A comparison between fatty acid methyl ester profiling methods (PLFA and EL‐FAME) as soil health indicators

Abstract

Fatty acid methyl ester (FAME) profiling for characterizing microbial community composition typically is conducted via phospholipid fatty acid (PLFA) or ester‐linked fatty acid methyl ester (EL‐FAME) methods. As soil health assessments aim to be utilized across the nation and globe, the robust measurement and interpretation of microbial communities across a range of soils and environments will be necessary. This study compared PLFA and EL‐FAME methods for detecting and interpreting profiles of microbial community composition in croplands across a wide geographic area using a total of 172 soil samples from 14 states representing a wide range of soil properties. Overall, PLFA and EL‐FAME provided comparable biomarkers in terms of microbial community composition. The Spearman's Rank correlation test showed positive correlations (r = 0.37–0.71) between PLFA and EL‐FAME methods for absolute abundance of total FAME and individual microbial groups including fungi (saprophytic fungi [SF], arbuscular mycorrhizal fungi [AMF], and general fungi [F]) and all bacterial groups (Gram positive [GMP], Gram negative [GMN], and Actinobacteria). In both methods, a common set of fatty acids were influential in differentiating samples. The main differences in biomarker abundances between the two methods were that fungal and Actinobacteria biomarkers (e.g., 16:1ω5c [AMF], 18:1ω9c [F], 18:3ω6c [F], and 10Me16:0 [Actinobacteria]) were more abundant or critical in EL‐FAME profiling (large variation among soil samples and sensitive to soil properties), but bacterial biomarkers such as i15:0 (GMP), 16:1ω7c (GMN), 18:1ω7c (GMN), and cy19:0ω7c (GMN) were more dominant and responsive to soil properties in PLFA profiling. The practical advantages of EL‐FAME are lower cost and simpler methodology. Although both methods produced similar microbial profile abundances for important microbial markers, PLFA was more sensitive to the wide range of soil chemical properties in this sample set including pH, clay content, soil organic matter, and active carbon.

Comparing biological methods for soil health assessments: EL‐FAME, enzyme activities, and qPCR

“…However, EL-FAME has become popular due to its simplicity and because it is less time consuming than PLFA analysis (Miura, Makoto, Niwa, Kaneko, & Sakamoto, 2017;Schutter and Dick, 2000). Additionally, the extraction in EL-FAME is directly from soil samples, and thus, may contain other lipid fractions including neutral lipids (Zelles, 1999;Miura et al, 2017), which give the advantage of evaluating the arbuscular mycorrhizal fungi (AMF) marker 16:1ω5c (Cotton & Acosta-Martínez, 2018;Li et al, 2020). The EL-FAME method has been shown to be sensitive at detecting changes in microbial communities under different management practices and regions (e.g., Mbuthia et al, 2015;Li et al, 2018), and after natural climatic disturbances such as drought, hurricanes, and extreme temperatures (Bérard, Bouchet, Sévenier, Pablo, & Gros, 2011; T A B L E 1 Quantitative polymerase chain reaction assays for genes associated with taxonomic groups and functional processes Cantrell et al, 2014;Pérez-Guzmán et al, 2020).…”

“…Additionally, these methods allow for the identification of broad groups such as Gram‐positive, Gram‐negative, Actinobacteria, and saprophytic fungi (Willers, Jansen van Rensburg, & Claassens, 2015; Zelles, 1999). Recently, Li, Cano, Acosta‐Martínez, Veum, and Moore‐Kucera (2020) compared PLFA and EL‐FAME using 172 soil samples representing a wide range of physicochemical properties, and provided detailed information regarding equipment, costs, practical advantages, and results. For example, although certain FAME markers may be of plant origin, leading to slight overestimation of some groups, total FAMEs have been used as a proxy of microbial biomass (e.g., Li et al., 2018; Li et al., 2020).…”

“…Recently, Li, Cano, Acosta‐Martínez, Veum, and Moore‐Kucera (2020) compared PLFA and EL‐FAME using 172 soil samples representing a wide range of physicochemical properties, and provided detailed information regarding equipment, costs, practical advantages, and results. For example, although certain FAME markers may be of plant origin, leading to slight overestimation of some groups, total FAMEs have been used as a proxy of microbial biomass (e.g., Li et al., 2018; Li et al., 2020). Also, since phospholipids are easily degraded upon cell death, fatty acids derived from PLFA analysis are thought to represent the viable microbial community (Zelles, 1999).…”

Phospholipid fatty acids in soil—drawbacks and future prospects

“…This contrasts neutral lipid fatty acids (NLFA), which are storage components, especially in fungi, and give interesting information on the nutritional status of fungi (Bååth 2003). Total fatty acid methyl ester (FAME) or ester-linked (EL) total FAME have been repeatedly determined in soil by in situ hydrolysis and methylation reactions of fatty acids, without the PLFA extraction step (Acosta-Martínez et al 2010;Li et al 2020). Total FAME and EL-FAME give similar information on the composition of the main microbial groups to that provided by PLFA (Acosta-Martínez et al 2010) but create an additional link to the formation of microbial necromass from decaying biomass by different microbial groups (Miltner et al 2012).…”

Early Effect of Pine Biochar on Peach-Tree Planting on Microbial Community Composition and Enzymatic Activity

“…Despite the growing popularity of next-generation sequencing methods, which allow for detailed analysis of soil microbial communities, the determination of soil organisms' fatty acid patterns is still one of the most commonly used methods for testing microbial biomass and community structures [16]. Ester-linked fatty acid methyl ester (EL-FAME) profiling provides a rapid, inexpensive, reproducible, and reliable approach to characterize the existing microbial community of soil.…”