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"Water is life!" All active cellular systems require water as the medium and solvent of their metabolic activities. Hydrophobic compounds and structures, which tend to exclude water, though providing inter alia excellent sources of energy and a means of biological compartmentalization, present problems of cellular handling, poor bioavailability and, in some cases, toxicity. Microbes both synthesize and exploit a vast range of hydrophobic organics, especially petroleum oil hydrocarbons and industrial pollutants, and the underlying interactions not only have major consequences for the lifestyles of the microbes involved, but also for biogeochemistry, climate change, environmental pollution, human health and a range of biotechnological applications. The aim of this handbook is to be the definitive resource of current knowledge on the diverse and multifaceted aspects of these interactions, the microbial players, and the physiological mechanisms and adaptive strategies characteristic of the microbial lifestyle that plays out at hydrophobic material: aqueous liquid interfaces.

Petroleum --- Lipids --- Biology --- Chemistry --- Microbiology & Immunology --- Organic Chemistry --- Physical Sciences & Mathematics --- Health & Biological Sciences --- Microbiology --- Hydrocarbons --- Organic compounds --- Biodegradation. --- Microbiology. --- Analysis. --- Life sciences. --- Biochemistry. --- Microbial ecology. --- Microbial genetics. --- Microbial genomics. --- Environmental engineering. --- Biotechnology. --- Life Sciences. --- Applied Microbiology. --- Environmental Engineering/Biotechnology. --- Biochemistry, general. --- Microbial Ecology. --- Microbial Genetics and Genomics. --- Chemical engineering --- Genetic engineering --- Environmental control --- Environmental effects --- Environmental stresses --- Engineering --- Environmental health --- Environmental protection --- Pollution --- Sustainable engineering --- Genomics --- Microbial genetics --- Microorganisms --- Genetics --- Environmental microbiology --- Ecology --- Biological chemistry --- Chemical composition of organisms --- Organisms --- Physiological chemistry --- Medical sciences --- Microbial biology --- Biosciences --- Sciences, Life --- Science --- Composition

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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 hydrocarbon:water interfaces, biofilms and microbe:mineral interfaces. Three forms of fluorescence in situ hybridization - CARD-FISH, MAR-FISH and Two-pass TSA-FISH - are described for the ecophysiological analysis of functionally active microbes in samples. The methods presented will enable readers to obtain an ultrastructural picture of, and identify the key functional microbes in, samples under investigation. This in turn will constitute a key framework for the interpretation of information from other experimental approaches, such as physicochemical analyses and genomic investigations. 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.

Microbiology. --- Biochemical engineering. --- Biochemical Engineering. --- Microbial biology --- Biology --- Microorganisms --- Bio-process engineering --- Bioprocess engineering --- Biochemistry --- Biotechnology --- Chemical engineering

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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. It complements a second Volume that describes protocols for systems and synthetic biology applications. The wet experimental tools presented in this Volume include protocols for the standardisation of transcriptional measurements, application of uracil excision-based DNA editing for, inter alia, multi-gene assembly, the use of fluxomics to optimise “reducing power availability”, and the incorporation of non-canonical amino acids into proteins for optimisation of activities. Phenome-ing microbes, using a combination of RNA-seq and bioinformatic algorithms, is presented, as is an illustration, using methylotrophs as an example, of how the different key omics approaches constitute a pipeline for functional analysis, acquisition of a systems overview, and metabolic optimisation. Complementary computational tools that are presented include protocols for probing the genome architecture of regulatory networks, genome-scale metabolic reconstruction, and bioinformatic approaches to guide metabolic engineering. The Volume also includes an overview of how synthetic biology approaches can be used to improve biocontainment. 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.

Microbiology. --- Biochemical engineering. --- Biochemical Engineering. --- Microbial biology --- Biology --- Microorganisms --- Bio-process engineering --- Bioprocess engineering --- Biochemistry --- Biotechnology --- Chemical engineering

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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 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.

Microbiology. --- Biochemical engineering. --- Biochemical Engineering. --- Microbial biology --- Biology --- Microorganisms --- Bio-process engineering --- Bioprocess engineering --- Biochemistry --- Biotechnology --- Chemical engineering

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This Volume presents a comprehensive series of generic protocols for the genetic and genomic analysis of prokaryotic isolates. Genetic methods for functional analyses employ the latest cloning vectors, gene fusion methods and transposon mutagenesis systems, as well as systems for introducing protease-cleavage sequences into permissive sites in proteins under investigation. Genomic methods described include protocols for transcriptomics, shotgun proteomics, interactomics, metabolic profiling, and lipidomics. Bioinformatic tools for genome annotation, transcriptome display and the integration of transcriptomic data into genome-scale metabolic reconstructions are described. Protocols for 13C-based metabolic flux determinations and analysis of the hierarchical and metabolic regulation of fluxes through pathways are included. The Volume thus enables investigators to functionally analyse an isolate over the entire cellular range spanning the gene, the genome, the transcript repertoire, the proteome, the interactome, the metabolic network with its nodes and their regulatory hierarchies, and the metabolic fluxes and their physiological controls. 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.

Microbiology. --- Biochemical engineering. --- Biochemical Engineering. --- Microbial biology --- Biology --- Microorganisms --- Bio-process engineering --- Bioprocess engineering --- Biochemistry --- Biotechnology --- Chemical engineering