Original Article

Subject Category: Microbial population and community ecology

The ISME Journal (2012) 6, 542–553; doi:10.1038/ismej.2011.132; published online 6 October 2011

Diversity and dynamics of rare and of resident bacterial populations in coastal sands

Angélique Gobet1,2,7, Simone I Böer1,8, Susan M Huse3, Justus E E van Beusekom4, Christopher Quince5, Mitchell L Sogin3, Antje Boetius1,6 and Alban Ramette1

  1. 1HGF-MPG Group for Deep Sea Ecology and Technology, Max Planck Institute for Marine Microbiology, Bremen, Germany
  2. 2Jacobs University Bremen GmbH, Bremen, Germany
  3. 3Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA
  4. 4Alfred Wegener Institute for Polar and Marine Research, List/Sylt, Germany
  5. 5School of Engineering, University of Glasgow, Glasgow, UK
  6. 6HGF-MPG Group for Deep Sea Ecology and Technology, Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany

Correspondence: A Ramette, HGF-MPG Group for Deep Sea Ecology and Technology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany. E-mail: aramette@mpi-bremen.de

7Current address: Evolution of Plankton and PaleoOceans (EPPO) team, UMR 7144 CNRS – UPMC, Station Biologique de Roscoff, Roscoff, France.

8Current address: Federal Institute of Hydrology, Koblenz, Germany.

Received 2 May 2011; Revised 29 July 2011; Accepted 25 August 2011; Published online 6 October 2011.



Coastal sands filter and accumulate organic and inorganic materials from the terrestrial and marine environment, and thus provide a high diversity of microbial niches. Sands of temperate climate zones represent a temporally and spatially highly dynamic marine environment characterized by strong physical mixing and seasonal variation. Yet little is known about the temporal fluctuations of resident and rare members of bacterial communities in this environment. By combining community fingerprinting via pyrosequencing of ribosomal genes with the characterization of multiple environmental parameters, we disentangled the effects of seasonality, environmental heterogeneity, sediment depth and biogeochemical gradients on the fluctuations of bacterial communities of marine sands. Surprisingly, only 3–5% of all bacterial types of a given depth zone were present at all times, but 50–80% of them belonged to the most abundant types in the data set. About 60–70% of the bacterial types consisted of tag sequences occurring only once over a period of 1 year. Most members of the rare biosphere did not become abundant at any time or at any sediment depth, but varied significantly with environmental parameters associated with nutritional stress. Despite the large proportion and turnover of rare organisms, the overall community patterns were driven by deterministic relationships associated with seasonal fluctuations in key biogeochemical parameters related to primary productivity. The maintenance of major biogeochemical functions throughout the observation period suggests that the small proportion of resident bacterial types in sands perform the key biogeochemical processes, with minimal effects from the rare fraction of the communities.


454 pyrosequencing; coastal seas; bacterial diversity; multivariate analysis; rare biosphere