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Courtesy of Caltech Information Science and Technology Initiative – Wierman Cray 2 Supercomputer

Grants List


 Courtesy of Armbrust Lab - assembled metagenomic DNA sequence from a marine microbial community

Oregon State University, Department of Microbiology

Lab of Stephen J. Giovannoni, Ph.D.

In support of research in the laboratory of Senior Investigator Dr. Stephen J. Giovannoni on the dynamics of a key group of marine planktonic microorganisms that require external sources of carbon for food and energy. This abundant, ecologically important group of bacteria will be studied with respect to its composition, gene and protein expression patterns, genome content, and nutritional requirements. The outcomes of this grant include a deeper understanding of how populations of these bacteria change in space and time in natural marine systems, how they have evolved to cope with low nutrient levels, and how this ubiquitous and numerically predominant group impacts marine biogeochemical cycles.

Title: Lab of Stephen J. Giovannoni, Ph.D.
Date Awarded: Sep 2008
Amount: $3,425,229
Term: 49 months
Grant ID: GBMF607.01
Funding Area: Science, Marine Microbiology Initiative

Publications as of August 2015:

  1. Carini, P., B.A.S. Van Mooy, J.C. Thrash, A.E. White, Y. Zhao, E.O. Campbell, H. Fredricks, and S.J. Giovannoni. 2015. SAR11 lipid renovation in response to phosphorus starvation.  Proc. Nat. Acad. Sci., 112(25): 7767-7772. doi: 10.1073/pnas.1505034112
  2. Worden, A.Z., M.J. Follows, S.J. Giovannoni, S. Wilken, A.E. Zimmerman, and P.J. Keeling. 2015. Rethinking the marine carbon cycle: factoring in multifarious lifestyles of microbes. Science, 347(6223). doi: 10.1126/science.1257594
  3. Carini, P., A.E. White, E.O. Campbell, and S.J. Giovannoni. 2014.  Methane production by phosphate-starved SAR11 chemoheterotrophic marine bacteria. Nature Communications, 5(4346). doi: 10.1038/ncomms5346
  4. Carini, P., E.O. Campbell, J. Morré, S.A. Sañudo-Wilhelmy, B. Temperton, S.E. Bennett, J.C. Thrash, T. Begley, and S.J. Giovannoni. 2014. Discovery of a SAR11 growth requirement for thiamin’s pyrimidine precursor and its distribution in the Sargasso Sea. ISME Journal, 8: 1727-1738. doi: 10.1038/ismej.2014.61
  5. Giovannoni, S.J. and D. Nemergut. 2014. Microbes ride the current. Science, 345(1246). doi: 10.1126/science.1259467
  6. Giovannoni, S.J., J.C. Thrash, and B. Temperton. 2014. Implications of streamlining theory for microbial ecology. ISME Journal, 8: 1553-1565.  doi: 10.1038/ismej.2014.60
  7. Parsons, R.J., C.E. Nelson, C.A. Carlson, C.C. Denman, A.J. Andersson, A.L. Kledzik, K.L. Vergin, S.P. McNally, A.H. Treusch, and S.J. Giovannoni. 2014. Marine bacterioplankton community turnover within seasonally hypoxic waters of a subtropical sound: Devil’s Hole, Bermuda. Environ. Microbiol. doi:10.1111/1462-2920.12445
  8. Thrash, J.C., B. Temperton, B.K. Swan, Z.C. Landry, T. Woyke, E.F. DeLong, R. Stepanauskas, and S.J. Giovannoni. 2013. Genome features of a deep ocean SAR11 bathytype revealed by single-cell genomics and metagenomics. ISME Journal, 7: 1322–1332. doi:10.1038/ismej.2013.32
  9. Ferla, M.P., J.C. Thrash, S.J. Giovannoni, and W.M. Patrick. 2013. New rRNA gene-based phylogenies of the Alphaproteobacteria provide perspective on major groups, mitochondrial ancestry and phylogenetic instability.  PLOS ONE. doi: 10.1371/journal.pone.0083383
  10. Giovannoni, S.J., B. Temperton, and Y. Zhao. 2013. Reply to SAR11 virus and defensive host strains (S. Våge, J.E. Storesund, T.F. Thingstad). Nature, 499: E4-5. doi: 10.1038/nature12388
  11. Landry, Z.C., S.J. Giovanonni, S.R. Quake, and P.C. Blainey. 2013. Optofluidic cell selection from complex microbial communities for single-genome analysis. Methods Enzymol., 531: 61-90. doi: 10.1016/B978-0-12-407863-5.00004-6
  12. Smith, D.P., J.C. Thrash, C.D. Nicora, M.S. Lipton, K.E. Burnum-Johnson, P. Carini, R.D. Smith, and S.J. Giovannoni. 2013. Proteomic and transcriptomic analysis of “Candidatus Pelagibacter ubique” describe the first PII-independent response to nitrogen limitation in a free-living alphaproteobacterium. mBio, 4(6): e00133-12. doi: 10.1128/mBio.00133-12
  13. Vergin, K.L., B. Done, C.A. Carlson, and S.J. Giovannoni. 2013. Spatiotemporal distributions of rare bacterioplankton populations indicate a variety of adaptive strategies in the oligotrophic ocean. Aquat. Microb. Ecol., 71(1): 1-13. doi: 10.3354/ame01661
  14. Vergin, K.L., B. Beszteri, A. Monier , J.C. Thrash, B. Temperton, A.T. Treusch, F. Kilpert, A.Z. Worden, and S.J. Giovannoni. 2013. High-resolution SAR11 ecotype dynamics at the Bermuda Atlantic Time-series Study site by phylogenetic placement of pyrosequences. ISME Journal, 7: 1322-1332. doi: 10.1038/ismej.2013.32
  15. Zhao, Y., B. Temperton, J.C. Thrash, M.S. Schwalbach, K.L. Vergin, Z.C. Landry, M. Ellisman, T. Deerinck, M.B. Sullivan, and S. J. Giovannoni. 2013. Abundant SAR11 viruses in the ocean. Nature, 494: 357-60. doi: 10.1038/nature11921
  16. Carini, P., L. Steindler, S. Beszteri, and S.J. Giovannoni. 2012. Nutrient requirements for growth of the extreme oligotroph ‘Candidatus Pelagibacter ubique’ HTCC1062 on a defined medium.  ISME Journal, 7: 592-602. doi: 10.1038/ismej.2012.122
  17. Grote, J., J.C. Thrash, M.J. Huggett, Z.C. Landry, P. Carini, S.J. Giovannoni, M.S. Rappé. 2012. Streamlining and Core Genome Conservation among Highly Divergent Members of the SAR11 Clade. mBio, 3(5): e00252-12. doi:10.1128/mBio.00252-12
  18. Giovannoni, S.J. 2012. Vitamins in the sea. Proc. Nat. Acad. Sci., 109(35): 13888-9. doi: 10.1073/pnas.1211722109
  19. Temperton, B. and Giovannoni, S.J. 2012. Metagenomics: microbial diversity through a scratched lens. Curr. Opin. Microbiol., 15: 605-612. doi:10.1016/j.mib.2012.07.001
  20. Giovannoni, S.J., and K.L. Vergin. 2012. Seasonality in ocean microbial communities. Science, 335(6069): 671-6. doi: 10.1126/science.1198078
  21. Halsey, K.H., A.E. Carter, and S.J. Giovannoni. 2011. Synergistic metabolism of a broad range of C1 compounds in the marine methylotrophic bacterium HTCC2181. Environ. Microbiol., 14(3): 630-640. doi: 10.1111/j.1462-2920.2011.02605.x
  22. Treusch, A.H., E. Demir-Hilton, K.L. Vergin, A.Z. Worden, C.A. Carlson, M.G. Donatz, R.M. Burton, and S.J. Giovannoni. 2011. Phytoplankton distribution patterns in the northwestern Sargasso Sea revealed by small subunit rRNA genes from plastids. ISME Journal, 6:481-492. doi: 10.1038/ismej.2011.117
  23. Sun, J., L. Steindler, J.C. Thrash, K.H. Halsey, D.P. Smith, A.E. Carter, Z.C. Landry, and S.J. Giovannoni. 2011. One carbon metabolism in SAR11 pelagic marine bacteria. PLOS ONE, 6(8): e23973. doi: 10.1371/journal.pone.0023973
  24. Bertagnolli, A.D., A.H. Treusch, O.U. Mason, U. Stingl, K.L. Vergin, F. Chan, B. Beszteri, and S.J. Giovannoni. 2011. Bacterial diversity in the bottom boundary layer of the intercontinental shelf of Oregon, USA. Aquat. Microb. Ecol., 64: 15-25. doi: 10.3354/ame01504
  25. Thrash, J.C., A. Boyd, M.J. Huggett, J. Grote, P. Carini, R.J. Yoder, B. Robbertse, J.W. Spatafora, M.S. Rappé, and S.J. Giovannoni. 2011. Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade. Scientific Reports, 1(13). doi: 10.1038/srep00013
  26. Steindler, L., M.S. Schwalbach, D.P. Smith, F. Chan, and S.J. Giovannoni. 2011. Energy starved Candidatus Pelagibacter ubique substitutes light-mediated ATP production for endogenous carbon respiration. PLOS ONE, 6(5): e19725. doi: 10.1371/journal.pone.0019725
  27. Wang, L., S. Chen, K.L. Vergin, S.J. Giovannoni, S.W. Chan, M.S. DeMott, K. Taghizadeh, O.X. Cordero, M. Cutler, S. Timberlake, E.J. Alm, M. Polz, J. Pinhassi, Z. Deng, and P.C. Dedon. 2011. DNA phosphorothioation is widespread and quantized in bacterial genomes. Proc. Nat. Acad. Sci., 108(7): 2963-8. doi: 10.1073/PNAS.1017261108
  28. Thrash, J.C., J.C. Cho, A.D. Bertagnolli, S. Ferriera, J. Johnson, K.L. Vergin, and S.J. Giovannoni. 2011. Genome sequence of the marine Janibacter sp. strain HTCC2649. Journal of Bacteriology, 193(2): 584-5. doi: 10.1128/JB.01298-10
  29. Kang, I., K.L. Vergin, H.M. Oh, A. Choi, S.J. Giovannoni, and J.C. Cho. 2011. Genome sequence of strain HTCC2083, a novel member of the marine Roseobacter clade. Journal of Bacteriology, 193(1): 319-320. doi: 10.1128/JB.01268-10
  30. Oh, H.-M., I. Kang, K.L. Vergin, K. Lee, S.J. Giovannoni, and J.-C. Cho. 2011. Genome sequence of Oceanicaulis sp. strain HTCC2633, isolated from the Western Sargasso Sea. Journal of Bacteriology, 193(1): 317-318. doi: 10.1128/JB.01267-10
  31. Oh, H.-M., I. Kang, K.L. Vergin, D. Kang, K.-H. Rhee, S.J. Giovannoni, and J.-C. Cho. 2011. Complete genome sequence of strain HTCC2503T of Parvularcula bermudensis, the type species of the order ‘Parvularculales’ in the Alphaproteobacteria. Journal of Bacteriology, 193(1): 305-306. doi: 10.1128/JB.01205-10
  32. Oh, H.-M., I. Kang, S.-J. Yang, Y. Jang, K.L. Vergin, S.J. Giovannoni, and J.-C. Cho. 2011. Complete genome sequence of strain HTCC2170, a novel member of the genus Maribacter in the family Flavobacteriaceae. Journal of Bacteriology, 193(1): 303-304. doi: 10.1128/JB.01207-10
  33. Sowell, S.M., P.E. Abraham, M. Shah, N.C. Verberkmoes, D.F. Barofsky, and S.J. Giovanonni. 2011. Environmental proteomics of microbial plankton in a highly productive coastal upwelling system.  ISME Journal, 5: 856-65. doi: 10.1038/ismej.2010.168
  34. Mason, O.U., T. Nakagawa, M. Rosner, J.D. Van Nostrand, J. Zhou, A. Maruyama, M.R. Fisk, and S.J. Giovannoni. 2010. First Investigation of the Microbiology of the Deepest Layer of Ocean Crust.  PLOS ONE, 5(11): e15399. doi: 10.1371/journal.pone.001539
  35. Beszteri, B., B. Temperton, S. Frickenhaus, and S.J. Giovannoni. 2010. Average genome size: a potential source of bias in comparative metagenomics. ISME Journal, 4: 1075-77. doi: 10.1038/ismej.2010.29
  36. Thrash, J.C., J.-C. Cho, K.L. Vergin, R.M. Morris, S.J. Giovannoni. 2010. Genome sequence of Lentisphaera araneosa HTCC2155T, the type species of the order Lentisphaerales in the phylum Lentisphaerae. Journal of Bacteriology, 192(11): 2938-39. doi: 10.1128/JB.00208-10
  37. Thrash, J.C., J.-C. Cho, K.L. Vergin, and S.J. Giovannoni. 2010. The genome sequences of Oceanicola granulosus HTCC2516T and O. batsensis HTCC2597T. Journal of Bacteriology, 192(13): 3549-3550. doi: 10.1128/JB.00412-10
  38. Smith, D.P., J.B. Kitner, A.D. Norbeck, T.R. Clauss, M.S. Lipton, M.S. Schwalbach, L. Steindler, C.D. Nicora, R.D. Smith, and S.J. Giovannoni. 2010. Transcriptional and translational regulatory responses to iron limitation in the globally distributed marine bacterium Candidatus Pelagibacter ubique. PLOS ONE, 5(5): e10487. doi: 10.1371/journal.pone.0010487
  39. Thrash, J.C., U. Stingl, J.-C. Cho, S. Ferriera, J. Johnson, K.L. Vergin, and S.J. Giovannoni. 2010. Genome sequence of the novel marine Gammaproteobacterium strain HTCC5015. Journal of Bacteriology, 192(14): 3838-9. doi:
  40. Thrash, J.C., J.-C. Cho, S. Ferriera, J. Johnson, K.L. Vergin, and S.J. Giovannoni. 2010. Genome sequences of strains HTCC2148 and HTCC2080 belonging to the OM60/NOR5 clade of the Gammaproteobacteria. Journal of Bacteriology, 192(14): 3842-3. doi: 10.1128/JB.00511-10
  41. Thrash, J.C., J.-C. Cho, S. Ferriera, J. Johnson, K.L. Vergin, and S.J. Giovannoni. 2010. Genome sequences of Pelagibaca bermudensis HTCC2601T and Maritimibacter alkaliphilus HTCC2654T, the type strains of two marine Roseobacter genera. Journal of Bacteriology, 192(20): 5552-5553. doi: 10.1128/JB.00873-10
  42. Kang, I., H.Y. Oh, S. Ferriera, K.L. Vergin, S.J. Giovannoni, and J.-C. Cho. 2010. Genome Sequence of the Marine Alphaproteobacterium HTCC2150, assigned to the Roseobacter clade. Journal of Bacteriology, 192(23): 6315-6316. doi: 10.1128/JB.01088-10
  43. Tripp, H.J., M.S. Schwalbach, M.M. Meyer, J.B. Kitner, R.R. Breaker, and S.J. Giovannoni. 2009. Unique glycine-activated riboswitch linked to glycine-serine auxotrophy in SAR11. Environ. Microbiol., 11: 230-238. doi: 10.1111/j.1462-2920.2008.01758.x
  44. Carlson, C.A., R. Morris, R. Parsons, A.H. Treusch, S.J. Giovannoni, and K. Vergin. 2009.  Seasonal patterns in SAR11 populations in the euphotic and mesopelagic zones of the Northwestern Sargasso Sea.  ISME Journal, 3: 283-95. doi: 10.1038/ismej.2008.117
  45. Kujawinski, E.B., K. Longnecker, N.V. Bloug, R. Del Vecchio, L. Finlay, J.B. Kitner, and S.J. Giovannoni. 2009.  Novel markers for terrestrial and marine sources in marine dissolved organic matter using ultrahigh resolution electrospray ionization Fourier-transform ion cyclotron resonance mass spectrometry. Geochem. et Cosmochem. Acta,  73: 4384-4399.
  46. Treusch, A.H., K.L. Vergin, L.A. Finlay, M.G. Donatz, R.M. Burton, C.A. Carlson, and S.J. Giovannoni. 2009. Seasonality and Vertical Structure of Microbial Communities in an Ocean Gyre. ISME Journal, 3(10): 1148-63. doi: 10.1038/ismej.2009.60
  47. Meyer, M.M., T.D. Ames, D. Smith, Z. Weinberg, M.S. Schwalbach, S.J. Giovannoni, and R.R. Breaker. 2009.  Identification of candidate structured RNAs in the marine organism ‘Candidatus Pelagibacter ubique’. BMC Genomics, 10: 268. doi: 10.1186/1471-2164-10-268
  48. Oh, H.M., S.J. Giovannoni, S. Ferriera, J. Johnson, and J.C. Cho. 2009. Complete Genome Sequence of Erythrobacter litoralis HTCC2594. Journal of Bacteriology, 191(7): 2419-20. doi: 10.1128/JB.00026-09
  49. Oh, H.M., S.J. Giovannoni, S. Ferriera, J. Johnson, and J.C. Cho. 2009. Complete Genome Sequence of Robiginitalea biformata HTCC2501. Journal of Bacteriology, 191: 7144-5. doi: 10.1128/JB.01191-09
  50. Schwalbach, M.S., H.J. Tripp, L. Steindler, D.P. Smith, and S.J. Giovannoni. 2009. The presence of the glycolysis operon in SAR11 genomes is positively correlated with ocean productivity. Environ. Microbiol., 12: 490-500. doi: 10.1111/j.1462-2920.2009.02092.x

Other grants to Oregon State University, Department of Microbiology (1)

Lab of Stephen J. Giovannoni, PhD $2,613,332 Nov 2004
All Grants