Shedding light on phytoplankton

Marine phytoplanktons represent approximately 1% of the Earth's photosynthetic biomass but account for nearly 50% of the net primary productivity of the biosphere. These organisms occupy the euphotic zone of the ocean—the upper, illuminated zone of aquatic ecosystems where photosynthesis is possible. High light adapted species, such as Synechococcus species, occupy the nutrient-poor, light-rich upper 25 m of the zone where white/blue-green light is available. Low light adapted species are found further down the euphotic zone where blue-violet penetrates and where the environment is nutrient rich. The high light adapted Synechococcus use phycobilisomes for light harvesting, while Prochlorococcus maintain the functionally analogous chlorophyll a2/b2 Pcbs proteins. Papers concurrently published in Nature and PNAS report analysis of the genomes of Prochlorococcus SS120, MED4, MIT9313, and Synechococcus WH8102.In the August 11 PNAS, Alexis Dufresne and colleagues at the Centre National de la Recherche Scientifique and Université Paris sequenced the genome of the low light adapted Prochlorococcus marinus SS120. The 1.7-Mbp single circularized chromosome encodes 1884 predicted orfs—1254 of these have been assigned a biological role. Comparison with other cyanobacterial genomes reveals that P. marinus SS120 has a number of genes that are either absent or underrepresented. These include protein products involved in photosynthesis, DNA repair, solute uptake, signal transduction, and environmental stress response. The organism appears to lack light receptors and a number of signaling proteins present in the majority of microbial genomes (PNAS, 100:10020-10025, August 19, 2003).P. marinus SS120 maintains a near-minimal genome. The authors suggest that the genome size is maintained by selection connected to the cell volume. "Small cell size has at least two distinct advantages for a phytoplanktonic organisms: (i) to increase the in vivo absorption coefficient by reducing the package effect and (ii) to increase the cell surface to volume ration and thereby improve nutrient uptake. Thus, P. marinus SS120 seems to be a rare case of a free-living organism for which a direct connection between fundamental characteristics of the genome and organism ecology is apparent," conclude the authors.In the 13 August Nature, Gabriele Rocap and colleagues at the University of Washington and Brian Palenik and colleagues at the University of California present comparative analyses of Synechococcus WH8102 with Prochlorococcus MED4 and MIT9313. The 1.6-Mbp genome of the high light adapted MED4 is the smallest of the oxygenic phototrophs and encodes 1716 genes. MIT9313—a low light adapted strain—has a 2.4-Mbp genome encoding 2275 genes. Although 1352 genes are present in both strains, there is a considerable number of strain-specific genes, suggesting that a proportion of the 923 MIT9313-specific genes have been lost from MED4, as nearly 50% of these are present in WH8102 (Nature, DOI:10.1038/nature01947, August 13, 2003; Nature, DOI:10.1038/nature01943, August 13, 2003).The Prochlorococcus genomes exhibit characteristics of selective genome reduction, and there are several differences that are indicative of the regions of the euphotic zone occupied by the three strains. For example, the nitrogen acquisition capabilities reflect the nitrogen species most readily available at the "preferred" light level—ammonium near the surface, nitrite at depths. WH8102 is able to utilize both nitrate, during spring upwellings, and nitrite. As a result of gene loss, MIT9313 cannot use nitrate, and MED4 cannot use nitrite or nitrate.Palenik et al. propose that WH8102 is more nutritionally versatile than the Prochlorococcus strains. Analysis suggests that Synechococcus can utilize organic nitrogen and phosphorous sources—of interest as inorganic nitrogen and phosphorous are often limiting. In addition, comparison with the Prochlorococcus strains indicates that WH8102 has been subject to a greater amount of horizontal gene transfer. Finally, the authors present evidence for a unique swimming motility mechanism for Synechococcus. "To understand the global carbon cycle, it is obvious that one must understand the physiological characteristics of marine cyanobacteria. Genomic analysis can provide all-encompassing and penetrating insights into the biochemical and physiological secrets of an organism," writes Donald Bryant of Pennsylvania State University in an accompanying PNAS commentary.

Shedding light on phytoplankton

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