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Applied and Environmental Microbiology, June 2007, p. 3547-3555, Vol. 73, No. 11
0099-2240/07/$08.00+0     doi:10.1128/AEM.02275-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.

Ammonia-Oxidizing ß-Proteobacteria from the Oxygen Minimum Zone off Northern Chile

Laboratorio de Procesos Oceanográficos y Clima, Departamento de Oceanografía & Centro de Investigación Oceanográfica en el Pacífico Sudoriental, Universidad de Concepción, Concepción, Chile,¹ Departamento de Microbiología, Universidad de Concepción, Concepción, Chile,² Max-Planck-Institut für Limnologie, Plön, Germany³

Received 26 September 2006/ Accepted 28 March 2007

The composition of ammonia-oxidizing bacteria from the ß-Proteobacteria subclass (ßAOB) was studied in the surface and upper-oxycline oxic waters (2- to 50-m depth, 200 to 44 µM O₂) and within the oxygen minimum zone (OMZ) suboxic waters (50- to 400-m depth, 10 µM O₂) of the eastern South Pacific off northern Chile. This study was carried out through cloning and sequencing of genes coding for 16S rRNA and the ammonia monooxygenase enzyme active subunit (amoA). Sequences affiliated with Nitrosospira-like cluster 1 dominated the 16S rRNA gene clone libraries constructed from both oxic and suboxic waters. Cluster 1 consists exclusively of yet-uncultivated ßAOB from marine environments. However, a single clone, out of 224 obtained from the OMZ, was found to belong to Nitrosospira lineage cluster 0. To our knowledge, cluster 0 sequences have been derived from ßAOB isolated only from sand, soil, and freshwater environments. Sequences in clone libraries of the amoA gene from the surface and upper oxycline could be grouped in a marine subcluster, also containing no cultured representatives. In contrast, all 74 amoA sequences originating from the OMZ were either closely affiliated with cultured Nitrosospira spp. from clusters 0 and 2 or with other yet-uncultured ßAOB from soil and an aerated-anoxic Orbal process waste treatment plant. Our results reveal the presence of Nitrosospira-like ßAOB in both oxic and suboxic waters associated with the OMZ but with a clear community shift at the functional level (amoA) along the strong oxygen gradient.

Published ahead of print on 6 April 2007.