Phospholipid, ester-linked fatty acid profiles showed changes in benthic prokaryotic community structure reflecting culture manipulations that were both quantitative and statistically significant. Fatty acid structures, including the position and cis/trans geometry of double bonds, were chemically verified by GC/MS after appropriate derivatization. The fatty acid profiles of independent flasks showed reproducible shifts when manipulated identically and significant differences when manipulated with different treatments. The absence of polyunsaturated fatty acids indicated that the consortia were predominantly prokaryotic. The prokaryotic consortia of different treatments could be differentiated by the proportions of cyclopropyl fatty acids and the proportions and geometry of monounsaturated fatty acids.