Protocol for Inferring Compound Biodegradation at Low Concentrations from Biomass Measurements
Biodegradation tests for organic compounds are usually performed at relatively high carbon concentrations (2–100 mg L−1), which can be problematic for toxic compounds. Here we describe a protocol to test compound biodegradation through the concomitant formation of bacterial biomass at relatively low carbon concentrations (0.5–5 mg C/L). The protocol is based on accurate cell counting of dilute cell suspensions by flow cytometry coupled to cell staining with fluorescent dyes. (Source: Springer protocols feed by Microbiology)
Source: Springer protocols feed by Microbiology - December 29, 2016 Category: Microbiology Source Type: news

Bioremediation of Hydrocarbons and Chlorinated Solvents in Groundwater: Characterisation, Design and Performance Assessment
Bioremediation is an accepted and widely implemented technology for the management of groundwater contaminated by hydrocarbon and chlorinated solvent compounds. This chapter reviews the general application of bioremediation processes within a cost–benefit and risk assessment framework, which considers different contaminant types and their properties, release contexts, and the strengths and limitations of available approaches. The pathways, reaction mechanisms and microorganisms responsible for biodegradation of hydrocarbons and chlorinated solvents under aerobic and different anaerobic conditions in groundwater are i...
Source: Springer protocols feed by Microbiology - December 29, 2016 Category: Microbiology Source Type: news

Bioaugmentation
The ability of microorganisms to transform pollutants is well documented. However, in many cases microbial communities with the desired capabilities may develop too slowly or may not be sustained. In these cases, manipulation of the microbial composition may be advantageous. Bioremediation has been established as an environmental friendly treatment capable of improving the removal of the contaminants in natural and environmentally systems by circumventing insufficient response time and initiating the removal with a minimal lag phase. Bioremediation exploits the microbial ability to transform contaminants into less harmful ...
Source: Springer protocols feed by Microbiology - December 29, 2016 Category: Microbiology Source Type: news

Ex Situ Bioremediation Treatment (Landfarming)
Landfarming provides a platform where soil conditions (pH, nutrient, moisture, and tilling) can be optimized to promote microbial activities and thus the desired degradation of soil pollutants can be achieved. The factors under which landfarming is applicable and leads to increased effectiveness are reviewed and design parameters for successful landfarming applications are provided. (Source: Springer protocols feed by Microbiology)
Source: Springer protocols feed by Microbiology - December 29, 2016 Category: Microbiology Source Type: news

Biostimulation of Marine Crude Oil Spills Using Dispersants
Dispersants provide a bioremediation option for oil spills at sea for both surface and subsea releases, as demonstrated in the Deepwater Horizon response. By decreasing the interfacial tension between oil and water, dispersants substantially reduce the amount of energy required to disperse oil as tiny droplets (
Source: Springer protocols feed by Microbiology - December 29, 2016 Category: Microbiology Source Type: news

Field Studies Demonstrating the Efficacy of Bioremediation in Marine Environments
The ultimate fate of most oil released into the biosphere is biodegradation. Yet oil lacks some of the essential nutrients for microbial life, and its biodegradation can be limited by the availability of such nutrients from the local environment. Bioremediation of oil on shorelines aims to at least partially alleviate this limitation by the judicious application of fertilizers. Bioremediation played a central role in the response to the Exxon Valdez spill in Prince William Sound, AK, being applied to more than 120 km of shoreline. This short paper describes the program designed by Exxon, the USEPA, and the Alaska Departmen...
Source: Springer protocols feed by Microbiology - December 29, 2016 Category: Microbiology Source Type: news

The Use of Multiple Lines of Evidence to Substantiate Anaerobic BTEX Degradation in Groundwater
Aromatic compounds are nowadays still of major environmental concern. These compounds have been proven to be biodegradable under both aerobic and anaerobic conditions. Under anaerobic conditions several biodegradation pathways are proposed, but the bacteria and specific genes involved remain largely unknown. The detection of the actual biological degradation potential and expected kinetics of degradation in the field are therefore a challenge. Usually, a combination of different lines of evidence is used to determine and predict the biodegradation of BTEX under anaerobic conditions in the field. These include compound-spec...
Source: Springer protocols feed by Microbiology - December 29, 2016 Category: Microbiology Source Type: news

Methods to Assess the Fate and Impacts of Biofuels in Aquifer Systems
Soil and groundwater contamination from accidental or incidental releases of biofuel blends is a growing concern in many countries. Improved understanding of how different biofuel releases behave in the environment and affect the fate and transport of priority pollutants in aquifers is critical for long-term management strategies. Different experimental approaches have been used to advance our understandings of the fate and impacts of biofuel releases in aquifer systems, to develop improved monitoring and remediation approaches, and to validate mathematical fate and transport models. This chapter summarizes currently used ...
Source: Springer protocols feed by Microbiology - December 29, 2016 Category: Microbiology Source Type: news

Protocol for Biopile Construction Treating Contaminated Soils with Petroleum Hydrocarbons
When investigating the treatment of contaminated soils, the application of biotreatment is growing rapidly. Factors influencing this rapid growth include that the bioremediation processes are cost-efficient, safe, and nature-based. In the past, thermal, chemical, and physical treatment methods have failed to eliminate the pollution problem because those methods only shift the environmental pollutants to a new environmental phase such as air and water. Bioremediation technology, which leads to degradation of pollutants, may be a lucrative and environmentally beneficial alternative. Two major groups of bioremediation treatme...
Source: Springer protocols feed by Microbiology - December 29, 2016 Category: Microbiology Source Type: news

Anaerobic Digestion of Lipid-Rich Waste
Lipids present in waste and wastewater, also referred as fat, oil, and grease (FOG), can be efficiently converted to methane. This fact constitutes an opportunity for conserving the high energy content of waste lipids, thus facilitating its storage and future use as fuel, electricity, and heat. In anaerobic bioreactors, long-chain fatty acids (LCFAs) are released during hydrolysis of FOG. LCFAs tend to form stable emulsions, adhere to all available surfaces, and adsorb on the microbial cell walls leading to foam formation, sludge flotation, and washout, as well as temporary inhibition of microbes. These problems can be pre...
Source: Springer protocols feed by Microbiology - December 29, 2016 Category: Microbiology Source Type: news

Bioremediation of Sludge Obtained from Oil/Biofuel Storage Tanks
Crude oil refinery leads to the production of a considerable amount of oil tank bottom sludge which can contaminate the environment and is toxic to human and environmental health. Among the methods available for cleaning up sludge-contaminated environments is bioremediation, which is a widely acceptable method for the remediation of different hydrocarbon-contaminated soils. This method is based on using microbes, mainly bacteria and fungi to degrade or remove the contaminants. Bioremediation technology can be applied to soil contaminated with oil tank bottom sludge using natural attenuation, biostimulation (addition of nut...
Source: Springer protocols feed by Microbiology - December 29, 2016 Category: Microbiology Source Type: news

Genetic Enzyme Screening System: A Method for High-Throughput Functional Screening of Novel Enzymes from Metagenomic Libraries
This protocol describes a single-cell high-throughput genetic enzyme screening system (GESS) in which GFP fluorescence is used to detect the production of phenolic compounds from a given substrate by metagenomic enzyme activity. One of the important features of this single-cell genetic circuit is that it can be used to screen more than 200 different types of enzymes that produce phenolic compounds from phenyl group-containing substrates. The highly sensitive and quantitative nature of the GESS, combined with flow cytometry techniques, will facilitate rapid finding and directed evolution of valuable new enzymes such as glyc...
Source: Springer protocols feed by Microbiology - December 9, 2016 Category: Microbiology Source Type: news

Protocols for the Isolation and Preliminary Characterization of Bacteria for Biodesulfurization and Biodenitrogenation of Petroleum-Derived Fuels
The use of microorganisms to improve fuel quality has been proposed, and in this chapter we describe basic experimental procedures for the isolation and characterization of bacteria for biodesulfurization and biodenitrogenation with dibenzothiophene and carbazole as model compounds for each application, respectively. The presented protocols should be considered as a starting point and adapted to other problematic compounds and conditions. Basic protocols for the evaluation of the treatment of real oil fractions are also presented. (Source: Springer protocols feed by Microbiology)
Source: Springer protocols feed by Microbiology - December 9, 2016 Category: Microbiology Source Type: news

Protocols for Monitoring Growth and Lipid Accumulation in Oleaginous Yeasts
Oleaginous yeasts can synthesize and store lipids up to 20% of their dry weight and have emerged as resources of choice for biotechnological applications, such as bio-lipid production. The number of species and mutant libraries consequently available for screening is exponentially growing. Cultivation strategies and growth media for bio-lipid production need to be optimized to accelerate screening and identification of production strains. In this chapter we describe methods for high-throughput cell growth in 96 microtiter plates in various media including opaque broth by using a fluorescent reporter, carbon/nitrogen ratio ...
Source: Springer protocols feed by Microbiology - December 9, 2016 Category: Microbiology Source Type: news

Use of Bacterial Polyhydroxyalkanoates in Protein Display Technologies
Protein display and immobilization are powerful tools used in industrial biocatalysts, bioremediation, biomolecule screening and purification, as well as biosensor applications. Immobilization can aid in the stability and function of a protein and can allow its recovery and potential reuse. Traditional protein immobilization techniques involving entrapment or non-covalent interactions between the protein and support materials are susceptible to leaching and often require additional cross-linking steps; which may be costly, potentially toxic and may negatively affect the function of the protein. All of these approaches requ...
Source: Springer protocols feed by Microbiology - December 9, 2016 Category: Microbiology Source Type: news

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

Bacterial Solvent Responses and Tolerance: Cis & ndash;Trans Isomerization
The protocol describes the application of the membrane adaptive mechanism of Gram-negative bacteria belonging to the genera Pseudomonas and Vibrio, the isomerization of cis- to trans-unsaturated membrane fatty acids as a tool for the measurement of the toxicity of membrane-disturbing compounds. The degree of isomerization directly depends on the toxicity and concentration of membrane-affecting agents. Synthesis of trans fatty acids is apparent within 30 min after addition of stressors by direct isomerization of the respective cis configuration of the double bond without shifting the position. The purpose of the conver...
Source: Springer protocols feed by Microbiology - November 16, 2016 Category: Microbiology Source Type: news

Protocols for Measuring Activity of Sulphate-Reducing Bacteria in Water Injection Systems by Radiorespirometric Assay
Growth and activity of sulphate-reducing bacteria (SRB) is a problem for offshore oil fields injecting sea water for pressure support. Oxygen is traditionally removed before injection to reduce corrosion. The anoxic conditions and high sulphate content of sea water promotes growth and activity of SRB in the water injection system and in the reservoir. The major concern top side in the water injection system is microbiologically influenced corrosion (MIC) caused by SRB activity. Combined with the assessment of corrosion rates, monitoring of SRB activity is applied to evaluate treatment methods and optimize treatment regimen...
Source: Springer protocols feed by Microbiology - November 16, 2016 Category: Microbiology Source Type: news

Respiration Rate Determined by Phosphorescence-Based Sensors
Respiration rates can be a powerful diagnostic tool that provides insight into the metabolic activity of the cells. An optical-based method is well suited for making oxygen consumption measurements in microbial populations, whether on a model organism or environmental sample. This approach utilizes phosphorescent dyes since the lifetime of their excited state depends on the oxygen concentration. Two systems are described using closed sample chambers which can be constructed at minimal costs from off-the-shelf parts. The first system is designed around a glass cuvette utilizing an oil layer as an oxygen barrier. The second ...
Source: Springer protocols feed by Microbiology - November 16, 2016 Category: Microbiology Source Type: news

Introduction to Activities and Phenotypes
Crude oil and lipids greatly influence the structure and function of microbial communities, owing to merely physical effects such as hindering the diffusion of oxygen or light to communities trapped beneath oil layers, to toxicity of the highly soluble oil hydrocarbons, or to the utilization of hydrocarbons or lipids as growth substrates by microorganisms. This chapter brings together methods to investigate the effects of crude oil or lipids on the diversity and function of microbial communities. These can be principally grouped into protocols devoted to analyze the functional diversity of microbial communities in response...
Source: Springer protocols feed by Microbiology - November 16, 2016 Category: Microbiology Source Type: news

Protocol for the Measurement of Hydrocarbon Transport in Bacteria
Due to the hydrophobicity, volatility, and relatively low aqueous solubility of aliphatic and aromatic hydrocarbons, transport of these chemicals by bacteria has not been extensively studied. These issues make transport assays difficult to carry out, and as a result, strong evidence for the active transport of hydrocarbons is lacking. Here we describe a detailed protocol for the measurement of hydrocarbon transport in bacteria and suggest key equipment and control experiments required to obtain convincing results. (Source: Springer protocols feed by Microbiology)
Source: Springer protocols feed by Microbiology - November 16, 2016 Category: Microbiology Source Type: news

Laboratory Protocols for Investigating Microbial Souring and Potential Treatments in Crude Oil Reservoirs
Oilfield souring is most frequently caused by the activities of sulfate-reducing microorganisms as they reduce sulfate to sulfide as their terminal electron-accepting process. Souring poses serious health and safety hazards to oilfield workers and can be detrimental to oil production processes by potentially plugging reservoirs and/or leading to infrastructure corrosion. Oilfield souring often occurs during secondary recovery operations based on waterflooding, especially when the water source contains an ample amount of sulfate that can stimulate sulfate reducers associated with the reservoir or other locations within an o...
Source: Springer protocols feed by Microbiology - November 16, 2016 Category: Microbiology Source Type: news

Protocols for the Measurement of Bacterial Chemotaxis to Hydrocarbons
Bacterial chemotaxis is the process by which bacteria sense and respond to environmental stimuli. While the mechanism for chemotaxis has been extensively studied in enteric bacteria, studies in soil bacteria that are attracted to aromatic acids and aromatic hydrocarbons in addition to sugars and amino acids are lacking. Here we describe detailed protocols for the quantitative and qualitative assessment of chemotaxis responses to analyze responses to hydrocarbon and aromatic acid attractants to identify the specific receptors involved. (Source: Springer protocols feed by Microbiology)
Source: Springer protocols feed by Microbiology - November 16, 2016 Category: Microbiology Source Type: news

Analysis of PHB Metabolism Applying Tn5 Mutagenesis in Ralstonia eutropha
Transposon mutagenesis presents a powerful and practicable method to generate single-gene disruption mutants of microorganisms. As naturally occurring transposons“jump” within the genome, molecular biology uses plasmid-bound transposons, which randomly disrupt genomic regions of the target organism. Obtained transposon mutants help to elucidate metabolic pathways and to identify essential genes, which are involved in syntheses or degradation of compounds or are important for other cell processes or cell structures. The best-known transposon, Tn5, codes for different antibiotic resistances as well as for a trans...
Source: Springer protocols feed by Microbiology - November 16, 2016 Category: Microbiology Source Type: news

Protocols for Measuring Biosurfactant Production in Microbial Cultures
Microbial biosurfactants have wide structural and functional diversity which consequently requires the adoption of a range of techniques to investigate these amphiphilic molecules. Literature on the production and analytical detection of biosurfactants is overwhelmed with assertions of high yields for such products which are mostly over exaggerated estimates due to the use of flawed or inaccurate analytical techniques. In this chapter we focus on quantitative methods available to allow accurate estimates of production and yield data to be generated. (Source: Springer protocols feed by Microbiology)
Source: Springer protocols feed by Microbiology - November 16, 2016 Category: Microbiology Source Type: news

Phenotyping Microarrays for the Characterization of Environmental Microorganisms
Culture-based methods for the characterization of microorganisms remain essential to advances in microbiology. Phenotyping arrays and microplates in which each well represents a different selective growth environment are important tools (1) in the identification of microbial isolates, (2) in the characterization of the phenotypic fingerprint of microbial communities, (3) for linking specific functions with specific organisms or genes, and (4) for the identification of evolutionary trade-offs in the establishment of phenotypes. The use of phenotyping arrays in the study of hydrocarbon and lipid degradation by microbial isol...
Source: Springer protocols feed by Microbiology - November 16, 2016 Category: Microbiology Source Type: news

Primers: Functional Genes for Aerobic Chlorinated Hydrocarbon-Degrading Microbes
Bioremediation offers a solution to the problem of chlorinated hydrocarbon pollution. Small chlorinated compounds can be mineralised by aerobic bacteria, acting as carbon and energy sources, and the genes that encode these processes can be detected and monitored by PCR. This provides a rapid, specific, culture-independent, and potentially quantitative tool of enormous utility to bioremediation practitioners. This chapter summarises and evaluates available PCR primers for genes encoding metabolism of organochlorines, especially chlorinated alkanes, alkenes, and alkanoic acids. The enzyme families involved include hydrolytic...
Source: Springer protocols feed by Microbiology - October 12, 2016 Category: Microbiology Source Type: news

Primers That Target Functional Genes of Organohalide-Respiring Bacteria
Halogenated organic hydrocarbons are problematic environmental pollutants that can be reductively dehalogenated by organohalide-respiring bacteria (OHRB) in anoxic environments. This energy-conserving process is mediated by reductive dehalogenases (RDases). To amplify the diversity of reductive dehalogenase-encoding genes, degenerate primers have been designed, most of which target the conserved regions of the encoded protein sequences of the catalytic subunit, RdhA. In addition, specific primer sets have been developed and widely used to quantify and characterise OHRB and the reductive dehalogenase homologous (rdh) genes ...
Source: Springer protocols feed by Microbiology - October 12, 2016 Category: Microbiology Source Type: news

Primers: Functional Genes for Anaerobic Hydrocarbon Degrading Microbes
The detection of anaerobic hydrocarbon degrader populations via catabolic gene markers is important for the understanding of processes at contaminated sites. The genes of fumarate-adding enzymes (FAEs; i.e., benzylsuccinate and alkylsuccinate synthases) are widely used as specific functional markers for anaerobic degraders of aliphatic and aromatic hydrocarbons. Several recent studies have shown the existence of new and deeply branching FAE gene lineages in the environment, and respective FAE gene-targeted primer systems have been advanced. Here, state-of-the art protocols for the PCR detection, T-RFLP fingerprinting as we...
Source: Springer protocols feed by Microbiology - October 12, 2016 Category: Microbiology Source Type: news

Primers: Functional Marker Genes for Methylotrophs and Methanotrophs
Methylotrophs are a diverse group of microorganisms that use compounds without a carbon–carbon bond as a sole source of carbon and energy for growth. Methylotrophs play an important role in most environments, including terrestrial, aquatic, and marine habitats. Several approaches to detect and identify methylotrophs in environmental samples have been developed. A common approach is to target protein-encoding genes since methylotrophs are phylogenetically diverse, making the design of 16S rRNA primers and probes with wide coverage difficult or impossible. The mxaF gene encoding the active site subunit of the methanol ...
Source: Springer protocols feed by Microbiology - October 12, 2016 Category: Microbiology Source Type: news

Introduction to Primer-Based Detection of Microbial Genes, Particularly Those Encoding Enzymes for Aromatic/Aliphatic Hydrocarbon Biodegradation
One major contribution to understand the microbial ecology of biodegradation of pollutants in the environment has been the retrieval of information by using primers targeting genes that code for enzymes acting on aromatic or aliphatic hydrocarbons, therefore helping to survey and understand the microbial catabolome related with pollutant biodegradation in contaminated environments. In this introduction the advantages and limitations of using oligonucleotides generally and for hydrocarbon catabolism specifically are presented, and some common technical and theoretical considerations about using primers are explained. (Sourc...
Source: Springer protocols feed by Microbiology - October 12, 2016 Category: Microbiology Source Type: news

Current Landscape of Biomolecular Approaches for Assessing Biodegradation of Aromatic Hydrocarbons
The ability of bacteria to degrade hazardous pollutants is a valuable tool that can be employed for cleaning contaminated sites. As a result of the complex mixtures of organic compounds present in contaminated areas, the combined genetic information of more than one organism is necessary to enhance the degradation process. Aromatic compounds are believed to constitute approximately 25% of all biomass on earth. Community profiling and other molecular techniques, such as quantitative real-time PCR and fluorescence in situ hybridization, provide the phylogenetic context of the potential key genes associated with the degradati...
Source: Springer protocols feed by Microbiology - October 12, 2016 Category: Microbiology Source Type: news

Primers: Functional Genes for Nitrogen-Cycling Microbes in Oil Reservoirs
Microbial communities found in the subsurface are important in the biogeochemical cycling of nitrogen (N) both in the oxidative and reductive processes, and changes in their functional structure might affect the stability of a petroleum reservoir. In petroleum reservoirs, where in situ conditions are predominantly anoxic, denitrification involving the stepwise reduction of nitrate (NO3−) via nitrite (NO2−) and nitric oxide (NO) to nitrous oxide (N2O) or dinitrogen gas (N2) is a major process. Microorganisms may also decompose organic N to ammonium (NH4 +) by ammonification, which can subsequently be oxi...
Source: Springer protocols feed by Microbiology - October 12, 2016 Category: Microbiology Source Type: news

Primers: Bacterial Genes Encoding Enzymes for Aerobic Hydrocarbon Degradation
Alkanes are saturated hydrocarbons that are ubiquitous in the environment. Microbial degradation pathways evolved to activate and catabolise these compounds in order to gain energy and building blocks for cell growth. These pathways involve a number of hydroxylases, which primarily differ according to the nature of the hydrocarbon itself (e.g. aromatic or aliphatic). Given the widespread distribution of alkanes in the environment, a number of variants of such enzymes are present among microbes. Hence, primers designed to detect such environmental variants would require a database with a sufficiently large number of sequenc...
Source: Springer protocols feed by Microbiology - October 12, 2016 Category: Microbiology Source Type: news

Primers: Functional Genes and 16S rRNA Genes for Methanogens
To date, a great number of oligonucleotide probes/primers targeting phylogenetic markers of methanogenic archaea (methanogens), such as 16S rRNA and the gene for theα-subunit of methyl-coenzyme M reductase (mcrA), have been developed and used for the identification and quantification of individuals and groups of methanogens in environmental samples. These probes/primers were designed for different taxonomic levels of methanogens and have been used for studies in environmental microbiology as hybridization probes or PCR primers of qualitative and quantitative molecular techniques, such as high-throughput sequencing, q...
Source: Springer protocols feed by Microbiology - October 12, 2016 Category: Microbiology Source Type: news

Introduction to Genetic, Genomic and System Analyses of Pure Cultures
Although considered to be only a minute fraction of global biodiversity, the handling of the culturable microbiota is still essential for exploring the interface of the bacterial world with lipids, hydrocarbons and other chemicals. This endeavour requires a suite of wet and computational tools that are the subject of the present volume. The protocols detailed below go from generating large volumes of data with a suite of omics to methods for distilling such a data into information and this in turn into new and useful knowledge. To this end, in silico approaches have to go hand-in-hand with new strategies for genome editing...
Source: Springer protocols feed by Microbiology - December 31, 2015 Category: Microbiology Source Type: news