Comparative Genomic Analysis of Archaeal Genotypic Variants in a Single Population and in Two Different Oceanic Provinces
ABSTRACT Planktonic crenarchaeotes are present in high abundance in Antarctic winter surface waters, and they also make up a large proportion of total cell numbers throughout deep ocean waters. To better characterize these uncultivated marine crenarchaeotes, we analyzed large genome fragments from i...
Published in: | Applied and Environmental Microbiology |
---|---|
Main Authors: | , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
American Society for Microbiology
2002
|
Subjects: | |
Online Access: | http://dx.doi.org/10.1128/aem.68.1.335-345.2002 https://journals.asm.org/doi/pdf/10.1128/AEM.68.1.335-345.2002 |
id |
crasmicro:10.1128/aem.68.1.335-345.2002 |
---|---|
record_format |
openpolar |
spelling |
crasmicro:10.1128/aem.68.1.335-345.2002 2024-06-23T07:46:03+00:00 Comparative Genomic Analysis of Archaeal Genotypic Variants in a Single Population and in Two Different Oceanic Provinces Béjà, Oded Koonin, Eugene V. Aravind, L. Taylor, Lance T. Seitz, Heidi Stein, Jefferey L. Bensen, Daniel C. Feldman, Robert A. Swanson, Ronald V. DeLong, Edward F. 2002 http://dx.doi.org/10.1128/aem.68.1.335-345.2002 https://journals.asm.org/doi/pdf/10.1128/AEM.68.1.335-345.2002 en eng American Society for Microbiology https://journals.asm.org/non-commercial-tdm-license Applied and Environmental Microbiology volume 68, issue 1, page 335-345 ISSN 0099-2240 1098-5336 journal-article 2002 crasmicro https://doi.org/10.1128/aem.68.1.335-345.2002 2024-06-10T04:07:27Z ABSTRACT Planktonic crenarchaeotes are present in high abundance in Antarctic winter surface waters, and they also make up a large proportion of total cell numbers throughout deep ocean waters. To better characterize these uncultivated marine crenarchaeotes, we analyzed large genome fragments from individuals recovered from a single Antarctic picoplankton population and compared them to those from a representative obtained from deeper waters of the temperate North Pacific. Sequencing and analysis of the entire DNA insert from one Antarctic marine archaeon (fosmid 74A4) revealed differences in genome structure and content between Antarctic surface water and temperate deepwater archaea. Analysis of the predicted gene products encoded by the 74A4 sequence and those derived from a temperate, deepwater planktonic crenarchaeote (fosmid 4B7) revealed many typical archaeal proteins but also several proteins that so far have not been detected in archaea. The unique fraction of marine archaeal genes included, among others, those for a predicted RNA-binding protein of the bacterial cold shock family and a eukaryote-type Zn finger protein. Comparison of closely related archaea originating from a single population revealed significant genomic divergence that was not evident from 16S rRNA sequence variation. The data suggest that considerable functional diversity may exist within single populations of coexisting microbial strains, even those with identical 16S rRNA sequences. Our results also demonstrate that genomic approaches can provide high-resolution information relevant to microbial population genetics, ecology, and evolution, even for microbes that have not yet been cultivated. Article in Journal/Newspaper Antarc* Antarctic ASM Journals (American Society for Microbiology) Antarctic Pacific Applied and Environmental Microbiology 68 1 335 345 |
institution |
Open Polar |
collection |
ASM Journals (American Society for Microbiology) |
op_collection_id |
crasmicro |
language |
English |
description |
ABSTRACT Planktonic crenarchaeotes are present in high abundance in Antarctic winter surface waters, and they also make up a large proportion of total cell numbers throughout deep ocean waters. To better characterize these uncultivated marine crenarchaeotes, we analyzed large genome fragments from individuals recovered from a single Antarctic picoplankton population and compared them to those from a representative obtained from deeper waters of the temperate North Pacific. Sequencing and analysis of the entire DNA insert from one Antarctic marine archaeon (fosmid 74A4) revealed differences in genome structure and content between Antarctic surface water and temperate deepwater archaea. Analysis of the predicted gene products encoded by the 74A4 sequence and those derived from a temperate, deepwater planktonic crenarchaeote (fosmid 4B7) revealed many typical archaeal proteins but also several proteins that so far have not been detected in archaea. The unique fraction of marine archaeal genes included, among others, those for a predicted RNA-binding protein of the bacterial cold shock family and a eukaryote-type Zn finger protein. Comparison of closely related archaea originating from a single population revealed significant genomic divergence that was not evident from 16S rRNA sequence variation. The data suggest that considerable functional diversity may exist within single populations of coexisting microbial strains, even those with identical 16S rRNA sequences. Our results also demonstrate that genomic approaches can provide high-resolution information relevant to microbial population genetics, ecology, and evolution, even for microbes that have not yet been cultivated. |
format |
Article in Journal/Newspaper |
author |
Béjà, Oded Koonin, Eugene V. Aravind, L. Taylor, Lance T. Seitz, Heidi Stein, Jefferey L. Bensen, Daniel C. Feldman, Robert A. Swanson, Ronald V. DeLong, Edward F. |
spellingShingle |
Béjà, Oded Koonin, Eugene V. Aravind, L. Taylor, Lance T. Seitz, Heidi Stein, Jefferey L. Bensen, Daniel C. Feldman, Robert A. Swanson, Ronald V. DeLong, Edward F. Comparative Genomic Analysis of Archaeal Genotypic Variants in a Single Population and in Two Different Oceanic Provinces |
author_facet |
Béjà, Oded Koonin, Eugene V. Aravind, L. Taylor, Lance T. Seitz, Heidi Stein, Jefferey L. Bensen, Daniel C. Feldman, Robert A. Swanson, Ronald V. DeLong, Edward F. |
author_sort |
Béjà, Oded |
title |
Comparative Genomic Analysis of Archaeal Genotypic Variants in a Single Population and in Two Different Oceanic Provinces |
title_short |
Comparative Genomic Analysis of Archaeal Genotypic Variants in a Single Population and in Two Different Oceanic Provinces |
title_full |
Comparative Genomic Analysis of Archaeal Genotypic Variants in a Single Population and in Two Different Oceanic Provinces |
title_fullStr |
Comparative Genomic Analysis of Archaeal Genotypic Variants in a Single Population and in Two Different Oceanic Provinces |
title_full_unstemmed |
Comparative Genomic Analysis of Archaeal Genotypic Variants in a Single Population and in Two Different Oceanic Provinces |
title_sort |
comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces |
publisher |
American Society for Microbiology |
publishDate |
2002 |
url |
http://dx.doi.org/10.1128/aem.68.1.335-345.2002 https://journals.asm.org/doi/pdf/10.1128/AEM.68.1.335-345.2002 |
geographic |
Antarctic Pacific |
geographic_facet |
Antarctic Pacific |
genre |
Antarc* Antarctic |
genre_facet |
Antarc* Antarctic |
op_source |
Applied and Environmental Microbiology volume 68, issue 1, page 335-345 ISSN 0099-2240 1098-5336 |
op_rights |
https://journals.asm.org/non-commercial-tdm-license |
op_doi |
https://doi.org/10.1128/aem.68.1.335-345.2002 |
container_title |
Applied and Environmental Microbiology |
container_volume |
68 |
container_issue |
1 |
container_start_page |
335 |
op_container_end_page |
345 |
_version_ |
1802643698645729280 |