Dr. Stephen Giovannoni, Distinguished Professor

giovannoni Office 248 Nash Hall PEOPLE EDUCATION:  Former Lab Members
Phone 541-737-1835 PRODUCTS  
Email steve.giovannoni@oregonstate.edu           
Education  Ph.D., University of Oregon

Research Interests:  Ecology, evolution and systems biology of Pelagibacterales (SAR11) marine bacteria; New technologies for culturing bacteria; The marine carbon cycle.

Courses Taught:  MB 420/520 Microbial Genomics, Biogeochemistry and Diversity; MB 668 Microbial Bioinformatics and Genome Evolution.  Course taught at Bermuda Institute of Ocean SciencesMicrobial Oceanography:  The Biogeochemistry, Ecology, and Genomics of Oceanic Microbial Ecosystems.



We made a strategic decision to isolate important uncultured bacteria from nature and study them in a controlled laboratory setting where hypotheses emerging from the study of genome and metagenome sequences could be tested, refined, and modeled using the principles of systems biology.  Frequently our approach incorporates oceanographic field-studies that link laboratory discoveries to natural processes.  The work described below was made possible by the success of OSU's High Throughput Culturing Laboratory (HTCL), a facility we developed to isolate and study bacteria at the extremely low nutrient concentrations found in many natural environments.  Our work is supported by the National Science Foundation and the Marine Microbiology Initiative of the Gordon and Betty Moore Foundation.

The High-Throughput Cultivation Laboratory (HTCL):  One of our major activities is the culturing of new microbial species from the oceans and the sequencing and analysis of genomes from these strains.  We also maintain 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.  Understanding these organisms 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 giovannoni twoand small molecules for the chemical industry, agriculture, and medicine.  OSU's HTCL addresses this problem with robotics, flow cytometry and cell arraying techniques that enable us to culture and identify cells at the very low growth rates and nutrient concentrations that are typical of natural ecosystems.

Genome Streamlining:  Our current research is focused on comparative genomics and building whole-cell metabolic models for streamlined chemoheterotrophs that are testable using metabolomics strategies.  Studies of SAR11 and another marine bacterium, OM43, have led us to the surprising conclusion that metabolic versatility has been sacrificed for simplicity and small genome size in some bacterioplankton, rendering them able to use ambient nutrient resources efficiently but reducing their metabolic versatility.  Most of our research is focused on isolates from the family Pelagibacterales.  Pelagibacter genomes (1.31 -1.46 Mbp) are the smallest, and have the highest core genome conservation reported for free-living heterotrophic cells.  The essence of the genome streamlining theory is that evolutionary selection is efficient at eliminating unnecessary DNA from very large successful microbial populations.  Recently, extraordinary examples of genome reduction in SAR11 emerged.  These cells are deficient in assimilatory sulphate reduction genes, making them dependent on exogenous sources of reduced sulphur, such as 3-dimethyl-sulphoniopropionate (DMSP) or methionine, for growth.  We also found that SAR11 cells are glycine auxotrophs that use a unique and elegantly simple glycine-activated riboswitch on malate synthase to control the assimilation of the key phytoplankton metabolite glycolate through the TCA cycle into biomass.

Sargasso Sea Microbial Observatory:  We collaborate with oceanographer Dr. Craig Carlson in this long-term NSF-sponsored project that takes an ecological perspective to understanding the role of microorganisms in the oceanic carbon cycle.  Our study site in the Western Sargasso Sea (a.k.a. BATS, the Bermuda Atlantic Time-series Study) is an example of an oligotrophic ocean gyre.  Seventy percent of the oceans are gyres, regions of clear water and low productivity.  At BATS we use a variety of experimental approaches, including metagenomics, metaproteomics, fluorescence in situ hybridization and chemical measurements, to understand how microbial communities recycle organic matter.

Proteomics Mass spectrometry can identify proteins extracted from cultures or complex microbial communities, revealing the endpoints of transcription and translation--the proteomes of cells.  To study the mechanisms of microbial survival in oligotrophic oceans, and to understand their participation in the carbon cycle, we work with Drs. Mary Lipton and Richard Smith of the Pacific Northwest National Laboratory, applying capillary LC-tandem mass spectrometry to detect microbial proteins in samples collected from seawater.  We have found that mass spectra from periplasmic substrate-binding proteins account for a disproportionately large fraction of the bacterial proteins in seawater, consistent with models that predict streamlining selection and high surface to volume ratios in oligotrophic bacterioplankton.  At our study site in the Sargasso Sea, the most abundant SAR11 peptides are from periplasmic substrate-binding proteins for phosphate, amino acids, phosphonate, sugars, and spermidine. 

Environmental Metabolomics:  Marine dissolved organic matter (DOM) has so far eluded comprehensive chemical description, veiling complex interactions between abiotic and biotic processes that control this vast pool of reactive carbon.  Ongoing research is identifying specific metabolic strategies used by marine bacteria to oxidize marine DOM  and testing these ideas using metabolomics tools located in OSU's Mass Spectrometry Facility.sargasso sea


Pub Med

  • Glass, J.B., Kretz, C.B., Ganesh, S., Ranjan, P., Seston, S.L., Buck, K.N., Landing, W.M., Morton, P.L., Moffett, J.W., Giovannoni, S.J., Vergin, K.L. and Stewart, F.J.  2015.  Meta-omic signatures of microbial metal and nitrogen cycling in marine oxygen nimimum zones.  Front Microbiol.  6:998.
  • Carini, P., Van Mooy, B.A.S., Thrash, J.C., White, A.E., Zhao, Y., Campbell, E.O., Fredricks, H., and Giovannoni, S.J.  2015.  SAR11 lipid renovation in response to phosphorus starvation.  Proc. Natl. Acad. Sci., In Press.
  • Worden, A.Z., Follows, M.J., Giovannoni, S.J., Wilken, S., Zimmerman, A.E., and Keeling, P.J.  2015.  Rethinking the marine carbon cycle:  factoring in multifarious lifestyles of microbes.  Science 347 DOI:  10.1126/Science.1257594.
  • Carini, P., White, A.E., Campbell, E.O., Giovannoni, S.J.  2014.  Methane production by phosphate-starved SAR11 chemoheterotrophic marine bacteria.  Nat. Commun. 5:4346.
  • Parsons, R. J., Nelson, C. E., Carlson, C. A., Denman, C. C., Andersson, A. J., Kledzik, A. L., Vergin, K. L., McNally, S. P., Treusch, A. H., and Giovannoni, S. J.  2014. Marine bacterioplankton community turnover within seasonally hypoxic waters of a subtropical sound: Devil's Hole, Bermuda. Environ. Microb. doi:10.1111/1462-2920.12445.
  • Giovannoni, S.J., J.C. Thrash, and B. Temperton.  2014.  Implications of streamlining theory for microbial ecology.  ISME J. doi:10.1038/ismej.2014.60.
  • Cho, J.-C. and Giovannoni, S. J. 2010. Genus XLV. Robiginitalea.Cho and Giovannoni 2004, 1104VP. pp. 266-267. In N.R. Krieg, W. Ludwig, W.B. Whitman, B.P. Hedlund, B.J. Paster, J.T. Staley, N. Ward, D. Brown, and A. Parte (eds.) Bergey’s Manual of Systematic Bacteriology, 2nd Edition, Volume 4, Springer-Verlag, New York, USA.
  • Cho, J.-C. and Giovannoni, S. J. 2010. Genus I. Lentisphaera.Cho, Vergin, Morris and Giovannoni 2004a, 1005VP (Effective publication: Cho, Vergin, Morris and Giovannoni 2004b, 618.). pp. 468-470. In N.R. Krieg, W. Ludwig, W.B. Whitman, B.P. Hedlund, B.J. Paster, J.T. Staley, N. Ward, D. Brown, and A. Parte (eds.) Bergey’s Manual of Systematic Bacteriology, 2nd Edition, Volume 4, Springer-Verlag, New York, USA.
  • Carlson, C. A. and Giovannoni, S. J. (Ed.). 2009. Annual Review of Marine Science. Annual Reviews: California, USA. ISBN 978-0-8243-4501-3. 466p.
  • Rappé, M. and Giovannoni, S. J. 2003. The Uncultured Microbial Majority. Ann. Rev. Microbio. 57:369-94.
  • Giovannoni, S. J. and Rappé, M. 2000. Evolution, Diversity and Molecular Ecology of Marine Prokaryotes. p. 47-48. In Kirchman, D. (ed.) Microbial Ecology of the Oceans. John Wiley & Sons, Inc., New York.
  • Giovannoni, S. J. and Rappé, M. 1999. Microbial Diversity: It'sA New World.  The NEB Transcript. 10:1-4.
  • Giovannoni, S. J., Rappé, M., Gordon, D., Urbach, E., Suzuki, M., and Field, K. G. 1996. Ribosomal RNA and the evolution of bacterial diversity. P. 63-85. In Roberts, D. McL., Sharp, P., Alderson, G., and Collins, M. (ed.)Evolution of Microbial Life. Society for General Microbiology Symposium 54. Cambridge University Press.
  • Giovannoni, S. J., Mullins, T., and Field, K. G. 1995. Microbial diversity in marine systems: rRNA approaches to the study of unculturable microbes. In: Molecular Ecology of Aquatic Microbes, ed. Ian Joint, Springer-Verlag, Berlin-Heidelberg-New York-Tokyo.
  • Giovannoni, S. J. and Cary, S. C. 1993. Probing marine systems with ribosomal RNAs. Oceanography 6:95-104.
  • Giovannoni, S. J., Wood, N., and Huss, V. A. R. 1993. Molecular Phylogeny of Oxygenic Phototrophic Cells and Organelles from Small-Subunit Ribosomal RNA Sequences. Pages 159-170. In: Origins of Plastids,Lewin, R. A. (ed.) Chapman and Hall, NY, NY
  • Staley, J. T., Fuerst, J. L., Giovannoni, S. J., and Schlesner, H. 1991. The Order Planctomycetales and the Genera Planctomyces, Pirellula, Gemmata and Isoshaera. Pages 3710-3731. In: M. Dworkin et al. (eds.) The Prokaryotes. Volume 4, Chapter 203. Spinger-Verlag, New York.
  • Giovannoni, S. J. 1991. The Polymerase chain reaction. Pages 177-203. In: E. Stackebrandt, and M. Goodfellow (eds.) Modern Microbiological Methods: Nucleic Acids Techniques in Bacterial Systematics. John Wiley and Sons, New York.
  • Giovannoni, S. J. and Castenholz, R. W. 1989. Genus Isosphaera Pages 1959-1961. In: Krieg, N. R. and Holt, N. R. (eds.) Bergeys Manual of Systematic Bacteriology, Volume 2. Williams and Wilkins, Baltimore/London
  • Raff, R. A., Field, K. G., Olsen, G. J., Giovannoni, S. J., Ghiselin, M. T., Lane, D. J., Pace, N. R., and Raff, E. C. 1989. The phylogeny of the animal kingdom: a molecular approach. In: B. Fernholm (ed.) The Hierarchy of Life.70th Nobel Symposium, Sweden. Elsevier.
  • Turner, S., DeLong, E. F., Giovannoni, S. J., Olsen, G. J., and Pace, N. R. 1989. Phylogenetic analysis of microorganisms and natural populations. Pages 390-401. In: Cohen, Y. and Rosenberg, E. (eds.) Microbial Mats: Ecological Physiology of Benthic Microbial Communities.
  • Olsen, G. J., Lane, D. L., Giovannoni, S. J., Pace, N. R., Stahl, D. A. 1986. Microbial ecology and evolution: a ribosomal RNA approach. Ann. Rev. Microbiol. 40:337-366.