Introduction to Activities and Phenotypes

Abstract

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 to hydrocarbons or lipids, protocols aiming to resolve the specific interactions of microorganisms with hydrophobic phases, protocols to study the effects of hydrocarbons or lipids on bulk metabolic activities of microbial communities, and tools to identify specific genes involved in metabolic processes. Most of the protocols presented here can be applied directly on environmental samples, or on laboratory-scale micro/mesocosms, thereby allowing a direct comparison between pristine samples and samples contaminated experimentally with hydrocarbons.