurface geochemical systems, and therefore may have significant impacts on the fate of radionuclides released into subsurface environments. In this paper, the authors present a general reaction-transport model for microbial metabolism, redox chemistry, and radionuclide migration in subsurface systems. The model explicitly accounts for biomass accumulation and the coupling of radionuclide redox reactions with major biogeochemical processes. Based on the consideration that the biomass accumulation in subsurface environments is likely to achieve a quasi-steady state, they have accordingly modified the traditional microbial growth kinetic equation. They justified the use of the biogeochemical models without the explicit representation of biomass accumulation, if the interest of modeling is in the net impact of microbial reactions on geochemical processes. They then applied their model to a scenario in which an oxic water flow containing both uranium and completing organic ligands is recharged into an oxic aquifer in a carbonate formation. The model simulation shows that uranium can be reduced and therefore immobilized in the anoxic zone created by microbial degradation

  5. Bacillus licheniformis affects the microbial community and metabolic profile in the spontaneous fermentation of Daqu starter for Chinese liquor making.

    Science.gov (United States)

    Wang, Peng; Wu, Qun; Jiang, Xuejian; Wang, Zhiqiang; Tang, Jingli; Xu, Yan

    2017-06-05

    Chinese liquor is produced from spontaneous fermentation starter (Daqu) that provides the microbes, enzymes and flavors for liquor fermentation. To improve the flavor character of Daqu, we inoculated Bacillus licheniformis and studied the effect of this strain on the community structure and metabolic profile in Daqu fermentation. The microbial relative abundance changed after the inoculation, including the increase in Bacillus, Clavispora and Aspergillus, and the decrease in Pichia, Saccharomycopsis and some other genera. This variation was also confirmed by pure culture and coculture experiments. Seventy-three metabolites were identified during Daqu fermentation process. After inoculation, the average content of aromatic compounds were significantly enriched from 0.37mg/kg to 0.90mg/kg, and the average content of pyrazines significantly increased from 0.35mg/kg to 5.71mg/kg. The increase in pyrazines was positively associated with the metabolism of the inoculated Bacillus and the native genus Clavispora, because they produced much more pyrazines in their cocultures. Whereas the increase in aromatic compounds might be related to the change of in situ metabolic activity of several native genera, in particular, Aspergillus produced more aromatic compounds in cocultures with B. licheniformis. It indicated that the inoculation of B. licheniformis altered the flavor character of Daqu by both its own metabolic activity and the variation of in situ metabolic activity. Moreover, B. licheniformis inoculation influenced the enzyme activity of Daqu, including the significant increase in amylase activity (from 1.3gstarch/g/h to 1.7gstarch/g/h), and the significant decrease in glucoamylase activity (from 627.6mgglucose/g/h to 445.6mgglucose/g/h) and esterase activity (from 28.1mgethylcaproate/g/100h to 17.2mgethylcaproate/g/100h). These effects of inoculation were important factors for regulating the metabolism of microbial communities, hence for improving the flavor profile

  6. Kinetic modeling of cell metabolism for microbial production.

    Science.gov (United States)

    Costa, Rafael S; Hartmann, Andras; Vinga, Susana

    2016-02-10

    Kinetic models of cellular metabolism are important tools for the rational design of metabolic engineering strategies and to explain properties of complex biological systems. The recent developments in high-throughput experimental data are leading to new computational approaches for building kinetic models of metabolism. Herein, we briefly survey the available databases, standards and software tools that can be applied for kinetic models of metabolism. In addition, we give an overview about recently developed ordinary differential equations (ODE)-based kinetic models of metabolism and some of the main applications of such models are illustrated in guiding metabolic engineering design. Finally, we review the kinetic modeling approaches of large-scale networks that are emerging, discussing their main advantages, challenges and limitations. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. Genome-based Modeling and Design of Metabolic Interactions in Microbial Communities.

    Science.gov (United States)

    Mahadevan, Radhakrishnan; Henson, Michael A

    2012-01-01

    Biotechnology research is traditionally focused on individual microbial strains that are perceived to have the necessary metabolic functions, or the capability to have these functions introduced, to achieve a particular task. For many important applications, the development of such omnipotent microbes is an extremely challenging if not impossible task. By contrast, nature employs a radically different strategy based on synergistic combinations of different microbial species that collectively achieve the desired task. These natural communities have evolved to exploit the native metabolic capabilities of each species and are highly adaptive to changes in their environments. However, microbial communities have proven difficult to study due to a lack of suitable experimental and computational tools. With the advent of genome sequencing, omics technologies, bioinformatics and genome-scale modeling, researchers now have unprecedented capabilities to analyze and engineer the metabolism of microbial communities. The goal of this review is to summarize recent applications of genome-scale metabolic modeling to microbial communities. A brief introduction to lumped community models is used to motivate the need for genome-level descriptions of individual species and their metabolic interactions. The review of genome-scale models begins with static modeling approaches, which are appropriate for communities where the extracellular environment can be assumed to be time invariant or slowly varying. Dynamic extensions of the static modeling approach are described, and then applications of genome-scale models for design of synthetic microbial communities are reviewed. The review concludes with a summary of metagenomic tools for analyzing community metabolism and an outlook for future research.

  8. Dissimilatory Arsenate Reduction and In Situ Microbial Activities and Diversity in Arsenic-rich Groundwater of Chianan Plain, Southwestern Taiwan.

    Science.gov (United States)

    Das, Suvendu; Liu, Chia-Chuan; Jean, Jiin-Shuh; Liu, Tsunglin

    2016-02-01

    Although dissimilatory arsenic reduction (DAsR) has been recognized as an important process for groundwater arsenic (As) enrichment, its characterization and association with in situ microbial activities and diversity in As-rich groundwater is barely studied. In this work, we collected As-rich groundwater at depths of 23, 300, and 313 m, respectively, from Yenshui-3, Budai-Shinwen, and Budai-4 of Chianan plain, southwestern Taiwan, and conducted incubation experiments using different electron donors, acceptors, and sulfate-reducing bacterial inhibitor (tungstate) to characterize DAsR. Moreover, bacterial diversity was evaluated using 454-pyrosequencing targeting bacterial 16S rRNAs. MPN technique was used to enumerate microorganisms with different in situ metabolic functions. The results revealed that DAsR in groundwater of Chianan plain was a biotic phenomenon (as DAsR was totally inhibited by filter sterilization), enhanced by the type of electron donor (in this case, lactate enhanced DAsR but acetate and succinate did not), and limited by the availability of arsenate. In addition to oxidative recycling of As(III), dissolution of As(V)-saturated manganese and iron minerals by indigenous dissimilatory Mn(IV)- and Fe(III)-reducing bacteria, and abiotic oxidation of As(III) with Mn(IV) regenerated As(V) in the groundwater. Sulfate-respiring bacteria contributed 7.4 and 28.2 % to the observed DAsR in groundwater of Yinshui-3 and Budai-Shinwen, respectively, whereas their contribution was negligible in groundwater of Budai-4. A noticeable variation in dominant genera Acinetobacter and Bacillus was observed within the groundwater. Firmicutes dominated in highly As-rich groundwater of Yenshui-3, whereas Proteobacteria dominated in comparatively less As-rich groundwater of Budai-Shinwen and Budai 4.

  9. Metagenomic approach reveals microbial diversity and predictive microbial metabolic pathways in Yucha, a traditional Li fermented food.

    Science.gov (United States)

    Zhang, Jiachao; Wang, Xiaoru; Huo, Dongxue; Li, Wu; Hu, Qisong; Xu, Chuanbiao; Liu, Sixin; Li, Congfa

    2016-08-31

    Yucha is a typical traditional fermented food of the Li population in the Hainan province of China, and it is made up of cooked rice and fresh fish. In the present study, metagenomic approach and culture-dependent technology were applied to describe the diversity of microbiota and identify beneficial microbes in the Yucha. At the genus level, Lactobacillus was the most abundant genus (43.82% of the total reads), followed by Lactococcus, Enterococcus, Vibrio, Weissella, Pediococcus, Enterobacter, Salinivibrio, Acinetobacter, Macrococcus, Kluyvera and Clostridium; this result was confirmed by q-PCR. PCoA based on Weighted UniFrac distances showed an apparent clustering pattern for Yucha samples from different locations, and Lactobacillus sakei, Lactobacillus saniviri and Staphylococcus sciuri represented OTUs according to the major identified markers. At the microbial functional level, it was observed that there was an enrichment of metabolic functional features, including amino acid and carbohydrate metabolism, which implied that the microbial metabolism in the Yucha samples tended to be vigorous. Accordingly, we further investigated the correlation between the predominant microbes and metabolic functional features. Thirteen species of Lactobacillus (147 strains) were isolated, and Lactobacillus plantarum (60 isolates) and Lactobacillus pentosus (34 isolates) were isolated from every sample.

  10. Metabolic-flux dependent regulation of microbial physiology.

    Science.gov (United States)

    Litsios, Athanasios; Ortega, Álvaro D; Wit, Ernst C; Heinemann, Matthias

    2018-04-01

    According to the most prevalent notion, changes in cellular physiology primarily occur in response to altered environmental conditions. Yet, recent studies have shown that changes in metabolic fluxes can also trigger phenotypic changes even when environmental conditions are unchanged. This suggests that cells have mechanisms in place to assess the magnitude of metabolic fluxes, that is, the rate of metabolic reactions, and use this information to regulate their physiology. In this review, we describe recent evidence for metabolic flux-sensing and flux-dependent regulation. Furthermore, we discuss how such sensing and regulation can be mechanistically achieved and present a set of new candidates for flux-signaling metabolites. Similar to metabolic-flux sensing, we argue that cells can also sense protein translation flux. Finally, we elaborate on the advantages that flux-based regulation can confer to cells. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  11. Metabolomic applications to decipher gut microbial metabolic influence in health and disease

    Directory of Open Access Journals (Sweden)

    Francois-Pierre eMartin

    2012-04-01

    Full Text Available Dietary preferences and nutrients composition have been shown to influence human and gut microbial metabolism, which ultimately has specific effects on health and diseases’ risk. Increasingly, results from molecular biology and microbiology demonstrate the key role of the gut microbiota metabolic interface to the overall mammalian host’s health status. There is therefore raising interest in nutrition research to characterize the molecular foundations of the gut microbial mammalian cross-talk at both physiological and biochemical pathway levels. Tackling these challenges can be achieved through systems biology approaches, such as metabolomics, to underpin the highly complex metabolic exchanges between diverse biological compartments, including organs, systemic biofluids and microbial symbionts. By the development of specific biomarkers for prediction of health and disease, metabolomics is increasingly used in clinical applications as regard to disease aetiology, diagnostic stratification and potentially mechanism of action of therapeutical and nutraceutical solutions. Surprisingly, an increasing number of metabolomics investigations in pre-clinical and clinical studies based on proton nuclear magnetic resonance (1H NMR spectroscopy and mass spectrometry (MS provided compelling evidence that system wide and organ-specific biochemical processes are under the influence of gut microbial metabolism. This review aims at describing recent applications of metabolomics in clinical fields where main objective is to discern the biochemical mechanisms under the influence of the gut microbiota, with insight into gastrointestinal health and diseases diagnostics and improvement of homeostasis metabolic regulation.

  12. The Importance of Transition Metals in the Expanding Network of Microbial Metabolism in the Archean Eon

    Science.gov (United States)

    Moore, E. K.; Jelen, B. I.; Giovannelli, D.; Prabhu, A.; Raanan, H.; Falkowski, P. G.

    2017-12-01

    Deep time changes in Earth surface redox conditions, particularly due to global oxygenation, has impacted the availability of different metals and substrates that are central in biology. Oxidoreductase proteins are molecular nanomachines responsible for all biological electron transfer processes across the tree of life. These enzymes largely contain transition metals in their active sites. Microbial metabolic pathways form a global network of electron transfer, which expanded throughout the Archean eon. Older metabolisms (sulfur reduction, methanogenesis, anoxygenic photosynthesis) accessed negative redox potentials, while later evolving metabolisms (oxygenic photosynthesis, nitrification/denitrification, aerobic respiration) accessed positive redox potentials. The incorporation of different transition metals facilitated biological innovation and the expansion of the network of microbial metabolism. Network analysis was used to examine the connections between microbial taxa, metabolic pathways, crucial metallocofactors, and substrates in deep time by incorporating biosignatures preserved in the geologic record. Nitrogen fixation and aerobic respiration have the highest level of betweenness among metabolisms in the network, indicating that the oldest metabolisms are not the most central. Fe has by far the highest betweenness among metals. Clustering analysis largely separates High Metal Bacteria (HMB), Low Metal Bacteria (LMB), and Archaea showing that simple un-weighted links between taxa, metabolism, and metals have phylogenetic relevance. On average HMB have the highest betweenness among taxa, followed by Archaea and LMB. There is a correlation between the number of metallocofactors and metabolic pathways in representative bacterial taxa, but Archaea do not follow this trend. In many cases older and more recently evolved metabolisms were clustered together supporting previous findings that proliferation of metabolic pathways is not necessarily chronological.

  13. In situ examination of microbial populations in a model drinking water distribution system

    DEFF Research Database (Denmark)

    Martiny, Adam Camillo; Nielsen, Alex Toftgaard; Arvin, Erik

    2002-01-01

    A flow cell set-up was used as a model drinking water distribution system to analyze the in situ microbial population. Biofilm growth was followed by transmission light microscopy for 81 days and showed a biofilm consisting of microcolonies separated by a monolayer of cells. Protozoans (ciliates...... of a mixed population of α- and β-Proteobacteria. 65 strains from the inlet water and 20 from the biofilm were isolated on R2A agar plates and sorted into groups with amplified rDNA restriction analysis. The 16S rDNA gene was sequenced for representatives of the abundant groups. A phylogenetic analysis...... revealed that the majority of the isolated strains from the bulk water and biofilm were affiliated to the family of Comamonadaceae in the β-lineage of Proteobacteria. The majority of the strains from the α-lineage were affiliated to the family of Sphingomonadaceae. We were unable to detect any strains from...

  14. Photochemical alteration of organic carbon draining permafrost soils shifts microbial metabolic pathways and stimulates respiration.

    Science.gov (United States)

    Ward, Collin P; Nalven, Sarah G; Crump, Byron C; Kling, George W; Cory, Rose M

    2017-10-03

    In sunlit waters, photochemical alteration of dissolved organic carbon (DOC) impacts the microbial respiration of DOC to CO 2 . This coupled photochemical and biological degradation of DOC is especially critical for carbon budgets in the Arctic, where thawing permafrost soils increase opportunities for DOC oxidation to CO 2 in surface waters, thereby reinforcing global warming. Here we show how and why sunlight exposure impacts microbial respiration of DOC draining permafrost soils. Sunlight significantly increases or decreases microbial respiration of DOC depending on whether photo-alteration produces or removes molecules that native microbial communities used prior to light exposure. Using high-resolution chemical and microbial approaches, we show that rates of DOC processing by microbes are likely governed by a combination of the abundance and lability of DOC exported from land to water and produced by photochemical processes, and the capacity and timescale that microbial communities have to adapt to metabolize photo-altered DOC.The role of dissolved organic carbon (DOC) photo-alteration in the microbial respiration of DOC to CO 2 is unclear. Here, the authors show that the impact of this mechanism depends on whether photo-alteration of DOC produces or removes molecules used by native microbial communities prior to light exposure.

  15. In situ formation of graphene layers on graphite surfaces for efficient anodes of microbial fuel cells.

    Science.gov (United States)

    Tang, Jiahuan; Chen, Shanshan; Yuan, Yong; Cai, Xixi; Zhou, Shungui

    2015-09-15

    Graphene can be used to improve the performance of the anode in a microbial fuel cell (MFC) due to its good biocompatibility, high electrical conductivity and large surface area. However, the chemical production and modification of the graphene on the anode are environmentally hazardous because of the use of various harmful chemicals. This study reports a novel method based on the electrochemical exfoliation of a graphite plate (GP) for the in situ formation of graphene layers on the surface of a graphite electrode. When the resultant graphene-layer-based graphite plate electrode (GL/GP) was used as an anode in an MFC, a maximum power density of 0.67 ± 0.034 W/m(2) was achieved. This value corresponds to 1.72-, 1.56- and 1.26-times the maximum power densities of the original GP, exfoliated-graphene-modified GP (EG/GP) and chemically-reduced-graphene-modified GP (rGO/GP) anodes, respectively. Electrochemical measurements revealed that the high performance of the GL/GP anode was attributable to its macroporous structure, improved electron transfer and high electrochemical capacitance. The results demonstrated that the proposed method is a facile and environmentally friendly synthesis technique for the fabrication of high-performance graphene-based electrodes for use in microbial energy harvesting. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. Facile in-situ fabrication of graphene/riboflavin electrode for microbial fuel cells

    International Nuclear Information System (INIS)

    Wang, Qian-Qian; Wu, Xia-Yuan; Yu, Yang-Yang; Sun, De-Zhen; Jia, Hong-Hua; Yong, Yang-Chun

    2017-01-01

    A novel graphene/riboflavin (RF) composite electrode was developed and its potential application as microbial fuel cell (MFC) anode was demonstrated. Graphene layers were first grown on the surface of graphite electrode by a one-step in-situ electrochemical exfoliation approach. Then, noncovalent functionalization of the graphene layers with RF was achieved by a simple spontaneous adsorption process. The graphene/RF electrode was extensively characterized by transmission electron microscopy, Fourier transform infrared spectroscopy, Raman analysis, and cyclic voltammetry analysis. Remarkably, when applied as the anode of Shewanella oneidensis MR-1 inoculated MFCs, the graphene/RF electrode significantly decreased charge transfer over-potential and enhanced cell attachment, which in turn delivered about 5.3- and 2.5-fold higher power output, when compared with that produced by the bare graphite paper electrode and graphene electrode, respectively. These results demonstrated that electron shuttle immobilization on the electrode surface could be a promising and practical strategy for improving the performance of microbial electrochemical systems.

  17. In Situ Microbial Community Control of the Stability of Bio-reduced Uranium

    International Nuclear Information System (INIS)

    Baldwin, Brett R.; Peacock, Aaron D.; Resch, Charles T.; Arntzen, Evan; Smithgall, Amanda N.; Pfiffner, Susan; Gan, M.; McKinley, James P.; Long, Philip E.; White, David C.

    2008-01-01

    In aerobic aquifers typical of many Department of Energy (DOE) legacy waste sites, uranium is present in the oxidized U(VI) form which is more soluble and thus more mobile. Field experiments at the Old Rifle UMTRA site have demonstrated that biostimulation by electron donor addition (acetate) promotes biological U(VI) reduction (2). However, U(VI) reduction is reversible and oxidative dissolution of precipitated U(IV) after the cessation of electron donor addition remains a critical issue for the application of biostimulation as a treatment technology. Despite the potential for oxidative dissolution, field experiments at the Old Rifle site have shown that rapid reoxidation of bio-reduced uranium does not occur and U(VI) concentrations can remain at approximately 20% of background levels for more than one year. The extent of post-amendment U(VI) removal and the maintenance of bioreduced uranium may result from many factors including U(VI) sorption to iron-containing mineral phases, generation of H2S or FeS0.9, or the preferential sorption of U(VI) by microbial cells or biopolymers, but the processes controlling the reduction and in situ reoxidation rates are not known. To investigate the role of microbial community composition in the maintenance of bioreduced uranium, in-well sediment incubators (ISIs) were developed allowing field deployment of amended and native sediments during on-going experiments at the site. Field deployment of the ISIs allows expedient interrogation of microbial community response to field environmental perturbations and varying geochemical conditions.

  18. In Situ Microbial Community Control of the Stability of Bio-reduced Uranium

    Energy Technology Data Exchange (ETDEWEB)

    Baldwin, Brett, R.; Peacock, Aaron, D.; Resch, Charles, T.; Arntzen, Evan; Smithgall, Amanda, N.; Pfiffner, Susan; Gan, M.; McKinley, James, P.; Long, Philip, E.; White, David, C.

    2008-03-28

    In aerobic aquifers typical of many Department of Energy (DOE) legacy waste sites, uranium is present in the oxidized U(VI) form which is more soluble and thus more mobile. Field experiments at the Old Rifle UMTRA site have demonstrated that biostimulation by electron donor addition (acetate) promotes biological U(VI) reduction (2). However, U(VI) reduction is reversible and oxidative dissolution of precipitated U(IV) after the cessation of electron donor addition remains a critical issue for the application of biostimulation as a treatment technology. Despite the potential for oxidative dissolution, field experiments at the Old Rifle site have shown that rapid reoxidation of bio-reduced uranium does not occur and U(VI) concentrations can remain at approximately 20% of background levels for more than one year. The extent of post-amendment U(VI) removal and the maintenance of bioreduced uranium may result from many factors including U(VI) sorption to iron-containing mineral phases, generation of H2S or FeS0.9, or the preferential sorption of U(VI) by microbial cells or biopolymers, but the processes controlling the reduction and in situ reoxidation rates are not known. To investigate the role of microbial community composition in the maintenance of bioreduced uranium, in-well sediment incubators (ISIs) were developed allowing field deployment of amended and native sediments during on-going experiments at the site. Field deployment of the ISIs allows expedient interrogation of microbial community response to field environmental perturbations and varying geochemical conditions.

  19. Microbial physiology-based model of ethanol metabolism in subsurface sediments

    Science.gov (United States)

    Jin, Qusheng; Roden, Eric E.

    2011-07-01

    A biogeochemical reaction model was developed based on microbial physiology to simulate ethanol metabolism and its influence on the chemistry of anoxic subsurface environments. The model accounts for potential microbial metabolisms that degrade ethanol, including those that oxidize ethanol directly or syntrophically by reducing different electron acceptors. Out of the potential metabolisms, those that are active in the environment can be inferred by fitting the model to experimental observations. This approach was applied to a batch sediment slurry experiment that examined ethanol metabolism in uranium-contaminated aquifer sediments from Area 2 at the U.S. Department of Energy Field Research Center in Oak Ridge, TN. According to the simulation results, complete ethanol oxidation by denitrification, incomplete ethanol oxidation by ferric iron reduction, ethanol fermentation to acetate and H 2, hydrogenotrophic sulfate reduction, and acetoclastic methanogenesis: all contributed significantly to the degradation of ethanol in the aquifer sediments. The assemblage of the active metabolisms provides a frame work to explore how ethanol amendment impacts the chemistry of the environment, including the occurrence and levels of uranium. The results can also be applied to explore how diverse microbial metabolisms impact the progress and efficacy of bioremediation strategies.

  20. Metabolic engineering of microbial competitive advantage for industrial fermentation processes.

    Science.gov (United States)

    Shaw, A Joe; Lam, Felix H; Hamilton, Maureen; Consiglio, Andrew; MacEwen, Kyle; Brevnova, Elena E; Greenhagen, Emily; LaTouf, W Greg; South, Colin R; van Dijken, Hans; Stephanopoulos, Gregory

    2016-08-05

    Microbial contamination is an obstacle to widespread production of advanced biofuels and chemicals. Current practices such as process sterilization or antibiotic dosage carry excess costs or encourage the development of antibiotic resistance. We engineered Escherichia coli to assimilate melamine, a xenobiotic compound containing nitrogen. After adaptive laboratory evolution to improve pathway efficiency, the engineered strain rapidly outcompeted a control strain when melamine was supplied as the nitrogen source. We additionally engineered the yeasts Saccharomyces cerevisiae and Yarrowia lipolytica to assimilate nitrogen from cyanamide and phosphorus from potassium phosphite, and they outcompeted contaminating strains in several low-cost feedstocks. Supplying essential growth nutrients through xenobiotic or ecologically rare chemicals provides microbial competitive advantage with minimal external risks, given that engineered biocatalysts only have improved fitness within the customized fermentation environment. Copyright © 2016, American Association for the Advancement of Science.

  1. Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism

    DEFF Research Database (Denmark)

    Broman, Elias; Sjöstedt, Johanna; Pinhassi, Jarone

    2017-01-01

    . In particular, the intermediate site sediments responded differently upon oxygenation compared to the anoxic and oxic site sediments. This included a microbial community composition with more habitat generalists, lower amounts of RNA transcripts attributed to methane oxidation, and a reduced rate of organic...... efforts, depend largely on the oxygenation history of sites. Furthermore, it was shown that re-oxygenation efforts to remediate dead zones could ultimately be facilitated by in situ microbial molecular mechanisms involved in removal of toxic H2S and the potent greenhouse gas methane....

  2. Microbial and Chemical Enhancement of In-Situ Carbon Mineralization in Geological Formation

    Energy Technology Data Exchange (ETDEWEB)

    Matter, J.; Chandran, K.

    2013-05-31

    Predictions of global energy usage suggest a continued increase in carbon emissions and rising concentrations of CO{sub 2} in the atmosphere unless major changes are made to the way energy is produced and used. Various carbon capture and storage (CCS) technologies are currently being developed, but unfortunately little is known regarding the fundamental characteristics of CO{sub 2}-mineral reactions to allow a viable in-situ carbon mineralization that would provide the most permanent and safe storage of geologically-injected CO{sub 2}. The ultimate goal of this research project was to develop a microbial and chemical enhancement scheme for in-situ carbon mineralization in geologic formations in order to achieve long-term stability of injected CO{sub 2}. Thermodynamic and kinetic studies of CO{sub 2}-mineral-brine systems were systematically performed to develop the in-situ mineral carbonation process that utilizes organic acids produced by a microbial reactor. The major participants in the project are three faculty members and their graduate and undergraduate students at the School of Engineering and Applied Science and at the Lamont-Doherty Earth Observatory at Columbia University: Alissa Park in Earth and Environmental Engineering & Chemical Engineering (PI), Juerg Matter in Earth and Environmental Science (Co-PI), and Kartik Chandran in Earth and Environmental Engineering (Co-PI). Two graduate students, Huangjing Zhao and Edris Taher, were trained as a part of this project as well as a number of graduate students and undergraduate students who participated part-time. Edris Taher received his MS degree in 2012 and Huangjing Zhao will defend his PhD on Jan. 15th, 2014. The interdisciplinary training provided by this project was valuable to those students who are entering into the workforce in the United States. Furthermore, the findings from this study were and will be published in referred journals to disseminate the results. The list of the papers is given at

  3. Detection of Metabolism Function of Microbial Community of Corpses by Biolog-Eco Method.

    Science.gov (United States)

    Jiang, X Y; Wang, J F; Zhu, G H; Ma, M Y; Lai, Y; Zhou, H

    2016-06-01

    To detect the changes of microbial community functional diversity of corpses with different postmortem interval (PMI) and to evaluate forensic application value for estimating PMI. The cultivation of microbial community from the anal swabs of a Sus scrofa and a human corpse placed in field environment from 0 to 240 h after death was performed using the Biolog-Eco Microplate and the variations of the absorbance values were also monitored. Combined with the technology of forensic pathology and flies succession, the metabolic characteristics and changes of microbial community on the decomposed corpse under natural environment were also observed. The diversity of microbial metabolism function was found to be negatively correlated with the number of maggots in the corpses. The freezing processing had the greatest impact on average well color development value at 0 h and the impact almost disappeared after 48 h. The diversity of microbial metabolism of the samples became relatively unstable after 192 h. The principal component analysis showed that 31 carbon sources could be consolidated for 5 principal components (accumulative contribution ratio >90%).The carbon source tsquare-analysis showed that N -acetyl- D -glucosamine and L -serine were the dominant carbon sources for estimating the PMI (0=240 h) of the Sus scrofa and human corpse. The Biolog-Eco method can be used to reveal the metabolic differences of the carbon resources utilization of the microbial community on the corpses during 0-240 h after death, which could provide a new basis for estimating the PMI. Copyright© by the Editorial Department of Journal of Forensic Medicine

  4. Use of genome-scale microbial models for metabolic engineering

    DEFF Research Database (Denmark)

    Patil, Kiran Raosaheb; Åkesson, M.; Nielsen, Jens

    2004-01-01

    Metabolic engineering serves as an integrated approach to design new cell factories by providing rational design procedures and valuable mathematical and experimental tools. Mathematical models have an important role for phenotypic analysis, but can also be used for the design of optimal metaboli...... network structures. The major challenge for metabolic engineering in the post-genomic era is to broaden its design methodologies to incorporate genome-scale biological data. Genome-scale stoichiometric models of microorganisms represent a first step in this direction....

  5. Genome-resolved metagenomics reveals that sulfur metabolism dominates the microbial ecology of rising hydrothermal plumes

    Science.gov (United States)

    Anantharaman, K.; Breier, J. A., Jr.; Jain, S.; Reed, D. C.; Dick, G.

    2015-12-01

    Deep-sea hydrothermal plumes occur when hot fluids from hydrothermal vents replete with chemically reduced elements and compounds like sulfide, methane, hydrogen, ammonia, iron and manganese mix with cold, oxic seawater. Chemosynthetic microbes use these reduced chemicals to power primary production and are pervasive throughout the deep sea, even at sites far removed from hydrothermal vents. Although neutrally-buoyant hydrothermal plumes have been well-studied, rising hydrothermal plumes have received little attention even though they represent an important interface in the deep-sea where microbial metabolism and particle formation processes control the transformation of important elements and impact global biogeochemical cycles. In this study, we used genome-resolved metagenomic analyses and thermodynamic-bioenergetic modeling to study the microbial ecology of rising hydrothermal plumes at five different hydrothermal vents spanning a range of geochemical gradients at the Eastern Lau Spreading Center (ELSC) in the Western Pacific Ocean. Our analyses show that differences in the geochemistry of hydrothermal vents do not manifest in microbial diversity and community composition, both of which display only minor variance across ELSC hydrothermal plumes. Microbial metabolism is dominated by oxidation of reduced sulfur species and supports a diversity of bacteria, archaea and viruses that provide intriguing insights into metabolic plasticity and virus-mediated horizontal gene transfer in the microbial community. The manifestation of sulfur oxidation genes in hydrogen and methane oxidizing organisms hints at metabolic opportunism in deep-sea microbes that would enable them to respond to varying redox conditions in hydrothermal plumes. Finally, we infer that the abundance, diversity and metabolic versatility of microbes associated with sulfur oxidation impart functional redundancy that could allow it to persist in the dynamic settings of hydrothermal plumes.

  6. Aerobic microbial metabolism of condensed thiophenes found in petroleum

    International Nuclear Information System (INIS)

    Kropp, K. G.

    1997-01-01

    The aerobic microbial degradation of 21 condensed thiophenes found in petroleum or synthetic fuels have been studied, motivated by recent research which showed that resistance to biodegradation increases with increasing methyl-substitution. The specific objective was to identify metabolites in pure cultures of aromatic hydrocarbon-degrading Pseudomonas spp. incubated in mineral medium in the presence of an aromatic growth substrate and a condensed thiophene. Over 80 metabolites of the condensed thiophenes were identified using gas chromatography analysis with an atomic emission detector. Among the metabolites identified were sulfoxides, sulfones, hydroxy- and carboxyl-substituted benzothiophenes, hydroxy-substituted dibenzothiophenes, substituted benzothiophene-2,3-diones, and 3-hydroxy-2-formylbenzothiophenes

  7. Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0.

    Directory of Open Access Journals (Sweden)

    Brian R Granger

    2016-04-01

    Full Text Available The complexity of metabolic networks in microbial communities poses an unresolved visualization and interpretation challenge. We address this challenge in the newly expanded version of a software tool for the analysis of biological networks, VisANT 5.0. We focus in particular on facilitating the visual exploration of metabolic interaction between microbes in a community, e.g. as predicted by COMETS (Computation of Microbial Ecosystems in Time and Space, a dynamic stoichiometric modeling framework. Using VisANT's unique metagraph implementation, we show how one can use VisANT 5.0 to explore different time-dependent ecosystem-level metabolic networks. In particular, we analyze the metabolic interaction network between two bacteria previously shown to display an obligate cross-feeding interdependency. In addition, we illustrate how a putative minimal gut microbiome community could be represented in our framework, making it possible to highlight interactions across multiple coexisting species. We envisage that the "symbiotic layout" of VisANT can be employed as a general tool for the analysis of metabolism in complex microbial communities as well as heterogeneous human tissues. VisANT is freely available at: http://visant.bu.edu and COMETS at http://comets.bu.edu.

  8. Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0.

    Science.gov (United States)

    Granger, Brian R; Chang, Yi-Chien; Wang, Yan; DeLisi, Charles; Segrè, Daniel; Hu, Zhenjun

    2016-04-01

    The complexity of metabolic networks in microbial communities poses an unresolved visualization and interpretation challenge. We address this challenge in the newly expanded version of a software tool for the analysis of biological networks, VisANT 5.0. We focus in particular on facilitating the visual exploration of metabolic interaction between microbes in a community, e.g. as predicted by COMETS (Computation of Microbial Ecosystems in Time and Space), a dynamic stoichiometric modeling framework. Using VisANT's unique metagraph implementation, we show how one can use VisANT 5.0 to explore different time-dependent ecosystem-level metabolic networks. In particular, we analyze the metabolic interaction network between two bacteria previously shown to display an obligate cross-feeding interdependency. In addition, we illustrate how a putative minimal gut microbiome community could be represented in our framework, making it possible to highlight interactions across multiple coexisting species. We envisage that the "symbiotic layout" of VisANT can be employed as a general tool for the analysis of metabolism in complex microbial communities as well as heterogeneous human tissues. VisANT is freely available at: http://visant.bu.edu and COMETS at http://comets.bu.edu.

  9. Functional Gene Diversity and Metabolic Potential of the Microbial Community in an Estuary-Shelf Environment

    Directory of Open Access Journals (Sweden)

    Yu Wang

    2017-06-01

    Full Text Available Microbes play crucial roles in various biogeochemical processes in the ocean, including carbon (C, nitrogen (N, and phosphorus (P cycling. Functional gene diversity and the structure of the microbial community determines its metabolic potential and therefore its ecological function in the marine ecosystem. However, little is known about the functional gene composition and metabolic potential of bacterioplankton in estuary areas. The East China Sea (ECS is a dynamic marginal ecosystem in the western Pacific Ocean that is mainly affected by input from the Changjiang River and the Kuroshio Current. Here, using a high-throughput functional gene microarray (GeoChip, we analyzed the functional gene diversity, composition, structure, and metabolic potential of microbial assemblages in different ECS water masses. Four water masses determined by temperature and salinity relationship showed different patterns of functional gene diversity and composition. Generally, functional gene diversity [Shannon–Weaner’s H and reciprocal of Simpson’s 1/(1-D] in the surface water masses was higher than that in the bottom water masses. The different presence and proportion of functional genes involved in C, N, and P cycling among the bacteria of the different water masses showed different metabolic preferences of the microbial populations in the ECS. Genes involved in starch metabolism (amyA and nplT showed higher proportion in microbial communities of the surface water masses than of the bottom water masses. In contrast, a higher proportion of genes involved in chitin degradation was observed in microorganisms of the bottom water masses. Moreover, we found a higher proportion of nitrogen fixation (nifH, transformation of hydroxylamine to nitrite (hao and ammonification (gdh genes in the microbial communities of the bottom water masses compared with those of the surface water masses. The spatial variation of microbial functional genes was significantly correlated

  10. Rumen microbial communities influence metabolic phenotypes in lambs

    DEFF Research Database (Denmark)

    Morgavi, Diego P.; Rahahao-Paris, Estelle; Popova, Milka

    2015-01-01

    and the metabolic phenotype of lambs for identifying host-microbe associations and potential biomarkers of digestive functions. Twin lambs, separated in two groups after birth were exposed to practices (isolation and gavage with rumen fluid with protozoa or protozoa-depleted) that differentially restricted...

  11. Microbial arsenic metabolism: New twists on an old poison

    Science.gov (United States)

    Stolz, J.F.; Basu, P.; Oremland, R.S.

    2010-01-01

    Phylogenetically diverse microorganisms metabolize arsenic despite its toxicity and are part of its robust iogeochemical cycle. Respiratory arsenate reductase is a reversible enzyme, functioning in some microbes as an arsenate reductase but in others as an arsenite oxidase. As(III) can serve as an electron donor for anoxygenic photolithoautotrophy and chemolithoautotrophy. Organoarsenicals, such as the feed additive roxarsone, can be used as a source of energy, releasing inorganic arsenic.

  12. Characterization and Modeling Of Microbial Carbon Metabolism In Thawing Permafrost

    Science.gov (United States)

    Graham, D. E.; Phelps, T. J.; Xu, X.; Carroll, S.; Jagadamma, S.; Shakya, M.; Thornton, P. E.; Elias, D. A.

    2012-12-01

    Increased annual temperatures in the Arctic are warming the surface and subsurface, resulting in thawing permafrost. Thawing exposes large pools of buried organic carbon to microbial degradation, increasing greenhouse gas generation and emission. Most global-scale land-surface models lack depth-dependent representations of carbon conversion and GHG transport; therefore they do not adequately describe permafrost thawing or microbial mineralization processes. The current work was performed to determine how permafrost thawing at moderately elevated temperatures and anoxic conditions would affect CO2 and CH4 generation, while parameterizing depth-dependent GHG production processes with respect to temperature and pH in biogeochemical models. These enhancements will improve the accuracy of GHG emission predictions and identify key biochemical and geochemical processes for further refinement. Three core samples were obtained from discontinuous permafrost terrain in Fairbanks, AK with a mean annual temperature of -3.3 °C. Each core was sectioned into surface/near surface (0-0.8 m), active layer (0.8-1.6 m), and permafrost (1.6-2.2 m) horizons, which were homogenized for physico-chemical characterization and microcosm construction. Surface samples had low pH values (6.0), low water content (18% by weight), low organic carbon (0.8%), and high C:N ratio (43). Active layer samples had higher pH values (6.4), higher water content (34%), more organic carbon (1.4%) and a lower C:N ratio (24). Permafrost samples had the highest pH (6.5), highest water content (46%), high organic carbon (2.5%) and the lowest C:N ratio (19). Most organic carbon was quantified as labile or intermediate pool versus stable pool in each sample, and all samples had low amounts of carbonate. Surface layer microcosms, containing 20 g sediment in septum-sealed vials, were incubated under oxic conditions, while similar active and permafrost layer samples were anoxic. These microcosms were incubated at -2

  13. Self-potential and Complex Conductivity Monitoring of In Situ Hydrocarbon Remediation in Microbial Fuel Cell

    Science.gov (United States)

    Zhang, C.; Revil, A.; Ren, Z.; Karaoulis, M.; Mendonca, C. A.

    2013-12-01

    Petroleum hydrocarbon contamination of soil and groundwater in both non-aqueous phase liquid and dissolved forms generated from spills and leaks is a wide spread environmental issue. Traditional cleanup of hydrocarbon contamination in soils and ground water using physical, chemical, and biological remedial techniques is often expensive and ineffective. Recent studies show that the microbial fuel cell (MFC) can simultaneously enhance biodegradation of hydrocarbons in soil and groundwater and yield electricity. Non-invasive geophysical techniques such as self-potential (SP) and complex conductivity (induced polarization) have shown the potential to detect and characterize the nature of electron transport mechanism of in situ bioremediation of organic contamination plumes. In this study, we deployed both SP and complex conductivity in lab scale MFCs to monitor time-laps geophysical response of degradation of hydrocarbons by MFC. Two different sizes of MFC reactors were used in this study (DI=15 cm cylinder reactor and 94.5cm x 43.5 cm rectangle reactor), and the initial hydrocarbon concentration is 15 g diesel/kg soil. SP and complex conductivity measurements were measured using non-polarizing Ag/AgCl electrodes. Sensitivity study was also performed using COMSOL Multiphysics to test different electrode configurations. The SP measurements showed stronger anomalies adjacent to the MFC than locations afar, and both real and imaginary parts of complex conductivity are greater in areas close to MFC than areas further away and control samples without MFC. The joint use of SP and complex conductivity could in situ evaluate the dynamic changes of electrochemical parameters during this bioremediation process at spatiotemporal scales unachievable with traditional sampling methods. The joint inversion of these two methods to evaluate the efficiency of MFC enhanced hydrocarbon remediation in the subsurface.

  14. Genome-centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion.

    Science.gov (United States)

    Vanwonterghem, Inka; Jensen, Paul D; Rabaey, Korneel; Tyson, Gene W

    2016-09-01

    Our understanding of the complex interconnected processes performed by microbial communities is hindered by our inability to culture the vast majority of microorganisms. Metagenomics provides a way to bypass this cultivation bottleneck and recent advances in this field now allow us to recover a growing number of genomes representing previously uncultured populations from increasingly complex environments. In this study, a temporal genome-centric metagenomic analysis was performed of lab-scale anaerobic digesters that host complex microbial communities fulfilling a series of interlinked metabolic processes to enable the conversion of cellulose to methane. In total, 101 population genomes that were moderate to near-complete were recovered based primarily on differential coverage binning. These populations span 19 phyla, represent mostly novel species and expand the genomic coverage of several rare phyla. Classification into functional guilds based on their metabolic potential revealed metabolic networks with a high level of functional redundancy as well as niche specialization, and allowed us to identify potential roles such as hydrolytic specialists for several rare, uncultured populations. Genome-centric analyses of complex microbial communities across diverse environments provide the key to understanding the phylogenetic and metabolic diversity of these interactive communities. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

  15. Genome-driven evolutionary game theory helps understand the rise of metabolic interdependencies in microbial communities.

    Science.gov (United States)

    Zomorrodi, Ali R; Segrè, Daniel

    2017-11-16

    Metabolite exchanges in microbial communities give rise to ecological interactions that govern ecosystem diversity and stability. It is unclear, however, how the rise of these interactions varies across metabolites and organisms. Here we address this question by integrating genome-scale models of metabolism with evolutionary game theory. Specifically, we use microbial fitness values estimated by metabolic models to infer evolutionarily stable interactions in multi-species microbial "games". We first validate our approach using a well-characterized yeast cheater-cooperator system. We next perform over 80,000 in silico experiments to infer how metabolic interdependencies mediated by amino acid leakage in Escherichia coli vary across 189 amino acid pairs. While most pairs display shared patterns of inter-species interactions, multiple deviations are caused by pleiotropy and epistasis in metabolism. Furthermore, simulated invasion experiments reveal possible paths to obligate cross-feeding. Our study provides genomically driven insight into the rise of ecological interactions, with implications for microbiome research and synthetic ecology.

  16. Summer investigations into the metabolic diversity of the microbial world

    Energy Technology Data Exchange (ETDEWEB)

    Breznak, J.; Dworkin, M.

    1993-05-17

    The philosophy of the course described here is to underscore the essence of microbiology which is diversity>: diversity of morphology and cellular development, behavior, and metabolic and physiological functions. Emphasis is on microbes other than those customarily covered in conventional microbiology courses and includes: the archaebacteria, extremophiles, and array of obligate anaerobes, various phototrophs, and those microbes exhibiting complex developmental cycles. Also included are microbes carrying out a variety of transformations of organic and inorganic compounds, as well as those which normally occur in symbiotic association with other microbes or with higher forms of life.

  17. Production of microbial rhamnolipid by Pseudomonas aeruginosa MM1011 for ex situ enhanced oil recovery.

    Science.gov (United States)

    Amani, Hossein; Müller, Markus Michael; Syldatk, Christoph; Hausmann, Rudolf

    2013-07-01

    Recently, several investigations have been carried out on the in situ bacteria flooding, but the ex situ biosurfactant production and addition to the sand pack as agents for microbial enhanced oil recovery (MEOR) has little been studied. In order to develop suitable technology for ex situ MEOR processes, it is essential to carry out tests about it. Therefore, this work tries to fill the gap. The intention of this study was to investigate whether the rhamnolipid mix could be produced in high enough quantities for enhanced oil recovery in the laboratory scale and prove its potential use as an effective material for field application. In this work, the ability of Pseudomonas aeruginosa MM1011 to grow and produce rhamnolipid on sunflower as sole carbon source under nitrogen limitation was shown. The production of Rha-C10-C10 and Rha2-C10-C10 was confirmed by thin-layer chromatography and high-performance liquid chromatography analysis. The rhamnolipid mixture obtained was able to reduce the surface and interfacial tension of water to 26 and 2 mN/m, respectively. The critical micelle concentration was 120 mg/L. Maximum rhamnolipid production reached to about 0.7 g/L in a shake flask. The yield of rhamnolipid per biomass (Y RL/x ), rhamnolipid per sunflower oil (Y RL/s ), and the biomass per sunflower oil (Y x/s ) for shake flask were obtained about 0.01, 0.0035, and 0.035 g g(-1), respectively. The stability of the rhamnolipid at different salinities, pH and temperature, and also, its emulsifying activity has been investigated. It is an effective surfactant at very low concentrations over a wide range of temperatures, pHs, and salt concentrations, and it also has the ability to emulsify oil, which is essential for enhanced oil recovery. With 120 mg/L rhamnolipid, 27 % of original oil in place was recovered after water flooding from a sand pack. This result not only suggests rhamnolipids as appropriate model biosurfactants for MEOR, but it even shows the potential as a

  18. Identification of bacteria used for microbial enhanced oil recovery process by fluorescence in situ hybridization technique

    Energy Technology Data Exchange (ETDEWEB)

    Fujiwara, K.; Tanaka, S.; Otsuka, M. [Kansai Research Institute, Kyoto (Japan). Lifescience Lab.; Yonebayashi, H. [Japan National Oil Corp., Chiba (Japan). Tech. Research Center; Enomoto, H. [Tohoku University, Sendai (Japan). Dept. of Geoscience and Tech.

    2000-01-01

    A fluorescence in situ hybridization (FISH) technique using 16S rRNA-targeted oligonucleotide probes was developed for rapid detection of microorganisms for use in the microbial enhancement of oil recovery (MEOR) process. Two microorganisms, Enterobacter cloacae TRC-322 and Bacillus licheniformis TRC-18-2-a, were selected from a collection of Enterobacter sp. and Bacillus sp. which were screened in previous studies as candidate microorganisms for injection, and were used for this experiment. Oligonucleotide probes, design based on specific sequences in the 16S rRNA gene were labeled with either fluorescein isothiocyanate (FITC), or 6-car-boxy-X-rhodamine (ROX), and were allowed to hybridize with fixed cells of the two microorganisms noted above. The fluorescence signal emitted from each microorganism cells could clearly be detected by an epifluorescence microscope. Moreover, E. cloacae TRC-322 and B, licheniformis TRC-18-2-a, suspended in actual reservoir brine, including inorganic salts, oil and aboriginal cells of the reservoir brine, could be detected directly by this hybridization method, without the need for cultivation and isolation. (author)

  19. In situ analysis of microbial reduction of a nitrate plume in Opalinus clay

    International Nuclear Information System (INIS)

    Bleyen, N.; Smets, S.; Valcke, E.; Albrecht, A.; De Canniere, P.; Schwyn, B.; Wittebroodt, C.

    2012-01-01

    Document available in extended abstract form only. In several countries, such as Belgium, France and Switzerland, clay formations are foreseen as the host rock for geological disposal of bituminized low-level and intermediate-level long-lived radioactive waste. Suitable clay formations exhibit favorable hydro-mechanical and geochemical characteristics, which are expected to retard the migration of leached radionuclides. Along with radionuclides, certain classes of bituminized radioactive waste may also contain high concentrations of NaNO 3 , dispersed into the hydrophobic bitumen matrix used to stabilize the waste. During and after saturation of the disposal gallery, this bituminized waste will start to take up water due to osmosis, resulting in the leaching of significant amounts of NaNO 3 and soluble organic bitumen degradation products (BDP) into the clay pore water. This nitrate plume could cause several geochemical and biochemical processes in the clay surrounding the waste disposal gallery, potentially affecting the barrier function of the host rock. To study these processes, an in situ experiment in the Opalinus Clay, named the Bitumen-Nitrate-Clay interaction (BN) experiment, is being performed at the Mont Terri Rock Laboratory (CH). The experiment consists of a vertical borehole rigged with a downhole equipment containing three packed-off intervals, each lined with a cylindrical sintered stainless steel filter screen to allow contact with the surrounding clay. Prior to the start of the tests, the intervals were injected with an artificial Opalinus Clay pore water, containing all major ions at pore water concentrations at Mont Terri, but no organic matter, and were equilibrated with the surrounding clay for ∼8 months. To ensure a continuous water flow during the tests, each interval is connected to a stainless steel water circulation unit, equipped with water sampling containers, circulation pumps and flow meters. In addition, to continuously monitor the

  20. A Status Report on the Global Research in Microbial Metabolic Engineering

    Energy Technology Data Exchange (ETDEWEB)

    Joe, Min Ho; Lim, Sang Yong; Kim, Dong Ho

    2008-09-15

    Biotechnology industry is now a global 'Mega-Trend' and metabolic engineering technology has important role is this area. Therefore, many countries has made efforts in this field to produce top value added bio-products efficiently using microorganisms. It has been applied to increase the production of chemicals that are already produced by the host organism, to produce desired chemical substances from less expensive feedstock, and to generate products that are new to the host organism. Recent experimental advances, the so-called '-omics' technologies, mainly functional genomics, proteomics and metabolomics, have enabled wholesale generation of new genomic, transcriptomic, proteomic, and metabolomic data. This report provides the insights of the integrated view of metabolism generated by metabolic engineering for biotechnological applications of microbial metabolic engineering.

  1. A Status Report on the Global Research in Microbial Metabolic Engineering

    International Nuclear Information System (INIS)

    Joe, Min Ho; Lim, Sang Yong; Kim, Dong Ho

    2008-09-01

    Biotechnology industry is now a global 'Mega-Trend' and metabolic engineering technology has important role is this area. Therefore, many countries has made efforts in this field to produce top value added bio-products efficiently using microorganisms. It has been applied to increase the production of chemicals that are already produced by the host organism, to produce desired chemical substances from less expensive feedstock, and to generate products that are new to the host organism. Recent experimental advances, the so-called '-omics' technologies, mainly functional genomics, proteomics and metabolomics, have enabled wholesale generation of new genomic, transcriptomic, proteomic, and metabolomic data. This report provides the insights of the integrated view of metabolism generated by metabolic engineering for biotechnological applications of microbial metabolic engineering

  2. A Status Report on the Global Research in Microbial Metabolic Engineering

    Energy Technology Data Exchange (ETDEWEB)

    Joe, Min Ho; Lim, Sang Yong; Kim, Dong Ho

    2008-09-15

    Biotechnology industry is now a global 'Mega-Trend' and metabolic engineering technology has important role is this area. Therefore, many countries has made efforts in this field to produce top value added bio-products efficiently using microorganisms. It has been applied to increase the production of chemicals that are already produced by the host organism, to produce desired chemical substances from less expensive feedstock, and to generate products that are new to the host organism. Recent experimental advances, the so-called '-omics' technologies, mainly functional genomics, proteomics and metabolomics, have enabled wholesale generation of new genomic, transcriptomic, proteomic, and metabolomic data. This report provides the insights of the integrated view of metabolism generated by metabolic engineering for biotechnological applications of microbial metabolic engineering.

  3. Effect of silver nanoparticles on growth performance, metabolism and microbial profile of broiler chickens

    DEFF Research Database (Denmark)

    Pineda, Lane Manalili; Chwalibog, André; Sawosz, Ewa

    2012-01-01

    and intestinal content were collected to evaluate the effects of AgNano on plasma concentration of immunoglobulins and the intestinal microflora, respectively. The provision of water solutions containing different concentrations of AgNano had no effect on postnatal growth performance and the energy metabolism...... (IgG) in the blood plasma of broilers supplemented with AgNano decreased at day 36 (p = 0.012). The results demonstrated that AgNano affects N utilisation and plasma IgG concentration; however, it does not influence the microbial populations in the digestive tract, the energy metabolism and growth...

  4. Metal availability and the expanding network of microbial metabolisms in the Archaean eon

    Science.gov (United States)

    Moore, Eli K.; Jelen, Benjamin I.; Giovannelli, Donato; Raanan, Hagai; Falkowski, Paul G.

    2017-09-01

    Life is based on energy gained by electron-transfer processes; these processes rely on oxidoreductase enzymes, which often contain transition metals in their structures. The availability of different metals and substrates has changed over the course of Earth's history as a result of secular changes in redox conditions, particularly global oxygenation. New metabolic pathways using different transition metals co-evolved alongside changing redox conditions. Sulfur reduction, sulfate reduction, methanogenesis and anoxygenic photosynthesis appeared between about 3.8 and 3.4 billion years ago. The oxidoreductases responsible for these metabolisms incorporated metals that were readily available in Archaean oceans, chiefly iron and iron-sulfur clusters. Oxygenic photosynthesis appeared between 3.2 and 2.5 billion years ago, as did methane oxidation, nitrogen fixation, nitrification and denitrification. These metabolisms rely on an expanded range of transition metals presumably made available by the build-up of molecular oxygen in soil crusts and marine microbial mats. The appropriation of copper in enzymes before the Great Oxidation Event is particularly important, as copper is key to nitrogen and methane cycling and was later incorporated into numerous aerobic metabolisms. We find that the diversity of metals used in oxidoreductases has increased through time, suggesting that surface redox potential and metal incorporation influenced the evolution of metabolism, biological electron transfer and microbial ecology.

  5. A bioenergetics-kinetics coupled modeling study on subsurface microbial metabolism in a field biostimulation experiment

    Science.gov (United States)

    Jin, Q.; Zheng, Z.; Zhu, C.

    2006-12-01

    Microorganisms in nature conserve energy by catalyzing various geochemical reactions. To build a quantitative relationship between geochemical conditions and metabolic rates, we propose a bioenergetics-kinetics coupled modeling approach. This approach describes microbial community as a metabolic network, i.e., fermenting microbes degrade organic substrates while aerobic respirer, nitrate reducer, metal reducer, sulfate reducer, and methanogen consume the fermentation products. It quantifies the control of substrate availability and biological energy conservation on the metabolic rates using thermodynamically consistent rate laws. We applied this simulation approach to study the progress of microbial metabolism during a field biostimulation experiment conducted in Oak Ridge, Tennessee. In the experiment, ethanol was injected into a monitoring well and groundwater was sampled to monitor changes in the chemistry. With time, concentrations of ethanol and SO42- decreased while those of NH4+, Fe2+, and Mn2+ increased. The simulation results fitted well to the observation, indicating simultaneous ethanol degradation and terminal electron accepting processes. The rates of aerobic respiration and denitrification were mainly controlled by substrate concentrations while those of ethanol degradation, sulfate reduction, and methanogenesis were controlled dominantly by the energy availability. The simulation results suggested two different microbial growth statuses in the subsurface. For the functional groups with significant growth, variations with time in substrate concentrations demonstrated a typical S curve. For the groups without significant growth, initial decreases in substrate concentrations were linear with time. Injecting substrates followed by monitoring environmental chemistry therefore provides a convenient approach to characterize microbial growth in the subsurface where methods for direct observation are currently unavailable. This research was funded by the

  6. Electronic Nose Technology to Measure Soil Microbial Activity and Classify Soil Metabolic Status

    OpenAIRE

    Fabrizio De Cesare; Elena Di Mattia; Simone Pantalei; Emiliano Zampetti; Vittorio Vinciguerra; Antonella Macagnano

    2011-01-01

    The electronic nose (E-nose) is a sensing technology that has been widely used to monitor environments in the last decade. In the present study, the capability of an E-nose, in combination with biochemical and microbiological techniques, of both detecting the microbial activity and estimating the metabolic status of soil ecosystems, was tested by measuring on one side respiration, enzyme activities and growth of bacteria in natural but simplified soil ecosystems over 23 days of incubation thr...

  7. Influence of Wastewater Discharge on the Metabolic Potential of the Microbial Community in River Sediments.

    Science.gov (United States)

    Li, Dong; Sharp, Jonathan O; Drewes, Jörg E

    2016-01-01

    To reveal the variation of microbial community functions during water filtration process in river sediments, which has been utilized widely in natural water treatment systems, this study investigates the influence of municipal wastewater discharge to streams on the phylotype and metabolic potential of the microbiome in upstream and particularly various depths of downstream river sediments. Cluster analyses based on both microbial phylogenetic and functional data collectively revealed that shallow upstream sediments grouped with those from deeper subsurface downstream regions. These sediment samples were distinct from those found in shallow downstream sediments. Functional genes associated with carbohydrate, xenobiotic, and certain amino acid metabolisms were overrepresented in upstream and deep downstream samples. In contrast, the more immediate contact with wastewater discharge in shallow downstream samples resulted in an increase in the relative abundance of genes associated with nitrogen, sulfur, purine and pyrimidine metabolisms, as well as restriction-modification systems. More diverse bacterial phyla were associated with upstream and deep downstream sediments, mainly including Actinobacteria, Planctomycetes, and Firmicutes. In contrast, in shallow downstream sediments, genera affiliated with Betaproteobacteria and Gammaproteobacteria were enriched with putative functions that included ammonia and sulfur oxidation, polyphosphate accumulation, and methylotrophic bacteria. Collectively, these results highlight the enhanced capabilities of microbial communities residing in deeper stream sediments for the transformation of water contaminants and thus provide a foundation for better design of natural water treatment systems to further improve the removal of contaminants.

  8. Genome-scale modelling of microbial metabolism with temporal and spatial resolution.

    Science.gov (United States)

    Henson, Michael A

    2015-12-01

    Most natural microbial systems have evolved to function in environments with temporal and spatial variations. A major limitation to understanding such complex systems is the lack of mathematical modelling frameworks that connect the genomes of individual species and temporal and spatial variations in the environment to system behaviour. The goal of this review is to introduce the emerging field of spatiotemporal metabolic modelling based on genome-scale reconstructions of microbial metabolism. The extension of flux balance analysis (FBA) to account for both temporal and spatial variations in the environment is termed spatiotemporal FBA (SFBA). Following a brief overview of FBA and its established dynamic extension, the SFBA problem is introduced and recent progress is described. Three case studies are reviewed to illustrate the current state-of-the-art and possible future research directions are outlined. The author posits that SFBA is the next frontier for microbial metabolic modelling and a rapid increase in methods development and system applications is anticipated. © 2015 Authors; published by Portland Press Limited.

  9. Influence of Wastewater Discharge on the Metabolic Potential of the Microbial Community in River Sediments

    KAUST Repository

    Li, Dong

    2015-09-24

    To reveal the variation of microbial community functions during water filtration process in river sediments, which has been utilized widely in natural water treatment systems, this study investigates the influence of municipal wastewater discharge to streams on the phylotype and metabolic potential of the microbiome in upstream and particularly various depths of downstream river sediments. Cluster analyses based on both microbial phylogenetic and functional data collectively revealed that shallow upstream sediments grouped with those from deeper subsurface downstream regions. These sediment samples were distinct from those found in shallow downstream sediments. Functional genes associated with carbohydrate, xenobiotic, and certain amino acid metabolisms were overrepresented in upstream and deep downstream samples. In contrast, the more immediate contact with wastewater discharge in shallow downstream samples resulted in an increase in the relative abundance of genes associated with nitrogen, sulfur, purine and pyrimidine metabolisms, as well as restriction–modification systems. More diverse bacterial phyla were associated with upstream and deep downstream sediments, mainly including Actinobacteria, Planctomycetes, and Firmicutes. In contrast, in shallow downstream sediments, genera affiliated with Betaproteobacteria and Gammaproteobacteria were enriched with putative functions that included ammonia and sulfur oxidation, polyphosphate accumulation, and methylotrophic bacteria. Collectively, these results highlight the enhanced capabilities of microbial communities residing in deeper stream sediments for the transformation of water contaminants and thus provide a foundation for better design of natural water treatment systems to further improve the removal of contaminants. © 2015, Springer Science+Business Media New York.

  10. Metagenomic analysis of an ecological wastewater treatment plant's microbial communities and their potential to metabolize pharmaceuticals.

    Science.gov (United States)

    Balcom, Ian N; Driscoll, Heather; Vincent, James; Leduc, Meagan

    2016-01-01

    Pharmaceuticals and other micropollutants have been detected in drinking water, groundwater, surface water, and soil around the world. Even in locations where wastewater treatment is required, they can be found in drinking water wells, municipal water supplies, and agricultural soils. It is clear conventional wastewater treatment technologies are not meeting the challenge of the mounting pressures on global freshwater supplies. Cost-effective ecological wastewater treatment technologies have been developed in response. To determine whether the removal of micropollutants in ecological wastewater treatment plants (WWTPs) is promoted by the plant-microbe interactions, as has been reported for other recalcitrant xenobiotics, biofilm microbial communities growing on the surfaces of plant roots were profiled by whole metagenome sequencing and compared to the microbial communities residing in the wastewater. In this study, the concentrations of pharmaceuticals and personal care products (PPCPs) were quantified in each treatment tank of the ecological WWTP treating human wastewater at a highway rest stop and visitor center in Vermont. The concentrations of detected PPCPs were substantially greater than values reported for conventional WWTPs likely due to onsite recirculation of wastewater. The greatest reductions in PPCPs concentrations were observed in the anoxic treatment tank where Bacilli dominated the biofilm community. Benzoate degradation was the most abundant xenobiotic metabolic category identified throughout the system. Collectively, the microbial communities residing in the wastewater were taxonomically and metabolically more diverse than the immersed plant root biofilm. However, greater heterogeneity and higher relative abundances of xenobiotic metabolism genes was observed for the root biofilm.

  11. Changes in Microbial Energy Metabolism Measured by Nanocalorimetry during Growth Phase Transitions

    Science.gov (United States)

    Robador, Alberto; LaRowe, Douglas E.; Finkel, Steven E.; Amend, Jan P.; Nealson, Kenneth H.

    2018-01-01

    Calorimetric measurements of the change in heat due to microbial metabolic activity convey information about the kinetics, as well as the thermodynamics, of all chemical reactions taking place in a cell. Calorimetric measurements of heat production made on bacterial cultures have recorded the energy yields of all co-occurring microbial metabolic reactions, but this is a complex, composite signal that is difficult to interpret. Here we show that nanocalorimetry can be used in combination with enumeration of viable cell counts, oxygen consumption rates, cellular protein content, and thermodynamic calculations to assess catabolic rates of an isolate of Shewanella oneidensis MR-1 and infer what fraction of the chemical energy is assimilated by the culture into biomass and what fraction is dissipated in the form of heat under different limiting conditions. In particular, our results demonstrate that catabolic rates are not necessarily coupled to rates of cell division, but rather, to physiological rearrangements of S. oneidensis MR-1 upon growth phase transitions. In addition, we conclude that the heat released by growing microorganisms can be measured in order to understand the physiochemical nature of the energy transformation and dissipation associated with microbial metabolic activity in conditions approaching those found in natural systems. PMID:29449836

  12. Ceramic Proppant Design for In-situ Microbially Enhanced Methane Recovery

    Energy Technology Data Exchange (ETDEWEB)

    Sparks, Taylor D. [Univ. of Utah, Salt Lake City, UT (United States); Mclennan, John [Univ. of Utah, Salt Lake City, UT (United States); Fuertez, John [Univ. of Utah, Salt Lake City, UT (United States); Han, Kyu-Bum [Univ. of Utah, Salt Lake City, UT (United States)

    2017-12-29

    This project designed a new type of multi-functional lightweight proppant. The proppant is utilized as the conventional lightweight proppant but also transports microorganisms to coalbed reservoirs. The proppant is coated with a polymer which protects the methanogenic microorganisms and serves as a time-release delivery for methane generation. To produce the multifunctional proppant, we assigned five tasks: 1) culturing methanogenic microbes from natural carbon sources; 2) identifying optimized growth and methanogenesis conditions for the microbial consortia; 3) synthesizing the lightweight ceramic proppant; 4) encapsulating the consortia and proppant; and 5) demonstrating lab scale simulated performance by monitoring in-situ methane generation and hydraulic conductivity. Task 1) To evaluate the feasibility of ex-situ cultivation, natural microbial populations were collected from various hydrocarbon-rich environments and locations characterized by natural methanogenesis. Different rank coals, complex hydrocarbon sources, hydrocarbon seeps, and natural biogenic environments were incorporated in the sampling. Three levels of screening allowed selection of microbial populations, favorable nutrient amendments, sources of the microbial community, and quantification of methane produced from various coal types. Incubation periods of up to 24 weeks were evaluated at 23°C. Headspace concentrations of CH4 and CO2 were analyzed by gas chromatography. After a two-week incubation period of the most promising microbes, generated headspace gas concentrations reached 873,400 ppm for methane and 176,370 ppm for carbon dioxide. Task 2) A central composite design (CCD) was used to explore a broad range of operational conditions, examine the effects of the important environmental factors, such as temperature, pH and salt concentration, and query a feasible region of operation to maximize methane production from coal. Coal biogasification was optimal for this

  13. Microbial catabolic activities are naturally selected by metabolic energy harvest rate.

    Science.gov (United States)

    González-Cabaleiro, Rebeca; Ofiţeru, Irina D; Lema, Juan M; Rodríguez, Jorge

    2015-12-01

    The fundamental trade-off between yield and rate of energy harvest per unit of substrate has been largely discussed as a main characteristic for microbial established cooperation or competition. In this study, this point is addressed by developing a generalized model that simulates competition between existing and not experimentally reported microbial catabolic activities defined only based on well-known biochemical pathways. No specific microbial physiological adaptations are considered, growth yield is calculated coupled to catabolism energetics and a common maximum biomass-specific catabolism rate (expressed as electron transfer rate) is assumed for all microbial groups. Under this approach, successful microbial metabolisms are predicted in line with experimental observations under the hypothesis of maximum energy harvest rate. Two microbial ecosystems, typically found in wastewater treatment plants, are simulated, namely: (i) the anaerobic fermentation of glucose and (ii) the oxidation and reduction of nitrogen under aerobic autotrophic (nitrification) and anoxic heterotrophic and autotrophic (denitrification) conditions. The experimentally observed cross feeding in glucose fermentation, through multiple intermediate fermentation pathways, towards ultimately methane and carbon dioxide is predicted. Analogously, two-stage nitrification (by ammonium and nitrite oxidizers) is predicted as prevailing over nitrification in one stage. Conversely, denitrification is predicted in one stage (by denitrifiers) as well as anammox (anaerobic ammonium oxidation). The model results suggest that these observations are a direct consequence of the different energy yields per electron transferred at the different steps of the pathways. Overall, our results theoretically support the hypothesis that successful microbial catabolic activities are selected by an overall maximum energy harvest rate.

  14. Iron oxides stimulate microbial monochlorobenzene in situ transformation in constructed wetlands and laboratory systems

    International Nuclear Information System (INIS)

    Schmidt, Marie; Wolfram, Diana; Birkigt, Jan; Ahlheim, Jörg; Paschke, Heidrun; Richnow, Hans-Hermann; Nijenhuis, Ivonne

    2014-01-01

    Natural wetlands are transition zones between anoxic ground and oxic surface water which may enhance the (bio)transformation potential for recalcitrant chloro-organic contaminants due to the unique geochemical conditions and gradients. Monochlorobenzene (MCB) is a frequently detected groundwater contaminant which is toxic and was thought to be persistent under anoxic conditions. Furthermore, to date, no degradation pathways for anoxic MCB removal have been proven in the field. Hence, it is important to investigate MCB biodegradation in the environment, as groundwater is an important drinking water source in many European countries. Therefore, two pilot-scale horizontal subsurface-flow constructed wetlands, planted and unplanted, were used to investigate the processes in situ contributing to the biotransformation of MCB in these gradient systems. The wetlands were fed with anoxic MCB-contaminated groundwater from a nearby aquifer in Bitterfeld, Germany. An overall MCB removal was observed in both wetlands, whereas just 10% of the original MCB inflow concentration was detected in the ponds. In particular in the gravel bed of the planted wetland, MCB removal was highest in summer season with 73 ± 9% compared to the unplanted one with 40 ± 5%. Whereas the MCB concentrations rapidly decreased in the transition zone of unplanted gravel to the pond, a significant MCB removal was already determined in the anoxic gravel bed of the planted system. The investigation of hydro-geochemical parameters revealed that iron and sulphate reduction were relevant redox processes in both wetlands. In parallel, the addition of ferric iron or nitrate stimulated the mineralisation of MCB in laboratory microcosms with anoxic groundwater from the same source, indicating that the potential for anaerobic microbial degradation of MCB is present at the field site. - Highlights: • MCB removal in anoxic gravel bed of a planted and an unplanted constructed wetland was accompanied by iron

  15. Field Deployment for In-situ Metal and Radionuclide Stabilization by Microbial Metabolites

    Energy Technology Data Exchange (ETDEWEB)

    Turick, C. E.; Knox, A. S.; Dixon, K. L.; Roseberry, R. J.; Kritzas, Y. G

    2005-09-26

    A novel biotechnology is reported here that was demonstrated at SRS that facilitates metal and actinide immobilization by incorporating the physiology and ecology of indigenous bacteria. This technology is based on our previous work with pyomelanin-producing bacteria isolated from SRS soils. Through tyrosine supplementation, overproduction of pyomelanin was achieved, which lead ultimately to metal and actinide immobilization, both in-vitro and in-situ. Pyomelanin is a recalcitrant microbial pigment and a humic type compound in the class of melanin pigments. Pyomelanin has electron shuttling and metal chelation capabilities and thus accelerates the bacterial reduction and/or immobilization of metals. Pyomelanin is produced outside the cell and either diffuses away or attaches to the cell surface. In either case, the reduced pyomelanin is capable of transferring electrons to metals as well as chelating metals. Because of its recalcitrance and redox cycling properties, pyomelanin molecules can be used over and over again for metal transformation. When produced in excess, pyomelanin produced by one bacterial species can be used by other species for metal reduction, thereby extending the utility of pyomelanin and further accelerating metal immobilization rates. Soils contaminated with Ni and U were the focus of this study in order to develop in-situ, metal bioimmobilization technologies. We have demonstrated pyomelanin production in soil from the Tims Branch area of SRS as a result of tyrosine amendments. These results were documented in laboratory soil column studies and field deployment studies. The amended soils demonstrated increased redox behavior and sequestration capacity of U and transition metals following pyomelanin production. Treatments incorporating tyrosine and lactate demonstrated the highest levels of pyomelanin production. In order to determine the potential use of this technology at other areas of SRS, pyomelanin producing bacteria were also quantified

  16. Iron oxides stimulate microbial monochlorobenzene in situ transformation in constructed wetlands and laboratory systems

    Energy Technology Data Exchange (ETDEWEB)

    Schmidt, Marie; Wolfram, Diana; Birkigt, Jan [Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research — UFZ, Permoserstrasse 15, 04318 Leipzig (Germany); Ahlheim, Jörg [Department of Groundwater Remediation, Helmholtz Centre for Environmental Research — UFZ, Permoserstrasse 15, 04318 Leipzig (Germany); Paschke, Heidrun [Department of Analytical Chemistry, Helmholtz Centre for Environmental Research — UFZ, Permoserstrasse 15, 04318 Leipzig (Germany); Richnow, Hans-Hermann [Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research — UFZ, Permoserstrasse 15, 04318 Leipzig (Germany); Nijenhuis, Ivonne, E-mail: ivonne.nijenhuis@ufz.de [Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research — UFZ, Permoserstrasse 15, 04318 Leipzig (Germany)

    2014-02-01

    Natural wetlands are transition zones between anoxic ground and oxic surface water which may enhance the (bio)transformation potential for recalcitrant chloro-organic contaminants due to the unique geochemical conditions and gradients. Monochlorobenzene (MCB) is a frequently detected groundwater contaminant which is toxic and was thought to be persistent under anoxic conditions. Furthermore, to date, no degradation pathways for anoxic MCB removal have been proven in the field. Hence, it is important to investigate MCB biodegradation in the environment, as groundwater is an important drinking water source in many European countries. Therefore, two pilot-scale horizontal subsurface-flow constructed wetlands, planted and unplanted, were used to investigate the processes in situ contributing to the biotransformation of MCB in these gradient systems. The wetlands were fed with anoxic MCB-contaminated groundwater from a nearby aquifer in Bitterfeld, Germany. An overall MCB removal was observed in both wetlands, whereas just 10% of the original MCB inflow concentration was detected in the ponds. In particular in the gravel bed of the planted wetland, MCB removal was highest in summer season with 73 ± 9% compared to the unplanted one with 40 ± 5%. Whereas the MCB concentrations rapidly decreased in the transition zone of unplanted gravel to the pond, a significant MCB removal was already determined in the anoxic gravel bed of the planted system. The investigation of hydro-geochemical parameters revealed that iron and sulphate reduction were relevant redox processes in both wetlands. In parallel, the addition of ferric iron or nitrate stimulated the mineralisation of MCB in laboratory microcosms with anoxic groundwater from the same source, indicating that the potential for anaerobic microbial degradation of MCB is present at the field site. - Highlights: • MCB removal in anoxic gravel bed of a planted and an unplanted constructed wetland was accompanied by iron

  17. Metabolic and demographic feedbacks shape the emergent spatial structure and function of microbial communities.

    Directory of Open Access Journals (Sweden)

    Sylvie Estrela

    Full Text Available Microbes are predominantly found in surface-attached and spatially structured polymicrobial communities. Within these communities, microbial cells excrete a wide range of metabolites, setting the stage for interspecific metabolic interactions. The links, however, between metabolic and ecological interactions (functional relationships, and species spatial organization (structural relationships are still poorly understood. Here, we use an individual-based modelling framework to simulate the growth of a two-species surface-attached community where food (resource is traded for detoxification (service and investigate how metabolic constraints of individual species shape the emergent structural and functional relationships of the community. We show that strong metabolic interdependence drives the emergence of mutualism, robust interspecific mixing, and increased community productivity. Specifically, we observed a striking and highly stable emergent lineage branching pattern, generating a persistent lineage mixing that was absent when the metabolic exchange was removed. These emergent community properties are driven by demographic feedbacks, such that aid from neighbouring cells directly enhances focal cell growth, which in turn feeds back to neighbour fecundity. In contrast, weak metabolic interdependence drives conflict (exploitation or competition, and in turn greater interspecific segregation. Together, these results support the idea that species structural and functional relationships represent the net balance of metabolic interdependencies.

  18. In situ and Enriched Microbial Community Composition and Function Associated with Coal Bed Methane from Powder River Basin Coals

    Science.gov (United States)

    Barnhart, Elliott; Davis, Katherine; Varonka, Matthew; Orem, William; Fields, Matthew

    2016-04-01

    Coal bed methane (CBM) is a relatively clean source of energy but current CBM production techniques have not sustained long-term production or produced enough methane to remain economically practical with lower natural gas prices. Enhancement of the in situ microbial community that actively generates CBM with the addition of specific nutrients could potentially sustain development. CBM production more than doubled from native microbial populations from Powder River Basin (PRB) coal beds, when yeast extract and several individual components of yeast extract (proteins and amino acids) were added to laboratory microcosms. Microbial populations capable of hydrogenotrophic (hydrogen production/utilization) methanogenesis were detected in situ and under non-stimulated conditions. Stimulation with yeast extract caused a shift in the community to microorganisms capable of acetoclastic (acetate production/utilization) methanogenesis. Previous isotope analysis from CBM production wells indicated a similar microbial community shift as observed in stimulation experiments: hydrogenotrophic methanogenesis was found throughout the PRB, but acetoclastic methanogenesis dominated major recharge areas. In conjunction, a high proportion of cyanobacterial and algal SSU rRNA gene sequences were detected in a CBM well within a major recharge area, suggesting that these phototrophic organisms naturally stimulate methane production. In laboratory studies, adding phototrophic (algal) biomass stimulated CBM production by PRB microorganisms similarly to yeast extract (~40μg methane increase per gram of coal). Analysis of the British thermal unit (BTU) content of coal from long-term incubations indicated >99.5% of BTU content remained after CBM stimulation with either algae or yeast extract. Biomimicry of in situ algal CBM stimulation could lead to technologies that utilize coupled biological systems (photosynthesis and methane production) that sustainably enhance CBM production and generate

  19. Evidence of in situ microbial activity and sulphidogenesis in perennially sub-0 °C and hypersaline sediments of a high Arctic permafrost spring.

    Science.gov (United States)

    Lamarche-Gagnon, Guillaume; Comery, Raven; Greer, Charles W; Whyte, Lyle G

    2015-01-01

    The lost hammer (LH) spring perennially discharges subzero hypersaline reducing brines through thick layers of permafrost and is the only known terrestrial methane seep in frozen settings on Earth. The present study aimed to identify active microbial communities that populate the sediments of the spring outlet, and verify whether such communities vary seasonally and spatially. Microcosm experiments revealed that the biological reduction of sulfur compounds (SR) with hydrogen (e.g., sulfate reduction) was potentially carried out under combined hypersaline and subzero conditions, down to -20 °C, the coldest temperature ever recorded for SR. Pyrosequencing analyses of both 16S rRNA (i.e., cDNA) and 16S rRNA genes (i.e., DNA) of sediments retrieved in late winter and summer indicated fairly stable bacterial and archaeal communities at the phylum level. Potentially active bacterial and archaeal communities were dominated by clades related to the T78 Chloroflexi group and Halobacteria species, respectively. The present study indicated that SR, hydrogenotrophy (possibly coupled to autotrophy), and short-chain alkane degradation (other than methane), most likely represent important, previously unaccounted for, metabolic processes carried out by LH microbial communities. Overall, the obtained findings provided additional evidence that the LH system hosts active communities of anaerobic, halophilic, and cryophilic microorganisms despite the extreme conditions in situ.

  20. Microbial and molecular techniques to evaluate and to implement in-situ biodegradation potential and activity at sites contaminated with aromatic and chlorinated hydrocarbons

    International Nuclear Information System (INIS)

    Karg, F.; Henkler, Ch.

    2005-01-01

    Intrinsic bio-remediation harnesses the ability of indigenous microorganisms to degrade contaminants that are present in soil and groundwater. Over the past decade many environmental regulatory agencies especially in Europe have come to recognize the importance of these natural processes in contaminant attenuation. In order to use in-situ bio-remediation to clean up a site successfully it is necessary to investigate the indigenous microbial population and its potential activity to degrade the contaminants of concern (COCs). The evaluation of naturally-occurring degradative activity in initial screening of soil and groundwater samples using recently developed molecular and microbial methods may allow for the implementation of a contaminant reduction and management program without the need for fully engineered remediation intervention. Limited engineering approaches (nutrient delivery etc.) can be implemented to support naturally-occurring bio-restoration processes to achieve a controlled, dynamic attenuation of COCs. Techniques for monitoring pollutant-degrading microorganisms were previously limited to standard culturing techniques. More recently, techniques based upon detection of genetic elements and metabolic activities have been developed in collaboration with university partners Europe, especially in France. The modern techniques are more sensitive for monitoring microbial populations, metabolic activity and the genetic potential to degrade the COCs, and avoid the need for cultivation of microbes under artificial conditions in the laboratory. Especially the application of PCR-Tests (Polymerase Chain Reaction) are able to quantify the Genetic Potential of Pollutant Microbiological Degradation on a contaminated site. This enables to use very economic in-situ site rehabilitation strategies as for example (Dynamic Natural Attenuation). For this modern application of these new strategies PLANREAL created with HPC Envirotec and together with a French University

  1. Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality.

    Science.gov (United States)

    Jiang, Yue; Xiong, Xuejian; Danska, Jayne; Parkinson, John

    2016-01-12

    Metatranscriptomics is emerging as a powerful technology for the functional characterization of complex microbial communities (microbiomes). Use of unbiased RNA-sequencing can reveal both the taxonomic composition and active biochemical functions of a complex microbial community. However, the lack of established reference genomes, computational tools and pipelines make analysis and interpretation of these datasets challenging. Systematic studies that compare data across microbiomes are needed to demonstrate the ability of such pipelines to deliver biologically meaningful insights on microbiome function. Here, we apply a standardized analytical pipeline to perform a comparative analysis of metatranscriptomic data from diverse microbial communities derived from mouse large intestine, cow rumen, kimchi culture, deep-sea thermal vent and permafrost. Sequence similarity searches allowed annotation of 19 to 76% of putative messenger RNA (mRNA) reads, with the highest frequency in the kimchi dataset due to its relatively low complexity and availability of closely related reference genomes. Metatranscriptomic datasets exhibited distinct taxonomic and functional signatures. From a metabolic perspective, we identified a common core of enzymes involved in amino acid, energy and nucleotide metabolism and also identified microbiome-specific pathways such as phosphonate metabolism (deep sea) and glycan degradation pathways (cow rumen). Integrating taxonomic and functional annotations within a novel visualization framework revealed the contribution of different taxa to metabolic pathways, allowing the identification of taxa that contribute unique functions. The application of a single, standard pipeline confirms that the rich taxonomic and functional diversity observed across microbiomes is not simply an artefact of different analysis pipelines but instead reflects distinct environmental influences. At the same time, our findings show how microbiome complexity and availability of

  2. Does canine inflammatory bowel disease influence gut microbial profile and host metabolism?

    Science.gov (United States)

    Xu, Jia; Verbrugghe, Adronie; Lourenço, Marta; Janssens, Geert P J; Liu, Daisy J X; Van de Wiele, Tom; Eeckhaut, Venessa; Van Immerseel, Filip; Van de Maele, Isabel; Niu, Yufeng; Bosch, Guido; Junius, Greet; Wuyts, Brigitte; Hesta, Myriam

    2016-06-16

    Inflammatory bowel disease (IBD) refers to a diverse group of chronic gastrointestinal diseases, and gut microbial dysbiosis has been proposed as a modulating factor in its pathogenesis. Several studies have investigated the gut microbial ecology of dogs with IBD but it is yet unclear if this microbial profile can alter the nutrient metabolism of the host. The aim of the present study was to characterize the faecal bacterial profile and functionality as well as to determine host metabolic changes in IBD dogs. Twenty-three dogs diagnosed with IBD and ten healthy control dogs were included. Dogs with IBD were given a clinical score using the canine chronic enteropathy clinical activity index (CCECAI). Faecal short-chain fatty acids (SCFA) and ammonia concentrations were measured and quantitative PCR was performed. The concentration of plasma amino acids, acylcarnitines, serum folate, cobalamin, and indoxyl sulfate was determined. No significant differences in the abundance of a selection of bacterial groups and fermentation metabolites were observed between the IBD and control groups. However, significant negative correlations were found between CCECAI and the faecal proportion of Lactobacillus as well as between CCECAI and total SCFA concentration. Serum folate and plasma citrulline were decreased and plasma valine was increased in IBD compared to control dogs. Increased plasma free carnitine and total acylcarnitines were observed in IBD compared with control dogs, whereas short-chain acylcarnitines (butyrylcarnitine + isobutyrylcarnitine and, methylmalonylcarnitine) to free carnitine ratios decreased. Dogs with IBD had a higher 3-hydroxyisovalerylcarnitine + isovalerylcarnitine to leucine ratio compared to control dogs. Canine IBD induced a wide range of changes in metabolic profile, especially for the plasma concentrations of short-chain acylcarnitines and amino acids, which could have evolved from tissue damage and alteration in host metabolism. In

  3. Impact of metabolism and growth phase on the hydrogen isotopic composition of microbial fatty acids

    Science.gov (United States)

    Heinzelmann, Sandra M.; Villanueva, Laura; Sinke-Schoen, Danielle; Sinninghe Damsté, Jaap S.; Schouten, Stefan; van der Meer, Marcel T. J.

    2015-01-01

    Microorganisms are involved in all elemental cycles and therefore it is important to study their metabolism in the natural environment. A recent technique to investigate this is the hydrogen isotopic composition of microbial fatty acids, i.e., heterotrophic microorganisms produce fatty acids enriched in deuterium (D) while photoautotrophic and chemoautotrophic microorganisms produce fatty acids depleted in D compared to the water in the culture medium (growth water). However, the impact of factors other than metabolism have not been investigated. Here, we evaluate the impact of growth phase compared to metabolism on the hydrogen isotopic composition of fatty acids of different environmentally relevant microorganisms with heterotrophic, photoautotrophic and chemoautotrophic metabolisms. Fatty acids produced by heterotrophs are enriched in D compared to growth water with εlipid/water between 82 and 359‰ when grown on glucose or acetate, respectively. Photoautotrophs (εlipid/water between −149 and −264‰) and chemoautotrophs (εlipid/water between −217 and −275‰) produce fatty acids depleted in D. Fatty acids become, in general, enriched by between 4 and 46‰ with growth phase which is minor compared to the influence of metabolisms. Therefore, the D/H ratio of fatty acids is a promising tool to investigate community metabolisms in nature. PMID:26005437

  4. [Effects of nitrogen application rate on faba bean fusarium wilt and rhizospheric microbial metabolic functional diversity].

    Science.gov (United States)

    Dong, Yan; Yang, Zhi-xian; Dong, Kun; Tang, Li; Zheng, Yi; Hu, Guo-bin

    2013-04-01

    A field plot experiment was conducted to study the effects of different nitrogen (N) application rates on the microbial functional diversity in faba bean rhizosphere and the relationships between the microbial functional diversity and the occurrence of faba bean fusarium wilt. Four nitrogen application rates were installed, i. e. , N0(0 kg hm-2 , N1 (56. 25 kg hm-2) , N2(112. 5 kg hm-2), and N3 (168.75 kg hm-2), and Biolog microbial analysis system was applied to study the damage of faba bean fusarium wilt and the rhizospheric microbial metabolic functional diversity. Applying N (N1 N2, and N3) decreased the disease index of faba bean fusarium wilt and the quantity of Fusarium oxysporum significantly, and increased the quantities of bacteria and actinomyces and the ratios of bacteria/fungi and actinomyces/fungi significantly, with the peak values of bacteria and actinomyces, bacteria/fungi, and actinomyces/fungi, and the lowest disease index and F. oxysporum density in N2. As compared with N0, applying N increased the AWCD value significantly, but the effects of different N application rates on the ability of rhizospheric microbes in utilizing six types of carbon sources had definite differences. Under the application of N, the utilization rates of carbohydrates, carboxylic acids, and amino acids by the rhizospheric microbes were higher. Principal component analysis demonstrated that applying N changed the rhizospheric microbial community composition obviously, and the carbohydrates, carboxylic acids, and amino acids were the sensitive carbon sources differentiating the changes of the microbial community induced by N application. Applying N inhibited the utilization of carbohydrates and carboxylic acids but improved the utilization of amino acids and phenolic acids by the rhizospheric microbes, which could be one of the main reasons of applying N being able to reduce the harm of faba bean fusarium wilt. It was suggested that rationally applying N could increase the

  5. The molecular dimension of microbial species: 3. Comparative genomics of Synechococcus strains with different light responses and in situ diel transcription patterns of associated ecotypes in the Mushroom Spring microbial mat

    Directory of Open Access Journals (Sweden)

    Millie T. Olsen

    2015-06-01

    Full Text Available Genomes were obtained for three closely related strains of Synechococcus that are representative of putative ecotypes that predominate at different depths in the 1 mm-thick, upper-green layer in the 60°C mat of Mushroom Spring, Yellowstone National Park, and exhibit different light adaptation and acclimation responses. The genomes were compared to the published genome of a previously obtained, closely related strain from a neighboring spring, and differences in both gene content and orthologous gene alleles between high-light-adapted and low-light-adapted strains were identified. Evidence of genetic differences that relate to adaptation to light intensity and/or quality, CO2 uptake, nitrogen metabolism, organic carbon metabolism, and uptake of other nutrients were found between strains of the different putative ecotypes. In situ diel transcription patterns of genes, including genes unique to either low-light-adapted or high-light-adapted strains and different alleles of an orthologous photosystem gene, revealed that expression is fine-tuned to the different light environments experienced by ecotypes prevalent at various depths in the mat. This study suggests that strains of closely related putative ecotypes have different genomic adaptations that enable them to inhabit distinct ecological niches while living in close proximity within a microbial community.

  6. Metatranscriptomics reveal differences in in situ energy and nitrogen metabolism among hydrothermal vent snail symbionts.

    Science.gov (United States)

    Sanders, J G; Beinart, R A; Stewart, F J; Delong, E F; Girguis, P R

    2013-08-01

    Despite the ubiquity of chemoautotrophic symbioses at hydrothermal vents, our understanding of the influence of environmental chemistry on symbiont metabolism is limited. Transcriptomic analyses are useful for linking physiological poise to environmental conditions, but recovering samples from the deep sea is challenging, as the long recovery times can change expression profiles before preservation. Here, we present a novel, in situ RNA sampling and preservation device, which we used to compare the symbiont metatranscriptomes associated with Alviniconcha, a genus of vent snail, in which specific host-symbiont combinations are predictably distributed across a regional geochemical gradient. Metatranscriptomes of these symbionts reveal key differences in energy and nitrogen metabolism relating to both environmental chemistry (that is, the relative expression of genes) and symbiont phylogeny (that is, the specific pathways employed). Unexpectedly, dramatic differences in expression of transposases and flagellar genes suggest that different symbiont types may also have distinct life histories. These data further our understanding of these symbionts' metabolic capabilities and their expression in situ, and suggest an important role for symbionts in mediating their hosts' interaction with regional-scale differences in geochemistry.

  7. Microbial pathways in colonic sulfur metabolism and links with health and disease

    Directory of Open Access Journals (Sweden)

    Franck eCarbonero

    2012-11-01

    Full Text Available Sulfur is both crucial to life and a potential threat to health. While colonic sulfur metabolism mediated by eukaryotic cells is relatively well studied, much less is known about sulfur metabolism within gastrointestinal microbes. Sulfated compounds in the colon are either of inorganic (e.g., sulfates, sulfites or organic (e.g., dietary amino acids and host mucins origin. The most extensively studied of the microbes involved in colonic sulfur metabolism are the sulfate-reducing bacteria, which are common colonic inhabitants. Many other microbial pathways are likely to shape colonic sulfur metabolism as well as the composition and availability of sulfated compounds, and these interactions need to be examined in more detail. Hydrogen sulfide is the sulfur derivative that has attracted the most attention in the context of colonic health, and the extent to which it is detrimental or beneficial remains in debate. Several lines of evidence point to sulfate-reducing bacteria or exogenous hydrogen sulfide as potential players in the etiology of intestinal disorders, inflammatory bowel diseases and colorectal cancer in particular. Generation of hydrogen sulfide via pathways other than dissimilatory sulfate reduction may be as, or more, important than those involving the sulfate-reducing bacteria. We suggest here that a novel axis of research is to assess the effects of hydrogen sulfide in shaping colonic microbiome structure. Clearly, in-depth characterization of the microbial pathways involved in colonic sulfur metabolism is necessary for a better understanding of its contribution to colonic disorders and development of therapeutic strategies.

  8. Soil Metabolome and Metabolic Fate: Microbial Insights into Freshwater Tidal Wetland Redox Biogeochemistry

    Science.gov (United States)

    Roy Chowdhury, T.; Bramer, L.; Hoyt, D. W.; Kim, Y. M.; Metz, T. O.; McCue, L. A.; Jansson, J.; Bailey, V. L.

    2017-12-01

    Earth System Models predict climate extremes that will impact regional and global hydrology. Aquatic-terrestrial transition zones like wetlands will experience the immediate consequence of climate change as shifts in the magnitude and dynamics of hydrologic flow. Such fluctuating hydrology can alter the structure and function of the soil microbial populations that in turn will alter the nature and rate of biogeochemical transformations and significantly impact the carbon balance of the ecosystem. We tested the impacts of shifting hydrology on the soil microbiome and the role of antecedent moisture condition on redox active microbial processes in soils sampled from a tidal freshwater wetland system in the lower Columbia River, WA, USA. Our objectives were to characterize changes in the soil microbial community composition in response to soil moisture legacy effects, and to elucidate relationships between community response, geochemical signatures and metabolite profiles in this soil. The 16S rRNA gene sequencing showed significant decreases in bacterial abundance capable of anaerobic metabolism in response to drying, but quickly recovered to the antecedent moisture condition, as observed by redox processes. Metabolomics and biogeochemical process rates generated evidence for moisture-driven redox conditions as principal controls on the community and metabolic function. Fluctuating redox conditions altered terminal electron acceptor and donor availability and recovery strengths of these pools in soil such that a disproportionate release of carbon dioxide stemmed from alternative anaerobic degradation processes like sulfate and iron reduction in compared to methanogenesis. Our results show that anoxic conditions impact microbial communities in both permanently and temporarily saturated conditions and that rapid change in hydrology can increase substrate availability for both aerobic and anaerobic decomposition processes, including methanogenesis.

  9. Sulfur metabolizing microbes dominate microbial communities in Andesite-hosted shallow-sea hydrothermal systems.

    Science.gov (United States)

    Zhang, Yao; Zhao, Zihao; Chen, Chen-Tung Arthur; Tang, Kai; Su, Jianqiang; Jiao, Nianzhi

    2012-01-01

    To determine microbial community composition, community spatial structure and possible key microbial processes in the shallow-sea hydrothermal vent systems off NE Taiwan's coast, we examined the bacterial and archaeal communities of four samples collected from the water column extending over a redoxocline gradient of a yellow and four from a white hydrothermal vent. Ribosomal tag pyrosequencing based on DNA and RNA showed statistically significant differences between the bacterial and archaeal communities of the different hydrothermal plumes. The bacterial and archaeal communities from the white hydrothermal plume were dominated by sulfur-reducing Nautilia and Thermococcus, whereas the yellow hydrothermal plume and the surface water were dominated by sulfide-oxidizing Thiomicrospira and Euryarchaeota Marine Group II, respectively. Canonical correspondence analyses indicate that methane (CH(4)) concentration was the only statistically significant variable that explains all community cluster patterns. However, the results of pyrosequencing showed an essential absence of methanogens and methanotrophs at the two vent fields, suggesting that CH(4) was less tied to microbial processes in this shallow-sea hydrothermal system. We speculated that mixing between hydrothermal fluids and the sea or meteoric water leads to distinctly different CH(4) concentrations and redox niches between the yellow and white vents, consequently influencing the distribution patterns of the free-living Bacteria and Archaea. We concluded that sulfur-reducing and sulfide-oxidizing chemolithoautotrophs accounted for most of the primary biomass synthesis and that microbial sulfur metabolism fueled microbial energy flow and element cycling in the shallow hydrothermal systems off the coast of NE Taiwan.

  10. Sulfur metabolizing microbes dominate microbial communities in Andesite-hosted shallow-sea hydrothermal systems.

    Directory of Open Access Journals (Sweden)

    Yao Zhang

    Full Text Available To determine microbial community composition, community spatial structure and possible key microbial processes in the shallow-sea hydrothermal vent systems off NE Taiwan's coast, we examined the bacterial and archaeal communities of four samples collected from the water column extending over a redoxocline gradient of a yellow and four from a white hydrothermal vent. Ribosomal tag pyrosequencing based on DNA and RNA showed statistically significant differences between the bacterial and archaeal communities of the different hydrothermal plumes. The bacterial and archaeal communities from the white hydrothermal plume were dominated by sulfur-reducing Nautilia and Thermococcus, whereas the yellow hydrothermal plume and the surface water were dominated by sulfide-oxidizing Thiomicrospira and Euryarchaeota Marine Group II, respectively. Canonical correspondence analyses indicate that methane (CH(4 concentration was the only statistically significant variable that explains all community cluster patterns. However, the results of pyrosequencing showed an essential absence of methanogens and methanotrophs at the two vent fields, suggesting that CH(4 was less tied to microbial processes in this shallow-sea hydrothermal system. We speculated that mixing between hydrothermal fluids and the sea or meteoric water leads to distinctly different CH(4 concentrations and redox niches between the yellow and white vents, consequently influencing the distribution patterns of the free-living Bacteria and Archaea. We concluded that sulfur-reducing and sulfide-oxidizing chemolithoautotrophs accounted for most of the primary biomass synthesis and that microbial sulfur metabolism fueled microbial energy flow and element cycling in the shallow hydrothermal systems off the coast of NE Taiwan.

  11. Nitrogen metabolism and microbial production of dairy cows fed sugarcane and nitrogen compounds

    OpenAIRE

    Gonçalves,Geógenes da Silva; Pedreira,Marcio dos Santos; Pereira,Mara Lúcia Albuquerque; Santos,Dimas Oliveira; Souza,Dicastro Dias de; Porto Junior,Antonio Ferraz

    2014-01-01

    The aim of this study was to evaluate the effect of dairy cow diets containing two different sources of urea on nitrogen metabolism and microbial synthesis. Eight crossbred cows were confined and distributed in two 4x4 Latin: FS - soybean meal (control), conventional urea (UC) 100%; ULL 44 UC = 56% / 44% ULL, ULL 88 UC = 12% / 88% ULL. Diets were offered to animals during 21 days with 14 days of adaptation. The N intake, retained nitrogen balance, nitrogen excretion in milk, urine, feces and ...

  12. Metabolic commensalism and competition in a two-species microbial consortium

    DEFF Research Database (Denmark)

    Christensen, Bjarke Bak; Haagensen, Janus Anders Juul; Heydorn, Arne

    2002-01-01

    We analyzed metabolic interactions and the importance of specific structural relationships in a benzyl alcohol-degrading microbial consortium comprising two species, Pseudomonas putida strain R1 and Acinetobacter strain C6, both of which are able to utilize benzyl alcohol as their sole carbon...... alcohol, which apparently gives Acinetobacter strain C6 a growth advantage, probably because it converts benzyl alcohol to benzoate with a higher yield per time unit than P. putida R1. In biofilms, however, the organisms establish structured, surface-attached consortia, in which heterogeneous ecological...... niches develop, and under these conditions competition for the primary carbon source is not the only determinant of biomass and population structure....

  13. The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism

    DEFF Research Database (Denmark)

    Birkel, Garrett W.; Ghosh, Amit; Kumar, Vinay S.

    2017-01-01

    analysis, new methods for the effective use of the ever more readily available and abundant -omics data (i.e. transcriptomics, proteomics and metabolomics) are urgently needed.Results: The jQMM library presented here provides an open-source, Python-based framework for modeling internal metabolic fluxes......, it introduces the capability to use C-13 labeling experimental data to constrain comprehensive genome-scale models through a technique called two-scale C-13 Metabolic Flux Analysis (2S-C-13 MFA). In addition, the library includes a demonstration of a method that uses proteomics data to produce actionable...... insights to increase biofuel production. Finally, the use of the jQMM library is illustrated through the addition of several Jupyter notebook demonstration files that enhance reproducibility and provide the capability to be adapted to the user's specific needs.Conclusions: jQMM will facilitate the design...

  14. Advances in metabolic engineering in the microbial production of fuels and chemicals from C1 gas.

    Science.gov (United States)

    Humphreys, Christopher M; Minton, Nigel P

    2018-04-01

    The future sustainable production of chemicals and fuels from non-petrochemical sources, while at the same time reducing greenhouse gas (GHG) emissions, represent two of society's greatest challenges. Microbial chassis able to grow on waste carbon monoxide (CO) and carbon dioxide (CO 2 ) can provide solutions to both. Ranging from the anaerobic acetogens, through the aerobic chemoautotrophs to the photoautotrophic cyanobacteria, they are able to convert C1 gases into a range of chemicals and fuels which may be enhanced and extended through appropriate metabolic engineering. The necessary improvements will be facilitated by the increasingly sophisticated gene tools that are beginning to emerge as part of the Synthetic Biology revolution. These tools, in combination with more accurate metabolic and genome scale models, will enable C1 chassis to deliver their full potential. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  15. Computational design of auxotrophy-dependent microbial biosensors for combinatorial metabolic engineering experiments.

    Science.gov (United States)

    Tepper, Naama; Shlomi, Tomer

    2011-01-21

    Combinatorial approaches in metabolic engineering work by generating genetic diversity in a microbial population followed by screening for strains with improved phenotypes. One of the most common goals in this field is the generation of a high rate chemical producing strain. A major hurdle with this approach is that many chemicals do not have easy to recognize attributes, making their screening expensive and time consuming. To address this problem, it was previously suggested to use microbial biosensors to facilitate the detection and quantification of chemicals of interest. Here, we present novel computational methods to: (i) rationally design microbial biosensors for chemicals of interest based on substrate auxotrophy that would enable their high-throughput screening; (ii) predict engineering strategies for coupling the synthesis of a chemical of interest with the production of a proxy metabolite for which high-throughput screening is possible via a designed bio-sensor. The biosensor design method is validated based on known genetic modifications in an array of E. coli strains auxotrophic to various amino-acids. Predicted chemical production rates achievable via the biosensor-based approach are shown to potentially improve upon those predicted by current rational strain design approaches. (A Matlab implementation of the biosensor design method is available via http://www.cs.technion.ac.il/~tomersh/tools).

  16. Enhancement of the sweep efficiency of waterflooding operations by the in-situ microbial population of petroleum reservoirs

    Energy Technology Data Exchange (ETDEWEB)

    Brown, L.R.; Vadie, A.A.; Stephens, J.O.; Azadpour, A.

    1995-12-31

    Live cores were obtained from five reservoirs using special precautions to prevent contamination by exogenous microorganisms and minimize exposure to oxygen. The depths from which the cores were obtained ranged from 2,705 ft to 6,568 ft. Core plugs were cut radially from live cores, encased in heat-shrink plastic tubes, placed in core holders, and fitted with inlets and outlets. Nutrient additions stimulated the in-situ microbial population to increase, dissolve stratal material, produce gases, and release oil. Reduction in flow through the core plugs was observed in some cases, while in other cases flow was increased, probably due to the dissolution of carbonates in the formation. A field demonstration of the ability of the in-situ microbial population to increase oil recovery by blocking the more permeable zones of the reservoir is currently underway. This demonstration is being conducted in the North Blowhorn Creek Unit situated in Lamar County, Alabama. Live cores were obtained from a newly drilled well in the field and tested as described above. The field project involves four test patterns each including one injector, four to five producers, and a comparable control injector with its four to five producers. Nutrient injection in the field began November 1994.

  17. Hydrodynamic chronoamperometry for probing kinetics of anaerobic microbial metabolism--case study of Faecalibacterium prausnitzii.

    Science.gov (United States)

    Prévoteau, Antonin; Geirnaert, Annelies; Arends, Jan B A; Lannebère, Sylvain; Van de Wiele, Tom; Rabaey, Korneel

    2015-07-01

    Monitoring in vitro the metabolic activity of microorganisms aids bioprocesses and enables better understanding of microbial metabolism. Redox mediators can be used for this purpose via different electrochemical techniques that are either complex or only provide non-continuous data. Hydrodynamic chronoamperometry using a rotating disc electrode (RDE) can alleviate these issues but was seldom used and is poorly characterized. The kinetics of Faecalibacterium prausnitzii A2-165, a beneficial gut microbe, were determined using a RDE with riboflavin as redox probe. This butyrate producer anaerobically ferments glucose and reduces riboflavin whose continuous monitoring on a RDE provided highly accurate kinetic measurements of its metabolism, even at low cell densities. The metabolic reaction rate increased linearly over a broad range of cell concentrations (9 × 10(4) to 5 × 10(7) cells.mL(-1)). Apparent Michaelis-Menten kinetics was observed with respect to riboflavin (KM = 6 μM; kcat = 5.3 × 10(5) s(-1), at 37 °C) and glucose (KM = 6 μM; kcat = 2.4 × 10(5) s(-1)). The short temporal resolution allows continuous monitoring of fast cellular events such as kinetics inhibition with butyrate. Furthermore, we detected for the first time riboflavin reduction by another potential probiotic, Butyricicoccus pullicaecorum. The ability of the RDE for fast, accurate, simple and continuous measurements makes it an ad hoc tool for assessing bioprocesses at high resolution.

  18. Microbial metaproteomics for characterizing the range of metabolic functions and activities of human gut microbiota.

    Science.gov (United States)

    Xiong, Weili; Abraham, Paul E; Li, Zhou; Pan, Chongle; Hettich, Robert L

    2015-10-01

    The human gastrointestinal tract is a complex, dynamic ecosystem that consists of a carefully tuned balance of human host and microbiota membership. The microbiome is not merely a collection of opportunistic parasites, but rather provides important functions to the host that are absolutely critical to many aspects of health, including nutrient transformation and absorption, drug metabolism, pathogen defense, and immune system development. Microbial metaproteomics provides the ability to characterize the human gut microbiota functions and metabolic activities at a remarkably deep level, revealing information about microbiome development and stability as well as their interactions with their human host. Generally, microbial and human proteins can be extracted and then measured by high performance MS-based proteomics technology. Here, we review the field of human gut microbiome metaproteomics, with a focus on the experimental and informatics considerations involved in characterizing systems ranging from low-complexity model gut microbiota in gnotobiotic mice, to the emerging gut microbiome in the GI tract of newborn human infants, and finally to an established gut microbiota in human adults. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Effects of Pheretima Guillelmi Cultivation Time on Microbial Community Diversity and Characteristics of Carbon Metabolism in Vegetable Soil

    Directory of Open Access Journals (Sweden)

    ZHENG Xian-qing

    2015-12-01

    Full Text Available In order to study the effect of different biological tillage time (Pheretima guillelmi on soil microbial community metabolic functions in different soil depths, we set a location test in vegetable field at Chongming Island in Shanghai to analyze the changes of soil microbial community and carbon utilization abilities (Average well- color development, AWCD by using biolog eco-plate method. The three-year results showed that: Bio-tillage significantly improved microbial community activity, and with the increase of tillage years, biological tillage could make the average AWCD 3 to 7 times higher. The Simpson index and Shannon index of the biological tillage treatments were significantly higher than that of the control. The cumulative increase of 0~5 cm soil layer was 49 and 6.28 respectively, and the cumulative increase of 5~20 cm soil layer was 31 and 2.55 respectively. Earthworm bio-tillage significantly increased the soil microbial metabolic ability of 6 kinds of carbon sources, and increased the carbohydrate metabolism activity. In this study, earthworm bio-tillage is an effective way to increase the microbial activity of microbial soil.

  20. Using isotopic tracers to assess the impact of tillage and straw management on the microbial metabolic network in soil

    Science.gov (United States)

    Van Groenigen, K.; Forristal, D.; Jones, M. B.; Schwartz, E.; Hungate, B. A.; Dijkstra, P.

    2013-12-01

    By decomposing soil organic matter, microbes gain energy and building blocks for biosynthesis and release CO2 to the atmosphere. Therefore, insight into the effect of management practices on microbial metabolic pathways and C use efficiency (CUE; microbial C produced per substrate C utilized) may help to predict long term changes in soil C stocks. We studied the effects of reduced (RT) and conventional tillage (CT) on the microbial central C metabolic network, using soil samples from a 12-year-old field experiment in an Irish winter wheat cropping system. Each year after harvest, straw was removed from half of the RT and CT plots or incorporated into the soil in the other half, resulting in four treatment combinations. We added 1-13C and 2,3-13C pyruvate and 1-13C and U-13C glucose as metabolic tracer isotopomers to composite soil samples taken at two depths (0-15 cm and 15-30 cm) from each treatment and used the rate of position-specific respired 13CO2 to parameterize a metabolic model. Model outcomes were then used to calculate CUE of the microbial community. We found that the composite samples differed in CUE, but the changes were small, with values ranging between 0.757-0.783 across treatments and soil depth. Increases in CUE were associated with a decrease in tricarboxylic acid cycle and reductive pentose phosphate pathway activity and increased consumption of metabolic intermediates for biosynthesis. Our results indicate that RT and straw incorporation promote soil C storage without substantially changing CUE or any of the microbial metabolic pathways. This suggests that at our site, RT and straw incorporation promote soil C storage mostly through direct effects such as increased soil C input and physical protection from decomposition, rather than by feedback responses of the microbial community.

  1. Succession of the functional microbial communities and the metabolic functions in maize straw composting process.

    Science.gov (United States)

    Wei, Huawei; Wang, Liuhong; Hassan, Muhammad; Xie, Bing

    2018-05-01

    Illumina MiSeq sequencing and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) were applied to study the dynamic changes and effects of microbial community structures as well as the metabolic function of bacterial community in maize straw composting process. Results showed that humic acid contents in loosely combined humus (HA1) and stably combined humus (HA2) increased after composting and Staphylococcus, Cellulosimicrobium and Ochrobactrum possibly participated in the transformation of the process. The bacterial communities differed in different stages of the composting. Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria were reported the dominant phyla throughout the process and the relative abundance of the dominant phyla varied significantly (p composting. Copyright © 2018 Elsevier Ltd. All rights reserved.

  2. MALDI Mass Spectrometry Imaging for Visualizing In Situ Metabolism of Endogenous Metabolites and Dietary Phytochemicals

    Science.gov (United States)

    Fujimura, Yoshinori; Miura, Daisuke

    2014-01-01

    Understanding the spatial distribution of bioactive small molecules is indispensable for elucidating their biological or pharmaceutical roles. Mass spectrometry imaging (MSI) enables determination of the distribution of ionizable molecules present in tissue sections of whole-body or single heterogeneous organ samples by direct ionization and detection. This emerging technique is now widely used for in situ label-free molecular imaging of endogenous or exogenous small molecules. MSI allows the simultaneous visualization of many types of molecules including a parent molecule and its metabolites. Thus, MSI has received much attention as a potential tool for pathological analysis, understanding pharmaceutical mechanisms, and biomarker discovery. On the other hand, several issues regarding the technical limitations of MSI are as of yet still unresolved. In this review, we describe the capabilities of the latest matrix-assisted laser desorption/ionization (MALDI)-MSI technology for visualizing in situ metabolism of endogenous metabolites or dietary phytochemicals (food factors), and also discuss the technical problems and new challenges, including MALDI matrix selection and metabolite identification, that need to be addressed for effective and widespread application of MSI in the diverse fields of biological, biomedical, and nutraceutical (food functionality) research. PMID:24957029

  3. In Situ Field Sequencing and Life Detection in Remote (79°26′N Canadian High Arctic Permafrost Ice Wedge Microbial Communities

    Directory of Open Access Journals (Sweden)

    J. Goordial

    2017-12-01

    Full Text Available Significant progress is being made in the development of the next generation of low cost life detection instrumentation with much smaller size, mass and energy requirements. Here, we describe in situ life detection and sequencing in the field in soils over laying ice wedges in polygonal permafrost terrain on Axel Heiberg Island, located in the Canadian high Arctic (79°26′N, an analog to the polygonal permafrost terrain observed on Mars. The life detection methods used here include (1 the cryo-iPlate for culturing microorganisms using diffusion of in situ nutrients into semi-solid media (2 a Microbial Activity Microassay (MAM plate (BIOLOG Ecoplate for detecting viable extant microorganisms through a colourimetric assay, and (3 the Oxford Nanopore MinION for nucleic acid detection and sequencing of environmental samples and the products of MAM plate and cryo-iPlate. We obtained 39 microbial isolates using the cryo-iPlate, which included several putatively novel strains based on the 16S rRNA gene, including a Pedobacter sp. (96% closest similarity in GenBank which we partially genome sequenced using the MinION. The MAM plate successfully identified an active community capable of L-serine metabolism, which was used for metagenomic sequencing with the MinION to identify the active and enriched community. A metagenome on environmental ice wedge soil samples was completed, with base calling and uplink/downlink carried out via satellite internet. Validation of MinION sequencing using the Illumina MiSeq platform was consistent with the results obtained with the MinION. The instrumentation and technology utilized here is pre-existing, low cost, low mass, low volume, and offers the prospect of equipping micro-rovers and micro-penetrators with aggressive astrobiological capabilities. Since potentially habitable astrobiology targets have been identified (RSLs on Mars, near subsurface water ice on Mars, the plumes and oceans of Europa and Enceladus

  4. IMGMD: A platform for the integration and standardisation of In silico Microbial Genome-scale Metabolic Models.

    Science.gov (United States)

    Ye, Chao; Xu, Nan; Dong, Chuan; Ye, Yuannong; Zou, Xuan; Chen, Xiulai; Guo, Fengbiao; Liu, Liming

    2017-04-07

    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.

  5. Hydrodynamic chronoamperometry for probing kinetics of anaerobic microbial metabolism - case study of Faecalibacterium prausnitzii

    Science.gov (United States)

    Prévoteau, Antonin; Geirnaert, Annelies; Arends, Jan B. A.; Lannebère, Sylvain; van de Wiele, Tom; Rabaey, Korneel

    2015-07-01

    Monitoring in vitro the metabolic activity of microorganisms aids bioprocesses and enables better understanding of microbial metabolism. Redox mediators can be used for this purpose via different electrochemical techniques that are either complex or only provide non-continuous data. Hydrodynamic chronoamperometry using a rotating disc electrode (RDE) can alleviate these issues but was seldom used and is poorly characterized. The kinetics of Faecalibacterium prausnitzii A2-165, a beneficial gut microbe, were determined using a RDE with riboflavin as redox probe. This butyrate producer anaerobically ferments glucose and reduces riboflavin whose continuous monitoring on a RDE provided highly accurate kinetic measurements of its metabolism, even at low cell densities. The metabolic reaction rate increased linearly over a broad range of cell concentrations (9 × 104 to 5 × 107 cells.mL-1). Apparent Michaelis-Menten kinetics was observed with respect to riboflavin (KM = 6 μM kcat = 5.3×105 s-1, at 37 °C) and glucose (KM = 6 μM kcat = 2.4 × 105 s-1). The short temporal resolution allows continuous monitoring of fast cellular events such as kinetics inhibition with butyrate. Furthermore, we detected for the first time riboflavin reduction by another potential probiotic, Butyricicoccus pullicaecorum. The ability of the RDE for fast, accurate, simple and continuous measurements makes it an ad hoc tool for assessing bioprocesses at high resolution.

  6. Microbial dynamics during and after in situ chemical oxidation of chlorinated solvents

    NARCIS (Netherlands)

    Sutton, N.B.; Atashgahi, S.; Wal, van der J.; Wijn, G.; Grotenhuis, J.T.C.; Smidt, H.; Rijnaarts, H.

    2015-01-01

    In situ chemical oxidation (ISCO) followed by a bioremediation step is increasingly being considered as an effective biphasic technology. Information on the impact of chemical oxidants on organohalide respiring bacteria (OHRB), however, is largely lacking. Therefore, we used quantitative PCR (qPCR)

  7. Quantitative assessment of in situ microbial communities affecting nuclear waste disposal

    International Nuclear Information System (INIS)

    White, D.C.

    1996-01-01

    Microbes in the environments surrounding nuclear waste depositories pose several questions regarding the protection of the surrounding communities. microbes can facilitate microbially influenced corrosion (MIC), mobilize and facilitate the transport of nuclides as well as produce gaseous emissions which can compromise containment. We have developed an analysis of the extant microbiota that is independent of quantitative recovery and subsequent growth, based on signature biomarkers analysis (SBA)

  8. Shifts in microbial community structure during in situ surfactant-enhanced bioremediation of polycyclic aromatic hydrocarbon-contaminated soil.

    Science.gov (United States)

    Wang, Lingwen; Li, Feng; Zhan, Yu; Zhu, Lizhong

    2016-07-01

    This study aims to reveal the microbial mechanism of in situ surfactant-enhanced bioremediation (SEBR). Various concentrations of rhamnolipids, Tween 80, and sodium dodecyl benzenesulfonate (SDBS) were separately sprayed onto soils contaminated with polycyclic aromatic hydrocarbons (PAHs) for years. Within 90 days, the highest level of degradation (95 %) was observed in the soil treated with rhamnolipids (10 mg/kg), followed by 92 % degradation with Tween 80 (50 mg/kg) and 90 % degradation with SDBS (50 mg/kg). The results of the microbial phospholipid fatty acids (PLFAs) suggest that bacteria dominated the enhanced PAH biodegradation (94 % of the maximum contribution). The shift of bacterial community structure during the surfactant treatment was analyzed by using the 16S rRNA gene high-throughput sequencing. In the presence of surfactants, the number of the operational taxonomic units (OTUs) associated with Bacillus, Pseudomonas, and Sphingomonas increased from 2-3 to 15-30 % at the end of the experiment (two to three times of control). Gene prediction with phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) shows that the PAH-degrading genes, such as 1-hydroxy-2-naphthoate dioxygenase and PAH dioxygenase large subunit, significantly increased after the surfactant applications (p bioremediation.

  9. Reply to 'Comment on kinetic modeling of microbially-driven redox chemistry of subsurface environments: coupling transport, microbial metabolism and geochemistry' by J. Griffioen

    Science.gov (United States)

    Hunter, K. S.; Van Cappellen, P.

    2000-01-01

    Our paper, 'Kinetic modeling of microbially-driven redox chemistry of subsurface environments: coupling transport, microbial metabolism and geochemistry' (Hunter et al., 1998), presents a theoretical exploration of biogeochemical reaction networks and their importance to the biogeochemistry of groundwater systems. As with any other model, the kinetic reaction-transport model developed in our paper includes only a subset of all physically, biologically and chemically relevant processes in subsurface environments. It considers aquifer systems where the primary energy source driving microbial activity is the degradation of organic matter. In addition to the primary biodegradation pathways of organic matter (i.e. respiration and fermentation), the redox chemistry of groundwaters is also affected by reactions not directly involving organic matter oxidation. We refer to the latter as secondary reactions. By including secondary redox reactions which consume reduced reaction products (e.g., Mn2+, FeS, H2S), and in the process compete with microbial heterotrophic populations for available oxidants (i.e. O2, NO3-, Mn(IV), Fe(III), SO42-), we predict spatio-temporal distributions of microbial activity which differ significantly from those of models which consider only the biodegradation reactions. That is, the secondary reactions have a significant impact on the distributions of the rates of heterotrophic and chemolithotrophic metabolic pathways. We further show that secondary redox reactions, as well as non-redox reactions, significantly influence the acid-base chemistry of groundwaters. The distributions of dissolved inorganic redox species along flowpaths, however, are similar in simulations with and without secondary reactions (see Figs. 3(b) and 7(b) in Hunter et al., 1998), indicating that very different biogeochemical reaction dynamics may lead to essentially the same chemical redox zonation of a groundwater system.

  10. Unusual metabolic diversity of hyperalkaliphilic microbial communities associated with subterranean serpentinization at The Cedars.

    Science.gov (United States)

    Suzuki, Shino; Ishii, Shun'ichi; Hoshino, Tatsuhiko; Rietze, Amanda; Tenney, Aaron; Morrill, Penny L; Inagaki, Fumio; Kuenen, J Gijs; Nealson, Kenneth H

    2017-11-01

    Water from The Cedars springs that discharge from serpentinized ultramafic rocks feature highly basic (pH=~12), highly reducing (E h serpentinizing system, was dominated by several bacterial taxa from the phyla OD1 ('Parcubacteria') and Chloroflexi. Members of the GPS1 community had, for the most part, the smallest genomes reported for their respective taxa, and encoded only archaeal (A-type) ATP synthases or no ATP synthases at all. Furthermore, none of the members encoded respiration-related genes and some of the members also did not encode key biosynthesis-related genes. In contrast, BS5, fed by shallow water, appears to have a community driven by hydrogen metabolism and was dominated by a diverse group of Proteobacteria similar to those seen in many terrestrial serpentinization sites. Our findings indicated that the harsh ultrabasic geological setting supported unexpectedly diverse microbial metabolic strategies and that the deep-water-fed springs supported a community that was remarkable in its unusual metagenomic and genomic constitution.

  11. The effect of gluten on the host-microbial metabolism assessed by urinary metabolomics

    DEFF Research Database (Denmark)

    Roager, Henrik Munch; Frandsen, Henrik Lauritz; Gøbel, Rikke Juul

    A gluten-free diet clearly improves the life of patients with celiac disease, but the scientific evidence supporting possible health benefits of a gluten-free diet for non-celiac adults is limited. Therefore, as urine reflects the host and gut microbial metabolism, the study aimed to assess...... a gluten-rich (21.6±5.7g/day) or a gluten-poor (~1g/day) diet for 8 weeks, crossing over to the other diet after 6 weeks washout. Urine samples were standardised collected at the beginning and end of each diet intervention period and were analysed by gas chromatography mass spectrometry (GC-MS) and liquid...... the long-term metabolic effect of gluten on the urine metabolome of non-celiac individuals by a cross-over intervention study (gluten-poor and gluten rich, respectively) using a non-targeted metabolomics approach. Fifty-one non-celiac adult participants (30 female, 21 male) were randomized to either...

  12. Metabolic Potential and Activity in Fluids of the Coast Range Ophiolite Microbial Observatory, California, USA

    Science.gov (United States)

    Hoehler, T.; Som, S.; Schrenk, M.; McCollom, T.; Cardace, D.

    2016-01-01

    Metabolic potential and activity associated with hydrogen and carbon monoxide were characterized in fluids sampled from the the Coast Range Ophiolite Microbial Observatory (CROMO). CROMO consists of two clusters of science-dedicated wells drilled to varying depths up to 35m in the actively serpentinizing, Jurassic-age Coast Range Ophiolite of Northern California, along with a suite of pre-existing monitoring wells at the same site. Consistent with the fluid chemistry observed in other serpentinizing systems, CROMO fluids are highly alkaline, with pH up to 12.5, high in methane, with concentrations up 1600 micromolar, and low in dissolved inorganic carbon (DIC), with concentrations of 10's to 100's of micromolar. CROMO is conspicuous for fluid H2 concentrations that are consistently sub-micromolar, orders of magnitude lower than is typical of other systems. However, higher H2 concentrations (10's -100's of micromolar) at an earlier stage of fluid chemical evolution are predicted by, or consistent with: thermodynamic models for fluid chemistry based on parent rock composition equivalent to local peridotite and with water:rock ratio constrained by observed pH; the presence of magnetite at several wt% in CROMO drill cores; and concentrations of formate and carbon monoxide that would require elevated H2 if formed in equilibrium with H2 and DIC. Calculated Gibbs energy changes for reaction of H2 and CO in each of several metabolisms, across the range of fluid composition encompassed by the CROMO wells, range from bioenergetically feasible (capable of driving ATP synthesis) to thermodynamically unfavorable. Active consumption relative to killed controls was observed for both CO and H2 during incubation of fluids from the pre-existing monitoring wells; in incubations of freshly cored solids, consumption was only observed in one sample set (corresponding to the lowest pH) out of three. The specific metabolisms by which H2 and CO are consumed remain to be determined.

  13. Microbial metabolic potential for carbon degradation and nutrient (nitrogen and phosphorus) acquisition in an ombrotrophic peatland.

    Science.gov (United States)

    Lin, Xueju; Tfaily, Malak M; Green, Stefan J; Steinweg, J Megan; Chanton, Patrick; Imvittaya, Aopeau; Chanton, Jeffrey P; Cooper, William; Schadt, Christopher; Kostka, Joel E

    2014-06-01

    This study integrated metagenomic and nuclear magnetic resonance (NMR) spectroscopic approaches to investigate microbial metabolic potential for organic matter decomposition and nitrogen (N) and phosphorus (P) acquisition in soils of an ombrotrophic peatland in the Marcell Experimental Forest (MEF), Minnesota, USA. This analysis revealed vertical stratification in key enzymatic pathways and taxa containing these pathways. Metagenomic analyses revealed that genes encoding laccases and dioxygenases, involved in aromatic compound degradation, declined in relative abundance with depth, while the relative abundance of genes encoding metabolism of amino sugars and all four saccharide groups increased with depth in parallel with a 50% reduction in carbohydrate content. Most Cu-oxidases were closely related to genes from Proteobacteria and Acidobacteria, and type 4 laccase-like Cu-oxidase genes were >8 times more abundant than type 3 genes, suggesting an important and overlooked role for type 4 Cu-oxidase in phenolic compound degradation. Genes associated with sulfate reduction and methanogenesis were the most abundant anaerobic respiration genes in these systems, with low levels of detection observed for genes of denitrification and Fe(III) reduction. Fermentation genes increased in relative abundance with depth and were largely affiliated with Syntrophobacter. Methylocystaceae-like small-subunit (SSU) rRNA genes, pmoA, and mmoX genes were more abundant among methanotrophs. Genes encoding N2 fixation, P uptake, and P regulons were significantly enriched in the surface peat and in comparison to other ecosystems, indicating N and P limitation. Persistence of inorganic orthophosphate throughout the peat profile in this P-limiting environment indicates that P may be bound to recalcitrant organic compounds, thus limiting P bioavailability in the subsurface. Comparative metagenomic analysis revealed a high metabolic potential for P transport and starvation, N2 fixation, and

  14. Water type and irrigation time effects on microbial metabolism of a soil cultivated with Bermuda-grass Tifton 85

    Directory of Open Access Journals (Sweden)

    Sandra Furlan Nogueira

    2011-06-01

    Full Text Available This study investigated the microbial metabolism in Bermuda-grass Tifton 85 areas after potable-water and effluent irrigation treatments. The experiment was carried out in Lins/SP with samples taken in the rainy and dry seasons (2006 after one year and three years of irrigation management, and set up on an entirely randomized block design with four treatments: C (control, without irrigation or fertilization, PW (potable water + 520 kg of N ha-1 year-1; TE3 and TE0 (treated effluent + 520 kg of N ha-1 year-1 for three years and one year, respectively. The parameters determined were: microbial biomass carbon, microbial activity, and metabolic quotient. Irrigation with wastewater after three years indicated no alteration in soil quality for C and ET3; for PW, a negative impact on soil quality (microbial biomass decrease suggested that water-potable irrigation in Lins is not an adequate option. Microbial activity alterations observed in TE0 characterize a priming effect.

  15. Nanoscale zero-valent iron/persulfate enhanced upflow anaerobic sludge blanket reactor for dye removal: Insight into microbial metabolism and microbial community

    Science.gov (United States)

    Pan, Fei; Zhong, Xiaohan; Xia, Dongsheng; Yin, Xianze; Li, Fan; Zhao, Dongye; Ji, Haodong; Liu, Wen

    2017-03-01

    This study investigated the efficiency of nanoscale zero-valent iron combined with persulfate (NZVI/PS) for enhanced degradation of brilliant red X-3B in an upflow anaerobic sludge blanket (UASB) reactor, and examined the effects of NZVI/PS on anaerobic microbial communities during the treatment process. The addition of NZVI (0.5 g/L) greatly enhanced the decolourization rate of X-3B from 63.8% to 98.4%. The Biolog EcoPlateTM technique was utilized to examine microbial metabolism in the reactor, and the Illumina MiSeq high-throughput sequencing revealed 22 phyla and 88 genera of the bacteria. The largest genera (Lactococcus) decreased from 33.03% to 7.94%, while the Akkermansia genera increased from 1.69% to 20.23% according to the abundance in the presence of 0.2 g/L NZVI during the biological treatment process. Meanwhile, three strains were isolated from the sludge in the UASB reactors and identified by 16 S rRNA analysis. The distribution of three strains was consistent with the results from the Illumina MiSeq high throughput sequencing. The X-ray photoelectron spectroscopy results indicated that Fe(0) was transformed into Fe(II)/Fe(III) during the treatment process, which are beneficial for the microorganism growth, and thus promoting their metabolic processes and microbial community.

  16. Nanoscale zero-valent iron/persulfate enhanced upflow anaerobic sludge blanket reactor for dye removal: Insight into microbial metabolism and microbial community

    Science.gov (United States)

    Pan, Fei; Zhong, Xiaohan; Xia, Dongsheng; Yin, Xianze; Li, Fan; Zhao, Dongye; Ji, Haodong; Liu, Wen

    2017-01-01

    This study investigated the efficiency of nanoscale zero-valent iron combined with persulfate (NZVI/PS) for enhanced degradation of brilliant red X-3B in an upflow anaerobic sludge blanket (UASB) reactor, and examined the effects of NZVI/PS on anaerobic microbial communities during the treatment process. The addition of NZVI (0.5 g/L) greatly enhanced the decolourization rate of X-3B from 63.8% to 98.4%. The Biolog EcoPlateTM technique was utilized to examine microbial metabolism in the reactor, and the Illumina MiSeq high-throughput sequencing revealed 22 phyla and 88 genera of the bacteria. The largest genera (Lactococcus) decreased from 33.03% to 7.94%, while the Akkermansia genera increased from 1.69% to 20.23% according to the abundance in the presence of 0.2 g/L NZVI during the biological treatment process. Meanwhile, three strains were isolated from the sludge in the UASB reactors and identified by 16 S rRNA analysis. The distribution of three strains was consistent with the results from the Illumina MiSeq high throughput sequencing. The X-ray photoelectron spectroscopy results indicated that Fe(0) was transformed into Fe(II)/Fe(III) during the treatment process, which are beneficial for the microorganism growth, and thus promoting their metabolic processes and microbial community. PMID:28300176

  17. An approach for in situ studies of deep-sea amphipods and their microbial gut flora

    Science.gov (United States)

    Jannasch, H. W.; Cuhel, R. L.; Wirsen, C. O.; Taylor, C. D.

    1980-10-01

    A technique has been developed and field-tested for the trapping, feeding, and timed incubation of amphipods on the deep-sea floor. Data obtained from experiments using radiolabeled foodstuffs indicate that shifts within the labeled fractions of the major biological polymers make it possible to distinguish between the metabolism of the amphipods and that of their intestinal microflora.

  18. Winter survival of microbial contaminants in soil: an in situ verification.

    Science.gov (United States)

    Bucci, Antonio; Allocca, Vincenzo; Naclerio, Gino; Capobianco, Giovanni; Divino, Fabio; Fiorillo, Francesco; Celico, Fulvio

    2015-01-01

    The aim of the research was to evaluate, at site scale, the influence of freezing and freeze/thaw cycles on the survival of faecal coliforms and faecal enterococci in soil, in a climate change perspective. Before the winter period and during grazing, viable cells of faecal coliforms and faecal enterococci were detected only in the first 10 cm below ground, while, after the winter period and before the new seasonal grazing, a lower number of viable cells of both faecal indicators was detected only in some of the investigated soil profiles, and within the first 5 cm. Taking into consideration the results of specific investigations, we hypothesise that the non-uniform spatial distribution of grass roots within the studied soil can play an important role in influencing this phenomenon, while several abiotic factors do not play any significant role. Taking into account the local trend in the increase of air temperature, a different distribution of microbial pollution over time is expected in spring waters, in future climate scenarios. The progressive increase in air temperature will cause a progressive decrease in freeze/thaw cycles at higher altitudes, minimising cold shocks on microbial cells, and causing spring water pollution also during winter. Copyright © 2014. Published by Elsevier B.V.

  19. Mineralogical controls on surface colonization by sulfur-metabolizing microbial communities

    Science.gov (United States)

    Jones, A. A.; Bennett, P.

    2012-12-01

    When characterizing microbial diversity and the microbial ecosystem of the shallow subsurface the mineral matrix is generally assumed to be homogenous and unreactive. We report here experimental evidence that microorganisms colonize rock surfaces according to the rock's chemistry and the organism's metabolic requirements and tolerances. We investigated this phenomenon using laboratory biofilm reactors with both a pure culture of sulfur-oxidizing Thiothrix unzii and a mixed environmental sulfur-metabolizing community from Lower Kane, Cave, WY, USA. Reactors contained rock and mineral chips (calcite, albite, microcline, quartz, chert, Madison Limestone (ML), Madison Dolostone (MD), and basalt) amended with one of the two inoculants. Biomass of attached microorganisms on each mineral surface was quantified. The 16S rRNA of attached microbial communities were compared using Roche FLX and Titanium 454 next generation pyrosequencing. A primary controlling factor on taxonomy of attached microorganisms in both pure and mixed culture experiments was mineral buffering capacity. In mixed culture experiments acid-buffering carbonates were preferentially colonized by neutrophilic sulfur-oxidizing microorganisms (~18% to ~27% of microorganisms), while acidophilic sulfur-oxidizing microorganisms colonized non-buffering quartz exclusively (~46% of microorganisms). The nutrient content of the rock was a controlling factor on biomass accumulation, with neutrophilic organisms selecting between carbonate surfaces of equivalent buffer capacities according to the availability of phosphate. Dry biomass on ML was 17.8 ± 2.3 mg/cm2 and MD was 20.6 ± 6.8 mg/cm2; while nutrient poor calcite accumulated 2.4 ± 0.3 mg/cm2. Biomass accumulation was minimal on non-buffering nutrient-limited surfaces. These factors are countered by the competitive exclusion of some populations. A pure culture of T. unzii preferentially colonizes carbonates while a very closely related Thiothrix spp is excluded

  20. Soil microbial metabolic quotient (qCO2) of twelve ecosystems of Mt. Kilimanjaro

    Science.gov (United States)

    Pabst, Holger; Gerschlauer, Friederike; Kiese, Ralf; Kuzyakov, Yakov

    2014-05-01

    Soil organic carbon, microbial biomass carbon (MBC) and the metabolic quotient qCO2 - as sensitive and important parameters for soil fertility and C turnover - are strongly affected by land-use changes all over the world. These effects are particularly distinct upon conversion of natural to agricultural ecosystems due to very fast carbon (C) and nutrient cycles and high vulnerability, especially in the tropics. In this study, we used an elevational gradient on Mt. Kilimanjaro to investigate the effects of land-use change and elevation on Corg, MBC and qCO2. Down to a soil depth of 18 cm we compared 4 natural (Helichrysum, Erica forest, Podocarpus forest, Ocotea forest), 5 seminatural (disturbed Podocarpus forest, disturbed Ocotea forest, lower montane forest, grassland, savannah), 1 sustainably used (homegarden) and 2 intensively used ecosystems (coffee plantation, maize field) on an elevation gradient from 950 to 3880 m a.s.l.. Using an incubation device, soil CO2-efflux of 18 cm deep soil cores was measured under field moist conditions and mean annual temperature. MBC to Corg ratios varied between 0.7 and 2.3%. qCO2 increased with magnitude of the disturbance, albeit this effect decreased with elevation. Following the annual precipitation of the ecosystems, both, Corg and MBC showed a hum-shaped distribution with elevation, whereas their maxima were between 2500 and 3000 m a.s.l.. Additionaly, Corg and MBC contents were significantly reduced in intensively used agricultural systems. We conclude that the soil microbial biomass and its activity in Mt. Kilimanjaro ecosystems are strongly altered by land-use. This effect is more distinct in lower than in higher elevated ecosystems and strongly dependent on the magnitude of disturbance.

  1. MbT-Tool: An open-access tool based on Thermodynamic Electron Equivalents Model to obtain microbial-metabolic reactions to be used in biotechnological process.

    Science.gov (United States)

    Araujo, Pablo Granda; Gras, Anna; Ginovart, Marta

    2016-01-01

    Modelling cellular metabolism is a strategic factor in investigating microbial behaviour and interactions, especially for bio-technological processes. A key factor for modelling microbial activity is the calculation of nutrient amounts and products generated as a result of the microbial metabolism. Representing metabolic pathways through balanced reactions is a complex and time-consuming task for biologists, ecologists, modellers and engineers. A new computational tool to represent microbial pathways through microbial metabolic reactions (MMRs) using the approach of the Thermodynamic Electron Equivalents Model has been designed and implemented in the open-access framework NetLogo. This computational tool, called MbT-Tool (Metabolism based on Thermodynamics) can write MMRs for different microbial functional groups, such as aerobic heterotrophs, nitrifiers, denitrifiers, methanogens, sulphate reducers, sulphide oxidizers and fermenters. The MbT-Tool's code contains eighteen organic and twenty inorganic reduction-half-reactions, four N-sources (NH4 (+), NO3 (-), NO2 (-), N2) to biomass synthesis and twenty-four microbial empirical formulas, one of which can be determined by the user (CnHaObNc). MbT-Tool is an open-source program capable of writing MMRs based on thermodynamic concepts, which are applicable in a wide range of academic research interested in designing, optimizing and modelling microbial activity without any extensive chemical, microbiological and programing experience.

  2. MbT-Tool: An open-access tool based on Thermodynamic Electron Equivalents Model to obtain microbial-metabolic reactions to be used in biotechnological process

    Directory of Open Access Journals (Sweden)

    Pablo Araujo Granda

    2016-01-01

    Full Text Available Modelling cellular metabolism is a strategic factor in investigating microbial behaviour and interactions, especially for bio-technological processes. A key factor for modelling microbial activity is the calculation of nutrient amounts and products generated as a result of the microbial metabolism. Representing metabolic pathways through balanced reactions is a complex and time-consuming task for biologists, ecologists, modellers and engineers. A new computational tool to represent microbial pathways through microbial metabolic reactions (MMRs using the approach of the Thermodynamic Electron Equivalents Model has been designed and implemented in the open-access framework NetLogo. This computational tool, called MbT-Tool (Metabolism based on Thermodynamics can write MMRs for different microbial functional groups, such as aerobic heterotrophs, nitrifiers, denitrifiers, methanogens, sulphate reducers, sulphide oxidizers and fermenters. The MbT-Tool's code contains eighteen organic and twenty inorganic reduction-half-reactions, four N-sources (NH4+, NO3−, NO2−, N2 to biomass synthesis and twenty-four microbial empirical formulas, one of which can be determined by the user (CnHaObNc. MbT-Tool is an open-source program capable of writing MMRs based on thermodynamic concepts, which are applicable in a wide range of academic research interested in designing, optimizing and modelling microbial activity without any extensive chemical, microbiological and programing experience.

  3. Intratumoral metabolic heterogeneity predicts invasive components in breast ductal carcinoma in situ

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Hai-Jeon [Ewha Womans University School of Medicine, Department of Nuclear Medicine, Yangchun-Ku, Seoul (Korea, Republic of); Kim, Yemi [Ewha Womans University, Clinical Research Institute, Seoul (Korea, Republic of); Kim, Bom Sahn [Ewha Womans University School of Medicine, Department of Nuclear Medicine, Yangchun-Ku, Seoul (Korea, Republic of); Ewha Womans University, Clinical Research Institute, Seoul (Korea, Republic of)

    2015-12-15

    This study investigated whether texture-based imaging parameters could identify invasive components of ductal carcinoma in situ (DCIS). We enrolled 65 biopsy-confirmed DCIS patients (62 unilateral, 3 bilateral) who underwent {sup 18}F-FDG PET, diffusion-weighted imaging (DWI), or breast-specific gamma imaging (BSGI). We measured SUV{sub max} and intratumoral metabolic heterogeneity by the area under the curve (AUC) of cumulative SUV histograms (CSH) on PET, tumour-to-normal ratio (TNR) and coefficient of variation (COV) as an index of heterogeneity on BSGI, minimum ADC (ADC{sub min}) and ADC difference (ADC{sub diff}) as an index of heterogeneity on DWI. After surgery, final pathology was categorized as pure-DCIS (DCIS-P), DCIS with microinvasion (DCIS-MI), or invasive ductal carcinoma (IDC). Clinicopathologic features of DCIS were correlated with final classification. Final pathology confirmed 44 DCIS-P, 14 DCIS-MI, and 10 IDC. The invasive component of DCIS was significantly correlated with higher SUV{sub max} (p = 0.017) and lower AUC-CSH (p < 0.001) on PET, higher TNR (p = 0.008) and COV (p = 0.035) on BSGI, lower ADC{sub min} (p = 0.016) and higher ADC{sub diff} (p = 0.009) on DWI, and larger pathologic size (p = 0.018). On multiple regression analysis, AUC-CSH was the only significant predictor of invasive components (p = 0.044). The intratumoral metabolic heterogeneity of {sup 18}F-FDG PET was the most important predictor of invasive components of DCIS. (orig.)

  4. Intratumoral metabolic heterogeneity predicts invasive components in breast ductal carcinoma in situ

    International Nuclear Information System (INIS)

    Yoon, Hai-Jeon; Kim, Yemi; Kim, Bom Sahn

    2015-01-01

    This study investigated whether texture-based imaging parameters could identify invasive components of ductal carcinoma in situ (DCIS). We enrolled 65 biopsy-confirmed DCIS patients (62 unilateral, 3 bilateral) who underwent 18 F-FDG PET, diffusion-weighted imaging (DWI), or breast-specific gamma imaging (BSGI). We measured SUV max and intratumoral metabolic heterogeneity by the area under the curve (AUC) of cumulative SUV histograms (CSH) on PET, tumour-to-normal ratio (TNR) and coefficient of variation (COV) as an index of heterogeneity on BSGI, minimum ADC (ADC min ) and ADC difference (ADC diff ) as an index of heterogeneity on DWI. After surgery, final pathology was categorized as pure-DCIS (DCIS-P), DCIS with microinvasion (DCIS-MI), or invasive ductal carcinoma (IDC). Clinicopathologic features of DCIS were correlated with final classification. Final pathology confirmed 44 DCIS-P, 14 DCIS-MI, and 10 IDC. The invasive component of DCIS was significantly correlated with higher SUV max (p = 0.017) and lower AUC-CSH (p < 0.001) on PET, higher TNR (p = 0.008) and COV (p = 0.035) on BSGI, lower ADC min (p = 0.016) and higher ADC diff (p = 0.009) on DWI, and larger pathologic size (p = 0.018). On multiple regression analysis, AUC-CSH was the only significant predictor of invasive components (p = 0.044). The intratumoral metabolic heterogeneity of 18 F-FDG PET was the most important predictor of invasive components of DCIS. (orig.)

  5. In situ Microbial Community Control of the Stability of Bio-Reduced Uranium

    International Nuclear Information System (INIS)

    Long, Phillip E.; McKinley, James P.; White, David C.

    2006-01-01

    In aerobic aquifers typical of many Department of Energy (DOE) legacy waste sites, uranium is present in the oxidized U(VI) form which is soluble and thus mobile compared to U(IV). Previous work at the Old Rifle Uranium Mill Tailings Remedial Action (UMTRA) site demonstrated that biostimulation by acetate injection promoted growth of Geobacteraceae and stimulated the microbial reduction of U(VI) to less soluble U(IV) (1, 4). Despite the potential for oxidative dissolution of bio-reduced U(IV), field experiments at the Old Rifle site show that although the rate of U(VI) reduction decreases following the on-set of sulfate reduction, U(VI) reduction continues even following the cessation of acetate injection (1, 4). However, U(VI) reduction is reversible and the basis for the observed maintenance of U(VI) reduction post-stimulation is a critical but as yet unresolved issue for the application of biostimulation as a treatment technology. The continued U(VI) reduction and the maintenance of reduced U(IV) may result from many factors including U(VI) reduction by sulfate reducing bacteria (SRB), generation of H2S or FeS0.9 which serves as an oxygen sink, or the preferential sorption of U(VI) by microbial cells or biopolymers. The overall goal of the project is to develop an understanding of the mechanisms for the maintenance of bio-reduced uranium in an aerobic aquifer under field conditions following the cessation of electron donor addition

  6. Microbial communities associated with uranium in-situ recovery mining process are related to acid mine drainage assemblages.

    Science.gov (United States)

    Coral, Thomas; Descostes, Michaël; De Boissezon, Hélène; Bernier-Latmani, Rizlan; de Alencastro, Luiz Felippe; Rossi, Pierre

    2018-07-01

    A large fraction (47%) of the world's uranium is mined by a technique called "In Situ Recovery" (ISR). This mining technique involves the injection of a leaching fluid (acidic or alkaline) into a uranium-bearing aquifer and the pumping of the resulting solution through cation exchange columns for the recovery of dissolved uranium. The present study reports the in-depth alterations brought to autochthonous microbial communities during acidic ISR activities. Water samples were collected from a uranium roll-front deposit that is part of an ISR mine in operation (Tortkuduk, Kazakhstan). Water samples were obtained at a depth of ca 500 m below ground level from several zones of the Uyuk aquifer following the natural redox zonation inherited from the roll front deposit, including the native mineralized orebody and both upstream and downstream adjacent locations. Samples were collected equally from both the entrance and the exit of the uranium concentration plant. Next-generation sequencing data showed that the redox gradient shaped the community structures, within the anaerobic, reduced, and oligotrophic habitats of the native aquifer zones. Acid injection induced drastic changes in the structures of these communities, with a large decrease in both cell numbers and diversity. Communities present in the acidified (pH values acid mine drainage, with the dominance of Sulfobacillus sp., Leptospirillum sp. and Acidithiobacillus sp., as well as the archaean Ferroplasma sp. Communities located up- and downstream of the mineralized zone under ISR and affected by acidic fluids were blended with additional facultative anaerobic and acidophilic microorganisms. These mixed biomes may be suitable communities for the natural attenuation of ISR mining-affected subsurface through the reduction of metals and sulfate. Assessing the effect of acidification on the microbial community is critical to evaluating the potential for natural attenuation or active bioremediation strategies

  7. Comparison of three 15N methods to correct for microbial contamination when assessing in situ protein degradability of fresh forages.

    Science.gov (United States)

    Kamoun, M; Ammar, H; Théwis, A; Beckers, Y; France, J; López, S

    2014-11-01

    The use of stable (15)N as a marker to determine microbial contamination in nylon bag incubation residues to estimate protein degradability was investigated. Three methods using (15)N were compared: (15)N-labeled forage (dilution method, LF), (15)N enrichment of rumen solids-associated bacteria (SAB), and (15)N enrichment of rumen liquid-associated bacteria (LAB). Herbage from forages differing in protein and fiber contents (early-cut Italian ryegrass, late-cut Italian ryegrass, and red clover) were freeze-dried and ground and then incubated in situ in the rumen of 3 steers for 3, 6, 12, 24, and 48 h using the nylon bag technique. The (15)N-labeled forages were obtained by fertilizing the plots where herbage was grown with (15)NH4 (15)NO3. Unlabeled forages (obtained from plots fertilized with NH4NO3) were incubated at the same time that ((15)NH4)2SO4 was continuously infused into the rumen of the steers, and then pellets of labeled SAB and LAB were isolated by differential centrifugation of samples of ruminal contents. The proportion of bacterial N in the incubation residues increased from 0.09 and 0.45 g bacterial N/g total N at 3 h of incubation to 0.37 and 0.85 g bacterial N/g total N at 48 h of incubation for early-cut and late-cut ryegrass, respectively. There were differences (P forage (late-cut ryegrass) was 0.51, whereas the corrected values were 0.85, 0.84, and 0.77 for the LF, SAB, and LAB methods, respectively. With early-cut ryegrass and red clover, the differences between uncorrected and corrected values ranged between 6% and 13%, with small differences among the labeling methods. Generally, methods using labeled forage or labeled SAB and LAB provided similar corrected degradability values. The accuracy in estimating the extent of degradation of protein in the rumen from in situ disappearance curves is improved when values are corrected for microbial contamination of the bag residue.

  8. Effect of Bioprocessing on the In Vitro Colonic Microbial Metabolism of Phenolic Acids from Rye Bran Fortified Breads

    DEFF Research Database (Denmark)

    Koistinen, Ville M; Nordlund, Emilia; Katina, Kati

    2017-01-01

    in an in vitro colon model, the metabolites were analyzed using two different methods applying mass spectrometry. While phenolic acids were released more extensively from the bioprocessed bran bread and ferulic acid had consistently higher concentrations in the bread type during fermentation, there were only......Cereal bran is an important source of dietary fiber and bioactive compounds, such as phenolic acids. We aimed to study the phenolic acid metabolism of native and bioprocessed rye bran fortified refined wheat bread and to elucidate the microbial metabolic route of phenolic acids. After incubation...

  9. Microbial metabolism alters pore water chemistry and increases consolidation of oil sands tailings.

    Science.gov (United States)

    Arkell, Nicholas; Kuznetsov, Petr; Kuznetsova, Alsu; Foght, Julia M; Siddique, Tariq

    2015-01-01

    Tailings produced during bitumen extraction from surface-mined oil sands ores (tar sands) comprise an aqueous suspension of clay particles that remain dispersed for decades in tailings ponds. Slow consolidation of the clays hinders water recovery for reuse and retards volume reduction, thereby increasing the environmental footprint of tailings ponds. We investigated mechanisms of tailings consolidation and revealed that indigenous anaerobic microorganisms altered porewater chemistry by producing CO and CH during metabolism of acetate added as a labile carbon amendment. Entrapped biogenic CO decreased tailings pH, thereby increasing calcium (Ca) and magnesium (Mg) cations and bicarbonate (HCO) concentrations in the porewater through dissolution of carbonate minerals. Soluble ions increased the porewater ionic strength, which, with higher exchangeable Ca and Mg, decreased the diffuse double layer of clays and increased consolidation of tailings compared with unamended tailings in which little microbial activity was observed. These results are relevant to effective tailings pond management strategies. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

  10. 2004 Molecular Basis of Microbial One-Carbon Metabolism Gordon Conference - August 1-6, 2004

    Energy Technology Data Exchange (ETDEWEB)

    Joseph A. Krzycki

    2005-09-15

    The Gordon Research Conference (GRC) on 2004 Molecular Basis of Microbial One-Carbon Metabolism Gordon Conference - August 1-6, 2004 was held at Mount Holyoke College, South Hadley, MA from August 1-6, 2004. The Conference was well-attended with 117 participants (attendees list attached). The attendees represented the spectrum of endeavor in this field coming from academia, industry, and government laboratories, both U.S. and foreign scientists, senior researchers, young investigators, and students. In designing the formal speakers program, emphasis was placed on current unpublished research and discussion of the future target areas in this field. There was a conscious effort to stimulate lively discussion about the key issues in the field today. Time for formal presentations was limited in the interest of group discussions. In order that more scientists could communicate their most recent results, poster presentation time was scheduled. Attached is a copy of the formal schedule and speaker program and the poster program. In addition to these formal interactions, 'free time' was scheduled to allow informal discussions. Such discussions are fostering new collaborations and joint efforts in the field.

  11. Genetic and metabolic engineering for microbial production of poly-γ-glutamic acid.

    Science.gov (United States)

    Cao, Mingfeng; Feng, Jun; Sirisansaneeyakul, Sarote; Song, Cunjiang; Chisti, Yusuf

    2018-05-28

    Poly-γ-glutamic acid (γ-PGA) is a natural biopolymer of glutamic acid. The repeating units of γ-PGA may be derived exclusively from d-glutamic acid, or l-glutamic acid, or both. The monomer units are linked by amide bonds between the α-amino group and the γ-carboxylic acid group. γ-PGA is biodegradable, edible and water-soluble. It has numerous existing and emerging applications in processing of foods, medicines and cosmetics. This review focuses on microbial production of γ-PGA via genetically and metabolically engineered recombinant bacteria. Strategies for improving production of γ-PGA include modification of its biosynthesis pathway, enhancing the production of its precursor (glutamic acid), and preventing loss of the precursor to competing byproducts. These and other strategies are discussed. Heterologous synthesis of γ-PGA in industrial bacterial hosts that do not naturally produce γ-PGA is discussed. Emerging trends and the challenges affecting the production of γ-PGA are reviewed. Copyright © 2018. Published by Elsevier Inc.

  12. Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine.

    Science.gov (United States)

    Louis, Petra; Flint, Harry J

    2009-05-01

    Butyrate-producing bacteria play a key role in colonic health in humans. This review provides an overview of the current knowledge of the diversity, metabolism and microbial ecology of this functionally important group of bacteria. Human colonic butyrate producers are Gram-positive firmicutes, but are phylogenetically diverse, with the two most abundant groups related to Eubacterium rectale/Roseburia spp. and to Faecalibacterium prausnitzii. Five different arrangements have been identified for the genes of the central pathway involved in butyrate synthesis, while in most cases butyryl-CoA : acetate CoA-transferase, rather than butyrate kinase, appears to perform the final step in butyrate synthesis. Mechanisms have been proposed recently in non-gut Clostridium spp. whereby butyrate synthesis can result in energy generation via both substrate-level phosphorylation and proton gradients. Here we suggest that these mechanisms also apply to the majority of butyrate producers from the human colon. The roles of these bacteria in the gut community and their influence on health are now being uncovered, taking advantage of the availability of cultured isolates and molecular methodologies. Populations of F. prausnitzii are reported to be decreased in Crohn's disease, for example, while populations of Roseburia relatives appear to be particularly sensitive to the diet composition in human volunteer studies.

  13. Elevated CO2 shifts the functional structure and metabolic potentials of soil microbial communities in a C4 agroecosystem.

    Science.gov (United States)

    Xiong, Jinbo; He, Zhili; Shi, Shengjing; Kent, Angela; Deng, Ye; Wu, Liyou; Van Nostrand, Joy D; Zhou, Jizhong

    2015-03-20

    Atmospheric CO2 concentration is continuously increasing, and previous studies have shown that elevated CO2 (eCO2) significantly impacts C3 plants and their soil microbial communities. However, little is known about effects of eCO2 on the compositional and functional structure, and metabolic potential of soil microbial communities under C4 plants. Here we showed that a C4 maize agroecosystem exposed to eCO2 for eight years shifted the functional and phylogenetic structure of soil microbial communities at both soil depths (0-5 cm and 5-15 cm) using EcoPlate and functional gene array (GeoChip 3.0) analyses. The abundances of key genes involved in carbon (C), nitrogen (N) and phosphorus (P) cycling were significantly stimulated under eCO2 at both soil depths, although some differences in carbon utilization patterns were observed between the two soil depths. Consistently, CO2 was found to be the dominant factor explaining 11.9% of the structural variation of functional genes, while depth and the interaction of depth and CO2 explained 5.2% and 3.8%, respectively. This study implies that eCO2 has profound effects on the functional structure and metabolic potential/activity of soil microbial communities associated with C4 plants, possibly leading to changes in ecosystem functioning and feedbacks to global change in C4 agroecosystems.

  14. Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations.

    Science.gov (United States)

    Wu, Xiaofen; Holmfeldt, Karin; Hubalek, Valerie; Lundin, Daniel; Åström, Mats; Bertilsson, Stefan; Dopson, Mark

    2016-05-01

    Microorganisms in the terrestrial deep biosphere host up to 20% of the earth's biomass and are suggested to be sustained by the gases hydrogen and carbon dioxide. A metagenome analysis of three deep subsurface water types of contrasting age (from 86% coverage. The populations were dominated by Proteobacteria, Candidate divisions, unclassified archaea and unclassified bacteria. The estimated genome sizes of the biosphere. The data were finally used to create a combined metabolic model of the deep terrestrial biosphere microbial community.

  15. [Advances in metabolic engineering for the microbial production of naturally occurring terpenes-limonene and bisabolene: a mini review].

    Science.gov (United States)

    Pang, Yaru; Hu, Zhihui; Xiao, Dongguang; Yu, Aiqun

    2018-01-25

    Limonene (C₁₀H₁₆) and bisabolene (C₁₅H₂₄) are both naturally occurring terpenes in plants. Depending on the number of C₅ units, limonene and bisabolene are recognized as representative monoterpenes and sesquiterpenes, respectively. Limonene and bisabolene are important pharmaceutical and nutraceutical products used in the prevention and treatment of cancer and many other diseases. In addition, they can be used as starting materials to produce a range of commercially valuable products, such as pharmaceuticals, nutraceuticals, cosmetics, and biofuels. The low abundance or yield of limonene and bisabolene in plants renders their isolation from plant sources non-economically viable. Isolation of limonene and bisabolene from plants also suffers from low efficiency and often requires harsh reaction conditions, prolonged reaction times, and expensive equipment cost. Recently, the rapid developments in metabolic engineering of microbes provide a promising alternative route for producing these plant natural products. Therefore, producing limonene and bisabolene by engineering microbial cells into microbial factories is becoming an attractive alternative approach that can overcome the bottlenecks, making it more sustainable, environmentally friendly and economically competitive. Here, we reviewed the status of metabolic engineering of microbes that produce limonene and bisabolene including microbial hosts, key enzymes, metabolic pathways and engineering of limonene/bisabolene biosynthesis. Furthermore, key challenges and future perspectives were discussed.

  16. Gut Microbial Metabolism of Polyphenols from Black Tea and Red Wine/Grape Juice Is Source-Specific and Colon-Region Dependent

    NARCIS (Netherlands)

    Dorsten, van F.A.; Peters, S.; Gross, G.; Gomez-Roldan, V.; Klinkenberg, M.; Vos, de Ric; Vaughan, E.E.; Duynhoven, van J.P.M.; Possemiers, S.; Wiele, van der T.; Jacobs, D.M.

    2012-01-01

    The colonic microbial degradation of a polyphenol-rich black tea extract (BTE) and red wine/grape juice extract (RWGE) was compared in a five-stage in vitro gastrointestinal model (TWINSHIME). Microbial metabolism of BTE and RWGE polyphenols in the TWINSHIME was studied subsequently in single- and

  17. Microbial communities from different subsystems in biological heap leaching system play different roles in iron and sulfur metabolisms.

    Science.gov (United States)

    Xiao, Yunhua; Liu, Xueduan; Ma, Liyuan; Liang, Yili; Niu, Jiaojiao; Gu, Yabing; Zhang, Xian; Hao, Xiaodong; Dong, Weiling; She, Siyuan; Yin, Huaqun

    2016-08-01

    The microbial communities are important for minerals decomposition in biological heap leaching system. However, the differentiation and relationship of composition and function of microbial communities between leaching heap (LH) and leaching solution (LS) are still unclear. In this study, 16S rRNA gene sequencing was used to assess the microbial communities from the two subsystems in ZiJinShan copper mine (Fujian province, China). Results of PCoA and dissimilarity test showed that microbial communities in LH samples were significantly different from those in LS samples. The dominant genera of LH was Acidithiobacillus (57.2 ∼ 87.9 %), while Leptospirillum (48.6 ∼ 73.7 %) was predominant in LS. Environmental parameters (especially pH) were the major factors to influence the composition and structure of microbial community by analysis of Mantel tests. Results of functional test showed that microbial communities in LH utilized sodium thiosulfate more quickly and utilized ferrous sulfate more slowly than those in LS, which further indicated that the most sulfur-oxidizing processes of bioleaching took place in LH and the most iron-oxidizing processes were in LS. Further study found that microbial communities in LH had stronger pyrite leaching ability, and iron extraction efficiency was significantly positively correlated with Acidithiobacillus (dominated in LH), which suggested that higher abundance ratio of sulfur-oxidizing microbes might in favor of minerals decomposition. Finally, a conceptual model was designed through the above results to better exhibit the sulfur and iron metabolism in bioleaching systems.

  18. In situ stimulation vs. bioaugmentation: Can microbial inoculation of plant roots enhance biodegradation of organic compounds?

    Energy Technology Data Exchange (ETDEWEB)

    Kingsley, M.T.; Metting, F.B. Jr.; Fredrickson, J.K. [Pacific Northwest Lab., Richland, WA (United States); Seidler, R.J. [Environmental Protection Agency, Corvallis, OR (United States). Environmental Research Lab.

    1993-06-01

    The use of plant roots and their associated rhizosphere bacteria for biocontainment and biorestoration offers several advantages for treating soil-dispersed contaminants and for application to large land areas. Plant roots function as effective delivery systems, since root growth transports bacteria vertically and laterally along the root in the soil column (see [ 1,2]). Movement of microbes along roots and downward in the soil column can be enhanced via irrigation [1-4]. For example, Ciafardini et al. [3] increased the nodulation and the final yield of soybeans during pod filling by including Bradyrhizobium japonicum in the irrigation water. Using rhizosphere microorganisms is advantageous for biodegradation of compounds that are degraded mainly by cometabolic processes, e.g., trichloroethylene (TCE). The energy source for bacterial growth and metabolism is supplied by the plant in the form of root exudates and other sloughed organic material. Plants are inexpensive, and by careful choice of species that possess either tap or fibrous root growth patterns, they can be used to influence mass transport of soil contaminants to the root surface via the transpiration stream [5]. Cropping of plants to remove heavy metals from contaminated soils has been proposed as a viable, low-cost, low-input treatment option [6]. The interest in use of plants as a remediation strategy has even reached the popular press [7], where the use of ragweed for the reclamation of sites contaminated with tetraethyl lead and other heavy metals was discussed.

  19. Genome-Enabled Modeling of Biogeochemical Processes Predicts Metabolic Dependencies that Connect the Relative Fitness of Microbial Functional Guilds

    Science.gov (United States)

    Brodie, E.; King, E.; Molins, S.; Karaoz, U.; Steefel, C. I.; Banfield, J. F.; Beller, H. R.; Anantharaman, K.; Ligocki, T. J.; Trebotich, D.

    2015-12-01

    Pore-scale processes mediated by microorganisms underlie a range of critical ecosystem services, regulating carbon stability, nutrient flux, and the purification of water. Advances in cultivation-independent approaches now provide us with the ability to reconstruct thousands of genomes from microbial populations from which functional roles may be assigned. With this capability to reveal microbial metabolic potential, the next step is to put these microbes back where they belong to interact with their natural environment, i.e. the pore scale. At this scale, microorganisms communicate, cooperate and compete across their fitness landscapes with communities emerging that feedback on the physical and chemical properties of their environment, ultimately altering the fitness landscape and selecting for new microbial communities with new properties and so on. We have developed a trait-based model of microbial activity that simulates coupled functional guilds that are parameterized with unique combinations of traits that govern fitness under dynamic conditions. Using a reactive transport framework, we simulate the thermodynamics of coupled electron donor-acceptor reactions to predict energy available for cellular maintenance, respiration, biomass development, and enzyme production. From metagenomics, we directly estimate some trait values related to growth and identify the linkage of key traits associated with respiration and fermentation, macromolecule depolymerizing enzymes, and other key functions such as nitrogen fixation. Our simulations were carried out to explore abiotic controls on community emergence such as seasonally fluctuating water table regimes across floodplain organic matter hotspots. Simulations and metagenomic/metatranscriptomic observations highlighted the many dependencies connecting the relative fitness of functional guilds and the importance of chemolithoautotrophic lifestyles. Using an X-Ray microCT-derived soil microaggregate physical model combined

  20. New transposon tools tailored for metabolic engineering of Gram-negative microbial cell factories

    Directory of Open Access Journals (Sweden)

    Esteban eMartínez-García

    2014-10-01

    Full Text Available Re-programming microorganisms to modify their existing functions and/or to bestow bacteria with entirely new-to-Nature tasks have largely relied so far on specialized molecular biology tools. Such endeavors are not only relevant in the burgeoning metabolic engineering arena, but also instrumental to explore the functioning of complex regulatory networks from a fundamental point of view. À la carte modification of bacterial genomes thus calls for novel tools to make genetic manipulations easier. We propose the use of a series of new broad-host-range mini-Tn5 vectors, termed pBAMDs, for the delivery of gene(s into the chromosome of Gram-negative bacteria and for generating saturated mutagenesis libraries in gene function studies. These delivery vectors endow the user with the possibility of easy cloning and subsequent insertion of functional cargoes with three different antibiotic resistance markers (kanamycin, streptomycin, and gentamicin. After validating the pBAMD vectors in the environmental bacterium Pseudomonas putida KT2440, their use was also illustrated by inserting the entire poly(3-hydroxybutyrate (PHB synthesis pathway from Cupriavidus necator in the chromosome of a phosphotransacetylase mutant of Escherichia coli. PHB is a completely biodegradable polyester with a number of industrial applications that make it attractive as a potential replacement of oil-based plastics. The non-selective nature of chromosomal insertions of the biosynthetic genes was evidenced by a large landscape of PHB synthesis levels in independent clones. One clone was selected and further characterized as a microbial cell factory for PHB accumulation, and it achieved polymer accumulation levels comparable to those of a plasmid-bearing recombinant. Taken together, our results demonstrate that the new mini-Tn5 vectors can be used to confer interesting phenotypes in Gram-negative bacteria that would be very difficult to engineer through direct manipulation of the

  1. New Transposon Tools Tailored for Metabolic Engineering of Gram-Negative Microbial Cell Factories

    International Nuclear Information System (INIS)

    Martínez-García, Esteban; Aparicio, Tomás; Lorenzo, Víctor de; Nikel, Pablo I.

    2014-01-01

    Re-programming microorganisms to modify their existing functions and/or to bestow bacteria with entirely new-to-Nature tasks have largely relied so far on specialized molecular biology tools. Such endeavors are not only relevant in the burgeoning metabolic engineering arena but also instrumental to explore the functioning of complex regulatory networks from a fundamental point of view. À la carte modification of bacterial genomes thus calls for novel tools to make genetic manipulations easier. We propose the use of a series of new broad-host-range mini-Tn5-vectors, termed pBAMDs, for the delivery of gene(s) into the chromosome of Gram-negative bacteria and for generating saturated mutagenesis libraries in gene function studies. These delivery vectors endow the user with the possibility of easy cloning and subsequent insertion of functional cargoes with three different antibiotic-resistance markers (kanamycin, streptomycin, and gentamicin). After validating the pBAMD vectors in the environmental bacterium Pseudomonas putida KT2440, their use was also illustrated by inserting the entire poly(3-hydroxybutyrate) (PHB) synthesis pathway from Cupriavidus necator in the chromosome of a phosphotransacetylase mutant of Escherichia coli. PHB is a completely biodegradable polyester with a number of industrial applications that make it attractive as a potential replacement of oil-based plastics. The non-selective nature of chromosomal insertions of the biosynthetic genes was evidenced by a large landscape of PHB synthesis levels in independent clones. One clone was selected and further characterized as a microbial cell factory for PHB accumulation, and it achieved polymer accumulation levels comparable to those of a plasmid-bearing recombinant. Taken together, our results demonstrate that the new mini-Tn5-vectors can be used to confer interesting phenotypes in Gram-negative bacteria that would be very difficult to engineer through direct manipulation of the structural genes.

  2. New Transposon Tools Tailored for Metabolic Engineering of Gram-Negative Microbial Cell Factories

    Energy Technology Data Exchange (ETDEWEB)

    Martínez-García, Esteban; Aparicio, Tomás; Lorenzo, Víctor de; Nikel, Pablo I., E-mail: pablo.nikel@cnb.csic.es [Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Madrid (Spain)

    2014-10-28

    Re-programming microorganisms to modify their existing functions and/or to bestow bacteria with entirely new-to-Nature tasks have largely relied so far on specialized molecular biology tools. Such endeavors are not only relevant in the burgeoning metabolic engineering arena but also instrumental to explore the functioning of complex regulatory networks from a fundamental point of view. À la carte modification of bacterial genomes thus calls for novel tools to make genetic manipulations easier. We propose the use of a series of new broad-host-range mini-Tn5-vectors, termed pBAMDs, for the delivery of gene(s) into the chromosome of Gram-negative bacteria and for generating saturated mutagenesis libraries in gene function studies. These delivery vectors endow the user with the possibility of easy cloning and subsequent insertion of functional cargoes with three different antibiotic-resistance markers (kanamycin, streptomycin, and gentamicin). After validating the pBAMD vectors in the environmental bacterium Pseudomonas putida KT2440, their use was also illustrated by inserting the entire poly(3-hydroxybutyrate) (PHB) synthesis pathway from Cupriavidus necator in the chromosome of a phosphotransacetylase mutant of Escherichia coli. PHB is a completely biodegradable polyester with a number of industrial applications that make it attractive as a potential replacement of oil-based plastics. The non-selective nature of chromosomal insertions of the biosynthetic genes was evidenced by a large landscape of PHB synthesis levels in independent clones. One clone was selected and further characterized as a microbial cell factory for PHB accumulation, and it achieved polymer accumulation levels comparable to those of a plasmid-bearing recombinant. Taken together, our results demonstrate that the new mini-Tn5-vectors can be used to confer interesting phenotypes in Gram-negative bacteria that would be very difficult to engineer through direct manipulation of the structural genes.

  3. Carbon isotopic patterns of amino acids associated with various microbial metabolic pathways and physiological conditions

    Science.gov (United States)

    Wang, P. L.; Hsiao, K. T.; Lin, L. H.

    2017-12-01

    Amino acids represent one of the most important categories of biomolecule. Their abundance and isotopic patterns have been broadly used to address issues related to biochemical processes and elemental cycling in natural environments. Previous studies have shown that various carbon assimilative pathways of microorganisms (e.g. autotrophy, heterotrophy and acetotrophy) could be distinguished by carbon isotopic patterns of amino acids. However, the taxonomic and catabolic coverage are limited in previous examination. This study aims to uncover the carbon isotopic patterns of amino acids for microorganisms remaining uncharacterized but bearing biogeochemical and ecological significance in anoxic environments. To fulfill the purpose, two anaerobic strains were isolated from riverine wetland and mud volcano in Taiwan. One strain is a sulfate reducing bacterium (related to Desulfovibrio marrakechensis), which is capable of utilizing either H2 or lactate, and the other is a methanogen (related to Methanolobus profundi), which grows solely with methyl-group compounds. Carbon isotope analyses of amino acids were performed on cells grown in exponential and stationary phase. The isotopic patterns were similar for all examined cultures, showing successive 13C depletion along synthetic pathways. No significant difference was observed for the methanogen and lactate-utilizing sulfate reducer harvested in exponential and stationary phases. In contrast, the H2-utilizing sulfate reducer harvested in stationary phase depleted and enriched 13C in aspartic acid and glycine, respectively when compared with that harvested in exponential phase. Such variations might infer the change of carbon flux during synthesis of these two amino acids in the reverse TCA cycle. In addition, the discriminant function analysis for all available data from culture studies further attests the capability of using carbon isotope patterns of amino acids in identifying microbial metabolisms.

  4. Impact of anti-acidification microbial consortium on carbohydrate metabolism of key microbes during food waste composting.

    Science.gov (United States)

    Song, Caihong; Li, Mingxiao; Qi, Hui; Zhang, Yali; Liu, Dongming; Xia, Xunfeng; Pan, Hongwei; Xi, Beidou

    2018-07-01

    This study investigated the effect of anti-acidification microbial consortium (AAMC), which act synergistically for rapid bioconversion of organic acids on carbohydrate metabolism of key microbes in the course of food waste (FW) composting by metaproteomics. AAMC was inoculated to the composting mass and compared with treatment with alkaline compounds and the control without any amendment. Inoculating AAMC could effectively accelerate carbohydrate degradation process and improve composting efficiency. Carbohydrate metabolic network profiles showed the inoculation with AAMC could increase significantly the types of enzymes catalysing the degradation of lignin, cellulose and hemicellulose. Furthermore, AAMC inoculum could increase not only diversities of microbes producing key enzymes in metabolism pathways of acetic and propionic acids, but also the amounts of these key enzymes. The increase of diversities of microbes could disperse the pressure from acidic adversity on microorganisms which were capable to degrade acetic and propionic acids. Copyright © 2018 Elsevier Ltd. All rights reserved.

  5. Radioactive tracers as a tool for the study of in situ meiofaunal-microbial trophic interactions in marine sediments

    International Nuclear Information System (INIS)

    Carman, K.R.

    1989-01-01

    Three methods of delivering labeled substrates to natural cores of sediments were compared. Slurried sediments disrupted the sedimentary structure and significantly altered uptake of labeled substrates by copepod species. Thus, disruption of sedimentary structure can significantly alter microbial-meiofaunal interactions and influence the results of grazing studies. The [ 3 H]-thymidine technique for measuring bacterial production was evaluated. The metabolic fate of labeled thymidine in a coastal marine sediment was not consistent with assumptions necessary for measuring bacterial production or its consumption by meiofauna. Microautoradiography was used to demonstrate the sedimentary microalgae and heterotrophic bacteria can be selectively labeled with [ 14 C]bicarbonate and labeled organic substrates, respectively. A study was performed to determine if radioactivity measured in copepods from grazing experiments was the result of ingestion of labeled microorganisms or the result of uptake by non-feeding processes. Uptake of label by copepods from [ 14 C]-bicarbonate was due almost exclusively to grazing on microalgae. Uptake of label by copepods from [ 14 C]-acetate, however, resulted from activity by epicuticular bacteria and was not due to ingestion of labeled bacteria

  6. A Green Microbial Fuel Cell-Based Biosensor for In Situ Chromium (VI) Measurement in Electroplating Wastewater.

    Science.gov (United States)

    Wu, Li-Chun; Tsai, Teh-Hua; Liu, Man-Hai; Kuo, Jui-Ling; Chang, Yung-Chu; Chung, Ying-Chien

    2017-10-27

    The extensive use of Cr(VI) in many industries and the disposal of Cr(VI)-containing wastes have resulted in Cr(VI)-induced environmental contamination. Cr(VI) compounds are associated with increased cancer risks; hence, the detection of toxic Cr(VI) compounds is crucial. Various methods have been developed for Cr(VI) measurement, but they are often conducted offsite and cannot provide real-time toxicity monitoring. A microbial fuel cell (MFC) is an eco-friendly and self-sustaining device that has great potential as a biosensor for in situ Cr(VI) measurement, especially for wastewater generated from different electroplating units. In this study, Exiguobacterium aestuarii YC211, a facultatively anaerobic, Cr(VI)-reducing, salt-tolerant, and exoelectrogenic bacterium, was isolated and inoculated into an MFC to evaluate its feasibility as a Cr(VI) biosensor. The Cr(VI) removal efficiency of E. aestuarii YC211 was not affected by the surrounding environment (pH 5-9, 20-35 °C, coexisting ions, and salinity of 0-15 g/L). The maximum power density of the MFC biosensor was 98.3 ± 1.5 mW/m² at 1500 Ω. A good linear relationship ( r ² = 0.997) was observed between the Cr(VI) concentration (2.5-60 mg/L) and the voltage output. The developed MFC biosensor is a simple device that can accurately measure Cr(VI) concentrations in the actual electroplating wastewater that is generated from different electroplating units within 30 min with low deviations (-6.1% to 2.2%). After treating the actual electroplating wastewater with the MFC, the predominant family in the biofilm was found to be Bacillaceae (95.3%) and was further identified as the originally inoculated E. aestuarii YC211 by next generation sequencing (NGS). Thus, the MFC biosensor can measure Cr(VI) concentrations in situ in the effluents from different electroplating units, and it can potentially help in preventing the violation of effluent regulations.

  7. In situ dynamics of O2, pH, light and photosynthesis in ikaite tufa columns (Ikka Fjord, Greenland – a unique microbial habitat.

    Directory of Open Access Journals (Sweden)

    Erik Christian Løvbjerg Trampe

    2016-05-01

    Full Text Available The Ikka Fjord (SW Greenland harbors a unique microbial habitat in the form of several hundred submarine tufa columns composed of ikaite, a special hexahydrate form of calcium carbonate that precipitates when alkaline phosphate- and carbonate-enriched spring water seeping out of the sea floor meets cold seawater. While several unique heterotrophic microbes have been isolated from the tufa columns, the microbial activity and the boundary conditions for microbial growth in ikaite have remained unexplored. We present the first detailed in situ characterization of the physico-chemical microenvironment and activity of oxygenic phototrophs thriving within the ikaite columns. In situ underwater microsensor measurements of pH, temperature, and irradiance in the porous ikaite crystal matrix, revealed an extreme microenvironment characterized by low temperatures, strong light attenuation, and gradients of pH changing from pH 9 at the outer column surface to above pH 10 over the first 1-2 cm of the ikaite. This outer layer of the freshly deposited ikaite matrix contained densely pigmented yellow and green zones harboring a diverse phototrophic community dominated by diatoms and cyanobacteria, respectively, as shown by amplicon sequencing. In situ O2 measurements, as well as underwater variable chlorophyll fluorescence measurements of photosynthetic activity, demonstrated high levels of oxygenic photosynthesis in this extreme gradient environment with strong irradiance-driven O2 dynamics ranging from anoxia to hyperoxic conditions in the ikaite matrix, albeit the local formation of gas bubbles buffered the day-night dynamics of O2 in the tufa columns. The microbial phototrophs in the ikaite matrix are embedded in exopolymers forming endolithic biofilms that may interact with mineral formation and cementing of ikaite crystals.

  8. In situ Dynamics of O2, pH, Light, and Photosynthesis in Ikaite Tufa Columns (Ikka Fjord, Greenland)-A Unique Microbial Habitat.

    Science.gov (United States)

    Trampe, Erik C L; Larsen, Jens E N; Glaring, Mikkel A; Stougaard, Peter; Kühl, Michael

    2016-01-01

    The Ikka Fjord (SW Greenland) harbors a unique microbial habitat in the form of several hundred submarine tufa columns composed of ikaite, a special hexahydrate form of calcium carbonate that precipitates when alkaline phosphate- and carbonate-enriched spring water seeping out of the sea floor meets cold seawater. While several unique heterotrophic microbes have been isolated from the tufa columns, the microbial activity, and the boundary conditions for microbial growth in ikaite have remained unexplored. We present the first detailed in situ characterization of the physico-chemical microenvironment and activity of oxygenic phototrophs thriving within the ikaite columns. In situ underwater microsensor measurements of pH, temperature, and irradiance in the porous ikaite crystal matrix, revealed an extreme microenvironment characterized by low temperatures, strong light attenuation, and gradients of pH changing from pH 9 at the outer column surface to above pH 10 over the first 1-2 cm of the ikaite. This outer layer of the freshly deposited ikaite matrix contained densely pigmented yellow and green zones harboring a diverse phototrophic community dominated by diatoms and cyanobacteria, respectively, as shown by amplicon sequencing. In situ O2 measurements, as well as underwater variable chlorophyll fluorescence measurements of photosynthetic activity, demonstrated high levels of oxygenic photosynthesis in this extreme gradient environment with strong irradiance-driven O2 dynamics ranging from anoxia to hyperoxic conditions in the ikaite matrix, albeit the local formation of gas bubbles buffered the day-night dynamics of O2 in the tufa columns. The microbial phototrophs in the ikaite matrix are embedded in exopolymers forming endolithic biofilms that may interact with mineral formation and cementing of ikaite crystals.

  9. In situ Dynamics of O2, pH, Light, and Photosynthesis in Ikaite Tufa Columns (Ikka Fjord, Greenland)—A Unique Microbial Habitat

    Science.gov (United States)

    Trampe, Erik C. L.; Larsen, Jens E. N.; Glaring, Mikkel A.; Stougaard, Peter; Kühl, Michael

    2016-01-01

    The Ikka Fjord (SW Greenland) harbors a unique microbial habitat in the form of several hundred submarine tufa columns composed of ikaite, a special hexahydrate form of calcium carbonate that precipitates when alkaline phosphate- and carbonate-enriched spring water seeping out of the sea floor meets cold seawater. While several unique heterotrophic microbes have been isolated from the tufa columns, the microbial activity, and the boundary conditions for microbial growth in ikaite have remained unexplored. We present the first detailed in situ characterization of the physico-chemical microenvironment and activity of oxygenic phototrophs thriving within the ikaite columns. In situ underwater microsensor measurements of pH, temperature, and irradiance in the porous ikaite crystal matrix, revealed an extreme microenvironment characterized by low temperatures, strong light attenuation, and gradients of pH changing from pH 9 at the outer column surface to above pH 10 over the first 1–2 cm of the ikaite. This outer layer of the freshly deposited ikaite matrix contained densely pigmented yellow and green zones harboring a diverse phototrophic community dominated by diatoms and cyanobacteria, respectively, as shown by amplicon sequencing. In situ O2 measurements, as well as underwater variable chlorophyll fluorescence measurements of photosynthetic activity, demonstrated high levels of oxygenic photosynthesis in this extreme gradient environment with strong irradiance-driven O2 dynamics ranging from anoxia to hyperoxic conditions in the ikaite matrix, albeit the local formation of gas bubbles buffered the day-night dynamics of O2 in the tufa columns. The microbial phototrophs in the ikaite matrix are embedded in exopolymers forming endolithic biofilms that may interact with mineral formation and cementing of ikaite crystals. PMID:27242741

  10. Does canine inflammatory bowel disease influence gut microbial profile and host metabolism?

    NARCIS (Netherlands)

    Xu, Jia; Verbrugghe, Adronie; Lourenço, Marta; Janssens, Geert P.J.; Liu, Daisy J.X.; Wiele, Van de Tom; Eeckhaut, Venessa; Immerseel, Van Filip; Maele, Van de Isabel; Niu, Yufeng; Bosch, Guido; Junius, Greet; Wuyts, Brigitte; Hesta, Myriam

    2016-01-01

    Background: Inflammatory bowel disease (IBD) refers to a diverse group of chronic gastrointestinal diseases, and gut microbial dysbiosis has been proposed as a modulating factor in its pathogenesis. Several studies have investigated the gut microbial ecology of dogs with IBD but it is yet unclear

  11. In situ detection of microbial c-type cytochrome based on intrinsic peroxidase-like activity using screen-printed carbon electrode.

    Science.gov (United States)

    Wen, Junlin; He, Daigui; Yu, Zhen; Zhou, Shungui

    2018-08-15

    C-type cytochromes (c-cyts) facilitate microbial extracellular electron transfer and play critical roles in biogeochemical cycling, bioelectricity generation and bioremediation. In this study, a simple and effective method has been developed to detect microbial c-cyts by means of peroxidase mimetic reaction on screen-printed carbon electrode (SPCE). To this end, bacteria cells were immobilized onto the working electrode surface of SPCE by a simple drop casting. After introducing 3,3',5,5'-tetramethylbenzidine (TMB) solution, microbial c-cyts with peroxidase-like activity catalyze the oxidation of TMB in the presence of hydrogen peroxide. The oxidized TMB was electrochemically determined and the current signal was employed to calculate the c-cyts content. This electrochemical method is highly sensitive for microbial c-cyts with a low detection limit of 40.78 fmol and a wide detection range between 51.70 fmol and 6.64 pmol. Moreover, the proposed technique can be universally expanded to detect c-cyts in other bacteria species such as Fontibacter ferrireducens, Pseudomonas aeruginosa, Comamonas guangdongensis and Escherichia coli. Furthermore, the proposed method confers an in situ facile and quantitative c-cyts detection without any destructive sample preparations, complex electrode modifications and expensive enzyme- or metal particle- based signal amplification. The suggested method advances an intelligent strategy for in situ quantification of microbial c-cyts and consequently holds promising application potential in microbiology and environmental science. Copyright © 2018 Elsevier B.V. All rights reserved.

  12. Anaerobic 4-hydroxyproline utilization: Discovery of a new glycyl radical enzyme in the human gut microbiome uncovers a widespread microbial metabolic activity.

    Science.gov (United States)

    Huang, Yolanda Y; Martínez-Del Campo, Ana; Balskus, Emily P

    2018-02-06

    The discovery of enzymes responsible for previously unappreciated microbial metabolic pathways furthers our understanding of host-microbe and microbe-microbe interactions. We recently identified and characterized a new gut microbial glycyl radical enzyme (GRE) responsible for anaerobic metabolism of trans-4-hydroxy-l-proline (Hyp). Hyp dehydratase (HypD) catalyzes the removal of water from Hyp to generate Δ 1 -pyrroline-5-carboxylate (P5C). This enzyme is encoded in the genomes of a diverse set of gut anaerobes and is prevalent and abundant in healthy human stool metagenomes. Here, we discuss the roles HypD may play in different microbial metabolic pathways as well as the potential implications of this activity for colonization resistance and pathogenesis within the human gut. Finally, we present evidence of anaerobic Hyp metabolism in sediments through enrichment culturing of Hyp-degrading bacteria, highlighting the wide distribution of this pathway in anoxic environments beyond the human gut.

  13. Investigation of the microbial metabolism of carbon dioxide and hydrogen in the kangaroo foregut by stable isotope probing.

    Science.gov (United States)

    Godwin, Scott; Kang, Alicia; Gulino, Lisa-Maree; Manefield, Mike; Gutierrez-Zamora, Maria-Luisa; Kienzle, Marco; Ouwerkerk, Diane; Dawson, Kerri; Klieve, Athol V

    2014-09-01

    Kangaroos ferment forage material in an enlarged forestomach analogous to the rumen, but in contrast to ruminants, they produce little or no methane. The objective of this study was to identify the dominant organisms and pathways involved in hydrogenotrophy in the kangaroo forestomach, with the broader aim of understanding how these processes are able to predominate over methanogenesis. Stable isotope analysis of fermentation end products and RNA stable isotope probing (RNA-SIP) were used to investigate the organisms and biochemical pathways involved in the metabolism of hydrogen and carbon dioxide in the kangaroo forestomach. Our results clearly demonstrate that the activity of bacterial reductive acetogens is a key factor in the reduced methane output of kangaroos. In in vitro fermentations, the microbial community of the kangaroo foregut produced very little methane, but produced a significantly greater proportion of acetate derived from carbon dioxide than the microbial community of the bovine rumen. A bacterial operational taxonomic unit closely related to the known reductive acetogen Blautia coccoides was found to be associated with carbon dioxide and hydrogen metabolism in the kangaroo foregut. Other bacterial taxa including members of the genera Prevotella, Oscillibacter and Streptococcus that have not previously been reported as containing hydrogenotrophic organisms were also significantly associated with metabolism of hydrogen and carbon dioxide in the kangaroo forestomach.

  14. Establishment and metabolic analysis of a model microbial community for understanding trophic and electron accepting interactions of subsurface anaerobic environments

    Directory of Open Access Journals (Sweden)

    Yang Zamin K

    2010-05-01

    Full Text Available Abstract Background Communities of microorganisms control the rates of key biogeochemical cycles, and are important for biotechnology, bioremediation, and industrial microbiological processes. For this reason, we constructed a model microbial community comprised of three species dependent on trophic interactions. The three species microbial community was comprised of Clostridium cellulolyticum, Desulfovibrio vulgaris Hildenborough, and Geobacter sulfurreducens and was grown under continuous culture conditions. Cellobiose served as the carbon and energy source for C. cellulolyticum, whereas D. vulgaris and G. sulfurreducens derived carbon and energy from the metabolic products of cellobiose fermentation and were provided with sulfate and fumarate respectively as electron acceptors. Results qPCR monitoring of the culture revealed C. cellulolyticum to be dominant as expected and confirmed the presence of D. vulgaris and G. sulfurreducens. Proposed metabolic modeling of carbon and electron flow of the three-species community indicated that the growth of C. cellulolyticum and D. vulgaris were electron donor limited whereas G. sulfurreducens was electron acceptor limited. Conclusions The results demonstrate that C. cellulolyticum, D. vulgaris, and G. sulfurreducens can be grown in coculture in a continuous culture system in which D. vulgaris and G. sulfurreducens are dependent upon the metabolic byproducts of C. cellulolyticum for nutrients. This represents a step towards developing a tractable model ecosystem comprised of members representing the functional groups of a trophic network.

  15. Microbial Metabolism in Soil at Subzero Temperatures: Adaptation Mechanisms Revealed by Position-Specific 13C Labeling

    Directory of Open Access Journals (Sweden)

    Ezekiel K. Bore

    2017-05-01

    Full Text Available Although biogeochemical models designed to simulate carbon (C and nitrogen (N dynamics in high-latitude ecosystems incorporate extracellular parameters, molecular and biochemical adaptations of microorganisms to freezing remain unclear. This knowledge gap hampers estimations of the C balance and ecosystem feedback in high-latitude regions. To analyze microbial metabolism at subzero temperatures, soils were incubated with isotopomers of position-specifically 13C-labeled glucose at three temperatures: +5 (control, -5, and -20°C. 13C was quantified in CO2, bulk soil, microbial biomass, and dissolved organic carbon (DOC after 1, 3, and 10 days and also after 30 days for samples at -20°C. Compared to +5°C, CO2 decreased 3- and 10-fold at -5 and -20°C, respectively. High 13C recovery in CO2 from the C-1 position indicates dominance of the pentose phosphate pathway at +5°C. In contrast, increased oxidation of the C-4 position at subzero temperatures implies a switch to glycolysis. A threefold higher 13C recovery in microbial biomass at -5 than +5°C points to synthesis of intracellular compounds such as glycerol and ethanol in response to freezing. Less than 0.4% of 13C was recovered in DOC after 1 day, demonstrating complete glucose uptake by microorganisms even at -20°C. Consequently, we attribute the fivefold higher extracellular 13C in soil than in microbial biomass to secreted antifreeze compounds. This suggests that with decreasing temperature, intracellular antifreeze protection is complemented by extracellular mechanisms to avoid cellular damage by crystallizing water. The knowledge of sustained metabolism at subzero temperatures will not only be useful for modeling global C dynamics in ecosystems with periodically or permanently frozen soils, but will also be important in understanding and controlling the adaptive mechanisms of food spoilage organisms.

  16. Methane Metabolizing Microbial Communities in the Cold Seep Areas in the Northern Continental Shelf of South China Sea

    Science.gov (United States)

    Wang, F.; Liang, Q.

    2016-12-01

    Marine sediment contains large amount of methane, estimated approximately 500-2500 gigatonnes of dissolved and hydrated methane carbon stored therein, mainly in continental margins. In localized specific areas named cold seeps, hydrocarbon (mainly methane) containing fluids rise to the seafloor, and support oases of ecosystem composed of various microorganisms and faunal assemblages. South China Sea (SCS) is surrounded by passive continental margins in the west and north and convergent margins in the south and east. Thick organic-rich sediments have accumulated in the SCS since the late Mesozoic, which are continuing sources to form gas hydrates in the sediments of SCS. Here, Microbial ecosystems, particularly those involved in methane transformations were investigated in the cold seep areas (Qiongdongnan, Shenhu, and Dongsha) in the northern continental shelf of SCS. Multiple interdisciplinary analytic tools such as stable isotope probing, geochemical analysis, and molecular ecology, were applied for a comprehensive understanding of the microbe mediated methane transformation in this project. A variety of sediments cores have been collected, the geochemical profiles and the associated microbial distribution along the sediment cores were recorded. The major microbial groups involved in the methane transformation in these sediment cores were revealed, known methane producing and oxidizing archaea including Methanosarcinales, anaerobic methane oxidizing groups ANME-1, ANME-2 and their niche preference in the SCS sediments were found. In-depth comparative analysis revealed the presence of SCS-specific archaeal subtypes which probably reflected the evolution and adaptation of these methane metabolizing microbes to the SCS environmental conditions. Our work represents the first comprehensive analysis of the methane metabolizing microbial communities in the cold seep areas along the northern continental shelf of South China Sea, would provide new insight into the

  17. 2012 Molecular Basis of Microbial One-Carbon Metabolism Gordon Research Conferences and Gordon Research Seminar, August 4-10,2012

    Energy Technology Data Exchange (ETDEWEB)

    Hanson, Thomas

    2012-08-10

    The 2012 Gordon Conference will present and discuss cutting-edge research in the field of microbial metabolism of C1 compounds. The conference will feature the roles and application of C1 metabolism in natural and synthetic systems at scales from molecules to ecosystems. The conference will stress molecular aspects of the unique metabolism exhibited by autotrophic bacteria, methanogens, methylotrophs, aerobic and anaerobic methanotrophs, and acetogens.

  18. A review of metabolic and enzymatic engineering strategies for designing and optimizing performance of microbial cell factories

    Directory of Open Access Journals (Sweden)

    Amanda K. Fisher

    2014-08-01

    Full Text Available Microbial cell factories (MCFs are of considerable interest to convert low value renewable substrates to biofuels and high value chemicals. This review highlights the progress of computational models for the rational design of an MCF to produce a target bio-commodity. In particular, the rational design of an MCF involves: (i product selection, (ii de novo biosynthetic pathway identification (i.e., rational, heterologous, or artificial, (iii MCF chassis selection, (iv enzyme engineering of promiscuity to enable the formation of new products, and (v metabolic engineering to ensure optimal use of the pathway by the MCF host. Computational tools such as (i de novo biosynthetic pathway builders, (ii docking, (iii molecular dynamics (MD and steered MD (SMD, and (iv genome-scale metabolic flux modeling all play critical roles in the rational design of an MCF. Genome-scale metabolic flux models are of considerable use to the design process since they can reveal metabolic capabilities of MCF hosts. These can be used for host selection as well as optimizing precursors and cofactors of artificial de novo biosynthetic pathways. In addition, recent advances in genome-scale modeling have enabled the derivation of metabolic engineering strategies, which can be implemented using the genomic tools reviewed here as well.

  19. Bacterial communities associated with Shinkaia crosnieri from the Iheya North, Okinawa Trough: Microbial diversity and metabolic potentials

    Science.gov (United States)

    Zhang, Jian; Zeng, Zhi-gang; Chen, Shuai; Sun, Li

    2018-04-01

    Shinkaia crosnieri is a galatheid crab endemic to the deep-sea hydrothermal systems in the Okinawa Trough. In this study, we systematically analyzed and compared the diversity and metabolic potentials of the microbial communities in different tissues (setae, gill, and intestine) of S. crosnieri by high-throughput sequencing technology and quantitative real-time polymerase chain reaction. Sequence analysis based on the V3-V4 regions of the 16S rRNA gene obtained 408,079 taxon tags, which covered 15 phyla, 22 classes, 32 orders, 42 families, and 25 genera. Overall, the microbial communities in all tissues were dominated by Epsilonproteobacteria and Gammaproteobacteria, of which Epsilonproteobacteria was the largest class and accounted for 85.24% of the taxon tags. In addition, 20 classes of bacteria were discovered for the first time to be associated with S. crosnieri and no archaea were detected. Comparative analysis showed that (i) bacteria from different tissues fell into different groups by β-diversity analysis, (ii) bacterial communities in intestine were similar to that in gill and much more diverse than that in setae, and the sulfur-oxidizing genus Sulfurovum was markedly enriched in intestine and gill. Furthermore, bacteria potentially involved in methane, nitrogen, and metal metabolisms were detected in all samples. The key genes of aprA/dsrA and pmoA involved in sulfate reducing and methane oxidization, respectively, were detected in the gill and gut communities for the first time, and pmoA was significantly more abundant in gill and setae than in intestine. These results provide the first comparative and relatively complete picture of the diversity and metabolic potentials of the bacteria in different tissues of S. crosnieri. These results also indicate that the composition of the microbial communities in hydrothermal fauna changes with time, suggesting the importance of environmental influence.

  20. Microbial Communities and Their Predicted Metabolic Functions in Growth Laminae of a Unique Large Conical Mat from Lake Untersee, East Antarctica

    Directory of Open Access Journals (Sweden)

    Hyunmin Koo

    2017-08-01

    Full Text Available In this study, we report the distribution of microbial taxa and their predicted metabolic functions observed in the top (U1, middle (U2, and inner (U3 decadal growth laminae of a unique large conical microbial mat from perennially ice-covered Lake Untersee of East Antarctica, using NextGen sequencing of the 16S rRNA gene and bioinformatics tools. The results showed that the U1 lamina was dominated by cyanobacteria, specifically Phormidium sp., Leptolyngbya sp., and Pseudanabaena sp. The U2 and U3 laminae had high abundances of Actinobacteria, Verrucomicrobia, Proteobacteria, and Bacteroidetes. Closely related taxa within each abundant bacterial taxon found in each lamina were further differentiated at the highest taxonomic resolution using the oligotyping method. PICRUSt analysis, which determines predicted KEGG functional categories from the gene contents and abundances among microbial communities, revealed a high number of sequences belonging to carbon fixation, energy metabolism, cyanophycin, chlorophyll, and photosynthesis proteins in the U1 lamina. The functional predictions of the microbial communities in U2 and U3 represented signal transduction, membrane transport, zinc transport and amino acid-, carbohydrate-, and arsenic- metabolisms. The Nearest Sequenced Taxon Index (NSTI values processed through PICRUSt were 0.10, 0.13, and 0.11 for U1, U2, and U3 laminae, respectively. These values indicated a close correspondence with the reference microbial genome database, implying high confidence in the predicted metabolic functions of the microbial communities in each lamina. The distribution of microbial taxa observed in each lamina and their predicted metabolic functions provides additional insight into the complex microbial ecosystem at Lake Untersee, and lays the foundation for studies that will enhance our understanding of the mechanisms responsible for the formation of these unique mat structures and their evolutionary significance.

  1. The woodrat gut microbiota as an experimental system for understanding microbial metabolism of dietary toxins

    Directory of Open Access Journals (Sweden)

    Kevin D. Kohl

    2016-07-01

    Full Text Available The microbial communities inhabiting the alimentary tracts of mammals, particularly those of herbivores, are estimated to be one of the densest microbial reservoirs on Earth. The significance of these gut microbes in influencing the physiology, ecology and evolution of their hosts is only beginning to be realized. To understand the microbiome of herbivores with a focus on nutritional ecology, while evaluating the roles of host evolution and environment in sculpting microbial diversity, we have developed an experimental system consisting of the microbial communities of several species of herbivorous woodrats (genus Neotoma that naturally feed on a variety of dietary toxins. We designed this system to investigate the long-standing, but experimentally neglected hypothesis that ingestion of toxic diets by herbivores is facilitated by the gut microbiota. Like several other rodent species, the woodrat stomach has a sacculated, nongastric foregut portion. We have documented a dense and diverse community of microbes in the woodrat foregut, with several genera potentially capable of degrading dietary toxins and/or playing a role in stimulating hepatic detoxification enzymes of the host. The biodiversity of these gut microbes appears to be a function of host evolution, ecological experience and diet, such that dietary toxins increase microbial diversity in hosts with experience with these toxins while novel toxins depress microbial diversity. These microbial communities are critical to the ingestion of a toxic diet as reducing the microbial community with antibiotics impairs the host’s ability to feed on dietary toxins. Furthermore, the detoxification capacity of gut microbes can be transferred from Neotoma both intra and interspecifically to naïve animals that lack ecological and evolutionary history with these toxins. In addition to advancing our knowledge of complex host-microbes interactions, this system holds promise for identifying microbes that

  2. Molecular Basis of Microbial One-Carbon Metabolism 2008 Gordon Research Conference (July 20-25, 2008)

    Energy Technology Data Exchange (ETDEWEB)

    Stephen W. Ragsdale

    2009-08-12

    One-carbon (C-1) compounds play a central role in microbial metabolism. C-1 compounds include methane, carbon monoxide, CO2, and methanol as well as coenzyme-bound one-carbon compounds (methyl-B12, CH3-H4folate, etc). Such compounds are of broad global importance because several C-1 compounds (e.g., CH4) are important energy sources, some (e.g., CO2 and CH4) are potent greenhouse gases, and others (e.g., CH2Cl2) are xenobiotics. They are central in pathways of energy metabolism and carbon fixation by microbes and many are of industrial interest. Research on the pathways of one-carbon metabolism has added greatly to our understanding of evolution, structural biology, enzyme mechanisms, gene regulation, ecology, and applied biology. The 2008 meeting will include recent important findings in the following areas: (a) genomics, metagenomics, and proteomic studies that have expanded our understanding of autotrophy and C-1 metabolism and the evolution of these pathways; (b) redox regulation of carbon cycles and the interrelationship between the carbon cycle and other biogeochemical cycles (sulfur, nitrogen, oxygen); (c) novel pathways for carbon assimilation; (d) biotechnology related to C-1 metabolism; (e) novel enzyme mechanisms including channeling of C-1 intermediates during metabolism; and (f) the relationship between metal homeostasis and the global carbon cycle. The conference has a diverse and gender-balanced slate of speakers and session leaders. The wide variety of disciplines brought to the study of C-1 metabolism make the field an excellent one in which to train young researchers.

  3. Analysis of the functional gene structure and metabolic potential of microbial community in high arsenic groundwater.

    Science.gov (United States)

    Li, Ping; Jiang, Zhou; Wang, Yanhong; Deng, Ye; Van Nostrand, Joy D; Yuan, Tong; Liu, Han; Wei, Dazhun; Zhou, Jizhong

    2017-10-15

    Microbial functional potential in high arsenic (As) groundwater ecosystems remains largely unknown. In this study, the microbial community functional composition of nineteen groundwater samples was investigated using a functional gene array (GeoChip 5.0). Samples were divided into low and high As groups based on the clustering analysis of geochemical parameters and microbial functional structures. The results showed that As related genes (arsC, arrA), sulfate related genes (dsrA and dsrB), nitrogen cycling related genes (ureC, amoA, and hzo) and methanogen genes (mcrA, hdrB) in groundwater samples were correlated with As, SO 4 2- , NH 4 + or CH 4 concentrations, respectively. Canonical correspondence analysis (CCA) results indicated that some geochemical parameters including As, total organic content, SO 4 2- , NH 4 + , oxidation-reduction potential (ORP) and pH were important factors shaping the functional microbial community structures. Alkaline and reducing conditions with relatively low SO 4 2- , ORP, and high NH 4 + , as well as SO 4 2- and Fe reduction and ammonification involved in microbially-mediated geochemical processes could be associated with As enrichment in groundwater. This study provides an overall picture of functional microbial communities in high As groundwater aquifers, and also provides insights into the critical role of microorganisms in As biogeochemical cycling. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Environmental spread of microbes impacts the development of metabolic phenotypes in mice transplanted with microbial communities from humans

    DEFF Research Database (Denmark)

    Zhang, Li; Bahl, Martin Iain; Roager, Henrik Munch

    2017-01-01

    Microbiota transplantation to germ-free animals is a powerful method to study involvement of gut microbes in the aetiology of metabolic syndrome. Owing to large interpersonal variability in gut microbiota, studies with broad coverage of donors are needed to elucidate the establishment of human......, thereby allowing us to explore the extent of microbial spread between cages in a well-controlled environment. Despite high group-wise similarity between obese and control human microbiotas, transplanted mice in the four isolators developed distinct gut bacterial composition and activity, body mass gain......, and insulin resistance. Spread of microbes between cages within isolators interacted with establishment of the transplanted microbiotas in mice, and contributed to the transmission of metabolic phenotypes. Our findings highlight the impact of donor variability and reveal that inter-individual spread...

  5. Microbial analysis of in situ biofilm formation in drinking water distribution systems: implications for monitoring and control of drinking water quality.

    Science.gov (United States)

    Douterelo, Isabel; Jackson, M; Solomon, C; Boxall, J

    2016-04-01

    Biofilm formation in drinking water distribution systems (DWDS) is influenced by the source water, the supply infrastructure and the operation of the system. A holistic approach was used to advance knowledge on the development of mixed species biofilms in situ, by using biofilm sampling devices installed in chlorinated networks. Key physico-chemical parameters and conventional microbial indicators for drinking water quality were analysed. Biofilm coverage on pipes was evaluated by scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM). The microbial community structure, bacteria and fungi, of water and biofilms was assessed using pyrosequencing. Conventional wisdom leads to an expectation for less microbial diversity in groundwater supplied systems. However, the analysis of bulk water showed higher microbial diversity in groundwater site samples compared with the surface water site. Conversely, higher diversity and richness were detected in biofilms from the surface water site. The average biofilm coverage was similar among sites. Disinfection residual and other key variables were similar between the two sites, other than nitrates, alkalinity and the hydraulic conditions which were extremely low at the groundwater site. Thus, the unexpected result of an exceptionally low diversity with few dominant genera (Pseudomonas and Basidiobolus) in groundwater biofilm samples, despite the more diverse community in the bulk water, is attributed to the low-flow hydraulic conditions. This finding evidences that the local environmental conditions are shaping biofilm formation, composition and amount, and hence managing these is critical for the best operation of DWDS to safeguard water quality.

  6. Impact of the electron donor on in situ microbial nitrate reduction in Opalinus Clay: results from the Mont Terri rock laboratory (Switzerland)

    Energy Technology Data Exchange (ETDEWEB)

    Bleyen, N.; Smets, S. [Belgian Nuclear Research Centre SCK-CEN, Mol (Belgium); Small, J. [National Nuclear Laboratory NLL, Warrington (United Kingdom); and others

    2017-04-15

    At the Mont Terri rock laboratory (Switzerland), an in situ experiment is being carried out to examine the fate of nitrate leaching from nitrate-containing bituminized radioactive waste, in a clay host rock for geological disposal. Such a release of nitrate may cause a geochemical perturbation of the clay, possibly affecting some of the favorable characteristics of the host rock. In this in situ experiment, combined transport and reactivity of nitrate is studied inside anoxic and water-saturated chambers in a borehole in the Opalinus Clay. Continuous circulation of the solution from the borehole to the surface equipment allows a regular sampling and online monitoring of its chemical composition. In this paper, in situ microbial nitrate reduction in the Opalinus Clay is discussed, in the presence or absence of additional electron donors relevant for the disposal concept and likely to be released from nitrate-containing bituminized radioactive waste: acetate (simulating bitumen degradation products) and H{sub 2} (originating from radiolysis and corrosion in the repository). The results of these tests indicate that - in case microorganisms would be active in the repository or the surrounding clay - microbial nitrate reduction can occur using electron donors naturally present in the clay (e.g. pyrite, dissolved organic matter). Nevertheless, non-reactive transport of nitrate in the clay is expected to be the main process. In contrast, when easily oxidizable electron donors would be available (e.g. acetate and H{sub 2}), the microbial activity will be strongly stimulated. Both in the presence of H{sub 2} and acetate, nitrite and nitrogenous gases are predominantly produced, although some ammonium can also be formed when H{sub 2} is present. The reduction of nitrate in the clay could have an impact on the redox conditions in the pore-water and might also lead to a gas-related perturbation of the host rock, depending on the electron donor used during denitrification

  7. In-situ studies of microbial CH4 oxidation efficiency in Arctic wetland soils. Applications of stable carbon isotopes

    International Nuclear Information System (INIS)

    Preuss, Inken-Marie

    2013-01-01

    Arctic wetland soils are significant sources of the climate-relevant trace gas methane (CH 4 ). The observed accelerated warming of the Arctic is expected to cause deeper permafrost thawing followed by increased carbon mineralization and CH 4 formation in water-saturated permafrost-affected tundra soils thus creating a positive feedback to climate change. Aerobic CH 4 oxidation is regarded as the key process reducing CH 4 emissions from wetlands, but quantification of turnover rates has remained difficult so far. This study improved the in-situ quantification of microbial CH 4 oxidation efficiency in arctic wetland soils in Russia's Lena River Delta based on stable isotope signatures of CH 4 . In addition to the common practice of determining the stable isotope fractionation during oxidation, additionally the fractionation effect of diffusion, an important gas transport mechanism in tundra soils, was investigated for both saturated and unsaturated conditions. The isotopic fractionation factors α ox and α diff were used to calculate the CH 4 oxidation efficiency from the CH 4 stable isotope signatures of wet polygonal tundra soils of different hydrology. Further, the method was used to study the short-term effects of temperature increase with a climate manipulation experiment. For the first time, the stable isotope fractionation of CH 4 diffusion through water-saturated soils was determined with α diff = 1.001 ± 0.0002 (n = 3). CH 4 stable isotope fractionation during diffusion through air-filled pores of the investigated polygonal tundra soils was α diff = 1.013 ± 0.003 (n = 18). For the studied sites the fractionation factor for diffusion under saturated conditions α diff = 1.001 seems to be of utmost importance for the quantification of the CH 4 oxidation efficiency, since most of the CH 4 is oxidized in the saturated part at the aerobic-anaerobic interface. Furthermore, it was found that α ox differs widely between sites and horizons (mean α ox = 1

  8. The Influence of Tallow on Rumen Metabolism, Microbial Biomass Synthesis and Fatty Acid Composition of Bacteria and Protozoa

    DEFF Research Database (Denmark)

    Weisbjerg, Martin Riis; Børsting, Christian Friis; Hvelplund, Torben

    1992-01-01

    Rumen metabolism, microbial biomass synthesis and microbial long chain fatty acid composition were studied in lactating cows fed at two levels of dry matter intake (L, 8.6 kg DM and H, 12.6 kg DM) with 0, 4 and 6% added tallow at the low feed level (L0, L4 and L6) and 0, 2, 4 and 6% at the high...... feed level (H0, H2, H4 and H6). Fibre digestibility was not significantly affected by tallow addition. Increasing tallow level in the diet decreased the total VFA concentration, the ratio of acetic acid to propionic acid and the ammonia concentration in the rumen. Crude fat and fatty acid content...... in bacterial and protozoal dry matter increased with increased tallow level, especially due to an increase in fatty acids originating from the feeds. Microbial synthesis in the rumen and flow of amino acids to the duodenum was highest for medium fat intake at the high feed level....

  9. Host genes related to paneth cells and xenobiotic metabolism are associated with shifts in human ileum-associated microbial composition.

    Directory of Open Access Journals (Sweden)

    Tianyi Zhang

    Full Text Available The aim of this study was to integrate human clinical, genotype, mRNA microarray and 16 S rRNA sequence data collected on 84 subjects with ileal Crohn's disease, ulcerative colitis or control patients without inflammatory bowel diseases in order to interrogate how host-microbial interactions are perturbed in inflammatory bowel diseases (IBD. Ex-vivo ileal mucosal biopsies were collected from the disease unaffected proximal margin of the ileum resected from patients who were undergoing initial intestinal surgery. Both RNA and DNA were extracted from the mucosal biopsy samples. Patients were genotyped for the three major NOD2 variants (Leufs1007, R702W, and G908R and the ATG16L1T300A variant. Whole human genome mRNA expression profiles were generated using Agilent microarrays. Microbial composition profiles were determined by 454 pyrosequencing of the V3-V5 hypervariable region of the bacterial 16 S rRNA gene. The results of permutation based multivariate analysis of variance and covariance (MANCOVA support the hypothesis that host mucosal Paneth cell and xenobiotic metabolism genes play an important role in host microbial interactions.

  10. Characterization of microbial metabolism of Syrah grape products in an in vitro colon model using targeted and non-targeted analytical approaches

    OpenAIRE

    Aura, Anna-Marja; Mattila, Ismo; Hyötyläinen, Tuulia; Gopalacharyulu, Peddinti; Cheynier, Veronique; Souquet, Jean-Marc; Bes, Magali; Le Bourvellec, Carine; Guyot, Sylvain; Orešič, Matej

    2012-01-01

    Purpose Syrah red grapes are used in the production of tannin-rich red wines. Tannins are high molecular weight molecules, proanthocyanidins (PAs), and poorly absorbed in the upper intestine. In this study, gut microbial metabolism of Syrah grape phenolic compounds was investigated. Methods Syrah grape pericarp was subjected to an enzymatic in vitro digestion model, and red wine and grape skin PA fraction were prepared. Microbial conversion was screened using an in vitro colon model with faec...

  11. Starter Culture Selection for Making Chinese Sesame-Flavored Liquor Based on Microbial Metabolic Activity in Mixed-Culture Fermentation

    Science.gov (United States)

    Wu, Qun; Ling, Jie

    2014-01-01

    Selection of a starter culture with excellent viability and metabolic activity is important for inoculated fermentation of traditional food. To obtain a suitable starter culture for making Chinese sesame-flavored liquor, the yeast and bacterium community structures were investigated during spontaneous and solid-state fermentations of this type of liquor. Five dominant species in spontaneous fermentation were identified: Saccharomyces cerevisiae, Pichia membranaefaciens, Issatchenkia orientalis, Bacillus licheniformis, and Bacillus amyloliquefaciens. The metabolic activity of each species in mixed and inoculated fermentations of liquor was investigated in 14 different cocultures that used different combinations of these species. The relationships between the microbial species and volatile metabolites were analyzed by partial least-squares (PLS) regression analysis. We found that S. cerevisiae was positively correlated to nonanal, and B. licheniformis was positively associated with 2,3-butanediol, isobutyric acid, guaiacol, and 4-vinyl guaiacol, while I. orientalis was positively correlated to butyric acid, isovaleric acid, hexanoic acid, and 2,3-butanediol. These three species are excellent flavor producers for Chinese liquor. Although P. membranaefaciens and B. amyloliquefaciens were not efficient flavor producers, the addition of them alleviated competition among the other three species and altered their growth rates and flavor production. As a result, the coculture of all five dominant species produced the largest amount of flavor compounds. The result indicates that flavor producers and microbial interaction regulators are important for inoculated fermentation of Chinese sesame-flavored liquor. PMID:24814798

  12. MicroScope—an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data

    Science.gov (United States)

    Vallenet, David; Belda, Eugeni; Calteau, Alexandra; Cruveiller, Stéphane; Engelen, Stefan; Lajus, Aurélie; Le Fèvre, François; Longin, Cyrille; Mornico, Damien; Roche, David; Rouy, Zoé; Salvignol, Gregory; Scarpelli, Claude; Thil Smith, Adam Alexander; Weiman, Marion; Médigue, Claudine

    2013-01-01

    MicroScope is an integrated platform dedicated to both the methodical updating of microbial genome annotation and to comparative analysis. The resource provides data from completed and ongoing genome projects (automatic and expert annotations), together with data sources from post-genomic experiments (i.e. transcriptomics, mutant collections) allowing users to perfect and improve the understanding of gene functions. MicroScope (http://www.genoscope.cns.fr/agc/microscope) combines tools and graphical interfaces to analyse genomes and to perform the manual curation of gene annotations in a comparative context. Since its first publication in January 2006, the system (previously named MaGe for Magnifying Genomes) has been continuously extended both in terms of data content and analysis tools. The last update of MicroScope was published in 2009 in the Database journal. Today, the resource contains data for >1600 microbial genomes, of which ∼300 are manually curated and maintained by biologists (1200 personal accounts today). Expert annotations are continuously gathered in the MicroScope database (∼50 000 a year), contributing to the improvement of the quality of microbial genomes annotations. Improved data browsing and searching tools have been added, original tools useful in the context of expert annotation have been developed and integrated and the website has been significantly redesigned to be more user-friendly. Furthermore, in the context of the European project Microme (Framework Program 7 Collaborative Project), MicroScope is becoming a resource providing for the curation and analysis of both genomic and metabolic data. An increasing number of projects are related to the study of environmental bacterial (meta)genomes that are able to metabolize a large variety of chemical compounds that may be of high industrial interest. PMID:23193269

  13. Effect of Lineage-Specific Metabolic Traits of Lactobacillus reuteri on Sourdough Microbial Ecology

    OpenAIRE

    Lin, Xiaoxi B.; Gänzle, Michael G.

    2014-01-01

    This study determined the effects of specific metabolic traits of Lactobacillus reuteri on its competitiveness in sourdoughs. The competitiveness of lactobacilli in sourdough generally depends on their growth rate; acid resistance additionally contributes to competitiveness in sourdoughs with long fermentation times. Glycerol metabolism via glycerol dehydratase (gupCDE) accelerates growth by the regeneration of reduced cofactors; glutamate metabolism via glutamate decarboxylase (gadB) increas...

  14. Marked Response in Microbial Community and Metabolism in the Ileum and Cecum of Suckling Piglets After Early Antibiotics Exposure

    Directory of Open Access Journals (Sweden)

    Miao Yu

    2018-05-01

    Full Text Available In modern swine husbandry systems, antibiotics have been used as growth promoters for piglets during suckling or weaning period. However, while early colonization of intestinal microbiota has been regarded crucial for the host’s later life performance and well-being, little is known about the impact of antibiotics on intestinal microbiota in suckling piglets. The present study aimed to investigate the effects of early antibiotics exposure on gut microbiota and microbial metabolism of suckling piglets. Sixteen litters of suckling piglets were fed a creep feed diet with (Antibiotic or without (Control antibiotics from postnatal days 7–23 (n = 8. The ileal and cecal digesta were obtained for microbial composition and microbial metabolites analysis. The results showed that the antibiotics significantly altered the bacterial community composition by decreasing (P < 0.05 the diversity and richness in the ileum. The antibiotics significantly reduced the abundance of Lactobacillus in both the ileum and cecum, increased the abundance of Streptococcus, unclassified Enterococcaceae, unclassified Fusobacteriales, and Corynebacterium in the ileum, and the abundance of unclassified Ruminococcaceae and unclassified Erysipelotrichaceae in the cecum. The antibiotics decreased (P < 0.05 ileal lactate concentration and cecal concentration of total short-chain fatty acids (SCFAs. But the antibiotics enhanced protein fermentation (P < 0.05 in the ileum and cecum, as ileal concentrations of putrescine and cadaverine, and cecal concentrations of isobutyrate, isovalerate, putrescine, cadaverine, spermine, and spermidine were significantly increased (P < 0.05. These results indicated that early antibiotics exposure significantly altered the microbial composition of suckling piglets toward a vulnerable and unhealthy gut environment. The findings provide a new insight on the antibiotics impact on neonates and may provide new framework for designing alternatives to the

  15. Effect of Microbial Interaction on Urea Metabolism in Chinese Liquor Fermentation

    NARCIS (Netherlands)

    Wu, Qun; Lin, Jianchun; Cui, Kaixiang; Du, Rubin; Zhu, Yang; Xu, Yan

    2017-01-01

    Urea is the primary precursor of the carcinogen ethyl carbamate in fermented foods. Understanding urea metabolism is important for controlling ethyl carbamate production. Using Chinese liquor as a model system, we used metatranscriptome analysis to investigate urea metabolism in spontaneous food

  16. Microbial Metabolism. Part 10. Metabolites of 7,8 Dimethoxyflavone and 5-Methoxyflavone

    Science.gov (United States)

    Microbial transformation of 7, 8-dimethoxyflavone (1) by Mucor ramannianus (ATCC 9628) produced five metabolites: 7, 8-dimethoxy-4'-hydroxyflavone (2), 3', 4'-dihydroxy-7, 8-dimethoxyflavone (3), 7, 3'-dihydroxy-8-methoxyflavone (4), 7, 4'-dihydroxy-8-methoxyflavone (5) and 8-methoxy-7, 3', 4'-trihy...

  17. Frozen in Time? Microbial strategies for survival and carbon metabolism over geologic time in a Pleistocene permafrost chronosequence

    Science.gov (United States)

    Mackelprang, R.; Douglas, T. A.; Waldrop, M. P.

    2014-12-01

    Permafrost soils have received tremendous interest due to their importance as a global carbon store with the potential to be thawed over the coming centuries. Instead of being 'frozen in time,' permafrost contains active microbes. Most metagenomic studies have focused on Holocene aged permafrost. Here, we target Pleistocene aged ice and carbon rich permafrost (Yedoma), which can differ in carbon content and stage of decay. Our aim was to understand how microbes in the permafrost transform organic matter over geologic time and to identify physiological and biochemical adaptations that enable long-term survival. We used next-generation sequencing to characterize microbial communities along a permafrost age gradient. Samples were collected from the Cold Regions Research and Engineering Laboratory (CRREL) Permafrost Tunnel near Fox, AK, which penetrates a hillside providing access to permafrost ranging in age from 12 to 40 kyr. DNA was extracted directly from unthawed samples. 16S rRNA amplicon (16S) and shotgun metagenome sequencing revealed significant age-driven differences. First, microbial diversity declines with permafrost age, likely due to long-term exposure to environmental stresses and a reduction in metabolic resources. Second, we observed taxonomic differences among ages, with an increasing abundance of Firmicutes (endospore-formers) in older samples, suggesting that dormancy is a common survival strategy in older permafrost. Ordination of 16S and metagenome data revealed age-based clustering. Genes differing significantly between age categories included those involved in lipopolysaccharide assembly, cold-response, and carbon processing. These data point to the physiological adaptations to long-term frozen conditions and to the metabolic processes utilized in ancient permafrost. In fact, a gene common in older samples is involved in cadaverine production, which could potentially explain the putrefied smell of Pleistocene aged permafrost. Coupled with soil

  18. Recent advances in engineering propionyl-CoA metabolism for microbial production of value-added chemicals and biofuels.

    Science.gov (United States)

    Srirangan, Kajan; Bruder, Mark; Akawi, Lamees; Miscevic, Dragan; Kilpatrick, Shane; Moo-Young, Murray; Chou, C Perry

    2017-09-01

    Diminishing fossil fuel reserves and mounting environmental concerns associated with petrochemical manufacturing practices have generated significant interests in developing whole-cell biocatalytic systems for the production of value-added chemicals and biofuels. Although acetyl-CoA is a common natural biogenic precursor for the biosynthesis of numerous metabolites, propionyl-CoA is unpopular and non-native to most organisms. Nevertheless, with its C3-acyl moiety as a discrete building block, propionyl-CoA can serve as another key biogenic precursor to several biological products of industrial importance. As a result, engineering propionyl-CoA metabolism, particularly in genetically tractable hosts with the use of inexpensive feedstocks, has paved an avenue for novel biomanufacturing. Herein, we present a systematic review on manipulation of propionyl-CoA metabolism as well as relevant genetic and metabolic engineering strategies for microbial production of value-added chemicals and biofuels, including odd-chain alcohols and organic acids, bio(co)polymers and polyketides. [Formula: see text].

  19. Metabolic mapping of proteinase activity with emphasis on in situ zymography of gelatinases: review and protocols.

    Science.gov (United States)

    Frederiks, Wilma M; Mook, Olaf R F

    2004-06-01

    Proteases are essential for protein catabolism, regulation of a wide range of biological processes, and in the pathogenesis of many diseases. Several techniques are available to localize activity of proteases in tissue sections or cell preparations. For localization of the activity of matrix metalloproteinases, in situ zymography was introduced some decades ago. The procedure is based on zymography using SDS polyacrylamide gels containing gelatin, casein, or fibrin as substrate. For in situ zymography, either a photographic emulsion containing gelatin or a fluorescence-labeled proteinaceous macromolecular substrate is brought into contact with a tissue section or cell preparation. After incubation, enzymatic activity is revealed as white spots in a dark background or as black spots in a fluorescent background. However, this approach does not allow precise localization of proteinase activity because of limited sensitivity. A major improvement in sensitivity was achieved with the introduction of dye-quenched (DQ-)gelatin, which is gelatin that is heavily labeled with FITC molecules so that its fluorescence is quenched. After cleavage of DQ-gelatin by gelatinolytic activity, fluorescent peptides are produced that are visible against a weakly fluorescent background. The incubation with DQ-gelatin can be combined with simultaneous immunohistochemical detection of a protein on the same section. To draw valid conclusions from the findings with in situ zymography, specific inhibitors need to be used and the technique has to be combined with immunohistochemistry and zymography. In that case, in situ zymography provides data that extend our understanding of the role of specific proteinases in various physiological and pathological conditions.

  20. Lessons learned from the Febex in situ test: geochemical processes associated to the microbial degradation and gas generation

    International Nuclear Information System (INIS)

    Fernandez, A. M.; Sanchez, D.M.; Melon, A.; Mingarro, M.; Wieczorek, K.

    2012-01-01

    Document available in extended abstract form only. Compacted bentonites are considered as backfill and sealing material in most high-level radioactive waste disposal (HLW) concepts because of their physico-chemical properties. Although they are very stable in their original natural ambient, any change in the physico-chemical, geochemical and mineralogical conditions may influence in their functions. Therefore, numerous studies have been performed during years in order to evaluate the bentonite barrier behaviour affected by thermo-hydro-mechanical and geochemical processes in tests at different scales. One of the key parameters in the safety assessment of a nuclear waste repository is the redox conditions of the bentonite pore water in the near field, due to their effect on the mobility and sorption of a lot of radionuclides. Among the factors that influence the Eh of the pore water are: a) the amount of oxygen in the barrier and in the clay-rocks, b) the type of existing minerals sensible to the redox potential, c) the production of radiolytic oxidants and reductants, d) the type and rate of the metal corrosion, f) the existence of organic matter, and e) the presence and viability of micro-organisms. However, the microbiological processes have not been taken into account during a lot of years because it is was thought that the microbial growth and activity at repository conditions are improbable due to: the low water activity as a consequence of the heat and the pore water salinity, the reduced space for their growth due to the compaction degree and swelling of the bentonite, etc. Different studies have shown that the microorganisms stop their activity at a w 2 MPa, low availability of water, small pore size 3 or a pore water salinity > 100 g NaCl/L. Nevertheless, during the transitory phase of the bentonite saturation, some modifications occur in the salinity of the pore water, the initial dry densities due to the hydration process, the swelling pressures, and the

  1. Deep subsurface microbial processes

    Science.gov (United States)

    Lovley, D.R.; Chapelle, F.H.

    1995-01-01

    Information on the microbiology of the deep subsurface is necessary in order to understand the factors controlling the rate and extent of the microbially catalyzed redox reactions that influence the geophysical properties of these environments. Furthermore, there is an increasing threat that deep aquifers, an important drinking water resource, may be contaminated by man's activities, and there is a need to predict the extent to which microbial activity may remediate such contamination. Metabolically active microorganisms can be recovered from a diversity of deep subsurface environments. The available evidence suggests that these microorganisms are responsible for catalyzing the oxidation of organic matter coupled to a variety of electron acceptors just as microorganisms do in surface sediments, but at much slower rates. The technical difficulties in aseptically sampling deep subsurface sediments and the fact that microbial processes in laboratory incubations of deep subsurface material often do not mimic in situ processes frequently necessitate that microbial activity in the deep subsurface be inferred through nonmicrobiological analyses of ground water. These approaches include measurements of dissolved H2, which can predict the predominant microbially catalyzed redox reactions in aquifers, as well as geochemical and groundwater flow modeling, which can be used to estimate the rates of microbial processes. Microorganisms recovered from the deep subsurface have the potential to affect the fate of toxic organics and inorganic contaminants in groundwater. Microbial activity also greatly influences 1 the chemistry of many pristine groundwaters and contributes to such phenomena as porosity development in carbonate aquifers, accumulation of undesirably high concentrations of dissolved iron, and production of methane and hydrogen sulfide. Although the last decade has seen a dramatic increase in interest in deep subsurface microbiology, in comparison with the study of

  2. Are pathogenic bacteria just looking for food? Metabolism and microbial pathogenesis

    Science.gov (United States)

    Rohmer, Laurence; Hocquet, Didier; Miller, Samuel I.

    2011-01-01

    It is interesting to speculate that the evolutionary drive of microbes to develop pathogenic characteristics was to access the nutrient resources that animals provided. Environments in animals that pathogens colonize have also driven the evolution of new bacterial characteristics to maximize these new nutritional opportunities. This review focuses on genomic and functional aspects of pathogen metabolism that allow efficient utilization of nutrient resources provided by animals. Similar to genes encoding specific virulence traits, some genes encoding metabolic functions have been horizontally acquired by pathogens to provide a selective advantage in host tissues. Selective advantage in host tissues can also be gained in some circumstances by loss of function due to mutations that alter metabolic capabilities. Greater understanding of bacterial metabolism within host tissues should be important for increased understanding of host-pathogen interactions and the development of future therapeutic strategies. PMID:21600774

  3. Influence of Wastewater Discharge on the Metabolic Potential of the Microbial Community in River Sediments

    KAUST Repository

    Li, Dong; Sharp, Jonathan O.; Drewes, Jorg

    2015-01-01

    , sulfur, purine and pyrimidine metabolisms, as well as restriction–modification systems. More diverse bacterial phyla were associated with upstream and deep downstream sediments, mainly including Actinobacteria, Planctomycetes, and Firmicutes. In contrast

  4. Investigations into the metabolic diversity of microorganisms as part of microbial diversity

    Energy Technology Data Exchange (ETDEWEB)

    Leadbetter, Jared [California Inst. of Technology (CalTech), Pasadena, CA (United States)

    2016-07-25

    DOE funds supported a key portion of the MBL Microbial Diversity (Woods Hole) program across 6 complete summers. The initial 4 years of the funded period were overseen by two co-Directors, Daniel Buckley (Cornell) and Steve Zinder (Cornell), who then completed their term. The final 2 summers were overseen by 2 new co-Directors, Jared R. Leadbetter (Caltech) and Dianne Newman (Caltech). The 6 funded summer iterations of the course included the incorporation of new themes such as single cell approaches applied to natural microbial communities (cell separation and sorting, genome amplification from single cells, and the use of Nano-SIMS to examine assimilation of carbon and nitrogen from isotopically labeled substrates into single cells), genetics and genomics on bacteria freshly isolated during the course of the programs, quantitative systems biology, and modern quantitative light microscopy.

  5. Microbial food webs and metabolic state across oligotrophic waters of the Mediterranean Sea during summer

    Directory of Open Access Journals (Sweden)

    U. Christaki

    2011-07-01

    Full Text Available The abundance and activity of the major members of the heterotrophic microbial community – from viruses to ciliates – were studied along a longitudinal transect across the Mediterranean Sea in the summer of 2008. The Mediterranean Sea is characterized by a west to-east gradient of deepening of DCM (deep chlorophyll maximum and increasing oligotrophy reflected in gradients of biomass and production. However, within this well documented longitudinal trend, hydrological mesoscale features exist and likely influence microbial dynamics. Here we present data from a W-E transect of 17 stations during the period of summer stratification. Along the transect the production and fate of organic matter was investigated at three selected sites each one located in the centre of an anticyclonic eddy: in the Algero-Provencal Basin (St. A, the Ionian Basin (St. B, and the Levantine Basin (St. C. The 3 geographically distant eddies showed low values of the different heterotrophic compartments of the microbial food web, and except for viruses in site C, all integrated (0–150 m stocks were higher in reference stations located in the same basin outside the eddies. During our study the 3 eddies showed equilibrium between GPP (Gross Primary Production and DCR (Dark Community Respiration. Integrated PPp (Particulate Primary Production values at A, B and C varied from ~140 to ~190 mg C m−2.

  6. A Novel Early Warning System Based on a Sediment Microbial Fuel Cell for In Situ and Real Time Hexavalent Chromium Detection in Industrial Wastewater.

    Science.gov (United States)

    Zhao, Shuai; Liu, Pu; Niu, Yongyan; Chen, Zhengjun; Khan, Aman; Zhang, Pengyun; Li, Xiangkai

    2018-02-22

    Hexavalent chromium (Cr(VI)) is a well-known toxic heavy metal in industrial wastewater, but in situ and real time monitoring cannot be achieved by current methods used during industrial wastewater treatment processes. In this study, a Sediment Microbial Fuel Cell (SMFC) was used as a biosensor for in situ real-time monitoring of Cr(VI), which was the organic substrate is oxidized in the anode and Cr(VI) is reduced at the cathode simultaneously. The pH 6.4 and temperature 25 °C were optimal conditions for the operation. Under the optimal conditions, linearity (R² = 0.9935) of the generated voltage was observed in the Cr(VI) concentration range from 0.2 to 0.7 mg/L. The system showed high specificity for Cr(VI), as other co-existing ions such as Cu 2+ , Zn 2+ , and Pb 2+ did not interfere with Cr(VI) detection. In addition, when the sediment MFC-based biosensor was applied for measuring Cr(VI) in actual wastewater samples, a low deviation (real time in situ detection of Cr(VI) in industrial wastewaters.

  7. A review on the bioenergetics of anaerobic microbial metabolism close to the thermodynamic limits and its implications for digestion applications.

    Science.gov (United States)

    Leng, Ling; Yang, Peixian; Singh, Shubham; Zhuang, Huichuan; Xu, Linji; Chen, Wen-Hsing; Dolfing, Jan; Li, Dong; Zhang, Yan; Zeng, Huiping; Chu, Wei; Lee, Po-Heng

    2018-01-01

    The exploration of the energetics of anaerobic digestion systems can reveal how microorganisms cooperate efficiently for cell growth and methane production, especially under low-substrate conditions. The establishment of a thermodynamically interdependent partnership, called anaerobic syntrophy, allows unfavorable reactions to proceed. Interspecies electron transfer and the concentrations of electron carriers are crucial for maintaining this mutualistic activity. This critical review summarizes the functional microorganisms and syntroph partners, particularly in the metabolic pathways and energy conservation of syntrophs. The kinetics and thermodynamics of propionate degradation to methane, reversibility of the acetate oxidation process, and estimation of microbial growth are summarized. The various routes of interspecies electron transfer, reverse electron transfer, and Poly-β-hydroxyalkanoate formation in the syntrophic community are also reviewed. Finally, promising and critical directions of future research are proposed. Fundamental insight in the activities and interactions involved in AD systems could serve as a guidance for engineered systems optimization and upgrade. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. Effect of Temperature on Precipitation Rate of Calcium Carbonate Produced through Microbial Metabolic Process of Bio Materials

    Directory of Open Access Journals (Sweden)

    Prima Yane Putri

    2016-09-01

    Full Text Available Concrete is the most widely used construction material in civil engineering. But plain concrete is a brittle material and has little resistance to cracking. The cracking in concrete promotes deterioration such as the corrosion of reinforcing rebar, therefore, repair in filling the crack is often carried out. Recently, repair methods using bio-based materials associated with microbial metabolic processes leading to precipitation of calcium carbonate have been intensively studied. In this study, influencing factors on the precipitation rate depending on the constituents of bio-based material comprising yeast, glucose and calcium acetate mixed in tris buffer solution was examined for improving the rate of initial reactions. In addition, effect of temperature change on the amount of calcium carbonate precipitation was also investigated. The precipitates were identified by X-ray diffraction. It was shown that the increase of temperature lead to a change on calcium carbonate precipitation and caused the pH decrease under 7.0.

  9. In situ phytoremediation of PAH-contaminated soil by intercropping alfalfa (Medicago sativa L.) with tall fescue (Festuca arundinacea Schreb.) and associated soil microbial activity

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Mingming; Fu, Dengqiang; Teng, Ying; Shen, Yuanyuan; Luo, Yongming; Li, Zhengao [Chinese Academy of Sciences, Nanjing (China). Key Laboratory of Soil Environment and Pollution Remediation; Christie, Peter [Agri-Food and Biosciences Institute, Belfast (United Kingdom). Agri-Environment Branch

    2011-09-15

    Purpose: A 7-month field experiment was conducted to investigate the polycyclic aromatic hydrocarbon (PAH) remediation potential of two plant species and changes in counts of soil PAH-degrading bacteria and microbial activity. Materials and methods: Alfalfa and tall fescue were grown in monoculture and intercropped for 7 months in contaminated field soil. Soil and plant samples were analyzed for PAHs. Plant biomass, densities of PAH-degradation soil bacteria, soil microbial biomass C and N, enzyme activities, and the physiological profile of the soil microbial community were determined. Results and discussion: Average removal percentage of total PAHs in intercropping (30.5%) was significantly higher than in monoculture (19.9%) or unplanted soil (-0.6%). About 7.5% of 3-ring, 12.3% of 4-ring, and 17.2% of 5(+6)-ring PAHs were removed from the soil by alfalfa, with corresponding values of 25.1%, 10.4%, and 30.1% for tall fescue. Intercropping significantly enhanced the remediation efficiency. About 18.9% of 3-ring, 30.9% of 4-ring, and 33.4% of 5(+6)-ring PAHs were removed by the intercropping system. Higher counts of soil culturable PAH-degrading bacteria and elevated microbial biomass and enzyme activities were found after intercropping. Soil from intercropping showed significantly higher (p < 0.05) average well-color development obtained by the BIOLOG Ecoplate assay and Shannon-Weaver index compared with monoculture. Conclusions: Cropping promoted the dissipation of soil PAHs. Tall fescue gave greater removal of soil PAHs than alfalfa, and intercropping was more effective than monoculture. Intercropping of alfalfa and tall fescue may be a promising in situ bioremediation strategy for PAH-contaminated soils. (orig.)

  10. Arabinoxylo-Oligosaccharides and Inulin Impact Inter-Individual Variation on Microbial Metabolism and Composition, Which Immunomodulates Human Cells.

    Science.gov (United States)

    Van den Abbeele, Pieter; Taminiau, Bernard; Pinheiro, Iris; Duysburgh, Cindy; Jacobs, Heidi; Pijls, Loek; Marzorati, Massimo

    2018-02-07

    Fecal batch fermentations coupled to cocultures of epithelial cells and macrophages were used to compare how arabinoxylo-oligosaccharides (AXOS) and inulin modulate gut microbial activity and composition of three different human donors and subsequently the epithelial permeability and immune response. Both inulin and AXOS decreased the pH during incubation (-1.5 pH units), leading to increased productions of acetate, propionate, and butyrate. Differences in terms of metabolites production could be linked to specific microbial alterations at genus level upon inulin/AXOS supplementation (i.e., Bifidobacterium, Bacteroides, Prevotella and unclassified Erysipelotrichaceae), as shown by 16S-targeted Illumina sequencing. Both products stimulated gut barrier and immune function with increases in TEER, NF-KB, IL-10, and IL-6. Ingredients with different structures selectively modulate the microbiota of a specific donor leading to differential changes at metabolic level. The extent of this effect is donor specific and is linked to a final specific modulation of the host's immune system.

  11. The Oxidative Metabolism of Fossil Hydrocarbons and Sulfide Minerals by the Lithobiontic Microbial Community Inhabiting Deep Subterrestrial Kupferschiefer Black Shale

    Directory of Open Access Journals (Sweden)

    Agnieszka Włodarczyk

    2018-05-01

    Full Text Available Black shales are one of the largest reservoirs of fossil organic carbon and inorganic reduced sulfur on Earth. It is assumed that microorganisms play an important role in the transformations of these sedimentary rocks and contribute to the return of organic carbon and inorganic sulfur to the global geochemical cycles. An outcrop of deep subterrestrial ~256-million-year-old Kupferschiefer black shale was studied to define the metabolic processes of the deep biosphere important in transformations of organic carbon and inorganic reduced sulfur compounds. This outcrop was created during mining activity 12 years ago and since then it has been exposed to the activity of oxygen and microorganisms. The microbial processes were described based on metagenome and metaproteome studies as well as on the geochemistry of the rock. The microorganisms inhabiting the subterrestrial black shale were dominated by bacterial genera such as Pseudomonas, Limnobacter, Yonghaparkia, Thiobacillus, Bradyrhizobium, and Sulfuricaulis. This study on black shale was the first to detect archaea and fungi, represented by Nitrososphaera and Aspergillus genera, respectively. The enzymatic oxidation of fossil aliphatic and aromatic hydrocarbons was mediated mostly by chemoorganotrophic bacteria, but also by archaea and fungi. The dissimilative enzymatic oxidation of primary reduced sulfur compounds was performed by chemolithotrophic bacteria. The geochemical consequences of microbial activity were the oxidation and dehydrogenation of kerogen, as well as oxidation of sulfide minerals.

  12. Metabolic and phylogenetic analysis of microbial communities during phytoremediation of soil contaminated with weathered hydrocarbons and heavy metals.

    Science.gov (United States)

    Palmroth, Marja R T; Koskinen, Perttu E P; Kaksonen, Anna H; Münster, Uwe; Pichtel, John; Puhakka, Jaakko A

    2007-12-01

    In the current study, the microbial ecology of weathered hydrocarbon and heavy metal contaminated soil undergoing phytoremediation was studied. The relationship of functional diversity, measured as carbon source utilisation in Biolog plates and extracellular enzymatic activities, and genetic diversity of bacteria was evaluated. Denaturing gradient gel electrophoresis was used for community analyses at the species level. Bulk soil and rhizosphere soil from pine and poplar plantations were analysed separately to determine if the plant rhizosphere impacted hydrocarbon degradation. Prevailing microbial communities in the field site were both genetically and metabolically diverse. Furthermore, both tree rhizosphere and fertilisation affected the compositions of these communities and increased activities of extracellular aminopeptidases. In addition, the abundance of alkane hydroxylase and naphthalene dioxygenase genes in the communities was low, but the prevalence of these genes was increased by the addition of bioavailable hydrocarbons. Tree rhizosphere communities had greater hydrocarbon degradation potential than those of bulk soil. Hydrocarbon utilising communities were dominated generally by the species Ralstonia eutropha and bacteria belonging to the genus Burkholderia. Despite the presence of viable hydrocarbon-degrading microbiota, decomposition of hydrocarbons from weathered hydrocarbon contaminated soil over four years, regardless of the presence of vegetation, was low in unfertilised soil. Compost addition enhanced the removal of hydrocarbons.

  13. Methane-metabolizing microbial communities in sediments of the Haima cold seep area, northwest slope of the South China Sea.

    Science.gov (United States)

    Niu, Mingyang; Fan, Xibei; Zhuang, Guangchao; Liang, Qianyong; Wang, Fengping

    2017-09-01

    Cold seeps are widespread chemosynthetic ecosystems in the deep-sea environment, and cold seep microbial communities of the South China Sea are poorly constrained. Here we report on the archaeal communities, particularly those involved in methane metabolization, in sediments of a newly discovered cold seep (named 'Haima') on the northwest slope of the South China Sea. Archaeal diversity, abundance and distribution were investigated in two piston cores collected from a seep area (QDN-14B) and a non-seep control site (QDN-31B). Geochemical investigation of the QDN-14B core identified an estimated sulfate-methane transition zone (Estimated SMTZ) at 300-400 cm below sea floor (cmbsf), where a high abundance of anaerobic methane-oxidizing archaea (ANME) occurred, as revealed by analysis of the 16S rRNA gene and the gene (mcrA) encoding the α-subunit of the key enzyme methyl-coenzyme M reductase. ANME-2a/b was predominant in the upper and middle layers of the estimated SMTZ, whereas ANME-1b outcompeted ANME-2 in the sulfate-depleted bottom layers of the estimated SMTZ and the methanogenic zone. Fine-scale phylogenetic analysis further divided the ANME-1b group into three subgroups with different distribution patterns: ANME-1bI, ANME-1bII and ANME-1bIII. Multivariate analyses indicated that dissolved inorganic carbon and sulfate may be important factors controlling the composition of the methane-metabolizing community. Our study on ANME niche separation and interactions with other archaeal groups improves our understanding of the metabolic diversity and flexibility of ANME, and the findings further suggest that ANME subgroups may have evolved diversified/specified metabolic capabilities other than syntrophic anaerobic oxidation of methane coupled with sulfate reduction in marine sediments. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  14. In situ environment rather than substrate type dictates microbial community structure of biofilms in a cold seep system

    KAUST Repository

    Lee, O.O.; Wang, Y.; Tian, R.; Zhang, W.; Shek, C.S.; Bougouffa, Salim; Al-Suwailem, A.; Batang, Z.B.; Xu, W.; Wang, G.C.; Zhang, Xixiang; Lafi, F.F.; Bajic, Vladimir B.; Qian, P.-Y.

    2014-01-01

    Using microscopic and molecular techniques combined with computational analysis, this study examined the structure and composition of microbial communities in biofilms that formed on different artificial substrates in a brine pool and on a seep vent of a cold seep in the Red Sea to test our hypothesis that initiation of the biofilm formation and spreading mode of microbial structures differs between the cold seep and the other aquatic environments. Biofilms on different substrates at two deployment sites differed morphologically, with the vent biofilms having higher microbial abundance and better structural features than the pool biofilms. Microbes in the pool biofilms were more taxonomically diverse and mainly composed of various sulfate-reducing bacteria whereas the vent biofilms were exclusively dominated by sulfur-oxidizing Thiomicrospira. These results suggest that the redox environments at the deployment sites might have exerted a strong selection on microbes in the biofilms at two sites whereas the types of substrates had limited effects on the biofilm development.

  15. In situ environment rather than substrate type dictates microbial community structure of biofilms in a cold seep system

    KAUST Repository

    Lee, O.O.

    2014-01-08

    Using microscopic and molecular techniques combined with computational analysis, this study examined the structure and composition of microbial communities in biofilms that formed on different artificial substrates in a brine pool and on a seep vent of a cold seep in the Red Sea to test our hypothesis that initiation of the biofilm formation and spreading mode of microbial structures differs between the cold seep and the other aquatic environments. Biofilms on different substrates at two deployment sites differed morphologically, with the vent biofilms having higher microbial abundance and better structural features than the pool biofilms. Microbes in the pool biofilms were more taxonomically diverse and mainly composed of various sulfate-reducing bacteria whereas the vent biofilms were exclusively dominated by sulfur-oxidizing Thiomicrospira. These results suggest that the redox environments at the deployment sites might have exerted a strong selection on microbes in the biofilms at two sites whereas the types of substrates had limited effects on the biofilm development.

  16. In situ exposure to low herbicide concentrations affects microbial population composition and catabolic gene frequency in an aerobic shallow aquifer

    DEFF Research Database (Denmark)

    de Lipthay, J.R.; Tuxen, Nina; Johnsen, Kaare

    2003-01-01

    and were analyzed for the presence of general microbial populations, Pseudomonas bacteria, and specific phenoxy acid degraders. Both culture-dependent and culture-independent methods were applied. The abundance of microbial phenoxy acid degraders (10(0) to 10(4) g(-1) sediment) was determined by most...... measured by either PCR or plating on selective agar media was higher in sediments subjected to high levels of phenoxy acid. Furthermore, high numbers of CFU compared to direct counting of 4',6-diamidino-2-phenylindole-stained cells in the microscope suggested an increased culturability of the indigenous...

  17. Metabolic enzyme cost explains variable trade-offs between microbial growth rate and yield.

    Directory of Open Access Journals (Sweden)

    Meike T Wortel

    2018-02-01

    Full Text Available Microbes may maximize the number of daughter cells per time or per amount of nutrients consumed. These two strategies correspond, respectively, to the use of enzyme-efficient or substrate-efficient metabolic pathways. In reality, fast growth is often associated with wasteful, yield-inefficient metabolism, and a general thermodynamic trade-off between growth rate and biomass yield has been proposed to explain this. We studied growth rate/yield trade-offs by using a novel modeling framework, Enzyme-Flux Cost Minimization (EFCM and by assuming that the growth rate depends directly on the enzyme investment per rate of biomass production. In a comprehensive mathematical model of core metabolism in E. coli, we screened all elementary flux modes leading to cell synthesis, characterized them by the growth rates and yields they provide, and studied the shape of the resulting rate/yield Pareto front. By varying the model parameters, we found that the rate/yield trade-off is not universal, but depends on metabolic kinetics and environmental conditions. A prominent trade-off emerges under oxygen-limited growth, where yield-inefficient pathways support a 2-to-3 times higher growth rate than yield-efficient pathways. EFCM can be widely used to predict optimal metabolic states and growth rates under varying nutrient levels, perturbations of enzyme parameters, and single or multiple gene knockouts.

  18. Influence of diet and microbial activity in the digestive tract on digestibility, and nitrogen and energy metabolism in rats and pigs

    DEFF Research Database (Denmark)

    Eggum, B O; Thorbek, G; Beames, R M

    1982-01-01

    -55 kg. Measurements were made on the influence of microbial activity in the digestive tract on digestibility and nitrogen and energy metabolism. Dietary inclusion of the antibiotic Nebacitin was the method used to reduce the microbial population. 2. The microbial activity in the hind-gut (mumol ATP....../g air-dry contents) of antibiotic-treated rats was reduced to approximately one-tenth of that of untreated rats. 3. Live-weight gain was not significantly affected in either species by a reduction in the microbial activity, in spite of a reduction in dry matter digestibility in animals with reduced...... microflora. 4. For rats on low-crude-fibre diets, a reduction in microflora reduced digestibility of all nutrients and energy and metabolizability of digestible energy by approximately 5.4%. All differences were highly significant. On high-crude-fibre diets the decrease was approximately 5.9%. In pigs...

  19. Effect of Microbial Interaction on Urea Metabolism in Chinese Liquor Fermentation.

    Science.gov (United States)

    Wu, Qun; Lin, Jianchun; Cui, Kaixiang; Du, Rubin; Zhu, Yang; Xu, Yan

    2017-12-20

    Urea is the primary precursor of the carcinogen ethyl carbamate in fermented foods. Understanding urea metabolism is important for controlling ethyl carbamate production. Using Chinese liquor as a model system, we used metatranscriptome analysis to investigate urea metabolism in spontaneous food fermentation processes. Saccharomyces cerevisiae was dominant in gene transcription for urea biosynthesis and degradation. Lysinibacillus sphaericus was dominant for urea degradation. S. cerevisiae degraded 18% and L. sphaericus degraded 13% of urea in their corresponding single cultures, whereas they degraded 56% of urea in coculture after 12 h. Compared to single cultures, transcription of CAR1, DAL2, and argA, which are related to urea biosynthesis, decreased by 51, 36, and 69% in coculture, respectively. Transcription of DUR1 and ureA, which are related to urea degradation, increased by 227 and 70%, respectively. Thus, coexistence of the two strains promoted degradation of urea via transcriptional regulation of genes related to urea metabolism.

  20. Metabolic potential and in situ activity of marine Marinimicrobia bacteria in an anoxic water column.

    Science.gov (United States)

    Bertagnolli, Anthony D; Padilla, Cory C; Glass, Jennifer B; Thamdrup, Bo; Stewart, Frank J

    2017-11-01

    Marinimicrobia bacteria are widespread in subeuphotic areas of the oceans and particularly abundant in oxygen minimum zones (OMZs). Information on Marinimicrobia metabolism is sparse, making the biogeochemical influence of this group challenging to predict. Here, metagenome-assembled genomes representing Marinimicrobia subgroups PN262000N21 and ARCTIC96B-7 were retrieved to near completion (97% and 94%) from OMZ metagenomes, with contamination (14.1%) observed only in ARCTIC96B-7. Genes for aerobic carbon monoxide (CO) oxidation, polysulfide metabolism and hydrogen utilization were identified only in PN262000N21, while genes for partial denitrification occurred in both genomes. Transcripts mapping to these genomes increased from utilizing proteins, including sulfur transferases, were enriched at sulfidic depths. PN262000N21 transcripts encoding a protein with fibronectin domains similar to those in cellulosome-producing bacteria were also abundant, suggesting a potential for high molecular weight carbon cycling. These data provide omic-level descriptions of metabolic potential and activity in OMZ-associated Marinimicrobia, suggesting differentiation between subgroups with roles in carbon and dissimilatory inorganic nitrogen and sulfur cycling. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  1. Probiotic modulation of symbiotic gut microbial-host metabolic interactions in a humanized microbiome mouse model

    NARCIS (Netherlands)

    Martin, F.P.J.; Wang, Y.; Sprenger, N.; Yap, K.S.; Rezzi, S.; Ramadan, Z.; Peré-Trepat, E.; Rochat, F.; Cherbut, C.; Bladeren, van P.J.; Fay, L.B.; Kochhar, S.; LindOn, J.C.; Holmes, E.; Nicholson, J.K.

    2008-01-01

    The transgenomic metabolic effects of exposure to either Lactobacillus paracasei or Lactobacillus rhamnosus probiotics have been measured and mapped in humanized extended genome mice (germ-free mice colonized with human baby flora). Statistical analysis of the compartmental fluctuations in diverse

  2. ReacKnock: identifying reaction deletion strategies for microbial strain optimization based on genome-scale metabolic network.

    Directory of Open Access Journals (Sweden)

    Zixiang Xu

    Full Text Available Gene knockout has been used as a common strategy to improve microbial strains for producing chemicals. Several algorithms are available to predict the target reactions to be deleted. Most of them apply mixed integer bi-level linear programming (MIBLP based on metabolic networks, and use duality theory to transform bi-level optimization problem of large-scale MIBLP to single-level programming. However, the validity of the transformation was not proved. Solution of MIBLP depends on the structure of inner problem. If the inner problem is continuous, Karush-Kuhn-Tucker (KKT method can be used to reformulate the MIBLP to a single-level one. We adopt KKT technique in our algorithm ReacKnock to attack the intractable problem of the solution of MIBLP, demonstrated with the genome-scale metabolic network model of E. coli for producing various chemicals such as succinate, ethanol, threonine and etc. Compared to the previous methods, our algorithm is fast, stable and reliable to find the optimal solutions for all the chemical products tested, and able to provide all the alternative deletion strategies which lead to the same industrial objective.

  3. An innovative bioelectrochemical-anaerobic digestion-coupled system for in-situ ammonia recovery and biogas enhancement: process performance and microbial ecology

    DEFF Research Database (Denmark)

    Zhang, Yifeng; Angelidaki, Irini

    (SMRC) and a continuous stirred tank reactor (CSTR), to prevent ammonia toxicity during anaerobic digestion by in-situ ammonia recovery and electricity production. In batch experiment, the ammonia concentration in the CSTR decreased from 6 to 0.7 g-N/L with an average recovery rate of 0.18 g-N/L(CSTR...... performance was enhanced. In addition, the coexistence of other cations in CSTR or cathode had no negative effect on the ammonia transportation. In continuous reactor operation, 112% extra biogas production was achieved due to ammonia recovery. High-throughput molecular sequencing analysis showed an impact...... of ammonia recovery on the microbial community composition in the integrated system. Results clearly indicate the great potential of the SMRC-CSTR-coupled system for efficient and cost-effective ammonia recovery, energy production and treatment of ammonia-rich residues....

  4. The application of fluorescence in situ hybridization (FISH technique for studying the microbial communities in intestinal tissues of white shrimp (Penaeus vannamei

    Directory of Open Access Journals (Sweden)

    Supamattaya, K.

    2005-02-01

    Full Text Available Fluorescence in situ hybridization technique is very useful for the evaluation of microbial communities in various environments. It is possible to apply this technique to study the intestinal microflora in white shrimp (Penaeus vannamei. Different fixatives and storage temperature were tested in this technique. It was found that fixation with 10% buffered formalin for 12 hours and changed to 70% ethanol shown positive results when compared to the fixation with Davidson's fixative or RF fixative. The best signaling was obtainedfrom the samples which were stored in -20ºC. By using the DNA probe targeted to the Eubacteria domain (EUB338 probe, 5′-GCT GCC TCC CGT AGG AGT-3′ labeled with fluorescein as a hybridizing probe, it was found that most intestinal microflora were aggregated with the intestinal contents, or dispersed in the lumen. There was not evidence of the attachment of the microflora with the intestinal epithelium in this study.

  5. In Situ Boundary Layer Coral Metabolism in the Atlantic Ocean Acidification Test Bed

    Science.gov (United States)

    McGillis, Wade

    2013-04-01

    and Chris Langdon, Brice Loose, Dwight Gledhill, Diana Hsueh, Derek Manzello, Ian Enochs, Ryan Moyer We present net ecosystem productivity (nep) and net ecosystem calcification (nec) in coral and seagrass ecosystems using the boundary layer gradient flux technique (CROSS). Coastal anthropogenic inputs and changes in global ocean chemistry in response to rising levels of atmospheric carbon dioxide has emerged in recent years as a topic of considerable concern. Coral reefs are particularly vulnerable from eroded environmental conditions including ocean acidification and water pollution. The Atlantic Ocean Acidification Testbed (AOAT) project monitors metabolism to ascertain the continuing health of coral reef ecosystems. The CROSS boundary layer nep/nec approach is one component of this diagnostic program. Certification of CROSS as an operational monitoring tool is underway in the AOAT. CROSS inspects a benthic community and measures productivity/respiration and calcification/dissolution over an area of 10 square meters. Being a boundary layer tool, advection and complex mesoscale flows are not a factor or concern and CROSS is autonomous and can be used at deep benthic sites. The interrogation area is not enclosed therefore exposed to ambient light, flow, and nutrient levels. CROSS is easy to deploy, unambiguous, and affordable. Repeated measurements have been made from 2011-2012 in reefal systems in La Parguera Puerto Rico and the Florida Keys, USA. Diurnal, seasonal and regional metabolism will be compared and discussed. The ability to accurately probe benthic ecosystems provides a powerful management and research tool to policy makers and researchers.

  6. Dynamics of Panax ginseng Rhizospheric Soil Microbial Community and Their Metabolic Function

    Directory of Open Access Journals (Sweden)

    Yong Li

    2014-01-01

    Full Text Available The bacterial communities of 1- to 6-year ginseng rhizosphere soils were characterized by culture-independent approaches, random amplified polymorphic DNA (RAPD, and amplified ribosomal DNA restriction analysis (ARDRA. Culture-dependent method (Biolog was used to investigate the metabolic function variance of microbe living in rhizosphere soil. Results showed that significant genetic and metabolic function variance were detected among soils, and, with the increasing of cultivating years, genetic diversity of bacterial communities in ginseng rhizosphere soil tended to be decreased. Also we found that Verrucomicrobia, Acidobacteria, and Proteobacteria were the dominants in rhizosphere soils, but, with the increasing of cultivating years, plant disease prevention or plant growth promoting bacteria, such as Pseudomonas, Burkholderia, and Bacillus, tended to be rare.

  7. Effect of lineage-specific metabolic traits of Lactobacillus reuteri on sourdough microbial ecology.

    Science.gov (United States)

    Lin, Xiaoxi B; Gänzle, Michael G

    2014-09-01

    This study determined the effects of specific metabolic traits of Lactobacillus reuteri on its competitiveness in sourdoughs. The competitiveness of lactobacilli in sourdough generally depends on their growth rate; acid resistance additionally contributes to competitiveness in sourdoughs with long fermentation times. Glycerol metabolism via glycerol dehydratase (gupCDE) accelerates growth by the regeneration of reduced cofactors; glutamate metabolism via glutamate decarboxylase (gadB) increases acid resistance by generating a proton motive force. Glycerol and glutamate metabolisms are lineage-specific traits in L. reuteri; therefore, this study employed glycerol dehydratase-positive sourdough isolates of human-adapted L. reuteri lineage I, glutamate decarboxylase-positive strains of rodent-adapted L. reuteri lineage II, as well as mutants with deletions in gadB or gupCDE. The competitivenesses of the strains were quantified by inoculation of wheat and sorghum sourdoughs with defined strains, followed by propagation of doughs with a 10% inoculum and 12-h or 72-h fermentation cycles. Lineage I L. reuteri strains dominated sourdoughs propagated with 12-h fermentation cycles; lineage II L. reuteri strains dominated sourdoughs propagated with 72-h fermentation cycles. L. reuteri 100-23ΔgadB was outcompeted by its wild-type strain in sourdoughs fermented with 72-h fermentation cycles; L. reuteri FUA3400ΔgupCDE was outcompeted by its wild-type strain in sourdoughs fermented with both 12-h and 72-h fermentation cycles. Competition experiments with isogenic pairs of strains resulted in a constant rate of strain displacement of the less competitive mutant strain. In conclusion, lineage-specific traits of L. reuteri determine the competitiveness of this species in sourdough fermentations. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  8. Unique Microbial Diversity and Metabolic Pathway Features of Fermented Vegetables From Hainan, China

    OpenAIRE

    Qiannan Peng; Shuaiming Jiang; Jieling Chen; Chenchen Ma; Dongxue Huo; Yuyu Shao; Jiachao Zhang; Jiachao Zhang

    2018-01-01

    Fermented vegetables are typically traditional foods made of fresh vegetables and their juices, which are fermented by beneficial microorganisms. Herein, we applied high-throughput sequencing and culture-dependent technology to describe the diversities of microbiota and identify core microbiota in fermented vegetables from different areas of Hainan Province, and abundant metabolic pathways in the fermented vegetables were simultaneously predicted. At the genus level, Lactobacillus bacteria we...

  9. Inhibition of microbial metabolism in anaerobic lagoons by selected sulfonamides, tetracyclines, lincomycin, and tylosin tartrate

    Science.gov (United States)

    Loftin, Keith A.; Henny, Cynthia; Adams, Craig D.; Surampali, Rao; Mormile, Melanie R.

    2005-01-01

    Antibiotics are used to maintain healthy livestock and to promote weight gain in concentrated animal feed operations. Antibiotics rarely are metabolized completely by livestock and, thus, are often present in livestock waste and in waste-treatment lagoons. The introduction of antibiotics into anaerobic lagoons commonly used for swine waste treatment has the potential for negative impacts on lagoon performance, which relies on a consortium of microbes ranging from fermentative microorganisms to methanogens. To address this concern, the effects of eight common veterinary antibiotics on anaerobic activity were studied. Anaerobic microcosms, prepared from freshly collected lagoon slurries, were amended with individual antibiotics at 10 mg/L for the initial screening study and at 1, 5, and 25 mg/L for the dose-response study. Monitored metabolic indicators included hydrogen, methane, and volatile fatty acid concentrations as well as chemical oxygen demand. The selected antibiotics significantly inhibited methane production relative to unamended controls, thus indicating that antibiotics at concentrations commonly found in swine lagoons can negatively impact anaerobic metabolism. Additionally, historical antibiotic usage seems to be a potential factor in affecting methane production. Specifically, less inhibition of methane production was noted in samples taken from the lagoon with a history of multiple-antibiotic use.

  10. Inhibition of microbial metabolism in anaerobic lagoons by selected sulfonamides, tetracyclines, lincomycin, and tylosin tartrate.

    Science.gov (United States)

    Loftin, Keith A; Henny, Cynthia; Adams, Craig D; Surampali, Rao; Mormile, Melanie R

    2005-04-01

    Antibiotics are used to maintain healthy livestock and to promote weight gain in concentrated animal feed operations. Antibiotics rarely are metabolized completely by livestock and, thus, are often present in livestock waste and in waste-treatment lagoons. The introduction of antibiotics into anaerobic lagoons commonly used for swine waste treatment has the potential for negative impacts on lagoon performance, which relies on a consortium of microbes ranging from fermentative microorganisms to methanogens. To address this concern, the effects of eight common veterinary antibiotics on anaerobic activity were studied. Anaerobic microcosms, prepared from freshly collected lagoon slurries, were amended with individual antibiotics at 10 mg/L for the initial screening study and at 1, 5, and 25 mg/L for the dose-response study. Monitored metabolic indicators included hydrogen, methane, and volatile fatty acid concentrations as well as chemical oxygen demand. The selected antibiotics significantly inhibited methane production relative to unamended controls, thus indicating that antibiotics at concentrations commonly found in swine lagoons can negatively impact anaerobic metabolism. Additionally, historical antibiotic usage seems to be a potential factor in affecting methane production. Specifically, less inhibition of methane production was noted in samples taken from the lagoon with a history of multiple-antibiotic use.

  11. Gold nanoparticles produced in situ mediate bioelectricity and hydrogen production in a microbial fuel cell by quantized capacitance charging.

    Science.gov (United States)

    Kalathil, Shafeer; Lee, Jintae; Cho, Moo Hwan

    2013-02-01

    Oppan quantized style: By adding a gold precursor at its cathode, a microbial fuel cell (MFC) is demonstrated to form gold nanoparticles that can be used to simultaneously produce bioelectricity and hydrogen. By exploiting the quantized capacitance charging effect, the gold nanoparticles mediate the production of hydrogen without requiring an external power supply, while the MFC produces a stable power density. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Effects of correcting in situ ruminal microbial colonization of feed particles on the relationship between ruminally undegraded and intestinally digested crude protein in concentrate feeds.

    Science.gov (United States)

    González, Javier; Mouhbi, Rabiaa; Guevara-González, Jesús Alberto; Arroyo, José María

    2018-02-01

    In situ estimates of ruminally undegraded protein (RUP) and intestinally digested protein (IDP) of ten concentrates, uncorrected or corrected for the ruminal microbial colonization, were used to examine the effects of this correction on the relationship between IDP and RUP values. Both variables were established for three rumen and duodenum cannulated wethers using 15 N labeling-techniques and considering measured rates of ruminal particle comminution (k c ) and outflow (k p ). A covariance analysis showed that the close relationship found between both variables (IDP = -0.0132 ± 0.00679 + 0.776 ± 0.0002 RUP; n = 60; P content in concentrates and industrial by-products can be predicted from RUP values, thus avoiding the laborious and complex procedure of determining intestinal digestibility; however, a larger sample of feeds is necessary to achieve more accurate predictions. The lack of influence of the correction for microbial contamination on the prediction observed in the present study increases the data available for this prediction. However, only the use of corrected values may provide an accurate evaluation. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  13. Characterization of the microbial community composition and the distribution of Fe-metabolizing bacteria in a creek contaminated by acid mine drainage.

    Science.gov (United States)

    Sun, Weimin; Xiao, Enzong; Krumins, Valdis; Dong, Yiran; Xiao, Tangfu; Ning, Zengping; Chen, Haiyan; Xiao, Qingxiang

    2016-10-01

    A small watershed heavily contaminated by long-term acid mine drainage (AMD) from an upstream abandoned coal mine was selected to study the microbial community developed in such extreme system. The watershed consists of AMD-contaminated creek, adjacent contaminated soils, and a small cascade aeration unit constructed downstream, which provide an excellent contaminated site to study the microbial response in diverse extreme AMD-polluted environments. The results showed that the innate microbial communities were dominated by acidophilic bacteria, especially acidophilic Fe-metabolizing bacteria, suggesting that Fe and pH are the primary environmental factors in governing the indigenous microbial communities. The distribution of Fe-metabolizing bacteria showed distinct site-specific patterns. A pronounced shift from diverse communities in the upstream to Proteobacteria-dominated communities in the downstream was observed in the ecosystem. This location-specific trend was more apparent at genus level. In the upstream samples (sampling sites just below the coal mining adit), a number of Fe(II)-oxidizing bacteria such as Alicyclobacillus spp., Metallibacterium spp., and Acidithrix spp. were dominant, while Halomonas spp. were the major Fe(II)-oxidizing bacteria observed in downstream samples. Additionally, Acidiphilium, an Fe(III)-reducing bacterium, was enriched in the upstream samples, while Shewanella spp. were the dominant Fe(III)-reducing bacteria in downstream samples. Further investigation using linear discriminant analysis (LDA) effect size (LEfSe), principal coordinate analysis (PCoA), and unweighted pair group method with arithmetic mean (UPGMA) clustering confirmed the difference of microbial communities between upstream and downstream samples. Canonical correspondence analysis (CCA) and Spearman's rank correlation indicate that total organic carbon (TOC) content is the primary environmental parameter in structuring the indigenous microbial communities

  14. Profiling of Indigenous Microbial Community Dynamics and Metabolic Activity During Enrichment in Molasses-Supplemented Crude Oil-Brine Mixtures for Improved Understanding of Microbial Enhanced Oil Recovery

    DEFF Research Database (Denmark)

    Halim, Amalia Yunita; Pedersen, Dorthe Skou; Nielsen, Sidsel Marie

    2015-01-01

    Anaerobic incubations using crude oil and brine from a North Sea reservoir were conducted to gain increased understanding of indigenous microbial community development, metabolite production, and the effects on the oil–brine system after addition of a complex carbon source, molasses, with or with...... of molasses has potential as microbial enhanced oil recovery (MEOR) strategy in North Sea oil reservoirs.......Anaerobic incubations using crude oil and brine from a North Sea reservoir were conducted to gain increased understanding of indigenous microbial community development, metabolite production, and the effects on the oil–brine system after addition of a complex carbon source, molasses....... The microbial growth caused changes in the crude oil–brine system: formation of oil emulsions, and reduction of interfacial tension (IFT). Reduction in IFT was associated with microbes being present at the oil–brine interphase. These findings suggest that stimulation of indigenous microbial growth by addition...

  15. Profiling of Indigenous Microbial Community Dynamics and Metabolic Activity During Enrichment in Molasses-Supplemented Crude Oil-Brine Mixtures for Improved Understanding of Microbial Enhanced Oil Recovery.

    Science.gov (United States)

    Halim, Amalia Yunita; Pedersen, Dorthe Skou; Nielsen, Sidsel Marie; Lantz, Anna Eliasson

    2015-06-01

    Anaerobic incubations using crude oil and brine from a North Sea reservoir were conducted to gain increased understanding of indigenous microbial community development, metabolite production, and the effects on the oil-brine system after addition of a complex carbon source, molasses, with or without nitrate to boost microbial growth. Growth of the indigenous microbes was stimulated by addition of molasses. Pyrosequencing showed that specifically Anaerobaculum, Petrotoga, and Methanothermococcus were enriched. Addition of nitrate favored the growth of Petrotoga over Anaerobaculum. The microbial growth caused changes in the crude oil-brine system: formation of oil emulsions, and reduction of interfacial tension (IFT). Reduction in IFT was associated with microbes being present at the oil-brine interphase. These findings suggest that stimulation of indigenous microbial growth by addition of molasses has potential as microbial enhanced oil recovery (MEOR) strategy in North Sea oil reservoirs.

  16. Methods for the Isolation of Genes Encoding Novel PHA Metabolism Enzymes from Complex Microbial Communities.

    Science.gov (United States)

    Cheng, Jiujun; Nordeste, Ricardo; Trainer, Maria A; Charles, Trevor C

    2017-01-01

    Development of different PHAs as alternatives to petrochemically derived plastics can be facilitated by mining metagenomic libraries for diverse PHA cycle genes that might be useful for synthesis of bio-plastics. The specific phenotypes associated with mutations of the PHA synthesis pathway genes in Sinorhizobium meliloti and Pseudomonas putida, allows the use of powerful selection and screening tools to identify complementing novel PHA synthesis genes. Identification of novel genes through their function rather than sequence facilitates the functional proteins that may otherwise have been excluded through sequence-only screening methodology. We present here methods that we have developed for the isolation of clones expressing novel PHA metabolism genes from metagenomic libraries.

  17. Corn silage in dairy cow diets to reduce ruminal methanogenesis: effects on the rumen metabolically active microbial communities.

    Science.gov (United States)

    Lettat, A; Hassanat, F; Benchaar, C

    2013-08-01

    Methane produced by the methanogenic Archaea that inhabit the rumen is a potent greenhouse gas and represents an energy loss for the animal. Although several strategies have been proposed to mitigate enteric CH4 production, little is known about the effects of dietary changes on the microbial consortia involved in ruminal methanogenesis. Thus, the current study aimed to examine how the metabolically active microbes are affected when dairy cows were fed diets with increasing proportions of corn silage (CS). For this purpose, 9 ruminally cannulated lactating dairy cows were used in a replicated 3 × 3 Latin square design and fed a total mixed ration (60:40 forage:concentrate ratio on a dry matter basis) with the forage portion being either alfalfa silage (0% CS), corn silage (100% CS), or a 50:50 mixture (50% CS). Enteric CH4 production was determined using respiration chambers and total rumen content was sampled for the determination of fermentation characteristics and molecular biology analyses (cDNA-based length heterogeneity PCR, quantitative PCR). The cDNA-based length heterogeneity PCR targeting active microbes revealed similar bacterial communities in cows fed 0% CS and 50% CS diets, whereas important differences were observed between 0% CS and 100% CS diets, including a reduction in the bacterial richness and diversity in cows fed 100% CS diet. As revealed by quantitative PCR, feeding the 100% CS diet increased the number of total bacteria, Prevotella spp., Archaea, and methanogenic activity, though it reduced protozoal number. Meanwhile, increasing the CS proportion in the diet increased propionate concentration but decreased ruminal pH, CH4 production (L/kg of dry matter intake), and concentrations of acetate and butyrate. Based on these microbial and fermentation changes, and because CH4 production was reduced by feeding 100% CS diet, this study shows that the use of cDNA-based quantitative PCR to estimate archaeal growth and activity is not reliable

  18. Polyphenols as enzyme inhibitors in different degraded peat soils: Implication for microbial metabolism in rewetted peatlands

    Science.gov (United States)

    Zak, Dominik; Roth, Cyril; Gelbrecht, Jörg; Fenner, Nathalie; Reuter, Hendrik

    2015-04-01

    Recently, more than 30,000 ha of drained minerotrophic peatlands (= fens) in NE Germany were rewetted to restore their ecological functions. Due to an extended drainage history, a re-establishment of their original state is not expected in the short-term. Elevated concentrations of dissolved organic carbon, ammonium and phosphate have been measured in the soil porewater of the upper degraded peat layers of rewetted fens at levels of one to three orders higher than the values in pristine systems; an indicator of increased microbial activity in the upper degraded soil layers. On the other hand there is evidence that the substrate availability within the degraded peat layer is lowered since the organic matter has formerly been subject to intense decomposition over the decades of drainage and intense agricultural use of the areas. Previously however, it was suggested that inhibition of hydrolytic enzymes by polyphenolic substances is suspended during aeration of peat soils mainly due to the decomposition of the inhibiting polyphenols by oxidising enzymes such as phenol oxidase. Accordingly we hypothesised a lack of enzyme inhibiting polyphenols in degraded peat soils of rewetted fens compared to less decomposed peat of more natural fens. We collected both peat samples at the soil surface (0-20 cm) and fresh roots of dominating vascular plants and mosses (as peat parent material) from five formerly drained rewetted sites and five more natural sites of NE Germany and NW Poland. Less decomposed peat and living roots were used to obtain an internal standard for polyphenol analysis and to run enzyme inhibition tests. For all samples we determined the total phenolic contents and in addition we distinguished between the contents of hydrolysable and condensed tannic substances. From a methodical perspective the advantage of internal standards compared to the commercially available standards cyanidin chloride and tannic acid became apparent. Quantification with cyanidin or

  19. Formate as an energy source for microbial metabolism in chemosynthetic zones of hydrothermal ecosystems.

    Science.gov (United States)

    Windman, Todd; Zolotova, Natalya; Schwandner, Florian; Shock, Everett L

    2007-12-01

    Formate, a simple organic acid known to support chemotrophic hyperthermophiles, is found in hot springs of varying temperature and pH. However, it is not yet known how metabolic strategies that use formate could contribute to primary productivity in hydrothermal ecosystems. In an effort to provide a quantitative framework for assessing the role of formate metabolism, concentration data for dissolved formate and many other solutes in samples from Yellowstone hot springs were used, together with data for coexisting gas compositions, to evaluate the overall Gibbs energy for many reactions involving formate oxidation or reduction. The result is the first rigorous thermodynamic assessment of reactions involving formate oxidation to bicarbonate and reduction to methane coupled with various forms of iron, nitrogen, sulfur, hydrogen, and oxygen for hydrothermal ecosystems. We conclude that there are a limited number of reactions that can yield energy through formate reduction, in contrast to numerous formate oxidation reactions that can yield abundant energy for chemosynthetic microorganisms. Because the energy yields are so high, these results challenge the notion that hydrogen is the primary energy source of chemosynthetic microbes in hydrothermal ecosystems.

  20. Weedy lignocellulosic feedstock and microbial metabolic engineering. Advancing the generation of 'Biofuel'

    Energy Technology Data Exchange (ETDEWEB)

    Chandel, Anuj K. [Jawaharlal Nehru Technological Univ., Hyderabad (India). Centre of Biotechnology; Singh, Om V. [Pittsburgh Univ., Bradford, PA (United States). Div. of Biological and Health Sciences

    2011-03-15

    Lignocellulosic materials are the most abundant renewable organic resources ({proportional_to}200 billion tons annually) on earth that are readily available for conversion to ethanol and other value-added products, but they have not yet been tapped for the commercial production of fuel ethanol. The lignocellulosic substrates include woody substrates such as hardwood (birch and aspen, etc.) and softwood (spruce and pine, etc.), agro residues (wheat straw, sugarcane bagasse, corn stover, etc.), dedicated energy crops (switch grass, and Miscanthus etc.), weedy materials (Eicchornia crassipes, Lantana camara etc.), and municipal solid waste (food and kitchen waste, etc.). Despite the success achieved in the laboratory, there are limitations to success with lignocellulosic substrates on a commercial scale. The future of lignocellulosics is expected to lie in improvements of plant biomass, metabolic engineering of ethanol, and cellulolytic enzyme-producing microorganisms, fullest exploitation of weed materials, and process integration of the individual steps involved in bioethanol production. Issues related to the chemical composition of various weedy raw substrates for bioethanol formation, including chemical composition-based structural hydrolysis of the substrate, need special attention. This area could be opened up further by exploring genetically modified metabolic engineering routes in weedy materials and in biocatalysts that would make the production of bioethanol more efficient. (orig.)

  1. The relationship between microbial metabolic activity and biocorrosion of carbon steel.

    Science.gov (United States)

    Dzierzewicz, Z; Cwalina, B; Chodurek, E; Wilczok, T

    1997-12-01

    The effect of metabolic activity (expressed by generation time, rate of H2S production and the activity of hydrogenase and adenosine phosphosulphate (APS)-reductase enzymes) of the 8 wild strains of Desulfovibrio desulfuricans and of their resistance to metal ions (Hg2+, Cu2+, Mn2+, Zn2+, Ni2+, Cr3+) on the rate of corrosion of carbon steel was studied. The medium containing lactate as the carbon source and sulphate as the electron acceptor was used for bacterial metabolic activity examination and in corrosive assays. Bacterial growth inhibition by metal ions was investigated in the sulphate-free medium. The rate of H2S production was approximately directly proportional to the specific activities of the investigated enzymes. These activities were inversely proportional to the generation time. The rate of microbiologically induced corrosion (MIC) of carbon steel was directly proportional to bacterial resistance to metal ions (correlation coefficient r = 0.95). The correlation between the MIC rate and the activity of enzymes tested, although weaker, was also observed (r = 0.41 for APS-reductase; r = 0.69 for hydrogenase; critical value rc = 0.30, p = 0.05, n = 40).

  2. Comparative analysis of fecal microbiota and intestinal microbial metabolic activity in captive polar bears.

    Science.gov (United States)

    Schwab, Clarissa; Gänzle, Michael

    2011-03-01

    The composition of the intestinal microbiota depends on gut physiology and diet. Ursidae possess a simple gastrointestinal system composed of a stomach, small intestine, and indistinct hindgut. This study determined the composition and stability of fecal microbiota of 3 captive polar bears by group-specific quantitative PCR and PCR-DGGE (denaturing gradient gel electrophoresis) using the 16S rRNA gene as target. Intestinal metabolic activity was determined by analysis of short-chain fatty acids in feces. For comparison, other Carnivora and mammals were included in this study. Total bacterial abundance was approximately log 8.5 DNA gene copies·(g feces)-1 in all 3 polar bears. Fecal polar bear microbiota was dominated by the facultative anaerobes Enterobacteriaceae and enterococci, and the Clostridium cluster I. The detection of the Clostridium perfringens α-toxin gene verified the presence of C. perfringens. Composition of the fecal bacterial population was stable on a genus level; according to results obtained by PCR-DGGE, dominant bacterial species fluctuated. The total short-chain fatty acid content of Carnivora and other mammals analysed was comparable; lactate was detected in feces of all carnivora but present only in trace amounts in other mammals. In comparison, the fecal microbiota and metabolic activity of captive polar bears mostly resembled the closely related grizzly and black bears.

  3. Single-cell genomics reveal metabolic strategies for microbial growth and survival in an oligotrophic aquifer

    Energy Technology Data Exchange (ETDEWEB)

    Wilkins, Michael J.; Kennedy, David W.; Castelle, Cindy; Field, Erin; Stepanauskas, Ramunas; Fredrickson, Jim K.; Konopka, Allan

    2014-02-09

    Bacteria from the genus Pedobacter are a major component of microbial assemblages at Hanford Site and have been shown to significantly change in abundance in response to the subsurface intrusion of Columbia River water. Here we employed single cell genomics techniques to shed light on the physiological niche of these microorganisms. Analysis of four Pedobacter single amplified genomes (SAGs) from Hanford Site sediments revealed a chemoheterotrophic lifestyle, with the potential to exist under both aerobic and microaerophilic conditions via expression of both aa3­-type and cbb3-type cytochrome c oxidases. These SAGs encoded a wide-range of both intra-and extra­-cellular carbohydrate-active enzymes, potentially enabling the degradation of recalcitrant substrates such as xylan and chitin, and the utilization of more labile sugars such as mannose and fucose. Coupled to these enzymes, a diversity of transporters and sugar-binding molecules were involved in the uptake of carbon from the extracellular local environment. The SAGs were enriched in TonB-dependent receptors (TBDRs), which play a key role in uptake of substrates resulting from degradation of recalcitrant carbon. CRISPR-Cas mechanisms for resisting viral infections were identified in all SAGs. These data demonstrate the potential mechanisms utilized for persistence by heterotrophic microorganisms in a carbon-limited aquifer, and hint at potential linkages between observed Pedobacter abundance shifts within the 300 Area subsurface and biogeochemical shifts associated with Columbia River water intrusion.

  4. In situ investigation of tubular microbial fuel cells deployed in an aeration tank at a municipal wastewater treatment plant.

    Science.gov (United States)

    Zhang, Fei; Ge, Zheng; Grimaud, Julien; Hurst, Jim; He, Zhen

    2013-05-01

    To examine the feasibility of integrating microbial fuel cells (MFCs) into an activated sludge process, three MFCs with different ion exchange membranes and/or cathode catalysts were installed in an aeration tank to treat primary effluent. Both contaminant treatment and electricity generation were studied during the operation for more than 400 days. The effects of membrane/catalysts on MFC performance were not observed, likely due to the low removal of chemical oxygen demand (COD) (tank, unless the key problems such as biofouling are solved. Copyright © 2013 Elsevier Ltd. All rights reserved.

  5. Effects of dairy manure management in annual and perennial cropping systems on soil microbial communities associated with in situ N2O fluxes

    Science.gov (United States)

    Dunfield, Kari; Thompson, Karen; Bent, Elizabeth; Abalos, Diego; Wagner-Riddle, Claudia

    2016-04-01

    Liquid dairy manure (LDM) application and ploughing events may affect soil microbial community functioning differently between perennial and annual cropping systems due to plant-specific characteristics stimulating changes in microbial community structure. Understanding how these microbial communities change in response to varied management, and how these changes relate to in situ N2O fluxes may allow the creation of predictive models for use in the development of best management practices (BMPs) to decrease nitrogen (N) losses through choice of crop, plough, and LDM practices. Our objectives were to contrast changes in the population sizes and community structures of genes associated with nitrifier (amoA, crenamoA) and denitrifier (nirK, nirS, nosZ) communities in differently managed annual and perennial fields demonstrating variation in N2O flux, and to determine if differences in these microbial communities were linked to the observed variation in N2O fluxes. Soil was sampled in 2012 and in 2014 in a 4-ha spring-applied LDM grass-legume (perennial) plot and two 4-ha corn (annual) treatments under fall or spring LDM application. Soil DNA was extracted and used to target N-cycling genes via qPCR (n=6) and for next-generation sequencing (Illumina Miseq) (n=3). Significantly higher field-scale N2O fluxes were observed in the annual plots compared to the perennial system; however N2O fluxes increased after plough down of the perennial plot. Nonmetric multidimensional scaling (NMS) indicated differences in N-cycling communities between annual and perennial cropping systems, and some communities became similar between annual and perennial plots after ploughing. Shifts in these communities demonstrated relationships with agricultural management, which were associated with differences in N2O flux. Indicator species analysis was used to identify operational taxonomic units (OTUs) most responsible for community shifts related to management. Nitrifying and denitrifying soil

  6. Diagnosis of rare inherited glyoxalate metabolic disorders through in-situ analysis of renal stones

    Science.gov (United States)

    Jacob, D. E.; Grohe, B.; Hoppe, B.; Beck, B. B.; Tessadri, R.

    2012-04-01

    The primary hyperoxalurias type I - III constitute rare autosomal-recessive inherited disorders of the human glyoxylate metabolism. By mechanisms that are ill understood progressive nephrocalcinosis and recurrent urolithiasis (kidney stone formation) often starting in early childhood, along with their secondary complications results in loss of nephron mass which progresses to end-stage renal failure over time. In the most frequent form, end-stage renal failure (ESRF) is the rule and combined liver/kidney transplantation respectively pre-emptive liver transplantation are the only causative treatment today. Hence, this contributes significantly to healthcare costs and early diagnosis is extremely important for a positive outcome for the patient. We are developing a stone-based diagnostic method by in-detail multi-methods investigation of the crystalline moiety in concert with urine and stone proteomics. Stone analysis will allow faster analysis at low-impact for the patients in the early stages of the disease. First results from combined spectroscopic (Raman, FTIR)and geochemical micro-analyses (Electron Microprobe and Laser Ablation ICP-MS) are presented here that show significant differences between stones from hyperoxaluria patients and those formed by patients without this disorder (idiopathic stones). Major differences exist in chemistry as well as in morphology and phase composition of the stones. Ca/P ratios and Mg contents differentiate between oxalate-stones from hyperoxaluria patients and idiopathic stones. Results show that also within the different subtypes of primary hyperoxaluria significant differences can be found in stone composition. These imply differences in stone formation which could be exploited for new therapeutic pathways. Furthermore, the results provide important feedback for suspected but yet unconfirmed cases of primary hyperoxaluria when used in concert with the genetic methods routinely applied.

  7. Volatile Gas Production by Methyl Halide Transferase: An In Situ Reporter Of Microbial Gene Expression In Soil.

    Science.gov (United States)

    Cheng, Hsiao-Ying; Masiello, Caroline A; Bennett, George N; Silberg, Jonathan J

    2016-08-16

    Traditional visual reporters of gene expression have only very limited use in soils because their outputs are challenging to detect through the soil matrix. This severely restricts our ability to study time-dependent microbial gene expression in one of the Earth's largest, most complex habitats. Here we describe an approach to report on dynamic gene expression within a microbial population in a soil under natural water levels (at and below water holding capacity) via production of methyl halides using a methyl halide transferase. As a proof-of-concept application, we couple the expression of this gas reporter to the conjugative transfer of a bacterial plasmid in a soil matrix and show that gas released from the matrix displays a strong correlation with the number of transconjugant bacteria that formed. Gas reporting of gene expression will make possible dynamic studies of natural and engineered microbes within many hard-to-image environmental matrices (soils, sediments, sludge, and biomass) at sample scales exceeding those used for traditional visual reporting.

  8. D/H Ratios in Lipids as a Tool to Elucidate Microbial Metabolism

    Science.gov (United States)

    Wijker, Reto S.; Sessions, Alex L.

    2016-04-01

    Large D/H fractionations have been observed in the lipids and growth water of most organisms studied today. These fractionations have generally been assumed to be constant across most biota because they originate solely from isotope effects imposed by the highly conserved lipid biosynthetic pathway. Recent data is illustrating this conclusion as incomplete. Lipids from field and laboratory samples exhibit huge variations in D/H fractionation. In environmental samples, lipids vary in δD by up to 300 ‰ and in laboratory cultures the documented variation is up to 500 ‰ within the same organism. Remarkably, the isotope fractionation appears to be correlated with the type of metabolism employed by the host organism. However, the underlying biochemical mechanisms leading to these isotopic variations are not yet fully understood. Because the largest proportion of H-bound C in fatty acids is derived directly from NADPH during biosynthesis, the original hypothesis was that large differences in the isotopic composition of NADPH, generated by different central metabolic pathways, were the primary source of D/H variation in lipids. However, recent observations indicate that this cannot be the whole story and lead us to the conclusion that additional processes must affect the isotope composition of NADPH. These processes may include the isotopic exchange of NADPH with water as well as fractionation of NADPH by transhydrogenases, interconverting NADH to NADPH by exhibiting large isotope effects. In this project, our objective is to ascertain whether D/H fractionation and these biochemical processes are correlated. We investigate correlations between cellular NADPH/NADP+ as well as NADH/NAD+ pool sizes and the D/H fractionation in a set of different microorganisms and will present the trends here. Our results will contribute to a more comprehensive understanding of the basic biological regulations over D/H fractionation and potentially enables their use as tracers and

  9. Autochthonous and allochthonous contributions of organic carbon to microbial food webs in Svalbard fjords

    OpenAIRE

    Holding, J.M.; Duarte, C.M.; Delgado-Huertas, A.; Soetaert, K.; Vonk, J.E.; Agusti, S.; Wassmann, P.; Middelburg, J.

    2017-01-01

    Rising temperatures in the Arctic Ocean are causing sea ice and glaciers to melt at record breaking rates, which has consequences for carbon cycling in the Arctic Ocean that are yet to be fully understood. Microbial carbon cycling is driven by internal processing of in situ produced organic carbon (OC), however recent research suggests that melt water from sea ice and glaciers could introduce an allochthonous source of OC to the microbial food web with ramifications for the metabolic balance ...

  10. Application of Tools to Measure PCB Microbial Dechlorination and Flux into Water During In-situ Treatment of Sediments

    Science.gov (United States)

    2011-08-01

    removal of sulfur. The copper treated extract was passed through a 3% deactivated silica gel column using hexane ( pesticide grade) as the eluting...the addition of microorganisms and/or chemicals to the sediments to initiate or enhance bioremediation . In situ solidification/stabilization...and a floc contact area. The detail settings are shown in Table 1……………………………………...……...87 Figure 6.5: Using Lick et al. (1996) experiment data to

  11. Effects of Secondary Plant Metabolites on Microbial Populations: Changes in Community Structure and Metabolic Activity in Contaminated Environments

    Directory of Open Access Journals (Sweden)

    Lucie Musilova

    2016-07-01

    Full Text Available Secondary plant metabolites (SPMEs play an important role in plant survival in the environment and serve to establish ecological relationships between plants and other organisms. Communication between plants and microorganisms via SPMEs contained in root exudates or derived from litter decomposition is an example of this phenomenon. In this review, the general aspects of rhizodeposition together with the significance of terpenes and phenolic compounds are discussed in detail. We focus specifically on the effect of SPMEs on microbial community structure and metabolic activity in environments contaminated by polychlorinated biphenyls (PCBs and polyaromatic hydrocarbons (PAHs. Furthermore, a section is devoted to a complex effect of plants and/or their metabolites contained in litter on bioremediation of contaminated sites. New insights are introduced from a study evaluating the effects of SPMEs derived during decomposition of grapefruit peel, lemon peel, and pears on bacterial communities and their ability to degrade PCBs in a long-term contaminated soil. The presented review supports the “secondary compound hypothesis” and demonstrates the potential of SPMEs for increasing the effectiveness of bioremediation processes.

  12. Modeling Late-State Serpentinization on Enceladus and Implications for Methane-Utilizing Microbial Metabolisms

    Science.gov (United States)

    Hart, R.; Cardace, D.

    2017-12-01

    Modeling investigations of Enceladus and other icy-satellites have included physicochemical properties (Sohl et al., 2010; Glein et al., 2015; Neveu et al., 2015), geophysical prospects of serpentinization (Malamud and Prialnik, 2016; Vance et al., 2016), and aqueous geochemistry across different antifreeze fluid-rock scenarios (Neveu et al., 2017). To more effectively evaluate the habitability of Enceladus, in the context of recent observations (Waite et al., 2017), we model the potential bioenergetic pathways that would be thermodynamically favorable at the interface of hydrothermal water-rock reactions resulting from late stage serpentinization (>90% serpentinized), hypothesized on Enceladus. Building on previous geochemical model outputs of Enceladus (Neveu et al., 2017), and bioenergetic modeling (as in Amend and Shock, 2001; Cardace et al., 2015), we present a model of late stage serpentinization possible at the water-rock interface of Enceladus, and report changing activities of chemical species related to methane utilization by microbes over the course of serpentinization using the Geochemist's Workbench REACT code [modified Extended Debye-Hückel (Helgeson, 1969) using the thermodynamic database of SUPCRT92 (Johnson et al., 1992)]. Using a model protolith speculated to exist at Enceladus's water-rock boundary, constrained by extraterrestrial analog analytical data for subsurface serpentinites of the Coast Range Ophiolite (Lower Lake, CA, USA) mélange rocks, we deduce evolving habitability conditions as the model protolith reacts with feasible, though hypothetical, planetary ocean chemistries (from Glien et al., 2015, and Neveu et al., 2017). Major components of modeled oceans, Na-Cl, Mg-Cl, and Ca-Cl, show shifts in the feasibility of CO2-CH4-H2 driven microbial habitability, occurring early in the reaction progress, with methanogenesis being bioenergetically favored. Methanotrophy was favored late in the reaction progress of some Na-Cl systems and in the

  13. [Effects of heavy metals pollution on soil microbial communities metabolism and soil enzyme activities in coal mining area of Tongchuan, Shaanxi Province of Northwest China].

    Science.gov (United States)

    Guo, Xing-Liang; Gu, Jie; Chen, Zhi-Xue; Gao, Hua; Qin, Qing-Jun; Sun, Wei; Zhang, Wei-Juan

    2012-03-01

    This paper studied the metabolism of soil microbes, functions of soil microbial communities, and activities of soil enzymes in a coal mining area of Tongchuan. In the coal mining area, the concentrations of soil Cu, Zn, Cd, and Pb were significantly higher than those in the non-mining area, of which, Cd contributed most to the heavy metals pollution. By adopting Biolog method combining with principal component analysis (PCA) and cluster analysis, it was found that the metabolic characteristics of different soil microbial communities varied significantly with increasing soil heavy metals pollution, and the variation was mainly manifested in the metabolic patterns of carbon sources such as saccharides and amino acids. In slightly and moderately polluted soils, the utilization of carbon sources by soil microbial communities was activated; while in heavily polluted soils, the carbon sources utilization was inhibited. The activities of soil urease, protease, alkaline phosphatase, and catalase all tended to decline with intensifying soil heavy metals pollution. The soil urease, protease, alkaline phosphatase, and catalase activities in the coal mining area were 50.5%-65.1%, 19.1%-57.1%, 87.2%-97.5%, and 77.3%-86.0% higher than those in the non-mining area, respectively. The activities of soil sucrase and cellulase were activated in slightly and moderately polluted soils, but inhibited in heavily polluted soils.

  14. In situ detection of anaerobic alkane metabolites in subsurface environments

    Directory of Open Access Journals (Sweden)

    Lisa eGieg

    2013-06-01

    Full Text Available Alkanes comprise a substantial fraction of crude oil and refined fuels. As such, they are prevalent within deep subsurface fossil fuel deposits and in shallow subsurface environments such as aquifers that are contaminated with hydrocarbons. These environments are typically anaerobic, and host diverse microbial communities that can potentially use alkanes as substrates. Anaerobic alkane biodegradation has been reported to occur under nitrate-reducing, sulfate-reducing, and methanogenic conditions. Elucidating the pathways of anaerobic alkane metabolism has been of interest in order to understand how microbes can be used to remediate contaminated sites. Alkane activation primarily occurs by addition to fumarate, yielding alkylsuccinates, unique anaerobic metabolites that can be used to indicate in situ anaerobic alkane metabolism. These metabolites have been detected in hydrocarbon-contaminated shallow aquifers, offering strong evidence for intrinsic anaerobic bioremediation. Recently, studies have also revealed that alkylsuccinates are present in oil and coal seam production waters, indicating that anaerobic microbial communities can utilize alkanes in these deeper subsurface environments. In many crude oil reservoirs, the in situ anaerobic metabolism of hydrocarbons such as alkanes may be contibuting to modern-day detrimental effects such as oilfield souring, or may lead to more benefical technologies such as enhanced energy recovery from mature oilfields. In this review, we briefly describe the key metabolic pathways for anaerobic alkane (including n-alkanes, isoalkanes, and cyclic alkanes metabolism and highlight several field reports wherein alkylsuccinates have provided evidence for anaerobic in situ alkane metabolism in shallow and deep subsurface environments.

  15. The feasibility of automated online flow cytometry for in-situ monitoring of microbial dynamics in aquatic ecosystems

    Science.gov (United States)

    Besmer, Michael D.; Weissbrodt, David G.; Kratochvil, Bradley E.; Sigrist, Jürg A.; Weyland, Mathias S.; Hammes, Frederik

    2014-01-01

    Fluorescent staining coupled with flow cytometry (FCM) is often used for the monitoring, quantification and characterization of bacteria in engineered and environmental aquatic ecosystems including seawater, freshwater, drinking water, wastewater, and industrial bioreactors. However, infrequent grab sampling hampers accurate characterization and subsequent understanding of microbial dynamics in all of these ecosystems. A logic technological progression is high throughput and full automation of the sampling, staining, measurement, and data analysis steps. Here we assess the feasibility and applicability of automated FCM by means of actual data sets produced with prototype instrumentation. As proof-of-concept we demonstrate examples of microbial dynamics in (i) flowing tap water from a municipal drinking water supply network and (ii) river water from a small creek subject to two rainfall events. In both cases, automated measurements were done at 15-min intervals during 12–14 consecutive days, yielding more than 1000 individual data points for each ecosystem. The extensive data sets derived from the automated measurements allowed for the establishment of baseline data for each ecosystem, as well as for the recognition of daily variations and specific events that would most likely be missed (or miss-characterized) by infrequent sampling. In addition, the online FCM data from the river water was combined and correlated with online measurements of abiotic parameters, showing considerable potential for a better understanding of cause-and-effect relationships in aquatic ecosystems. Although several challenges remain, the successful operation of an automated online FCM system and the basic interpretation of the resulting data sets represent a breakthrough toward the eventual establishment of fully automated online microbiological monitoring technologies. PMID:24917858

  16. Bioethanol a Microbial Biofuel Metabolite; New Insights of Yeasts Metabolic Engineering

    Directory of Open Access Journals (Sweden)

    Khaled A. Selim

    2018-03-01

    Full Text Available Scarcity of the non-renewable energy sources, global warming, environmental pollution, and raising the cost of petroleum are the motive for the development of renewable, eco-friendly fuels production with low costs. Bioethanol production is one of the promising materials that can subrogate the petroleum oil, and it is considered recently as a clean liquid fuel or a neutral carbon. Diverse microorganisms such as yeasts and bacteria are able to produce bioethanol on a large scale, which can satisfy our daily needs with cheap and applicable methods. Saccharomyces cerevisiae and Pichia stipitis are two of the pioneer yeasts in ethanol production due to their abilities to produce a high amount of ethanol. The recent focus is directed towards lignocellulosic biomass that contains 30–50% cellulose and 20–40% hemicellulose, and can be transformed into glucose and fundamentally xylose after enzymatic hydrolysis. For this purpose, a number of various approaches have been used to engineer different pathways for improving the bioethanol production with simultaneous fermentation of pentose and hexoses sugars in the yeasts. These approaches include metabolic and flux analysis, modeling and expression analysis, followed by targeted deletions or the overexpression of key genes. In this review, we highlight and discuss the current status of yeasts genetic engineering for enhancing bioethanol production, and the conditions that influence bioethanol production.

  17. Distance-dependent varieties of microbial community structure and metabolic functions in the rhizosphere of Sedum alfredii Hance during phytoextraction of a cadmium-contaminated soil.

    Science.gov (United States)

    Yang, Wenhao; Zhang, Taoxiang; Lin, Sen; Ni, Wuzhong

    2017-06-01

    The recovery of microbial community and activities is crucial to the remediation of contaminated soils. Distance-dependent variations of microbial community composition and metabolic characteristics in the rhizospheric soil of hyperaccumulator during phytoextraction are poorly understood. A 12-month phytoextraction experiment with Sedum alfredii in a Cd-contaminated soil was conducted. A pre-stratified rhizobox was used for separating sub-layer rhizospheric (0-2, 2-4, 4-6, 6-8, 8-10 mm from the root mat)/bulk soils. Soil microbial structure and function were analyzed by phospholipid fatty acid (PLFA) and MicroResp™ methods. The concentrations of total and specified PLFA biomarkers and the utilization rates for the 14 substrates (organic carbon) in the 0-2-mm sub-layer rhizospheric soil were significantly increased, as well as decreased with the increase in the distance from the root mat. Microbial structure measured by the ratios of different groups of PLFAs such as fungal/bacterial, monounsaturated/saturated, ratios of Gram-positive to Gram-negative (GP/GN) bacterial, and cyclopropyl/monoenoic precursors and 19:0 cyclo/18:1ω7c were significantly changed in the 0-2-mm soil. The PLFA contents and substrate utilization rates were negatively correlated with pH and total, acid-soluble, and reducible fractions of Cd, while positively correlated with labile carbon. The dynamics of microbial community were likely due to root exudates and Cd uptake by S. alfredii. This study revealed the stimulations and gradient changes of rhizosphere microbial community through phytoextraction, as reduced Cd concentration, pH, and increased labile carbons are due to the microbial community responses.

  18. Microbial diversity in hydrothermal surface to subsurface environments of Suiyo Seamount, Izu-Bonin Arc, using a catheter-type in situ growth chamber.

    Science.gov (United States)

    Higashi, Yowsuke; Sunamura, Michinari; Kitamura, Keiko; Nakamura, Ko-ichi; Kurusu, Yasurou; Ishibashi, Jun-ichiro; Urabe, Tetsuro; Maruyama, Akihiko

    2004-03-01

    After excavation using a portable submarine driller near deep-sea hydrothermal vents in the Suiyo Seamount, Izu-Bonin Arc, microbial diversity was examined in samples collected from inside the boreholes using an in situ growth chamber called a vent catheter. This instrument, which we devised for this study, consists of a heat-tolerant pipe tipped with a titanium mesh entrapment capsule that is packed with sterilized inorganic porous grains, which serve as an adhesion substrate. After this instrument was deployed inside each of the boreholes, as well as a natural vent, for 3-10 days in the vicinity of hot vent fluids (maxima: 156-305 degrees C), DNA was extracted from the adhesion grains, 16S rDNA was amplified, and randomly selected clones were sequenced. In phylogenetic analysis of more than 120 clones, several novel phylotypes were detected within the epsilon-Proteobacteria, photosynthetic bacteria (PSB)-related alpha-Proteobacteria, and Euryarchaeota clusters. Members of epsilon-Proteobacteria were frequently encountered. Half of these were classified between two known groups, Corre's B and D. The other half of the clones were assigned to new groups, SSSV-BE1 and SSSV-BE2 (Suiyo Seamount sub-vent origin, Bacteria domain, epsilon-Proteobacteria, groups 1 and 2). From this hydrothermal vent field, we detected a novel lineage within the PSB cluster, SSNV-BA1 (Suiyo Seamount natural vent origin, Bacteria domain, alpha-Proteobacteria, group 1), which is closely related to Rhodopila globiformis isolated from a hot spring. A number of archaeal clones were also detected from the borehole samples. These clones formed a novel monophyletic clade, SSSV-AE1 (Suiyo Seamount sub-vent origin, Archaea domain, Euryarchaeota, group 1), approximately between methanogenic hyperthermophilic members of Methanococcales and environmental clone members of DHVE Group II. Thus, this hydrothermal vent environment appears to be a noteworthy microbial and genetic resource. It is also

  19. Metabolic versatility of Gram-positive microbial isolates from contaminated river sediments

    International Nuclear Information System (INIS)

    Narancic, Tanja; Djokic, Lidija; Kenny, Shane T.; O’Connor, Kevin E.; Radulovic, Vanja; Nikodinovic-Runic, Jasmina; Vasiljevic, Branka

    2012-01-01

    Highlights: ► Thirty-four isolated Gram-positive bacteria could degrade wide range of aromatic pollutants. ► Nine isolates could grow in the presence of extremely high levels of heavy metals. ► Twelve isolates accumulated polyphosphate, 3 polyhydroxybutyrate, 4 exopolysaccharides. ► The incidence of multiple antibiotic resistance markers among isolates was low. - Abstract: Gram-positive bacteria from river sediments affected by the proximity of a petrochemical industrial site were isolated and characterized with respect to their ability to degrade a wide range of aromatic compounds. In this study we identified metabolically diverse Gram-positive bacteria capable of growth on wide range aromatic compounds in the presence of heavy metals and with the ability to accumulate biopolymers. Thirty-four isolates that were able to use 9 or more common aromatic pollutants, such as benzene, biphenyl, naphthalene etc. as a sole source of carbon and energy included members of Bacillus, Arthrobacter, Rhodococcus, Gordonia, Streptomyces, and Staphylococcus genus. Rhodococcus sp. TN105, Gordonia sp. TN103 and Arthrobacter sp. TN221 were identified as novel strains. Nine isolates were able to grow in the presence of one or more metals (mercury, cadmium, nickel) at high concentration (100 mM). Seven isolates could degrade 15 different aromatic compounds and could grow in the presence of one or more heavy metals. Two of these isolates were resistant to multiple antibiotics including erythromycin and nalidixic acid. One third of isolates could accumulate at least one biopolymer. Twelve isolates (mainly Bacillus sp. and Arthrobacter sp.) accumulated polyphosphate, 3 Bacillus sp. accumulated polyhydroxybutyrate, while 4 isolates could accumulate exopolysaccharides.

  20. Medium factors on anaerobic production of rhamnolipids by Pseudomonas aeruginosa SG and a simplifying medium for in situ microbial enhanced oil recovery applications.

    Science.gov (United States)

    Zhao, Feng; Zhou, Jidong; Han, Siqin; Ma, Fang; Zhang, Ying; Zhang, Jie

    2016-04-01

    Aerobic production of rhamnolipid by Pseudomonas aeruginosa was extensively studied. But effect of medium composition on anaerobic production of rhamnolipid by P. aeruginosa was unknown. A simplifying medium facilitating anaerobic production of rhamnolipid is urgently needed for in situ microbial enhanced oil recovery (MEOR). Medium factors affecting anaerobic production of rhamnolipid were investigated using P. aeruginosa SG (Genbank accession number KJ995745). Medium composition for anaerobic production of rhamnolipid by P. aeruginosa is different from that for aerobic production of rhamnolipid. Both hydrophobic substrate and organic nitrogen inhibited rhamnolipid production under anaerobic conditions. Glycerol and nitrate were the best carbon and nitrogen source. The commonly used N limitation under aerobic conditions was not conducive to rhamnolipid production under anaerobic conditions because the initial cell growth demanded enough nitrate for anaerobic respiration. But rhamnolipid was also fast accumulated under nitrogen starvation conditions. Sufficient phosphate was needed for anaerobic production of rhamnolipid. SO4(2-) and Mg(2+) are required for anaerobic production of rhamnolipid. Results will contribute to isolation bacteria strains which can anaerobically produce rhamnolipid and medium optimization for anaerobic production of rhamnolipid. Based on medium optimization by response surface methodology and ions composition of reservoir formation water, a simplifying medium containing 70.3 g/l glycerol, 5.25 g/l NaNO3, 5.49 g/l KH2PO4, 6.9 g/l K2HPO4·3H2O and 0.40 g/l MgSO4 was designed. Using the simplifying medium, 630 mg/l of rhamnolipid was produced by SG, and the anaerobic culture emulsified crude oil to EI24 = 82.5 %. The simplifying medium was promising for in situ MEOR applications.

  1. Label-free in vivo in situ diagnostic imaging by cellular metabolism quantification with a flexible multiphoton endomicroscope (Conference Presentation)

    Science.gov (United States)

    Leclerc, Pierre; Hage, Charles-Henri; Fabert, Marc; Brevier, Julien; O'Connor, Rodney P.; Bardet-Coste, Sylvia M.; Habert, Rémi; Braud, Flavie; Kudlinski, Alexandre; Louradour, Frederic

    2017-02-01

    Multiphoton microscopy is a cutting edge imaging modality leading to increasing advances in biology and also in the clinical field. To use it at its full potential and at the very heart of clinical practice, there have been several developments of fiber-based multiphoton microendoscopes. The application for those probes is now limited by few major restrictions, such as the difficulty to collect autofluorescence signals from tissues and cells theses being inherently weak (e.g. the ones from intracellular NADH or FAD metabolites). This limitation reduces the usefulness of microendoscopy in general, effectively restraining it to morphological imaging modality requiring staining of the tissues. Our aim is to go beyond this limitation, showing for the first time label-free cellular metabolism monitoring, in vivo in situ in real time. The experimental setup is an upgrade of a recently published one (Ducourthial et.al, Scientific Reports, 2016) where femtosecond pulse fiber delivery is further optimized thank's to a new transmissive-GRISM-based pulse stretcher permitting high energy throughput and wide bandwidth. This device allows fast sequential operation with two different excitation wavelengths for efficient two-photon excited NADH and FAD autofluorescence endoscopic detection (i.e. 860 nm for FAD and 760 nm for NADH), enabling cellular optical redox ratio quantification at 8 frames/s. The obtained results on cell models in vitro and also on animal models in vivo (e.g. neurons of a living mouse) prove that we accurately assess the level of NADH and FAD at subcellular resolution through a 3-meters-long fiber with our miniaturized probe (O.D. =2.2 mm).

  2. Application of in situ biosparging to remediate a petroleum-hydrocarbon spill site: field and microbial evaluation.

    Science.gov (United States)

    Kao, C M; Chen, C Y; Chen, S C; Chien, H Y; Chen, Y L

    2008-02-01

    In this study, a full-scale biosparging investigation was conducted at a petroleum-hydrocarbon spill site. Field results reveal that natural attenuation was the main cause of the decrease in major contaminants [benzene, toluene, ethylbenzene, and xylenes (BTEX)] concentrations in groundwater before the operation of biosparging system. Evidence of the occurrence of natural attenuation within the BTEX plume includes: (1) decrease of DO, nitrate, sulfate, and redox potential, (2) production of dissolved ferrous iron, sulfide, methane, and CO(2), (3) decreased BTEX concentrations along the transport path, (4) increased microbial populations, and (5) limited spreading of the BTEX plume. Field results also reveal that the operation of biosparging caused the shifting of anaerobic conditions inside the plume to aerobic conditions. This variation can be confirmed by the following field observations inside the plume due to the biosparging process: (1) increase in DO, redox potential, nitrate, and sulfate, (2) decrease dissolved ferrous iron, sulfide, and methane, (3) increased total cultivable heterotrophs, and (4) decreased total cultivable anaerobes as well as methanogens. Results of polymerase chain reaction, denaturing gradient gel electrophoresis, and nucleotide sequence analysis reveal that three BTEX biodegraders (Candidauts magnetobacterium, Flavobacteriales bacterium, and Bacteroidetes bacterium) might exist at this site. Results show that more than 70% of BTEX has been removed through the biosparging system within a 10-month remedial period at an averaged groundwater temperature of 18 degrees C. This indicates that biosparging is a promising technology to remediate BTEX contaminated groundwater.

  3. Pyrosequencing reveals high-temperature cellulolytic microbial consortia in Great Boiling Spring after in situ lignocellulose enrichment.

    Directory of Open Access Journals (Sweden)

    Joseph P Peacock

    Full Text Available To characterize high-temperature cellulolytic microbial communities, two lignocellulosic substrates, ammonia fiber-explosion-treated corn stover and aspen shavings, were incubated at average temperatures of 77 and 85°C in the sediment and water column of Great Boiling Spring, Nevada. Comparison of 109,941 quality-filtered 16S rRNA gene pyrosequences (pyrotags from eight enrichments to 37,057 quality-filtered pyrotags from corresponding natural samples revealed distinct enriched communities dominated by phylotypes related to cellulolytic and hemicellulolytic Thermotoga and Dictyoglomus, cellulolytic and sugar-fermenting Desulfurococcales, and sugar-fermenting and hydrogenotrophic Archaeoglobales. Minor enriched populations included close relatives of hydrogenotrophic Thermodesulfobacteria, the candidate bacterial phylum OP9, and candidate archaeal groups C2 and DHVE3. Enrichment temperature was the major factor influencing community composition, with a negative correlation between temperature and richness, followed by lignocellulosic substrate composition. This study establishes the importance of these groups in the natural degradation of lignocellulose at high temperatures and suggests that a substantial portion of the diversity of thermophiles contributing to consortial cellulolysis may be contained within lineages that have representatives in pure culture.

  4. Metabolism

    Science.gov (United States)

    ... Are More Common in People With Type 1 Diabetes Metabolic Syndrome Your Child's Weight Healthy Eating Endocrine System Blood Test: Basic Metabolic Panel (BMP) Activity: Endocrine System Growth Disorders Diabetes Center Thyroid Disorders Your Endocrine System Movie: Endocrine ...

  5. Carbon monoxide as a metabolic energy source for extremely halophilic microbes: implications for microbial activity in Mars regolith.

    Science.gov (United States)

    King, Gary M

    2015-04-07

    Carbon monoxide occurs at relatively high concentrations (≥800 parts per million) in Mars' atmosphere, where it represents a potentially significant energy source that could fuel metabolism by a localized putative surface or near-surface microbiota. However, the plausibility of CO oxidation under conditions relevant for Mars in its past or at present has not been evaluated. Results from diverse terrestrial brines and saline soils provide the first documentation, to our knowledge, of active CO uptake at water potentials (-41 MPa to -117 MPa) that might occur in putative brines at recurrent slope lineae (RSL) on Mars. Results from two extremely halophilic isolates complement the field observations. Halorubrum str. BV1, isolated from the Bonneville Salt Flats, Utah (to our knowledge, the first documented extremely halophilic CO-oxidizing member of the Euryarchaeota), consumed CO in a salt-saturated medium with a water potential of -39.6 MPa; activity was reduced by only 28% relative to activity at its optimum water potential of -11 MPa. A proteobacterial isolate from hypersaline Mono Lake, California, Alkalilimnicola ehrlichii MLHE-1, also oxidized CO at low water potentials (-19 MPa), at temperatures within ranges reported for RSL, and under oxic, suboxic (0.2% oxygen), and anoxic conditions (oxygen-free with nitrate). MLHE-1 was unaffected by magnesium perchlorate or low atmospheric pressure (10 mbar). These results collectively establish the potential for microbial CO oxidation under conditions that might obtain at local scales (e.g., RSL) on contemporary Mars and at larger spatial scales earlier in Mars' history.

  6. Biotechnology in petroleum recovery. The microbial EOR

    Energy Technology Data Exchange (ETDEWEB)

    Sen, Ramkrishna [Department of Biotechnology, Indian Institute of Technology (IIT), Kharagpur, West Bengal 721302 (India)

    2008-12-15

    Biotechnology has played a significant role in enhancing crude oil recovery from the depleted oil reservoirs to solve stagnant petroleum production, after a three-stage recovery process employing mechanical, physical and chemical methods. Biotechnologically enhanced oil recovery processes, known as microbial enhanced oil recovery (MEOR), involve stimulating indigenous reservoir microbes or injecting specially selected consortia of natural bacteria into the reservoir to produce specific metabolic events that lead to improved oil recovery. This also involves flooding with oil recovery agents produced ex situ by industrial or pilot scale fermentation. This paper essentially reviews the operating mechanisms and the progress made in enhanced oil recovery through the use of microbes and their metabolic products. Improvement in oil recovery by injecting solvents and gases or by energizing the reservoir microflora to produce them in situ for carbonate rock dissolution and reservoir re-pressurization has been enunciated. The role of biosurfactants in oil mobilization through emulsification and that of biopolymers for selective plugging of oil-depleted zones and for biofilm formation have been delineated. The spoil sport played by sulfate-reducing bacteria (SRB) in MEOR has also been briefly reviewed. The importance of mathematical models used in predicting the applicability of an MEOR strategy and the microbial growth and transport has been qualitatively discussed. The results of some laboratory studies and worldwide field trials applying ex situ and in situ MEOR technologies were compiled and interpreted. However, the potential of the MEOR technologies has not been fully realized due to poor yield of the useful microbial metabolic products, growth inhibition by accumulated toxic metabolites and longer time of incubation. A complete evaluation and assessment of MEOR from an engineering standpoint based on economics, applicability and performance is required to further

  7. Tracing biofouling to the structure of the microbial community and its metabolic products: a study of the three-stage MBR process.

    Science.gov (United States)

    Gao, Dawen; Fu, Yuan; Ren, Nanqi

    2013-11-01

    The biofouling characteristics of a sequential anoxic/aerobic-membrane bioreactor (A/O MBR) were analyzed during the three-stage process (fast-slow-fast transmembrane pressure (TMP) increasing). The results indicated: during the stage 1 (before day 1), the microbial communities in the activated sludge (AS), cake sludge (CS) and biofilm (BF) were similar to each other, and the adsorption of microbes and the metabolic products was the main factor that led to TMP increase; during the stage 2 (between day 1 and day 7), the cake layer begun to form and the TMP continued to rise gradually at a reduced rate compared to stage 1, at this point a characteristic microbial community colonized the CS with microorganisms such as Saprospiraceae and Comamonadaceae thriving on the membrane surface (BF) probably due to greater nutrient availability, and the predominance of these species in the microbial population led to the accumulation of biofouling metabolic products in the CS, which resulted in membrane fouling and the associated rise in TMP; during the final stage (after day 7), the biofilm had matured, and the activity of anaerobes stimulated cake compaction. The statistical analysis showed a correlation between the TMP changing rate and the carbonhydrates of soluble microbial products (SMPc) content in the CS. When the SMPc concentration rose slowly there was a low level of biofouling. However, when the SMPc accumulating rate was greater, it resulted in the more severe biofouling associated with the TMP jump. Furthermore, the correlation coefficient for the TMP increase and protein concentrations of extracellular polymeric substances (EPSp) in the CS was highly significant. The cluster analysis suggested that the AS microbial community remained stable during the three TMP change stages, while the CS and BF community were changed accompanied with the TMP change. The interaction between the microbial communities and the metabolic products lead to the significant correlation

  8. Microbial biosensors

    International Nuclear Information System (INIS)

    Le Yu; Chen, Wilfred; Mulchandani, Ashok

    2006-01-01

    A microbial biosensor is an analytical device that couples microorganisms with a transducer to enable rapid, accurate and sensitive detection of target analytes in fields as diverse as medicine, environmental monitoring, defense, food processing and safety. The earlier microbial biosensors used the respiratory and metabolic functions of the microorganisms to detect a substance that is either a substrate or an inhibitor of these processes. Recently, genetically engineered microorganisms based on fusing of the lux, gfp or lacZ gene reporters to an inducible gene promoter have been widely applied to assay toxicity and bioavailability. This paper reviews the recent trends in the development and application of microbial biosensors. Current advances and prospective future direction in developing microbial biosensor have also been discussed

  9. Investigating the impact of microbial interactions with geologic media on geophysical properties

    Science.gov (United States)

    Davis, Caroline Ann

    The goals of this study were to investigate the effect of: (1) microbial metabolic byproducts, microbial growth, and biofilm formation on the low frequency electrical properties of porous media, (2) biofilm formation on acoustic wave properties, and (3) the natural electrical (self-potential) signatures associated with an in-situ biological permeable reactive barrier (PRB). The results suggest: (1) increases in electrolytic conductivity are consistent with increased concentrations of organic acids and biosurfactants; (2) mineral weathering promoted by organic acids causes increases in electrolytic conductivity, concomitant with increases in major cation concentrations; (3) interfacial conductivity generally parallels microbial cell concentrations and biofilm formation; (4) variations in microbial growth and biofilms causes spatiotemporal heterogeneity in the elastic properties of porous media; (5) SP signatures associated with the injection of groundwater into an in-situ biological PRB are dominated by diffusion potentials induced by the injections. The results suggest that electrolytic conductivity may be useful as an indicator of metabolism, while interfacial conductivity may be used as proxy indicator for microbial growth and biofilm formation in porous media. In addition, acoustic measurements may provide diagnostic spatiotemporal data for the validation of bioclogging models/simulations. Collectively, this study provides further evidence that geophysical measurements are sensitive to microbial-induced changes to geologic media, and may be useful for the detection and monitoring of subsurface microbial growth, activity, and distribution such as in microbial enhanced oil recovery, assessing biofilm barriers used for contaminant remediation, or as sealants for reservoirs in CO2 sequestration studies.

  10. A 3D-printed microbial cell culture platform with in situ PEGDA hydrogel barriers for differential substrate delivery.

    Science.gov (United States)

    Kadilak, Andrea L; Rehaag, Jessica C; Harrington, Cameron A; Shor, Leslie M

    2017-09-01

    Additive manufacturing, or 3D-printing techniques have recently begun to enable simpler, faster, and cheaper production of millifluidic devices at resolutions approaching 100-200  μ m. At this resolution, cell culture devices can be constructed that more accurately replicate natural environments compared with conventional culturing techniques. A number of microfluidics researchers have begun incorporating additive manufacturing into their work, using 3D-printed devices in a wide array of chemical, fluidic, and even some biological applications. Here, we describe a 3D-printed cell culture platform and demonstrate its use in culturing Pseudomonas putida KT2440 bacteria for 44 h under a differential substrate gradient. Polyethylene glycol diacrylate (PEGDA) hydrogel barriers are patterned in situ within a 3D-printed channel. Transport of the toluidine blue tracer dye through the hydrogel barriers is characterized. Nutrients and oxygen were delivered to cells in the culture region by diffusion through the PEGDA hydrogel barriers from adjacent media or saline perfusion channels. Expression of green fluorescent protein by P. putida KT2440 enabled real time visualization of cell density within the 3D-printed channel, and demonstrated cells were actively expressing protein over the course of the experiment. Cells were observed clustering near hydrogel barrier boundaries where fresh substrate and oxygen were being delivered via diffusive transport, but cells were unable to penetrate the barrier. The device described here provides a versatile and easy to implement platform for cell culture in readily controlled gradient microenvironments. By adjusting device geometry and hydrogel properties, this platform could be further customized for a wide variety of biological applications.

  11. Characterization of microbial metabolism of Syrah grape products in an in vitro colon model using targeted and non-targeted analytical approaches.

    Science.gov (United States)

    Aura, Anna-Marja; Mattila, Ismo; Hyötyläinen, Tuulia; Gopalacharyulu, Peddinti; Cheynier, Veronique; Souquet, Jean-Marc; Bes, Magali; Le Bourvellec, Carine; Guyot, Sylvain; Orešič, Matej

    2013-03-01

    Syrah red grapes are used in the production of tannin-rich red wines. Tannins are high molecular weight molecules, proanthocyanidins (PAs), and poorly absorbed in the upper intestine. In this study, gut microbial metabolism of Syrah grape phenolic compounds was investigated. Syrah grape pericarp was subjected to an enzymatic in vitro digestion model, and red wine and grape skin PA fraction were prepared. Microbial conversion was screened using an in vitro colon model with faecal microbiota, by measurement of short-chain fatty acids by gas chromatography (GC) and microbial phenolic metabolites using GC with mass detection (GC-MS). Red wine metabolites were further profiled using two-dimensional GC mass spectrometry (GCxGC-TOFMS). In addition, the effect of PA structure and dose on conversion efficiency was investigated by GC-MS. Red wine exhibited a higher degree of C1-C3 phenolic acid formation than PA fraction or grape pericarp powders. Hydroxyphenyl valeric acid (flavanols and PAs as precursors) and 3,5-dimethoxy-4-hydroxybenzoic acid (anthocyanin as a precursor) were identified from the red wine metabolite profile. In the absence of native grape pericarp or red wine matrix, the isolated PAs were found to be effective in the dose-dependent inhibition of microbial conversions and short-chain fatty acid formation. Metabolite profiling was complementary to targeted analysis. The identified metabolites had biological relevance, because the structures of the metabolites resembled fragments of their grape phenolic precursors or were in agreement with literature data.

  12. Legacy effects of continuous chloropicrin-fumigation for 3-years on soil microbial community composition and metabolic activity

    NARCIS (Netherlands)

    Zhang, Shuting; Liu, Xiaojiao; Jiang, Qipeng; Shen, Guihua; Ding, Wei

    2017-01-01

    Chloropicrin is widely used to control ginger wilt in China, which have an enormous impact on soil microbial diversity. However, little is known on the possible legacy effects on soil microbial community composition with continuous fumigation over different years. In this report, we used high

  13. Effects of Conservation Tillage on Topsoil Microbial Metabolic Characteristics and Organic Carbon within Aggregates under a Rice (Oryza sativa L.) –Wheat (Triticum aestivum L.) Cropping System in Central China

    Science.gov (United States)

    Liu, Tian-Qi; Cao, Cou-Gui; Li, Cheng-Fang

    2016-01-01

    Investigating microbial metabolic characteristics and soil organic carbon (SOC) within aggregates and their relationships under conservation tillage may be useful in revealing the mechanism of SOC sequestration in conservation tillage systems. However, limited studies have been conducted to investigate the relationship between SOC and microbial metabolic characteristics within aggregate fractions under conservation tillage. We hypothesized that close relationships can exist between SOC and microbial metabolic characteristics within aggregates under conservation tillage. In this study, a field experiment was conducted from June 2011 to June 2013 following a split-plot design of a randomized complete block with tillage practices [conventional intensive tillage (CT) and no tillage (NT)] as main plots and straw returning methods [preceding crop residue returning (S, 2100−2500 kg C ha−1) and removal (NS, 0 kg C ha-1)] as subplots with three replications. The objective of this study was to reveal the effects of tillage practices and residue-returning methods on topsoil microbial metabolic characteristics and organic carbon (SOC) fractions within aggregates and their relationships under a rice–wheat cropping system in central China. Microbial metabolic characteristics investigated using the Biolog system was examined within two aggregate fractions (>0.25 and 0.25 aggregate, and 0.25 mm aggregate (11.3%), and 0.25 mm aggregate, and 0.25 mm aggregate, and tillage (NT and S) increased microbial metabolic activities and Shannon index in >0.25 and directly improved SOC by promoting DOC in >0.25 mm aggregate in the upper (0−5 cm) soil layer under conservation tillage systems, as well as directly and indirectly by promoting DOC and MBC in tillage increased SOC in aggregates in the topsoil by improving microbial metabolic activities. PMID:26731654

  14. River Metabolism and Nutrient Cycling at the Point Scale: Insights from In Situ Sensors in Benthic Chambers

    Science.gov (United States)

    Cohen, M. J.; Reijo, C. J.; Hensley, R. T.

    2017-12-01

    Riverine processing of nutrients and carbon is a local process, subject to heterogeneity in sediment, biotic, insolation, and flow velocity drivers. Measurements at the reach scale aggregate across riverscapes, limiting their utility for enumerating these drivers, and thus for scaling to river networks. Using a combination of in situ sensors that sample water chemistry at high temporal resolution and open benthic chambers that isolate the biogeochemical impacts of a small footprint of benthic surface area, we explored controls on metabolism and nutrient cycling. We specifically sought to answer two questions. First, what are the controls on primary production, with a particular emphasis on the relative roles of light vs. nutrient limitation? Second, what are the pathways of nutrient retention, and do the reaction kinetics of these different pathways differ? We demonstrate the considerable utility of these benthic chambers, reasoning that they provide experimental units for river processes that are not attainable at the reach or network scale. Specifically, in addition to their ability to sample the heterogeneity of the river bed as well as observe nutrient depletion to create concentrations well below ambient levels, they enable manipulative experiments (e.g., nutrient enrichment, light reduction, grazer adjustments) while retaining key elements of the natural system. Across several of Florida's spring-fed river sites, our results strongly support the primacy of light limitation of primary production, with very little evidence of any incremental effects of nutrient enrichment. Nutrient depletion assays further support the dominance of two N retention mechanisms (denitrification and assimilation), the kinetics of which differ markedly, with denitrification exhibiting nearly first-order reactions, and assimilation following zero-order or Michaelis-Menten kinetics over the range of observed concentrations. This latter result helps explain the absence of strong

  15. Degradation of 1,1,2,2-tetrachloroethane and accumulation of vinyl chloride in wetland sediment microcosms and in situ porewater: biogeochemical controls and associations with microbial communities

    Science.gov (United States)

    Lorah, Michelle M.; Voytek, Mary A.

    2004-05-01

    The biodegradation pathways of 1,1,2,2-tetrachloroethane (TeCA) and 1,1,2-trichloroethane (112TCA) and the associated microbial communities in anaerobic wetland sediments were evaluated using concurrent geochemical and genetic analyses over time in laboratory microcosm experiments. Experimental results were compared to in situ porewater data in the wetland to better understand the factors controlling daughter product distributions in a chlorinated solvent plume discharging to a freshwater tidal wetland at Aberdeen Proving Ground, Maryland. Microcosms constructed with wetland sediment from two sites showed little difference in the initial degradation steps of TeCA, which included simultaneous hydrogenolysis to 112TCA and dichloroelimination to 1,2-dichloroethene (12DCE). The microcosms from the two sites showed a substantial difference, however, in the relative dominance of subsequent dichloroelimination of 112TCA. A greater dominance of 112TCA dichloroelimination in microcosms constructed with sediment that was initially iron-reducing and subsequently simultaneously iron-reducing and methanogenic caused approximately twice as much vinyl chloride (VC) production as microcosms constructed with sediment that was methanogenic only throughout the incubation. The microcosms with higher VC production also showed substantially more rapid VC degradation. Field measurements of redox-sensitive constituents, TeCA, and its anaerobic degradation products along flowpaths in the wetland porewater also showed greater production and degradation of VC with concurrent methanogenesis and iron reduction. Molecular fingerprinting indicated that bacterial species [represented by a peak at a fragment size of 198 base pairs (bp) by MnlI digest] are associated with VC production from 112TCA dichloroelimination, whereas methanogens (190 and 307 bp) from the Methanococcales or Methanobacteriales family are associated with VC production from 12DCE hydrogenolysis. Acetate-utilizing methanogens

  16. The effect of feed rations containing high moisture crimped corn ensiled with microbial inoculant or chemical additive on milk production and metabolism of dairy cows

    Directory of Open Access Journals (Sweden)

    László Könyves

    2015-01-01

    Full Text Available The study evaluated the effects of crimped corn preserved either with organic acids or with a microbial inoculant on a range of metabolic and production indicators of dairy cows. Two hundred and sixty in-calf, second and third parity cows were selected into pairs on basis of age, parity, milk production in previous lactation, days in milk and body condition score with the greatest possible conformity within pairs. Cow pairs were assigned into a 2-period crossover experiment (2 × 45 days and kept in separate groups within the same shed. Dietary treatments were TMR with crimped corn preserved with either organic acids (treatment K or microbial inoculant (treatment B. Ten superbly matched cow-pairs were selected to form nucleus pairs for metabolic studies. The preservatives had no effect on the nutrient content of crimped corn. Crimped corn preserved with the microbial inoculant were found mouldy, predominantly with Mucor sp. at a number high enough to inhibit the growth of lactic acid bacteria, and had significantly higher pH and ammonium concentration compared to the chemical treatment. The milk yield of treatment K cows was significantly higher than that of treatment B cows with identical feed intake. Blood beta-hydroxy-butyrate concentration was lower and blood aspartate amino transferase activity higher with treatment K compared to treatment B. Results of this study suggest the superiority of total mixed rations containing chemically preserved crimped corn in terms of ammonia and microbiological indicators of crimped corn, significantly higher milk yield, and balanced energy metabolism.

  17. Metabolism

    Science.gov (United States)

    ... lin), which signals cells to increase their anabolic activities. Metabolism is a complicated chemical process, so it's not ... how those enzymes or hormones work. When the metabolism of body chemicals is ... Hyperthyroidism (pronounced: hi-per-THIGH-roy-dih-zum). Hyperthyroidism ...

  18. Groundbreaking technology: in-situ anaerobic bioremediation for treatment of contaminated soil and groundwater

    International Nuclear Information System (INIS)

    Fernandes, K.A.

    2002-01-01

    Anaerobic in-situ bioremediation is a technique often used to cleanse contaminated soil and groundwater. 'Anaerobic in-situ bioremediation' is a phrase with distinct terms all having relevance in the application of this technique. Anaerobic implies the absence of dissolved oxygen, while 'in-situ' simply means that the environmental cleansing occurs with out removing, displacing, or significantly disturbing the specimen or surrounding area. 'Bioremediation' is a term used to describe the biological use of microbes or plants to detoxify the environment. In order to properly implement this complex process, one must have an understanding of microbiology, biochemistry, genetics, metabolic processes, and structure and function of natural microbial communities. (author)

  19. IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes.

    Science.gov (United States)

    Hadjithomas, Michalis; Chen, I-Min A; Chu, Ken; Huang, Jinghua; Ratner, Anna; Palaniappan, Krishna; Andersen, Evan; Markowitz, Victor; Kyrpides, Nikos C; Ivanova, Natalia N

    2017-01-04

    Secondary metabolites produced by microbes have diverse biological functions, which makes them a great potential source of biotechnologically relevant compounds with antimicrobial, anti-cancer and other activities. The proteins needed to synthesize these natural products are often encoded by clusters of co-located genes called biosynthetic gene clusters (BCs). In order to advance the exploration of microbial secondary metabolism, we developed the largest publically available database of experimentally verified and predicted BCs, the Integrated Microbial Genomes Atlas of Biosynthetic gene Clusters (IMG-ABC) (https://img.jgi.doe.gov/abc/). Here, we describe an update of IMG-ABC, which includes ClusterScout, a tool for targeted identification of custom biosynthetic gene clusters across 40 000 isolate microbial genomes, and a new search capability to query more than 700 000 BCs from isolate genomes for clusters with similar Pfam composition. Additional features enable fast exploration and analysis of BCs through two new interactive visualization features, a BC function heatmap and a BC similarity network graph. These new tools and features add to the value of IMG-ABC's vast body of BC data, facilitating their in-depth analysis and accelerating secondary metabolite discovery. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  20. Acquired tolerance and in situ detoxification of furfural and HMF through glucose metabolic pathways by Saccharomyces cerevisiae

    Science.gov (United States)

    Lignocellulosic biomass conversion inhibitors furfural and HMF inhibit microbial growth and interfere with subsequent fermentation of ethanol. Numerous yeast genes were found to be associated with the inhibitor tolerance. However, little is known about system mechanisms of the tolerance and detoxi...

  1. In situ Dynamics of O2, pH, Light, and Photosynthesis in Ikaite Tufa Columns (Ikka Fjord, Greenland)?A Unique Microbial Habitat

    OpenAIRE

    Trampe, Erik C. L.; Larsen, Jens E. N.; Glaring, Mikkel A.; Stougaard, Peter; K?hl, Michael

    2016-01-01

    The Ikka Fjord (SW Greenland) harbors a unique microbial habitat in the form of several hundred submarine tufa columns composed of ikaite, a special hexahydrate form of calcium carbonate that precipitates when alkaline phosphate- and carbonate-enriched spring water seeping out of the sea floor meets cold seawater. While several unique heterotrophic microbes have been isolated from the tufa columns, the microbial activity, and the boundary conditions for microbial growth in ikaite have remaine...

  2. Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales

    Energy Technology Data Exchange (ETDEWEB)

    Daly, Rebecca A.; Borton, Mikayla A.; Wilkins, Michael J.; Hoyt, David W.; Kountz, Duncan J.; Wolfe, Richard A.; Welch, Susan A.; Marcus, Daniel N.; Trexler, Ryan V.; MacRae, Jean D.; Krzycki, Joseph A.; Cole, David R.; Mouser, Paula J.; Wrighton, Kelly C.

    2016-09-05

    Hydraulic fracturing is the industry standard for extracting hydrocarbons from shale formations. Attention has been paid to the economic benefits and environmental impacts of this process, yet the biogeochemical changes induced in the deep subsurface are poorly understood. Recent single-gene investigations revealed that halotolerant microbial communities were enriched after hydraulic fracturing. Here the reconstruction of 31 unique genomes coupled to metabolite data from the Marcellus and Utica shales revealed that methylamine cycling supports methanogenesis in the deep biosphere. Fermentation of injected chemical additives also sustains long-term microbial persistence, while sulfide generation from thiosulfate represents a poorly recognized corrosion mechanism in shales. Extensive links between viruses and microbial hosts demonstrate active viral predation, which may contribute to the release of labile cellular constituents into the extracellular environment. Our analyses show that hydraulic fracturing provides the organismal and chemical inputs for colonization and persistence in the deep terrestrial subsurface.

  3. Pyrogallol, an absorbable microbial gallotannins-metabolite and mango polyphenols (Mangifera Indica L.) suppress breast cancer ductal carcinoma in situ proliferation in vitro.

    Science.gov (United States)

    Nemec, Matthew J; Kim, Hyemee; Marciante, Alexandria B; Barnes, Ryan C; Talcott, Stephen T; Mertens-Talcott, Susanne U

    2016-09-14

    Mango is rich in bioactive absorbable polyphenols, but also contains considerable amounts of unabsorbable gallotannins at varying degrees of polymerization. Gallotannins are not absorbable upon consumption and have rarely been considered in the discussion of health benefits of polyphenols. Therefore, the objective of this study was to investigate the anti-proliferative activities of the major microbial metabolite of gallotannins, pyrogallol (PG) and a low molecular weight fraction of mango (Mangifera Indica L.) polyphenols (ML) and involved pathways including the AKT/mTOR signaling axis in an in situ breast cancer cell line, MCF10DCIS.COM. Fluorouracil (5-FU), a widely used genotoxic cancer therapeutic, was used a positive control and in combination with ML and PG to assess potential interactions. Concentrations that were non-cytotoxic in non-cancer cells were identified in non-cancer mammary fibroblasts (MCF-12F) and only non-cytotoxic dietarily relevant concentrations were selected for the investigation in MCF10DCIS.COM cancer cells. In addition to proliferation and viability, mRNA and expression of total and phosphorylated protein were investigated. Results show that both, ML and PG significantly reduced proliferation in MCF10DCIS.COM, but did not significantly reduce viability following a 48 h exposure. ML significantly reduced mRNA expression of mTOR and HIF-1α, while PG significantly reduced mRNA of IGF-1R, AKT, mTOR and HIF-1α. ML and PG reduced total protein expression of IGF-1R, IR, AKT, mTOR, and P70S6K. In addition, PG reduced IRS protein. Both treatments also had an effect on phosphorylated protein levels, with PG significantly reducing IGF-1R, AKT, and P70S6K levels. ML had a similar effect and significantly decreased IR, AKT, and P70S6K phosphorylation levels. Within the low concentration-range, ML and PG did not interact with the cytotoxic activities of 5-FU. Overall, the AKT/mTOR signaling axis appears to be implicated as causal in decreased

  4. The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. II. Metabolic Functions of Abundant Community Members Predicted from Metagenomic Analyses.

    Science.gov (United States)

    Thiel, Vera; Hügler, Michael; Ward, David M; Bryant, Donald A

    2017-01-01

    Microbial mat communities in the effluent channels of Octopus and Mushroom Springs within the Lower Geyser Basin of Yellowstone National Park have been extensively characterized. Previous studies have focused on the chlorophototrophic organisms of the phyla Cyanobacteria and Chloroflexi . However, the diversity and metabolic functions of the other portion of the community in the microoxic/anoxic region of the mat are poorly understood. We recently described the diverse but extremely uneven microbial assemblage in the undermat of Mushroom Spring based on 16S rRNA amplicon sequences, which was dominated by Roseiflexus members, filamentous anoxygenic chlorophototrophs. In this study, we analyzed the orange-colored undermat portion of the community of Mushroom Spring mats in a genome-centric approach and discuss the metabolic potentials of the major members. Metagenome binning recovered partial genomes of all abundant community members, ranging in completeness from ~28 to 96%, and allowed affiliation of function with taxonomic identity even for representatives of novel and Candidate phyla. Less complete metagenomic bins correlated with high microdiversity. The undermat portion of the community was found to be a mixture of phototrophic and chemotrophic organisms, which use bicarbonate as well as organic carbon sources derived from different cell components and fermentation products. The presence of rhodopsin genes in many taxa strengthens the hypothesis that light energy is of major importance. Evidence for the usage of all four bacterial carbon fixation pathways was found in the metagenome. Nitrogen fixation appears to be limited to Synechococcus spp. in the upper mat layer and Thermodesulfovibrio sp. in the undermat, and nitrate/nitrite metabolism was limited. A closed sulfur cycle is indicated by biological sulfate reduction combined with the presence of genes for sulfide oxidation mainly in phototrophs. Finally, a variety of undermat microorganisms have genes for

  5. The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. II. Metabolic Functions of Abundant Community Members Predicted from Metagenomic Analyses

    Directory of Open Access Journals (Sweden)

    Vera Thiel

    2017-06-01

    Full Text Available Microbial mat communities in the effluent channels of Octopus and Mushroom Springs within the Lower Geyser Basin of Yellowstone National Park have been extensively characterized. Previous studies have focused on the chlorophototrophic organisms of the phyla Cyanobacteria and Chloroflexi. However, the diversity and metabolic functions of the other portion of the community in the microoxic/anoxic region of the mat are poorly understood. We recently described the diverse but extremely uneven microbial assemblage in the undermat of Mushroom Spring based on 16S rRNA amplicon sequences, which was dominated by Roseiflexus members, filamentous anoxygenic chlorophototrophs. In this study, we analyzed the orange-colored undermat portion of the community of Mushroom Spring mats in a genome-centric approach and discuss the metabolic potentials of the major members. Metagenome binning recovered partial genomes of all abundant community members, ranging in completeness from ~28 to 96%, and allowed affiliation of function with taxonomic identity even for representatives of novel and Candidate phyla. Less complete metagenomic bins correlated with high microdiversity. The undermat portion of the community was found to be a mixture of phototrophic and chemotrophic organisms, which use bicarbonate as well as organic carbon sources derived from different cell components and fermentation products. The presence of rhodopsin genes in many taxa strengthens the hypothesis that light energy is of major importance. Evidence for the usage of all four bacterial carbon fixation pathways was found in the metagenome. Nitrogen fixation appears to be limited to Synechococcus spp. in the upper mat layer and Thermodesulfovibrio sp. in the undermat, and nitrate/nitrite metabolism was limited. A closed sulfur cycle is indicated by biological sulfate reduction combined with the presence of genes for sulfide oxidation mainly in phototrophs. Finally, a variety of undermat

  6. In-situ studies of microbial CH{sub 4} oxidation efficiency in Arctic wetland soils. Applications of stable carbon isotopes

    Energy Technology Data Exchange (ETDEWEB)

    Preuss, Inken-Marie

    2013-07-05

    Arctic wetland soils are significant sources of the climate-relevant trace gas methane (CH{sub 4}). The observed accelerated warming of the Arctic is expected to cause deeper permafrost thawing followed by increased carbon mineralization and CH{sub 4} formation in water-saturated permafrost-affected tundra soils thus creating a positive feedback to climate change. Aerobic CH{sub 4} oxidation is regarded as the key process reducing CH{sub 4} emissions from wetlands, but quantification of turnover rates has remained difficult so far. This study improved the in-situ quantification of microbial CH{sub 4} oxidation efficiency in arctic wetland soils in Russia's Lena River Delta based on stable isotope signatures of CH{sub 4}. In addition to the common practice of determining the stable isotope fractionation during oxidation, additionally the fractionation effect of diffusion, an important gas transport mechanism in tundra soils, was investigated for both saturated and unsaturated conditions. The isotopic fractionation factors α{sub ox} and α{sub diff} were used to calculate the CH{sub 4} oxidation efficiency from the CH{sub 4} stable isotope signatures of wet polygonal tundra soils of different hydrology. Further, the method was used to study the short-term effects of temperature increase with a climate manipulation experiment. For the first time, the stable isotope fractionation of CH{sub 4} diffusion through water-saturated soils was determined with α{sub diff} = 1.001 ± 0.0002 (n = 3). CH{sub 4} stable isotope fractionation during diffusion through air-filled pores of the investigated polygonal tundra soils was α{sub diff} = 1.013 ± 0.003 (n = 18). For the studied sites the fractionation factor for diffusion under saturated conditions α{sub diff} = 1.001 seems to be of utmost importance for the quantification of the CH{sub 4} oxidation efficiency, since most of the CH{sub 4} is oxidized in the saturated part at the aerobic-anaerobic interface. Furthermore

  7. Metagenomic analysis revealed highly diverse microbial arsenic metabolism genes in paddy soils with low-arsenic contents

    International Nuclear Information System (INIS)

    Xiao, Ke-Qing; Li, Li-Guan; Ma, Li-Ping; Zhang, Si-Yu; Bao, Peng; Zhang, Tong; Zhu, Yong-Guan

    2016-01-01

    Microbe-mediated arsenic (As) metabolism plays a critical role in global As cycle, and As metabolism involves different types of genes encoding proteins facilitating its biotransformation and transportation processes. Here, we used metagenomic analysis based on high-throughput sequencing and constructed As metabolism protein databases to analyze As metabolism genes in five paddy soils with low-As contents. The results showed that highly diverse As metabolism genes were present in these paddy soils, with varied abundances and distribution for different types and subtypes of these genes. Arsenate reduction genes (ars) dominated in all soil samples, and significant correlation existed between the abundance of arr (arsenate respiration), aio (arsenite oxidation), and arsM (arsenite methylation) genes, indicating the co-existence and close-relation of different As resistance systems of microbes in wetland environments similar to these paddy soils after long-term evolution. Among all soil parameters, pH was an important factor controlling the distribution of As metabolism gene in five paddy soils (p = 0.018). To the best of our knowledge, this is the first study using high-throughput sequencing and metagenomics approach in characterizing As metabolism genes in the five paddy soil, showing their great potential in As biotransformation, and therefore in mitigating arsenic risk to humans. - Highlights: • Use metagenomics to analyze As metabolism genes in paddy soils with low-As content. • These genes were ubiquitous, abundant, and associated with diverse microbes. • pH as an important factor controlling their distribution in paddy soil. • Imply combinational effect of evolution and selection on As metabolism genes. - Metagenomics was used to analyze As metabolism genes in paddy soils with low-As contents. These genes were ubiquitous, abundant, and associated with diverse microbes.

  8. Development of an integrated, in-situ remediation technology. Topical report for task No. 6: lab-scale development of microbial degradation process, September 26, 1994--May 25, 1996

    International Nuclear Information System (INIS)

    Odom, J.M.

    1997-01-01

    Contamination in low permeability soils poses a significant technical challenge to in situ remediation efforts. Poor accessibility to the contaminants and difficulty in delivery of treatment reagents have rendered existing in situ treatments such as bioremediation, vapor extraction, and pump and treat rather ineffective when applied to low permeability soils present at many contaminated sites. The technology is an integrated in situ treatment in which established geotechnical methods are used to install degradation zones directly in the contaminated soil, and electro-osmosis is utilized to move the contaminants back and forth through those zones until the treatment is completed. The present Topical Report for Task No. 6 summarizes the results of a study of the potential for stimulating microbial reductive dehalogenation as part of the integrated in situ treatment process at the field experiment test site at DOE's Gaseous Diffusion Plant in Paducah, Kentucky. A series of open-quotes microcosm bottle testsclose quotes were performed on samples of contaminated soil and groundwater taken from the Paducah site and spiked with trichloroethene (TCE). A number of bottles were set up, each spiked with a different carbon source in order to enhance the growth of different microbial subpopulations already present within the indigenous population in the soil. In addition, a series of bottle tests were completed with samples of the granular activated carbon (GAC) treatment zone material retrieved from the test site during the Paducah field experiment. In these tests, the GAC samples were used in place of the soil. Results of the soil-groundwater microcosms yielded a negative indication of the presence of dechlorinating bacteria at the site. However, charcoal (GAC) samples from one location in the test plot exhibited marked dechlorination with conversion of TCE to dichloroethene

  9. In situ bioventing in deep soils at arid sites

    International Nuclear Information System (INIS)

    Frishmuth, R.A.; Ratz, J.W.; Blicker, B.R.; Hall, J.F.; Downey, D.C.

    1995-01-01

    In situ bioventing has been shown to be a cost-effective remedial alternative for vadose zone soils. The success of the technology relies on the ability of indigenous soil microorganisms to utilize petroleum hydrocarbon contaminants as a primary metabolic substrate. Soil microbial populations are typically elevated in shallow soils due to an abundance of naturally occurring substrates and nutrients, but may be limited at greater depths due to a lack of these constituents. Therefore, the effectiveness of in situ bioventing is questionable in contaminated soil zones that extend far below the ground surface. Also, because the soil microbial population relies on soil moisture to sustain hydrocarbon degradation, the viability of bioventing is questionable in arid climates, where the soil moisture content is suspected to be minimal

  10. Microbial Mineralization of cis-Dichloroethene and Vinyl Chloride as a Component of Natural Attenuation of Chloroethene Contaminants under Conditions Identified in the Field as Anoxic

    Science.gov (United States)

    2012-01-01

    16 2. cis-DCE mineralization kinetics under hypoxic and anoxic conditions .............................17 Conversion Factors Inch/Pound...situ conditions. Vmax is influenced by micro- bial biomass , metabolic activity, and the availability of nutri- ents and substrates that support...were incapable of growth at atmospheric oxygen levels (Morris 1976). Enzymatic defenses against oxygen radicals have been documented 20 Microbial

  11. Recent advances in microbial production of fuels and chemicals using tools and strategies of systems metabolic engineering

    DEFF Research Database (Denmark)

    Cho, Changhee; Choi, So Young; Luo, Zi Wei

    2015-01-01

    The advent of various systems metabolic engineering tools and strategies has enabled more sophisticated engineering of microorganisms for the production of industrially useful fuels and chemicals. Advances in systems metabolic engineering have been made in overproducing natural chemicals...... and producing novel non-natural chemicals. In this paper, we review the tools and strategies of systems metabolic engineering employed for the development of microorganisms for the production of various industrially useful chemicals belonging to fuels, building block chemicals, and specialty chemicals......, in particular focusing on those reported in the last three years. It was aimed at providing the current landscape of systems metabolic engineering and suggesting directions to address future challenges towards successfully establishing processes for the bio-based production of fuels and chemicals from renewable...

  12. Recent advances in microbial production of fuels and chemicals using tools and strategies of systems metabolic engineering.

    Science.gov (United States)

    Cho, Changhee; Choi, So Young; Luo, Zi Wei; Lee, Sang Yup

    2015-11-15

    The advent of various systems metabolic engineering tools and strategies has enabled more sophisticated engineering of microorganisms for the production of industrially useful fuels and chemicals. Advances in systems metabolic engineering have been made in overproducing natural chemicals and producing novel non-natural chemicals. In this paper, we review the tools and strategies of systems metabolic engineering employed for the development of microorganisms for the production of various industrially useful chemicals belonging to fuels, building block chemicals, and specialty chemicals, in particular focusing on those reported in the last three years. It was aimed at providing the current landscape of systems metabolic engineering and suggesting directions to address future challenges towards successfully establishing processes for the bio-based production of fuels and chemicals from renewable resources. Copyright © 2014 Elsevier Inc. All rights reserved.

  13. Microbial protein synthesis and nitrogen metabolism in cows bred on tropical pasture and fed on cassava root and corn

    Directory of Open Access Journals (Sweden)

    Ádler Carvalho da Silva

    2014-05-01

    Full Text Available Current experiment evaluated the effect of replacement of full corn meal by dehydrated ground cassava roots at levels 0%, 25%, 50%, 75% and 100% in experimental supplements for lactating cows grazing on irrigated and fertilized tropical pastures. Ten Holstein cows were divided into two 5 x 5 Latin squares, with average initial 150 days of lactation, milk production 22±3.30 kg day-1 at the beginning of experiment and initial body weight of 603±65 kg. Cows were maintained on pasture consisting of elephant grass (Pennisetum purpureum, Schum cultivar Pioneiro, intercropped with Tifton 85 (Cynodon nlemfuensis, fertilized with 600 kg nitrogen per hectare year-1. There was no significant difference (p > 0.05 between the substitution levels of corn meal by ground and dehydrated cassava root in the concentrate on the synthesis of microbial protein with an estimated average of 1,288.49 g day-1 and efficiency in the synthesis of microbial protein per kilogram of TDN with estimated average of 91.30 g kg-1 TDN. Nitrogen equilibrium showed an estimated average of 218.79 g day-1 of retained nitrogen. The microbial protein synthesis and nitrogen balance were not affected by treatments.

  14. IN SITU BIOREMEDIATION OF TRICHLOROETHYLENE USING BURKHOLDERIA CEPACIA G4 PR1: ANALYSIS OF MICROBIAL ECOLOGY PARAMETERS FOR RISK ASSESSMENT (RESEARCH BRIEF)

    Science.gov (United States)

    The introduction of bacteria into aquifers for bioremediation purposes requires monitoring of the persistence and activity of microbial populations for efficacy and risk assessment purposes. Burkholderia cepacia G4 PR1 constitutively expresses a toluene ortho-monooxygenase (tom) ...

  15. Evaluation of some feedstuffs with special emphasis on the effect of nitrate and other non-protein nitrogen fractions on ruminal microbial metabolism

    International Nuclear Information System (INIS)

    Nikolic, J.A.

    1988-01-01

    Green herbage grown under widely different conditions was examined for nitrate content. The mean value was 0.14% (range 0.01-0.32%) NO 3 -N in the dry matter (DM). It was concluded that the cut green fodder would induce high levels of blood methaemoglobin when fed to ruminants in mixed diets. Nevertheless, experiments in vitro indicated that relatively small amounts of dietary nitrate induced considerable microbial nitrate reducing activity in rumen contents. Moreover, nitrate reduction to ammonia was accompanied by alterations in microbial sulphur and energy metabolism. A technique for determining organic matter digestibility (OMD) in vitro was standardized and used to evaluate the potential nutritive value of some fruit wastes. Studies on apple pomace silage indicated that added urea did not significantly increase the silage protein content but remained as a potential source of non-protein nitrogen for rumen microorganisms. Apple pomace ensiled alone or preferably with other ingredients was acceptable to sheep and cattle, particularly as a supplement to their winter rations. (author). 27 refs, 2 figs, 5 tabs

  16. MicroScope-an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data.

    Science.gov (United States)

    Médigue, Claudine; Calteau, Alexandra; Cruveiller, Stéphane; Gachet, Mathieu; Gautreau, Guillaume; Josso, Adrien; Lajus, Aurélie; Langlois, Jordan; Pereira, Hugo; Planel, Rémi; Roche, David; Rollin, Johan; Rouy, Zoe; Vallenet, David

    2017-09-12

    The overwhelming list of new bacterial genomes becoming available on a daily basis makes accurate genome annotation an essential step that ultimately determines the relevance of thousands of genomes stored in public databanks. The MicroScope platform (http://www.genoscope.cns.fr/agc/microscope) is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. Starting from the results of our syntactic, functional and relational annotation pipelines, MicroScope provides an integrated environment for the expert annotation and comparative analysis of prokaryotic genomes. It combines tools and graphical interfaces to analyze genomes and to perform the manual curation of gene function in a comparative genomics and metabolic context. In this article, we describe the free-of-charge MicroScope services for the annotation and analysis of microbial (meta)genomes, transcriptomic and re-sequencing data. Then, the functionalities of the platform are presented in a way providing practical guidance and help to the nonspecialists in bioinformatics. Newly integrated analysis tools (i.e. prediction of virulence and resistance genes in bacterial genomes) and original method recently developed (the pan-genome graph representation) are also described. Integrated environments such as MicroScope clearly contribute, through the user community, to help maintaining accurate resources. © The Author 2017. Published by Oxford University Press.

  17. III. Cellular ultrastructures in situ as key to understanding tumor energy metabolism: biological significance of the Warburg effect.

    Science.gov (United States)

    Witkiewicz, Halina; Oh, Phil; Schnitzer, Jan E

    2013-01-01

    Despite the universality of metabolic pathways, malignant cells were found to have their metabolism reprogrammed to generate energy by glycolysis even under normal oxygen concentrations (the Warburg effect). Therefore, the pathway energetically 18 times less efficient than oxidative phosphorylation was implicated to match increased energy requirements of growing tumors. The paradox was explained by an abnormally high rate of glucose uptake, assuming unlimited availability of substrates for tumor growth in vivo. However, ultrastructural analysis of tumor vasculature morphogenesis showed that the growing tissue regions did not have continuous blood supply and intermittently depended on autophagy for survival. Erythrogenic autophagy, and resulting ATP generation by glycolysis, appeared critical to initiating vasculature formation where it was missing. This study focused on ultrastructural features that reflected metabolic switch from aerobic to anaerobic. Morphological differences between and within different types of cells were evident in tissue sections. In cells undergoing nucleo-cytoplasmic conversion into erythrosomes (erythrogenesis), gradual changes led to replacing mitochondria with peroxisomes, through an intermediate form connected to endoplasmic reticulum. Those findings related to the issue of peroxisome biogenesis and to the phenomenon of hemogenic endothelium. Mitochondria were compacted also during mitosis. In vivo, cells that lost and others that retained capability to use oxygen coexisted side-by-side; both types were important for vasculature morphogenesis and tissue growth. Once passable, the new vasculature segment could deliver external oxygen and nutrients. Nutritional and redox status of microenvironment had similar effect on metabolism of malignant and non-malignant cells demonstrating the necessity to maintain structure-energy equivalence in all living cells. The role of glycolysis in initiating vasculature formation, and in progression of

  18. A liquid chromatography – tandem mass spectrometry method to measure a selected panel of uremic retention solutes derived from endogenous and colonic microbial metabolism

    Energy Technology Data Exchange (ETDEWEB)

    Loor, Henriette de; Poesen, Ruben [KU Leuven – University of Leuven, Department of Microbiology and Immunology, Laboratory of Nephrology, B-3000 Leuven (Belgium); De Leger, Wout; Dehaen, Wim [KU Leuven – University of Leuven, Department of Chemistry, Division of Molecular Design and Synthesis, B-3000 Leuven (Belgium); Augustijns, Patrick [KU Leuven – University of Leuven, Department of Pharmaceutical and Pharmacological Sciences, Drug Delivery and Disposition, B-3000 Leuven (Belgium); Evenepoel, Pieter [KU Leuven – University of Leuven, Department of Microbiology and Immunology, Laboratory of Nephrology, B-3000 Leuven (Belgium); University Hospitals Leuven, Department of Nephrology and Renal Transplantation, B-3000 Leuven (Belgium); Meijers, Björn, E-mail: bjorn.meijers@uzleuven.be [KU Leuven – University of Leuven, Department of Microbiology and Immunology, Laboratory of Nephrology, B-3000 Leuven (Belgium); University Hospitals Leuven, Department of Nephrology and Renal Transplantation, B-3000 Leuven (Belgium)

    2016-09-14

    Chronic kidney disease (CKD) is associated with an increased risk of mortality and cardiovascular disease, which is, at least partly, mediated by the accumulation of so-called uremic retention solutes. Although there has been an increasing interest in the behavior of these solutes, derived from both the endogenous and colonic microbial metabolism, methods to simultaneously and accurately measure a broad panel of relevant uremic retention solutes remain scarce. We developed a highly sensitive ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method. A high throughput sample preparation was used with extraction of analytes from 50 μl serum using Ostro plate technology. For most solutes, stable isotopes labelled metabolites were used as internal standards. Chromatography was achieved using an Acquity UPLC CSH Fluoro Phenyl column. The total run time was 8 min, the mobile phase was a gradient of 0.1% formic acid in Milli-Q water and pure methanol at a flow rate of 0.5 ml min{sup −1}. Detection was performed using a tandem mass spectrometer with alternated positive and negative electrospray ionization. Calibration curves were linear for all solutes. Precision was assessed according to the NCCLS EP5-T guideline, being below 15% for all metabolites. Mean recoveries were between 83 and 104% for all metabolites. The validated method was successfully applied in a cohort of 488 patients with CKD. We developed and validated a sensitive and robust UPLC-MS/MS method for quantification of 15 uremic retention solutes derived from endogenous and colonic microbial metabolism. This method allows for studying the behavior and relevance of these solutes in patients with CKD. - Highlights: • Simultaneous quantification of fifteen relevant uremic retention solutes. • Comprehensive validation, highly sensitive and high through-put LC-MSMS method. • Comparison of different blood tubes. • Freeze-thaw stability. • Successful implementation in a

  19. Suppression of microbial metabolic pathways inhibits the generation of the human body odor component diacetyl by Staphylococcus spp.

    Directory of Open Access Journals (Sweden)

    Takeshi Hara

    Full Text Available Diacetyl (2,3-butanedione is a key contributor to unpleasant odors emanating from the axillae, feet, and head regions. To investigate the mechanism of diacetyl generation on human skin, resident skin bacteria were tested for the ability to produce diacetyl via metabolism of the main organic acids contained in human sweat. L-lactate metabolism by Staphylococcus aureus and Staphylococcus epidermidis produced the highest amounts of diacetyl, as measured by high-performance liquid chromatography. Glycyrrhiza glabra root extract (GGR and α-tocopheryl-L-ascorbate-2-O-phosphate diester potassium salt (EPC-K1, a phosphate diester of α-tocopherol and ascorbic acid, effectively inhibited diacetyl formation without bactericidal effects. Moreover, a metabolic flux analysis revealed that GGR and EPC-K1 suppressed diacetyl formation by inhibiting extracellular bacterial conversion of L-lactate to pyruvate or by altering intracellular metabolic flow into the citrate cycle, respectively, highlighting fundamentally distinct mechanisms by GGR and EPC-K1 to suppress diacetyl formation. These results provide new insight into diacetyl metabolism by human skin bacteria and identify a regulatory mechanism of diacetyl formation that can facilitate the development of effective deodorant agents.

  20. Suppression of microbial metabolic pathways inhibits the generation of the human body odor component diacetyl by Staphylococcus spp.

    Science.gov (United States)

    Hara, Takeshi; Matsui, Hiroshi; Shimizu, Hironori

    2014-01-01

    Diacetyl (2,3-butanedione) is a key contributor to unpleasant odors emanating from the axillae, feet, and head regions. To investigate the mechanism of diacetyl generation on human skin, resident skin bacteria were tested for the ability to produce diacetyl via metabolism of the main organic acids contained in human sweat. L-lactate metabolism by Staphylococcus aureus and Staphylococcus epidermidis produced the highest amounts of diacetyl, as measured by high-performance liquid chromatography. Glycyrrhiza glabra root extract (GGR) and α-tocopheryl-L-ascorbate-2-O-phosphate diester potassium salt (EPC-K1), a phosphate diester of α-tocopherol and ascorbic acid, effectively inhibited diacetyl formation without bactericidal effects. Moreover, a metabolic flux analysis revealed that GGR and EPC-K1 suppressed diacetyl formation by inhibiting extracellular bacterial conversion of L-lactate to pyruvate or by altering intracellular metabolic flow into the citrate cycle, respectively, highlighting fundamentally distinct mechanisms by GGR and EPC-K1 to suppress diacetyl formation. These results provide new insight into diacetyl metabolism by human skin bacteria and identify a regulatory mechanism of diacetyl formation that can facilitate the development of effective deodorant agents.

  1. Effects of wastewater treatment plant effluent inputs on planktonic metabolic rates and microbial community composition in the Baltic Sea

    DEFF Research Database (Denmark)

    Vaquer-Sunyer, Raquel; Reader, Heather E.; Muthusamy, Saraladevi

    2016-01-01

    ) contribute to eutrophication as they are important sources of nitrogen to coastal areas. Here, we evaluated the effects of wastewater treatment plant effluent inputs on Baltic Sea planktonic communities in four experiments. We tested for effects of effluent inputs on chlorophyll a content, bacterial....... An increase in BP and decrease in CR could be caused by high lability of the DOM that can support secondary bacterial production, without an increase in respiration. Increases in bacterial production and simultaneous decreases of primary production lead to more carbon being consumed in the microbial loop...

  2. Long-term oil contamination causes similar changes in microbial communities of two distinct soils.

    Science.gov (United States)

    Liao, Jingqiu; Wang, Jie; Jiang, Dalin; Wang, Michael Cai; Huang, Yi

    2015-12-01

    Since total petroleum hydrocarbons (TPH) are toxic and persistent in environments, studying the impact of oil contamination on microbial communities in different soils is vital to oil production engineering, effective soil management and pollution control. This study analyzed the impact of oil contamination on the structure, activity and function in carbon metabolism of microbial communities of Chernozem soil from Daqing oil field and Cinnamon soil from Huabei oil field through both culture-dependent techniques and a culture-independent technique-pyrosequencing. Results revealed that pristine microbial communities in these two soils presented disparate patterns, where Cinnamon soil showed higher abundance of alkane, (polycyclic aromatic hydrocarbons) PAHs and TPH degraders, number of cultivable microbes, bacterial richness, bacterial biodiversity, and stronger microbial activity and function in carbon metabolism than Chernozem soil. It suggested that complicated properties of microbes and soils resulted in the difference in soil microbial patterns. However, the changes of microbial communities caused by oil contamination were similar in respect of two dominant phenomena. Firstly, the microbial community structures were greatly changed, with higher abundance, higher bacterial biodiversity, occurrence of Candidate_division_BRC1 and TAO6, disappearance of BD1-5 and Candidate_division_OD1, dominance of Streptomyces, higher percentage of hydrocarbon-degrading groups, and lower percentage of nitrogen-transforming groups. Secondly, microbial activity and function in carbon metabolism were significantly enhanced. Based on the characteristics of microbial communities in the two soils, appropriate strategy for in situ bioremediation was provided for each oil field. This research underscored the usefulness of combination of culture-dependent techniques and next-generation sequencing techniques both to unravel the microbial patterns and understand the ecological impact of

  3. Mineral absorption and excretion as affected by microbial phytase and their effect on energy metabolism in young piglets

    NARCIS (Netherlands)

    Kies, A.K.; Gerrits, W.J.J.; Schrama, J.W.; Heetkamp, M.J.W.; Linden, van der K.L.; Zandstra, T.; Verstegen, M.W.A.

    2005-01-01

    Positive effects of dietary phytase supplementation on pig performance are observed not only when phosphorus is limiting. Improved energy utilization might be one explanation. Using indirect calorimetry, phytase-induced changes in energy metabolism were evaluated in young piglets with adequate

  4. Transitory microbial habitat in the hyperarid Atacama Desert

    Science.gov (United States)

    Schulze-Makuch, Dirk; Wagner, Dirk; Kounaves, Samuel P.; Mangelsdorf, Kai; Devine, Kevin G.; de Vera, Jean-Pierre; Schmitt-Kopplin, Philippe; Grossart, Hans-Peter; Parro, Victor; Kaupenjohann, Martin; Galy, Albert; Schneider, Beate; Airo, Alessandro; Frösler, Jan; Davila, Alfonso F.; Arens, Felix L.; Cáceres, Luis; Solís Cornejo, Francisco; Carrizo, Daniel; Dartnell, Lewis; DiRuggiero, Jocelyne; Flury, Markus; Ganzert, Lars; Gessner, Mark O.; Grathwohl, Peter; Guan, Lisa; Heinz, Jacob; Hess, Matthias; Keppler, Frank; Maus, Deborah; McKay, Christopher P.; Meckenstock, Rainer U.; Montgomery, Wren; Oberlin, Elizabeth A.; Probst, Alexander J.; Sáenz, Johan S.; Sattler, Tobias; Schirmack, Janosch; Sephton, Mark A.; Schloter, Michael; Uhl, Jenny; Valenzuela, Bernardita; Vestergaard, Gisle; Wörmer, Lars; Zamorano, Pedro

    2018-03-01

    Traces of life are nearly ubiquitous on Earth. However, a central unresolved question is whether these traces always indicate an active microbial community or whether, in extreme environments, such as hyperarid deserts, they instead reflect just dormant or dead cells. Although microbial biomass and diversity decrease with increasing aridity in the Atacama Desert, we provide multiple lines of evidence for the presence of an at times metabolically active, microbial community in one of the driest places on Earth. We base this observation on four major lines of evidence: (i) a physico-chemical characterization of the soil habitability after an exceptional rain event, (ii) identified biomolecules indicative of potentially active cells [e.g., presence of ATP, phospholipid fatty acids (PLFAs), metabolites, and enzymatic activity], (iii) measurements of in situ replication rates of genomes of uncultivated bacteria reconstructed from selected samples, and (iv) microbial community patterns specific to soil parameters and depths. We infer that the microbial populations have undergone selection and adaptation in response to their specific soil microenvironment and in particular to the degree of aridity. Collectively, our results highlight that even the hyperarid Atacama Desert can provide a habitable environment for microorganisms that allows them to become metabolically active following an episodic increase in moisture and that once it decreases, so does the activity of the microbiota. These results have implications for the prospect of life on other planets such as Mars, which has transitioned from an earlier wetter environment to today’s extreme hyperaridity.

  5. THE EFFECTS OF AEROBIC EXERCISE ON SKELETAL MUSCLE METABOLISM, MORPHOLOGY AND IN SITU ENDURANCE IN DIABETIC RATS

    Directory of Open Access Journals (Sweden)

    Nilay Ergen

    2005-12-01

    Full Text Available The effects of aerobic exercise training on skeletal muscle endurance capacity were examined in diabetic rats in situ. Moderate diabetes was induced by iv injection of streptozotocin and an exercise training program on a treadmill was carried out for 8 weeks. The animals randomly assigned to one of the four experimental groups: control-sedentary (CS, control-exercise (CE, diabetic-sedentary (DS or diabetic-exercise (DE. The changes in the muscle endurance capacity were evaluated through the square wave impulses (supramaximal of 0.2-ms duration at 1 Hz in the in situ gastrocnemius-soleus muscle complex. Muscle was stimulated continuously until tension development reduced to the half of this maximal value. Time interval between the beginning and the end of stimulation period is defined as contraction duration. Following the training period, blood glucose level reduced significantly in the DE group compared to DS group (p < 0.05. The soles muscle citrate synthase activity was increased significantly in both of the trained groups compared to sedentary animals (p < 0.05. Fatigued muscle lactate values were not significantly different from each other. Ultrastractural abnormality of the skeletal muscle in DS group disappeared with training. Presence of increased lipid droplets, mitochondria clusters and glycogen accumulation was observed in the skeletal muscle of DE group. The contraction duration was longer in the DE group than others (p < 0.001. Fatigue resistance of exercised diabetic animals may be explained by increased intramyocellular lipid droplets, high blood glucose level and muscle citrate synthase activity

  6. GM2-ganglioside metabolism in hexosaminidase A deficiency states: determination in situ using labeled GM2 added to fibroblast cultures

    International Nuclear Information System (INIS)

    Raghavan, S.S.; Krusell, A.; Krusell, J.; Lyerla, T.A.; Kolodny, E.H.

    1985-01-01

    To clarify the relationship between hexosaminidase A (HEX A) activity and GM2-ganglioside hydrolysis in atypical clinical situations of HEX A deficiency, we have developed a simple method to assess GM2-ganglioside metabolism in cultured fibroblasts utilizing GM2 labeled with tritium in the sphingosine portion of the molecule. The radioactive lipid is added to the media of cultured skin fibroblasts, and after 10 days the cells are thoroughly washed, then harvested, and their lipid composition analyzed by HPLC. The degree of hydrolysis of the ingested GM2 is determined by comparing the amount of radioactive counts recovered in undegraded substrate with total cellular radioactivity. A deficiency in GM2-ganglioside hydrolysis was demonstrated in seven HEX A-deficient adults with neurological signs and in two healthy-appearing adolescents with older affected siblings. In each case, an analysis of endogenous monosialoganglioside composition revealed an increase in GM2-ganglioside, confirming the presence of a block in the metabolism of GM2. No defect in GM2-catabolism was found in four other healthy individuals with HEX A deficiency. This method of assay is especially helpful in the evaluation of atypical cases of HEX A deficiency for the definitive diagnosis of GM2-gangliosidosis

  7. Enteric short-chain fatty acids: microbial messengers of metabolism, mitochondria, and mind: implications in autism spectrum disorders

    Directory of Open Access Journals (Sweden)

    Derrick F. MacFabe

    2015-05-01

    Full Text Available Clinical observations suggest that gut and dietary factors transiently worsen and, in some cases, appear to improve behavioral symptoms in a subset of persons with autism spectrum disorders (ASDs, but the reason for this is unclear. Emerging evidence suggests ASDs are a family of systemic disorders of altered immunity, metabolism, and gene expression. Pre- or perinatal infection, hospitalization, or early antibiotic exposure, which may alter gut microbiota, have been suggested as potential risk factors for ASD. Can a common environmental agent link these disparate findings? This review outlines basic science and clinical evidence that enteric short-chain fatty acids (SCFAs, present in diet and also produced by opportunistic gut bacteria following fermentation of dietary carbohydrates, may be environmental triggers in ASD. Of note, propionic acid, a major SCFA produced by ASD-associated gastrointestinal bacteria (clostridia, bacteroides, desulfovibrio and also a common food preservative, can produce reversible behavioral, electrographic, neuroinflammatory, metabolic, and epigenetic changes closely resembling those found in ASD when administered to rodents. Major effects of these SCFAs may be through the alteration of mitochondrial function via the citric acid cycle and carnitine metabolism, or the epigenetic modulation of ASD-associated genes, which may be useful clinical biomarkers. It discusses the hypothesis that ASDs are produced by pre- or post-natal alterations in intestinal microbiota in sensitive sub-populations, which may have major implications in ASD cause, diagnosis, prevention, and treatment.

  8. Metabolic and microbial community dynamics during the hydrolytic and acidogenic fermentation in a leach-bed process

    Energy Technology Data Exchange (ETDEWEB)

    Straeuber, Heike; Kleinsteuber, Sabine [UFZ - Helmholtz Centre for Environmental Research, Leipzig (Germany). Dept. of Bioenergy; UFZ - Helmholtz Centre for Environmental Research, Leipzig (Germany). Dept. of Environmental Microbiology; Schroeder, Martina [UFZ - Helmholtz Centre for Environmental Research, Leipzig (Germany). Dept. of Bioenergy

    2012-12-15

    Biogas production from lignocellulosic feedstock not competing with food production can contribute to a sustainable bioenergy system. The hydrolysis is the rate-limiting step in the anaerobic digestion of solid substrates such as straw. Hence, a detailed understanding of the metabolic processes during the steps of hydrolysis and acidogenesis is required to improve process control strategies. The fermentation products formed during the acidogenic fermentation of maize silage as a model substrate in a leach-bed process were determined by gas and liquid chromatography. The bacterial community dynamics was monitored by terminal restriction fragment length polymorphism analysis. The community profiles were correlated with the process data using multivariate statistics. The batch process comprised three metabolic phases characterized by different fermentation products. The bacterial community dynamics correlated with the production of the respective metabolites. In phase 1, lactic and acetic acid fermentations dominated. Accordingly, bacteria of the genera Lactobacillus and Acetobacter were detected. In phase 2, the metabolic pathways shifted to butyric acid fermentation, accompanied by the production of hydrogen and carbon dioxide and a dominance of the genus Clostridium. In phase 3, phylotypes affiliated with Ruminococcaceae and Lachnospiraceae prevailed, accompanied by the formation of caproic and acetic acids, and a high gas production rate. A clostridial butyric type of fermentation was predominant in the acidogenic fermentation of maize silage, whereas propionic-type fermentation was marginal. As the metabolite composition resulting from acidogenesis affects the subsequent methanogenic performance, process control should focus on hydrolysis/acidogenesis when solid substrates are digested. (orig.)

  9. Summer investigations into the metabolic diversity of the microbial world. Progress report, May 5, 1992--April 30, 1993

    Energy Technology Data Exchange (ETDEWEB)

    Breznak, J.; Dworkin, M.

    1993-05-17

    The philosophy of the course described here is to underscore the essence of microbiology which is diversity>: diversity of morphology and cellular development, behavior, and metabolic and physiological functions. Emphasis is on microbes other than those customarily covered in conventional microbiology courses and includes: the archaebacteria, extremophiles, and array of obligate anaerobes, various phototrophs, and those microbes exhibiting complex developmental cycles. Also included are microbes carrying out a variety of transformations of organic and inorganic compounds, as well as those which normally occur in symbiotic association with other microbes or with higher forms of life.

  10. Metaproteome analysis to determine the metabolically active part of a thermophilic microbial community producing biogas from agricultural biomass.

    Science.gov (United States)

    Hanreich, Angelika; Heyer, Robert; Benndorf, Dirk; Rapp, Erdmann; Pioch, Markus; Reichl, Udo; Klocke, Michael

    2012-07-01

    Complex consortia of microorganisms are responsible for biogas production. A lot of information about the taxonomic structure and enzymatic potential of such communities has been collected by a variety of gene-based approaches, yet little is known about which of all the assumable metabolic pathways are active throughout the process of biogas formation. To tackle this problem, we established a protocol for the metaproteomic analysis of samples taken from biogas reactors fed with agricultural biomass. In contrast to previous studies where an anaerobic digester was fed with synthetic wastewater, the complex matrix in this study required the extraction of proteins with liquid phenol and the application of paper bridge loading for 2-dimensional gel electrophoresis. Proteins were subjected to nanoHPLC (high-performance liquid chromatography) coupled to tandem mass spectrometry for characterization. Several housekeeping proteins as well as methanogenesis-related enzymes were identified by a MASCOT search and de novo sequencing, which proved the feasibility of our approach. The establishment of such an approach is the basis for further metaproteomic studies of biogas-producing communities. In particular, the apparent status of metabolic activities within the communities can be monitored. The knowledge collected from such experiments could lead to further improvements of biogas production.

  11. Sensitive and substrate-specific detection of metabolically active microorganisms in natural microbial consortia using community isotope arrays.

    Science.gov (United States)

    Tourlousse, Dieter M; Kurisu, Futoshi; Tobino, Tomohiro; Furumai, Hiroaki

    2013-05-01

    The goal of this study was to develop and validate a novel fosmid-clone-based metagenome isotope array approach - termed the community isotope array (CIArray) - for sensitive detection and identification of microorganisms assimilating a radiolabeled substrate within complex microbial communities. More specifically, a sample-specific CIArray was used to identify anoxic phenol-degrading microorganisms in activated sludge treating synthetic coke-oven wastewater in a single-sludge predenitrification-nitrification process. Hybridization of the CIArray with DNA from the (14) C-phenol-amended sample indicated that bacteria assimilating (14) C-atoms, presumably directly from phenol, under nitrate-reducing conditions were abundant in the reactor, and taxonomic assignment of the fosmid clone end sequences suggested that they belonged to the Gammaproteobacteria. The specificity of the CIArray was validated by quantification of fosmid-clone-specific DNA in density-resolved DNA fractions from samples incubated with (13) C-phenol, which verified that all CIArray-positive probes stemmed from microorganisms that assimilated isotopically labeled carbon. This also demonstrated that the CIArray was more sensitive than DNA-SIP, as the former enabled positive detection at a phenol concentration that failed to yield a 'heavy' DNA fraction. Finally, two operational taxonomic units distantly related to marine Gammaproteobacteria were identified to account for more than half of 16S rRNA gene clones in the 'heavy' DNA library, corroborating the CIArray-based identification. © 2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  12. In Situ Analysis of Metabolic Characteristics Reveals the Key Yeast in the Spontaneous and Solid-State Fermentation Process of Chinese Light-Style Liquor

    Science.gov (United States)

    Kong, Yu; Wu, Qun; Zhang, Yan

    2014-01-01

    The in situ metabolic characteristics of the yeasts involved in spontaneous fermentation process of Chinese light-style liquor are poorly understood. The covariation between metabolic profiles and yeast communities in Chinese light-style liquor was modeled using the partial least square (PLS) regression method. The diversity of yeast species was evaluated by sequence analysis of the 26S ribosomal DNA (rDNA) D1/D2 domains of cultivable yeasts, and the volatile compounds in fermented grains were analyzed by gas chromatography (GC)-mass spectrometry (MS). Eight yeast species and 58 volatile compounds were identified, respectively. The modulation of 16 of these volatile compounds was associated with variations in the yeast population (goodness of prediction [Q2] > 20%). The results showed that Pichia anomala was responsible for the characteristic aroma of Chinese liquor, through the regulation of several important volatile compounds, such as ethyl lactate, octanoic acid, and ethyl tetradecanoate. Correspondingly, almost all of the compounds associated with P. anomala were detected in a pure culture of this yeast. In contrast to the PLS regression results, however, ethyl lactate and ethyl isobutyrate were not detected in the same pure culture, which indicated that some metabolites could be generated by P. anomala only when it existed in a community with other yeast species. Furthermore, different yeast communities provided different volatile patterns in the fermented grains, which resulted in distinct flavor profiles in the resulting liquors. This study could help identify the key yeast species involved in spontaneous fermentation and provide a deeper understanding of the role of individual yeast species in the community. PMID:24727269

  13. Fluorescence in situ hybridization mapping of six loci containing genes involved in the dioxin metabolism of domestic bovids.

    Science.gov (United States)

    Genualdo, Viviana; Spalenza, Veronica; Perucatti, Angela; Iannuzzi, Alessandra; Di Meo, Giulia Pia; Caputi-Jambrenghi, Annamaria; Vonghia, Gino; Rasero, Roberto; Nebbia, Carlo; Sacchi, Paola; Iannuzzi, Leopoldo

    2011-05-01

    Six loci containing genes involved in the dioxin metabolism (ARNT, AHR, CYP1A1, CYP1A2, CYP1B1 and AHRR) were assigned, for the first time, to cattle (Bos taurus, 2n = 60, BTA), river buffalo (Bubalus bubalis, 2n = 50, BBU), sheep (Ovis aries, 2n = 54, OAR) and goat (Capra hircus, 2n = 60, CHI) chromosomes by comparative FISH-mapping and R-banding using bovine BAC-clones. The following chromosome locations were found: ARNT to BTA3q21, BBU6q21, OAR1p21 and CHI3q21, AHR to BTA4q15, BBU8q15, OAR4q15 and CHI4q15; CYP1A1 and CYP1A2 to BTA21q17, BBU20q17, OAR18q17 and CHI21q17; CYP1B1 to BTA11q16, BBU12q22, OAR3p16 and CHI11q16, AHRR to BTA20q24, BBU19q24, OAR16q24 and CHI20q24. All loci were mapped at the same homoeologous chromosomes and chromosome bands of the four bovid species. Comparisons with corresponding human locations were also reported.

  14. Proof-of-Concept Study: Novel Microbially-Driven Fenton Reaction for In Situ Remediation of Groundwater Contaminated with 1,4-Dioxane, Tetrachloroethene (PCE) and Trichloroethene (TCE)

    Science.gov (United States)

    2014-09-17

    with 1,4-Dioxane, Tetrachloroethene (PCE) and Trichloroethene ( TCE ) SERDP Project ER-2305 September 2014 Thomas DiChristina Georgia...HO) radicals that degrade 1,4- dioxane, TCE , and PCE. In comparison to conventional (purely abiotic) Fenton reactions, the microbially-driven Fenton...reaction operates at circumneutral pH and does not require addition of exogenous H2O2 or UV irradiation to regenerate Fe(II). The 1,4-dioxane, TCE

  15. Methanosarcina Play an Important Role in Anaerobic Co-Digestion of the Seaweed Ulva lactuca: Taxonomy and Predicted Metabolism of Functional Microbial Communities.

    Directory of Open Access Journals (Sweden)

    Jamie A FitzGerald

    Full Text Available Macro-algae represent an ideal resource of third generation biofuels, but their use necessitates a refinement of commonly used anaerobic digestion processes. In a previous study, contrasting mixes of dairy slurry and the macro-alga Ulva lactuca were anaerobically digested in mesophilic continuously stirred tank reactors for 40 weeks. Higher proportions of U. lactuca in the feedstock led to inhibited digestion and rapid accumulation of volatile fatty acids, requiring a reduced organic loading rate. In this study, 16S pyrosequencing was employed to characterise the microbial communities of both the weakest (R1 and strongest (R6 performing reactors from the previous work as they developed over a 39 and 27-week period respectively. Comparing the reactor communities revealed clear differences in taxonomy, predicted metabolic orientation and mechanisms of inhibition, while constrained canonical analysis (CCA showed ammonia and biogas yield to be the strongest factors differentiating the two reactor communities. Significant biomarker taxa and predicted metabolic activities were identified for viable and failing anaerobic digestion of U. lactuca. Acetoclastic methanogens were inhibited early in R1 operation, followed by a gradual decline of hydrogenotrophic methanogens. Near-total loss of methanogens led to an accumulation of acetic acid that reduced performance of R1, while a slow decline in biogas yield in R6 could be attributed to inhibition of acetogenic rather than methanogenic activity. The improved performance of R6 is likely to have been as a result of the large Methanosarcina population, which enabled rapid removal of acetic acid, providing favourable conditions for substrate degradation.

  16. Methanosarcina Play an Important Role in Anaerobic Co-Digestion of the Seaweed Ulva lactuca: Taxonomy and Predicted Metabolism of Functional Microbial Communities.

    Science.gov (United States)

    FitzGerald, Jamie A; Allen, Eoin; Wall, David M; Jackson, Stephen A; Murphy, Jerry D; Dobson, Alan D W

    2015-01-01

    Macro-algae represent an ideal resource of third generation biofuels, but their use necessitates a refinement of commonly used anaerobic digestion processes. In a previous study, contrasting mixes of dairy slurry and the macro-alga Ulva lactuca were anaerobically digested in mesophilic continuously stirred tank reactors for 40 weeks. Higher proportions of U. lactuca in the feedstock led to inhibited digestion and rapid accumulation of volatile fatty acids, requiring a reduced organic loading rate. In this study, 16S pyrosequencing was employed to characterise the microbial communities of both the weakest (R1) and strongest (R6) performing reactors from the previous work as they developed over a 39 and 27-week period respectively. Comparing the reactor communities revealed clear differences in taxonomy, predicted metabolic orientation and mechanisms of inhibition, while constrained canonical analysis (CCA) showed ammonia and biogas yield to be the strongest factors differentiating the two reactor communities. Significant biomarker taxa and predicted metabolic activities were identified for viable and failing anaerobic digestion of U. lactuca. Acetoclastic methanogens were inhibited early in R1 operation, followed by a gradual decline of hydrogenotrophic methanogens. Near-total loss of methanogens led to an accumulation of acetic acid that reduced performance of R1, while a slow decline in biogas yield in R6 could be attributed to inhibition of acetogenic rather than methanogenic activity. The improved performance of R6 is likely to have been as a result of the large Methanosarcina population, which enabled rapid removal of acetic acid, providing favourable conditions for substrate degradation.

  17. Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life.

    Science.gov (United States)

    Brown, Christopher T; Sharon, Itai; Thomas, Brian C; Castelle, Cindy J; Morowitz, Michael J; Banfield, Jillian F

    2013-12-17

    The premature infant gut has low individual but high inter-individual microbial diversity compared with adults. Based on prior 16S rRNA gene surveys, many species from this environment are expected to be similar to those previously detected in the human microbiota. However, the level of genomic novelty and metabolic variation of strains found in the infant gut remains relatively unexplored. To study the stability and function of early microbial colonizers of the premature infant gut, nine stool samples were taken during the third week of life of a premature male infant delivered via Caesarean section. Metagenomic sequences were assembled and binned into near-complete and partial genomes, enabling strain-level genomic analysis of the microbial community.We reconstructed eleven near-complete and six partial bacterial genomes representative of the key members of the microbial community. Twelve of these genomes share >90% putative ortholog amino acid identity with reference genomes. Manual curation of the assembly of one particularly novel genome resulted in the first essentially complete genome sequence (in three pieces, the order of which could not be determined due to a repeat) for Varibaculum cambriense (strain Dora), a medically relevant species that has been implicated in abscess formation.During the period studied, the microbial community undergoes a compositional shift, in which obligate anaerobes (fermenters) overtake Escherichia coli as the most abundant species. Other species remain stable, probably due to their ability to either respire anaerobically or grow by fermentation, and their capacity to tolerate fluctuating levels of oxygen. Metabolic predictions for V. cambriense suggest that, like other members of the microbial community, this organism is able to process various sugar substrates and make use of multiple different electron acceptors during anaerobic respiration. Genome comparisons within the family Actinomycetaceae reveal important differences

  18. Involvement of gut microbial fermentation in the metabolic alterations occurring in n-3 polyunsaturated fatty acids-depleted mice

    Directory of Open Access Journals (Sweden)

    Carpentier Yvon A

    2011-06-01

    Full Text Available Abstract Backround Western diet is characterized by an insufficient n-3 polyunsaturated fatty acid (PUFA consumption which is known to promote the pathogenesis of several diseases. We have previously observed that mice fed with a diet poor in n-3 PUFA for two generations exhibit hepatic steatosis together with a decrease in body weight. The gut microbiota contributes to the regulation of host energy metabolism, due to symbiotic relationship with fermentable nutrients provided in the diet. In this study, we have tested the hypothesis that perturbations of the gut microbiota contribute to the metabolic alterations occurring in mice fed a diet poor in n-3 PUFA for two generations (n-3/- mice. Methods C57Bl/6J mice fed with a control or an n-3 PUFA depleted diet for two generations were supplemented with prebiotic (inulin-type Fructooligosaccharides, FOS, 0.20 g/day/mice during 24 days. Results n-3/-mice exhibited a marked drop in caecum weight, a decrease in lactobacilli and an increase in bifidobacteria in the caecal content as compared to control mice (n-3/+ mice. Dietary supplementation with FOS for 24 days was sufficient to increase caecal weight and bifidobacteria count in both n-3/+ and n-3/-mice. Moreover, FOS increased lactobacilli content in n-3/-mice, whereas it decreased their level in n-3/+ mice. Interestingly, FOS treatment promoted body weight gain in n-3/-mice by increasing energy efficiency. In addition, FOS treatment decreased fasting glycemia and lowered the higher expression of key factors involved in the fatty acid catabolism observed in the liver of n-3/-mice, without lessening steatosis. Conclusions the changes in the gut microbiota composition induced by FOS are different depending on the type of diet. We show that FOS may promote lactobacilli and counteract the catabolic status induced by n-3 PUFA depletion in mice, thereby contributing to restore efficient fat storage.

  19. Novel mode of microbial energy metabolism: organic carbon oxidation coupled to dissimilatory reduction of iron or manganese.

    Science.gov (United States)

    Lovley, D R; Phillips, E J

    1988-06-01

    A dissimilatory Fe(III)- and Mn(IV)-reducing microorganism was isolated from freshwater sediments of the Potomac River, Maryland. The isolate, designated GS-15, grew in defined anaerobic medium with acetate as the sole electron donor and Fe(III), Mn(IV), or nitrate as the sole electron acceptor. GS-15 oxidized acetate to carbon dioxide with the concomitant reduction of amorphic Fe(III) oxide to magnetite (Fe(3)O(4)). When Fe(III) citrate replaced amorphic Fe(III) oxide as the electron acceptor, GS-15 grew faster and reduced all of the added Fe(III) to Fe(II). GS-15 reduced a natural amorphic Fe(III) oxide but did not significantly reduce highly crystalline Fe(III) forms. Fe(III) was reduced optimally at pH 6.7 to 7 and at 30 to 35 degrees C. Ethanol, butyrate, and propionate could also serve as electron donors for Fe(III) reduction. A variety of other organic compounds and hydrogen could not. MnO(2) was completely reduced to Mn(II), which precipitated as rhodochrosite (MnCO(3)). Nitrate was reduced to ammonia. Oxygen could not serve as an electron acceptor, and it inhibited growth with the other electron acceptors. This is the first demonstration that microorganisms can completely oxidize organic compounds with Fe(III) or Mn(IV) as the sole electron acceptor and that oxidation of organic matter coupled to dissimilatory Fe(III) or Mn(IV) reduction can yield energy for microbial growth. GS-15 provides a model for how enzymatically catalyzed reactions can be quantitatively significant mechanisms for the reduction of iron and manganese in anaerobic environments.

  20. Insights from quantitative metaproteomics and protein-stable isotope probing into microbial ecology.

    Science.gov (United States)

    von Bergen, Martin; Jehmlich, Nico; Taubert, Martin; Vogt, Carsten; Bastida, Felipe; Herbst, Florian-Alexander; Schmidt, Frank; Richnow, Hans-Hermann; Seifert, Jana

    2013-10-01

    The recent development of metaproteomics has enabled the direct identification and quantification of expressed proteins from microbial communities in situ, without the need for microbial enrichment. This became possible by (1) significant increases in quality and quantity of metagenome data and by improvements of (2) accuracy and (3) sensitivity of modern mass spectrometers (MS). The identification of physiologically relevant enzymes can help to understand the role of specific species within a community or an ecological niche. Beside identification, relative and absolute quantitation is also crucial. We will review label-free and label-based methods of quantitation in MS-based proteome analysis and the contribution of quantitative proteome data to microbial ecology. Additionally, approaches of protein-based stable isotope probing (protein-SIP) for deciphering community structures are reviewed. Information on the species-specific metabolic activity can be obtained when substrates or nutrients are labeled with stable isotopes in a protein-SIP approach. The stable isotopes ((13)C, (15)N, (36)S) are incorporated into proteins and the rate of incorporation can be used for assessing the metabolic activity of the corresponding species. We will focus on the relevance of the metabolic and phylogenetic information retrieved with protein-SIP studies and for detecting and quantifying the carbon flux within microbial consortia. Furthermore, the combination of protein-SIP with established tools in microbial ecology such as other stable isotope probing techniques are discussed.

  1. Methylobacterium genome sequences: a reference blueprint to investigate microbial metabolism of C1 compounds from natural and industrial sources.

    Science.gov (United States)

    Vuilleumier, Stéphane; Chistoserdova, Ludmila; Lee, Ming-Chun; Bringel, Françoise; Lajus, Aurélie; Zhou, Yang; Gourion, Benjamin; Barbe, Valérie; Chang, Jean; Cruveiller, Stéphane; Dossat, Carole; Gillett, Will; Gruffaz, Christelle; Haugen, Eric; Hourcade, Edith; Levy, Ruth; Mangenot, Sophie; Muller, Emilie; Nadalig, Thierry; Pagni, Marco; Penny, Christian; Peyraud, Rémi; Robinson, David G; Roche, David; Rouy, Zoé; Saenampechek, Channakhone; Salvignol, Grégory; Vallenet, David; Wu, Zaining; Marx, Christopher J; Vorholt, Julia A; Olson, Maynard V; Kaul, Rajinder; Weissenbach, Jean; Médigue, Claudine; Lidstrom, Mary E

    2009-01-01

    Methylotrophy describes the ability of organisms to grow on reduced organic compounds without carbon-carbon bonds. The genomes of two pink-pigmented facultative methylotrophic bacteria of the Alpha-proteobacterial genus Methylobacterium, the reference species Methylobacterium extorquens strain AM1 and the dichloromethane-degrading strain DM4, were compared. The 6.88 Mb genome of strain AM1 comprises a 5.51 Mb chromosome, a 1.26 Mb megaplasmid and three plasmids, while the 6.12 Mb genome of strain DM4 features a 5.94 Mb chromosome and two plasmids. The chromosomes are highly syntenic and share a large majority of genes, while plasmids are mostly strain-specific, with the exception of a 130 kb region of the strain AM1 megaplasmid which is syntenic to a chromosomal region of strain DM4. Both genomes contain large sets of insertion elements, many of them strain-specific, suggesting an important potential for genomic plasticity. Most of the genomic determinants associated with methylotrophy are nearly identical, with two exceptions that illustrate the metabolic and genomic versatility of Methylobacterium. A 126 kb dichloromethane utilization (dcm) gene cluster is essential for the ability of strain DM4 to use DCM as the sole carbon and energy source for growth and is unique to strain DM4. The methylamine utilization (mau) gene cluster is only found in strain AM1, indicating that strain DM4 employs an alternative system for growth with methylamine. The dcm and mau clusters represent two of the chromosomal genomic islands (AM1: 28; DM4: 17) that were defined. The mau cluster is flanked by mobile elements, but the dcm cluster disrupts a gene annotated as chelatase and for which we propose the name "island integration determinant" (iid). These two genome sequences provide a platform for intra- and interspecies genomic comparisons in the genus Methylobacterium, and for investigations of the adaptive mechanisms which allow bacterial lineages to acquire methylotrophic

  2. Studies of the Ecophysiology of Single Cells in Microbial Communities by (Quantitative) Microautoradiography and Fluorescence In Situ Hybridization (MAR-FISH)

    DEFF Research Database (Denmark)

    Nierychlo, Marta; Nielsen, Jeppe Lund; Nielsen, Per Halkjær

    2015-01-01

    image analysis (MARQuant). Quantification of MAR signals can answer more specific questions regarding metabolic activity and function of the microbes. Here, we give an overview of how to use MAR-FISH in various ecosystems and provide a detailed protocol for MAR-FISH, including sampling, incubation...

  3. Microbial community evolution of black and stinking rivers during in situ remediation through micro-nano bubble and submerged resin floating bed technology.

    Science.gov (United States)

    Sun, Yanmei; Wang, Shiwei; Niu, Junfeng

    2018-06-01

    Microbes play important roles during river remediation and the interaction mechanism illustration between microorganisms and sewage is of great significance to improve restoration technology. In this study, micro-nano bubble and submerged resin floating bed composite technology (MBSR) was firstly used to restore two black and stinking urban rivers. After restoration, the water pollution indices such as dissolved oxygen (DO), ammonia nitrogen (NH 4 + -N), total phosphorous (TP), chemical oxygen demand (COD Cr ), water clarity, and the number of facial coliform were significantly improved. Microbial community composition and relative abundance both varied and more aerobic microbes emerged after remediation. The microbial changes showed correlation with DO, NH 4 + -N, TP and COD Cr of the rivers. In summary, the MBSR treatment improved the physiochemical properties of the two black and stinking urban rivers probably through oxygen enrichment of micro-nano bubble and adsorption of submerged resin floating bed, which thereby stimulated functional microbes to degrade pollutants. Copyright © 2018 Elsevier Ltd. All rights reserved.

  4. Solar energy powered microbial fuel cell with a reversible bioelectrode

    NARCIS (Netherlands)

    Strik, D.P.B.T.B.; Hamelers, H.V.M.; Buisman, C.J.N.

    2010-01-01

    The solar energy powered microbial fuel cell is an emerging technology for electricity generation via electrochemically active microorganisms fueled by solar energy via in situ photosynthesized metabolites from algae, cyanobacteria, or living higher plants. A general problem with microbial fuel

  5. Methylobacterium genome sequences: a reference blueprint to investigate microbial metabolism of C1 compounds from natural and industrial sources.

    Directory of Open Access Journals (Sweden)

    Stéphane Vuilleumier

    Full Text Available Methylotrophy describes the ability of organisms to grow on reduced organic compounds without carbon-carbon bonds. The genomes of two pink-pigmented facultative methylotrophic bacteria of the Alpha-proteobacterial genus Methylobacterium, the reference species Methylobacterium extorquens strain AM1 and the dichloromethane-degrading strain DM4, were compared.The 6.88 Mb genome of strain AM1 comprises a 5.51 Mb chromosome, a 1.26 Mb megaplasmid and three plasmids, while the 6.12 Mb genome of strain DM4 features a 5.94 Mb chromosome and two plasmids. The chromosomes are highly syntenic and share a large majority of genes, while plasmids are mostly strain-specific, with the exception of a 130 kb region of the strain AM1 megaplasmid which is syntenic to a chromosomal region of strain DM4. Both genomes contain large sets of insertion elements, many of them strain-specific, suggesting an important potential for genomic plasticity. Most of the genomic determinants associated with methylotrophy are nearly identical, with two exceptions that illustrate the metabolic and genomic versatility of Methylobacterium. A 126 kb dichloromethane utilization (dcm gene cluster is essential for the ability of strain DM4 to use DCM as the sole carbon and energy source for growth and is unique to strain DM4. The methylamine utilization (mau gene cluster is only found in strain AM1, indicating that strain DM4 employs an alternative system for growth with methylamine. The dcm and mau clusters represent two of the chromosomal genomic islands (AM1: 28; DM4: 17 that were defined. The mau cluster is flanked by mobile elements, but the dcm cluster disrupts a gene annotated as chelatase and for which we propose the name "island integration determinant" (iid.These two genome sequences provide a platform for intra- and interspecies genomic comparisons in the genus Methylobacterium, and for investigations of the adaptive mechanisms which allow bacterial lineages to acquire

  6. Binding of heavy metal ions in aggregates of microbial cells, EPS and biogenic iron minerals measured in-situ using metal- and glycoconjugates-specific fluorophores

    Science.gov (United States)

    Hao, Likai; Guo, Yuan; Byrne, James M.; Zeitvogel, Fabian; Schmid, Gregor; Ingino, Pablo; Li, Jianli; Neu, Thomas R.; Swanner, Elizabeth D.; Kappler, Andreas; Obst, Martin

    2016-05-01

    Aggregates consisting of bacterial cells, extracellular polymeric substances (EPS) and Fe(III) minerals formed by Fe(II)-oxidizing bacteria are common at bulk or microscale chemical interfaces where Fe cycling occurs. The high sorption capacity and binding capacity of cells, EPS, and minerals controls the mobility and fate of heavy metals. However, it remains unclear to which of these component(s) the metals will bind in complex aggregates. To clarify this question, the present study focuses on 3D mapping of heavy metals sorbed to cells, glycoconjugates that comprise the majority of EPS constituents, and Fe(III) mineral aggregates formed by the phototrophic Fe(II)-oxidizing bacteria Rhodobacter ferrooxidans SW2 using confocal laser scanning microscopy (CLSM) in combination with metal- and glycoconjugates-specific fluorophores. The present study evaluated the influence of glycoconjugates, microbial cell surfaces, and (biogenic) Fe(III) minerals, and the availability of ferrous and ferric iron on heavy metal sorption. Analyses in this study provide detailed knowledge on the spatial distribution of metal ions in the aggregates at the sub-μm scale, which is essential to understand the underlying mechanisms of microbe-mineral-metal interactions. The heavy metals (Au3+, Cd2+, Cr3+, CrO42-, Cu2+, Hg2+, Ni2+, Pd2+, tributyltin (TBT) and Zn2+) were found mainly sorbed to cell surfaces, present within the glycoconjugates matrix, and bound to the mineral surfaces, but not incorporated into the biogenic Fe(III) minerals. Statistical analysis revealed that all ten heavy metals tested showed relatively similar sorption behavior that was affected by the presence of sorbed ferrous and ferric iron. Results in this study showed that in addition to the mineral surfaces, both bacterial cell surfaces and the glycoconjugates provided most of sorption sites for heavy metals. Simultaneously, ferrous and ferric iron ions competed with the heavy metals for sorption sites on the organic

  7. Combining Push Pull Tracer Tests and Microbial DNA and mRNA Analysis to Assess In-Situ Groundwater Nitrate Transformations

    Science.gov (United States)

    Henson, W.; Graham, W. D.; Huang, L.; Ogram, A.

    2015-12-01

    Nitrogen transformation mechanisms in the Upper Floridan Aquifer (UFA) are still poorly understood because of karst aquifer complexity and spatiotemporal variability in nitrate and carbon loading. Transformation rates have not been directly measured in the aquifer. This study quantifies nitrate-nitrogen transformation potential in the UFA using single well push-pull tracer injection (PPT) experiments combined with microbial characterization of extracted water via qPCR and RT-qPCR of selected nitrate reduction genes. Tracer tests with chloride and nitrate ± carbon were executed in two wells representing anoxic and oxic geochemical end members in a spring groundwater contributing area. A significant increase in number of microbes with carbon addition suggests stimulated growth. Increases in the activities of denitrification genes (nirK and nirS) as measured by RT-qPCR were not observed. However, only microbes suspended in the tracer were obtained, ignoring effects of aquifer material biofilms. Increases in nrfA mRNA and ammonia concentrations were observed, supporting Dissimilatory Reduction of Nitrate to Ammonia (DNRA) as a reduction mechanism. In the oxic aquifer, zero order nitrate loss rates ranged from 32 to 89 nmol /L*hr with no added carbon and 90 to 240 nmol /L*hr with carbon. In the anoxic aquifer, rates ranged from 18 to 95 nmol /L*hr with no added carbon and 34 to 207 nmol /L*hr with carbon. These loss rates are low; 13 orders of magnitude less than the loads applied in the contributing area each year, however they do indicate that losses can occur in oxic and anoxic aquifers with and without carbon. These rates may include, ammonia adsorption, uptake, or denitrification in aquifer material biofilms. Rates with and without carbon addition for both aquifers were similar, suggesting aquifer redox state and carbon availability alone are insufficient to predict response to nutrient additions without characterization of microbial response. Surprisingly, these

  8. Measurement of microbial activity in soil by colorimetric observation of in situ dye reduction: an approach to detection of extraterrestrial life

    Directory of Open Access Journals (Sweden)

    Barnes Bruce

    2002-07-01

    Full Text Available Abstract Background Detecting microbial life in extraterrestrial locations is a goal of space exploration because of ecological and health concerns about possible contamination of other planets with earthly organisms, and vice versa. Previously we suggested a method for life detection based on the fact that living entities require a continual input of energy accessed through coupled oxidations and reductions (an electron transport chain. We demonstrated using earthly soils that the identification of extracted components of electron transport chains is useful for remote detection of a chemical signature of life. The instrument package developed used supercritical carbon dioxide for soil extraction, followed by chromatography or electrophoresis to separate extracted compounds, with final detection by voltammetry and tandem mass-spectrometry. Results Here we used Earth-derived soils to develop a related life detection system based on direct observation of a biological redox signature. We measured the ability of soil microbial communities to reduce artificial electron acceptors. Living organisms in pure culture and those naturally found in soil were shown to reduce 2,3-dichlorophenol indophenol (DCIP and the tetrazolium dye 2,3-bis(2-methoxy-4-nitro-5-sulfophenyl-2H-tetrazolium-5-carboxanilide inner salt (XTT. Uninoculated or sterilized controls did not reduce the dyes. A soil from Antarctica that was determined by chemical signature and DNA analysis to be sterile also did not reduce the dyes. Conclusion Observation of dye reduction, supplemented with extraction and identification of only a few specific signature redox-active biochemicals such as porphyrins or quinones, provides a simplified means to detect a signature of life in the soils of other planets or their moons.

  9. Effect of forage conservation method on ruminal lipid metabolism and microbial ecology in lactating cows fed diets containing a 60:40 forage-to-concentrate ratio.

    Science.gov (United States)

    Halmemies-Beauchet-Filleau, A; Kairenius, P; Ahvenjärvi, S; Crosley, L K; Muetzel, S; Huhtanen, P; Vanhatalo, A; Toivonen, V; Wallace, R J; Shingfield, K J

    2013-04-01

    The effect of forage conservation method on ruminal lipid metabolism and microbial ecology was examined in 2 complementary experiments in cows. Treatments comprised fresh chopped grass, barn-dried hay, or untreated (UTS) or formic acid-treated silage (FAS) prepared from the same grass sward. Preparation of conserved forages coincided with the collection of samples from cows offered fresh grass. In the first experiment, 5 multiparous Finnish Ayrshire cows (229 d in milk) were used to compare the effects of feeding diets based on grass followed by hay during 2 consecutive 14-d periods separated by a 5-d transition during which extensively wilted grass was fed. In the second experiment, 5 multiparous Finnish Ayrshire cows (53 d in milk) were assigned to 1 of 2 blocks and allocated treatments according to a replicated 3×3 Latin square design with 14-d periods to compare the effects of hay, UTS, and FAS. Cows received 7 or 9 kg/d of the same concentrate in experiments 1 and 2, respectively. Conservation of grass by drying, but not ensiling, decreased forage fatty acid content primarily due to losses of 18:2n-6 and 18:3n-3. Compared with grass, feeding hay had no effect on dry matter intake (DMI), rumen pH, or fermentation characteristics, other than increasing ammonia content, but lowered whole-tract organic matter and fiber digestibility (experiment 1). Relative to hay, silage increased DMI, rumen volatile fatty acid (VFA) concentrations, and molar proportions of butyrate, and decreased molar acetate proportions (experiment 2). Compared with UTS, FAS increased DMI, had no effect on rumen ammonia or VFA concentrations, but tended to lower rumen pH and the molar ratio of lipogenic to glucogenic VFA. Conservation method had no substantial effect on ruminal or whole-tract digestibility coefficients. Compared with fresh grass and silages, hay decreased lipolysis and biohydrogenation (BH) of dietary unsaturates in the rumen, resulting in similar flows of 18:2n-6 and 18:3n-3

  10. MICROBIAL MATS - A JOINT VENTURE

    NARCIS (Netherlands)

    VANGEMERDEN, H

    Microbial mats characteristically are dominated by a few functional groups of microbes: cyanobacteria, colorless sulfur bacteria, purple sulfur bacteria, and sulfate-reducing bacteria. Their combined metabolic activities result in steep environmental microgradients, particularly of oxygen and

  11. Functional gene diversity of soil microbial communities from five oil-contaminated fields in China.

    Science.gov (United States)

    Liang, Yuting; Van Nostrand, Joy D; Deng, Ye; He, Zhili; Wu, Liyou; Zhang, Xu; Li, Guanghe; Zhou, Jizhong

    2011-03-01

    To compare microbial functional diversity in different oil-contaminated fields and to know the effects of oil contaminant and environmental factors, soil samples were taken from typical oil-contaminated fields located in five geographic regions of China. GeoChip, a high-throughput functional gene array, was used to evaluate the microbial functional genes involved in contaminant degradation and in other major biogeochemical/metabolic processes. Our results indicated that the overall microbial community structures were distinct in each oil-contaminated field, and samples were clustered by geographic locations. The organic contaminant degradation genes were most abundant in all samples and presented a similar pattern under oil contaminant stress among the five fields. In addition, alkane and aromatic hydrocarbon degradation genes such as monooxygenase and dioxygenase were detected in high abundance in the oil-contaminated fields. Canonical correspondence analysis indicated that the microbial functional patterns were highly correlated to the local environmental variables, such as oil contaminant concentration, nitrogen and phosphorus contents, salt and pH. Finally, a total of 59% of microbial community variation from GeoChip data can be explained by oil contamination, geographic location and soil geochemical parameters. This study provided insights into the in situ microbial functional structures in oil-contaminated fields and discerned the linkages between microbial communities and environmental variables, which is important to the application of bioremediation in oil-contaminated sites.

  12. In-situ growing NiCo2O4 nanoplatelets on carbon cloth as binder-free catalyst air-cathode for high-performance microbial fuel cells

    International Nuclear Information System (INIS)

    Cao, Chun; Wei, Liling; Wang, Gang; Shen, Jianquan

    2017-01-01

    Highlights: • NiCo 2 O 4 nanoplatelets were in-situ growing on carbon cloth as ORR catalyst in biofuel cells. • Binder-free cathode with the lower internal resistance. • Binder-free cathode was low-cost. • NiCo 2 O 4 -CFC shows better power generation performance than Pt/C. - Abstract: Air-cathode microbial fuel cells (MFCs) was one of most promising sustainable new energy device as well as an advanced sewage treatment technology, and thoroughly studies have been devoted to lower its cost and enhance its power generation. Herein, a binder-free and low-cost catalyst air-cathode was fabricated by in-situ electro-deposition of NiCo 2 O 4 nanoplatelets on carbon cloth, followed by feasible calcinations. The catalytic activity of catalyst air-cathode was optimized by varying the deposition time. And the optimal air-cathode was installed in real MFCs and exhibited distinct maximum out-put power density (645 ± 6 mW m −2 ), which was 12.96% higher than commercial Pt/C (571 ± 11 mW m −2 ). Noted that its remarkable electricity generation performance in MFCs should absolutely attributed to the well catalytic activity for oxygen reduction reaction, and more likely ascribed to its low internal resistance since binder-free catalyst air-cathode can facilitate the electron/charge transfer process. Therefore, it was an efficient strategy to improve the electricity generation performance of MFCs by using this binder-free catalyst air-cathode, which was also potential for application in many other electrochemical devices.

  13. Effects of feeding dry or modified wet distillers grains with solubles with or without supplemental calcium oxide on ruminal metabolism and microbial enzymatic activity of beef cattle.

    Science.gov (United States)

    Schroeder, A R; Iakiviak, M; Felix, T L

    2014-09-01

    concentration were found when comparing DGS type or supplemental CaO. In conclusion, the type of DGS fed had little effect on ruminal metabolism. Even though CaO increased ruminal pH and cellulase activity at some times postfeeding, it was not enough to affect in situ fiber disappearance.

  14. Microbial diversity and impact on carbonate geochemistry across a changing geochemical gradient in a karst aquifer.

    Science.gov (United States)

    Gray, Cassie J; Engel, Annette S

    2013-02-01

    Although microbes are known to influence karst (carbonate) aquifer ecosystem-level processes, comparatively little information is available regarding the diversity of microbial activities that could influence water quality and geological modification. To assess microbial diversity in the context of aquifer geochemistry, we coupled 16S rRNA Sanger sequencing and 454 tag pyrosequencing to in situ microcosm experiments from wells that cross the transition from fresh to saline and sulfidic water in the Edwards Aquifer of central Texas, one of the largest karst aquifers in the United States. The distribution of microbial groups across the transition zone correlated with dissolved oxygen and sulfide concentration, and significant variations in community composition were explained by local carbonate geochemistry, specifically calcium concentration and alkalinity. The waters were supersaturated with respect to prevalent aquifer minerals, calcite and dolomite, but in situ microcosm experiments containing these minerals revealed significant mass loss from dissolution when colonized by microbes. Despite differences in cell density on the experimental surfaces, carbonate loss was greater from freshwater wells than saline, sulfidic wells. However, as cell density increased, which was correlated to and controlled by local geochemistry, dissolution rates decreased. Surface colonization by metabolically active cells promotes dissolution by creating local disequilibria between bulk aquifer fluids and mineral surfaces, but this also controls rates of karst aquifer modification. These results expand our understanding of microbial diversity in karst aquifers and emphasize the importance of evaluating active microbial processes that could affect carbonate weathering in the subsurface.

  15. Co-digestion of manure and whey for in situ biogas upgrading by the addition of H2: process performance and microbial insights

    DEFF Research Database (Denmark)

    Luo, Gang; Angelidaki, Irini

    2013-01-01

    composition. The best biogas composition (75:6.6:18.4) was obtained at stirring speed 150 rpmand using ceramic diffuser, while the biogas in the control reactor consisted of CH4 and CO2 at a ratio of 55:45. The consumed hydrogen was almost completely converted to CH4, and there was no significant accumulation......In situ biogas upgrading was conducted by introducing H2 directly to the anaerobic reactor. As H2 addition is associated with consumption of the CO2 in the biogas reactor, pH increased to higher than 8.0 when manure alone was used as substrate. By co-digestion of manure with acidic whey, the p......H in the anaerobic reactor with the addition of hydrogen could be maintained below 8.0, which did not have inhibition to the anaerobic process. The H2 distribution systems (diffusers with different pore sizes) and liquid mixing intensities were demonstrated to affect the gas-liquid mass transfer of H2 and the biogas...

  16. Effects of Pulp and Na-Bentonite Amendments on the Mobility of Trace Elements, Soil Enzymes Activity and Microbial Parameters under Ex Situ Aided Phytostabilization

    Science.gov (United States)

    Wasilkowski, Daniel; Mrozik, Agnieszka

    2017-01-01

    The objective of this study was to explore the potential use of pulp (by-product) from coffee processing and Na-bentonite (commercial product) for minimizing the environmental risk of Zn, Pb and Cd in soil collected from a former mine and zinc-lead smelter. The effects of soil amendments on the physicochemical properties of soil, the structural and functional diversity of the soil microbiome as well as soil enzymes were investigated. Moreover, biomass of Festuca arundinacea Schreb. (cultivar Asterix) and the uptake of trace elements in plant tissues were studied. The outdoor pot set contained the following soils: control soil (initial), untreated soil (without additives) with grass cultivation and soils treated (with additives) with and without plant development. All of the selected parameters were measured at the beginning of the experiment (t0), after 2 months of chemical stabilization (t2) and at the end of the aided phytostabilization process (t14). The obtained results indicated that both amendments efficiently immobilized the bioavailable fractions of Zn (87–91%) and Cd (70–83%) at t14; however, they were characterized by a lower ability to bind Pb (33–50%). Pulp and Na-bentonite drastically increased the activity of dehydrogenase (70- and 12-fold, respectively) at t14, while the activities of urease, acid and alkaline phosphatases differed significantly depending on the type of material that was added into the soil. Generally, the activities of these enzymes increased; however, the increase was greater for pulp (3.5-6-fold) than for the Na-bentonite treatment (1.3–2.2-fold) as compared to the control. Soil additives significantly influenced the composition and dynamics of the soil microbial biomass over the experiment. At the end, the contribution of microbial groups could be ordered as follows: gram negative bacteria, fungi, gram positive bacteria, actinomycetes regardless of the type of soil enrichment. Conversely, the shift in the functional

  17. Effects of Pulp and Na-Bentonite Amendments on the Mobility of Trace Elements, Soil Enzymes Activity and Microbial Parameters under Ex Situ Aided Phytostabilization.

    Directory of Open Access Journals (Sweden)

    Daniel Wasilkowski

    Full Text Available The objective of this study was to explore the potential use of pulp (by-product from coffee processing and Na-bentonite (commercial product for minimizing the environmental risk of Zn, Pb and Cd in soil collected from a former mine and zinc-lead smelter. The effects of soil amendments on the physicochemical properties of soil, the structural and functional diversity of the soil microbiome as well as soil enzymes were investigated. Moreover, biomass of Festuca arundinacea Schreb. (cultivar Asterix and the uptake of trace elements in plant tissues were studied. The outdoor pot set contained the following soils: control soil (initial, untreated soil (without additives with grass cultivation and soils treated (with additives with and without plant development. All of the selected parameters were measured at the beginning of the experiment (t0, after 2 months of chemical stabilization (t2 and at the end of the aided phytostabilization process (t14. The obtained results indicated that both amendments efficiently immobilized the bioavailable fractions of Zn (87-91% and Cd (70-83% at t14; however, they were characterized by a lower ability to bind Pb (33-50%. Pulp and Na-bentonite drastically increased the activity of dehydrogenase (70- and 12-fold, respectively at t14, while the activities of urease, acid and alkaline phosphatases differed significantly depending on the type of material that was added into the soil. Generally, the activities of these enzymes increased; however, the increase was greater for pulp (3.5-6-fold than for the Na-bentonite treatment (1.3-2.2-fold as compared to the control. Soil additives significantly influenced the composition and dynamics of the soil microbial biomass over the experiment. At the end, the contribution of microbial groups could be ordered as follows: gram negative bacteria, fungi, gram positive bacteria, actinomycetes regardless of the type of soil enrichment. Conversely, the shift in the functional

  18. Effects of Synchronization of Carbohydrate and Protein Supply in Total Mixed Ration with Korean Rice Wine Residue on Ruminal Fermentation, Nitrogen Metabolism and Microbial Protein Synthesis in Holstein Steers

    Directory of Open Access Journals (Sweden)

    Min Yu Piao

    2012-11-01

    Full Text Available Three Holstein steers in the growing phase, each with a ruminal cannula, were used to test the hypothesis that the synchronization of the hourly rate of carbohydrate and nitrogen (N released in the rumen would increase the amount of retained nitrogen for growth and thus improve the efficiency of microbial protein synthesis (EMPS. In Experiment 1, in situ degradability coefficients of carbohydrate and N in feeds including Korean rice wine residue (RWR were determined. In Experiment 2, three total mixed ration (TMR diets having different rates of carbohydrate and N release in the rumen were formulated using the in situ degradability of the feeds. All diets were made to contain similar contents of crude protein (CP and neutral detergent fiber (NDF but varied in their hourly pattern of nutrient release. The synchrony index of the three TMRs was 0.51 (LS, 0.77 (MS and 0.95 (HS, respectively. The diets were fed at a restricted level (2% of the animal’s body weight in a 3×3 Latin-square design. Synchronizing the hourly supply of energy and N in the rumen did not significantly alter the digestibility of dry matter, organic matter, crude protein, NDF or acid detergent fiber (ADF (p>0.05. The ruminal NH3-N content of the LS group at three hours after feeding was significantly higher (p0.05. In addition, the purine derivative (PD excretion in urine and microbial-N production (MN among the three groups were not significantly different (p>0.05. In conclusion, synchronizing dietary energy and N supply to the rumen did not have a major effect on nutrient digestion or microbial protein synthesis (MPS in Holstein steers.

  19. Simultaneous monitoring of biofilm growth, microbial activity, and inorganic deposits on surfaces with an in situ, online, real-time, non-destructive, optical sensor.

    Science.gov (United States)

    Strathmann, Martin; Mittenzwey, Klaus-Henrik; Sinn, Gert; Papadakis, Wassilios; Flemming, Hans-Curt

    2013-01-01

    Deposits on surfaces in water-bearing systems, also known as 'fouling', can lead to substantial losses in the performance of industrial processes as well as a decreased product quality. Early detection and localization of such deposits can, to a considerable extent, save such losses. However, most of the surfaces that become fouled, for example, in process water pipes, membrane systems, power plants, and food and beverage industries, are difficult to access and analyses conducted on the water phase do not reveal the site or extent of deposits. Furthermore, it is of interest to distinguish biological from non-biological deposits. Although they usually occur together, different countermeasures are necessary. Therefore, sensors are required that indicate the development of surface fouling in real-time, non-destructively, and in situ, preferably allowing for discrimination between chemical and/or biological deposits. In this paper, an optical deposit sensor is presented which fulfills these requirements. Based on multiple fluorescence excitation emission matrix analysis, it detects autofluorescence of amino acids as indicators of biomass. Autofluorescence of nicotinamide adenine dinucleotide + hydrogen is interpreted as an indicator of biological activity, thus it acts as a viability marker, making the method suited for assessing the efficacy of disinfection treatments. Scattering signals from abiotic deposits such as calcium carbonate or corrosion products can clearly be distinguished from biotic substances and monitored separately. The sensor provides an early warning of fouling, allowing for timely countermeasures to be deployed. It also provides an assessment of the success of cleaning treatments and is a promising tool for integrated antifouling strategies.

  20. Towards a universal microbial inoculum for dissolved organic carbon degradation experiments

    Science.gov (United States)

    Pastor, Ada; Catalán, Núria; Gutiérrez, Carmen; Nagar, Nupur; Casas-Ruiz, Joan P.; Obrador, Biel; von Schiller, Daniel; Sabater, Sergi; Petrovic, Mira; Borrego, Carles M.; Marcé, Rafael

    2017-04-01

    Dissolved organic carbon (DOC) is the largest biologically available pool of organic carbon in aquatic ecosystems and its degradation along the land-to-ocean continuum has implications for carbon cycling from local to global scales. DOC biodegradability is usually assessed by incubating filtered water inoculated with native microbial assemblages in the laboratory. However, the use of a native inoculum from several freshwaters, without having a microbial-tailored design, hampers our ability to tease apart the relative contribution of the factors driving DOC degradation from the effects of local microbial communities. The use of a standard microbial inoculum would allow researchers to disentangle the drivers of DOC degradation from the metabolic capabilities of microbial communities operating in situ. With this purpose, we designed a bacterial inoculum to be used in experiments of DOC degradation in freshwater habitats. The inoculum is composed of six bacterial strains that easily grow under laboratory conditions, possess a versatile metabolism and are able to grow under both aerobic and anaerobic conditions. The mixed inoculum showed higher DOC degradation rates than those from their isolated bacterial components and the consumption of organic substrates was consistently replicated. Moreover, DOC degradation rates obtained using the designed inoculum were responsive across a wide range of natural water types differing in DOC concentration and composition. Overall, our results show the potential of the designed inoculum as a tool to discriminate between the effects of environmental drivers and intrinsic properties of DOC on degradation dynamics.

  1. Final report for DOE Grant No. DE-SC0006609 - Persistence of Microbially Facilitated Calcite Precipitation as an in situ Treatment for Strontium-90

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Robert W. [Univ. of Idaho, Idaho Falls, ID (United States); Fujita, Yoshiko [Idaho National Lab. (INL), Idaho Falls, ID (United States); Hubbard, Susan S. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2013-11-15

    Subsurface radionuclide and metal contaminants throughout the U.S. Department of Energy (DOE) complex pose one of DOE's greatest challenges for long-term stewardship. One promising stabilization mechanism for divalent ions, such as the short-lived radionuclide 90Sr, is co-precipitation in calcite. We have previously found that nutrient addition can stimulate microbial ureolytic activity, that this activity accelerates calcite precipitation and co-precipitation of Sr, and that higher calcite precipitation rates can result in increased Sr partitioning. We have conducted integrated field, laboratory, and computational research to evaluate the relationships between ureolysis and calcite precipitation rates and trace metal partitioning under environmentally relevant conditions, and investigated the coupling between flow/flux manipulations and precipitate distribution. A field experimental campaign conducted at the Integrated Field Research Challenge (IFRC) site located at Rifle, CO was based on a continuous recirculation design; water extracted from a down-gradient well was amended with urea and molasses (a carbon and electron donor) and re-injected into an up-gradient well. The goal of the recirculation design and simultaneous injection of urea and molasses was to uniformly accelerate the hydrolysis of urea and calcite precipitation over the entire inter-wellbore zone. The urea-molasses recirculation phase lasted, with brief interruptions for geophysical surveys, for 12 days and was followed by long-term monitoring which continued for 13 months. A post experiment core located within the inter-wellbore zone was collected on day 321 and characterized with respect to cation exchange capacity, mineral carbonate content, urease activity, ureC gene abundance, extractable ammonium (a urea hydrolysis product) content, and the 13C isotopic composition of solid carbonates. It was also subjected to selective extractions for strontium and uranium. Result

  2. Influência do nitrogênio degradável no rúmen sobre a degradabilidade in situ, os parâmetros ruminais e a eficiência de síntese microbiana em novilhos alimentados com cana-de-açúcar Ruminal degradable nitrogen for steers fed sugar cane: in situ degradability, ruminal parameters and microbial synthesis efficiency

    Directory of Open Access Journals (Sweden)

    Roselene Nunes da Silveira

    2009-03-01

    Full Text Available Objetivou-se avaliar o efeito da deficiência de nitrogênio degradável no rúmen (NDR, utilizando como volumoso cana-de-açúcar suplementada com uréia, farelo de soja ou farelo de glúten de milho - 60, sobre a eficiência de síntese microbiana e a degradabilidade in situ da matéria seca (MS e da fibra em detergente neutro (FDN em novilhos mestiços. Utilizaram-se oito novilhos canulados no rúmen e duodeno, distribuídos em dois quadrados latinos 4 × 4 e alimentados com cana-de-açúcar e cana-de-açúcar suplementada com uréia, farelo de soja ou farelo de glúten de milho-60. O pH e a concentração de N-NH3 foram mensurados no fluido ruminal antes e 2, 4, 6 e 8 horas após o fornecimento da ração. Utilizou-se a fibra em detergente ácido indigestível como indicador de fluxo duodenal. A eficiência microbiana foi determinada pelas bases purinas.As fontes de proteína degradável no rúmen não influenciaram a degradabilidade da matéria seca, entretanto, o maior valor de degradabilidade efetiva da FDN foi obtido com a cana-de-açúcar com farelo de soja. O pH e a concentração de N-NH3 observados com todas as dietas foram adequados para o crescimento dos microrganismos ruminais. A deficiência de nitrogênio degradável no rúmen não influencia a síntese de proteína microbiana e a dinâmica de fase líquida.The objective of this work was to evaluate the ruminal degradable nitrogen (RDN deficit using as roughage sugar cane supplemented with urea, soybean meal, or corn gluten meal 60 on the microbial synthesis efficiency, in situ dry matter (DM and neutral detergent fiber (NDF degradability. The treatments were: sugar cane, sugar cane with urea, soybean meal or corn gluten meal 60. Eight rumen and duodenum cannulated steers were used and arranged according to two 4 × 4 Latin Squares. The pH and N-NH3 were determined in the ruminal fluid before and 2, 4, 6 and 8 hours after feeding. The duodenal flow was estimated by indigestible

  3. Recent Advances in Microbial Single Cell Genomics Technology and Applications

    Science.gov (United States)

    Stepanauskas, R.

    2016-02-01

    Single cell genomics is increasingly utilized as a powerful tool to decipher the metabolic potential, evolutionary histories and in situ interactions of environmental microorganisms. This transformative technology recovers extensive information from cultivation-unbiased samples of individual, unicellular organisms. Thus, it does not require data binning into arbitrary phylogenetic or functional groups and therefore is highly compatible with agent-based modeling approaches. I will present several technological advances in this field, which significantly improve genomic data recovery from individual cells and provide direct linkages between cell's genomic and phenotypic properties. I will also demonstrate how these new technical capabilities help understanding the metabolic potential and viral infections of the "microbial dark matter" inhabiting aquatic and subsurface environments.

  4. Microbial ecology of denitrification in biological wastewater treatment.

    Science.gov (United States)

    Lu, Huijie; Chandran, Kartik; Stensel, David

    2014-11-01

    Globally, denitrification is commonly employed in biological nitrogen removal processes to enhance water quality. However, substantial knowledge gaps remain concerning the overall community structure, population dynamics and metabolism of different organic carbon sources. This systematic review provides a summary of current findings pertaining to the microbial ecology of denitrification in biological wastewater treatment processes. DNA fingerprinting-based analysis has revealed a high level of microbial diversity in denitrification reactors and highlighted the impacts of carbon sources in determining overall denitrifying community composition. Stable isotope probing, fluorescence in situ hybridization, microarrays and meta-omics further link community structure with function by identifying the functional populations and their gene regulatory patterns at the transcriptional and translational levels. This review stresses the need to integrate microbial ecology information into conventional denitrification design and operation at full-scale. Some emerging questions, from physiological mechanisms to practical solutions, for example, eliminating nitrous oxide emissions and supplementing more sustainable carbon sources than methanol, are also discussed. A combination of high-throughput approaches is next in line for thorough assessment of wastewater denitrifying community structure and function. Though denitrification is used as an example here, this synergy between microbial ecology and process engineering is applicable to other biological wastewater treatment processes. Copyright © 2014 Elsevier Ltd. All rights reserved.

  5. Metabolite secretion in microorganisms: the theory of metabolic overflow put to the test

    DEFF Research Database (Denmark)

    Pinu, Farhana R.; Granucci, Ninna; Daniell, James

    2018-01-01

    Introduction Microbial cells secrete many metabolites during growth, including important intermediates of the central carbon metabolism. This has not been taken into account by researchers when modeling microbial metabolism for metabolic engineering and systems biology studies. Materials and Meth...

  6. Key players and team play: anaerobic microbial communities in hydrocarbon-contaminated aquifers.

    Science.gov (United States)

    Kleinsteuber, Sabine; Schleinitz, Kathleen M; Vogt, Carsten

    2012-05-01

    Biodegradation of anthropogenic pollutants in shallow aquifers is an important microbial ecosystem service which is mainly brought about by indigenous anaerobic microorganisms. For the management of contaminated sites, risk assessment and control of natural attenuation, the assessment of in situ biodegradation and the underlying microbial processes is essential. The development of novel molecular methods, "omics" approaches, and high-throughput techniques has revealed new insight into complex microbial communities and their functions in anoxic environmental systems. This review summarizes recent advances in the application of molecular methods to study anaerobic microbial communities in contaminated terrestrial subsurface ecosystems. We focus on current approaches to analyze composition, dynamics, and functional diversity of subsurface communities, to link identity to activity and metabolic function, and to identify the ecophysiological role of not yet cultured microbes and syntrophic consortia. We discuss recent molecular surveys of contaminated sites from an ecological viewpoint regarding degrader ecotypes, abiotic factors shaping anaerobic communities, and biotic interactions underpinning the importance of microbial cooperation for microbial ecosystem services such as contaminant degradation.

  7. Biotechnological Aspects of Microbial Extracellular Electron Transfer

    Science.gov (United States)

    Kato, Souichiro

    2015-01-01

    Extracellular electron transfer (EET) is a type of microbial respiration that enables electron transfer between microbial cells and extracellular solid materials, including naturally-occurring metal compounds and artificial electrodes. Microorganisms harboring EET abilities have received considerable attention for their various biotechnological applications, in addition to their contribution to global energy and material cycles. In this review, current knowledge on microbial EET and its application to diverse biotechnologies, including the bioremediation of toxic metals, recovery of useful metals, biocorrosion, and microbial electrochemical systems (microbial fuel cells and microbial electrosynthesis), were introduced. Two potential biotechnologies based on microbial EET, namely the electrochemical control of microbial metabolism and electrochemical stimulation of microbial symbiotic reactions (electric syntrophy), were also discussed. PMID:26004795

  8. Final Scientific/Technical Report, DE-FG02-06ER64171, Integrated Nucleic Acid System for In-Field Monitoring of Microbial Community Dynamics and Metabolic Activity – Subproject to Co-PI Eric E. Roden

    Energy Technology Data Exchange (ETDEWEB)

    Eric E. Roden

    2009-07-08

    This report summarizes research conducted in conjunction with a project entitled “Integrated Nucleic Acid System for In-Field Monitoring of Microbial Community Dynamics and Metabolic Activity”, which was funded through the Integrative Studies Element of the former NABIR Program (now the Environmental Remediation Sciences Program) within the Office of Biological and Environmental Research. Dr. Darrell Chandler (originally at Argonne National Laboratory, now with Akonni Biosystems) was the overall PI/PD for the project. The overall project goals were to (1) apply a model iron-reducer and sulfate-reducer microarray and instrumentation systems to sediment and groundwater samples from the Scheibe et al. FRC Area 2 field site, UMTRA sediments, and other DOE contaminated sites; (2) continue development and expansion of a 16S rRNA/rDNA¬-targeted probe suite for microbial community dynamics as new sequences are obtained from DOE-relevant sites; and (3) address the fundamental molecular biology and analytical chemistry associated with the extraction, purification and analysis of functional genes and mRNA in environmental samples. Work on the UW subproject focused on conducting detailed batch and semicontinuous culture reactor experiments with uranium-contaminated FRC Area 2 sediment. The reactor experiments were designed to provide coherent geochemical and microbiological data in support of microarray analyses of microbial communities in Area 2 sediments undergoing biostimulation with ethanol. A total of four major experiments were conducted (one batch and three semicontinuous culture), three of which (the batch and two semicontinuous culture) provided samples for DNA microarray analysis. A variety of other molecular analyses (clone libraries, 16S PhyloChip, RT-PCR, and T-RFLP) were conducted on parallel samples from the various experiments in order to provide independent information on microbial community response to biostimulation.

  9. Enhanced microbial coalbed methane generation: A review of research, commercial activity, and remaining challenges

    Science.gov (United States)

    Ritter, Daniel J.; Vinson, David S.; Barnhart, Elliott P.; Akob, Denise M.; Fields, Matthew W.; Cunningham, Al B.; Orem, William H.; McIntosh, Jennifer C.

    2015-01-01

    Coalbed methane (CBM) makes up a significant portion of the world’s natural gas resources. The discovery that approximately 20% of natural gas is microbial in origin has led to interest in microbially enhanced CBM (MECoM), which involves stimulating microorganisms to produce additional CBM from existing production wells. This paper reviews current laboratory and field research on understanding processes and reservoir conditions which are essential for microbial CBM generation, the progress of efforts to stimulate microbial methane generation in coal beds, and key remaining knowledge gaps. Research has been primarily focused on identifying microbial communities present in areas of CBM generation and attempting to determine their function, in-situ reservoir conditions that are most favorable for microbial CBM generation, and geochemical indicators of metabolic pathways of methanogenesis (i.e., acetoclastic or hydrogenotrophic methanogenesis). Meanwhile, researchers at universities, government agencies, and companies have focused on four primary MECoM strategies: 1) microbial stimulation (i.e., addition of nutrients to stimulate native microbes); 2) microbial augmentation (i.e., addition of microbes not native to or abundant in the reservoir of interest); 3) physically increasing microbial access to coal and distribution of amendments; and 4) chemically increasing the bioavailability of coal organics. Most companies interested in MECoM have pursued microbial stimulation: Luca Technologies, Inc., successfully completed a pilot scale field test of their stimulation strategy, while two others, Ciris Energy and Next Fuel, Inc., have undertaken smaller scale field tests. Several key knowledge gaps remain that need to be addressed before MECoM strategies can be implemented commercially. Little is known about the bacterial community responsible for coal biodegradation and how these microorganisms may be stimulated to enhance microbial methanogenesis. In addition, research

  10. Microbial Mineral Colonization Across a Subsurface Redox Transition Zone

    Directory of Open Access Journals (Sweden)

    Brandon eConverse

    2015-08-01

    Full Text Available This study employed 16S rRNA gene amplicon pyrosequencing to examine the hypothesis that chemolithotrophic Fe(II-oxidizing bacteria (FeOB would preferentially colonize the Fe(II-bearing mineral biotite compared to quartz sand when the minerals were incubated in situ within a subsurface redox transition zone (RTZ at the Hanford 300 Area site in Richland, WA, USA. The work was motivated by the recently documented presence of neutral-pH chemolithotrophic FeOB capable of oxidizing structural Fe(II in primary silicate and secondary phyllosilicate minerals in 300 Area sediments and groundwater (Benzine et al., 2013. Sterilized portions of sand+biotite or sand alone were incubated in situ for five months within a multilevel sampling (MLS apparatus that spanned a ca. 2-m interval across the RTZ in two separate groundwater wells. Parallel MLS measurements of aqueous geochemical species were performed prior to deployment of the minerals. Contrary to expectations, the 16S rRNA gene libraries showed no significant difference in microbial communities that colonized the sand+biotite versus sand-only deployments. Both mineral-associated and groundwater communities were dominated by heterotrophic taxa, with organisms from the Pseudomonaceae accounting for up to 70% of all reads from the colonized minerals. These results are consistent with previous results indicating the capacity for heterotrophic metabolism (including anaerobic metabolism below the RTZ as well as the predominance of heterotrophic taxa within 300 Area sediments and groundwater. Although heterotrophic organisms clearly dominated the colonized minerals, several putative lithotrophic (NH4+, H2, Fe(II, and HS- oxidizing taxa were detected in significant abundance above and within the RTZ. Such organisms may play a role in the coupling of anaerobic microbial metabolism to oxidative pathways with attendant impacts on elemental cycling and redox-sensitive contaminant behavior in the vicinity of the

  11. Polyphasic characterization of a PCP-to-phenol dechlorinating microbial community enriched from paddy soil

    Energy Technology Data Exchange (ETDEWEB)

    Yoshida, Naoko [EcoTopia Science Institute, Nagoya University Nagoya 464-8603 (Japan)]. E-mail: ysd75@esi.nagoya-u.ac.jp; Yoshida, Yukina [Graduate School of Engineering, Nagoya University, Nagoya 464-8603 (Japan); Handa, Yuko [Graduate School of Engineering, Nagoya University, Nagoya 464-8603 (Japan); Kim, Hyo-Keun [Korea Ginseng and Tobacco Research Institute, Taejon 305-345 (Korea, Republic of); Ichihara, Shigeyuki [Faculty of Agriculture, Meijo University, Nagoya 468-8502 (Japan); Katayama, Arata [EcoTopia Science Institute, Nagoya University Nagoya 464-8603 (Japan); Graduate School of Engineering, Nagoya University, Nagoya 464-8603 (Japan)

    2007-08-01

    Dechlorination of PCP has been observed previously under anaerobic condition in paddy soil. However, there is poor information about the dechlorination pathway of PCP and the microbial community associated with the PCP dechlorination in paddy soil. In this study, an anaerobic microbial community dechlorinating PCP was enriched by serial transfers from a paddy soil using a medium containing PCP, lactate and the steam-sterilized paddy soil. The enriched microbial community dechlorinated PCP completely to phenol under the anaerobic condition by a dechlorinating pathway as follows; PCP {sup {yields}} 2,3,4,5-tetrachlorophenol {sup {yields}} 3,4,5-trichlorophenol {sup {yields}} 3,5-dichlorophenol {sup {yields}} 3-chlorophenol {sup {yields}} phenol. Intermediate products such as 3-chlorophenol were not accumulated, which were immediately dechlorinated to phenol. The enriched microbial community was characterized physiologically by testing the effects of electron donors and electron acceptors on the dechlorinating activity. The dechlorinating activity was promoted with lactate, pyruvate, and hydrogen as electron donors but not with acetate. Electron acceptors, nitrate and sulphate, inhibited the dechlorinating activity competitively but not iron (III). The microbial group associated with the anaerobic dechlorination was characterized by the effect of specific inhibitors on the PCP dechlorination. Effects of specific metabolic inhibitors and antibiotics indicated the involvement of Gram-positive spore-forming bacteria with the PCP dechlorinating activity, which was represented as bacteria of phylum Firmicutes. The structure of the microbial community was characterized by fluorescence in situ hybridization, quinone profiling, and PCR-DGGE (denaturing gel gradient electrophoresis). The combined results indicated the predominance of Clostridium species of phylum Firmicutes in the microbial community. Desulfitobacterium spp. known as anaerobic Gram-positive spore

  12. Polyphasic characterization of a PCP-to-phenol dechlorinating microbial community enriched from paddy soil

    International Nuclear Information System (INIS)

    Yoshida, Naoko; Yoshida, Yukina; Handa, Yuko; Kim, Hyo-Keun; Ichihara, Shigeyuki; Katayama, Arata

    2007-01-01

    Dechlorination of PCP has been observed previously under anaerobic condition in paddy soil. However, there is poor information about the dechlorination pathway of PCP and the microbial community associated with the PCP dechlorination in paddy soil. In this study, an anaerobic microbial community dechlorinating PCP was enriched by serial transfers from a paddy soil using a medium containing PCP, lactate and the steam-sterilized paddy soil. The enriched microbial community dechlorinated PCP completely to phenol under the anaerobic condition by a dechlorinating pathway as follows; PCP → 2,3,4,5-tetrachlorophenol → 3,4,5-trichlorophenol → 3,5-dichlorophenol → 3-chlorophenol → phenol. Intermediate products such as 3-chlorophenol were not accumulated, which were immediately dechlorinated to phenol. The enriched microbial community was characterized physiologically by testing the effects of electron donors and electron acceptors on the dechlorinating activity. The dechlorinating activity was promoted with lactate, pyruvate, and hydrogen as electron donors but not with acetate. Electron acceptors, nitrate and sulphate, inhibited the dechlorinating activity competitively but not iron (III). The microbial group associated with the anaerobic dechlorination was characterized by the effect of specific inhibitors on the PCP dechlorination. Effects of specific metabolic inhibitors and antibiotics indicated the involvement of Gram-positive spore-forming bacteria with the PCP dechlorinating activity, which was represented as bacteria of phylum Firmicutes. The structure of the microbial community was characterized by fluorescence in situ hybridization, quinone profiling, and PCR-DGGE (denaturing gel gradient electrophoresis). The combined results indicated the predominance of Clostridium species of phylum Firmicutes in the microbial community. Desulfitobacterium spp. known as anaerobic Gram-positive spore-forming bacteria dechlorinating PCP were not detected by PCR using a

  13. The microbial community of a biofilm contact reactor for the treatment of winery wastewater.

    Science.gov (United States)

    de Beer, D M; Botes, M; Cloete, T E

    2018-02-01

    To utilize a three-tiered approach to provide insight into the microbial community structure, the spatial distribution and the metabolic capabilities of organisms of a biofilm in the two towers of a high-rate biological contact reactor treating winery wastewater. Next-generation sequencing indicated that bacteria primarily responsible for the removal of carbohydrates, sugars and alcohol were more abundant in tower 1 than tower 2 while nitrifying and denitrifying bacteria were more abundant in tower 2. Yeast populations differed in each tower. Fluorescent in situ hybridization coupled with confocal microscopy showed distribution of organisms confirming an oxygen gradient across the biofilm depth. The Biolog system (ECO plates) specified the different carbon-metabolizing profiles of the two biofilms. The three-tiered approach confirmed that the addition of a second subunit to the bioreactor, expanded the treatment capacity by augmenting the microbial and metabolic diversity of the system, improving the treatment scope of the system. A three-tiered biofilm analysis provided data required to optimize the design of a bioreactor to provide favourable conditions for the development of a microbial consortium, which has optimal waste removal properties for the treatment requirements at hand. © 2017 The Society for Applied Microbiology.

  14. Metaproteomics: Harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities

    Science.gov (United States)

    Hettich, Robert L.; Pan, Chongle; Chourey, Karuna; Giannone, Richard J.

    2013-01-01

    Summary The availability of extensive genome information for many different microbes, including unculturable species in mixed communities from environmental samples, has enabled systems-biology interrogation by providing a means to access genomic, transcriptomic, and proteomic information. To this end, metaproteomics exploits the power of high performance mass spectrometry for extensive characterization of the complete suite of proteins expressed by a microbial community in an environmental sample. PMID:23469896

  15. The maturing of microbial ecology.

    Science.gov (United States)

    Schmidt, Thomas M

    2006-09-01

    A.J. Kluyver and C.B. van Niel introduced many scientists to the exceptional metabolic capacity of microbes and their remarkable ability to adapt to changing environments in The Microbe's Contribution to Biology. Beyond providing an overview of the physiology and adaptability of microbes, the book outlined many of the basic principles for the emerging discipline of microbial ecology. While the study of pure cultures was highlighted, provided a unifying framework for understanding the vast metabolic potential of microbes and their roles in the global cycling of elements, extrapolation from pure cultures to natural environments has often been overshadowed by microbiologists inability to culture many of the microbes seen in natural environments. A combination of genomic approaches is now providing a culture-independent view of the microbial world, revealing a more diverse and dynamic community of microbes than originally anticipated. As methods for determining the diversity of microbial communities become increasingly accessible, a major challenge to microbial ecologists is to link the structure of natural microbial communities with their functions. This article presents several examples from studies of aquatic and terrestrial microbial communities in which culture and culture-independent methods are providing an enhanced appreciation for the microbe's contribution to the evolution and maintenance of life on Earth, and offers some thoughts about the graduate-level educational programs needed to enhance the maturing field of microbial ecology.

  16. Winter ecology of a subalpine grassland: Effects of snow removal on soil respiration, microbial structure and function.

    Science.gov (United States)

    Gavazov, Konstantin; Ingrisch, Johannes; Hasibeder, Roland; Mills, Robert T E; Buttler, Alexandre; Gleixner, Gerd; Pumpanen, Jukka; Bahn, Michael

    2017-07-15

    Seasonal snow cover provides essential insulation for mountain ecosystems, but expected changes in precipitation patterns and snow cover duration due to global warming can influence the activity of soil microbial communities. In turn, these changes have the potential to create new dynamics of soil organic matter cycling. To assess the effects of experimental snow removal and advanced spring conditions on soil carbon (C) and nitrogen (N) dynamics, and on the biomass and structure of soil microbial communities, we performed an in situ study in a subalpine grassland in the Austrian Alps, in conjunction with soil incubations under controlled conditions. We found substantial winter C-mineralisation and high accumulation of inorganic and organic N in the topsoil, peaking at snowmelt. Soil microbial biomass doubled under the snow, paralleled by a fivefold increase in its C:N ratio, but no apparent change in its bacteria-dominated community structure. Snow removal led to a series of mild freeze-thaw cycles, which had minor effects on in situ soil CO 2 production and N mineralisation. Incubated soil under advanced spring conditions, however, revealed an impaired microbial metabolism shortly after snow removal, characterised by a limited capacity for C-mineralisation of both fresh plant-derived substrates and existing soil organic matter (SOM), leading to reduced priming effects. This effect was transient and the observed recovery in microbial respiration and SOM priming towards the end of the winter season indicated microbial resilience to short-lived freeze-thaw disturbance under field conditions. Bacteria showed a higher potential for uptake of plant-derived C substrates during this recovery phase. The observed temporary loss in microbial C-mineralisation capacity and the promotion of bacteria over fungi can likely impede winter SOM cycling in mountain grasslands under recurrent winter climate change events, with plausible implications for soil nutrient availability and

  17. Microbial transformation of xenobiotics for environmental ...

    African Journals Online (AJOL)

    Microbial transformation of xenobiotics for environmental bioremediation. ... anaerobic and reductive biotransformation by co-metabolic processes and an overview of ... of xenobiotic compounds in context to the modern day biotechnology.

  18. Microbial food web components, bulk metabolism, and single-cell physiology of piconeuston in surface microlayers of high-altitude lakes

    Directory of Open Access Journals (Sweden)

    Hugo eSarmento

    2015-05-01

    Full Text Available Sharp boundaries in the physical environment are usually associated with abrupt shifts in organism’s abundance, activity and diversity. Aquatic surface microlayers (SML form a steep gradient between two contrasted environments, the atmosphere and surface waters, where they regulate the gas exchange between both environments. They usually harbor an abundant and active microbial life: the neuston. Few ecosystems are subjected to such a high UVR regime as high altitude lakes during summer. Here, we measured bulk estimates of heterotrophic activity, community structure and single-cell physiological properties by flow cytometry in 19 high-altitude remote Pyrenean lakes and compared the biological processes in the SML with those in the underlying surface waters. Phototrophic picoplankton (PPP populations, were generally present in high abundances and in those lakes containing PPP populations with phycoerythrin (PE, total PPP abundance was higher at the SML. Heterotrophic nanoflagellates (HNF were also more abundant in the SML. Bacteria in the SµL had lower leucine incorporation rates, lower percentages of live cells, and higher numbers of highly-respiring cells, likely resulting in a lower growth efficiency. No simple and direct linear relationships could be found between microbial abundances or activities and environmental variables, but factor analysis revealed that, despite their physical proximity, microbial life in SML and underlying waters was governed by different and independent processes. Overall, we demonstrate that piconeuston in high altitude lakes has specific features different from those of the picoplankton, and that they are highly affected by potential stressful environmental factors, such as high UVR radiation.

  19. Boom clay pore water, home of a diverse microbial community

    International Nuclear Information System (INIS)

    Wouters, Katinka; Moors, Hugo; Leys, Natalie

    2012-01-01

    Document available in extended abstract form only. Boom Clay pore water (BCPW) has been studied in the framework of geological disposal of nuclear waste for over two decades, thereby mainly addressing its geochemical properties. A reference composition for synthetic clay water has been derived earlier by modelling and spatial calibration efforts, mainly based on interstitial water sampled from different layers within the Boom clay. However, since microbial activity is found in a range of extreme circumstances, the possibility of microbes interacting with future radioactive waste in a host formation like Boom Clay, cannot be ignored. In this respect, BCPW was sampled from different Boom Clay layers using the Morpheus piezometer and subsequently analysed by a complementary set of microbiological and molecular techniques, in search for overall shared and abundant microorganisms. Similar to the previous characterization of the 'average' BCPW chemical composition, the primary aim of this microbiological study is to determine a representative BCPW microbial community which can be used in laboratory studies. Secondly, the in situ activity and the metabolic properties of members of this community were addressed, aiming to assess their survival and proliferation chances in repository conditions. In a first approach, total microbial DNA of the community was extracted from the BCPW samples. This molecular approach allows a broad insight in the total microbial ecology of the BCPW samples. By polymerase chain reaction (PCR) on the highly conserved 16S rRNA genes in this DNA pool and subsequent sequencing and bio-informatics analysis, operational taxonomic units (OTUs) could be assigned to the microbial community. The bacterial community was found to be quite diverse, with OTUs belonging to 8 different phyla (Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, Chlorobi, Spirochetes, Chloroflexi and Deinococcus-Thermus). These results provide an overall view of the

  20. Boom clay pore water, home of a diverse microbial community

    Energy Technology Data Exchange (ETDEWEB)

    Wouters, Katinka; Moors, Hugo; Leys, Natalie [SCK.CEN, Environment, Health and Safety Institute, B-2400 Mol (Belgium)

    2012-10-15

    Document available in extended abstract form only. Boom Clay pore water (BCPW) has been studied in the framework of geological disposal of nuclear waste for over two decades, thereby mainly addressing its geochemical properties. A reference composition for synthetic clay water has been derived earlier by modelling and spatial calibration efforts, mainly based on interstitial water sampled from different layers within the Boom clay. However, since microbial activity is found in a range of extreme circumstances, the possibility of microbes interacting with future radioactive waste in a host formation like Boom Clay, cannot be ignored. In this respect, BCPW was sampled from different Boom Clay layers using the Morpheus piezometer and subsequently analysed by a complementary set of microbiological and molecular techniques, in search for overall shared and abundant microorganisms. Similar to the previous characterization of the 'average' BCPW chemical composition, the primary aim of this microbiological study is to determine a representative BCPW microbial community which can be used in laboratory studies. Secondly, the in situ activity and the metabolic properties of members of this community were addressed, aiming to assess their survival and proliferation chances in repository conditions. In a first approach, total microbial DNA of the community was extracted from the BCPW samples. This molecular approach allows a broad insight in the total microbial ecology of the BCPW samples. By polymerase chain reaction (PCR) on the highly conserved 16S rRNA genes in this DNA pool and subsequent sequencing and bio-informatics analysis, operational taxonomic units (OTUs) could be assigned to the microbial community. The bacterial community was found to be quite diverse, with OTUs belonging to 8 different phyla (Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, Chlorobi, Spirochetes, Chloroflexi and Deinococcus-Thermus). These results provide an overall view of the

  1. Gaining electricity from in situ oxidation of hydrogen produced by fermentative cellulose degradation.

    Science.gov (United States)

    Niessen, J; Schröder, U; Harnisch, F; Scholz, F

    2005-01-01

    To exploit the fermentative hydrogen generation and direct hydrogen oxidation for the generation of electric current from the degradation of cellulose. Utilizing the metabolic activity of the mesophilic anaerobe Clostridium cellulolyticum and the thermophilic Clostridium thermocellum we show that electricity generation is possible from cellulose fermentation. The current generation is based on an in situ oxidation of microbially synthesized hydrogen at platinum-poly(tetrafluoroaniline) (Pt-PTFA) composite electrodes. Current densities of 130 mA l(-1) (with 3 g cellulose per litre medium) were achieved in poised potential experiments under batch and semi-batch conditions. The presented results show that electricity generation is possible by the in situ oxidation of hydrogen, product of the anaerobic degradation of cellulose by cellulolytic bacteria. For the first time, it is shown that an insoluble complex carbohydrate like cellulose can be used for electricity generation in a microbial fuel cell. The concept represents a first step to the utilization of macromolecular biomass components for microbial electricity generation.

  2. In situ bioremediation of chlorinated solvent with natural gas

    International Nuclear Information System (INIS)

    Rabold, D.E.

    1996-01-01

    A bioremediation system for the removal of chlorinated solvents from ground water and sediments is described. The system involves the the in-situ injection of natural gas (as a microbial nutrient) through an innovative configuration of horizontal wells

  3. Effects of dietary resistant starch content on metabolic status, milk composition, and microbial profiling in lactating sows and on offspring performance.

    Science.gov (United States)

    Yan, H; Lu, H; Almeida, V V; Ward, M G; Adeola, O; Nakatsu, C H; Ajuwon, K M

    2017-02-01

    In the present study, the effects of dietary resistant starch (RS) content on serum metabolite and hormone concentrations, milk composition, and faecal microbial profiling in lactating sows, as well as on offspring performance was investigated. Sixteen sows were randomly allotted at breeding to two treatments containing low- and high-RS contents from normal and high-amylose corn varieties, respectively, and each treatment had eight replicates (sows). Individual piglet body weight (BW) and litter size were recorded at birth and weaning. Milk samples were obtained on day 10 after farrowing for composition analysis. On day 2 before weaning, blood and faecal samples were collected to determine serum metabolite and hormone concentrations and faecal microbial populations, respectively. Litter size at birth and weaning were not influenced (p > 0.05) by the sow dietary treatments. Although feeding the RS-rich diet to sows reduced (p = 0.004) offspring birth BW, there was no difference in piglet BW at weaning (p > 0.05). High-RS diet increased (p content, and tended (p = 0.09) to increase milk fat content in lactating sows. Feeding the RS-rich diet to sows increased (p bacterial population diversity. These results indicate that high-RS diets induce fatty acid mobilization and a greater intestinal bacterial richness in lactating sows, as well as a greater nutrient density in maternal milk, without affecting offspring performance at weaning. Journal of Animal Physiology and Animal Nutrition © 2016 Blackwell Verlag GmbH.

  4. Improved Access To Aging Ocean Basement Biosphere For Microbial Geochemical Studies

    Science.gov (United States)

    Cowen, J. P.; Glazer, B.; Rappe, M.; Kenig, F.; Fisher, A.; Copson, D.; Harris, D.; Jolly, J.; Nuzzio, D.

    2005-12-01

    CORK observatories affixed to Integrated Ocean Drilling Program (IODP) boreholes offer an unprecedented opportunity to study biogeochemical properties and microbial diversity in circulating fluids from sediment-buried ocean basement. Preliminary 16S rRNA gene sequence data from 65 degrees C fluids escaping from the top of the over-pressured ODP borehole 1026B, on the flanks of the Juan de Fuca Ridge indicated the presence of diverse Bacteria and Archaea, including gene clones with varying degrees of relatedness to known dissimilatory nitrate reducers (with ammonia production), thermophilic sulfate reducers, and thermophilic fermentative heterotrophs, consistent with fluid chemistry measurements. However, questions remain regarding microbial community structure, key metabolic pathways and rates, and redox chemistry of the basement fluids, along with concerns for contamination issues. We describe ongoing developments intended to address key in situ analytical and sampling challenges including: 1) The new generation CORKs' dedicated microbiological/geochemical fluid delivery system specifically designed to minimize chemical contamination and surface biofouling; and 2) Development of a seafloor instrument sled for coupling to the CORK's bio-fluid delivery system for acquisition of real-time, in situ electrochemical (voltammetry) redox chemistry data on basement fluids, in addition to in situ particle filtration of basement fluids for molecular genetics, culturing and biogeochemical studies. Results of the first deployment of this instrument sled to new CORK observatory 1301A in Cascadia Basin, on the flanks of the Juan de Fuca Ridge, will be described.

  5. Geochemical and Microbiological Characteristics during in Situ Chemical Oxidation and in Situ Bioremediation at a Diesel Contaminated Site

    NARCIS (Netherlands)

    Sutton, N.B.; Kalisz, M.; Krupanek, J.; Marek, J.; Grotenhuis, J.T.C.; Smidt, H.; Weert, de J.; Rijnaarts, H.H.M.; Gaans, van P.; Keijzer, T.

    2014-01-01

    While in situ chemical oxidation with persulfate has seen wide commercial application, investigations into the impacts on groundwater characteristics, microbial communities and soil structure are limited. To better understand the interactions of persulfate with the subsurface and to determine the

  6. Global microbialization of coral reefs.

    Science.gov (United States)

    Haas, Andreas F; Fairoz, Mohamed F M; Kelly, Linda W; Nelson, Craig E; Dinsdale, Elizabeth A; Edwards, Robert A; Giles, Steve; Hatay, Mark; Hisakawa, Nao; Knowles, Ben; Lim, Yan Wei; Maughan, Heather; Pantos, Olga; Roach, Ty N F; Sanchez, Savannah E; Silveira, Cynthia B; Sandin, Stuart; Smith, Jennifer E; Rohwer, Forest

    2016-04-25

    Microbialization refers to the observed shift in ecosystem trophic structure towards higher microbial biomass and energy use. On coral reefs, the proximal causes of microbialization are overfishing and eutrophication, both of which facilitate enhanced growth of fleshy algae, conferring a competitive advantage over calcifying corals and coralline algae. The proposed mechanism for this competitive advantage is the DDAM positive feedback loop (dissolved organic carbon (DOC), disease, algae, microorganism), where DOC released by ungrazed fleshy algae supports copiotrophic, potentially pathogenic bacterial communities, ultimately harming corals and maintaining algal competitive dominance. Using an unprecedented data set of >400 samples from 60 coral reef sites, we show that the central DDAM predictions are consistent across three ocean basins. Reef algal cover is positively correlated with lower concentrations of DOC and higher microbial abundances. On turf and fleshy macroalgal-rich reefs, higher relative abundances of copiotrophic microbial taxa were identified. These microbial communities shift their metabolic potential for carbohydrate degradation from the more energy efficient Embden-Meyerhof-Parnas pathway on coral-dominated reefs to the less efficient Entner-Doudoroff and pentose phosphate pathways on algal-dominated reefs. This 'yield-to-power' switch by microorganism directly threatens reefs via increased hypoxia and greater CO2 release from the microbial respiration of DOC.

  7. Microbial diversity arising from thermodynamic constraints

    Science.gov (United States)

    Großkopf, Tobias; Soyer, Orkun S

    2016-01-01

    The microbial world displays an immense taxonomic diversity. This diversity is manifested also in a multitude of metabolic pathways that can utilise different substrates and produce different products. Here, we propose that these observations directly link to thermodynamic constraints that inherently arise from the metabolic basis of microbial growth. We show that thermodynamic constraints can enable coexistence of microbes that utilise the same substrate but produce different end products. We find that this thermodynamics-driven emergence of diversity is most relevant for metabolic conversions with low free energy as seen for example under anaerobic conditions, where population dynamics is governed by thermodynamic effects rather than kinetic factors such as substrate uptake rates. These findings provide a general understanding of the microbial diversity based on the first principles of thermodynamics. As such they provide a thermodynamics-based framework for explaining the observed microbial diversity in different natural and synthetic environments. PMID:27035705

  8. Microbial diversity arising from thermodynamic constraints.

    Science.gov (United States)

    Großkopf, Tobias; Soyer, Orkun S

    2016-11-01

    The microbial world displays an immense taxonomic diversity. This diversity is manifested also in a multitude of metabolic pathways that can utilise different substrates and produce different products. Here, we propose that these observations directly link to thermodynamic constraints that inherently arise from the metabolic basis of microbial growth. We show that thermodynamic constraints can enable coexistence of microbes that utilise the same substrate but produce different end products. We find that this thermodynamics-driven emergence of diversity is most relevant for metabolic conversions with low free energy as seen for example under anaerobic conditions, where population dynamics is governed by thermodynamic effects rather than kinetic factors such as substrate uptake rates. These findings provide a general understanding of the microbial diversity based on the first principles of thermodynamics. As such they provide a thermodynamics-based framework for explaining the observed microbial diversity in different natural and synthetic environments.

  9. Effect of long-term fertilization on humic redox mediators in multiple microbial redox reactions.

    Science.gov (United States)

    Guo, Peng; Zhang, Chunfang; Wang, Yi; Yu, Xinwei; Zhang, Zhichao; Zhang, Dongdong

    2018-03-01

    This study investigated the effects of different long-term fertilizations on humic substances (HSs), humic acids (HAs) and humins, functioning as redox mediators for various microbial redox biotransformations, including 2,2',4,4',5,5'- hexachlorobiphenyl (PCB 153 ) dechlorination, dissimilatory iron reduction, and nitrate reduction, and their electron-mediating natures. The redox activity of HSs for various microbial redox metabolisms was substantially enhanced by long-term application of organic fertilizer (pig manure). As a redox mediator, only humin extracted from soils with organic fertilizer amendment (OF-HM) maintained microbial PCB 153 dechlorination activity (1.03 μM PCB 153 removal), and corresponding HA (OF-HA) most effectively enhanced iron reduction and nitrate reduction by Shewanella putrefaciens. Electrochemical analysis confirmed the enhancement of their electron transfer capacity and redox properties. Fourier transform infrared analysis showed that C=C and C=O bonds, and carboxylic or phenolic groups in HSs might be the redox functional groups affected by fertilization. This research enhances our understanding of the influence of anthropogenic fertility on the biogeochemical cycling of elements and in situ remediation ability in agroecosystems through microorganisms' metabolisms. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. Microbial Propionic Acid Production

    Directory of Open Access Journals (Sweden)

    R. Axayacatl Gonzalez-Garcia

    2017-05-01

    Full Text Available Propionic acid (propionate is a commercially valuable carboxylic acid produced through microbial fermentation. Propionic acid is mainly used in the food industry but has recently found applications in the cosmetic, plastics and pharmaceutical industries. Propionate can be produced via various metabolic pathways, which can be classified into three major groups: fermentative pathways, biosynthetic pathways, and amino acid catabolic pathways. The current review provides an in-depth description of the major metabolic routes for propionate production from an energy optimization perspective. Biological propionate production is limited by high downstream purification costs which can be addressed if the target yield, productivity and titre can be achieved. Genome shuffling combined with high throughput omics and metabolic engineering is providing new opportunities, and biological propionate production is likely to enter the market in the not so distant future. In order to realise the full potential of metabolic engineering and heterologous expression, however, a greater understanding of metabolic capabilities of the native producers, the fittest producers, is required.

  11. Magnetic resonance diffusion and relaxation characterization of water in the unfrozen vein network in polycrystalline ice and its response to microbial metabolic products

    Science.gov (United States)

    Brown, Jennifer R.; Brox, Timothy I.; Vogt, Sarah J.; Seymour, Joseph D.; Skidmore, Mark L.; Codd, Sarah L.

    2012-12-01

    Polycrystalline ice, as found in glaciers and the ice sheets of Antarctica, is a low porosity porous media consisting of a complicated and dynamic pore structure of liquid-filled intercrystalline veins within a solid ice matrix. In this work, Nuclear Magnetic Resonance measurements of relaxation rates and molecular diffusion, useful for probing pore structure and transport dynamics in porous systems, were used to physically characterize the unfrozen vein network structure in ice and its response to the presence of metabolic products produced by V3519-10, a cold tolerant microorganism isolated from the Vostok ice core. Recent research has found microorganisms that can remain viable and even metabolically active within icy environments at sub-zero temperatures. One potential mechanism of survival for V3519-10 is secretion of an extracellular ice binding protein that binds to the prism face of ice crystals and inhibits ice recrystallization, a coarsening process resulting in crystal growth with ice aging. Understanding the impact of ice binding activity on the bulk vein network structure in ice is important to modeling of frozen geophysical systems and in development of ice interacting proteins for biotechnology applications, such as cryopreservation of cell lines, and manufacturing processes in food sciences. Here, we present the first observations of recrystallization inhibition in low porosity ice containing V3519-10 extracellular protein extract as measured with Nuclear Magnetic Resonance and Magnetic Resonance Imaging.

  12. From position-specific isotope labeling towards soil fluxomics: a novel toolbox to assess the microbial impact on biogeochemical cycles

    Science.gov (United States)

    Apostel, C.; Dippold, M. A.; Kuzyakov, Y.

    2015-12-01

    Understanding the microbial impact on C and nutrient cycles is one of the most important challenges in terrestrial biogeochemistry. Transformation of low molecular weight organic substances (LMWOS) is a key step in all biogeochemical cycles because 1) all high molecular substances pass the LMWOS pool during their degradation and 2) only LMWOS can be taken up by microorganisms intact. Thus, the transformations of LMWOS are dominated by biochemical pathways of the soil microorganisms. Thus, understanding fluxes and transformations in soils requires a detailed knowledge on the microbial metabolic network and its control mechanism. Tracing C fate in soil by isotopes became on of the most applied and promising biogeochemistry tools but studies were nearly exclusively based on uniformly labeled substances. However, such tracers do not allow the differentiation of the intact use of the initial substances from its transformation to metabolites. The novel tool of position-specific labeling enables to trace molecule atoms separately and thus to determine the cleavage of molecules - a prerequisite for metabolic tracing. Position-specific labeling of basic metabolites and quantification of isotope incorporation in CO2 and bulk soil enabled following the basic metabolic pathways of microorganisms. However, the combination of position-specific 13C labeling with compound-specific isotope analysis of microbial biomarkers and metabolites like phospholipid fatty acids (PLFA) or amino sugars revealed new insights into the soil fluxome: First, it enables tracing specific anabolic pathways in diverse microbial communities in soils e.g. carbon starvation pathways versus pathways reflecting microbial growth. Second, it allows identification of specific pathways of individual functional microbial groups in soils in situ. Tracing metabolic pathways and understanding their regulating factors are crucial for soil C fluxomics i.e. the unravaling of the complex network of C transformations

  13. Microbial products II

    Energy Technology Data Exchange (ETDEWEB)

    Pape, H; Rehm, H J [eds.

    1986-01-01

    The present volume deals mainly with compounds which have been detected as natural microbial products. Part 1 of this volume introduces the general aspects of the overproduction of metabolites and the concepts and genetics of secondary metabolism. Compounds such as nucleosides, nucleotides, coenzymes, vitamins and lipids are dealt with in part 2. Part 3 then is devoted to products and antibiotics with uses im medicine, veterinary medicine, plant protection and metabolites with antitumor activity. Several secondary metabolites have found uses in human and animal health care. With 244 figs., 109 tabs.

  14. Microbial syntrophy: interaction for the common good.

    Science.gov (United States)

    Morris, Brandon E L; Henneberger, Ruth; Huber, Harald; Moissl-Eichinger, Christine

    2013-05-01

    Classical definitions of syntrophy focus on a process, performed through metabolic interaction between dependent microbial partners, such as the degradation of complex organic compounds under anoxic conditions. However, examples from past and current scientific discoveries suggest that a new, simple but wider definition is necessary to cover all aspects of microbial syntrophy. We suggest the term 'obligately mutualistic metabolism', which still focuses on microbial metabolic cooperation but also includes an ecological aspect: the benefit for both partners. By the combined metabolic activity of microorganisms, endergonic reactions can become exergonic through the efficient removal of products and therefore enable a microbial community to survive with minimal energy resources. Here, we explain the principles of classical and non-classical syntrophy and illustrate the concepts with various examples. We present biochemical fundamentals that allow microorganism to survive under a range of environmental conditions and to drive important biogeochemical processes. Novel technologies have contributed to the understanding of syntrophic relationships in cultured and uncultured systems. Recent research highlights that obligately mutualistic metabolism is not limited to certain metabolic pathways nor to certain environments or microorganisms. This beneficial microbial interaction is not restricted to the transfer of reducing agents such as hydrogen or formate, but can also involve the exchange of organic, sulfurous- and nitrogenous compounds or the removal of toxic compounds. © 2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  15. Metabolic Activity and Biosignatures of Microbes in the Lower Ocean Crust of Atlantis Bank, IODP Expedition 360

    Science.gov (United States)

    Wee, S. Y.; Edgcomb, V. P.; Burgaud, G.; Klein, F.; Schubotz, F.; Yvon-Lewis, S. A.; Sylvan, J. B.

    2017-12-01

    International Ocean Discovery Program (IODP) Expedition 360 represents the first leg of a multi-phase drilling program, SloMo, aimed at investigating the nature of the lower crust and Moho at slow spreading ridges. The goal of Expedition 360 was to recover a representative transect of the lower oceanic crust formed at Atlantis Bank, an oceanic core complex on the SW Indian Ridge. Recovered cores were primarily gabbro and olivine gabbro, which may potentially host serpentinization reactions and associated microbial life. Our goal was to sample this subseafloor environment and determine quantity, diversity and metabolic capabilities of any resident microbial life. Hole U1473A was drilled during Expedition 360 down to 790 m below seafloor and samples for detection of microbial communities and microbial biosignatures were collected throughout. We present here quantification of microbial biomass via fluorescence microscopy, preliminary analysis of nutrient addition experiments, data from sequencing of microbial 16S rRNA genes, analysis of microbial lipids, and data from Raman spectra of subsurface isolates. We initiated and sampled 12 nutrient addition experiments from 71-745 mbsf by adding sampled rocks to artificial seawater with no additions, added ammonium, added ammonium plus phosphate, and added organic acids. In nearly all of the experiment bottles, methane was detected when samples were collected at six months and again after one year of incubation. Phosphate in the incubations was drawn down, indicating active microbial metabolism, and archaeal lipids from in situ samples indicate the presence of methanogens, corroborating the likelihood of methanogens as the source of detected methane in the nutrient addition incubations. Altogether, the interdisciplinary approach used here provides a peek into life in the subseafloor upper ocean crust.

  16. Monitoring Genetic and Metabolic Potential for In-Site Bioremediation: Mass Spectrometry

    International Nuclear Information System (INIS)

    Buchanan, M.V.

    2000-01-01

    A number of DOE sites are contaminated with mixtures of dense non-aqueous phase liquids (DNAPLs) such as carbon tetrachloride, chloroform, perchloroethylene, and trichloroethylene. At many of these sites, in situ microbial bioremediation is an attractive strategy for cleanup, since it has the potential to degrade DNAPLs in situ without the need for pump-and-treat or soil removal procedures, and without producing toxic byproducts. A rapid screening method to determine broad range metabolic and genetic potential for contaminant degradation would greatly reduce the cost and time involved in assessment for in situ bioremediation, as well as for monitoring ongoing bioremediation treatment. The objective of this project was the development of mass-spectrometry-based methods to screen for genetic potential for both assessment and monitoring of in situ bioremediation of DNAPLs. These methods were designed to provide more robust and routine methods for DNA-based characterization of the genetic potential of subsurface microbes for degrading pollutants. Specifically, we sought to (1) Develop gene probes that yield information equivalent to conventional probes, but in a smaller size that is more amenable to mass spectrometric detection, (2) Pursue improvements to matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) methodology in order to allow its more general application to gene probe detection, and (3) Increase the throughput of microbial characterization by integrating gene probe preparation, purification, and MALDI-MS analysis

  17. Competing pathways in drug metabolism. I. Effect of input concentration on the conjugation of gentisamide in the once-through in situ perfused rat liver preparation

    International Nuclear Information System (INIS)

    Morris, M.E.; Yuen, V.; Tang, B.K.; Pang, K.S.

    1988-01-01

    Sulfation and glucuronidation are two parallel pathways for the metabolism of phenolic substrates. Gentisamide (GAM) was used as a model compound to examine the effects of parallel competing pathways on drug disappearance and metabolite formation in the once-through perfused rat liver preparation. GAM was found to form one glucuronide (GAM-5G) and two sulfate (GAM-2S and GAM-5S) conjugates. These GAM conjugates were biosynthesized in recirculating rat liver preparations, and were isolated by preparative high-performance liquid chromatography. Specific incorporation of 35S-sodium sulfate and [14C]glucose into GAM sulfate and glucuronide conjugates revealed corresponding elution patterns as labeled GAM metabolites. Their identities were characterized by enzymatic and acid hydrolyses and by NMR spectroscopy. Gentisamide-5-sulfate (GAM-5S) and gentisamide-5-glucuronide (GAM-5G) are major metabolites, and gentisamide-2-sulfate (GAM-2S) is a minor metabolite. Single-pass rat liver perfusions were used to examine the effect of stepwise increases/decreases of input GAM concentration (CIn) on the extraction ratio (E) of GAM and formation of metabolites. The E of GAM remained constant (about 0.89) at input concentrations from 0.9 to 120 microM and decreased at CIn greater than 120 microM. Metabolite patterns, however, changed with GAM CIn, even when E was constant at CIn up to 120 microM. GAM-5S was present as the major metabolite of GAM at all GAM CInS in most liver preparations but the proportions of GAM-5S and GAM-2S decreased at increasing CIn; the proportion of GAM-5G, a minor metabolite at low CIn, increased with increasing CIn. Biliary excretion rates at steady state accounted for 5.3 +/- 2.7% (mean +/- S.D.) of the input rate: GAM-5G was the predominant metabolite found

  18. Copper (II) addition to accelerate lactic acid production from co-fermentation of food waste and waste activated sludge: Understanding of the corresponding metabolisms, microbial community and predictive functional profiling.

    Science.gov (United States)

    Ye, Tingting; Li, Xiang; Zhang, Ting; Su, Yinglong; Zhang, Wenjuan; Li, Jun; Gan, Yanfei; Zhang, Ai; Liu, Yanan; Xue, Gang

    2018-03-20

    Bio-refinery of food waste and waste activated sludge to high value-added chemicals, such as lactic acid, has attracted particular interest in recent years. In this paper, the effect of copper (II) dosing to the organic waste fermentation system on lactic acid production was evaluated, which proved to be a promising method to stimulate high yield of lactic acid (77.0% higher than blank) at dosage of 15 μM-Cu 2+ /g VSS. As mechanism study suggested, copper addition enhanced the activity of α-glycosidase and glycolysis, which increased the substrate for subsequent acidification; whereas, the high dosage (70 μM-Cu 2+ /g VSS) inhibited the conversion of lactic acid to VFA, thus stabilized lactic acid concentration. Microbial community study revealed that small amount of copper (II) at 15 μM/g VSS resulted in the proliferation of Lactobacillus to 82.6%, which mainly produced lactic acid. Finally, the variation of functional capabilities implied that the proposed homeostatic system II was activated at relatively low concentration of copper. Meanwhile, membrane transport function and carbohydrate metabolism were also strengthened. This study provides insights into the effect of copper (II) on the enhancement of lactic acid production from co-fermentation of food waste and waste activated sludge. Copyright © 2018 Elsevier Ltd. All rights reserved.

  19. Monitoring in situ biodegradation of hydrocarbons by using stable carbon isotopes

    International Nuclear Information System (INIS)

    Aggarwal, P.K.; Hinchee, R.E.

    1991-01-01

    Spilled or leaked nonhalogenated petroleum hydrocarbons in the soil can generally be metabolized by indigenous, aerobic bacteria. In situ biological degradation of hydrocarbons may be accelerated by supplying inorganic nutrients and/or oxygen. Approaches to monitoring and verifying enhanced in situ biodegradation have included measurements of changes over time in the (a) concentration of hydrocarbons, (b) temperature, (c) number of hydrocarbon-degrading microorganisms, (d) ratio of fast-degrading hydrocarbons (e.g., pristanes or phytanes), and (e) metabolic intermediates. Measurements of oxygen consumption over time and elevated carbon dioxide concentrations in soil gas also have been used as indicators of hydrocarbon degradation. An alternative approach that may help substantiate biodegradation is to measure stable carbon isotope ratios in soil gas CO 2 . Stable carbon isotope ratio analysis is inexpensive and commercially available at many laboratories. Carbon dioxide produced by hydrocarbon degradation may be distinguished from that produced by other processes based on the carbon isotopic compositions characteristic of the source material and/or fractionation accompanying microbial metabolism. Here the authors demonstrate the applicability of the stable isotope technique for monitoring enhanced. aerobic biodegradation of hydrocarbons using data from three locations in the United States

  20. Visualizing Microbial Biogeochemistry: NanoSIMS and Stable Isotope Probing (Invited)

    Science.gov (United States)

    Pett-Ridge, J.; Weber, P. K.

    2009-12-01

    Linking phylogenetic information to function in microbial communities is a key challenge for microbial ecology. Isotope-labeling experiments provide a useful means to investigate the ecophysiology of microbial populations and cells in the environment and allow measurement of nutrient transfers between cell types, symbionts and consortia. The combination of Nano-Secondary Ion Mass Spectrometry (NanoSIMS) analysis, in situ labeling and high resolution microscopy allows isotopic analysis to be linked to phylogeny and morphology and holds great promise for fine-scale studies of microbial systems. In NanoSIMS analysis, samples are sputtered with an energetic primary beam (Cs+, O-) liberating secondary ions that are separated by the mass spectrometer and detected in a suite of electron multipliers. Five isotopic species may be analyzed concurrently with spatial resolution as fine as 50nm. A high sensitivity isotope ratio ‘map’ can then be generated for the analyzed area. NanoSIMS images of 13C, 15N and Mo (a nitrogenase co-factor) localization in diazotrophic cyanobacteria show how cells differentially allocate resources within filaments and allow calculation of nutrient uptake rates on a cell by cell basis. Images of AM fungal hyphae-root and cyanobacteria-rhizobia associations indicate the mobilization and sharing (stealing?) of newly fixed C and N. In a related technique, “El-FISH”, stable isotope labeled biomass is probed with oligonucleotide-elemental labels and then imaged by NanoSIMS. In microbial consortia and cyanobacterial mats, this technique helps link microbial structure and function simultaneously even in systems with unknown and uncultivated microbes. Finally, the combination of re-engineered universal 16S oligonucleotide microarrays with NanoSIMS analyses may allow microbial identity to be linked to functional roles in complex systems such as mats and cellulose degrading hindgut communities. These newly developed methods provide correlated

  1. Aerobic microbial dolomite at the nanometer scale : Implications for the geologic record

    NARCIS (Netherlands)

    Sánchez-Román, Mónica; Vasconcelos, Crisógono; Schmid, Thomas; Dittrich, Maria; McKenzie, Judith A.; Zenobi, Renato; Rivadeneyra, Maria A.

    2008-01-01

    Microbial experiments are the only proven approach to produce experimental dolomite under Earth's surface conditions. Although microbial metabolisms are known to induce dolomite precipitation by favoring dolomite growth kinetics, the involvement of microbes in the dolomite nucleation process is

  2. Evolution of Microbial Quorum Sensing to Human Global Quorum Sensing: An Insight into How Gap Junctional Intercellular Communication Might Be Linked to the Global Metabolic Disease Crisis.

    Science.gov (United States)

    Trosko, James E

    2016-06-15

    The first anaerobic organism extracted energy for survival and reproduction from its source of nutrients, with the genetic means to ensure protection of its individual genome but also its species survival. While it had a means to communicate with its community via simple secreted molecules ("quorum sensing"), the eventual shift to an aerobic environment led to multi-cellular metazoan organisms, with evolutionary-selected genes to form extracellular matrices, stem cells, stem cell niches, and a family of gap junction or "connexin" genes. These germinal and somatic stem cells responded to extracellular signals that triggered intra-cellular signaling to regulate specific genes out of the total genome. These extra-cellular induced intra-cellular signals also modulated gap junctional intercellular communication (GJIC) in order to regulate the new cellular functions of symmetrical and asymmetrical cell division, cell differentiation, modes of cell death, and senescence. Within the hierarchical and cybernetic concepts, differentiated by neurons organized in the brain of the Homo sapiens, the conscious mind led to language, abstract ideas, technology, myth-making, scientific reasoning, and moral decision-making, i.e., the creation of culture. Over thousands of years, this has created the current collision between biological and cultural evolution, leading to the global "metabolic disease" crisis.

  3. Evolution of Microbial Quorum Sensing to Human Global Quorum Sensing: An Insight into How Gap Junctional Intercellular Communication Might Be Linked to the Global Metabolic Disease Crisis

    Directory of Open Access Journals (Sweden)

    James E. Trosko

    2016-06-01

    Full Text Available The first anaerobic organism extracted energy for survival and reproduction from its source of nutrients, with the genetic means to ensure protection of its individual genome but also its species survival. While it had a means to communicate with its community via simple secreted molecules (“quorum sensing”, the eventual shift to an aerobic environment led to multi-cellular metazoan organisms, with evolutionary-selected genes to form extracellular matrices, stem cells, stem cell niches, and a family of gap junction or “connexin” genes. These germinal and somatic stem cells responded to extracellular signals that triggered intra-cellular signaling to regulate specific genes out of the total genome. These extra-cellular induced intra-cellular signals also modulated gap junctional intercellular communication (GJIC in order to regulate the new cellular functions of symmetrical and asymmetrical cell division, cell differentiation, modes of cell death, and senescence. Within the hierarchical and cybernetic concepts, differentiated by neurons organized in the brain of the Homo sapiens, the conscious mind led to language, abstract ideas, technology, myth-making, scientific reasoning, and moral decision–making, i.e., the creation of culture. Over thousands of years, this has created the current collision between biological and cultural evolution, leading to the global “metabolic disease” crisis.

  4. Microbial glycoproteomics

    DEFF Research Database (Denmark)

    Halim, Adnan; Anonsen, Jan Haug

    2017-01-01

    Mass spectrometry-based "-omics" technologies are important tools for global and detailed mapping of post-translational modifications. Protein glycosylation is an abundant and important post translational modification widespread throughout all domains of life. Characterization of glycoproteins...... and research in this area is rapidly accelerating. Here, we review recent developments in glycoproteomic technologies with a special focus on microbial protein glycosylation....

  5. Microbial Energy Conversion

    Energy Technology Data Exchange (ETDEWEB)

    Buckley, Merry [American Society for Microbiology (ASM), Washington, DC (United States); Wall, Judy D. [Univ. of Missouri, Columbia, MO (United States)

    2006-10-01

    production. Research should focus on the actions of enzymes and enzyme complexes within the context of the whole cell, how they’re regulated, where they’re placed, and what they interact with. Better modeling tools are needed to facilitate progress in microbial energy transformations. Models of metabolic dynamics, including levels of reductants and regulation of electron flow need to be improved. Global techno-economic models of microbial energy conversion systems, which seek to simultaneously describe the resource flows into and out of a system as well as its economics, are needed and should be made publicly available on the internet. Finally, more emphasis needs to be placed on multidisciplinary education and training and on cooperation between disciplines in order to make the most of microbial energy conversion technologies and to meet the research needs of the future.

  6. Microbial stratification and microbially catalyzed processes along a hypersaline chemocline

    Science.gov (United States)

    Hyde, A.; Joye, S. B.; Teske, A.

    2017-12-01

    Orca Basin is the largest deep hypersaline anoxic basin in the world, covering over 400 km2. Located at the bottom of the Gulf of Mexico, this body of water reaches depths of 200 meters and is 8 times denser (and more saline) than the overlying seawater. The sharp pycnocline prevents any significant vertical mixing and serves as a particle trap for sinking organic matter. These rapid changes in salinity, oxygen, organic matter, and other geochemical parameters present unique conditions for the microbial communities present. We collected samples in 10m intervals throughout the chemocline. After filtering the water, we used high-throughput bacterial and archaeal 16S rRNA gene sequencing to characterize the changing microbial community along the Orca Basin chemocline. The results reveal a dominance of microbial taxa whose biogeochemical function is entirely unknown. We then used metagenomic sequencing and reconstructed genomes for select samples, revealing the potential dominant metabolic processes in the Orca Basin chemocline. Understanding how these unique geochemical conditions shape microbial communities and metabolic capabilities will have implications for the ocean's biogeochemical cycles and the consequences of expanding oxygen minimum zones.

  7. Microbial xanthophylls.

    Science.gov (United States)

    Bhosale, Prakash; Bernstein, Paul S

    2005-09-01

    Xanthophylls are oxygenated carotenoids abundant in the human food supply. Lutein, zeaxanthin, and cryptoxanthin are major xanthophyll carotenoids in human plasma. The consumption of these xanthophylls is directly associated with reduction in the risk of cancers, cardiovascular disease, age-related macular degeneration, and cataract formation. Canthaxanthin and astaxanthin also have considerable importance in aquaculture for salmonid and crustacean pigmentation, and are of commercial interest for the pharmaceutical and food industries. Chemical synthesis is a major source for the heavy demand of xanthophylls in the consumer market; however, microbial producers also have potential as commercial sources. In this review, we discuss the biosynthesis, commercial utility, and major microbial sources of xanthophylls. We also present a critical review of current research and technologies involved in promoting microbes as potential commercial sources for mass production.

  8. Assessing the potential of spectral induced polarization to detect in situ changes in iron reduction

    Science.gov (United States)

    Rosier, C. L.; Price, A.; Sharma, S.; Atekwana, E. A.

    2016-12-01

    The near surface geophysical technique Spectral Induced Polarization (SIP), provides promise as an effective method measuring in situ biofilm formation/development. Yet, potential mechanisms responsible for observed shifts in SIP response due to biofilm are not clearly understood. In order to address possible mechanisms we assessed the influence of Shewanella oneidensis (MR1) cell density (colony forming units; CFU), biofilm production (Bradford assay) and iron reduction metabolism (colorimetric assay) on SIP response. Laboratory measurements were collected over three months on columns packed with either iron-coated or iron-free sands and amended with artificial ground water and acetate in order to stimulate biofilm production and microbial iron reduction. Additionally, scanning electron microscopy (SEM) was used to confirm the presence of S. oneidensis cells and biofilm. Our results suggest that during early/initial stage (75 days) of column incubation, SIP measurements revealed that phase and imaginary conductivity responses decreased as the concentration of reduced iron decreased below 2.0 mM. In contrast, we observed only a moderate increase in phase and imaginary conductivity ( 30%) within iron-free columns as a result of increases in S. oneidensis cells (CFU 1.5 x 1011) and biofilm production (7.0 mg ml-1). SEM analysis confirmed the presence of biofilm and cells within both iron-coated and iron-free columns. We hypothesize that the production of microbial metabolic byproducts is a potential mechanism explaining large phase shits observed in previous studies ( 50 mrads) rather than the conductivity of cells or biofilm. Our findings provide support for the following: i) ratio of cells to biofilm production only moderately influences both phase and imaginary conductivity response and ii) largest phase and imaginary conductivity response resulted from microbial metabolism (i.e. iron reduction) and potentially biofilm trapping of conductive materials (i

  9. Studies about behavior of microbial degradation of organic compounds

    International Nuclear Information System (INIS)

    Ohtsuka, Makiko

    2003-02-01

    Some of TRU waste include organic compounds, thus these organic compounds might be nutrients for microbial growth at disposal site. This disposal system might be exposed to high alkali condition by cement compounds as engineering barrier material. In the former experimental studies, it has been supposed that microbial exist under pH = 12 and the microbial activity acclimated to high alkali condition are able to degrade asphalt under anaerobic condition. Microbes are called extremophile that exist in cruel habitat as high alkali or reductive condition. We know less information about the activity of extremophile, though any recent studies reveal them. In this study, the first investigation is metabolic pathway as microbial activity, the second is microbial degradation of aromatic compounds in anaerobic condition, and the third is microbial activity under high alkali. Microbial metabolic pathway consist of two systems that fulfill their function each other. One system is to generate energy for microbial activities and the other is to convert substances for syntheses of organisms' structure materials. As these systems are based on redox reaction between substances, it is made chart of the microbial activity region using pH, Eh, and depth as parameter, There is much report that microbe is able to degrade aromatic compounds under aerobic or molecular O 2 utilizing condition. For degradation of aromatic compounds in anaerobic condition, supplying electron acceptor is required. Co-metabolism and microbial consortia has important role, too. Alcalophile has individual transporting system depending Na + and acidic compounds contained in cell wall. Generating energy is key for survival and growth under high alkali condition. Co-metabolism and microbial consortia are effective for microbial degradation of aromatic compounds under high alkali and reductive condition, and utilizable electron acceptor and degradable organic compounds are required for keeping microbial activity and

  10. The nanostructure of microbially-reduced graphene oxide fosters thick and highly-performing electrochemically-active biofilms

    Science.gov (United States)

    Virdis, Bernardino; Dennis, Paul G.

    2017-07-01

    Biofilms of electrochemically-active organisms are used in microbial electrochemical technologies (METs) to catalyze bioreactions otherwise not possible at bare electrodes. At present, however, achievable current outputs are still below levels considered sufficient for economic viability of large-scale METs implementations. Here, we report three-dimensional, self-aggregating biofilm composites comprising of microbial cells embedded with microbially-reduced graphene oxide (rGO) nanoparticles to form a thick macro-porous network with superior electrochemical properties. In the presence of metabolic substrate, these hybrid biofilms are capable of producing up to five times more catalytic current than the control biofilms. Cyclic voltammetry, linear sweep voltammetry, and electrochemical impedance spectroscopy, show that in spite of the increased thickness, the biofilms amended with GO display lower polarization/charge transfer resistance compared to the controls, which we ascribe to the incorporation of rGO into the biofilms, which (1) promotes fast electron transfer, yet conserving a macroporous structure that allows free diffusion of reactants and products, and (2) enhances the interfacial dynamics by allowing a higher load of microbial cells per electrode surface area. These results suggest an easy-to-apply and cost-effective method to produce high-performing electrochemically-active biofilms in situ.

  11. Stability of U(VI) and Tc(VII) Reducing Microbial Communities to Environmental Perturbation: Development and Testing of a Thermodynamic Network Model

    International Nuclear Information System (INIS)

    McKinley, James P.; Istok, Jonathan

    2005-01-01

    Previously published research from in situ field experiments at the NABIR Field Research Center have shown that cooperative metabolism of denitrifiers and Fe(III)/sulfate reducers is essential for creating subsurface conditions favorable for U(VI) and Tc(VII) bioreduction (Istok et al., 2004). The overall goal of this project is to develop and test a thermodynamic network model for predicting the effects of substrate additions and environmental perturbations on the composition and functional stability of subsurface microbial communities. The overall scientific hypothesis is that a thermodynamic analysis of the energy-yielding reactions performed by broadly defined groups of microorganisms can be used to make quantitative and testable predictions of the change in microbial community composition that will occur when a substrate is added to the subsurface or when environmental conditions change. An interactive computer program was developed to calculate the overall growth equation and free energy yield for microorganisms that grow by coupling selected combinations of electron acceptor and electron donor half-reactions. Each group performs a specific function (e.g. oxidation of acetate coupled to reduction of nitrate); collectively the groups provide a theoretical description of the entire natural microbial community. The microbial growth data are combined with an existing thermodynamic data base for associated geochemical reactions and used to simulate the coupled microbial-geochemical response of a complex natural system to substrate addition or any other environmental perturbations

  12. Dissecting the genetic and metabolic mechanisms of adaptation to the knockout of a major metabolic enzyme in Escherichia coli

    DEFF Research Database (Denmark)

    Long, Christopher P.; Gonzalez, Jacqueline E.; Feist, Adam M.

    2018-01-01

    Unraveling the mechanisms of microbial adaptive evolution following genetic or environmental challenges is of fundamental interest in biological science and engineering. When the challenge is the loss of a metabolic enzyme, adaptive responses can also shed significant insight into metabolic...

  13. Microbial effects

    International Nuclear Information System (INIS)

    Sharpe, V.J.

    1985-10-01

    The long term safety and integrity of radioactive waste disposal sites proposed for use by Ontario Hydro may be affected by the release of radioactive gases. Microbes mediate the primary pathways of waste degradation and hence an assessment of their potential to produce gaseous end products from the breakdown of low level waste was performed. Due to a number of unknown variables, assumptions were made regarding environmental and waste conditions that controlled microbial activity; however, it was concluded that 14 C and 3 H would be produced, albeit over a long time scale of about 1500 years for 14 C in the worst case situation

  14. Ecological distribution and population physiology defined by proteomics in a natural microbial community

    Science.gov (United States)

    Mueller, Ryan S.; Denef, Vincent J.; Kalnejais, Linda H.; Suttle, K. Blake; Thomas, Brian C.; Wilmes, Paul; Smith, Richard L.; Nordstrom, D. Kirk; McCleskey, R. Blaine; Shah, Menesh B.; VerBekmoes, Nathan C.; Hettich, Robert L.; Banfield, Jillian F.

    2010-01-01

    An important challenge in microbial ecology is developing methods that simultaneously examine the physiology of organisms at the molecular level and their ecosystem level interactions in complex natural systems. We integrated extensive proteomic, geochemical, and biological information from 28 microbial communities collected from an acid mine drainage environment and representing a range of biofilm development stages and geochemical conditions to evaluate how the physiologies of the dominant and less abundant organisms change along environmental gradients. The initial colonist dominates across all environments, but its proteome changes between two stable states as communities diversify, implying that interspecies interactions affect this organism's metabolism. Its overall physiology is robust to abiotic environmental factors, but strong correlations exist between these factors and certain subsets of proteins, possibly accounting for its wide environmental distribution. Lower abundance populations are patchier in their distribution, and proteomic data indicate that their environmental niches may be constrained by specific sets of abiotic environmental factors. This research establishes an effective strategy to investigate ecological relationships between microbial physiology and the environment for whole communities in situ.

  15. Microbial degradation of furanic compounds : Biochemistry, genetics, and impact

    NARCIS (Netherlands)

    Wierckx, N.; Koopman, F.; Ruijssenaars, H.J.; De Winde, J.H.

    2011-01-01

    Microbial metabolism of furanic compounds, especially furfural and 5-hydroxymethylfurfural (HMF), is rapidly gaining interest in the scientific community. This interest can largely be attributed to the occurrence of toxic furanic aldehydes in lignocellulosic hydrolysates. However, these compounds

  16. Phylogenetic and functional analysis of metagenome sequence from high-temperature archaeal habitats demonstrate linkages between metabolic potential and geochemistry

    Directory of Open Access Journals (Sweden)

    William P. Inskeep

    2013-05-01

    Full Text Available Geothermal habitats in Yellowstone National Park (YNP provide an unparalled opportunity to understand the environmental factors that control the distribution of archaea in thermal habitats. Here we describe, analyze and synthesize metagenomic and geochemical data collected from seven high-temperature sites that contain microbial communities dominated by archaea relative to bacteria. The specific objectives of the study were to use metagenome sequencing to determine the structure and functional capacity of thermophilic archaeal-dominated microbial communities across a pH range from 2.5 to 6.4 and to discuss specific examples where the metabolic potential correlated with measured environmental parameters and geochemical processes occurring in situ. Random shotgun metagenome sequence (~40-45 Mbase Sanger sequencing per site was obtained from environmental DNA extracted from high-temperature sediments and/or microbial mats and subjected to numerous phylogenetic and functional analyses. Analysis of individual sequences (e.g., MEGAN and G+C content and assemblies from each habitat type revealed the presence of dominant archaeal populations in all environments, 10 of whose genomes were largely reconstructed from the sequence data. Analysis of protein family occurrence, particularly of those involved in energy conservation, electron transport and autotrophic metabolism, revealed significant differences in metabolic strategies across sites consistent with differences in major geochemical attributes (e.g., sulfide, oxygen, pH. These observations provide an ecological basis for understanding the distribution of indigenous archaeal lineages across high temperature systems of YNP.

  17. Biosurfactants during in situ bioremediation: factors that influence the production and challenges in evalution.

    Science.gov (United States)

    Decesaro, Andressa; Machado, Thaís Strieder; Cappellaro, Ângela Carolina; Reinehr, Christian Oliveira; Thomé, Antônio; Colla, Luciane Maria

    2017-09-01

    Research on the influence of biosurfactants on the efficiency of in situ bioremediation of contaminated soil is continuously growing. Despite the constant progress in understanding the mechanisms involved in the effects of biosurfactants, there are still many factors that are not sufficiently elucidated. There is a lack of research on autochthonous or exogenous microbial metabolism when biostimulation or bioaugmentation is carried out to produce biosurfactants at contaminated sites. In addition, studies on the application of techniques that measure the biosurfactants produced in situ are needed. This is important because, although the positive influence of biosurfactants is often reported, there are also studies where no effect or negative effects have been observed. This review aimed to examine some studies on factors that can improve the production of biosurfactants in soils during in situ bioremediation. Moreover, this work reviews the methodologies that can be used for measuring the production of these biocomposts. We reviewed studies on the potential of biosurfactants to improve the bioremediation of hydrocarbons, as well as the limitations of methods for the production of these biomolecules by microorganisms in soil.

  18. Harnessing a methane-fueled, sediment-free mixed microbial community for utilization of distributed sources of natural gas.

    Science.gov (United States)

    Marlow, Jeffrey J; Kumar, Amit; Enalls, Brandon C; Reynard, Linda M; Tuross, Noreen; Stephanopoulos, Gregory; Girguis, Peter

    2018-06-01

    Harnessing the metabolic potential of uncultured microbial communities is a compelling opportunity for the biotechnology industry, an approach that would vastly expand the portfolio of usable feedstocks. Methane is particularly promising because it is abundant and energy-rich, yet the most efficient methane-activating metabolic pathways involve mixed communities of anaerobic methanotrophic archaea and sulfate reducing bacteria. These communities oxidize methane at high catabolic efficiency and produce chemically reduced by-products at a comparable rate and in near-stoichiometric proportion to methane consumption. These reduced compounds can be used for feedstock and downstream chemical production, and at the production rates observed in situ they are an appealing, cost-effective prospect. Notably, the microbial constituents responsible for this bioconversion are most prominent in select deep-sea sediments, and while they can be kept active at surface pressures, they have not yet been cultured in the lab. In an industrial capacity, deep-sea sediments could be periodically recovered and replenished, but the associated technical challenges and substantial costs make this an untenable approach for full-scale operations. In this study, we present a novel method for incorporating methanotrophic communities into bioindustrial processes through abstraction onto low mass, easily transportable carbon cloth artificial substrates. Using Gulf of Mexico methane seep sediment as inoculum, optimal physicochemical parameters were established for methane-oxidizing, sulfide-generating mesocosm incubations. Metabolic activity required >∼40% seawater salinity, peaking at 100% salinity and 35 °C. Microbial communities were successfully transferred to a carbon cloth substrate, and rates of methane-dependent sulfide production increased more than threefold per unit volume. Phylogenetic analyses indicated that carbon cloth-based communities were substantially streamlined and were

  19. Mass spectral molecular networking of living microbial colonies

    NARCIS (Netherlands)

    Watrous, J.; Roach, P.; Alexandrov, T.; Heath, B.S.; Yang, J.Y.; Kersten, R.D.; Voort, van der M.; Pogliano, K.; Gross, H.; Raaijmakers, J.; Moore, B.S.; Laskin, J.; Bandeira, N.; Dorrestein, P.C.

    2012-01-01

    Integrating the governing chemistry with the genomics and phenotypes of microbial colonies has been a “holy grail” in microbiology. This work describes a highly sensitive, broadly applicable, and cost-effective approach that allows metabolic profiling of live microbial colonies directly from a Petri

  20. Microbial metatranscriptomics in a permanent marine oxygen minimum zone

    OpenAIRE

    Stewart, Frank J.; Ulloa, Osvaldo; DeLong, Edward

    2010-01-01

    Simultaneous characterization of taxonomic composition, metabolic gene content and gene expression in marine oxygen minimum zones (OMZs) has potential to broaden perspectives on the microbial and biogeochemical dynamics in these environments. Here, we present a metatranscriptomic survey of microbial community metabolism in the Eastern Tropical South Pacific OMZ off northern Chile. Community RNA was sampled in late austral autumn from four depths (50, 85, 110, 200 m) extending across the oxycl...

  1. In situ experimentation at the water/sediment interface in the deep sea: 2. Biotransformation of dissolved organic substrates by microbial communities at 2000m depth in the Bay of Biscay

    Science.gov (United States)

    Cahet, Guy; Daumas, Raoul; Sibuet, Myriam

    Few attempts have been made to quantify the utilization of organic matter by the bacteria of the superficial layers of deep sea sediment. During two BIOCYAN cruises (August 1986 and June 1987) we used the submersible Cyana, to incubate sediment samples in situ in a specially designed box core in presence of 14C-glutamic acid and 3H leucine. These experiments were conducted at 2000m depth in the Bay of Biscay. Bacterial activity was stopped by the injection of formaldehyde. Samples were retrieved with the research submersible Cyana and its accompanying free vehicle shuttle. Sediment organic matter was fractioned into four components: 1) 14CO 2; 2) nucleic components and polysacharids; 3) labile proteins; and 4) condensed hydrolysable polymers. To evaluate the barotolerance of deep-sea bacteria, undisturbed superficial layer samples were also incubated with the same labelled substrates at 4°C at the atmospheric pressure. In both cases, and except for glucose, our results show that distributions of radioactivity in the different components of the organic material were almost similar. However, the rate of incorporation was usually higher for in situ experiments than for decompressed samples. Bacterial utilization of both 14C glutamic acid and 14C glucose were higher in June than in August. Such differences may result from changes in the food supply arriving as sinking particles and deriving from the photosynthetically productive surface waters. Food input was probably more important in June than in August leading to corresponding increases in: 1) the abundance of derived bacteria, and 2) deep-sea bacterial activities.

  2. Nitrate metabolism in the gromiid microbial universe

    DEFF Research Database (Denmark)

    Høgslund, Signe; Risgaard-Petersen, Nils; Cedhagen, Tomas

    enclose and regulate a small biogeochemical universe within their cell. Their transparent proteinaceous cell wall surrounds a complex matrix consisting of sediment, bacteria and nitrate which is concentrated to hundreds of mM in the gromiid cell. The nitrate is respired to dinitrogen, but in contrast...

  3. Microbial metabolism part 13 metabolites of hesperetin

    Science.gov (United States)

    The fungal culture, Mucor ramannianus (ATCC 2628) transformed hesperitin to four metabolites: 4'-methoxy -5, 7, 8, 3'-tetrahydroxyflavanone (8-hydroxyhesperetin), 5, 7, 3', 4'-tetrahydroxyflavanone (eriodictyol), 4'-methoxy-5, 3'-dihydroxyflavanone 7-sulfate (hesperetin 7-sulfate) and 5, 7, 3'-tri...

  4. Impact of simulated acid rain on soil microbial community function in Masson pine seedlings

    Directory of Open Access Journals (Sweden)

    Lin Wang

    2014-09-01

    Conclusion: The results obtained indicated that the higher acid load decreased the soil microbial activity and no effects on soil microbial diversity assessed by Biolog of potted Masson pine seedlings. Simulated acid rain also changed the metabolic capability of the soil microbial community.

  5. Microbial changes during pregnancy, birth and infancy

    Directory of Open Access Journals (Sweden)

    Meital Nuriel-Ohayon

    2016-07-01

    Full Text Available Several healthy developmental processes such as pregnancy, fetal development and infant development include a multitude of physiological changes: weight gain, hormonal and metabolic changes, as well as immune changes. In this review we present an additional important factor which both influences and is affected by these physiological processes- the microbiome. We summarize the known changes in microbiota composition at a variety of body sites including gut, vagina, oral cavity and placenta, throughout pregnancy, fetal development and early childhood. There is still a lot to be discovered; yet several pieces of research point to the healthy desired microbial changes. Future research is likely to unravel precise roles and mechanisms of the microbiota in gestation; perhaps linking the metabolic, hormonal and immune changes together. Although some research has started to link microbial dysbiosis and specific microbial populations with unhealthy pregnancy complications, it is important to first understand the context of the natural healthy microbial changes occurring. Until recently the placenta and developing fetus were considered to be germ free, containing no apparent microbiome. We present multiple study results showing distinct microbiota compositions in the placenta and meconium, alluding to early microbial colonization. These results may change dogmas and our overall understanding of the importance and roles of microbiota from the beginning of life. We further review the main factors shaping the infant microbiome- modes of delivery, feeding, weaning, and exposure to antibiotics. Taken together, we are starting to build a broader understanding of healthy vs. abnormal microbial alterations throughout major developmental time-points.

  6. The information science of microbial ecology.

    Science.gov (United States)

    Hahn, Aria S; Konwar, Kishori M; Louca, Stilianos; Hanson, Niels W; Hallam, Steven J

    2016-06-01

    A revolution is unfolding in microbial ecology where petabytes of 'multi-omics' data are produced using next generation sequencing and mass spectrometry platforms. This cornucopia of biological information has enormous potential to reveal the hidden metabolic powers of microbial communities in natural and engineered ecosystems. However, to realize this potential, the development of new technologies and interpretative frameworks grounded in ecological design principles are needed to overcome computational and analytical bottlenecks. Here we explore the relationship between microbial ecology and information science in the era of cloud-based computation. We consider microorganisms as individual information processing units implementing a distributed metabolic algorithm and describe developments in ecoinformatics and ubiquitous computing with the potential to eliminate bottlenecks and empower knowledge creation and translation. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  7. The Role of Microbial Amino Acid Metabolism in Host Metabolism

    OpenAIRE

    Evelien P. J. G. Neis; Cornelis H. C. Dejong; Sander S. Rensen

    2015-01-01

    Disruptions in gut microbiota composition and function are increasingly implicated in the pathogenesis of obesity, insulin resistance, and type 2 diabetes mellitus. The functional output of the gut microbiota, including short-chain fatty acids and amino acids, are thought to be important modulators underlying the development of these disorders. Gut bacteria can alter the bioavailability of amino acids by utilization of several amino acids originating from both alimentary and endogenous protei...

  8. Technical and Regulatory Requirements for Enhanced In Situ Bioremediation of Chlorinated Solvents in Groundwater

    National Research Council Canada - National Science Library

    1998-01-01

    Enhanced in situ bioremediation (EISB) of chlorinated solvents in groundwater involves the input of an organic carbon source, nutrients, electron acceptors, and/or microbial cultures to stimulate degradation...

  9. In situ bioreduction of technetium and uranium in a nitrate-contaminated aquifer

    International Nuclear Information System (INIS)

    IstokD, Jonathan; Senko, J.M.; Krumholz, Lee R.; Watson, David B.; Bogle, Mary Anna; Peacock, Aaron D.; Change, Y.J.; White, David C.

    2004-01-01

    The potential to stimulate an indigenous microbial community to reduce a mixture of U(VI) and Tc(VII) in the presence of high (120 mM) initial NO 3 - co-contamination was evaluated in a shallow unconfined aquifer using a series of single-well, push-pull tests. In the absence of added electron donor, NO 3 - , Tc(VII), and U(VI) reduction was not detectable. However, in the presence of added ethanol, glucose, or acetate to serve as electron donor, rapid NO 3 - utilization was observed. The accumulation of NO 2 - , the absence of detectable NH 4 + accumulation, and the production of N 2 O during in situ acetylene-block experiments suggest that NO 3 - was being consumed via denitrification. Tc(VII) reduction occurred concurrently with NO 3 - reduction, but U(VI) reduction was not observed until two or more donor additions resulted in iron-reducing conditions, as detected by the production of Fe(II). Reoxidation/remobilization of U(IV) was also observed in tests conducted with high (120 mM) but not low (1 mM) initial NO 3 - concentrations and not during acetylene-block experiments conducted with high initial NO 3 - . These results suggest that NO 3 - -dependent microbial U(IV) oxidation may inhibit or reverse U(VI) reduction and decrease the stability of U(IV) in this environment. Changes in viable biomass, community composition, metabolic status, and respiratory state of organisms harvested from down-well microbial samplers deployed during these tests were consistent with the conclusions that electron donor additions resulted in microbial growth, the creation of anaerobic conditions, and an increase in activity of metal-reducing organisms (e.g., Geobacter). The results demonstrate that it is possible to stimulate the simultaneous bioreduction of U(VI) and Tc(VII) mixtures commonly found with NO 3 - co-contamination at radioactive waste sites.

  10. Glycerol supplementation of the growth medium enhances in situ detoxification of furfural by Clostridium beijerinckii during butanol fermentation.

    Science.gov (United States)

    Ujor, Victor; Agu, Chidozie Victor; Gopalan, Venkat; Ezeji, Thaddeus Chukwuemeka

    2014-01-01

    Lignocellulose-derived microbial inhibitors such as furfural and 5-hydroxymethyl furfural adversely affect fermentation of lignocellulosic biomass hydrolysates to fuels and chemicals due to their toxicity on fermenting microbes. To harness the potential of lignocellulose as a cheap source of fermentable sugars, in situ detoxification of furfural and other lignocellulose-derived microbial inhibitors is essential. To enhance in situ detoxification and tolerance of furfural by Clostridium beijerinckii NCIMB 8052 during acetone-butanol-ethanol (ABE) fermentation, the effect of glycerol on NADH/NADPH generation and ABE production by furfural (4, 5, and 6 g/L)-challenged cultures was investigated in this study. In all instances, beneficial outcomes were observed. For example, the fermentation medium supplemented with glycerol and subjected to 5 g/L furfural elicited up to 1.8- and 3-fold increases, respectively, in NADH and NADPH levels in C. beijerinckii 8052 relative to the control culture. These critical changes are the likely underpinnings for the glycerol-mediated 2.3-fold increase in the rate of detoxification of 5 g/L furfural, substrate consumption, and ABE production compared to the unsupplemented medium. Collectively, these results demonstrate that increased intracellular NADH/NADPH in C. beijerinckii 8052 due to glycerol utilization engenders favorable effects on many aspects of cellular metabolism, including enhanced furfural reduction and increased ABE production.

  11. Deep microbial life in the Altmark natural gas reservoir: baseline characterization prior CO2 injection

    Science.gov (United States)

    Morozova, Daria; Shaheed, Mina; Vieth, Andrea; Krüger, Martin; Kock, Dagmar; Würdemann, Hilke

    2010-05-01

    Within the framework of the CLEAN project (CO2 Largescale Enhanced gas recovery in the Altmark Natural gas field) technical basics with special emphasis on process monitoring are explored by injecting CO2 into a gas reservoir. Our study focuses on the investigation of the in-situ microbial community of the Rotliegend natural gas reservoir in the Altmark, located south of the city Salzwedel, Germany. In order to characterize the microbial life in the extreme habitat we aim to localize and identify microbes including their metabolism influencing the creation and dissolution of minerals. The ability of microorganisms to speed up dissolution and formation of minerals might result in changes of the local permeability and the long-term safety of CO2 storage. However, geology, structure and chemistry of the reservoir rock and the cap rock as well as interaction with saline formation water and natural gases and the injected CO2 affect the microbial community composition and activity. The reservoir located at the depth of about 3500m, is characterised by high salinity fluid and temperatures up to 127° C. It represents an extreme environment for microbial life and therefore the main focus is on hyperthermophilic, halophilic anaerobic microorganisms. In consequence of the injection of large amounts of CO2 in the course of a commercial EGR (Enhanced Gas Recovery) the environmental conditions (e.g. pH, temperature, pressure and solubility of minerals) for the autochthonous microorganisms will change. Genetic profiling of amplified 16S rRNA genes are applied for detecting structural changes in the community by using PCR- SSCP (PCR-Single-Strand-Conformation Polymorphism) and DGGE (Denaturing Gradient Gel Electrophoresis). First results of the baseline survey indicate the presence of microorganisms similar to representatives from other saline, hot, anoxic, deep environments. However, due to the hypersaline and hyperthermophilic reservoir conditions, cell numbers are low, so that

  12. Efeitos hemodinâmicos e metabólicos iniciais da perfusão hipotérmica intestinal in situ.: avaliação de um novo modelo canino de autotransplante intestinal Initial hemodynamic and metabolic effects of intestinal hypothermic perfusion in situ: an alternative model of canine intestinal autotransplantation

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