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Chapter 64 : Lipid Fingerprinting of Soil Microbial Communities
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).
CCA of microcosm and field soil PLFA profiles. (A) Ordination biplot of the fatty acids and environmental variable scores. Three circles were added to panel A following statistical analysis to aid in identifying the plotted fatty acids. The circle furthest to the left includes the fatty acids i15:0, 16:0, 16:1ω5c, 16:1ω7t, and i17:1ω5. The middle circle includes the fatty acids 16:1ω11c, i17:0, 17:0cy, 18:0, and sum 7. The circle furthest to the right includes the fatty acids 10Me 16:0, 10Me 17:0, 17:1ω9c, and sum 9. (B) Ordination biplot of the sample and the environmental variable scores. Each sample point is the average of three treatment replicates. Black squares indicate +C samples, and gray circles indicate –C samples. Following statistical analysis, circles were added to the biplots to indicate treatment groupings, but these circles do not indicate confidence ellipsoids. In both plots (A and B) the environmental variables are plotted as discrete points. Reprinted with permission from Drenovsky et al. ( 32 ).
CCA of 42 sites classified by nine land use types. Vectors represent soil characteristics, and centroids show statistically significant management factors. Reprinted with permission from Steenwerth et al. ( 115 ).
Common multivariate methods for fatty acid fingerprint analysis a