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Applied and Environmental Microbiology, January 1999, p. 213-220, Vol. 65, No. 1
0099-2240/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.

Nitrogen Cycling and Community Structure of Proteobacterial beta -Subgroup Ammonia-Oxidizing Bacteria within Polluted Marine Fish Farm Sediments

Allison E. McCaig,1 Carol J. Phillips,2,3 John R. Stephen,1,4,dagger George A. Kowalchuk,5 S. Martyn Harvey,2 Rodney A. Herbert,3 T. Martin Embley,4 and James I. Prosser1,*

Department of Molecular and Cell Biology, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD,1 Dunstaffnage Marine Laboratory, Oban, Argyll PA34 4AD,2 and Department of Biological Sciences, University of Dundee, Dundee DD1 4HN,3 Scotland, and Department of Zoology, The Natural History Museum, London SW7 5BD, England,4 United Kingdom, and Department of Plant Microorganism Interactions, Netherlands Institute of Ecology, 6666 ZG Heteren, The Netherlands5

Received 22 June 1998/Accepted 20 October 1998

A multidisciplinary approach was used to study the effects of pollution from a marine fish farm on nitrification rates and on the community structure of ammonia-oxidizing bacteria in the underlying sediment. Organic content, ammonium concentrations, nitrification rates, and ammonia oxidizer most-probable-number counts were determined in samples of sediment collected from beneath a fish cage and on a transect at 20 and 40 m from the cage. The data suggest that nitrogen cycling was significantly disrupted directly beneath the fish cage, with inhibition of nitrification and denitrification. Although visual examination indicated some slight changes in sediment appearance at 20 m, all other measurements were similar to those obtained at 40 m, where the sediment was considered pristine. The community structures of proteobacterial beta -subgroup ammonia-oxidizing bacteria at the sampling sites were compared by PCR amplification of 16S ribosomal DNA (rDNA), using primers which target this group. PCR products were analyzed by denaturing gradient gel electrophoresis (DGGE) and with oligonucleotide hybridization probes specific for different ammonia oxidizers. A DGGE doublet observed in PCR products from the highly polluted fish cage sediment sample was present at a lower intensity in the 20-m sample but was absent from the pristine 40-m sample station. Band migration, hybridization, and sequencing demonstrated that the doublet corresponded to a marine Nitrosomonas group which was originally observed in 16S rDNA clone libraries prepared from the same sediment samples but with different PCR primers. Our data suggest that this novel Nitrosomonas subgroup was selected for within polluted fish farm sediments and that the relative abundance of this group was influenced by the extent of pollution.

* Corresponding author. Mailing address: Department of Molecular and Cell Biology, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, United Kingdom. Phone: 44 1224 273148. Fax: 44 1224 273144. E-mail: j.prosser{at}abdn.ac.uk.

dagger Present address: Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37932-2575.

Applied and Environmental Microbiology, January 1999, p. 213-220, Vol. 65, No. 1
0099-2240/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.


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