Principal Investigator Sallie Chisholm
Discovered only 25 years ago, Prochlorococcus is thought to be the most abundant photosynthetic cell in the oceans, often reaching 108 cells L-1 and with an estimated global population of 1027 cells. Their global abundance is due in part to the existence of physiologically and genetically distinct “ecotypes” which have different light and temperature optima for growth, and a myriad of other differences that provide opportunities for niche differentiation. All of this diversity is contained within a group that shares 97% similarity in rRNA sequence, and as such would be considered a single microbial species.
There is now a rich database of Prochlorococcus genomic information from cultures, single cell genomes, and metagenomic databases. The average genome size is about 2000 genes, 1100 of which represent the core set of genes shared by all Prochlorococcus. Each new sequenced variant contributes roughly 200 unique genes to the global “pan-genome”. This increment shows no signs of diminishing as we add new genomes, suggesting that the global gene pool of Prochlorococcus is enormous. Many of the non-core genes in Prochlorococcus are clustered in genomic ‘islands’ some of which appear to have been acquired by horizontal gene transfer, sometimes bearing the signature of phage involvement.
We are also studying Prochlorococcus as a model cell for advancing systems biology, through analysis of its transcriptome, proteome and regulatory networks. Since the cell has a very small genome, is an autotroph, and has a very streamline regulatory system, it is a ‘minimal’ living unit and this simplifies analysis and modeling.
At the other extreme of systems biology, we are studying the distribution and abundance of Prochlorococcus ecotypes in the global oceans to develop a framework for unveiling the selective pressures that have shaped their genotypic and phenotypic differences. Work is focused on two study sites: a station near Bermuda and a station near Hawaii, and we use the Global Ocean Survey metagenomic dataset to better understand the biogeography of Prochlorococcus genes. Because the ocean environment is simple, and fluid, it offers a unique opportunity to study the relationship between genomic composition and environmental parameters.