The use of phospholipid fatty acids to determine microbial community structure

Abstract

The most difficult task facing microbial ecologists is the quantitative description of microbial communities. This is due to the fact that, unlike higher organisms, there is little correlation between the observable structure of a microorganism and its ecological function. Hence, the tried and true method of plant and animal ecologists, careful visual observation, is often of little value when applied to the problem of describing microbial communities. Indeed, the vast majority of microbial diversity is best described in terms of their varied metabolic functions. Unfortunately, measures of metabolic processes, while yielding important ecological information, rarely yield estimates of the biomass of microorganisms effecting the measured rate. Classical methods of isolation and identification, as well as many modern molecular methods, are highly selective — that is they fail to detect most organisms in a given environment. Only two accepted methods overcome the difficulty of selectivity and provide a relatively unbiased view of the structure of complex microbial communities. These are analysis of microbial populations using ribosomal RNA (or its corresponding DNA sequences) and phospholipid fatty acid analysis. Both techniques have advantages and disadvantages and should not be viewed as competing, rather, as complementary. Community analysis using rRNA (or rDNA) sequencing can commonly detect and identify community members with a high degree of specificity (to species and even strains), as well as, detect and suggest phylogenetic affinities of as yet uncultured organisms.