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Applied and Environmental Microbiology, May 2003, p. 2430-2443, Vol. 69, No. 5
0099-2240/03/$08.00+0     DOI: 10.1128/AEM.69.5.2430-2443.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.

Clade-Specific 16S Ribosomal DNA Oligonucleotides Reveal the Predominance of a Single Marine Synechococcus Clade throughout a Stratified Water Column in the Red Sea

Nicholas J. Fuller,1 Dominique Marie,2 Frédéric Partensky,2 Daniel Vaulot,2 Anton F. Post,3 and David J. Scanlan1*

Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom,1 Station Biologique de Roscoff, UMR 7127 CNRS et Université Pierre et Marie Curie, 29682 Roscoff Cedex, France,2 The H. Steinitz Marine Biology Laboratory, The Interuniversity Institute for Marine Science, Coral Beach, 88103 Eilat, Israel3

Received 14 November 2002/ Accepted 5 February 2003

Phylogenetic relationships among members of the marine Synechococcus genus were determined following sequencing of the 16S ribosomal DNA (rDNA) from 31 novel cultured isolates from the Red Sea and several other oceanic environments. This revealed a large genetic diversity within the marine Synechococcus cluster consistent with earlier work but also identified three novel clades not previously recognized. Phylogenetic analyses showed one clade, containing halotolerant isolates lacking phycoerythrin (PE) and including strains capable, or not, of utilizing nitrate as the sole N source, which clustered within the MC-A (Synechococcus subcluster 5.1) lineage. Two copies of the 16S rRNA gene are present in marine Synechococcus genomes, and cloning and sequencing of these copies from Synechococcus sp. strain WH 7803 and genomic information from Synechococcus sp. strain WH 8102 reveal these to be identical. Based on the 16S rDNA sequence information, clade-specific oligonucleotides for the marine Synechococcus genus were designed and their specificity was optimized. Using dot blot hybridization technology, these probes were used to determine the in situ community structure of marine Synechococcus populations in the Red Sea at the time of a Synechococcus maximum during April 1999. A predominance of genotypes representative of a single clade was found, and these genotypes were common among strains isolated into culture. Conversely, strains lacking PE, which were also relatively easily isolated into culture, represented only a minor component of the Synechococcus population. Genotypes corresponding to well-studied laboratory strains also appeared to be poorly represented in this stratified water column in the Red Sea.

* Corresponding author. Mailing address: Department of Biological Sciences, University of Warwick, Gibbet Hill Rd., Coventry CV4 7AL, United Kingdom. Phone: 44 24 76 528363. Fax: 44 24 76 523701. E-mail: dscanlan{at}bio.warwick.ac.uk.

Applied and Environmental Microbiology, May 2003, p. 2430-2443, Vol. 69, No. 5
0099-2240/03/$08.00+0     DOI: 10.1128/AEM.69.5.2430-2443.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.



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