Accuracy, Reproducibility, and Interpretation of Fatty Acid Methyl Ester Profiles of Model Bacterial Communities

Abstract

We determined the accuracy and reproducibility of whole-community fatty acid methyl ester (FAME) analysis with two model bacterial communities differing in composition by using the Microbial ID, Inc. (MIDI), system. The biomass, taxonomic structure, and expected MIDI-FAME profiles under a variety of environmental conditions were known for these model communities a priori. Not all members of each community could be detected in the composite profile because of lack of fatty acid "signatures" in some isolates or because of variations (approximately fivefold) in fatty acid yield across taxa. MIDI-FAME profiles of replicate subsamples of a given community were similar in terms of fatty acid yield per unit of community dry weight and relative proportions of specific fatty acids. Principal-components analysis (PCA) of MIDI-FAME profiles resulted in a clear separation of the two different communities and a clustering of replicates of each community from two separate experiments on the first PCA axis. The first PCA axis accounted for 57.1% of the variance in the data and was correlated with fatty acids that varied significantly between communities and reflected the underlying community taxonomic structure. On the basis of our data, community fatty acid profiles can be used to assess the relative similarities and differences of microbial communities that differ in taxonomic composition. However, detailed interpretation of community fatty acid profiles in terms of biomass or community taxonomic composition must be viewed with caution until our knowledge of the quantitative and qualitative distribution of fatty acids over a wide variety of taxa and the effects of growth conditions on fatty acid profiles is more extensive.

The concentrations of fatty acids in organo‐mineral particle‐size fractions of a Chernozem

“…For example, the concentration of n-C 28:0 in the NPK þ FYM treatment was less by factor of about 7 than in the FYM treatment of the Phaeozem nearby. This difference cannot be explained by environmental effects on bacterial populations as shown by Haack et al (1994) and Kennedy (1994).…”

Fatty acid analysis and spoilage potential of biofilms from two breweries

“…These can be colonized by anaerobic beer-spoiling bacteria. The usage of the FAME analysis for differentiating complex artificial communities has been validated by Haack et al (1994) and it has been successfully used for the characterization of soil communities (Schutter and Dick 2000;Drenovsky et al 2004). An advantage of the MIDI-FAME procedure is the about 10-fold lower amount of required sample mass for getting a reliable community fingerprint than for analysing PLFA (Drenovsky et al 2004).…”

“…The extraction and analysis of fatty acids is well established in microbial ecology for characterizing microbial communities (Vestal and White 1989;Haack et al 1994). This method allows the processing of large, representative samples of biomass and it detects all taxa present, except the Archaea.…”

Diversity of bacterial communities in the rhizosphere and root interior of field-grown genetically modified Brassica napus

“…The changes in the fatty acid composition found in our study may be an indicator of increased presence of Gramnegative, Gram-positive and fungal isolates in the root interior of the transgenic canola varieties. However, Haack et al [32] caution that conclusions about community structure derived from analysis of signature fatty acids may be oversimpli¢ed. In addition, Buyer and Drinkwater [33] suggest that soil fatty acid composition may change without accompanying changes in the microbial species composition, due in part to extraction of fatty acids associated with soil organic matter and plant roots.…”