ABSTRACT
Direct cultivation or indirect molecular approaches can be used to explore and exploit the microbial diversity present in soil. Cultivation and isolation of microorganisms is the traditional method but, as only 0.1% to 1.0% of the soil bacteria are culturable using standard cultivation methods. Methods described for metagenomic DNA isolation from soil and sediment samples can be broadly classified into direct and indirect extraction procedures. Direct DNA isolation is based on cell lysis within the sample matrix and subsequent separation of DNA from the matrix and cell debris. Theoretically, the microbial DNA isolated from a soil sample represents the collective DNA of all the indigenous soil microorganisms, and is named the soil metagenome. Construction of a soil metagenomic library begins with sample collection. As soil samples are heterogeneous, details of physical, chemical and biotic factors such as particle size, soil type, water content, pH, temperature and plant cover are useful for evaluation and comparison of the outcomes of soil-based studies.
