Comparing the Diversity Present in Forests Soils Metagenomic Libraries and the Soil Sources Using Denaturing Gradient Gel Electrophoresis

Metagenomics evaluates genomes in an environment, unraveling function and diversity using culture independent approaches. Our laboratory generated two Metagenomic Libraries (MgL) from a Tropical Forest (TF) and a Dry Forest (DF) in Puerto Rico. Our goal is compare microbial diversity present in the MgL and their respective soil sample using Denaturing Gradient Gel Electrophoresis (DGGE). Fosmid DNA from induced MgL from both forests was extracted, and DNA extraction was done to the soil samples used to generate the MgL. Then, a 16S rDNA PCR using domain-specific primer was performed. The amplicons were run thru DGGE. A second DGGE comparison was done using 16S rDNA gene library amplicons generated from the TF-MgL and 16S-rDNA amplified from the soil. DNA extraction revealed bands in all the Fosmids and the soil samples. Amplicons were obtained from all the samples. Different DGGE band patterns were obtained from the MgL and from the soil samples. All the bands in TF soil sample DGGE are present in the MgL-DGGE pattern. This MgL contains bands not present in the soil sample, suggesting PCR, and/or the extraction method bias. The DF-MgL DGGE showed a band pattern in the soil sample that was not detected in the MgL, suggesting that the microbial diversity is not completely represented. In the second DGGE, the cloned 16S rDNA gene libraries used from the MgL were present in the respective soil sample. DGGE demonstrated that the MgL partially represent the diversity present in the soil source.  In silico analysis comparison is still needed.