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Applied and Environmental Microbiology, December 2006, p. 7767-7777, Vol. 72, No. 12
0099-2240/06/$08.00+0     doi:10.1128/AEM.00946-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Diversity of Ammonia-Oxidizing Archaea and Bacteria in the Sediments of a Hypernutrified Subtropical Estuary: Bahía del Tóbari, Mexico{triangledown}

J. Michael Beman* and Christopher A. Francis

Department of Geological and Environmental Sciences, Stanford University, Stanford, California 94305

Received 20 April 2006/ Accepted 22 September 2006

Nitrification within estuarine sediments plays an important role in the nitrogen cycle, both at the global scale and in individual estuaries. Although bacteria were once thought to be solely responsible for catalyzing the first and rate-limiting step of this process, several recent studies have suggested that mesophilic Crenarchaeota are capable of performing ammonia oxidation. Here we examine the diversity (richness and community composition) of ammonia-oxidizing archaea (AOA) and bacteria (AOB) within sediments of Bahía del Tóbari, a hypernutrified estuary receiving substantial amounts of ammonium in agricultural runoff. Using PCR primers designed to specifically target the archaeal ammonia monooxygenase {alpha}-subunit (amoA) gene, we found AOA to be present at five sampling sites within this estuary and at two sampling time points (January and October 2004). In contrast, the bacterial amoA gene was PCR amplifiable from only 40% of samples. Bacterial amoA libraries were dominated by a few widely distributed Nitrosomonas-like sequence types, whereas AOA diversity showed significant variation in both richness and community composition. AOA communities nevertheless exhibited consistent spatial structuring, with two distinct end member assemblages recovered from the interior and the mouths of the estuary and a mixed assemblage from an intermediate site. These findings represent the first detailed examination of archaeal amoA diversity in estuarine sediments and demonstrate that diverse communities of Crenarchaeota capable of ammonia oxidation are present within estuaries, where they may be actively involved in nitrification.

* Corresponding author. Mailing address: Department of Geological and Environmental Sciences, Building 320, Room 118, Stanford University, Stanford, CA 94305-2115. Phone: (650) 724-1535. Fax: (650) 725-2199. E-mail: beman{at}stanford.edu.

{triangledown} Published ahead of print on 29 September 2006.

Applied and Environmental Microbiology, December 2006, p. 7767-7777, Vol. 72, No. 12
0099-2240/06/$08.00+0     doi:10.1128/AEM.00946-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.



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