Springer protocols feed by Microbiology 
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This is an RSS file. You can use it to subscribe to this data in your favourite RSS reader or to display this data on your own website or blog.Protocol for the Application of Bioluminescence Full-Cell Bioreporters for Monitoring of Terrestrial Bioremediation
Microbial full-scale bioreporters are associated with a variety of names that include biosensors, bio-indicators and bio-reactive agents. The role of such microbial agents is to respond to the bioavailable fraction of a given analyte under“near environmental conditions”. Making use of appropriate assays with relevant and biologically compatible extraction procedures means that such techniques can be applied to develop site specific risk and hazard assessments, an appraisal of constraints inhibiting biodegradation and a prediction of potential for biodegradation. The effectiveness of an assay requires: (1) the c...
Source: Springer protocols feed by Microbiology - December 9, 2016 Category: Microbiology Source Type: news
Screening for Enantioselective Lipases
Many lipolytic enzymes are enantioselective thus being able to distinguish between two enantiomers of a given racemic substrate. This property together with ample availability and comparatively easy handling makes lipolytic enzymes the most widely used class of biocatalysts in the chemical and pharmaceutical industries. However, lipase activity as well as selectivity is often negligible towards typical industrial substrates which usually do not resemble natural ones. Therefore, suitable enzymes must first be identified, usually by activity-based screening methods which, however, differ in reliability, throughput and surrog...
Source: Springer protocols feed by Microbiology - December 9, 2016 Category: Microbiology Source Type: news
Protocol for Start-Up and Operation of CSTR Biogas Processes
There is currently a lack of consensus on how biogas processes should be started and run in order to obtain stable, efficient operation. Agreement on start-up and operating parameters would increase the quality of research, allow better comparison of scientific results and increase the applicability of new findings in a general perspective. It would also help full-scale operators avoid common costly mistakes during start-up and operation of biogas processes. The biogas protocol presented in this paper describes appropriate approaches for characterisation of substrate, determination of methane potential, formulation of a su...
Source: Springer protocols feed by Microbiology - December 9, 2016 Category: Microbiology Source Type: news
Introduction to Bioproducts, Biofuels, Biocatalysts and Facilitating Tools
In this volume, two main aspects are addressed. First, there is the enzymatic machinery dealing with hydrocarbons, fats, and oils. There is great progress in this domain and plenty of novel routes are still possible to explore and to upgrade to bring better microbial derived toolboxes to market implementation. Secondly there is the vast array of microbial lipid-associated molecules, ranging from volatile fatty acids to alkanoates and oils. Also in this domain, novel breakthroughs are at hand. The fact that enzymes capable of acting towards greasy molecules both in the bioconversion and the cleantech industry are of great i...
Source: Springer protocols feed by Microbiology - December 9, 2016 Category: Microbiology Source Type: news
Production of Biofuel-Related Isoprenoids Derived from Botryococcus braunii Algae
The colony algae Botryococcus braunii produces large amounts of C30+ triterpene hydrocarbons. Recent discovery of the associated biosynthetic genes has facilitated the metabolic engineering of these triterpene hydrocarbons in alternative hosts– where squalene has served as an analytical standard and a closely associated model hydrocarbon biosynthetic pathway. An extraction and analysis method is provided for both the native and heterologous systems. In the case of the native algae, the hydrocarbons are tightly associated with a complex wall matrix. In addition to quantification of extracted triterpenes by GC-FID, sec...
Source: Springer protocols feed by Microbiology - December 9, 2016 Category: Microbiology Source Type: news
Syngas Fermentation for Polyhydroxyalkanoate Production in Rhodospirillum rubrum
Bioconversion of organic waste into value-added products by a process called syngas fermentation is gaining considerable interest during the last years. Syngas is a gaseous mixture composed mainly of hydrogen and carbon monoxide and smaller quantities of other gases like CO2 that can be fermented by Rhodospirillum rubrum, a natural producer of polyhydroxybutyrate (PHB). R. rubrum is a highly versatile, purple, non-sulfur bacterium that can grow in a broad range of anaerobic and aerobic conditions. In anaerobiosis, it can utilize CO as carbon and energy source in the presence or absence of light. When exposed to CO, CO dehy...
Source: Springer protocols feed by Microbiology - December 9, 2016 Category: Microbiology Source Type: news
Genetic Strategies on Kennedy Pathway to Improve Triacylglycerol Production in Oleaginous Rhodococcus Strains
During the last years, microorganisms (yeasts, fungi, microalgae, and bacteria) have been receiving increasing attention as alternative lipid sources (also called single cell oils). Some lipid-accumulating bacteria, in particular those belonging to actinomycetes, are able to synthesize remarkably high amounts of triacylglycerides (TAGs) (up to 70% of the cellular dry weight) from simple carbon sources such as glucose, which are accumulated as intracellular lipid bodies. The applied potential of bacterial TAG may be similar to that of vegetable oil sources, such as additives for feed, cosmetics, oleochemicals, lubricants, a...
Source: Springer protocols feed by Microbiology - December 9, 2016 Category: Microbiology Source Type: news
Protocols for the Use of Gut Models to Study the Potential Contribution of the Gut Microbiota to Human Nutrition Through the Production of Short-Chain Fatty Acids
The colonic microbiota influences human energy status through the metabolic activity of the taxonomically diverse prokaryotic residents that number up to 1012 cells per gram. The principal means by which this happens is probably via short-chain fatty acids (SCFAs) (mainly acetate, propionate and butyrate), which are continually produced by fermentation of dietary fibre, absorbed through the colonic epithelium, transported via the hepatic portal vein to the liver and then converted to glucose and other lipids. SCFAs may also regulate appetite via G protein-coupled receptor (GPR43) activation and signalling. Since the coloni...
Source: Springer protocols feed by Microbiology - December 9, 2016 Category: Microbiology Source Type: news
Bacterial Secretion Systems for Use in Biotechnology: Autotransporter-Based Cell Surface Display and Ultrahigh-Throughput Screening of Large Protein Libraries
In recent years, continuous progress was made in our understanding of bacterial secretion pathways and the application of protein secretion for biotechnology. Efficient protein export is a prerequisite for cost-effective downstream processing, and secretion of a protein of interest may also be useful for certain enzyme assays, for biotransformation reactions, and, in particular, for screening enzyme variants in libraries generated by directed evolution. Cells that display a particular enzyme variant can be exposed to a broad spectrum of different chemical environments, can sustain a broad pH range, and can therefore allow ...
Source: Springer protocols feed by Microbiology - December 9, 2016 Category: Microbiology Source Type: news
Functional Screening of Metagenomic Libraries: Enzymes Acting on Greasy Molecules as Study Case
Greasy molecules such as aromatic and aliphatic hydrocarbons are ubiquitous and chemically heterogeneous microbial substrates that occur in the biosphere through human activities as well as natural inputs. Organic compounds consisting of one, two, or more fused aromatic rings are due to their toxicity considered as pollutants of a great concern; however, they are also important chemical building blocks of relevance for biology, chemistry, and materials sciences. Biological approaches are known to provide exquisite ecologically friendly methods, as compared to chemical ones, for their biodegradation or bioconversions. For t...
Source: Springer protocols feed by Microbiology - December 9, 2016 Category: Microbiology Source Type: news
Protocols for Measuring Methanogenesis
Methanogenesis is one of the most important terminal processes in the microbial degradation of organic matter in many anoxic environments. Since ancient times, methane was known as a combustion gas, but its microbiological origin was proved only in the nineteenth century. The contribution of methane to the global warming and its beneficial importance in ecological biotechnology and bioenergetics dictate the need in proper estimations of its fluxes and measurements of its production rates in different microbiological processes. (Source: Springer protocols feed by Microbiology)
Source: Springer protocols feed by Microbiology - November 16, 2016 Category: Microbiology Source Type: news
Determining the Tendency of Microorganisms to Interact with Hydrocarbon Phases
Three procedures for the determination of the hydrophobicity of microorganisms and/or their tendency to physically interact with hydrocarbon phases are presented. These include the bacterial/microbial adhesion to hydrocarbon (BATH/MATH) test, hydrophobic interaction chromatography and contact angle measurements of filter-retained microbial cell layers. (Source: Springer protocols feed by Microbiology)
Source: Springer protocols feed by Microbiology - November 16, 2016 Category: Microbiology Source Type: news
Protocol for Evaluating the Biological Stability of Fuel Formulations and Their Relationship to Carbon Steel Biocorrosion
The microbial metabolism of conventional and alternative fuels can be associated with the biocorrosion of the mostly carbon steel energy infrastructure. This phenomenon is particularly acute in anaerobic sulfate-rich environments. It is therefore important to reliably assess the inherent susceptibility of fuels to anaerobic biodegradation in marine waters as well as provide a measure of the impact of this metabolism on the integrity of steel. Such an assessment of fuels is increasingly important since the exact chemical makeup of both traditional and biofuels can vary and even subtle changes have a profound impact on steel...
Source: Springer protocols feed by Microbiology - November 16, 2016 Category: Microbiology Source Type: news
Measuring the Impact of Hydrocarbons on Rates of Nitrogen Fixation
We describe two methods to measure the bulk N2 fixation by the entire microcosm: the acetylene reduction assay and the analysis of bulk N isotope ratios following incubations with 15N2. Also, we present a method to determine N2 fixation at cellular level, based on nanoSIMS analysis of individual cells from microcosms incubated with 15N2. (Source: Springer protocols feed by Microbiology)
Source: Springer protocols feed by Microbiology - November 16, 2016 Category: Microbiology Source Type: news
Microbial Control of the Concentrations of Dissolved Aquatic Hydrocarbons
Hydrocarbon oxidizing bacteria have a major effect on the chemistry of natural water systems, particularly with increased inputs of anthropogenic petroleum products. We review the basic kinetics helpful in understanding the equilibrium between nutrient concentrations and microbial populations, and describe some techniques useful in establishing that equilibrium with emphasis on hydrocarbons. Topics include oil spills, naturally occurring hydrocarbons such as terpenes, and some peculiarities of the metabolism of these hydrophilic solutes, isolation of ambient hydrocarbon-using bacteria, liberation of partly oxidized product...
Source: Springer protocols feed by Microbiology - November 16, 2016 Category: Microbiology Source Type: news
