Evaluation of DNA extraction methods and DNA preservation solution to study soil microbial communities
During high-throughput sequencing, the outcome microbial community composition can be altered when DNA is incomplete purified or by DNase activity. The objectives are to estimate biases associated with the DNA purification of soils and evaluate the effect of a DNA preservation solution in the composition of the microbial community. To do this, DNA extractions efficiencies were compared among single strains, a mix of strains and soil microbial communities. The 16S ribosomal RNA gene of soils was amplified and sequenced to compare structural differences of microbial communities resulted from two commercial DNA purification kits. Besides, soil samples were collected from the Delta Nigeria and transported to the Netherlands using a DNA preservation solution to evaluate the stabilization of the DNA microbial community. The results suggest a bias in the quantification of Gram positives that is related meanly with cell lysis capacity of the DNA extraction kits. This bias would have important repercussions in microbial ecology studies were the abundance and function of Gram positives may be underestimated.
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