Diversity and Distribution of DNA Sequences with Affinity to Ammonia-Oxidizing Bacteria of the β Subdivision of the Class Proteobacteria in the Arctic Ocean
ABSTRACT The spatial distribution and diversity of ammonia-oxidizing bacteria of the β subdivision of the class Proteobacteria (hereinafter referred to as ammonia oxidizers) in the Arctic Ocean were determined. The presence of ammonia oxidizers was detected by PCR amplification of 16S rRNA genes usi...
Published in: | Applied and Environmental Microbiology |
---|---|
Main Authors: | , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
American Society for Microbiology
2000
|
Subjects: | |
Online Access: | http://dx.doi.org/10.1128/aem.66.5.1960-1969.2000 https://journals.asm.org/doi/pdf/10.1128/AEM.66.5.1960-1969.2000 |
id |
crasmicro:10.1128/aem.66.5.1960-1969.2000 |
---|---|
record_format |
openpolar |
spelling |
crasmicro:10.1128/aem.66.5.1960-1969.2000 2024-09-15T17:53:12+00:00 Diversity and Distribution of DNA Sequences with Affinity to Ammonia-Oxidizing Bacteria of the β Subdivision of the Class Proteobacteria in the Arctic Ocean Bano, Nasreen Hollibaugh, James T. 2000 http://dx.doi.org/10.1128/aem.66.5.1960-1969.2000 https://journals.asm.org/doi/pdf/10.1128/AEM.66.5.1960-1969.2000 en eng American Society for Microbiology https://journals.asm.org/non-commercial-tdm-license Applied and Environmental Microbiology volume 66, issue 5, page 1960-1969 ISSN 0099-2240 1098-5336 journal-article 2000 crasmicro https://doi.org/10.1128/aem.66.5.1960-1969.2000 2024-08-05T04:09:41Z ABSTRACT The spatial distribution and diversity of ammonia-oxidizing bacteria of the β subdivision of the class Proteobacteria (hereinafter referred to as ammonia oxidizers) in the Arctic Ocean were determined. The presence of ammonia oxidizers was detected by PCR amplification of 16S rRNA genes using a primer set specific for this group of organisms (nitA and nitB, which amplifies a 1.1-kb fragment between positions 137 and 1234, corresponding to Escherichia coli 16S rDNA numbering). We analyzed 246 samples collected from the upper water column (5 to 235 m) during March and April 1995, September and October 1996, and September 1997. Ammonia oxidizers were detected in 25% of the samples from 5 m, 80% of the samples from 55 m, 88% of the samples from 133 m, and 50% of the samples from 235 m. Analysis of nitA-nitB PCR product by nested PCR-denaturing gradient gel electrophoresis (DGGE) showed that all positive samples contained the same major band (band A), indicating the presence of a dominant, ubiquitous ammonia oxidizer in the Arctic Ocean basin. Twenty-two percent of the samples contained additional major bands. These samples were restricted to the Chukchi Sea shelf break, the Chukchi cap, and the Canada basin; areas likely influenced by Pacific inflow. The nucleotide sequence of the 1.1-kb nitA-nitB PCR product from a sample that contained only band A grouped with sequences designated group 1 marine Nitrosospira -like sequences. PCR-DGGE analysis of 122 clones from four libraries revealed that 67 to 71% of the inserts contained sequences with the same mobility as band A. Nucleotide sequences (1.1 kb) of another distinct group of clones, found only in 1995 samples (25%), fell into the group 5 marine Nitrosomonas -like sequences. Our results suggest that the Arctic Ocean β-proteobacterial ammonia oxidizers have low diversity and are dominated by marine Nitrosospira -like organisms. Diversity appears to be higher in Western Arctic Ocean regions influenced by inflow from the Pacific Ocean through the Bering and ... Article in Journal/Newspaper Arctic Ocean canada basin Chukchi Chukchi Sea ASM Journals (American Society for Microbiology) Applied and Environmental Microbiology 66 5 1960 1969 |
institution |
Open Polar |
collection |
ASM Journals (American Society for Microbiology) |
op_collection_id |
crasmicro |
language |
English |
description |
ABSTRACT The spatial distribution and diversity of ammonia-oxidizing bacteria of the β subdivision of the class Proteobacteria (hereinafter referred to as ammonia oxidizers) in the Arctic Ocean were determined. The presence of ammonia oxidizers was detected by PCR amplification of 16S rRNA genes using a primer set specific for this group of organisms (nitA and nitB, which amplifies a 1.1-kb fragment between positions 137 and 1234, corresponding to Escherichia coli 16S rDNA numbering). We analyzed 246 samples collected from the upper water column (5 to 235 m) during March and April 1995, September and October 1996, and September 1997. Ammonia oxidizers were detected in 25% of the samples from 5 m, 80% of the samples from 55 m, 88% of the samples from 133 m, and 50% of the samples from 235 m. Analysis of nitA-nitB PCR product by nested PCR-denaturing gradient gel electrophoresis (DGGE) showed that all positive samples contained the same major band (band A), indicating the presence of a dominant, ubiquitous ammonia oxidizer in the Arctic Ocean basin. Twenty-two percent of the samples contained additional major bands. These samples were restricted to the Chukchi Sea shelf break, the Chukchi cap, and the Canada basin; areas likely influenced by Pacific inflow. The nucleotide sequence of the 1.1-kb nitA-nitB PCR product from a sample that contained only band A grouped with sequences designated group 1 marine Nitrosospira -like sequences. PCR-DGGE analysis of 122 clones from four libraries revealed that 67 to 71% of the inserts contained sequences with the same mobility as band A. Nucleotide sequences (1.1 kb) of another distinct group of clones, found only in 1995 samples (25%), fell into the group 5 marine Nitrosomonas -like sequences. Our results suggest that the Arctic Ocean β-proteobacterial ammonia oxidizers have low diversity and are dominated by marine Nitrosospira -like organisms. Diversity appears to be higher in Western Arctic Ocean regions influenced by inflow from the Pacific Ocean through the Bering and ... |
format |
Article in Journal/Newspaper |
author |
Bano, Nasreen Hollibaugh, James T. |
spellingShingle |
Bano, Nasreen Hollibaugh, James T. Diversity and Distribution of DNA Sequences with Affinity to Ammonia-Oxidizing Bacteria of the β Subdivision of the Class Proteobacteria in the Arctic Ocean |
author_facet |
Bano, Nasreen Hollibaugh, James T. |
author_sort |
Bano, Nasreen |
title |
Diversity and Distribution of DNA Sequences with Affinity to Ammonia-Oxidizing Bacteria of the β Subdivision of the Class Proteobacteria in the Arctic Ocean |
title_short |
Diversity and Distribution of DNA Sequences with Affinity to Ammonia-Oxidizing Bacteria of the β Subdivision of the Class Proteobacteria in the Arctic Ocean |
title_full |
Diversity and Distribution of DNA Sequences with Affinity to Ammonia-Oxidizing Bacteria of the β Subdivision of the Class Proteobacteria in the Arctic Ocean |
title_fullStr |
Diversity and Distribution of DNA Sequences with Affinity to Ammonia-Oxidizing Bacteria of the β Subdivision of the Class Proteobacteria in the Arctic Ocean |
title_full_unstemmed |
Diversity and Distribution of DNA Sequences with Affinity to Ammonia-Oxidizing Bacteria of the β Subdivision of the Class Proteobacteria in the Arctic Ocean |
title_sort |
diversity and distribution of dna sequences with affinity to ammonia-oxidizing bacteria of the β subdivision of the class proteobacteria in the arctic ocean |
publisher |
American Society for Microbiology |
publishDate |
2000 |
url |
http://dx.doi.org/10.1128/aem.66.5.1960-1969.2000 https://journals.asm.org/doi/pdf/10.1128/AEM.66.5.1960-1969.2000 |
genre |
Arctic Ocean canada basin Chukchi Chukchi Sea |
genre_facet |
Arctic Ocean canada basin Chukchi Chukchi Sea |
op_source |
Applied and Environmental Microbiology volume 66, issue 5, page 1960-1969 ISSN 0099-2240 1098-5336 |
op_rights |
https://journals.asm.org/non-commercial-tdm-license |
op_doi |
https://doi.org/10.1128/aem.66.5.1960-1969.2000 |
container_title |
Applied and Environmental Microbiology |
container_volume |
66 |
container_issue |
5 |
container_start_page |
1960 |
op_container_end_page |
1969 |
_version_ |
1810295192799936512 |