Lipid Fingerprinting of Soil Microbial Communities

Abstract

This chapter provides an overview of lipid-based methods used to characterize microbial communities, specifically targeting the soil environment. The authors summarize the methods commonly used in investigations of soil communities, consider analytical and technical challenges of soil, describe statistical approaches for analyzing fingerprint data, and present applications to illustrate the types of information generated and questions that can be addressed with these methods. Types of lipid-based methods applied to soil include analyses of phospholipid fatty acids (PLFA), whole-cell fatty acid methyl esters (FAME) (also called EL-MIDI, MIDI method, and TS-FAME) in soil, sterols, and respiratory quinones. Fatty acid-based methods such as PLFA generally produce chromatographs (gas chromatography (GC) or gas chromatography-mass spectrophotometer (GC-MS)) consisting of multiple fatty acids. Some of the fatty acids have masses that are close to detection. PLFA analysis has provided insights into how soil microbial communities respond, in agricultural soils, to different management practices and, in natural ecosystems, to invasion by exotic plant species. In a comparison of the effects of different hay and fertilizer inputs, microbial community composition, based on PLFA fingerprinting, was significantly affected by the different treatments yet microbial C and N pools, as well as respiration, did not specifically respond to inputs. PLFA analysis is a direct wet-chemistry method (unlike, e.g., PCR-based methods) and generates quantitative information (e.g., nanomoles of different fatty acids).