Abstract
The urge of understanding soil microbial function and diversity of peatland soils either forested or non-forested has emerged since over a decade ago concerning the ongoing the ecosystem deterioration and its environmental impacts it causes. Like any other soil environments, this unique ecosystem possesses great challenges in isolating quality DNA prerequisite for microbial ecology studies in virtue of its physicochemical characteristics. Two general approaches have been extensively applied for soil microbial DNA extraction which are termed as 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 microaggregates 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 soil peatland metagenomics studies.
Highlights
Soil is a huge reservoir of carbon sources and organic matter, providing valuable nutrient-rich habitat for growth and energy for diverse organism
The success of isolating quality DNA from soil relies on different method used in the extraction protocol
Direct extraction methods are perceived as an ideal approach concerning its lesslaborious, rapid, and cost-effective processes requirement
Summary
Soil is a huge reservoir of carbon sources and organic matter, providing valuable nutrient-rich habitat for growth and energy for diverse organism. The microbial abundance has been extensively explored by the classical laboratory cultivation techniques which 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 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. This review highlights the modification and improvement in soil DNA extractions and purification techniques as well as their effectiveness in obtaining high quality DNA from peatland soil for metagenomic study
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