Marine cyanobacteria contribute perhaps 25% of global primary productivity and are thus of major importance in the global carbon and other element cycles. Multiple whole genomes are now available for model isolated strains of these organisms. These have been invaluable for understanding some of the different ecological strategies of these organisms and their ability to thrive in diverse environments from the coast to the open ocean. An important issue however is to what extent does the whole genome of a model organism isolated as a single cell from an environment really reflect the total repertoire of that species (referred to as its pan-genome). Some microbes seem to be able to access a larger pool of genes through horizontal transfer of DNA from other organisms. The types of genes they are obtaining and the mechanisms by which they are obtaining them is largely unknown, but could be very important to their ability to fix carbon and compete in an ecosystem. On the other hand, some microbes seem less able to gain genes through horizontal gene transfer. This research seeks to address these issues by performing metagenomic sequencing (DNA sequencing on a pool of environmental DNA) using 454 sequencing technology. Coastal marine cyanobacteria are sorted out of the sample before sequencing, greatly increasing the information available to understand the genetic diversity of these microbes. In this way the pan-genome of two major marine cyanobacteria (Synechococcus) species will be investigated and likely lead to the discovery of novel genes in these microorganisms.
Understanding the genetic diversity of these important microbes will help us understand how they fix carbon and compete in the constantly changing marine environment. It will provide a window into how genes can move between microbes in aquatic environments, a topic of great interest because of its similarity to horizontal gene transfer and associated antibiotic resistance in human health and agriculture. The metagenomic analyses used here are in their infancy in the aquatic sciences and training scientists in this cross-disciplinary area will spur its development. The broader impact of this research thus includes the interdisciplinary research training of an undergraduate, a graduate student, and a post-doctoral fellow. Mentoring undergraduates in an environmental microbiology lab course at UCSD will also further broaden the outreach of the work.
