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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
-Subgroup Ammonia-Oxidizing Bacteria within
Polluted Marine Fish Farm Sediments
Allison E.
McCaig,1
Carol J.
Phillips,2,3
John R.
Stephen,1,4,
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
-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.
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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