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Analysis of Bacterial Communities in Seagrass Bed Sediments by Double-Gradient Denaturing Gradient Gel Electrophoresis of PCR-Amplified 16S rRNA Genes

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Abstract

Bacterial communities associated with seagrass bed sediments are not well studied. The work presented here investigated several factors and their impact on bacterial community diversity, including the presence or absence of vegetation, depth into sediment, and season. Double-gradient denaturing gradient gel electrophoresis (DG-DGGE) was used to generate banding patterns from the amplification products of 16S rRNA genes in 1-cm sediment depth fractions. Bioinformatics software and other statistical analyses were used to generate similarity scores between sections. Jackknife analyses of these similarity coefficients were used to group banding patterns by depth into sediment, presence or absence of vegetation, and by season. The effects of season and vegetation were strong and consistent, leading to correct grouping of banding patterns. The effects of depth were not consistent enough to correctly group banding patterns using this technique. While it is not argued that bacterial communities in sediment are not influenced by depth in sediment, this study suggests that the differences are too fine and inconsistent to be resolved using 1-cm depth fractions and DG-DGGE. The effects of vegetation and season on bacterial communities in sediment were more consistent than the effects of depth in sediment, suggesting they exert stronger controls on microbial community structure.

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Acknowledgments

The assistance of Joseph A. Ringbauer Jr. was vital to the completion of this study. The US Environmental Protection Agency (EPA), through its Office of Research and Development, funded the research described here. It has been subjected to the agency’s peer review and has been approved as an EPA publication. Mention of trade names or commercial products does not constitute endorsement or recommendation by the EPA for use.

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Authors and Affiliations

  1. Office of Research and Development, US Environmental Protection Agency, NHEERL–Gulf Ecology Division, 1 Sabine Island Drive, Gulf Breeze, FL, 32561, USA

    J. B. James & R. Devereux

  2. Department of Biology, University of South Alabama, Mobile, AL, 36688, USA

    T. D. Sherman

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  1. J. B. James
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  2. T. D. Sherman
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  3. R. Devereux
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Correspondence to J. B. James.

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James, J.B., Sherman, T.D. & Devereux, R. Analysis of Bacterial Communities in Seagrass Bed Sediments by Double-Gradient Denaturing Gradient Gel Electrophoresis of PCR-Amplified 16S rRNA Genes. Microb Ecol 52, 655–661 (2006). https://doi.org/10.1007/s00248-006-9075-3

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  • DOI: https://doi.org/10.1007/s00248-006-9075-3

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