Bacteria diversity in paddy field soil by 16S rDNA-RFLP analysis in Ningxia
Jianping Zhang, Naiyuan Dong, Haobin Yu, Yongjun Zhou, Yongliang Lu, Ruimei Geng, Liuqing Yu
Biodiv Sci. 2008, 16 (6):
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Rice is one of the most important crops in the Ningxia region of China, and rice planting helps to maintain ecosystem balance and prevent land desertification. Soil microbial diversity provides basic functions for rice field soil ecosystems. To better understand bacterial diversity and community composition in Ningxia paddy soil, the total bacterial DNA was extracted from paddy soil collected from a typical rice field of Ningxia using the culture independent method. A 16S ribosomal DNA (16S rDNA) clone library of soil bacteria was constructed. The 16S rDNA fragments were analyzed by PCR-RFLP. Further sequencing and cluster analysis were conducted to elucidate the bacterial diversity. Over 23 kb DNA fragments were obtained from the paddy soil and 74 MspI restriction endonuclease types were detected by PCR-RFLP analysis. Sequence analysis revealed that 77.3% of clone sequences were similar to those of uncultured bacteria in the environment, while only 22.7% clone sequences were most closely related to those of cultured bacteria in GenBank, suggesting great potential for undeveloped bacterial resources was available in paddy fields. Our phylogenetic analysis found that the sequenced clones fell into 12 major lineages within the domain bacteria. Among them, members of the Proteobacteria were the dominant group, accounting for 37.8%, including -Proteobacteria (13.5%), γ-Proteobacteria (12.2%), δ-Proteobacteria (6.8%) and -Proteobacteria (5.4%), followed by Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi and Planctomycetes division with 16.2%, 12.2%, 10.8%, 10.8%, 8.1%, respectively. Firmicutes, Gemmatimonadetes, and Verrucomicrobia were less well represented. Our study revealed an extensive diversity of soil bacteria in a paddy field in Ningxia.