Linking microbial community analysis and ecosystem studies: A rapid lipid analysis protocol for high throughput

Teri C. Balser, Chao Liang, Jessica L.M. Gutknecht

Research output: Contribution to journalArticlepeer-review

7 Scopus citations


During the past two decades interest in linking soil microbial community composition and activity with ecosystem scale field studies of nutrient cycling or plant community response to disturbances has grown. Despite its importance there are challenges in making this linkage. Foremost is the question of analytical feasibility. In general, microbiological community-level methodologies have not been readily adaptable to the large sample sizes necessary for ecosystem-scale research. As a result, it has been difficult to generate compatible microbial and ecosystem data sets. Soil lipid analysis shows potential as a middle ground between simple biomass measures and molecular profiling. However, the two protocols that have most often been followed are either rapid but indiscriminate (total lipid analysis or fatty acid methyl ester analysis; FAME), or precise but time consuming (phospholipid fatty acid analysis; PLFA). In this paper we report results from a standardized soil used test a modified extraction method (the ‘hybrid’ method) developed to balance the speed of FAME and the precision of PLFA in order to increase sample throughput. In comparing the three methods, we find that FAME and PLFA are qualitatively and quantitatively distinct. The FAME method yielded the highest fatty acid abundance, but also had high variance resulting in low precision. The PLFA method had precision, but low yield. The ‘hybrid’ method fell midway between FAME and PLFA for quantitative fatty acid yield. In addition, the hybrid extraction can be completed in a fraction of the time it takes for PLFA. The hybrid protocol appears to provide an optimal balance between effort and accuracy and therefore is a good choice for large-scale ecosystem studies.

Original languageEnglish (US)
Pages (from-to)22-32
Number of pages11
JournalSoil Ecology Letters
Issue number1-2
StatePublished - Jun 2019

Bibliographical note

Funding Information:
This study was supported by grants from the Kearney Foundation, the Andrew W. Mellon Foundation and the Department of Energy-Great Lakes Bioenergy Research Center DOE-GLBRC) funding. We would also like to thank the Matson laboratory (Stanford University) and Balser laboratory (University of Wisconsin-Madison) where method testing was performed. We are also grateful for the assistance of Carrie Nielsen and Phil Barak.

Publisher Copyright:
© 2019, Higher Education Press.


  • Ecosystem studies
  • Lipid analysis
  • Microbial community composition
  • PLFA


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