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The marine cyanobacteria of the genus Synechococcus carry out a large portion of carbon fixation in the oceans, and their genomes are among the most abundant on the planet. Together with their relatives from the genus Prochlorococcus, these photosynthetic prokaryotic cells are the predominant members of the marine phytoplankton, which is responsible for about half of the world’s photosynthesis. Therefore, the study of these organisms is of great biological and ecological interest. Although the genus Synechococcus is less abundant than Prochlorococcus on a global scale, it is more ubiquitous and more diverse. In tropical and equatorial zones, both genera co-inhabit the central zones of the oceans which are characterized by a lack of mineral elements (oligotrophy). Although it is Prochlorococcus which predominates in these regions, Synechococcus gains the upper hand as soon as the waters become richer, i.e. in upwelling zones where deep water rises to the surface, or in coastal areas. The great ubiquity of the genus Synechococcus can be explained by the fact that there are strains which are genetically and physiologically adapted to different environmental conditions; some prefer central oceanic zones and others like coastal areas which are rich in nutrients. (It is important to note that the marine Synechococci are phylogenetically very distant from the Synechocococci found in fresh water or in hydrothermal vents; they are closer to the genus Prochlorococcus with which they form a monophyletic group).
In contrast to the cells of unicellular algae such as diatoms, the cells of Prochlorococcus and Synechococcus are very small - of the order of one micron - which explains the fact that despite their abundance, they were unnoticed for a long time, and the central ocean zones were considered to be a biological desert. Measurements of chlorophyll, however, had suggested that part of the plankton was not being detected. The marine representatives of the genus Synechococcus, discovered in 1979, were the first described elements of this “picoplankton” which, as we now know, plays an important role in the function of the global ocean: although the oligotrophic regions of the oceans possess a small biomass per unit of volume compared to the rich coastal areas, on the other hand, they extend over a very large surface.
The marine strains of Synechococcus possess several remarkable characteristics:
The first genome of Synechococcus to be sequenced was in fact one of these motile marine strains: WH8102, a strain that dwell in the most nutrient-poor zones of the oceans. Its 2.4 Mb genome was sequenced by the Joint Genome Institute (Walnut Creek, California) and the analysis of this sequence has been published in Nature in August 2003, at the same time as those of the sequences of three strains of Prochlorococcus. Two members of the "Oceanic Phytoplankton" group from the Roscoff Biological Station, Frederic Partensky and Alexis Dufresne, participated in the annotation of the WH8102 genome, by describing the photosynthetic genes.
One of the reasons for sequencing WH8102 is that this strain can be manipulated genetically. All the conditions for making this a model organism are thus now fulfilled, and several groups from the Department of Energy (DOE, GTL program) in the United States are working to model carbon fixation in this cyanobacterium. The choice by DOE can be explained by the present interest in carbon sequestration in the framework of the fight against climate warming. There has been some initiatives to increase locally the primary productivity of the oceans (to which Synechococcus is a major contributor, as we have seen) via an iron “seeding” operation. Beyond these controversial ecologic applications, studies on Synechococcus have a more fundamental goal. They will produce a large quantity of various types of data (genomic, transcriptomic, proteomic, etc.), for which a Synechococcus encyclopedia will soon provide access.
However, the WH8102 strain has not been extensively characterized in physiologic terms until recently. Furthermore, this strain does not reflect the large ecophysiologic and genetic diversity of the genus. It is therefore important to sequence Synechococcus strains which are representative of other clades and other environments. A consortium of laboratories, mainly European, coordinated by Frederic Partensky at the Roscoff Biological Station, has selected two strains for this purpose: WH7803, which is a strain representative of mesotrophic waters (rich in nutrient salts) and is the best characterized physiologically as well as being easy to manipulate genetically; and RCC307, an oceanic strain which presents great phylogenetic interest because the trees obtains using the 16S RNA gene seem to indicate that it is rooted at the base of the radiation of marine cyanobacteria.
The analysis of genomic sequences should lead to an understanding of the ecophysiologic and pigmentary characteristics of the two strains, as well as their mechanisms of adaptation to their specific ecological niches. Moreover, the comparison of these genomes with that of WH8102, as well as those of the strains of Prochlorococcus and other cyanobacteria which have been sequenced, will provide information on the evolution of genomes within this very important group of photosynthetic prokaryotes. Also, the WH7803 strain, which can be easily manipulated genetically, can be used for post genomic studies with the goal of identifying, for example, genes which are specific for ecological niches. Several mutants of this strain have already been obtained by two members of the consortium. Sequence data from these two strains can therefore be used in a whole series of research projects in marine genomics, a domain which has been identified as a priority initiative by the French ministry of research (creation of the GIS “Institut de la Génomique Marine”, 2003-2006) as well as the European research authorities (the “Marine Genomics” networks of excellence that have been recently accepted in the framework of the sixth PCRD).
The Synechococcus spp. WH7803 and RCC307 sequencing project was initiated by an international consortium composed of the following laboratories: “Oceanic phytoplankton” team at the Roscoff center for oceanography studies and marine biology (UMR 7127 CNRS and University Paris 6); Cyanobacteria unit at the Pasteur Institute (URA 2172 CNRS); Ocean Genome Legacy, Beverly, United States; Department of Biological Sciences, Warwick University, Coventry, United Kingdom; The Interuniversity Institute for Marine Science, Eilat, Israël.