Fatty acid profiling of soil microbial communities : a comparison of extraction methods and temporal dynamics in plant residue amended soils

Graduation date: 2007A method based on fatty acid (FA) analysis is used to profile microbial community structure (MCS). Various extraction protocols are available, which alter the types of FAs extracted from soils. The more time consuming but widely used protocol extracts only FAs from phospholipids (PLFA). This technique is desirable because PLFAs are largely of microbial origin and from viable cells, since they rapidly degrade upon microbial death. This stands in contrast to other more rapid methods that directly extract FAs but may extract FAs of non-microbial origin. In this thesis, two such methods of FA extraction (EL-FAME and MIDI) were compared to PLFA extracts for detecting shifts and interpreting profiles of MSC. Soil samples from a wide array of vegetation and climatic conditions were extracted by these methods, and their FA composition analyzed by gas chromatography. MIDI extracts contained major plant-specific FAs. Ordination multivariate analysis showed that separation of MCS among samples was driven mostly by these FAs, rather than by microbial FA markers. The degree of similarity between EL-FAME and PLFA results was affected by the environmental conditions. The major differences among methods were in the general fungal and arbuscular-mycorrhizal fungal markers that were related to the vegetation type where soils were found. Nevertheless, cross-sample relative differences in the amounts of prokaryote FAs were not impacted by EL-FAME relative to PLFA.\ud \ud PLFA also was used to track shifts in MCS during the decomposition of two residues of contrasting chemical composition (maize stover, MS; and coconut husk, CH), under two N rates in a Brazilian soil. Microbial biomass-C (MBC), respiration rates and activity of C-cycle enzymes were concomitantly evaluated. A laboratory incubation was conducted for 425 d that included a simulated drought period between days 160 and 290. MS significantly impacted MCS and increased respiration rates, MBC, and enzyme activities; while changes due to CH were more subtle or non-existent. In MS, N reduced the CO2-C losses from soil, but caused no change in MBC. Higher respiration rates under low N were associated with a more bacterial-dominated community, and a higher laccase activity