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Applied and Environmental Microbiology, September 2006, p. 5689-5701, Vol. 72, No. 9
0099-2240/06/$08.00+0     doi:10.1128/AEM.03007-05
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Microbial Community Diversity Associated with Carbon and Nitrogen Cycling in Permeable Shelf Sediments{dagger}

Evan M. Hunter, Heath J. Mills, and Joel E. Kostka*

Department of Oceanography, Florida State University, Tallahassee, Florida 32306

Received 20 December 2005/ Accepted 15 May 2006

Though a large fraction of primary production and organic matter cycling in the oceans occurs on continental shelves dominated by sandy deposits, the microbial communities associated with permeable shelf sediments remain poorly characterized. Therefore, in this study, we provide the first detailed characterization of microbial diversity in marine sands of the South Atlantic Bight through parallel analyses of small-subunit (SSU) rRNA gene (Bacteria), nosZ (denitrifying bacteria), and amoA (ammonia-oxidizing bacteria) sequences. Communities were analyzed by parallel DNA extractions and clone library construction from both sediment core material and manipulated sediment within column experiments designed for geochemical rate determinations. Rapid organic-matter degradation and coupled nitrification-denitrification were observed in column experiments at flow rates resembling in situ conditions over a range of oxygen concentrations. Numerous SSU rRNA phylotypes were affiliated with the phyla Proteobacteria (classes Alpha-, Delta-, and Gammaproteobacteria), Planctomycetes, Cyanobacteria, Chloroflexi, and Bacteroidetes. Detectable sequence diversity of nosZ and SSU rRNA genes increased in stratified redox-stabilized columns compared to in situ sediments, with the Alphaproteobacteria comprising the most frequently detected group. Alternatively, nitrifier communities showed a relatively low and stable diversity that did not covary with the other gene targets. Our results elucidate predominant phylotypes that are likely to catalyze carbon and nitrogen cycling in marine sands. Although overall diversity increased in response to redox stabilization and stratification in column experiments, the major phylotypes remained the same in all of our libraries, indicating that the columns sufficiently mimic in situ conditions.

* Corresponding author. Mailing address: Department of Oceanography, Florida State University, FSU Collins Research Lab, 255 Atomic Way, Bldg. 42, Tallahassee, FL 32306-4470. Phone: (850) 644-5719. Fax: (850) 644-2581. E-mail: jkostka{at}ocean.fsu.edu.

{dagger} Supplemental material for this article may be found at http://aem.asm.org/.

Applied and Environmental Microbiology, September 2006, p. 5689-5701, Vol. 72, No. 9
0099-2240/06/$08.00+0     doi:10.1128/AEM.03007-05
Copyright © 2006, American Society for Microbiology. All Rights Reserved.



This article has been cited by other articles:

  • Mills, H. J., Hunter, E., Humphrys, M., Kerkhof, L., McGuinness, L., Huettel, M., Kostka, J. E. (2008). Characterization of Nitrifying, Denitrifying, and Overall Bacterial Communities in Permeable Marine Sediments of the Northeastern Gulf of Mexico. Appl. Environ. Microbiol. 74: 4440-4453 [Abstract] [Full Text]  
  • Urakawa, H., Tajima, Y., Numata, Y., Tsuneda, S. (2008). Low Temperature Decreases the Phylogenetic Diversity of Ammonia-Oxidizing Archaea and Bacteria in Aquarium Biofiltration Systems. Appl. Environ. Microbiol. 74: 894-900 [Abstract] [Full Text]  


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