African Journal of
Biotechnology

  • Abbreviation: Afr. J. Biotechnol.
  • Language: English
  • ISSN: 1684-5315
  • DOI: 10.5897/AJB
  • Start Year: 2002
  • Published Articles: 12496

Full Length Research Paper

Spatial variation of bacterial community composition near the Luzon strait assessed by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and multivariate analyses

Ling Juan1,2,3,4, Zhang Yanying1,3, Dong Junde1,3*, Wang Youshao2, Chen Lei1,3,4, Feng Jingbin1,3, Sun Hongyan1,3, Wang Dongxiao2 and Zhang Si1
1Key Laboratory of marine Bio-resourses Sustainable utilization, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China. 2State Key Laboratory of Oceanography in the Tropics, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China. 3National Experiment Station of Tropical Marine Biology, Sanya, 572000, China. 4Graduate school of Chinese academy of science, Beijing, 100049, China.
Email: [email protected]

  •  Accepted: 24 October 2011
  •  Published: 23 November 2011

Abstract

Different water masses have distinct natural physical and chemical properties, which may influence the bacterial community structure. In the western pacific on both sides of the Luzon strait, which is covered with three water masses including the South China Sea (SCS) water mass, the Kuroshio water mass and the SCS-Kuroshio transition water mass, we selected 11 stations to estimate the spatial variation of surface water bacterial community composition using denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR)-amplified bacterial 16S ribosomal deoxyribonucleic acid (DNA) gene fragments and interpreted the results; its relationship with physical and chemical factors based on multivariate statistical analysis. A total of 343 bands at 105 different positions were detected in DGGE profiles and 18 distinct DGGE bands were sequenced. Sequence analysis revealed that most of the phylotypes were typical marine uncultured bacteria, and predominant bacteria came from three major phyla; Proteobacteria, Actinobacteria and Cyanobacteria. Apparent phylotype richness near the Luzon strait area varied between 24 and 35 bands (mean 31). Similarity and cluster analysis indicate that the distribution and composition of bacterial community at transition area were more affected by the SCS water mass than Kuroshio current. Redundancy analysis (RDA) revealed that temperature, salinity and the concentration of nitrate accounted for a significant amount of the variability in the bacterial community composition (P=0.004, P=0.014 and P=0.038, respectively, P<0.05).

 

Key words: Bacterial community composition, spatial distribution, Luzon strait; Kuroshio Current, denaturing gradient gel electrophoresis (DGGE), redundancy analysis (RDA).

Abbreviation

SCS, South China Sea; DGGE, denaturing gradient gel electrophoresis; PCR, polymerase chain reaction; RDA, redundancy analysis; CTD, conductivity-temperature-depth; DCA, detrended correspondence analysis; PAH,polycyclic aromatic hydrocarbons; NCBI, national center for biotechnology information; MVSP, multivariate statistical    package;   UPGMA,   unweighted   pair-group method with arithmetic mean; BLAST, basic local alignment search tool; TAE,Tris–acetate– ethylene diamine tetraacetic acid; dNTP, deoxyribonucleotide triphosphate; EDTA, ethylene diamine tetraacetic acid; rDNA, ribosomaldeoxyribonucleic acid; UV, ultraviolet; DNA, deoxyribonucleic acid; PCR-DGGE,polymerase chain reaction-denaturing gradient gel electrophoresis.