Hydrocarbon and Lipid Microbiology Protocols
Hydrocarbon and Lipid Microbiology Protocols

Author: Terry J McGenity

Publisher: Springer

Published: 2018-05-06

Total Pages: 216

ISBN-13: 9783662569825

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This Volume presents relevant single-cell and single-molecule approaches in the study of microbes producing and utilizing hydrocarbons and lipids. While generically applicable for all microorganisms, the approaches described are, wherever possible, adapted to the field of study of hydrocarbon and lipid microbiology. The methods include basic procedures for isolating single cells by means of microfluidics and flow cytometry, and their cultivation in arrays as pure clones; for isolating, amplifying and sequencing single-cell genomes and transcriptomes; and for analysing single-cell metabolomes by means of Raman spectroscopy. Single-molecule approaches include the use of protein: fluorescent dye fusions for protein localization and methods for the production of cell division protostructures and lipid monolayers. Methods for the functional analysis of single cells include detection of metabolically active (protein-synthesizing) cells in environmental samples by bioorthogonal non-canonical amino acid tagging, Raman spectroscopy combined with stable isotope labelling and fluorescent in situ hybridisation, and visualization of single cells participating in gene transfer activity. Lastly, protocols are presented for single-cell biotechnological applications, including biofuel production. Hydrocarbon and Lipid Microbiology ProtocolsThere are tens of thousands of structurally different hydrocarbons, hydrocarbon derivatives and lipids, and a wide array of these molecules are required for cells to function. The global hydrocarbon cycle, which is largely driven by microorganisms, has a major impact on our environment and climate. Microbes are responsible for cleaning up the environmental pollution caused by the exploitation of hydrocarbon reservoirs and will also be pivotal in reducing our reliance on fossil fuels by providing biofuels, plastics and industrial chemicals. Gaining an understanding of the relevant functions of the wide range of microbes that produce, consume and modify hydrocarbons and related compounds will be key to responding to these challenges. This comprehensive collection of current and emerging protocols will facilitate acquisition of this understanding and exploitation of useful activities of such microbes.

Hydrocarbon and Lipid Microbiology Protocols
Hydrocarbon and Lipid Microbiology Protocols

Author: Terry J. McGenity

Publisher: Springer

Published: 2018-06-15

Total Pages: 137

ISBN-13: 9783662569818

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This Volume presents protocols for systems and synthetic biology applications in the field of hydrocarbon and lipid microbiology. It complements another Volume that describes generic protocols for wet experimental and computer-based systems and synthetic biology studies. The protocols in this Volume demonstrate how to employ systems and synthetic biology approaches in the design of microbes for the production of esters, isoprenoids, hydrophobic polymers, rhamnolipid biosurfactant, and peptide antimicrobial and thioether-stabilised molecules. Also presented is a protocol for the engineering of transcription factor-based biosensors for intracellular products, and another for the creation of a synthetic hydroxylase with novel activity for the selective oxyfunctionalisation of linear alkanes. Hydrocarbon and Lipid Microbiology ProtocolsThere are tens of thousands of structurally different hydrocarbons, hydrocarbon derivatives and lipids, and a wide array of these molecules are required for cells to function. The global hydrocarbon cycle, which is largely driven by microorganisms, has a major impact on our environment and climate. Microbes are responsible for cleaning up the environmental pollution caused by the exploitation of hydrocarbon reservoirs and will also be pivotal in reducing our reliance on fossil fuels by providing biofuels, plastics and industrial chemicals. Gaining an understanding of the relevant functions of the wide range of microbes that produce, consume and modify hydrocarbons and related compounds will be key to responding to these challenges. This comprehensive collection of current and emerging protocols will facilitate acquisition of this understanding and exploitation of useful activities of such microbes.

Hydrocarbon and Lipid Microbiology Protocols
Hydrocarbon and Lipid Microbiology Protocols

Author: Terry J. McGenity

Publisher: Springer

Published: 2016-12-16

Total Pages: 0

ISBN-13: 9783662531167

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This Volume describes methods for investigating microbes in their natural environment and how to obtain representative samples and preserve them for subsequent analyses. Chapters are arranged according to the environments under investigation, which include: oil reservoirs, fracking fluids, aquifers, coal beds, oil sands and their tailing ponds, lakes, rivers, leaves, polar seas and ice, the sea-surface microlayer, mud flats, microbialites, and deep-sea fauna. A variety of downstream analytical procedures are described, including: nucleic-acid extraction and preparation for high-throughput sequencing, fluorescence in-situ hybridisation, and cultivation of aerobic and anaerobic hydrocarbon-degrading microbes. Though most chapters focus on hydrocarbon-rich environments, many of the approaches used are generic, and as such will be of value to researchers embarking on studies of microbes and their processes in the field. Hydrocarbon and Lipid Microbiology Protocols There are tens of thousands of structurally different hydrocarbons, hydrocarbon derivatives and lipids, and a wide array of these molecules are required for cells to function. The global hydrocarbon cycle, which is largely driven by microorganisms, has a major impact on our environment and climate. Microbes are responsible for cleaning up the environmental pollution caused by the exploitation of hydrocarbon reservoirs and will also be pivotal in reducing our reliance on fossil fuels by providing biofuels, plastics and industrial chemicals. Gaining an understanding of the relevant functions of the wide range of microbes that produce, consume and modify hydrocarbons and related compounds will be key to responding to these challenges. This comprehensive collection of current and emerging protocols will facilitate acquisition of this understanding and exploitation of useful activities of such microbes.

Hydrocarbon and Lipid Microbiology Protocols
Hydrocarbon and Lipid Microbiology Protocols

Author: Terry J. McGenity

Publisher: Springer

Published: 2016-12-02

Total Pages: 0

ISBN-13: 9783662504277

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This Volume addresses the pros and cons of oligonucleotide probes, primers and primer combinations, and importantly considers how to design the best tools for the microbial taxa and/or processes being investigated. Individual chapters focus on the design of primers targeting genes that code for enzymes associated with the following functions: degradation of aromatic, aliphatic and chlorinated hydrocarbons under aerobic and anaerobic conditions, methanogenesis, methane oxidation, and the nitrogen cycle. Hydrocarbon and Lipid Microbiology Protocols There are tens of thousands of structurally different hydrocarbons, hydrocarbon derivatives and lipids, and a wide array of these molecules are required for cells to function. The global hydrocarbon cycle, which is largely driven by microorganisms, has a major impact on our environment and climate. Microbes are responsible for cleaning up the environmental pollution caused by the exploitation of hydrocarbon reservoirs and will also be pivotal in reducing our reliance on fossil fuels by providing biofuels, plastics and industrial chemicals. Gaining an understanding of the relevant functions of the wide range of microbes that produce, consume and modify hydrocarbons and related compounds will be key to responding to these challenges. This comprehensive collection of current and emerging protocols will facilitate acquisition of this understanding and exploitation of useful activities of such microbes.

Hydrocarbon and Lipid Microbiology Protocols
Hydrocarbon and Lipid Microbiology Protocols

Author: Terry J McGenity

Publisher: Springer

Published: 2018-12-09

Total Pages: 256

ISBN-13: 9783662569856

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This Volume features protocols for investigating the hydrocarbon- and lipid-specific activities of microbes. They include methods for studying chemotaxis, the colonisation of hydrocarbon surfaces, hydrocarbon uptake, respiration, nitrogen fixation, sulphate reduction, membrane stabilisation through cis-trans isomerisation of membrane fatty acids, and the production of biosurfactants and biopolymers in response to the presence of hydrocarbons. A protocol for studying the ability of microbes to control the concentration of hydrocarbons in their aqueous environment is also described, and phenotyping methods to reveal microbes' more general metabolic activities are presented. Several protocols for investigating acid production in connection with oil souring and biocorrosion by microbes in oil well, oil transportation and storage settings are presented. Lastly, protocols for measuring methanogenesis, as an example of microbial hydrocarbon production, are described.Hydrocarbon and Lipid Microbiology ProtocolsThere are tens of thousands of structurally different hydrocarbons, hydrocarbon derivatives and lipids, and a wide array of these molecules are required for cells to function. The global hydrocarbon cycle, which is largely driven by microorganisms, has a major impact on our environment and climate. Microbes are responsible for cleaning up the environmental pollution caused by the exploitation of hydrocarbon reservoirs and will also be pivotal in reducing our reliance on fossil fuels by providing biofuels, plastics and industrial chemicals. Gaining an understanding of the relevant functions of the wide range of microbes that produce, consume and modify hydrocarbons and related compounds will be key to responding to these challenges. This comprehensive collection of current and emerging protocols will facilitate acquisition of this understanding and exploitation of useful activities of such microbes.

Hydrocarbon and Lipid Microbiology Protocols
Hydrocarbon and Lipid Microbiology Protocols

Author: Terry J. McGenity

Publisher: Springer

Published: 2017-01-06

Total Pages: 0

ISBN-13: 9783662504499

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This Volume presents protocols for investigating the genetic, metabolic and ecological potential and functional analysis of microbial communities. Methods are described for the creation and bioinformatic assessment of metagenomic and metatranscriptomic libraries, and for metaproteomic analyses, which provide important insights into the metabolic potential and interactions of community members. These in turn lead to specific hypotheses concerning the functional contributions of individual populations in the community, which may be investigated by the stable isotope probing approaches described in this Volume, making it possible to identify those community members primarily responsible for particular functions. Methods for the direct extraction of proteins from environmental samples for sequencing and activity tests are presented, providing a broad overview of prevailing metabolic activities and of the types of microbe involved in them. Protocols for the analysis of nutrient flow through microbial communities and for the modelling of dynamic physiological interactions in communities are also provided. Lastly, the book presents a protocol for the quantitative assessment of permissiveness for the transfer of conjugative plasmids, important agents of physiological change and evolution in microbial communities. Hydrocarbon and Lipid Microbiology ProtocolsThere are tens of thousands of structurally different hydrocarbons, hydrocarbon derivatives and lipids, and a wide array of these molecules are required for cells to function. The global hydrocarbon cycle, which is largely driven by microorganisms, has a major impact on our environment and climate. Microbes are responsible for cleaning up the environmental pollution caused by the exploitation of hydrocarbon reservoirs and will also be pivotal in reducing our reliance on fossil fuels by providing biofuels, plastics and industrial chemicals. Gaining an understanding of the relevant functions of the wide range of microbes that produce, consume and modify hydrocarbons and related compounds will be key to responding to these challenges. This comprehensive collection of current and emerging protocols will facilitate acquisition of this understanding and exploitation of useful activities of such microbes.

Hydrocarbon and Lipid Microbiology Protocols
Hydrocarbon and Lipid Microbiology Protocols

Author: Terry J. McGenity

Publisher:

Published: 2016

Total Pages: 252

ISBN-13: 9783662527788

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This Volume presents methods for quantifying microbial populations and characterising microbial communities by extracting and analysing biomarkers such as RNA, DNA and lipids. The chapters cover a wide range of topics, including: cell separation from oil-rich environments, enumeration of hydrocarbon degraders and sulphate reducers using most-probable-number techniques, and quantification by means of real-time PCR. A variety of molecular methods are described for microbial community profiling, such as phospholipid fatty acid analysis, DGGE, T-RFLP and SSCP. One chapter examines high-throughput sequencing, and provides important information on the associated procedures required for thorough data analysis. A further chapter is devoted to the characterisation of protistan communities, while the closing chapter describes multiplex fluorescent antibody microarrays for detecting microbial biomarkers. Hydrocarbon and Lipid Microbiology Protocols There are tens of thousands of structurally different hydrocarbons, hydrocarbon derivatives and lipids, and a wide array of these molecules are required for cells to function. The global hydrocarbon cycle, which is largely driven by microorganisms, has a major impact on our environment and climate. Microbes are responsible for cleaning up the environmental pollution caused by the exploitation of hydrocarbon reservoirs and will also be pivotal in reducing our reliance on fossil fuels by providing biofuels, plastics and industrial chemicals. Gaining an understanding of the relevant functions of the wide range of microbes that produce, consume and modify hydrocarbons and related compounds will be key to responding to these challenges. This comprehensive collection of current and emerging protocols will facilitate acquisition of this understanding and exploitation of useful activities of such microbes.

Hydrocarbon and Lipid Microbiology Protocols
Hydrocarbon and Lipid Microbiology Protocols

Author: Terry J. McGenity

Publisher:

Published: 2017

Total Pages: 245

ISBN-13: 9783662531143

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This Volume covers protocols for various applications in hydrocarbon microbiology, including those of interest for industrial processes, biocatalysis, lipid and biofuel production, bioproducts, or the human microbiome. It presents detailed protocols for the functional screening of enzymes acting on greasy molecules (i.e. lipases, esterases), including assays for enantioselective biocatalysts, as well as approaches for protein display technologies. Protocols for improving fuel quality and production of biofuel and lipids in different hosts (bacteria, algae, yeast) are also provided. The production of biogas from organic waste and its fermentation into value-added products such as polyhydroxyalkanoates is covered, as well as an in-vitro model of the gut microbiome for short-chain fatty acid metabolism and microbial diversity analyses. The applications presented are examples of the many potential applications in hydrocarbon and lipid microbiology, and many (i.e. protein-display technologies) will also be of interest in other research fields. Hydrocarbon and Lipid Microbiology Protocols There are tens of thousands of structurally different hydrocarbons, hydrocarbon derivatives and lipids, and a wide array of these molecules are required for cells to function. The global hydrocarbon cycle, which is largely driven by microorganisms, has a major impact on our environment and climate. Microbes are responsible for cleaning up the environmental pollution caused by the exploitation of hydrocarbon reservoirs and will also be pivotal in reducing our reliance on fossil fuels by providing biofuels, plastics and industrial chemicals. Gaining an understanding of the relevant functions of the wide range of microbes that produce, consume and modify hydrocarbons and related compounds will be key to responding to these challenges. This comprehensive collection of current and emerging protocols will facilitate acquisition of this understanding and exploitation of useful activities of such microbes.

Hydrocarbon and Lipid Microbiology Protocols
Hydrocarbon and Lipid Microbiology Protocols

Author: Terry J. McGenity

Publisher:

Published: 2016

Total Pages: 188

ISBN-13: 9783662491379

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This Volume provides protocols for the biochemical analysis of hydrocarbon- and lipid-relevant products, cell components and activities of microbes that interact with hydrophobic compounds. They include methods for the extraction, purification and characterisation of surface tension-reducing bioemulsifiers and biosurfactants that increase the surface area and hence bioavailability of hydrophobic substrates. Protocols for the isolation and biochemical analysis of lipids and polyhydroxyalkanoates, food storage products made during nutrient abundance that represent important biotechnological products, are presented. The extraction of membrane lipid rafts, sub-organelles that fulfil important functional roles for the cell membrane, and the isolation and characterisation of membrane phospholipid biomarkers, are also described. The purification and characterisation of integral membrane hydrocarbon-oxidising enzymes are addressed. Lastly, two generic methods for the genetic analysis of catabolic pathways and analysis of ligand binding are presented. Hydrocarbon and Lipid Microbiology Protocols There are tens of thousands of structurally different hydrocarbons, hydrocarbon derivatives and lipids, and a wide array of these molecules are required for cells to function. The global hydrocarbon cycle, which is largely driven by microorganisms, has a major impact on our environment and climate. Microbes are responsible for cleaning up the environmental pollution caused by the exploitation of hydrocarbon reservoirs and will also be pivotal in reducing our reliance on fossil fuels by providing biofuels, plastics and industrial chemicals. Gaining an understanding of the relevant functions of the wide range of microbes that produce, consume and modify hydrocarbons and related compounds will be key to responding to these challenges. This comprehensive collection of current and emerging protocols will facilitate acquisition of this understanding and exploitation of useful activities of such microbes.