High-Quality Dna From Peat Soil for Metagenomic Studies: A Minireview on Dna Extraction Methods

Abstract

The understanding of microorganism's biodiversity in the peatland soil through non-cultivation based approach provide important inputs towards prediction of the ecosystem response towards the changing environment. The challenge that hindered the success to obtain high quality DNA from peat soil lies in the physicochemical characteristics such as low pH and high humic acid content. There are two general approaches that have been extensively applied for soil microbial DNA extraction, which are direct DNA extraction protocol and indirect DNA extraction protocol. The only step differentiate between these two protocols is the later includes additional cell separation method from soil micro-aggregates preceding DNA extraction process. Therefore, several improved and modified methods in conventional DNA extraction and purification methods are reviewed in this paper to cater all the highlighted issues as to obtain high-quality DNA for peatland metagenomics soil studies. INTRODUCTIONSoil is a huge reservoir of carbon sources and organic matter, providing valuable nutrient-rich habitat for growth and energy for diverse organism. The biological interaction amongst soil indigenous microorganisms is significant to maintain soil function, composition and fertility. In estimation, up to 10 8 microbial cells were found in a gram of bulk soil with at most 100 species diversity [1]. The role and complexity of soil microbial metabolisms and interactions have been broadly exploited with respect to various biotechnological applications such as plant microbial inoculation, bioremediation, enzyme isolation and bioactive compounds production [2-9].The microbial abundance has been extensively explored by the classical laboratory cultivation techniques which however bears only limited biodiversity of approximately less than 1% cultivable microbes from the natural environments [10][11][12]. These conventional culture-dependent methods heavily rely on the optimum supply of nutrient sources, growth media and other physical and chemical parameters such as pH, temperature and metal ions concentration that suit optimally to only certain groups of microorganisms hence dramatically underestimating the accurate number of microorganisms in the nature. The limitation of these growth techniques hinders the process of comprehensive soil microbial community analysis making it almost impossible and practically tedious to uncover more uncultivable and novel microorganism species.To overcome such limitations, the later development of rapid and direct access of genetic material from environmental samples without cultivation has been introduced. The term metagenomics is then used to describe the study of the collective unknown genetic material which give insights not just into the taxonomy diversity of the environmental samples but also their ecological function [13]. This discovery has revolutionized the way we perceive and understand the microbial world due to their ability to expose the previously unknown microscopic life diversity. However, the...

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