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PMID: 11422319 Published · ppublish English Journal Article Research Support, U.S. Gov't, Non-P.H.S.

Phylogenetic analysis of ribosomal RNA operons from uncultivated coastal marine bacterioplankton.

Environmental microbiology ·Vol. 3 ·No. 5 ·2001-05-00 ·Pages 323-31

Suzuki MT, Béjà O, Taylor LT, Delong EF

Abstract

Analyses of small subunit ribosomal RNA genes (SSU rDNAs) have significantly influenced our understanding of the composition of aquatic microbial assemblages. Unfortunately, SSU rDNA sequences often do not have sufficient resolving power to differentiate closely related species. To address this general problem for uncultivated bacterioplankton taxa, we analysed and compared sequences of polymerase chain reaction (PCR)-generated and bacterial artificial chromosome (BAC)-derived clones that contained most of the SSU rDNAs, the internal transcribed spacer (ITS) and the large subunit ribosomal RNA gene (LSU rDNA). The phylogenetic representation in the rRNA operon PCR library was similar to that reported previously in coastal bacterioplankton SSU rDNA libraries. We observed good concordance between the phylogenetic relationships among coastal bacterioplankton inferred from SSU or LSU rDNA sequences. ITS sequences confirmed the close intragroup relationships among members of the SAR11, SAR116 and SAR86 clades that were predicted by SSU and LSU rDNA sequence analyses. We also found strong support for homologous recombination between the ITS regions of operons from the SAR11 clade.

MeSH Terms

Bacteria/classification,cytology,genetics Base Sequence Cloning, Molecular DNA, Ribosomal/genetics Marine Biology Molecular Sequence Data Operon/genetics Phylogeny RNA, Ribosomal/genetics RNA, Transfer/genetics Water Microbiology

Chemicals

DNA, Ribosomal RNA, Ribosomal RNA, Transfer

Authors & Affiliations

4 authors, click to expand affiliations / ORCID

Suzuki M T

Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, CA 95039, USA.

Béjà O

Taylor L T

Delong E F

Article Info

Journal

Environmental microbiology

Abbr.

Environ Microbiol

ISSN

1462-2912

DOI

10.1046/j.1462-2920.2001.00198.x

Published

2001-05-00

Pages

323-31

Language

English

Region

England

NLM ID

100883692

Subset

Databases

GENBANK

AF268216, AF268217, AF268220, AF268221, AF268222, AF268236, AY033295, AY033296, AY033297, AY033298, AY033299, AY033300, AY033301, AY033302, AY033303, AY033304, AY033305, AY033306, AY033307, AY033308, AY033309, AY033310, AY033311, AY033312, AY033313, AY033314, AY033315, AY033316, AY033317, AY033318, AY033319, AY033320, AY033321, AY033322, AY033323, AY033324, AY033325, AY033326, AY033327, AY033328

External Links

PubMed source DOI: 10.1046/j.1462-2920.2001.00198.x View journal details

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Phylogenetic analysis of ribosomal RNA operons from uncultivated coastal marine bacterioplankton.

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