Skip to main content

Advertisement

SpringerLink
Log in

Topographic effects of coastal seas on the composition of the culturable bacterial communities in marine sediments

  • Primary Research Paper
  • Published:
Hydrobiologia Aims and scope Submit manuscript

Abstract

The influence of the topographical structure of natural coastal marine environments on the composition of culturable microbial communities in marine sediments was analyzed by comparing the composition of the culturable fraction of sedimental bacterial communities from five topographically disparate marine ecosystems. The sampling areas included open, enclosed and semi-closed coastal seas near Nagasaki, Japan. Bacterial identification and phylogenetic analyses based on 16S rDNA gene sequencing showed that 84.0% of the isolated strains belonged to known species. The marine indigenous γ-Proteobacteria were significantly higher (P < 0.05) in abundance among the strains isolated from the open coastal seas, but were less abundant in the enclosed and the semi-closed coastal seas. Conversely, the abundance of the low G + C gram-positive bacteria, mainly soil-derived Bacillus species, was significantly higher (P < 0.001) in the enclosed sea than in the open coastal seas. It was found that the composition of the culturable fraction of coastal sediment bacterial communities might be influenced by topographic factors and could be utilized as a microbiological tool for the assessment of the deterioration of environmental conditions in enclosed coastal seas.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Agogué, H., E. O. Casamayor, M. Bourrain, I. Obernosterer, F. Joux, G. J. Herndl & P. Lebaron, 2005. A survey on bacteria inhabiting the sea surface microlayer of coastal ecosystems. FEMS Microbiology Ecology 54: 269–280.

    Article  PubMed  CAS  Google Scholar 

  • Akagi, S. & F. Hirayama, 1991. Formation of oxygen-deficient water mass in Omura Bay. Marine Pollution Bulletin 23: 661–663.

    Article  CAS  Google Scholar 

  • Bernard, L., H. Schäfer, F. Joux, C. Courties, G. Muyzer & P. Lebaron, 2000. Genetic diversity of total, active and culturable marine bacteria in coastal seawater. Aquatic Microbial Ecology 23: 1–11.

    Google Scholar 

  • Chandler, D. P., S. M. Li, C. M. Spadoni, G. R. Drake, D. L. Balkwill, J. K. Fredrickson & F. J. Brockman, 1997. A molecular comparison of culturable aerobic heterotrophic bacteria and 16S rDNA clones derived from a deep subsurface sediment. FEMS Microbiology Ecology 23: 131–144.

    Article  CAS  Google Scholar 

  • Cho, J. C. & S. J. Giovannoni, 2004. Cultivation and growth characteristics of a diverse group of oligotrophic marine Gamma-Proteobacteria. Applied and Environmental Microbiology 70: 432–440.

    Article  PubMed  CAS  Google Scholar 

  • Cytryn, E., I. Gelfand, Y. Barak, J. van Rijn & D. Minz, 2003. Diversity of microbial communities correlated to physiochemical parameters in a digestion basin of a zero-discharge mariculture system. Environmental Microbiology 5: 55–63.

    Article  PubMed  CAS  Google Scholar 

  • Danovaro, R., D. Marrale, A. Dell’Anno, N. Delia Croce, A. Tselepides & M. Fabiano, 2000. Bacterial response to seasonal changes in labile organic matter composition on the continental shelf and bathyal sediments of the Cretan Sea. Progress in Oceanography 46: 345–366.

    Article  Google Scholar 

  • Ellis, R. J., P. Morgan, A. J. Weightman & J. C. Fry, 2003. Cultivation-dependent and -independent approaches for determining bacterial diversity in heavy-metal-contaminated soil. Applied and Environmental Microbiology 69: 3223–3230.

    Article  PubMed  CAS  Google Scholar 

  • Fujioka, R. S., 2001. Monitoring coastal marine waters for spore-forming bacteria of faecal and soil origin to determine point from non-point source pollution. Water Science and Technology 44: 181–188.

    PubMed  CAS  Google Scholar 

  • Fukumoto, T. & N. Kobayashi, 2005. Bottom stratification and water exchange in enclosed bay with narrow entrance. Journal of Coastal Research 21: 135–145.

    Article  Google Scholar 

  • Grossart, H. P., A. Schlingloff, M. Bernhard, M. Simon & T. Brinkhoff, 2004. Antagonistic activity of bacteria isolated from organic aggregates of the German Wadden Sea. FEMS Microbiology Ecology 47: 387–396.

    Article  CAS  PubMed  Google Scholar 

  • Gugliandolo, C. & T. L. Maugeri, 1998. Temporal variations in heterotrophic mesophilic bacteria from a marine shallow hydrothermal vent off the island of vulcano (Eolian Islands, Italy). Microbial Ecology 36: 13–22.

    Article  PubMed  CAS  Google Scholar 

  • Ivanova, E. P., M. V. Vysotskii, V. I. Svetashev, O. I. Nedashkovskaya, N. M. Gorshkova, V. V. Mikhailov, N. Yumoto, Y. Shigeri, T. Taguchi & S. Yoshikawa, 1999. Characterization of Bacillus strains of marine origin. International Microbiology 2: 267–271.

    PubMed  CAS  Google Scholar 

  • Lebaron, P., P. Servais, M. Troussellier, C. Courties, G.. Muyzer, L. Bernard, H. Schäfer, R. Pukall, E. Stackebrandt, T. Guindulain & J. Vives-Rego, 2001. Microbial community dynamics in Mediterranean nutrient-enriched seawater mesocosms: changes in abundances, activity and composition. FEMS Microbiology Ecology 34: 255–266.

    Article  PubMed  CAS  Google Scholar 

  • Lee, M. J., D. Y. Jeong, W. S. Kim, H. D. Kim, C. H. Kim, W. W. Park, Y. H. Park, K. S. Kim, H. M. Kim & D. S. Kim, 2000. A Tetrodotoxin-Producing Vibrio Strain, LM-1, from the Puffer Fish Fugu vermicularis radiatus. Applied and Environmental Microbiology 66: 1698–1701.

    Article  PubMed  CAS  Google Scholar 

  • Long, R. A. & F. Azam, 2001. Antagonistic interactions among marine pelagic bacteria. Applied and Environmental Microbiology 67: 4975–4983.

    Article  PubMed  CAS  Google Scholar 

  • Luna, G. M., E. Manini & R. Danovaro, 2002. Large fraction of dead and inactive bacteria in coastal marine sediments: comparison of protocols for determination and ecological significance. Applied and Environmental Microbiology 68: 3509–3513.

    Article  PubMed  CAS  Google Scholar 

  • McCaig, A. E., C. J. Phillips, J. R. Stephen, G. A. Kowalchuk, S. M. Harvey, R. A. Herbert, T. M. Embley & J. I. Prosser, 1999. Nitrogen cycling and community structure of Proteobacterial Beta-subgroup ammonia-oxidizing bacteria within polluted marine fish farm sediments. Applied and Environmental Microbiology 65: 213–220.

    PubMed  CAS  Google Scholar 

  • Meyer-Reil, L. A. & M. Köster, 2000. Eutrophication of marine waters: effects on benthic microbial communities. Marine Pollution Bulletin 41: 255–263.

    Article  CAS  Google Scholar 

  • Nogami, M., T. Matsuno, T. Nakamura & T. Fukumoto, 2000. Estimation of oxygen consumption rate using T-DO diagram in the benthic layer of Ohmura Bay, Kyushu, Japan. Journal of Oceanography 56: 319–329.

    Article  CAS  Google Scholar 

  • Paerl, H.W., J. Dyble, P. H. Moisander, R. T. Noble, M. F. Piehler, J. L. Pinckney, T. F. Steppe, L. Twomey & L. M. Valdes, 2003. Microbial indicators of aquatic ecosystem change: current applications to eutrophication studies. FEMS Microbiology Ecology 46: 233–246.

    Article  CAS  PubMed  Google Scholar 

  • Rajendran, N., O. Matsuda, Y. Urushigawa & U. Simidu, 1994. Characterization of microbial community structure in the surface sediment of Osaka Bay, Japan, by phospholipid fatty acid analysis. Applied and Environmental Microbiology 60: 248–257.

    PubMed  CAS  Google Scholar 

  • Schmidt, J. L., J. W. Deming, P. A. Jumars & R. G. Keil, 1998. Constancy of bacterial abundance in surficial marine sediments. Limnology and Oceanography 43: 976–982.

    Article  Google Scholar 

  • Shiba, T., U. Simidu & N. Taga, 1979. Distribution of aerobic bacteria which contain bacteriochlorophyll a. Applied and Environmental Microbiology 38: 43–45.

    PubMed  CAS  Google Scholar 

  • Stackebrandt, E. & B. M. Goebel, 1994. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. International Journal of Systematic Bacteriology 44: 846–849.

    Article  CAS  Google Scholar 

  • Swannell, R. P. J., K. Lee & M. McDonagh, 1996. Field evaluations of marine oil spill bioremediation. Microbiological Reviews 60: 342–365.

    PubMed  CAS  Google Scholar 

  • Thompson, J. D., D. G. Higgins & T. J. Gibson, 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22: 4673–4680.

    Article  PubMed  CAS  Google Scholar 

  • Urakawa, H., K. Kita-Tsukamoto & K. Ohwada, 1999. Microbial diversity in marine sediments from Sagami Bay and Tokyo Bay, Japan, as determined by 16S rRNA gene analysis. Microbiology 145: 3305–3315.

    PubMed  CAS  Google Scholar 

  • von Wintzingerode, F., S. Böcker, C. Schlötelburg, N. H. L. Chiu, N. Storm, C. Jurinke, C. R. Cantor, U. B. Göbel & D. van den Boom, 2002. Base-specific fragmentation of amplified 16S rRNA genes analyzed by mass spectrometry: a tool for rapid bacterial identification. Proceedings of the National Academy of Science USA 99: 7039–7044.

    Article  CAS  Google Scholar 

  • Yoon, J. H., I. G. Kim, K. H. Kang, T. K. Oh & Y. H. Park, 2003. Bacillus marisflavi sp. nov. and Bacillus aquimaris sp. nov., isolated from sea water of a tidal flat of the Yellow Sea in Korea. International Journal of Systematic and Evolutionary Microbiology 53: 1297–1303.

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgements

We thank Dr. S. Takeshita, Ph.D., Nagasaki University Joint Research Center for the field sampling of the marine sediment bacterial isolates. This work was supported partially by a grant from the Prefectural Collaboration of Regional Entities for the Advancement of Technology Excellence, JST.

Author information

Authors and Affiliations

  1. Laboratory of Molecular Biology of Infectious Agents, Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-Machi, Nagasaki, 852-8521, Japan

    Herizo Fabien Rafidinarivo, Satoshi Fujimoto, Ken Watanabe, Kaio Kitazato & Nobuyuki Kobayashi

Authors
  1. Herizo Fabien Rafidinarivo
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Satoshi Fujimoto
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ken Watanabe
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Kaio Kitazato
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Nobuyuki Kobayashi
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Herizo Fabien Rafidinarivo.

Additional information

Handling editor: K. Martens

Rights and permissions

Reprints and permissions

About this article

Cite this article

Rafidinarivo, H.F., Fujimoto, S., Watanabe, K. et al. Topographic effects of coastal seas on the composition of the culturable bacterial communities in marine sediments. Hydrobiologia 583, 205–212 (2007). https://doi.org/10.1007/s10750-006-0527-z

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10750-006-0527-z

Keywords

Search

Navigation