Aquatic Sciences Meeting, Albuquerque 2001

SS04 Environmental Microbial Genomics (Environmental and Disciplinary Connections)

Date: Wednesday, February 14, 2001, Time: 10:45:00 AM

Location: Brazos

Wawrik, B, , University of South Florida, St. Petersburg, USA, bwawrik@seas.marine.usf.edu

Paul, J, H, University of South Florida, St. Petersburg, USA,

Campbell, L, , Texas A & M University, College Station, USA, lcampbell@ocean.tamu.edu

Sequence Analysis of Transcriptionally-active Carbon Fixation Genes Indicates Near-Surface and Sub-Surface Clades of Prochlorococcus in the Gulf of Mexico

Cloning and amplification strategies form the molecular fishing poles that microbial ecologists use to catch the microbes (or snippets of their genomes) to interrogate the diversity and structure of aquatic microbial communities. Shotgun cloning into BAC or PAC systems and the more traditional PCR-based amplification are the fishing poles currently used in such studies. We have designed PCR primers to target three of the four Form I rbcL clades believed to occur in oceanic phytoplankton. Analysis of one station in the Gulf of Mexico using our Form IA/B primer set yielded 21 unique Prochlorococcus-like clones that could be divided into two subclades, twelve from the upper water column (10 to 60 m depth) and nine from greater depths (78 to 130 m). The deeper clade contained members possessing greater sequence diversity than the shallow clade. We hypothsisize that these are high light and low light adapted Prochlorococcus strains as have been previously described by physiologic studies and sequencing other loci. A low salinity plume (0-10 m depth) overlaid these waters and was characterized by a high abundance (5x104 /ml) of Synechococcus cells as determined by flow cytometry. However, no Synechococcus-like sequences were found in this plume, although high levels of Form IA transcripts were found there. Analysis of recently deposited PE-containing Synechococcus rbcL sequences in GenBank indicated differences in sequence with the FormIA/IB primer set used. These finding emphasize the inherent limitation of PCR-base methods for diversity analysis which require constant tuning of primer sets. New primer sets are being tested along with probe development for Taqman quantitation of rbcL gene expression.

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Aquatic Sciences Meeting, Albuquerque 2001

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