Bigelow Laboratory for Ocean Sciences

Ocean Life, Planet Health


Stepanauskas - Publications


  1. 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, in press.
  2. Martinez-Garcia M, Brazel DM, Poulton N, Swan BK, Lluesma Gomez M, Masland D, Sieracki ME, Stepanauskas R. 2012. Unveiling in situ interactions between marine protists and bacteria through single cell sequencing. The ISME Journal 6:703-707.
  3. Martinez-Garcia M, Swan BK, Poulton NJ, Lluesma Gomez M, Masland D, Sieracki ME, Stepanauskas R. 2012. High throughput single cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton. The ISME Journal 6: 113-123.


  1. 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.
  2. 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
  3. Woyke T, Sczyrba A, Lee J, Rinke C, Tighe D, Clingenpeel S, Malmstrom R, Stepanauskas R, Cheng J-F (2011) Contamination-free single cell amplification. PLoS ONE 10:e26161
  4. Martinez-Martinez J, Poulton N, Stepanauskas R, Sieracki M, Wilson WH (2011) Targeted Sorting of Single Virus-Infected Cells of the Coccolithophore Emiliania huxleyi. Plos ONE 6:e22520
  5. Heywood JL, Sieracki ME, Bellows W, Poulton NJ, Stepanauskas R. 2011. Capturing diversity of marine heterotrophic protists: one cell at a time. The ISME Journal 5:674-684
  6. Fleming EJ, Langdon AE, Martinez-Garcia M, Stepanauskas R, Poulton N, Masland D, Emerson D. 2011. What's new is old: resolving the identity of Leptothrix ochracea using single cell genomics, pyrosequencing and FISH. PLoS ONE 6:e17769 
  7. Ghai R, Pasic L, Fernandez AB, Martin-Cuadrado AB, Mizuno CM, McMahon KD, Papke RT, Stepanauskas R, Rodriguez-Brito B, Rohwer F, Sanchez-Porro C, Ventosa A, Rodriguez-Valera F. 2011. New abundant microbial groups in aquatic hypersaline environments. Scientific Reports 1:srep00135


  1. 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 
  2. Baker-Austin C, McArthur JV, Lindell AH, Wright MS, Tuckfield RC, Gooch J, Warner L, Oliver J, Stepanauskas R. 2009. Multi-site analysis reveals widespread antibiotic resistance in the marine pathogen Vibrio vulnificus. Microbial Ecology 57:151-159 
  3. Jorgensen NOG, Stepanauskas R. 2009. Biomass of pelagic fungi in Baltic rivers. Hydrobiologia 623:105-112
  4. Baker-Austin C, McArthur JV, Tuckfield RC, Najarro M, Lindell AH, Gooch J, Stepanauskas R. 2008. Antibiotic resistance in the shellfish pathogen Vibrio parahaemolyticus isolated from the coastal water and sediment of Georgia and South Carolina, USA. Journal of Food Protection 71:2552-2558
  5. Fricke WF, Wright MS, Lindell AH, Harkins DM, Baker-Austin C, Ravel J, Stepanauskas R. 2008. Insights into the environmental resistance gene pool from the genome sequence of the multidrug-resistant environmental isolate E. coli SMS-3-5. Journal of Bacteriology 190:6779-6794
  6. Ishoey T, Woyke T, Stepanauskas R, Novotny M, Lasken RS. 2008. Genomic sequencing of single microbial cells from environmental samples. Current Opinion in Microbiology 11:198-204
  7. Kraus TEC, Bergamaschi BA, Hernes PJ, Spencer RGM, Stepanauskas R, Kendall C, Losee RF, Fujii R. 2008. Assessing the contribution of wetlands and subsided islands to dissolved organic matter and disinfection byproduct precursors in the Sacramento-San Joaquin River Delta: A geochemical approach. Organic Geochemistry 39:1302-1318
  8. Wright MS, Baker-Austin C, Lindell AH, Stepanauskas R, Stokes HW, McArthur JV. 2008. Influence of industrial contamination on mobile genetic elements: Class 1 integron abundance and gene cassette structure in aquatic bacterial communities. The ISME Journal 2:417-428
  9. Stepanauskas R, Sieracki ME. 2007. Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time. Proceedings of the National Academy of Sciences of the United States of America 104:9052-9057
  10. Eckard RS, Hernes PJ, Bergamaschi BA, Stepanauskas R, Kendall, C. 2007. Landscape scale controls on the vascular plant component of dissolved organic carbon across a freshwater delta. Geochemica et Cosmochemica Acta 71:5968-5984
  11. Stepanauskas R, Glenn TC, Jagoe CH, Tuckfield RC, Lindell AH, King CJ, McArthur JV. 2006. Co-selection for microbial resistance to metals and antibiotics in freshwater microcosms. Environmental Microbiology 8:1510-1514
  12. Wright MS, Peltier GL, Stepanauskas R, McArthur JV. 2006. Bacterial tolerances to metals and antibiotics in metal-contaminated and reference streams. FEMS Microbiology Ecology 58: 293-302
  13. Baker BJ, Wright MS, Stepanauskas R, McArthur JV.2006. Co-selection of antibiotic and metal resistance. TRENDS In Microbiology 14:176-182
  14. Stepanauskas R, Glenn TC, Jagoe CH, Tuckfield RC, Lindell AH, McArthur JV.2005. Elevated bacterioplankton tolerance to metals and antibiotics in metal-contaminated industrial environments. Environmental Science & Technology 39:3671-3678
  15. Stepanauskas R, Moran MA, Bergamaschi BA, Hollibaugh JT. 2005. Sources, bioavailability, and photoreactivity of dissolved organic carbon in the Sacramento-San Joaquin River Delta. Biogeochemistry 74:131-149
  16. Mou XZ, Moran MA, Stepanauskas R, Gonzalez JM, Hodson RE. 2005. Flow-cytometric cell sorting and subsequent molecular analyses for culture-independent identification of bacterioplankton involved in dimethylsulfoniopropionate transformations. Applied and Environmental Microbiology 71:1405-1416
  17. Stepanauskas R, Moran MA, Bergamaschi BA, Hollibaugh JT. 2003. Covariance of bacterioplankton composition and environmental variables in a temperate delta system. Aquatic Microbial Ecology 31:85-98
  18. Jorgensen NOG, Stepanauskas R, Pedersen A-GU, Hansen M, Nybroe O. 2003. Occurence and degradation of peptidoglycan in aquatic environments. FEMS Microbiology Ecology 46:269-280
  19. Kekli A, Aldahan A, Meili M, Possnert G, Buraglio N, Stepanauskas R. 2003. I-129 in Swedish rivers: distribution and sources. Science of the Total Environment 309:161-172
  20. Stepanauskas R, Jorgensen NOG, Eigaard OR, Zvikas A, Tranvik LJ, Leonardson L. 2002. Summer inputs of riverine nutrients to the Baltic Sea: Bioavailability and eutrophication relevance. Ecological Monographs 72:579-597
  21. Stepanauskas R, Laudon H, Jorgensen NOG. 2000. High DON bioavailability in boreal streams during a spring flood. Limnology and Oceanography 45:1298-1307
  22. Stepanauskas R, Farjalla VF, Tranvik LJ, Svensson JM, Esteves FA, Graneli W. 2000. Bioavailability and sources of DOC and DON in macrophyte stands of a tropical coastal lake. Hydrobiologia 436:241-248
  23. Stepanauskas R, Leonardson L, Tranvik LJ. 1999. Bioavailability of wetland-derived DON to freshwater and marine bacterioplankton. Limnology and Oceanography 44:1477-1485
  24. Stepanauskas R, Edling H, Tranvik LJ. 1999. Differential dissolved organic nitrogen availability and bacterial aminopeptidase activity in limnic and marine waters. Microbial Ecology 38:264-272
  25. Bertilsson S, Stepanauskas R, Cuadros-Hansson R, Graneli W, Wikner J, Tranvik L. 1999. Photochemically induced changes in bioavailable carbon and nitrogen pools in a boreal watershed. Aquatic Microbial Ecology 19:47-56
  26. Davidsson TE, Stepanauskas R, Leonardson L. 1997. Vertical patterns of nitrogen transformations during infiltration in two wetland soils. Applied and Environmental Microbiology 63:3648-3656
  27. Stepanauskas R, Davidsson ET, Leonardson L. 1996. Nitrogen transformations in wetland soil cores measured by N-15 isotope pairing and dilution at four infiltration rates. Applied and Environmental Microbiology 62:2345-2351