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Bacterial Community Composition in Different Sediments from the Eastern Mediterranean Sea: a Comparison of Four 16S Ribosomal DNA Clone Libraries

Microbial Ecology volume 50, pages 447–462 (2005)Cite this article

Abstract

The regional variability of sediment bacterial community composition and diversity was studied by comparative analysis of four large 16S ribosomal DNA (rDNA) clone libraries from sediments in different regions of the Eastern Mediterranean Sea (Thermaikos Gulf, Cretan Sea, and South lonian Sea). Amplified rDNA restriction analysis of 664 clones from the libraries indicate that the rDNA richness and evenness was high: for example, a near-1:1 relationship among screened clones and number of unique restriction patterns when up to 190 clones were screened for each library. Phylogenetic analysis of 207 bacterial 16S rDNA sequences from the sediment libraries demonstrated that Gamma-, Delta-, and Alphaproteobacteria, Holophaga/Acidobacteria, Planctomycetales, Actinobacteria, Bacteroidetes, and Verrucomicrobia were represented in all four libraries. A few clones also grouped with the Betaproteobacteria, Nitrospirae, Spirochaetales, Chlamydiae, Firmicutes, and candidate division OPl 1. The abundance of sequences affiliated with Gammaproteobacteria was higher in libraries from shallow sediments in the Thermaikos Gulf (30 m) and the Cretan Sea (100 m) compared to the deeper South Ionian station (2790 m). Most sequences in the four sediment libraries clustered with uncultured 16S rDNA phylotypes from marine habitats, and many of the closest matches were clones from hydrocarbon seeps, benzene-mineralizing consortia, sulfate reducers, sulk oxidizers, and ammonia oxidizers. LIBSHUFF statistics of 16S rDNA gene sequences from the four libraries revealed major differences, indicating either a very high richness in the sediment bacterial communities or considerable variability in bacterial community composition among regions, or both.

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Acknowledgments

The officers and the crew of the R/Vs Aegaeo and Philia are acknowledged for their assistance during the sampling. This work was supported by the Swedish Research Council (grant 2002-4580 to S.B.) and the Swedish Research Council for Environment, Agricultural Sciences and Special Planning (grant 2002-0291 to S.B.). Sampling cruises were supported by the commission of the European Communities (through the Energy and Environment projects INTERPOL and ADIOS) and the Greek Ministry of Development (General Secretariat of Research and Technology).

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  1. Hellenic Center for Marine Research, Gournes Pediados, GR 71003, Heraklion, Crete, Greece

    Paraskevi N. Polymenakou & Anastasios Tselepides

  2. Environmental Chemical Processes Laboratory, Department of Chemistry, University of Crete, 71409, Heraklion, Greece

    Paraskevi N. Polymenakou & Euripides G. Stephanou

  3. Limnology/Department of Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Norbyv. 20, SE-75236, Uppsala, Sweden

    Stefan Bertilsson

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  1. Paraskevi N. Polymenakou
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Correspondence to Stefan Bertilsson.

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Polymenakou, P.N., Bertilsson, S., Tselepides, A. et al. Bacterial Community Composition in Different Sediments from the Eastern Mediterranean Sea: a Comparison of Four 16S Ribosomal DNA Clone Libraries. Microb Ecol 50, 447–462 (2005). https://doi.org/10.1007/s00248-005-0005-6

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Keywords

  • Bacterial Community
  • Clone Library
  • Terminal Restriction Fragment Length Polymorphism
  • Bacterial Community Composition
  • Candidate Division