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Microbial diversity in the Bassin d’Arcachon coastal lagoon (SW France)

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Abstract

The high biodiversity observed in coastal lagoons can often be related to a very high degree of environmental heterogeneity (β-biodiversity). In this article, I describe many physical factors that contribute to create environmental heterogeneity and different habitats within the Bassin d’Arcachon, a mesotidal lagoon in S.W. France. The microbial biodiversity has been studied in this coastal lagoon by culture-dependent and culture-independent techniques. The sediments of the meadows of the seagrass Zostera noltii have received a specific focus. During the last 15 years, several novel bacterial species have been isolated from these sediments and obtained in culture. Among these, five different species have been fully described as novel species according the Bacteriological Code and two of them represent also the type strain for a novel genus. The bacterial biodiversity has also been studied by molecular ecology techniques. An early study was focused on water column bacteria and a comparison has been made with the same community from the more eutrophic Prévost lagoon (France, Mediterranean coast). A clone library was also constructed for 16-S rRNA genes isolated and amplified from the 1–2 cm depth layer of the Z. noltii sediment. These studies showed a high degree of biodiversity and the importance of sulfate-reducing bacteria in the sediment, pointing to species that have not been obtained in culture. Collectively, these data show that there is still a large discrepancy between culture-dependent and culture-independent prokaryotic biodiversity. It is important to link the functional biogeochemical approach with the biodiversity approach. For the Bassin d’Arcachon studies, the biogeochemical approach has successfully nurtured the biodiversity studies, while the reverse has not yet been the case as the biogeochemical studies have lumped prokaryotes in functional groups.

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References

  • Amtoft Neubauer, A. T., A.-G. Underlien Pedersen, K. Finster, R. A. Herbert, A. P. Donnelly, P. Viaroli, G. Giordani, R. De Wit & B. Aa. Lomstein, 2004. Benthic decomposition of Zostera marina roots: a controlled laboratory experiment. Journal of Experimental Marine Biology and Ecology 313: 105–124.

    Article  Google Scholar 

  • Auby, I. & P. J. Labourg, 1996. Seasonal dynamics of Zostera noltii Hornem in the Bay of Arcachon (France). Journal of Sea Research 35: 269–277.

    Article  Google Scholar 

  • Barnes, R. S. K., 1980. Coastal Lagoons; The Natural History of a Neglected Habitat. Cambridge University Press, Cambridge: 106 pp.

    Google Scholar 

  • Benlloch, S., F. Rodríguez-Valera & A. J. Martínez-Murcia, 1995. Bacterial diversity in two coastal lagoons deduced from 16 S rDNA PCR amplification and partial sequencing. FEMS Microbiology Ecology 18: 267–280.

    Article  CAS  Google Scholar 

  • Bourguès, S., 1996. Ecologie des bactéries sulfato-réductrices en milieu lagunaire. Mineralisation de la matire organique et fixation de l’azote atmospherique. Ph.D. Thesis, University of Bordeaux.

  • Caumette, P., J. Castel & R.A. Herbert (eds), 1996. Coastal Lagoon Eutrophication and Anaerobic Processes (C.L.E.A.N.). Developments in Hydrobiology (reprinted from Hydrobiologia 329). Kluwer, Dordrecht.

  • Cifuentes, A., 2003. Diversidad procariótica en sedimentos marinos costeros mediante técnicas moleculares y de cultivo. PhD thesis Universidad Miquel Hernandez, Alicante, Spain.

  • Cifuentes, A., J. Antón, S. Benloch, A. Donnelly, R. A. Herbert & F. Rodríguez-Valera, 2000. Prokaryotic diversity in Zostera noltii colonized marine sediments. Applied Environmental Microbiology 66: 1715–1719.

    Article  CAS  Google Scholar 

  • Cifuentes, A., J. Antón, R. De Wit & F. Rodríguez-Valera, 2003. Diversity of Bacteria and Archaea in sulfate-reducing enrichment cultures inoculated from serial dilution of Zostera noltii rhizosphere samples. Environmental Microbiology 5: 754–764.

    Article  PubMed  CAS  Google Scholar 

  • De Wit, R., 2007. Biodiversity and ecosystem functioning in transitional waters; the point of view of a microbial ecologist. Transitional Waters Bulletin 1: 3–16.

    Google Scholar 

  • De Wit, R., L. J. Stal, B. Aa. Lomstein, R. A. Herbert, H. Van Gemerden, P. Viaroli, V.-U. Cecherelli, F. Rodríguez-Valera, B. Bartoli, G. Giordani, R. Azzoni, B. Schaub, D. T. Welsh, A. Donelly, A. Cifuentes, J. Antón, K. Finster, L. B. Nielsen, A.-G. Underlien Pedersen, A. Turi Neubeurer, M. A. Colangelo & S. K. Heijs, 2001. ROBUST: The ROle of BUffering capacities in STabilising coastal lagoon ecosystems. Continental Shelf Research 21: 2021–2041.

  • De Wit, R., J. Leibreich, F. Vernier, F. Delmas, H. Beuffe, Ph. Maison, J.-C. Chossat, C. Laplace-Treyture, R. Laplana, V. Clavé, M. Torre, I. Auby, G. Trut, D. Maurer & P. Capdeville, 2005. Relationship between land-use in the agro-forestry system of les Landes, nitrogen loading to and risk of macro-algal blooming in the Bassin d’Arcachon coastal lagoon (SW France). Estuarine. Coastal and Shelf Science 62: 453–465.

    Article  CAS  Google Scholar 

  • Duarte, C. M., 1995. Submerged aquatic vegetation in relation to different nutrient regimes. Ophelia 41: 87–112.

    Google Scholar 

  • Finster, K., W. Liesack & B. J. Tindall, 1997a. Sulfurospirillum arcachonense sp. nov., a new microaerophilic sulfur-reducing bacterium. International Journal of Systematic Bacteriology 39: 159–167.

    Google Scholar 

  • Finster, K., W. Liesack & B. J. Tindall, 1997b. Desulfospira joergensenii, gen. nov., sp. nov., a new sulfate-reducing bacterium isolated from marine surface sediment. Systematic and Applied Microbiology 20: 201–208.

    CAS  Google Scholar 

  • Finster, K., W. Liesack & B. Thamdrup, 1998. Elemental sulfur and thiosulfate disproportionation by Desulfocapsa sulfoexigens sp. nov., a new anaerobic bacterium isolated from marine surface sediment. Applied Environmental Microbiology 64: 119–125.

    CAS  Google Scholar 

  • Flindt, M. R., M. A. Pardal, A. I. Lillebø, I. Martins & J. C. Marques, 1999. Nutrient cycling and plant dynamics in estuaries: a brief review. Acta Oecologica 20: 237–248.

    Article  Google Scholar 

  • Guyoneaud, R., R. Matheron, R. Baulaigue, K. Podeur, A. Hirschler, P. Caumette, 1996. Anoxygenic phototrophic bacteria in eutrophic lagoons of the French Mediterranean and Atlantic coast (Prévost Lagoon, Arcachon Bay, Certes fishponds). In Caumette, P., J. Castel & R. A. Herbert (eds), Coastal Lagoon Eutrophication and Anaerobic Processes. Hydrobiologia 329. Reprinted as Developments in Hydrobiology 117 (H.J. Dumont, Series editor). Kluwer, Dordrecht: 253 pp.

  • Guyoneaud, R., R. Matheron, W. Liesack, J. F. Imhoff & P. Caumette, 1997. Thiorhodococcus minus, gen. nov., sp. nov., a new purple sulphur bacterium isolated from coastal lagoon sediments. Archives of Microbiology 168: 16–23.

    Article  PubMed  CAS  Google Scholar 

  • Guyoneaud, R., S. Mouné, C. Eatcock, V. Bothorel, A. Hirschler-Réa, J. Willison, R. Duran, W. Liesack, R. A. Herbert, R. Matheron & P. Caumette, 2002. Characterization of three spiral-shaped purple nonsulfur bacteria isolated from coastal lagoon sediments, saline sulfur springs, and microbial mats: emended description of the genus Roseospira and description of Roseospira marina sp. nov., Roseospira navarensis sp. nov., and Roseospira thiosulfatophila sp. nov. Archives of Microbiology 178: 315–324.

    Article  PubMed  CAS  Google Scholar 

  • Hauxwell, J., J. Cebrián & I. Valiela, 2003. Eelgrass Zostera marina loss in temperate estuaries: relationship to land-derived nitrogen-loads and the Effect of light limitation by algae. Marine Ecology Progress Series 247: 59–73.

    Article  CAS  Google Scholar 

  • Heijs, S. K., H. M. Jonkers, H. van Gemerden, B. E. M. Schaub & L. J. Stal, 1999. The buffering capacity towards free sulfide in sediments of a coastal lagoon (Bassin d’Arcachon, France)—the relative importance of chemical and biological processes. Estuarine & Coastal Shelf Science 49: 21–35.

    Article  CAS  Google Scholar 

  • Hemminga, M. A., 1998. The root rhizome system of seagrasses: an asset and a burden. Journal of Sea Research 39: 183–196.

    Article  Google Scholar 

  • Hill, T. C. J., K. A. Walsh, J. A. Harris & B. F. Moffet, 2003. Using ecological diversity measures with bacterial communities. FEMS Microbiology Ecology 43: 1–11.

    Article  CAS  PubMed  Google Scholar 

  • Imhoff, J. F., 2003. Phylogenetic taxonomy of the family Chlorobiaceae on the basis of 16S rRNA and fmo (Fenna-Matthews-Olson protein) gene sequences. International Journal of Systematic and Evolutionary Microbiology 53: 941–951.

    Article  PubMed  CAS  Google Scholar 

  • Jickells, T., J. Andrews, G. Samways, R. Sanders, S. Malcolm, D. Sivyer, R. Parker, D. Nedwell, M. Trimmer & J. Ridgway, 2000. Nutrient fluxes through the Humber estuary—past, present and future. Ambio 29: 130–135.

    Article  Google Scholar 

  • Kjerfve, B., 1994. Coastal lagoons, chapter 1. In Kjerfve, B. (ed.), Coastal Lagoon Processes. Elsevier Oceanography Series, Amsterdam: 1–8.

    Chapter  Google Scholar 

  • Lapage, S. P., P. H. A. Sneath, E. F. Lessel, V. B. D. Skerman, H. P. R. Seelinger & W. A. Clark (eds), 1992. International Code of Nomenclature of Bacteria (1990 revision) Bacteriological Code. Washington DC, American Society for Microbiology.

    Google Scholar 

  • Monsen, N. E., J. E. Cloern, L. V. Lucas & S. G. Monsmith, 2002. The use of flushing time, residence time, and age as transport time scales. Limnology Oceanography 47: 1545–1553.

    Google Scholar 

  • Nielsen, J. T., W. Liesack & K. Finster, 1999. Desulfovibrio zosterae sp. nov., a new sulfate reducer isolated from surface sterilized roots of the seagrass Zostera marina. International Journal of Systematic Bacteriology 49: 859–865.

    Article  PubMed  CAS  Google Scholar 

  • Nielsen, L. B., K. Kinster, D. T. Welsh, A. Donellly, R. A. Herbert, R. De Wit & B. Aa. Lomstein, 2001. Sulphate reduction and nitrogen fixation rates associated with roots, rhizomes and sediments from Zostera noltii and Spartina maritima meadows. Environmental Microbiology 3: 63–71.

    Article  PubMed  CAS  Google Scholar 

  • Pedersen, A.-G. U., J. Berntsen & B. Aa. Lomstein, 1999. The effect of eelgrass decomposition on sediment carbon and nitrogen cycling: a controlled laboratory experiment. Limnology & Oceanography 44: 1978–1992.

    Article  CAS  Google Scholar 

  • Rimmelin, P., J.-C. Dumon, E. Maneux & A. Gonçalves, 1998. Study of annual and seasonal dissolved inorganic nitrogen inputs into the Arcachon lagoon, Atlantic coast (France). Estuarine and Coastal Shelf Science 47: 649–659.

    Article  CAS  Google Scholar 

  • Sargos, J., 1997. Histoire de la forêt landaise, du désert à l’age d’or. Horizon chimérique, Bordeaux: 559.

    Google Scholar 

  • Seitzinger, S. P., C. Kroeze, A. F. Bouwman, N. Caraco, F. Dentener & R. V. Styles, 2002. Global patterns of dissolved inorganic and particulate nitrogen inputs to coastal systems: recent conditions and future projections. Estuaries 25: 640–655.

    Article  CAS  Google Scholar 

  • Valiela, I., J. McClelland, J. Hauxwell, P. J. Behr, D. Hersh & K. Foreman, 1997a. Macroalgal blooms in shallow estuaries: control and ecophysiological and ecosystem consequences. Limnology & Oceanography 42: 1105–1118.

    Google Scholar 

  • Valiela, I., G. Collins, J. Kremer, K. Lajtha, M. Geist, B. Seely, J. Brawley & C. H. Sham, 1997b. Nitrogen loadings from coastal watersheds to receiving estuaries: new mathod and application. Ecological Applications 7: 358–380.

    Article  Google Scholar 

  • Verger, F., 2005. Marais et estuaires du littoral français. Belin, Paris: 335 pp.

    Google Scholar 

  • Welsh, D. T., S. Bourguès, R. A. Herbert & R. De Wit, 1996. Seasonal variation in nitrogen fixation (acetylene reduction) and sulphate reduction rates in the rhizosphere of Zostera noltii: nitrogen fixation by sulphate reducing bacteria. Marine Biology 125: 619–628.

    Article  CAS  Google Scholar 

  • Welsh, D. T., S. Bourguès, R. De Wit & I. Auby, 1997. Effect of plant photosynthesis, carbon sources and ammonium availability on nitrogen fixation in the rhizosphere of Zostera noltii. Aquatic Microbial Ecology 12: 285–290.

    Article  Google Scholar 

  • Welsh, D. T., G. Castadelli, M. Bartoli, D. Polio, M. Careri, R. De Wit & P. Viaroli, 2001. Denitrification in an intertidal seagrass meadow, a comparison of 15N-isotope and acetylene block techniques. Marine Biology 139: 1029–1036.

    Article  CAS  Google Scholar 

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Acknowledgments

This review article has been largely based on my participation in the E.U. projects CLEAN and ROBUST, in the EU thematic network ELOISE and the French national program LITEAU. I thank my colleagues and students that participated in different projects for their contributions and stimulating discussions. This work was partially supported by the French program LITEAU, project “Gestion des richesses écologiques et des ressources économiques du Bassin d’Arcachon : Limites du pouvoir tampon de la lagune vis-à-vis des apports du bassin versant” contract N° LT 99064, financed by the Ministry of Ecology and Sustainable Development (MEDD, Paris).

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  1. Centre National de la Recherche Scientifique (CNRS) & Université Montpellier 2, UMR 5119 “Ecosystèmes lagunaires” Université Montpellier II & Ifremer, Case 093, Place Eugène Bataillon, 34095, Montpellier Cedex 05, France

    Rutger de Wit

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Correspondence to Rutger de Wit.

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Guest editors: A. Razinkovas, Z. R. Gasiūnaitė, J. M. Zaldivar & P. Viaroli

European Lagoons and their Watersheds: Function and Biodiversity

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de Wit, R. Microbial diversity in the Bassin d’Arcachon coastal lagoon (SW France). Hydrobiologia 611, 5–15 (2008). https://doi.org/10.1007/s10750-008-9461-6

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