Tracking down microbial communities via fatty acids analysis: analytical strategy for solid organic samples

Analysis of phospholipid fatty acid (PLFA) composition is one of the most commonly used culture-independent tools for investigating microbial populations in ecological studies. This methodology provides qualitative and quantitative insights into the structure of the microbial community and indicates the main groups of microorganisms present and their abundance. Perhaps the biggest strength of this lipid-based approach, as compared to other microbial community assays, is that because PLFAs are rapidly synthesized during microbial growth, are not found in storage molecules and degrade rapidly during cell death, it provides an accurate census of the current living community. All cells contain fatty acids (FAs) that can be extracted and esterified to form fatty acid methyl esters (FAMEs). When the FAMEs are analyzed using gas chromatography–mass spectrometry, the resulting profile constitutes a ‘fingerprint’ of the microorganisms in the sample, since it contains some microbial biomarkers. Although the methods usually used for soil samples have been applied in the analysis of PLFAs in organic samples, it is important to determine the best analytical strategy for solid samples with high organic matter content. We compared different combinations of extraction and derivatization methods for determining FAs, leading to a successful analytical procedure that involves a significant reduction in the complexity and sample preparation time. The application of the optimized methodology to characterize microbial communities is shown for a variety of solid environmental samples.