*5.3.4 Terminal restriction fragment length polymorphism (T-RFLP)*

T-RFLP follows the same principle as RFLP except that one PCR primer is labeled with a fluorescent dye, such as TET (4,7,2V,7V-tetrachloro-6 carboxyfluorescein) or 6-FAM (phosphoramidite fluorochrome 5-carboxyfluorescein), which allows detection of only the labeled terminal restriction fragment [33]. This simplifies the banding pattern, allowing the analysis of complex communities as well as providing information on diversity as each visible band represents a single operational taxonomic unit or ribotype. The banding pattern can be used to measure species richness and evenness as well as similarities between samples. Terminal restriction fragment length polymorphism (T-RFLP) has higher resolution and is more comprehensive than cultivation-based methods [13]. This procedure can be automated to allow sampling and analysis of a large number of soil samples with recent developments in bioinformatics, several Web-based T-RFLP analysis programs have been developed, which enable researchers to rapidly assign putative identities based on a database of fragments produced by known 16S rDNA

**Figure 2.** *RAPD profile of bulk soil DNA.*

#### *Soil Metagenomics: Concepts and Applications DOI: http://dx.doi.org/10.5772/intechopen.88958*

sequences. This technique has been successfully applied to the composition and diversity analysis of soil microbial communities under different environmental conditions [34–36]. T-RFLP analysis was used to reveal the composition and diversity of soil bacterial communities along an altitude gradient in Wuyi Mountains addressing relationship between the composition and structure of the soil microbial communities and the vegetation types and cause of the difference in soil microbial communities under different vegetation types [13].
