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.

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...

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...

This Volume presents key microscopy and imaging methods for revealing the structure and ultrastructure of environmental and experimental samples, of microbial communities and cultures, and of individual cells. Method adaptations that specifically address problems concerning the hydrophobic components of samples are highlighted and discussed. The methods described range from electron microscopy and light and fluorescence microscopy, to confocal laser-scanning microscopy, and include experimental set-ups for the analysis of interfacial processes like microbial growth and activities at...

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...

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...

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...

This Volume presents generic protocols for wet experimental and computer-based systems and synthetic biology approaches relevant to the field of hydrocarbon and lipid microbiology.