Metagenomic approach to soil microbial diversity and functions

The improved methods to analyze DNA or RNA from soil enable us to study microbial diversity and functions in soil which have never been revealed by conventional culture methods. Using one of such metagenomic approaches, polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), we succeeded in monitoring the change of microbial diversity in the soil treated with a chemicals or various fertilizer. Based on these achievements, since 2006, National Institute for Agro-Environmental Sciences (NIAES) play a central role in a Japanese national project addressing development of analytical methods for soil biological properties using environmental DNA (eDNA). In the project, we have optimized and standardized the conditions for preparation of DNA from soil and PCR-DGGE using soil metagenome to compare the microbial communities in different soil samples. The obtained PCR-DGGE data accompanying the physical and chemical soil properties and information about crop productivity have been used to construct a database (eDDASs: eDNA database for agricultural soils). In the project, we also succeeded in detecting microbial gene expression in soil using RNA extracted from soil. Our final goal is to determine the relationships between the biological properties evaluated by eDNA or RNA analysis and the soil physicochemical properties as affected by cultivation practice.