Protein Extraction from Contaminated Soils and Sediments

Abstract

Greasy molecules such as crude oil and polycyclic aromatic hydrocarbons (PAHs) are widely distributed in the environment and easily accumulate in soils and marine sediments. They may primarily be considered as an ecological problem, but at the same time constituted a factor influencing microbial populations and the biodegradation processes they mediate. Several strategies have been used to study the relationship between the PAHs input and ecosystem functioning and population structure. Among them, the preparation of protein extracts becomes overriding to obtain information about microbial function and for inferring active set of reactions associated to proteins being expressed. However, apart from the technical limitations for protein identifications, the isolation of microbial proteins from soil or sediments constitutes per se a key step, which should be optimized. Here we describe several methods for efficient extraction of proteins from contaminated soils or sediments. Such methods allow obtaining high protein yields which could be used for shotgun proteomic approaches or any kind of proteomic approach, including enzymatic activity tests. These approaches include those based on the direct extraction of proteins from raw samples and those based on the separation of microbial cells from material prior protein extraction. Although the majority of described methods are performed under denaturing conditions, we also provided details about approaches to obtain protein in native state, which could be used for biochemical tests.