One gram of soil may harbor up to 10 billion microorganisms belonging to possibly more than 10⁴ different species, most of which play vital roles in various biogeochemical cycles such as the release and fixation of nutrient elements and decomposition of organic matter. The microbial community is considered to be a functional indicator because changes in the soil environments in which they live can affect their structure and diversity. Microbial diversity is a growing field of study in soil science and microbial ecology. Increases in knowledge of soil microbial diversity depend on improvement in the approaches to its study. Over the last four decades, culture-dependent and culture-independent technologies have been developed to assess microbial diversity in soil.
Conventional culture-dependent methods such as plate counts, morphology analysis and community level physiological profiling (CLPP) provide information on the active heterotrophic component and the functional role of the population. However, the evaluation of soil microbial diversity based on these methods has been limited to the cultivable cells, amounts of which are less than 1% of the microorganisms observed under the microscope. To overcome this issue, profiles based on biochemical components of cell membrane have been used to characterize the soil microbial community. The profiles mainly include phospholipids fatty acids and respiratory quinines, the structure of which can be used to classify microorganisms. Since these methods avoid the limits of selective culturing and isolating, they have been considered to be an approach to objectively reflecting soil microbial community diversity.
With improvements in DNA extraction and polymerase chain reaction (PCR) technologies, a number of molecular-based methods, which are more reliable and accurate than the above-mentioned methods, have been developed to assess soil microbial diversity. These approaches include DNA reassociation, guanine+cytosine (G+C)% content, nucleic acid hybridization technologies such as fluorescent in situ hybridization (FISH) and DNA microarrays, soil metagenomics based on cloning and library screening of soil genomic DNA, PCR-based genetic fingerprinting such as terminal restriction fragment length polymorphism (T-RFLP), denaturing/temperature gradient gel electrophoresis (DGGE/TGGE), single strand conformation polymorphism (SSCP) and two-dimensional DNA gel electrophoresis(2-DGE)with high resolution. These molecular-based technologies can potentially provide excellent insights into diversity information of the cultivable as well as uncultivable soil microorganisms. Without a doubt, they have opened up novel ways to study soil microbial diversity in detail, and thus enable us to acquire a better understanding of the relationship between function and diversity of soil microorganisms. Genetic fingerprinting especially is a very suitable approach to monitoring changes of soil quality through analyzing temporal and spatial dynamics of microbial diversity.
The culture-independent methods do not require the selection of culture media and conditions, and also enable us to obtain more abundant and accurate information of microbial diversity than the culture-dependent methods. However, each method has its own limitations. Therefore, when applying these methods to the assessment of soil microbial community, a combination of more than two methods is recommended. This review introduces their principles, advantages and disadvantages, as well as summarizing their application and progress in studying soil microbial diversity.