Characterization of depth-related microbial communities in lake sediment by denaturing gradient gel electrophoresis of amplified 16S rRNA fragments

• Published in: Journal of environmental sciences (China) Vol. 20; no. 2; pp. 224 - 230
• Main Authors: ZHAO, Xingqing, YANG, Liuyan, YU, Zhenyang, PENG, Naiying, XIAO, Lin, YIN, Daqiang, QIN, Boqiang
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.02.2008
• Subjects: 16S; 16S rRNA; Acinetobacter; Bacillus; Bacteria - classification; Bacteria - genetics; Base Sequence; Brevibacillus; China; denaturing gradient gel electrophoresis (DGGE); Electrophoresis; Exiguobacterium; Fresh Water - microbiology; Freshwater; Geologic Sediments - microbiology; Hydrogen-Ion Concentration; Lake Taihu; microbial diversity; Molecular Sequence Data; Nitrogen; Oxygen; Phosphorus; Phylogeny; Polymerase Chain Reaction; RNA, Bacterial - genetics; RNA, Ribosomal, 16S - genetics; rRNA; sediment; vertical distribution; Water Microbiology; 微生物; 水质污染; China; 16S rRNA; vertical distribution; microbial diversity; denaturing gradient gel electrophoresis (DGGE); sediment; Lake Taihu
• ISSN: 1001-0742; 1878-7320
• DOI: 10.1016/s1001-0742(08)60035-2

The characterization of microbial communities of different depth sediment samples was examined by a culture-independent method and compared with physicochemical parameters, those are organic matter （OM）, total nitrogen （TN）, total phosphorus （TP）, pH and redox potential （Eh）. Total genomic DNA was extracted from samples derived from different depths. After they were amplified with the GC-341 f/907r primer sets of partial bacterial 16S rRNA genes, the products were separated by denaturing gradient gel electrophoresis （DGGE）. The profile of DGGE fingerprints of different depth sediment samples revealed that the community structure remained relatively stable along the entire 45 cm sediment core, however, principal-component analysis of DGGE patterns revealed that at greater sediment depths, successional shifts in community structure were evident. The principle coordinates analysis suggested that the bacterial communities along the sediment core could be separated into two groups, which were located 0-20 cm and 21-45 cm, respectively. The sequencing dominant bands demonstrated that the major phylogenetic groups identified by DGGE belonged to Bacillus, Bacterium, Brevibacillus, Exiguobacterium, γ-Proteobacterium, Acinetobacter sp. and some uncultured or unidentified bacteria. The results indicated the existence of highly diverse bacterial community in the lake sediment core.