Genomes to Life Contractor-Grantee Workshop III
February 6-9, 2005, Washington, D.C.
Microbial Genomics
71
Pelagibacter ubique: A Post-Genomic Investigation of Carbon Metabolism and Photochemistry in an Extraordinarily Abundant Oceanic Bacterium
Stephen J. Giovannoni1 * (steve.giovannoni@oregonstate.edu), Lisa Bibbs2, James Tripp1, Scott Givan1, Jang-Cheon Cho1, Martha D. Stapels3, Russell Desiderio1, Mercha Podar2, Kevin L. Vergin1, Mick Noordeweir2, Michael S. Rappé4, Samuel Laney1, Douglas F. Barofsky1, and Eric Mathur2
1Oregon State University, Corvallis, OR; 2 Diversa Corporation, San Diego, CA; 3Waters Corporation, Milford, MA; and 4Hawaii Institute of Marine Biology, Kaneohe, HI
The alphaproteobacterium SAR11, now known as Pelagibacter ubique, is arguably the most abundant organism in the oceans, 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, which is approximately equivalent in size to the atmospheric carbon dioxide 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). During the sequencing of the 1.3 million base pair genome of Pelagibacter ubique, in collaboration with Diversa Corp., 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. Laser flash excitation experiments with whole, cultured cells revealed absorption transients with decay kinetics characteristic of retinylidene ion pumps, and light-dependent drops in pH provided confirmation that this PR is a light-dependent proton pump. 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. The Pelagibacter genome is almost exactly the size of the genomes of the obligate intracellular parasites R. conorii and W. pipientis, but it appears to encode a relatively complete metabolic repertoire governed by unusually simple regulatory circuits. 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..
* Presenting author
