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Microbial Metabolism (microbial + metabolism)
Selected AbstractsApplication of Bacterial Biocathodes in Microbial Fuel CellsELECTROANALYSIS, Issue 19-20 2006Zhen He Abstract This review addresses the development and experimental progress of biocathodes in microbial fuel cells (MFCs). Conventional MFCs consist of biological anodes and abiotic cathodes. The abiotic cathode usually requires a catalyst or an electron mediator to achieve high electron transfer, increasing the cost and lowering the operational sustainability. Such disadvantages can be overcome by biocathodes, which use microorganisms to assist cathodic reactions. Biocathodes are feasible in potentiostat-poised half cells, but only very few studies have investigated them in complete MFCs. The classification of biocathodes is based on which terminal electron acceptor is available. For aerobic biocathodes with oxygen as the terminal electron acceptor, electron mediators, such as iron and manganese, are first reduced by the cathode (abiotically) and then reoxidized by bacteria. Anaerobic biocathodes directly reduce terminal electron acceptors, such as nitrate and sulfate, by accepting electrons from a cathode electrode through microbial metabolism. Biocathodes are promising in MFCs, and we anticipate a successful application after several breakthroughs are made. [source] The Dry Limit of Microbial Life in the Atacama Desert Revealed by Calorimetric ApproachesENGINEERING IN LIFE SCIENCES (ELECTRONIC), Issue 5 2008N. Barros Abstract The Atacama desert in Chile is one of the driest and most lifeless environments on Earth. It rains possibly once a decade. NASA examined these soils as a model for the Martian environment by comparing their degradation activity with Martian soil and looking for "the dry limit of life". The existence of heterotrophic bacteria in Atacama soil was demonstrated by DNA extraction and by the isolation of microorganisms. So far, however, no data have been available about the metabolic activities in these soils due to the limitations of the existing methodologies when applied to desert soils. Calorimetry was used to obtain information on the metabolic and thermal properties of eleven soil samples collected at different sites in the Atacama desert. Differential scanning calorimetry and isothermal calorimetry were employed to determine the pyrolysis properties of the carbon-containing matter and to measure biomass and microbial metabolism. They were compared to other soil properties such as total carbon and nitrogen, carbon to nitrogen ratio and pH. There was measurable organic matter in nine of the eleven samples and the heat of pyrolysis of those soils was correlated to the carbon content. In five of the eleven samples no biomass could be detected and the existence of basal microbial metabolism could not be established because all samples showed endothermic activity, probably from inorganic reactions with water. Six samples showed microbial activation after the addition of glucose. Carbon content, nitrogen content and the microbial activity after glucose amendment were correlated to the altitude and to the average minimum temperature of the sampling sites calculated from meteorological data. The detectable microbial metabolism was more dissipative with increasing altitude and decreasing temperature. [source] Thermophilic anaerobes in Arctic marine sediments induced to mineralize complex organic matter at high temperatureENVIRONMENTAL MICROBIOLOGY, Issue 4 2010Casey Hubert Summary Marine sediments harbour diverse populations of dormant thermophilic bacterial spores that become active in sediment incubation experiments at much higher than in situ temperature. This response was investigated in the presence of natural complex organic matter in sediments of two Arctic fjords, as well as with the addition of freeze-dried Spirulina or individual high-molecular-weight polysaccharides. During 50°C incubation experiments, Arctic thermophiles catalysed extensive mineralization of the organic matter via extracellular enzymatic hydrolysis, fermentation and sulfate reduction. This high temperature-induced food chain mirrors sediment microbial processes occurring at cold in situ temperatures (near 0°C), yet it is catalysed by a completely different set of microorganisms. Using sulfate reduction rates (SRR) as a proxy for organic matter mineralization showed that differences in organic matter reactivity determined the extent of the thermophilic response. Fjord sediments with higher in situ SRR also supported higher SRR at 50°C. Amendment with Spirulina significantly increased volatile fatty acids production and SRR relative to unamended sediment in 50°C incubations. Spirulina amendment also revealed temporally distinct sulfate reduction phases, consistent with 16S rRNA clone library detection of multiple thermophilic Desulfotomaculum spp. enriched at 50°C. Incubations with four different fluorescently labelled polysaccharides at 4°C and 50°C showed that the thermophilic population in Arctic sediments produce a different suite of polymer-hydrolysing enzymes than those used in situ by the cold-adapted microbial community. Over time, dormant marine microorganisms like these are buried in marine sediments and might eventually encounter warmer conditions that favour their activation. Distinct enzymatic capacities for organic polymer degradation could allow specific heterotrophic populations like these to play a role in sustaining microbial metabolism in the deep, warm, marine biosphere. [source] THIS ARTICLE HAS BEEN RETRACTED Tn5530 from Burkholderia cepacia strain 2a encodes a chloride channel protein essential for the catabolism of 2,4-dichlorophenoxyacetic acidENVIRONMENTAL MICROBIOLOGY, Issue 1 2007Antonio Sebastianelli Summary Chloride channel proteins (ClC) are found in living systems where they transport chloride ions across cell membranes. Recently, the structure/function of two prokaryotic ClC has been determined but little is known about the role of these proteins in the microbial metabolism of chlorinated compounds. Here we show that transposon Tn5530 from Burkholderia cepacia strain 2a encodes a ClC protein (BcClC) which is responsible for expelling Cl, ions generated during the catabolism of 2,4-dichlorophenoxyacetic acid (a chlorinated herbicide). We found that BcClC has the ability to transport Cl, ions across reconstituted proteoliposome membranes. We created two mutants in which the intrachannel glutamate residue of the protein, known to be responsible for opening and closing the channel (i.e. gating), was changed in order to create constitutively open and closed forms. We observed that cells carrying the closed-channel protein accumulated Cl, ions intracellularly leading to a decrease in intracellular pH, cell stasis and death. Further, we established that BcClC has the same gating mechanism as that reported for the ClC protein from Salmonella typhimurium. Our results show that the physiological role of ClC is to maintain cellular homeostasis which can be impaired by the catabolism of chlorinated compounds. [source] Microbial degradation of isoproturon and related phenylurea herbicides in and below agricultural fieldsFEMS MICROBIOLOGY ECOLOGY, Issue 1 2003Sebastian R Sørensen Abstract The phenylurea herbicides are an important group of pesticides used extensively for pre- or post-emergence weed control in cotton, fruit and cereal crops worldwide. The detection of phenylurea herbicides and their metabolites in surface and ground waters has raised the awareness of the important role played by agricultural soils in determining water quality. The degradation of phenylurea herbicides following application to agricultural fields is predominantly microbial. However, evidence suggests a slow degradation of the phenyl ring, and substantial spatial heterogeneity in the distribution of active degradative populations, which is a key factor determining patterns of leaching losses from agricultural fields. This review summarises current knowledge on the microbial metabolism of isoproturon and related phenylurea herbicides in and below agricultural soils. It addresses topics such as microbial degradation of phenylurea herbicides in soil and subsurface environments, characteristics of known phenylurea-degrading soil micro-organisms, and similarities between metabolic pathways for different phenylurea herbicides. Finally, recent studies in which molecular and microbiological techniques have been used to provide insight into the in situ microbial metabolism of isoproturon within an agricultural field will be discussed. [source] Energetics of overall metabolic reactions of thermophilic and hyperthermophilic Archaea and BacteriaFEMS MICROBIOLOGY REVIEWS, Issue 2 2001Jan P. Amend Abstract Thermophilic and hyperthermophilic Archaea and Bacteria have been isolated from marine hydrothermal systems, heated sediments, continental solfataras, hot springs, water heaters, and industrial waste. They catalyze a tremendous array of widely varying metabolic processes. As determined in the laboratory, electron donors in thermophilic and hyperthermophilic microbial redox reactions include H2, Fe2+, H2S, S, S2O32,, S4O62,, sulfide minerals, CH4, various mono-, di-, and hydroxy-carboxylic acids, alcohols, amino acids, and complex organic substrates; electron acceptors include O2, Fe3+, CO2, CO, NO3,, NO2,, NO, N2O, SO42,, SO32,, S2O32,, and S. Although many assimilatory and dissimilatory metabolic reactions have been identified for these groups of microorganisms, little attention has been paid to the energetics of these reactions. In this review, standard molal Gibbs free energies (,Gr°) as a function of temperature to 200°C are tabulated for 370 organic and inorganic redox, disproportionation, dissociation, hydrolysis, and solubility reactions directly or indirectly involved in microbial metabolism. To calculate values of ,Gr° for these and countless other reactions, the apparent standard molal Gibbs free energies of formation (,G°) at temperatures to 200°C are given for 307 solids, liquids, gases, and aqueous solutes. It is shown that values of ,Gr° for many microbially mediated reactions are highly temperature dependent, and that adopting values determined at 25°C for systems at elevated temperatures introduces significant and unnecessary errors. The metabolic processes considered here involve compounds that belong to the following chemical systems: H,O, H,O,N, H,O,S, H,O,N,S, H,O,Cinorganic, H,O,C, H,O,N,C, H,O,S,C, H,O,N,S,Camino acids, H,O,S,C,metals/minerals, and H,O,P. For four metabolic reactions of particular interest in thermophily and hyperthermophily (knallgas reaction, anaerobic sulfur and nitrate reduction, and autotrophic methanogenesis), values of the overall Gibbs free energy (,Gr) as a function of temperature are calculated for a wide range of chemical compositions likely to be present in near-surface and deep hydrothermal and geothermal systems. [source] Exoenzyme activities as indicators of dissolved organic matter composition in the hyporheic zone of a floodplain riverFRESHWATER BIOLOGY, Issue 8 2010SANDRA M. CLINTON Summary 1. We measured the hyporheic microbial exoenzyme activities in a floodplain river to determine whether dissolved organic matter (DOM) bioavailability varied with overlying riparian vegetation patch structure or position along flowpaths. 2. Particulate organic matter (POM), dissolved organic carbon (DOC), dissolved oxygen (DO), electrical conductivity and temperature were sampled from wells in a riparian terrace on the Queets River, Washington, U.S.A. on 25 March, 15 May, 20 July and 09 October 1999. Dissolved nitrate, ammonium and soluble reactive phosphorus were also collected on 20 July and 09 October 1999. Wells were characterised by their associated overlying vegetation: bare cobble/young alder, mid-aged alder (8,20 years) and old alder/old-growth conifer (25 to >100 years). POM was analysed for the ash-free dry mass and the activities of eight exoenzymes (,-glucosidase, ,-glucosidase, , -N-acetylglucosaminidase, xylosidase, phosphatase, leucine aminopeptidase, esterase and endopeptidase) using fluorogenic substrates. 3. Exoenzyme activities in the Queets River hyporheic zone indicated the presence of an active microbial community metabolising a diverse array of organic molecules. Individual exoenzyme activity (mean ± standard error) ranged from 0.507 ± 0.1547 to 22.8 ± 5.69 ,mol MUF (g AFDM),1 h,1, was highly variable among wells and varied seasonally, with the lowest rates occurring in March. Exoenzyme activities were weakly correlated with DO, DOC and inorganic nutrient concentrations. 4. Ratios of leucine aminopeptidase : ,-glucosidase were low in March, May and October and high in July, potentially indicating a switch from polysaccharides to proteins as the dominant component of microbial metabolism. 5. Principal components analysis indicated that there were patch effects and that these effects were strongest in the summer. 6. DOM degradation patterns did not change systematically along hyporheic flowpaths but varied with overlying forest patch type in the Queets River hyporheic zone, suggesting that additional carbon inputs exist. We hypothesise that the most likely input is the downward movement of DOM from overlying riparian soils. Understanding this movement of DOM from soils to subsurface water is essential for understanding both the hyporheic metabolism and the carbon budget of streams and rivers. [source] The potential for abiotic organic synthesis and biosynthesis at seafloor hydrothermal systemsGEOFLUIDS (ELECTRONIC), Issue 1-2 2010E. SHOCK Geofluids (2010) 10, 161,192 Abstract Calculations are presented of the extent to which chemical disequilibria are generated when submarine hydrothermal fluids mix with sea water. These calculations involve quantifying the chemical affinity for individual reactions by comparing equilibrium compositions with the compositions of mixtures in which oxidation,reduction reactions are inhibited. The oxidation,reduction reactions that depart from equilibrium in these systems provide energy for chemotrophic microbial metabolism. Methanogenesis is an example of this phenomenon, in which the combination of carbon dioxide, hydrogen and methane induced by fluid mixing is far from equilibrium, which can be approached if more methane is generated. Similarly, the production of other organic compounds is also favorable under the same conditions that permit methanogenesis. Alkanes, alkenes, alcohols, aldehydes, carboxylic acids and amino acids are among the compounds that, if formed, would lower the energetic state of the chemical composition generated in mixed fluids. The resulting positive values of chemical affinity correspond to the thermodynamic drive required for abiotic organic synthesis. It is also possible that energy release accompanies biosynthesis by chemotrophic organisms. In this way, hydrothermal ecosystems differ radically from familiar ecosystems at Earth's surface. If captured, the energy released may be sufficient to drive biosynthesis of carbohydrates, purines, pyrimidines and other compounds which require energy inputs. [source] Partitioning sources of soil respiration in boreal black spruce forest using radiocarbonGLOBAL CHANGE BIOLOGY, Issue 2 2006Edward A.G. Schuur Abstract Separating ecosystem and soil respiration into autotrophic and heterotrophic component sources is necessary for understanding how the net ecosystem exchange of carbon (C) will respond to current and future changes in climate and vegetation. Here, we use an isotope mass balance method based on radiocarbon to partition respiration sources in three mature black spruce forest stands in Alaska. Radiocarbon (,14C) signatures of respired C reflect the age of substrate C and can be used to differentiate source pools within ecosystems. Recently-fixed C that fuels plant or microbial metabolism has ,14C values close to that of current atmospheric CO2, while C respired from litter and soil organic matter decomposition will reflect the longer residence time of C in plant and soil C pools. Contrary to our expectations, the ,14C of C respired by recently excised black spruce roots averaged 14, greater than expected for recently fixed photosynthetic products, indicating that some portion of the C fueling root metabolism was derived from C storage pools with turnover times of at least several years. The ,14C values of C respired by heterotrophs in laboratory incubations of soil organic matter averaged 60, higher than the contemporary atmosphere ,14CO2, indicating that the major contributors to decomposition are derived from a combination of sources consistent with a mean residence time of up to a decade. Comparing autotrophic and heterotrophic ,14C end members with measurements of the ,14C of total soil respiration, we calculated that 47,63% of soil CO2 emissions were derived from heterotrophic respiration across all three sites. Our limited temporal sampling also observed no significant differences in the partitioning of soil respiration in the early season compared with the late season. Future work is needed to address the reasons for high ,14C values in root respiration and issues of whether this method fully captures the contribution of rhizosphere respiration. [source] Linking microbial activity and soil organic matter transformations in forest soils under elevated CO2GLOBAL CHANGE BIOLOGY, Issue 2 2005S. A. Billings Abstract Soil organic matter (SOM) dynamics ultimately govern the ability of soil to provide long-term C sequestration and the nutrients required for ecosystem productivity. Predicting belowground responses to elevated CO2 requires an integrated understanding of SOM transformations and the microbial activity that governs them. It remains unclear how the microorganisms upon which these transformations depend will function in an elevated CO2 world. This study examines SOM transformations and microbial metabolism in soils from the Duke Free Air Carbon Enrichment site in North Carolina, USA. We assessed microbial respiration and net nitrogen (N) mineralization in soils with and without elevated CO2 exposure during a 100-day incubation. We also traced the depleted C isotopic signature of the supplemental CO2 into SOM and the soils' phospholipid fatty acids (PLFA), which serve as biomarkers for living cells. Cumulative net N mineralization in elevated CO2 soils was 50% that in control soils after a 100-day incubation. Respiration was not altered with elevated CO2. C : N ratios of bulk SOM did not change with elevated CO2, but incubation data suggest that the C : N ratios of mineralized organic matter increased with elevated CO2. Values of SOM ,13C were depleted with elevated CO2 (,26.7±0.2 vs. ,30.2±0.3,), reflecting the depleted signature of the supplemental CO2. We compared ,13C of individual PLFA with the ,13C of SOM to discern incorporation of the depleted C isotopic signature into soil microbial groups in elevated CO2 plots. PLFA i15:0, a15:0, and 10Met18:0 reflected significant incorporation of recently produced photosynthate, suggesting that the bacterial groups defined by these biomarkers are active metabolizers in elevated CO2 soils. At least one of these groups (actinomycetes, 10Met18:0) specializes in metabolizing less labile substrates. Because control plots did not receive an equivalent 13C tracer, we cannot determine from these data whether this group of organisms was stimulated by elevated CO2 compared with these organisms in control soils. Stimulation of this group, if it occurred in the elevated CO2 plot, would be consistent with a decline in the availability of mineralizable organic matter with elevated CO2, which incubation data suggest may be the case in these soils. [source] Redox Processes and Water Quality of Selected Principal Aquifer SystemsGROUND WATER, Issue 2 2008P.B. McMahon Reduction/oxidation (redox) conditions in 15 principal aquifer (PA) systems of the United States, and their impact on several water quality issues, were assessed from a large data base collected by the National Water-Quality Assessment Program of the USGS. The logic of these assessments was based on the observed ecological succession of electron acceptors such as dissolved oxygen, nitrate, and sulfate and threshold concentrations of these substrates needed to support active microbial metabolism. Similarly, the utilization of solid-phase electron acceptors such as Mn(IV) and Fe(III) is indicated by the production of dissolved manganese and iron. An internally consistent set of threshold concentration criteria was developed and applied to a large data set of 1692 water samples from the PAs to assess ambient redox conditions. The indicated redox conditions then were related to the occurrence of selected natural (arsenic) and anthropogenic (nitrate and volatile organic compounds) contaminants in ground water. For the natural and anthropogenic contaminants assessed in this study, considering redox conditions as defined by this framework of redox indicator species and threshold concentrations explained many water quality trends observed at a regional scale. An important finding of this study was that samples indicating mixed redox processes provide information on redox heterogeneity that is useful for assessing common water quality issues. Given the interpretive power of the redox framework and given that it is relatively inexpensive and easy to measure the chemical parameters included in the framework, those parameters should be included in routine water quality monitoring programs whenever possible. [source] A Simple Pore Water Hydrogen Diffusion Syringe SamplerGROUND WATER, Issue 6 2007Don A. Vroblesky Molecular hydrogen (H2) is an important intermediate product and electron donor in microbial metabolism. Concentrations of dissolved H2 are often diagnostic of the predominant terminal electron-accepting processes in ground water systems or aquatic sediments. H2 concentrations are routinely measured in ground water monitoring wells but are rarely measured in saturated aquatic sediments due to a lack of simple and practical sampling methods. This report describes the design and development (including laboratory and field testing) of a simple, syringe-based H2 sampler in (1) saturated, riparian sediments, (2) surface water bed sediments, and (3) packed intervals of a fractured bedrock borehole that are inaccessible by standard pumped methods. [source] Microbial degradation of the biocide polyhexamethylene biguanide: isolation and characterization of enrichment consortia and determination of degradation by measurement of stable isotope incorporation into DNAJOURNAL OF APPLIED MICROBIOLOGY, Issue 4 2007L.P. O'Malley Abstract Aims:, To isolate micro-organisms capable of utilizing polyhexamethylene biguanide (PHMB) as a sole source of nitrogen, and to demonstrate biodegradation of the biocide. Methods and Results:, Two consortia of bacteria were successfully enriched at the expense of PHMB, using sand from PHMB-treated swimming pools as inoculum. Both consortia were shown to contain bacteria belonging to the genera Sphingomonas, Azospirillum and Mesorhizobium. It was shown that the presence of both Sphingomonas and Azospirillum spp. was required for extensive growth of the consortia. In addition, the Sphingomonads were the only isolates capable of growth in axenic cultures dosed with PHMB. Using a stable isotope (15N),labelled PHMB, metabolism of the biocide by both consortia was demonstrated. By comparing the level of 15N atom incorporation into bacterial DNA after growth on either 15N-PHMB or 15N-labelled NH4Cl, it was possible to estimate the percentage of PHMB biodegradation. Conclusions:, The microbial metabolism of nitrogen from the biguanide moiety of PHMB has been demonstrated. It was revealed that Sphingomonas and Azospirillum spp. are the principal organisms responsible for growth at the expense of PHMB. Significance and Impact of the Study:, This is the first study to demonstrate the microbial metabolism of PHMB. [source] Influence of nitrogen on the degradation of toluene in a compost-based biofilterJOURNAL OF CHEMICAL TECHNOLOGY & BIOTECHNOLOGY, Issue 9 2001Marie-Caroline Delhoménie Abstract Two identical laboratory-scale bioreactors were operated simultaneously, each treating an input air flow rate of 1,m3,h,1. The biofilters consisted of multi-stage columns, each stage packed with a compost-based filtering material, which was not previously inoculated. The toluene inlet concentration was fixed at 1.5,g,m,3 of air. Apart from the necessary carbon, the elements nitrogen, phosphorus, sulfur, potassium and other micro-elements are also essential for microbial metabolism. These were distributed throughout the filter bed material by periodic ,irrigations' with various test nutrient solutions. The performance of each biofilter was quantified by determining its toluene removal efficiency, and elimination capacity. Nutrient solution nitrogen levels were varied from 0 to 6.0,g,dm,3, which led to elimination capacities of up to 50,g,m,3,h,1 being obtained for a toluene inlet load of 80,g,m,3,h,1. A theoretical analysis also confirmed that the optimum nitrogen solution concentration lays in the range 4.0,6.0,g,dm,3. Validation of the irrigation mode was achieved by watering each biofilter stage individually. Vertical stage-by-stage stratification of the biofilter performance was not detected, ie each filter bed section removed the same amount of pollutant, the elimination capacity per stage being about 16,g,m,3,h,1 per section of column. © 2001 Society of Chemical Industry [source] A general model of the public goods dilemmaJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 6 2010S. A. Frank Abstract An individually costly act that benefits all group members is a public good. Natural selection favours individual contribution to public goods only when some benefit to the individual offsets the cost of contribution. Problems of sex ratio, parasite virulence, microbial metabolism, punishment of noncooperators, and nearly all aspects of sociality have been analysed as public goods shaped by kin and group selection. Here, I develop two general aspects of the public goods problem that have received relatively little attention. First, variation in individual resources favours selfish individuals to vary their allocation to public goods. Those individuals better endowed contribute their excess resources to public benefit, whereas those individuals with fewer resources contribute less to the public good. Thus, purely selfish behaviour causes individuals to stratify into upper classes that contribute greatly to public benefit and social cohesion and to lower classes that contribute little to the public good. Second, if group success absolutely requires production of the public good, then the pressure favouring production is relatively high. By contrast, if group success depends weakly on the public good, then the pressure favouring production is relatively weak. Stated in this way, it is obvious that the role of baseline success is important. However, discussions of public goods problems sometimes fail to emphasize this point sufficiently. The models here suggest simple tests for the roles of resource variation and baseline success. Given the widespread importance of public goods, better models and tests would greatly deepen our understanding of many processes in biology and sociality. [source] FOREST-RIVER INTERACTIONS: INFLUENCE ON HYPORHEIC DISSOLVED ORGANIC CARBON CONCENTRATIONS IN A FLOODPLAIN TERRACE,JOURNAL OF THE AMERICAN WATER RESOURCES ASSOCIATION, Issue 3 2002Sandra M. Clinton ABSTRACT: In large floodplain rivers, hyporheic (subsurface) flow-paths transfer nutrients from productive riparian terraces to oligotrophic off-channel habitats. Because dissolved organic carbon (DOC) fuels microbial processes and hyporheic microorganisms represent the first stage of retention and transformation of these nutrients, understanding DOC flux can provide information on the constraints of microbial metabolism in the hyporheic zone of rivers. We monitored hydrology, physicochemical indicators, and dissolved organic carbon (DOC) dynamics during low and high discharge periods in the hyporheic zone of a riparian terrace on the Queets River, Washington, to understand what processes control the supply of carbon to subsurface microbial communities. As discharge increased, terrace hyporheic flowpaths changed from parallel to focused, and the location of surface water inputs to the terrace shifted from the terrace edge to head. Overall, DOC concentrations decreased along hyporheic flowpaths; however, concentrations at points along the flowpaths varied with position along the head gradient and age of the overlying vegetation. We estimated that there is insufficient DOC in adverting surface water to support hyporheic microbial metabolism in this riparian terrace. These trends indicate that there are additional carbon sources to the subsurface water, and we conclude that DOC is leaching from overlying riparian soils within the forest patches. Thus, subsurface DOC concentrations reflect a balance between surface water inputs, metabolic uptake, and allochthonous inputs from forest soils. [source] Web alert: systems biology relevant to microbial metabolismMICROBIAL BIOTECHNOLOGY, Issue 3 2008An annotated selection of World Wide Web sites relevant to the topics in Microbial Biotechnology [source] Cover Picture , Mol.MOLECULAR NUTRITION & FOOD RESEARCH (FORMERLY NAHRUNG/FOOD), Issue S1 2009Nutr. There is increasing interest in how dietary flavonoids and related compounds that make their way to the large intestine are broken down to simple phenolic acids by the colonic microflora and what potential impact they may have on the microflora itself and on colonic health. Find out more by reading this issue on dietary phenolics, absorption, mammalian and microbial metabolism and colonic health. [source] The detection of antibacterial actions of whole herb tinctures using luminescent Escherichia coliPHYTOTHERAPY RESEARCH, Issue 12 2007Kathryn Watt Abstract Two whole cell Escherichia coli luminescent biosensors were used to determine the antibacterial actions of 16 herbal tinctures. These bioassays can detect genotoxic (strain DPD2794) and general oxidative stress (DE135) events when challenged with antibacterial substances. Many of the herbal tinctures were active against these Gram-negative bacteria, affecting their metabolism without, in some cases, arresting cell growth or causing cell death. Antibacterial activity ranged from undetectable for Curcuma longa, Cinnamomum zeylanicum and Apium graveolens to highly effective against both E. coli strains in the case of Rosmarinus officinalis. Some of the results were unexpected. Althaea officinalis affected microbial metabolism in spite of the lack of literature precedent, and Cinnamomum zeylanicum did not appear to be antimicrobial, as claimed in some literature. It is concluded that studies using luminescent bacterial biosensors can provide important new insights into the potency and modes of the lethal and sub-lethal antibacterial action of whole herbs, and thereby provide crucial evidence for efficacy demanded by modern science and medicine. Copyright © 2007 John Wiley & Sons, Ltd. [source] Comparative analysis on microbial and rat metabolism of ginsenoside Rb1 by high-performance liquid chromatography coupled with tandem mass spectrometryBIOMEDICAL CHROMATOGRAPHY, Issue 7 2008Guangtong Chen Abstract Ginsenoside Rb1 is an active protopanaxadiol saponin from Panax species. In order to compare the similarities and differences of microbial and mammalian metabolisms of ginsenoside Rb1, the microbial transformation by Acremonium strictum and metabolism in rats were comparatively studied. Microbial transformation of ginsenoside Rb1 by Acremonium strictum AS 3.2058 resulted in the formation of eight metabolites. Ten metabolites (M1,M10) were detected from the in vivo study in rats and eight of them were identified as the same compounds as those obtained from microbial metabolism by liquid chromatography,tandem mass spectrometry analysis and comparison with reference standards obtained from microbial metabolism. Their structures were identified as ginsenoside Rd, gypenoside XVII, 20(S)-ginsenoside Rg3, 20(R)-ginsenoside Rg3, ginsenoside F2, compound K, 12, -hydroxydammar-3-one-20(S) -O-, -d- glucopyranoside, and 25-hydroxyl-(E)-20(22)-ene-ginsenoside Rg3, respectively. The structures of the additional two metabolites were tentatively characterized as 20(22),24-diene-ginsenoside Rg3 and 25-hydroxyginsenoside Rd by HPLC-MS/MS analysis. M7,M10 are the first four reported metabolites in vivo. The time course of rat metabolism of ginsenoside Rb1 was also investigated. Copyright © 2008 John Wiley & Sons, Ltd. [source] Liquid chromatography,tandem mass spectrometry for the identification of l -tetrahydropalmatine metabolites in Penicillium janthinellum and ratsBIOMEDICAL CHROMATOGRAPHY, Issue 1 2006Li Li Abstract l-Tetrahydropalmatine (l-THP) is an active alkaloid from Stephania ainiaca Diels. In order to compare the similarities and differences of microbial and mammalian metabolisms of l-THP, the microbial transformation by Penicillium janthinellum and metabolism in rats were investigated. Biotransformation of l-THP by Penicillium janthinellum AS 3.510 resulted in the formation of three metabolites. Their structures were identified as l-corydalmine, l-corypalmine and 9- O -desmethyl-l-THP, respectively, by comprehensive nuclear magnetic resonance and mass spectrometry (MS) analysis. Six metabolites (M1,M6) were detected from the in vivo study in rats and three of which (l-corydalmine, l-corypalmine and 9- O -desmethyl-l-THP) were identified as the same compounds as those obtained from microbial metabolism by liquid chromatography,tandem mass spectrometry (LC-MS[sol ]MS) analysis and comparison with reference standards obtained from microbial metabolism. The structures of the additional three metabolites were tentatively deduced as 2- O -desmethyl-l-THP and two di- O -demethylated l-THP by LC-MS[sol ]MS analysis. Time courses of microbial and rat metabolisms of l-THP were also investigated. Copyright © 2005 John Wiley & Sons, Ltd. [source] Microfluidic biolector,microfluidic bioprocess control in microtiter platesBIOTECHNOLOGY & BIOENGINEERING, Issue 3 2010Matthias Funke Abstract In industrial-scale biotechnological processes, the active control of the pH-value combined with the controlled feeding of substrate solutions (fed-batch) is the standard strategy to cultivate both prokaryotic and eukaryotic cells. On the contrary, for small-scale cultivations, much simpler batch experiments with no process control are performed. This lack of process control often hinders researchers to scale-up and scale-down fermentation experiments, because the microbial metabolism and thereby the growth and production kinetics drastically changes depending on the cultivation strategy applied. While small-scale batches are typically performed highly parallel and in high throughput, large-scale cultivations demand sophisticated equipment for process control which is in most cases costly and difficult to handle. Currently, there is no technical system on the market that realizes simple process control in high throughput. The novel concept of a microfermentation system described in this work combines a fiber-optic online-monitoring device for microtiter plates (MTPs),the BioLector technology,together with microfluidic control of cultivation processes in volumes below 1,mL. In the microfluidic chip, a micropump is integrated to realize distinct substrate flow rates during fed-batch cultivation in microscale. Hence, a cultivation system with several distinct advantages could be established: (1) high information output on a microscale; (2) many experiments can be performed in parallel and be automated using MTPs; (3) this system is user-friendly and can easily be transferred to a disposable single-use system. This article elucidates this new concept and illustrates applications in fermentations of Escherichia coli under pH-controlled and fed-batch conditions in shaken MTPs. Biotechnol. Bioeng. 2010;107: 497,505. © 2010 Wiley Periodicals, Inc. [source] Modeling with a view to target identification in metabolic engineering: A critical evaluation of the available toolsBIOTECHNOLOGY PROGRESS, Issue 2 2010Jo Maertens Abstract The state of the art tools for modeling metabolism, typically used in the domain of metabolic engineering, were reviewed. The tools considered are stoichiometric network analysis (elementary modes and extreme pathways), stoichiometric modeling (metabolic flux analysis, flux balance analysis, and carbon modeling), mechanistic and approximative modeling, cybernetic modeling, and multivariate statistics. In the context of metabolic engineering, one should be aware that the usefulness of these tools to optimize microbial metabolism for overproducing a target compound depends predominantly on the characteristic properties of that compound. Because of their shortcomings not all tools are suitable for every kind of optimization; issues like the dependence of the target compound's synthesis on severe (redox) constraints, the characteristics of its formation pathway, and the achievable/desired flux towards the target compound should play a role when choosing the optimization strategy. © 2010 American Institute of Chemical Engineers Biotechnol. Prog., 2010 [source] Rapid media transition: An experimental approach for steady state analysis of metabolic pathwaysBIOTECHNOLOGY PROGRESS, Issue 1 2010Hannes Link Abstract Commonly steady state analysis of microbial metabolism is performed under well defined physiological conditions in continuous cultures with fixed external rates. However, most industrial bioprocesses are operated in fed-batch mode under non-stationary conditions, which cannot be realized in chemostat cultures. A novel experimental setup,rapid media transition,enables steady state perturbation of metabolism on a time scale of several minutes in parallel to operating bioprocesses. For this purpose, cells are separated from the production process and transferred into a lab-scale stirred-tank reactor with modified environmental conditions. This new approach was evaluated experimentally in four rapid media transition experiments with Escherichia coli from a fed-batch process. We tested the reaction to different carbon sources entering at various points of central metabolism. In all cases, the applied substrates (glucose, succinate, acetate, and pyruvate) were immediately utilized by the cells. Extracellular rates and metabolome data indicate a metabolic steady state during the short-term cultivation. Stoichiometric analysis revealed distribution of intracellular fluxes, which differs drastically subject to the applied carbon source. For some reactions, the variation of flux could be correlated to changes of metabolite concentrations. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2010 [source] Tectonic control of bioalteration in modern and ancient oceanic crust as evidenced by carbon isotopesISLAND ARC, Issue 1 2006Harald Furnes Abstract We review the carbon-isotope data for finely disseminated carbonates from bioaltered, glassy pillow rims of basaltic lava flows from in situ slow- and intermediate-spreading oceanic crust of the central Atlantic Ocean (CAO) and the Costa Rica Rift (CRR). The ,13C values of the bioaltered glassy samples from the CAO show a large range, between ,17 and +3, (Vienna Peedee belemnite standard), whereas those from the CRR define a much narrower range, between ,17, and ,7,. This variation can be interpreted as the product of different microbial metabolisms during microbial alteration of the glass. In the present study, the generally low ,13C values (less than ,7,) are attributed to carbonate precipitated from microbially produced CO2 during oxidation of organic matter. Positive ,13C values >0, likely result from lithotrophic utilization of CO2 by methanogenic Archaea that produce CH4 from H2 and CO2. High production of H2 at the slow-spreading CAO crust may be a consequence of fault-bounded, high-level serpentinized peridotites near or on the sea floor, in contrast to the CRR crust, which exhibits a layer-cake pseudostratigraphy with much less faulting and supposedly less H2 production. A comparison of the ,13C data from glassy pillow margins in two ophiolites interpreted to have formed at different spreading rates supports this interpretation. The Jurassic Mirdita ophiolite complex in Albania shows a structural architecture similar to that of the slow-spreading CAO crust, with a similar range in ,13C values of biogenic carbonates. The Late Ordvician Solund,Stavfjord ophiolite complex in western Norway exhibits structural and geochemical evidence for evolution at an intermediate-spreading mid-ocean ridge and displays ,13C signatures in biogenic carbonates similar to those of the CRR. Based on the results of this comparative study, it is tentatively concluded that the spreading rate-dependent tectonic evolution of oceanic lithosphere has a significant control on the evolution of microbial life and hence on the ,13C biosignatures preserved in disseminated biogenic carbonates in glassy, bioaltered lavas. [source] | ||||||||||||||||||||||||||||||||||