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Marine Ecology Progress Series

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MEPS 316:23-33 (2006)  -  doi:10.3354/meps316023

Gene diversity and organization in rbcL-containing genome fragments from uncultivated Synechococcus in the Gulf of Mexico

David E. John1, Boris Wawrik2, F. Robert Tabita3, John H. Paul1,*

1College of Marine Science, University of South Florida, 140 7th Avenue S, St. Petersburg, Florida 33701, USA
2Biotechnology Center for Agriculture and the Environment, Foran Hall, Cook College, Rutgers—The State University of New Jersey, 59 Dudley Road, New Brunswick, New Jersey 08901, USA
3Department of Microbiology and Plant Molecular Biology/Biotechnology Program, The Ohio State University, Columbus, Ohio 43210, USA
*Corresponding author. Email:

ABSTRACT: Factors controlling phytoplankton distribution and activity in the marine environment are often poorly understood. Knowledge of genomic content and organization may aid in understanding these processes. To this end, bulk environmental DNA was extracted from Gulf of Mexico seawater and cloned into a bacterial artificial chromosome (BAC) vector to generate a library of 3000 large-insert clones. This library was probed for various types of RubisCO gene (rbcL); 8 rbcL-containing clones (20 to 73 kb in size) were detected and sequenced. rbcL sequences indicated that they originated from marine α-Synechococcus spp. Genomic organization was highly similar to that of the sequenced genome of Synechococcus sp. strain WH 8102 in the region surrounding rbcL. Several differences from known α-Synechococcus were also observed, including putative monoamine oxidase and amino acid transport genes, and electron transport, photosynthesis and hypothetical protein genes similar to those of Prochlorococcus spp. (i.e. flavodoxin, thioredoxin reductase and iron-stress-induced chlorophyll-binding proteins). These findings indicate that the order and composition of the carbon fixation operon (cbbX to ccmK) is highly conserved in α-Synechococcus, while adjacent genomic composition indicates expanded metabolic capabilities obtained from gene-transfer events with Prochlorococcus spp. and other cyanobacteria.

KEY WORDS: Metagenomics · Synechococcus · rbcL · Carbon fixation · Monoamine oxidase · Iron stress · isiA · Chlorophyll-binding proteins

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