Application of PCR-DGGE technique in studying the effect of agricultural activities on soil microbial communities

Intensive agriculture has reduced soil fertility and has had harmful effects on human health and the environment. Therefore, the use of low-input and environmentally-friendly agricultural methods such as sustainable agriculture is necessary to achieve the required sustainability in food supply. Preservation and revitalization of beneficial microbial communities in the soil, is one of the important strategies of sustainable agriculture. These microorganisms with diverse activities (such as residue decomposition, mineralization and fixation of nutrients for plant growth, production of plant hormones, decomposition of pollutants, plant growth and biological control of plant pathogens), play very important roles in the function and sustainability of terrestrial ecosystems. Understanding the factors affecting these communities particularly the different methods of managing agricultural lands helps to manage them towards improving soil fertility, optimal plant growth and health, and increasing the productivity and stability of agricultural ecosystems. For selecting the best cultivation methods that preserve the diversity and strengthen microbial communities as well as avoiding activities that lead to the destruction and reduction of its diversity of microorganisms, fast, reliable, sensitive and specific methods are needed that provide comprehensive knowledge about the effect of different agricultural activities on the structure and diversity of these communities, including its unculturable part. Among molecular techniques, polymerase chain reaction-based methods have been widely used to study the diversity and structure of soil microorganisms, and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) is one of the most well-known and widely used methods. PCR-DGGE has been used successfully for more than two decades to investigate the effect of different crop managements on the diversity and structure of microorganisms in different soils or in a soil under different crop managements. Despite the availability of new generation of high-throughput sequencing technologies in the study of soil microbial communities, PCR-DGGE method due to various advantages with less hassle, cost and time and immediate presentation of components in both qualitative and semi-quantitative form is still an important way to study the impact of various agricultural practices and managements on microbial communities. With the help of the findings of this technique, the best management methods in agriculture could be selected and the way can be paved for the realization of sustainable agriculture and stable food supply. In this review, some researches and references that have used the efficacy of PCR-DGGE in studying the impact of various agricultural managements and activities on the composition and diversity of soil microbial communities and some of their results have been mentioned. The features, advantages, limitations, and principles of this method have also been outlined.