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This Volume describes methods for simulating natural environments by using reproducible and controllable meso- and microcosm experiments to analyse hydrocarbon-degrading microorganisms and to test hypotheses. It presents important aspects of the preparation of experimental set-ups, hydrocarbon application and sampling, and features protocols for experiments with different types of samples, such as biofilms, aquatic systems (e.g. groundwater, streams), and sediments, including oscillating oxic-anoxic mesocosms, as well as for in-situ experimentation in subtidal and deep sediments. Two chapters are dedicated to cultivation under high-pressure conditions, and several chapters include protocols for processing samples for downstream chemical, microbial or activity analyses. Several of the approaches presented are generic and will benefit anyone embarking on designing meso- and microcosm experiments. <

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: Meso- and Microcosms

Introduction.- Preparing the hydrocarbon / crude oil.- High pressure cultivation of hydrocarbonoclastic aerobic bacteria.- In vitro high pressure incubation and activity measurement of deep-sea, methanogenic archaea.- Bioreactor design to emulate deep-sea hydrocarbon releases including formation of gas hydrates.- Mudflat benthic spill simulations.- Protocols for subtidal and deep sea benthic oil spill simulations.- Simulation of anoxic/oxic oscillations in crude oil-degrading bioreactors.- Protocols for microcosms for growing biofilms on hydrophobic substrates - a polyphasic approach to study biodiversity, metabolic activity and biofilm architecture.- Application of micro- and mesocosms experiments to pollutant effects in biofilms.- Mini sediment columns and two-dimensional sediment flow-through microcosms - versatile model systems for studying biodegradation of organic contaminants in groundwater ecosystems.