Analysis of soil bacterial diversity by Using the 16S rRNA gene Library

Abstract:

[Objective] Soil microorganisms play an important role in the vegetable soil ecosystem. Through 16S rRNA gene cloning library technology to analysis the composition of bacteria community structure in the typical vegetable soil. To revealed the microbial diversity in the typical vegetable soil, and laid the foundation for the relationship between land-use changed and the ecological environment. [Methods] Total microbial DNA was directly extracted from a typical vegetable soil of Beijing and Shandong province. The clone library of 16S ribosomal RNA genes was amplified using PCR with universal bacterial primer sets. The PCR products were then subcloned into pGEM-T vector. Each unique restriction fragment polymorphism pattern, created by using two restriction endonucleases (HinfⅠand HaeⅢ), was designated as an operational taxonomic unit (OTU). Amplified DNA was used for diversity analysis. [Results] Constructed bacterial phylogenetic trees of the samples revealed the γ-proteobacteria, b-proteobacteria and α-proteobacteria groups were dominant in both clone libraries. Bacte-rial species composition from Beijing and Shandong province included 124 OTUs and 92 OTUs, respectively. [Conclusion] the dominant species of bacteria populations are proteobacteria in the typical vegetable soil of Beijing and Shandong areas. But bacte-rial diversity in the two typical vegetable soil samples was reduced. This phenomenon may be directly related to Continuous cul-tivation for many years and plant a single vegetable species. At the same time, this phenomenon may also be an important reason to cause vegetable soil diseases widespread occurred and soil degradation.