Comparison of phospholipid fatty acid (PLFA) and total soil fatty acid methyl esters (TSFAME) for characterizing soil microbial communities Rebecca E. Drenovsky a, * , Geoff N. Elliott b , Kenneth J. Graham c , Kate M. Scow a a Department of Land, Air and Water Resources, University of California, Davis, One Shields Avenue, Davis, CA 95616-8627, USA b Institute of Biological Sciences, University of Wales Aberystwyth, Aberystwyth, Ceredigion SY23 3DA, UK c Department of Biological Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616-8627, USA Received 30 June 2003; received in revised form 6 January 2004; accepted 31 May 2004 Abstract Phospholipid fatty acid (PLFA) and total soil fatty acid methyl esters (TSFAME), both lipid-based approaches used to characterize microbial communities, were compared with respect to their reliable detection limits, extraction precision, and ability to differentiate agricultural soils. Two sets of soil samples, representing seven crop types from California’s Central Valley, were extracted using PLFA and TSFAME procedures. PLFA analysis required 10 times more soil than TSFAME analysis to obtain a reliable microbial community fingerprint and total fatty acid content measurement. Although less soil initially was extracted with TSFAME, total fatty acid (FA) content g K1 soil (DW) was more than 7-fold higher in TSFAME– versus PLFA-extracted samples. Sample extraction precision was much lower with TSFAME analysis than PLFA analysis, with the coefficient of variation between replicates being as much as 4-fold higher with TSFAME extraction. There were significant differences between PLFA– and TSFAME-extracted samples when biomarker pool sizes (mol% values) for bacteria, actinomycetes, and fungi were compared. Correspondence analysis (CA) of PLFA and TSFAME samples indicated that extraction method had the greatest influence on sample FA composition. Soil type also influenced FA composition, with samples grouping by soil type with both extraction methods. However, separate CAs of PLFA– and TSFAME extracted samples depicted strong differences in underlying sample groupings. Recommendations for the selection of extraction method are presented and discussed. q 2004 Elsevier Ltd. All rights reserved. Keywords: Fatty acid; PLFA; TSFAME; Microbial community composition; Biomarker 1. Introduction Recent methodological advances in soil microbial ecology are increasing our understanding of soil microbial community composition and how community composition relates to soil processes. Many of the new methods extract the cellular constituents of microorganisms directly from soil, eliminating the bias inherent in culture-based methods (Fry, 1982; Pedros-Alio, 1993). Due to their chemical diversity and cellular abundance, lipids and nucleic acids are particularly promising constituents for investigating and characterizing microbial communities. Lipids, a major cellular component, constitute a wide variety of structurally and functionally diverse compounds. Using multivariate statistical analyses, this variation in fatty acid (FA) composition between microorganisms can be exploited, revealing differences between microbial commu- nities (Macalady et al., 2000). In addition, some FAs are considered biomarkers for specific groups of micro- organisms, based on their lipid profiles from pure culture (Zelles, 1999). Phospholipid fatty acids (PLFA) are major cell membrane constituents, and their polar head groups and ester-linked side chains (i.e. FAs) vary in composition between eukaryotes and prokaryotes, as well as among many pro- karyotic groups. These compounds rapidly degrade upon cell death (Pinkart et al., 2002), making them good indicators of living organisms (White et al., 1979). Phospholipids are extracted directly from soil, and following hydrolysis, their 0038-0717/$ - see front matter q 2004 Elsevier Ltd. All rights reserved. doi:10.1016/j.soilbio.2004.05.002 Soil Biology & Biochemistry 36 (2004) 1793–1800 www.elsevier.com/locate/soilbio * Corresponding author. Tel.: C1-530-752-0146; fax: C1-530-752- 1552. E-mail address: redrenovsky@ucdavis.edu (R.E. Drenovsky).