Bigelow Laboratory for Ocean Sciences

Ocean Life, Planet Health

Ramunas Stepanauskas


Senior Research Scientist
Bigelow Laboratory for Ocean Sciences
60 Bigelow Drive
P.O. Box 380
East Boothbay, ME   04544

Phone: +1-207-315-2567, ext. 308
Fax: +1-207-315-2329
Mobile: +1-207-380-4688

Curriculum Vitae

Stepanauskas CV (PDF)


Ph.D., Ecology, Lund University, Sweden, 2000
M.A.,  Limnology, Lund University, Sweden, 1995
B.A.,  Limnology, Uppsala University, Sweden, 1993

Research Interests

Stepanauskas’ research group studies biogeochemical roles, trophic interactions, evolutionary histories and biotechnological potential of microorganisms inhabiting oceans, deep subsurface, and other environments. Unicellular, microscopic bacteria, archaea and eukaryotes constitute the oldest, the most abundant, and the most diverse forms of life on our planet. Remarkably, this fundamental insight is fairly new to science, and was enabled by technological advances in culture-independent, molecular research tools. However, microbial diversity remains severely underexplored and poorly defined, due to its sheer vastness, fundamental biology differences from the better-studied multicellular organisms, technical limitations of commonly used techniques, and paucity of unifying concepts that are based on adequate field data. For example, many microbial ecology studies rely on surveys of the SSU rRNA genes, although biological features and evolutionary histories of most microorganisms carrying these genes remain completely unknown. To overcome these challenges, my colleagues and I developed robust methods and high-throughput infrastructure for microbial single cell genomics, which uncovers hereditary information at the most basic level of biological organization and provides genomic blueprints of the vast “microbial dark matter”. This novel technology, in combination with other research tools, is transforming a broad spectrum of microbial study areas. Active research projects include:

  • Global inventory of chemoautotrophs in the aphotic realm of the oceans
  • Microbial Carbon Transformations in Rock-Hosted Deep Subsurface Habitats
  • Integrated Study of Energy Metabolism, Carbon Fixation, and Colonization Mechanisms in Chemosynthetic Microbial Communities at Deep-Sea Vents
  • The antiquity, iron oxidation, and respiration on oxygen by modern Fe-oxidizing bacteria
  • Diversity of marine protists: Single cell genomics and imaging for TARA Oceans

Select Publications

  1. Swan BK, Tupper B, Sczyrba A, Lauro FM, Martinez-Garcia M, Gonzalez JM, Luo H, Wright JJ, Landry ZC, Hanson NW, Thompson B, Poulton NJ, Schwientek P, Gonzalez-Acinas S, Giovannoni SJ, Moran MA, Hallam SJ, Cavicchioli R, Woyke T, Stepanauskas R (2013) Prevalent genome streamlining and latitudinal divergence of marine bacteria in the surface ocean. PNAS 110:11463-11468.
  2. Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng J-F, Darling A, Malfatti S, Swan BK, Gies EA, Dodsworth JA, Hedlund BP, Tsiamis G, Sievert SM, Liu W-T, Eisen JA, Hallam S, Kyrpides N, Stepanauskas R, Rubin E, Hugenholtz P, Woyke T. 2013. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499:431-437. 
  3. Lloyd KG, Schreiber L, Petersen DG, Kjeldsen K, Lever MA, Stepanauskas R, Richter M, Kleindienst S, Lenk S, Schramm A, Jorgensen BB. 2013. Predominant archaea in marine sediments degrade detrital proteins. Nature 496:215-218.
  4. Stepanauskas, R. 2012. Single cell genomics: An individual look at microbes. Current Opinion in Microbiology, 15:613–620. 
  5. Martinez-Garcia M, Brazel DM, Swan BK, Arnosti C, Chain PSG, Reitenga KG, Xie G, Poulton NJ, Lluesma Gomez M, Masland DED, Thompson B, Bellows WK, Ziervogel K, Lo CC, Ahmed S, Gleasner CD, Detter CJ, Stepanauskas R. 2012. Capturing single cell genomes of active polysaccharide degraders: An unexpected contribution of Verrucomicrobia. PLoS ONE 7:e35314
  6. Swan BK, Martinez-Garcia M, Preston CM, Sczyrba A, Woyke T, Lamy D, Reinthaler T, Poulton NJ, Masland D, Lluesma Gomez M, Sieracki ME, DeLong EF, Herndl GJ, Stepanauskas R. 2011. Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean. Science 333:1296-1300.
  7. Yoon HS, Price DC, Stepanauskas R, Rajah VD, Sieracki ME, Wilson WH, Yang EC, Duffy S, Bhattacharya D. 2011 Single-cell genomics reveals organismal interactions in uncultivated marine protists. Science 332:714-717
  8. Woyke T, Xie G, Copeland A, Gonzalez JM, Han C, Kiss H, Saw J, Senin P, Yang C, Chatterji S, Cheng J-F, Eisen JA, Sieracki ME, Stepanauskas R. 2009. Assembling the marine metagenome, one cell at a time. PLoS ONE 4:e5299
  9. Stepanauskas R, Sieracki ME. 2007. Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time. PNAS 104:9052-9057

Bigelow Laboratory Single Cell Genomics Center