Canopy Trimming Experiment (CTE) Microbial EL-FAME Data



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The canopy trimming experiment at El Verde simulates some aspects (canopy openness and biomass redistribution) of hurricane disturbances. Soil samples and leaf litter were gathered from three replicate blocks, each with four treatment plots in Tabonuco Forest at in El Verde. Treatments (canopy trimming and debris addition) were applied in a 2 x 2 factorial design. Samples were obtained both before and after the canopy were trimmed and debris was applied in the appropriate treatments. Samples were collected every four months before and after treatments were applied. Molecular approaches such as EL-FAME are useful indicators of microbial community shifts in response to environmental change. In this experiment we analyzed microbial community composition and abundance in soil and leaf litter samples as reflected by EL-FAME profiles. All soil samples were cleaned by removing rocks and roots, and leaf litter samples were ground.

Fatty acid nomenclature: Fatty acids are named according to the conversion X:YωZ, where X represents the number of carbon atoms in the chain, followed by Y after the colon which represents the degree of the unsaturation. The symbol ω and Z represent the number of double bonds nearest to the carboxyl end. The prefixes a, i, cy and d refer to anteiso, iso, cyclopropyl branching and dicarboxylic fatty acid respectively; br indicates that the type of branching is unknown, while a number followed by Me indicates position of methyl group. Prefixes a and b indicate that the OH groups of an OH fatty acid are located at positions 2 and 3 respectively. Numbers preceded by w indicate the position of OH groups from the aliphatic end of the fatty acids (Kaur et al 2005).

Community analysis based on fatty acids: Fatty acid biomarkers could represent a group of particular microorganisms present in soil and leaf litter. Fatty acids used in literature as biomarkers are: Branched chain fatty acids (br 17:0, br 18:0, i17:0, a17:0, i16:0, i16:1, 10Me16:0, 10Me17:0), iso and anteiso isomers of 15:0 for gram positive bacteria; Cyclopropane fatty acids (cy17:0, cy19:0, 16:1w9, 16:1w7c, 16:1w5, 18:1w7,19:1) for gram-negative bacteria; 18:2w6 for fungi; 10Me16:0, 10Me17 : 0 and 10Me18 : 0 for Actinomycetes; cy17:0 and 10Me16:0 for Sulphate reducing bacteria; 16:1w8, 18:1w8 for Methanogens (Modified from Zelles, 1999; Kaur et al 2005).

Date Range: 
2002-11-02 00:00:00 to 2006-03-31 00:00:00

Publication Date: 

2011-06-07 00:00:00

Additional Project roles: 

Name: Miguel C Leon Role: Data Manager
Name: Francisco Rivera Role: Associated Researcher
Name: D. Jean Lodge Role: Associated Researcher
Name: Marirosa Molina Role: Associated Researcher


A PVC core (5cm diameter) was used to collect 0-10cm soil samples from five sub plots in each treatment plot. The five sub plot samples were clean (rocks, wood and invertebrates debris and roots) and pooled. Approximately 20 g of leaf litter samples were gathered close to where the soil cores were taken, then pooled and ground. All samples were kept at -4 °C after being pre-processed then moved to a -70 °C for longer storage.Lipids were extracted directly from soil and leaf litter using the EL-FAME method described by Schutter and Dick (2000). The lipid extraction procedure used a mild alkaline methylation, which in theory, remove the cellular ester linked fatty acid and not free fatty acids. After extracting the fatty acids by this method, they were cleaned with an amilopropyl (NH2) column to remove any humic substances. Fatty acid samples were kept frozen at -20 °C in darkness until their analysis in gas chromatograph.



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