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Analysis of RNA Polymerase Beta Subunit (rpoB) Gene Sequences for the Discriminative Power of Marine Vibrio Species

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Abstract

In the present study, we sequenced the RNA polymerase beta subunit (rpoB) gene of marine Vibrio species and assessed its discriminative power in identifying vibrios. Both the rpoB and 16S rRNA sequences of 29 phenotypically different Vibrio strains isolated from coastal waters were determined. Molecular and phylogenetic comparisons of the sequences of these two genes classified the 29 strains into 11 different species. The resolution of the Vibrio spp. on the rpoB phylogenetic tree was approximately three times greater than that on the 16S rRNA phylogenetic tree. Moreover, by comparing the rpoB sequences of 98 marine γ-Proteobacteria, including 38 marine Vibrio species, Vibrio-specific primers were developed to amplify a 730-bp fragment of the rpoB gene. Using these primers, we successfully detected Vibrio signals in environmental samples and determined their relative abundances via comparisons with known standards. This rpoB-targeting polymerase chain reaction assay can be used efficiently to monitor relative Vibrio abundance in marine waters.

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Acknowledgment

We are grateful to Dr. Tam Yin Ki for the technical help and to all members of the Area of Excellence (AoE) Project for the field assistance. This work was supported by the HKSAR governmental grant AoE04/04-02 awarded to P.-Y. Qian.

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Authors and Affiliations

  1. Department of Biology, Coastal Marine Laboratory, Hong Kong University of Science and Technology, Clearwater Bay, Kowloon, Hong Kong SAR, China

    Jang-Seu Ki, Rui Zhang, Wen Zhang, Yi-Li Huang & Pei-Yuan Qian

  2. Department of Life Science, College of Natural Sciences, Sangmyung University, Seoul, 110-743, South Korea

    Jang-Seu Ki

  3. Foreign Economic Cooperation Office (FECO) State Environmental Protection Administration (SEPA) P.R. China, China Global Environment Facility (GEF) Office, No.115 Xizhimennei, Nanxiaojie, Beijing, 100035, China

    Wen Zhang

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  1. Jang-Seu Ki
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Correspondence to Pei-Yuan Qian.

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Ki, JS., Zhang, R., Zhang, W. et al. Analysis of RNA Polymerase Beta Subunit (rpoB) Gene Sequences for the Discriminative Power of Marine Vibrio Species. Microb Ecol 58, 679–691 (2009). https://doi.org/10.1007/s00248-009-9519-7

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  • DOI: https://doi.org/10.1007/s00248-009-9519-7

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