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Evaluation of Homogenization Methods for Extraction of Live Bacteria and Recombinant DNA in Soil

In many soil types, ubiquitous bacteria are present very in low quantities due to the inherent challenges of microorganism survival in environmental conditions. While, in some cases, only present in low quantity, soil microorganisms are a critical component of our ecosystem. Soil microbiome studies aim to characterize the microbial repertoire and to correlate the microbial population with soil and ecological functions. While many studies involve culturing and isolation of bacteria harvested from the soil, some organisms are hard to propagate in the laboratory or require the sample to be processed directly to maintain analyte integrity. Given time involved and complexity of culture based enrichments, many modern studies involve direct cell lysis and DNA recovery from soil followed by PCR for target enrichment and detection. In order to infer absolute taxa abundance non‐conserved, targeted gene products are quantified by qPCR. While this approach is rapid and robust, qPCR is subject to inhibitory effects of soil based compounds such as humic acids and polysaccharides.