A comparison between fatty acid methyl ester profiling methods (PLFA and EL-FAME) as soil health indicators for microbial community composition

Authors: LI, CHENHUI - US Department Of Agriculture (USDA); CANO, AMANDA - US Department Of Agriculture (USDA); Acosta-Martinez, Veronica; Veum, Kristen; MOORE-KUCERA, JENNIFER - American Farmland Trust; SCHIPANSKI, MEAGAN - Colorado State University

Submitted to: Soil Science Society of America Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/15/2020
Publication Date: 8/26/2020
Citation: Li, C., Cano, A., Acosta-Martinez, V., Veum, K.S., Moore-Kucera, J., Schipanski, M. 2020. A comparison between fatty acid methyl ester profiling methods (PLFA and EL-FAME) as soil health indicators for microbial community composition. Soil Science Society of America Journal. 84:1153-1169. https://doi.org/10.1002/saj2.20118.
DOI: https://doi.org/10.1002/saj2.20118

Interpretive Summary: It is important to describe the distribution of fungi and bacteria of soil as they carry out different processes that provide nutrients and water for plant growth, and influence overall soil health. Scientists from ARS in Lubbock TX and Columbia MO with colleagues from other organizations compared two methods widely used to describe the microbial communities in soils from 14 states. Although the scientists found similar trends across the samples, one method was more sensitive to differences in the soil chemical properties, while the other method took less time to be performed and is more cost effective per sample. The group concluded that selecting from the two methods will depend on the resources available.

Technical 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 = 0.53-0.71) between PLFA and EL-FAME methods for absolute abundance of total FAME and individual microbial groups including, fungi [saprophytic fungi (SF) and arbuscular mycorrhizal fungi (AMF)], and all bacterial groups [Gram positive (GMP), Gram negative (GMN), and actinobacteria)]. In both methods, a common set of fatty acids were influential in the differentiating samples. The main differences of biomarker abundances between the two methods were that fungal and actinobacteria biomarkers [e.g., 16:1'5c (AMF), 18:1'9c (SF), 18:3'6c (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), 16:1'7c (GMN), 18:1'7c (GMN), and cy19:0'7c (GMN) were more dominant and responsive to soil properties in PLFA profiling. The advantages of EL-FAME are lower costs 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.