Nucleic acid extraction for studying plant-microbe interactions in rhizosphere

Abstract

Studies on diversity of microbial community in the field of rhizosphere ecology vastly rely on nucleic acid markers for analysis. The extraction can be a tedious and complicated task owing to the vast heterogeneity present in soil in terms of organic and inorganic constituents, texture and moisture content, and also the huge repertoire of life forms that it nurtures. There is no universal method of extraction for all soil types. The various challenges presented by the soil constituents make it an ever-evolving process. Cell lysis is an inherent part of any extraction process, with the extraction methodology exerting a huge impact on purity and yield of nucleic acid. Different extraction methods employed so far can be classified under two main categories based on the step of lysis: Indirect lysis and direct lysis methods. Humic acid is a persistent contaminant that has the maximum impact on nucleic acid quality, along with its interference with several downstream analyses. Several methods have been optimized for removal of soil organic content. With the realization of the importance of RNA component in providing a deeper insight into the functionality of the system, the co-extraction of DNA and RNA is a trending technique, with vast emphasis on the removal of humic acid, and purity of the extracted DNA/RNA.