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.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
