This action funds an NSF Postdoctoral Research Fellowship for FY 2010. The fellowship supports a research and training plan entitled "Understanding the genetic variety of the world's most dominant marine bacterium" for Cameron Thrash. The host institution for this research is the Oregon State University, and the sponsoring scientist is Stephen Giovannoni.
SAR11 is the abbreviation used to describe a type of globally important bacteria constituting 25-50% of the bacterial cells in the world's oceans and is therefore expected to have significant impact on global biogeochemical cycling. Variants of SAR11 are found at specific times and places in marine environments and are referred to as ecotypes. SAR11 ecotypes have observable variation in their genetic content but it is unknown how this variation defines the observed ecotypes. The proposed research aims to understand the genetic basis for these different SAR11 ecotypes by looking at the similarities and differences between multiple genomes of different SAR11 organisms. By determining the genes of these organisms, it is possible to determine if specific genes are responsible for the phenotypic differences observed for distinct ecotypes, and if genetic recombination is occurring at different rates within an ecotype compared to between ecotypes. Knowledge of the genetic basis for these different ecotypes will lead to a better understanding of how these organisms interact both with their environment (e.g., what nutrients may be required for a given ecotype) and with each other (e.g., why one ecotype dominates others in a specific place), and thus strengthen ecological theory regarding SAR11 organisms.
Broader motivation for this research is that understanding the basic ecology of marine microorganisms allows more accurate modeling of biogeochemical cycling of carbon in the world's oceans. This is of critical importance for anticipating the effects of climate change and informing policy regarding the global economy and resource allocation and use. Training objectives of this fellowship include achieving proficiency in computational biology and comparative genomics to compliment the Fellow's expertise in microbial physiology, with the ultimate goal being study of microbial contributions to marine biogeochemistry through a combined genomics and physiology approach.
The goals of this project were to elucidate the mechanisms by which SAR11 bacterioplankton create and maintain ecotype diversification. These organisms make up between 25 and 50% of the bacterial content of seawater, globally, and yet they have diversified in to subgroups that have specific spatial and temporal distribution (ecotypes) (Figure 1). Since SAR11 organisms are heterotrophs, and degrade a variety of carbon compounds for growth and survival, knowledge about the evolution of these ecotypes, and what maintains them, is essential for accurate understanding and prediction of the global carbon cycle. The comparative genomics research on SAR11 has demonstrated that many of the qualities found in the initial model organism extend to an unprecedented diversity of SAR11 strains. Small, streamlined genomes are the norm throughout the clade and conserved core genome content and synteny are higher than most other organisms (Figures 2 & 3). The presence of a conserved hypervariable region in all strains suggests that there are evolutionarily conserved mechanisms for exploring novel genetic content (Figure 4). Extended comparative genomics of SAR11 with near neighbors ought to yield valuable information about the origin of the clade and the nature of the common ancestor of Alphaproteobacteria. Strain-specific genetic variation also points to environmental adaptations which may help explain how ecotypes of SAR11 diversify and are maintained. Further research into clade-specific genetic variation should will light on these issues. Demonstration of conserved C1 metabolic pathways in a variety of SAR11 ecotypes (Figure 5) sheds new light on what types of compounds SAR11 cells utilize in the environment. The turnover of C1 compounds in ocean systems has not been extensively studied, and the prevalence of this metabolism in such a ubiquitous and dominant group as SAR11 points to new areas of research for the marine carbon cycle, and modeling carbon cycling in general. Since our research increased the overall resolution of the SAR11 clade to include at least 10 subclades with unique spatiotemporal variability, we can begin to form targeted strategies for isolating and sequencing new organisms from within the clade. Also, we can begin to correlate these new subclades with biogeochemical data to form hypotheses about specific roles these subclades serve in marine systems Knowing that diverse SAR11 strains can utilize C1 and methylated compounds will help model turnover and abiotic reaction kinetics that may involve these compounds. The extended diversity of subclade structure for SAR11 demonstrates the degrees of complexity that need to be kept in mind. In turn, this will help refine models of how CO2 is produced by marine heterotrophs like SAR11, and how CO2 is cycled though the atmosphere and the oceans overall. Better models of CO2 cycling will be able to contribute greatly to predicting the impact of global industrial activities and influence policy decisions where technologies that produce CO2 are concerned The findings also add to the debate about the hypotheses for the evolutionary history of mitochondria, and thereby, Eukaryotic cells. By showing evidence that these organelles are most closely related to free-living marine organisms (Figure 6), we can now broadly focus attention on the oceans as the site of the original endosymbiosis, and form new hypotheses regarding the circumstances surrounding this event.
