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Microbial Strains (microbial + strain)
Selected AbstractsArsenite oxidation and arsenate respiration by a new Thermus isolateFEMS MICROBIOLOGY LETTERS, Issue 2 2001Thomas M Gihring Abstract A new microbial strain was isolated from an arsenic-rich terrestrial geothermal environment. The isolate, designated HR13, was identified as a Thermus species based on 16S rDNA phylogenetic relationships and close sequence similarity within the Thermus genus. Under aerobic conditions, Thermus HR13 was capable of rapidly oxidizing inorganic As(III) to As(V). As(III) was oxidized at a rate approximately 100-fold greater than abiotic rates. Metabolic energy was not gained from the oxidation reaction. In the absence of oxygen, Thermus HR13 grew by As(V) respiration coupled with lactate oxidation. The ability to oxidize and reduce arsenic has not been previously described within the Thermus genus. [source] Applications of the rep-PCR DNA fingerprinting technique to study microbial diversity, ecology and evolutionENVIRONMENTAL MICROBIOLOGY, Issue 4 2009Satoshi Ishii Summary A large number of repetitive DNA sequences are found in multiple sites in the genomes of numerous bacteria, archaea and eukarya. While the functions of many of these repetitive sequence elements are unknown, they have proven to be useful as the basis of several powerful tools for use in molecular diagnostics, medical microbiology, epidemiological analyses and environmental microbiology. The repetitive sequence-based PCR or rep-PCR DNA fingerprint technique uses primers targeting several of these repetitive elements and PCR to generate unique DNA profiles or ,fingerprints' of individual microbial strains. Although this technique has been extensively used to examine diversity among variety of prokaryotic microorganisms, rep-PCR DNA fingerprinting can also be applied to microbial ecology and microbial evolution studies since it has the power to distinguish microbes at the strain or isolate level. Recent advancement in rep-PCR methodology has resulted in increased accuracy, reproducibility and throughput. In this minireview, we summarize recent improvements in rep-PCR DNA fingerprinting methodology, and discuss its applications to address fundamentally important questions in microbial ecology and evolution. [source] Genetic improvement of processes yielding microbial productsFEMS MICROBIOLOGY REVIEWS, Issue 2 2006Jose L. Adrio Abstract Although microorganisms are extremely good in presenting us with an amazing array of valuable products, they usually produce them only in amounts that they need for their own benefit; thus, they tend not to overproduce their metabolites. In strain improvement programs, a strain producing a high titer is usually the desired goal. Genetics has had a long history of contributing to the production of microbial products. The tremendous increases in fermentation productivity and the resulting decreases in costs have come about mainly by mutagenesis and screening/selection for higher producing microbial strains and the application of recombinant DNA technology. [source] Multienzyme Profiling of Thermophilic Microorganisms with a Substrate Cocktail AssayADVANCED SYNTHESIS & CATALYSIS (PREVIOUSLY: JOURNAL FUER PRAKTISCHE CHEMIE), Issue 7-8 2005Renaud Sicard Abstract Labeled substrates for 16 different catalytic activities were combined into a cocktail reagent for multienzyme functional profiling, called PHENOZYMTM. The assay involves a single reaction followed by determination of substrate consumption by HPLC-analysis. The method allows a rapid identification of multiple enzyme activities, and is compatible with a diversity of growth media and reaction conditions (pH, temperature). The PHENOZYMTM cocktail was used to analyze the activity of 16 enzyme activities in a series of microbial strains, including thermophilic microorganisms. The functional profiles were used for a functional classification of the different microbial strains tested by hierarchical cluster analysis. The resulting "phylo-enzymatic" tree revealed associations consistent with the known phylogenetic classification of the strains. The influence of the culture medium on the enzyme activity profiles was also apparent. [source] Newly isolated Streptomyces spp. as enantioselective biocatalysts: hydrolysis of 1,2-O-isopropylidene glycerol racemic estersJOURNAL OF APPLIED MICROBIOLOGY, Issue 4 2005F. Molinari Abstract Aims:, To identify microbial strains with esterase activity able to enantioselectively hydrolyse esters of (R,S)-1,2-O-isopropylidene glycerol. Methods and Results:, The microbial hydrolysis of various racemic esters of 1,2-O-isopropylidene glycerol (IPG) was attempted by screening among Streptomyces spp. previously selected on the basis of their carboxylesterase activity. The best results were observed in the hydrolysis of butyrate ester and two strains appeared promising as they showed opposite enantioselectivity: Streptomyces sp. 90852 gave predominantly (S)-IPG, while strain 90930 mostly gave the R -alcohol. Streptomyces sp. 90930 was identified as Streptomyces violaceusniger, whereas Streptomyces sp. 90852 is a new species belonging to the Streptomyces violaceus taxon. The carboxylesterase belonging to strain 90852 gave a maximum value of enantiomeric ratio (E) of 14,16. This strain was lyophilized and used as dry mycelium for catalysing the synthesis of isopropylidene glycerol butyrate in heptane showing reaction rate and enantioselectivity (E = 6·6) lower than what observed for the hydrolysis. Conclusions:, A new esterase with enantioselective activity towards (R,S)-IPG butyrate has been selected. The best enantioselectivity is similar or even better than the highest reported value in the literature with commercial enzymes. The enzyme is produced by a new species belonging to the S. violaceus taxon. Significance and Impact of the Study:, New esterases from streptomycetes can be employed for the enantioselective hydrolysis of chiral esters derived from primary alcohols, not efficiently resolved with commercial enzymes. [source] Assessment of naphthalene biodegradation efficiency of Pseudomonas and Burkholderia strains tested in soil model systems,JOURNAL OF CHEMICAL TECHNOLOGY & BIOTECHNOLOGY, Issue 2 2006Andrei E Filonov Abstract The kinetic parameters of the naphthalene degradation process performed by indigenous and introduced microorganisms were studied in soil model systems. The introduction of active naphthalene-degrading strains Pseudomonas putida BS3701 and G7 in soil model systems accelerated the naphthalene destruction process by a factor of three to four. Moreover, the addition of salicylate (0.1 mg g,1 dry soil) to the systems containing the introduced microbial strains again doubled the rate of the naphthalene degradation process. To provide a quantitative assessment of the naphthalene biodegradation process, a mathematical model describing the bacterial growth, the consumption of the naphthalene, the production and subsequent consumption of naphthalene cleavage products, and the consumption of organic soil substances in soil model systems was developed. An approach for assessment of the degradation efficiency of low solubility polycyclic aromatic hydrocarbon provided by bacteria of genera Pseudomonas and Burkholderia in soil was suggested. The approach will enable comparison and selection of the most active degraders, which have the potential for application in biotechnologies for cleaning of soils contaminated by polycyclic aromatic hydrocarbons. Copyright © 2005 Society of Chemical Industry [source] Panose, a new prebiotic candidateLETTERS IN APPLIED MICROBIOLOGY, Issue 6 2009H. Mäkeläinen Abstract Aims:, To investigate the prebiotic potential of two novel candidates, sophorose and panose, with in vitro methods. Methods and Results:, The growth of single microbial strains was first assessed for both substrates in pure cultures, and panose was further analysed in the simulated colon model with mixed human faecal culture. Quantitative PCR and flow cytometry were used to determine the microbial group and strain densities after the simulated colonic fermentation of panose, and chromatographic methods were utilized to analyse metabolite concentrations. In pure cultures, sophorose and panose were both fermented only by few beneficial strains, and in the colon simulator, panose gave a significant increase in the numbers of Bifidobacterium and Bifidobacterium lactis, concomitantly decreasing Bacteroides group. Butyrate and acetate production was significantly increased together with decreased markers of protein fermentation as a result of panose fermentation. Conclusions:, Panose had bifidogenic activities in vitro, and these potential beneficial effects should be further assessed in vitro and in vivo. Significance and Impact of the Study:, The current study has provided the first data on pure panose fermentation by the endogenous microbiota and extends our knowledge of the selective fermentation of oligosaccharides by the intestinal microbes. [source] Review: Biodegradation of tributyltins (organotins) by marine bacteriaAPPLIED ORGANOMETALLIC CHEMISTRY, Issue 1 2003S. K. Dubey Abstract Many marine bacterial strains have an inherent capability to degrade toxic organotin compounds, especially tributyltins (TBTs), that enter into the environment in the form of insecticides, fungicides and antifouling paints as a result of anthropogenic and industrial activities. Significant degradation of these compounds in the ambient environment may take several years, and it is necessary to consider methods or strategies that can accelerate the degradation process. There have been few demonstrations of biological degradation of these organotin biocides exclusively in laboratory-scale experiments. Compared with the few bench-scale degradation processes, there are no reports of field-scale processes for TBT bioremediation, in spite of its serious environmental threat to non-target organisms in the aquatic environment. Implementation of field-scale biodegradation of TBT requires inputs from biology, hydrology, geology, chemistry and civil engineering. A framework is emerging that can be adapted to develop new processes for bioremediation of toxic environmental wastes. In the case of TBT bioremediation, this framework incorporates screening and identification of natural bacterial strains, determination of optimal conditions for growth of isolates and TBT degradation, establishment of new metabolic pathways involved in TBT degradation, identification, localization and cloning of genes involved in degradation and in TBT resistance, development of suitable microbial strains using genetic manipulation techniques for practical applications and optimization of practical engineering processes for bioremediation of organotin-contaminated sites. The present review mainly addresses the aspect of TBT biodegradation with special reference to environmental sources of TBT, chemical structure and biological activity, resistant and degrading bacterial strains, possible mechanisms of resistance and degradation and the genetic and biochemical basis of TBT degradation and resistance. It also evaluates the feasibility and potential of natural and genetically modified TBT-degrading bacterial strains in field-scale experiments to bioremediate TBT-contaminated marine sites, and makes recommendations for more intensive and focused research in the area of TBT bioremediation mediated by marine bacterial strains. Copyright © 2002 John Wiley & Sons, Ltd. [source] A novel microplate-based screening strategy to assess the cellulolytic potential of Trichoderma strainsBIOTECHNOLOGY & BIOENGINEERING, Issue 3 2010Stefano Cianchetta Abstract Bioconversion of lignocellulosic biomass to fuel requires a hydrolysis step to obtain fermentable sugars, generally accomplished by fungal enzymes. An assorted library of cellulolytic microbial strains should facilitate the development of optimal enzyme cocktails specific for locally available feedstocks. Only a limited number of strains can be simultaneously assayed in screening based on large volume cultivation methods, as in shake flasks. This study describes a miniaturization strategy aimed at allowing parallel assessment of large numbers of fungal strains. Trichoderma strains were cultivated stationary on microcrystalline cellulose using flat bottom 24-well plates containing an agarized medium. Supernatants obtained by a rapid centrifugation step of the whole culture plates were evaluated for extracellular total cellulase activity, measured as filter paper activity, using a microplate-based assay. The results obtained were consistent with those observed in shake-flask experiments and more than 300 Trichoderma strains were accordingly characterized for cellulase production. Five strains, displaying on shake-flasks at least 80% of the activity shown by the hyper-cellulolytic mutant Trichoderma Rut-C30, were correctly recognized by the screening on 24-well plates, demonstrating the feasibility of this approach. Cellulase activity distribution for the entire Trichoderma collection is also reported. One strain (T. harzianum Ba8/86) displayed the closest profile to the reference strain Rut-C30 in time course experiments. The method is scalable and addresses a major bottleneck in screening programs, allowing small-scale parallel cultivation and rapid supernatant extraction. It can also be easily integrated with high-throughput enzyme assays and could be suitable for automation. Biotechnol. Bioeng. 2010;107: 461,468. © 2010 Wiley Periodicals, Inc. [source] Cooperation and cheating in microbial exoenzyme production , Theoretical analysis for biotechnological applicationsBIOTECHNOLOGY JOURNAL, Issue 7 2010Stefan Schuster Abstract The engineering of microorganisms to produce a variety of extracellular enzymes (exoenzymes), for example for producing renewable fuels and in biodegradation of xenobiotics, has recently attracted increasing interest. Productivity is often reduced by "cheater" mutants, which are deficient in exoenzyme production and benefit from the product provided by the "cooperating" cells. We present a game-theoretical model to analyze population structure and exoenzyme productivity in terms of biotechnologically relevant parameters. For any given population density, three distinct regimes are predicted: when the metabolic effort for exoenzyme production and secretion is low, all cells cooperate; at intermediate metabolic costs, cooperators and cheaters coexist; while at high costs, all cells use the cheating strategy. These regimes correspond to the harmony game, snowdrift game, and Prisoner's Dilemma, respectively. Thus, our results indicate that microbial strains engineered for exoenzyme production will not, under appropriate conditions, be outcompeted by cheater mutants. We also analyze the dependence of the population structure on cell density. At low costs, the fraction of cooperating cells increases with decreasing cell density and reaches unity at a critical threshold. Our model provides an estimate of the cell density maximizing exoenzyme production. [source] Modeling and Parameter Identification of the Simultaneous Saccharification-Fermentation Process for Ethanol ProductionBIOTECHNOLOGY PROGRESS, Issue 6 2007Silvia Ochoa Despite many environmental advantages of using alcohol as a fuel, there are still serious questions about its economical feasibility when compared with oil-based fuels. The bioethanol industry needs to be more competitive, and therefore, all stages of its production process must be simple, inexpensive, efficient, and "easy" to control. In recent years, there have been significant improvements in process design, such as in the purification technologies for ethanol dehydration (molecular sieves, pressure swing adsorption, pervaporation, etc.) and in genetic modifications of microbial strains. However, a lot of research effort is still required in optimization and control, where the first step is the development of suitable models of the process, which can be used as a simulated plant, as a soft sensor or as part of the control algorithm. Thus, toward developing good, reliable, and simple but highly predictive models that can be used in the future for optimization and process control applications, in this paper an unstructured and a cybernetic model are proposed and compared for the simultaneous saccharification-fermentation process (SSF) for the production of ethanol from starch by a recombinant Saccharomyces cerevisiae strain. The cybernetic model proposed is a new one that considers the degradation of starch not only into glucose but also into dextrins (reducing sugars) and takes into account the intracellular reactions occurring inside the cells, giving a more detailed description of the process. Furthermore, an identification procedure based on the Metropolis Monte Carlo optimization method coupled with a sensitivity analysis is proposed for the identification of the modelapos;s parameters, employing experimental data reported in the literature. [source] High-throughput epidemiologic typing in clinical microbiologyCLINICAL MICROBIOLOGY AND INFECTION, Issue 2 2003A. Van Belkum Mapping, and ultimately preventing, the dissemination of infectious agents is an important topic in public health. Newly developed molecular,microbiological methods have contributed significantly to recent advances in the efficient tracking of the nosocomial and environmental spread of microbial pathogens. Not only has the application of novel technologies led to improved understanding of microbial epidemiology, but the concepts of population structure and dynamics of many of the medically significant microorganisms have advanced significantly also. Currently, genetic identification of microbes is also within the reach of clinical microbiology laboratory professionals including those without specialized technology research interests. This review summarizes the possibilities for high-throughput molecular,microbiological typing in adequately equipped medical microbiology laboratories from both clinical and fundamental research perspectives. First, the development and application of methods for large-scale comparative typing of serially isolated microbial strains are discussed. The outcome of studies employing these methods allows for long-term epidemiologic surveillance of infectious diseases. Second, recent methods enable an almost nucleotide-by-nucleotide genetic comparison of smaller numbers of strains, thereby facilitating the identification of the genetic basis of, for instance, medically relevant microbiological traits. Whereas the first approach provides insights into the dynamic spread of infectious agents, the second provides insights into intragenomic dynamics and genetic functionality. The current state of technology is summarized, and future perspectives are sketched. [source] | |||||||||||||||||||||||||