Pelagibacter ubique: A perfect engineering solution?
Stephen Giovannoni, Ph.D.
Oregon State University
Friday, April 15, 2005
Pacific Forum – 11:00 a.m.
The title, chosen for MBARI scientists, refers to evidence that extraordinary evolutionary circumstances have "streamlined" the genome of Pelagibacter ubique. Apparently, this strategy is very effective in the oceans. Pelagibacter ubique is arguably the most abundant organism in seawater, where it accounts for approximately 25% of all microbial plankton cells. During summer periods it may exceed 50% of the cells in the surface waters of temperate ocean gyres. Pelagibacter plays a key role in the oxidation of the oceanic dissolved organic carbon pool. The first cultured strains of Pelagibacter were isolated by high throughput methods for culturing cells by dilution into natural seawater media, and screening using a new cell array technology. Pelagibacter cultures are routinely propagated in autoclaved seawater, where they attain cell densities that are typical of native populations (ca. 106 cells/ml).
P. ubique has a genome of 1,308,506 bp. The pattern of genome reduction observed in P. ubique is consistent with the hypothesis of genome streamlining driven by selection acting on a very large population which resides in a very low nutrient habitat. P. ubique appears to employ an adaptive strategy different from other heterotrophic marine bacteria which have been studied by genome sequencing, and instead resembles the highly successful marine unicellular cyanobacteria in its simple metabolism and small genome size.
During the sequencing of the genome, in collaboration with Diversa Corporation, it was discovered that this organism has a proteorhodopsin (PR) gene. Liquid chromatography and tandem mass spectrometry were used to prove that the Pelagibacter PR gene is expressed in culture and that an identical protein is abundant in coastal Oregon seawater. Pelagibacter ubique is the first cultured bacterial isolate to exhibit the PR genes discovered by Bejá, Delong, and coworkers, and the only experimental choice at present for understanding how light-dependent proton pumps influence the efficiency of dissolved organic carbon (DOC) assimilation by heterotrophic bacteria in the ocean surface.
One objective of our current research is to predict the organic carbon sources used by Pelagibacter by metabolic reconstruction. Another major thrust of our research is the application of mass spectrometry methods to understand the regulatory responses of Pelagibacter to environmental variables, and to explore the proteome state of Pelagibacter cells in the oceans, so that they can be used as proxies to report the biological state of the system. Metabolic modeling of Pelagibacter is an attractive long range goal because it is one of the smallest and simplest cells known. Its remarkable success may be attributable to the integration and optimization of metabolic processes for efficiency at low nutrient fluxes.