Stephen Giovannoni

Ribosomal RNA , Molecular Phylogeny, Microbial Ecology

Research Interests:  Marine microbiology and genomics

Office:  248 Nash Hall

Courses taught:

MB 420/520 Microbial Diversity, MB/MCB 668/669 Genomics and Cellular Evolution

Degrees:  Ph.D. University of Oregon

RESEARCH

The long-term goal of our research is to understand the cellular adaptations and ecology of prokaryotes in nature by focusing on species that are abundant and important in biogeochemical cycles. Discovering new organisms is one of our major activities. We study the oceans and the oceanic lithosphere. Our work often includes both laboratory experimental work and field studies. Our major sources of funding are grants the Gordon and Betty Moore Foundation and National Science Foundation (NSF).

SAR11. We cultured one of the most abundant organisms on the planet, SAR11, which has been renamed Pelagibacter ubique. SAR11 is the dominant microorganism in the ocean surface.  Genome sequencing revealed that it has one of the smallest genomes known for a free-living cell: 1,308,759 bp.  It is one of the smallest cells known.   Using the genome sequence to guide experimental research, we are seeking to identify the sources of carbon and energy that are used by Pelagibacter.

Sargasso Sea Microbial Observatory. This collaborate with oceanographer Craig Carlson in this NSF-sponsored project. It is focused on understanding the role of microorganisms in the oceanic carbon cycle. Our study site in the Western Sargasso Sea (a.k.a. BATS) is an example of an oligotrophic ocean gyre. Seventy percent of the oceans are gyres, regions of clear water and low productivity. The amount of dissolved organic carbon in these regions of the ocean is about the same as the total amount of CO2 in the atmosphere; hence, understanding how microorganisms use this carbon is important for deciphering the global carbon cycle. We employ bioinformatics techniques to design DNA probes for ribosomal RNAs, and use them to monitor long-term changes in the ocean surface microbial community. For these measurements we use technologies such as quantitative DNA/RNA hybridization, PCR, fluorescence in situ hybridization, and image analysis. To gain insight into the complex interactions taking place within whole microbial plankton communities we study their responses to experimental manipulation. To test our ideas under more controlled conditions we use laboratory experiments study the responses of cultured bacterioplankton to environmental variables.

High-Throughput Microbial Cultivation. One of our major activities is the culturing of new microbial species, and the maintenance of a culture collection that distributes these strains and their DNA to other investigators.  Our earlier research on applications of molecular biology to microbial ecology helped establish the broad and fundamental observation that a majority of the microorganisms in natural ecosystems have not been cultured in scientific laboratories. Bacteria that have never been cultured are among the most numerous organisms on our planet. Understanding their activities is critical to the development of local and global geochemical models, as well as socially relevant issues such as bioremediation. They are also a major reservoir of natural diversity that is yielding new enzymes and small molecules for the chemical industry, agriculture, and medicine. To address this problem we devised and built a new experimental facility at OSU for studying high throughput microbial cultivation methods. This facility uses robotics, flow cytometry and cell arraying techniques to culture and identify cells at the very low growth rates and nutrient concentrations that are typical of natural ecosystems.

Genome Sequencing. Genome sequences from new microorganisms offer insight into their activities in nature, and produce hypotheses about cellular functions that can be tested in the laboratory.  With support from the Gordon and Betty Moore Foundation we are sequencing the genomes of twenty-three strains of marine bacteria.

Ocean Lithosphere. Together with geologist Martin Fisk and Oceanographer Jim Cowen we have been studying microbial life in deep ocean rocks. The goals of this research are to identify microorganisms that are associated with igneous rocks in the deep ocean, determine the source of energy they use for metabolism, and culture them for biochemical study.

SELECTED PUBLICATIONS

Pub Med

Giovannoni, S. J., H. J. Tripp, S. Givan, M. Podar, K. L. Vergin, D. Baptista, L. Bibbs, J. Eads, T. H. Richardson, M. Noordewier, M. S. Rappé, J. Short, J. C. Carrington and E. J. Mathur. 2005.  Genome streamlining in a cosmopolitan oceanic bacterium. Science 309:1242-1245.

Giovannoni, S. J., L. Bibbs, J. C. Cho, M. D. Stapels, R.  Desiderio, K. L. Vergin, M. S. Rappé, S. Laney, L. Wilhelm, H. J. Tripp, E. J. Mathur and D. F. Barofsky.  2005.  Proteorhodopsin in the ubiquitous marine bacterium SAR11. Nature 483:82-85
Cowen J., S.J. Giovannoni, H. P. Johnson, F. Kenig, D. Butterfield, M. Rappé, M. Hutnak, and P. Lam. 2003. Fluids from aging ocean crust that support microbial life. Science 299:120-123.

Morris, R.M., M. S. Rappé, S. A. Connon, K. L. Vergin, W. A. Siebold, C.A. Carlson, S. J. Giovannoni. 2002. High cellular abundance of the SAR11 bacterioplankton clade in seawater. Nature 420:806-810.

Rappé, M.S , S. Connon, S., K. L. Vergin, and S. J. Giovannoni. 2002. Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418:630-631.

Connon, S and S.J Giovannoni. 2002. High throughput methods for culturing microorganisms in very low nutrient media yield diverse new marine isolates. Appl. Environ. Microbiol . 68: 3878-3885.

Urbach, E., K. L. Vergin, L. Young, A. Morse, G. Larson and S.J. Giovannoni. 2001. Unusual bacterioplankton in Crater Lake Oregon. Limnol. Oceanog . 46:557-572.

Fisk, M. R., S.J. Giovannoni and I. Thorseth. 1998. Alteration of oceanic volcanic glass: textural evidence for microbial activity. Science 281: 978-980.

Rappé, M.S., P.F. Kemp and S.J. Giovannoni. 1997. Phylogenetic diversity of marine coastal picoplankton 16S rRNA genes cloned from the continental shelf off Cape Hatteras, N.C. Limnol. Oceanog . 42:811-826.

Giovannoni, S.J., M. S. Rappé, K. L. Vergin and N. Adair. 1996. 16S rRNA genes reveal stratified open ocean bacterioplankton populations related to the Green Non-Sulfur bacteria. Proc. Natl. Acad. Sci. U.S.A . 93:7979-7984.

Suzuki, M., and S. J. Giovannoni. 1996. Bias caused by template annealing in the amplification of 16S rRNA genes by PCR. Appl. Environ. Microbiol . 62:625-630.

Giovannoni, S. J., T. B. Britschgi, C. L. Moyer, and K. G. Field. 1990. Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60-63.

Giovannoni, S. J., E. DeLong, G. J. Olsen, and N. R. Pace. 1988. Phylogenetic group-specific oligodeoxynucleotide probes for in situ microbial identification. J. Bacteriol. 170:720-726.

Giovannoni, S. J., S. Turner, G. T. Olsen, S. Barns, D. T. Lane, and N. R. Pace. 1988. Evolutionary relationships among cyanobacteria and green chloroplasts. J. Bacteriol. 170:3584-3592