Ramunas Stepanauskas, PhD


Senior Research Scientist
SCGC Director
Director SCGC
Phone: +1 (207) 315-2567, ext. 308
Fax: +1 (207) 315-2329
rstepanauskas@bigelow.org

For media inquiries, please contact sprofaizer@bigelow.org



Education

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

  • Untangling the Deep Genealogy of Microbial Dark Matter (NSF)
  • Ocean's dark energy: Global inventory of chemoautotrophs in the aphotic realm (NSF)
  • An Integrated Study of Energy Metabolism, Carbon Fixation, and Colonization Mechanisms in Chemosynthetic Microbial Communities at Deep-Sea Vents (NSF)
  • From genome to mechanism: understanding microbial iron metabolism in situ (NASA)

Personal Website

www.rstepanauskaslab.org

Publications

2016

  • Wasmund K, Cooper M, Schreiber L, Lloyd KG, Baker BJ, Petersen DJ, Jørgensen BB, Stepanauskas R, Reinhardt R, Schramm A, Loy A and Adrian L (2016). Single cell genome and group-specific dsrAB sequencing implicate marine members of the class Dehalococcoidia (phylum Chloroflexi) in sulfur cycling. Mbio, in press
  • Zhang Y, Sun Y, Jiao N, Stepanauskas R, Luo H (2016) Ecological genomics of CHAB-I-5, an uncultivated lineage in the globally abundant marine Roseobacter clade. Applied and Environmental Microbiology, in press
  • Eiler A, Mondav R, Sinclair L, Fernandez-Vidal L, Scofield DG, Schwientek P, Martinez-Garcia M, Torrents D, McMahon KD, Andersson SGE, Stepanauskas R, Woyke T, Bertilsson S (2016) Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria. ISME Journal, advance online publication
  • Dyksma S, Bischof K, Fuchs BM, Hoffmann K, Meier D, Meyerdierks A, Pjevac P, Probandt D, Richter M, Stepanauskas R, Mußmann M (2016) Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments. ISME Journal, advance online publication

2015

  • Ngugi DK, Blom J, Stepanauskas R, Stingl U (2015) Diversification and niche adaptations of Nitrospina-like bacteria in the polyextreme interfaces of Red Sea brines. ISME Journal, advance online publication.
  • Field EK, Sczyrba A, Lyman AE, Harris CC, Woyke T, Stepanauskas R, Emerson D (2015) Genomic insights into the uncultivated marine Zetaproteobacteria at Loihi Seamount. ISME Journal 9:857-870
  • Labonté JM, Swan BK, Poulos B, Luo H, Koren S, Hallam SJ, Sullivan MB, Woyke T, Eric Wommack K, Stepanauskas R (2015) Single-cell genomics-based analysis of virus-host interactions in marine surface bacterioplankton. ISME Journal 9:2386-2399.
  • Martijn J, Schulz F, Zaremba-Niedzwiedzka K, Viklund J, Stepanauskas R, Andersson SGE, Horn M, Guy L, Ettema TJG (2015) Single-cell genomics of a rare environmental alphaproteobacterium provides unique insights into Rickettsiaceae evolution. ISME Journal 9:2373-2385
  • Munson-McGee JH, Field EK, Bateson M, Rooney C, Stepanauskas R, Young MJ (2015) Nanoarchaeota, their Sulfolobales Host, and Nanoarchaeota virus distribution across Yellowstone National Park hot springs. Applied and Environmental Microbiology 81:7860-7868
  • Stepanauskas R (2015) Re-defining microbial diversity from its single-celled building blocks. Environmental Microbiology Reports 7:36-37
  • Stepanauskas R (2015) Wiretapping into microbial interactions by single cell genomics. Frontiers in Microbiology 6:e258.
  • Labonte JM, Field EK, Lau M, Chivian D, van Heerden E, Wommack KE, Kieft TL, Onstott TC, Stepanauskas R (2015) Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population. Frontiers in Microbiology 6:article649.
  • Youssef NH, Rinke C, Stepanauskas R, Farag I, Woyke T, Elshahed MS (2015) Insights into the metabolism, lifestyle and putative evolutionary history of the novel archaeal phylum 'Diapherotrites'. The ISME Journal 9:447–460.

2014

  • Roux S, Hawley AK, Beltran MT, Scofield M, Schwientek P, Stepanauskas R, Woyke T, Hallam SJ, Sullivan MB. 2014. Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics. eLife 3:e03125.
  • Engel P, Stepanauskas R, Moran NA. 2014. Hidden diversity in honey bee gut symbionts detected by single-cell genomics. PLoS Genetics 10:e1004596.
  • Ghylin TW, Garcia SL, Moya F, Oyserman BO, Schwientek P, Forest KT, Mutschler J, Dwulit-Smith J, Chan LK, Martinez-Garcia M, Sczyrba A, Stepanauskas R, Grossart HP, Woyke T, Warnecke F, Malmstrom R, Bertilsson S, McMahon KD. 2014. Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage. The ISME Journal, 8:2503–2516.
  • Eiler A, Zaremba-Niedzwiedzka K, Martinez-Garcia M, McMahon KD, Stepanauskas R, Andersson SGE, Bertilsson S. 2014. Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics. Environmental Microbiology 16: 2682-2698.
  • Luo H, Swan BK, Stepanauskas R, Hughes AL, Moran MA. 2014. Evolutionary analysis of a streamlined lineage of surface ocean Roseobacters. The ISME Journal, 8:1428-1439.
  • Thrash JC, Temperton B, Swan BK, Landry ZC, DeLong E, Stepanauskas R, Giovannoni SJ. 2014. Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype. The ISME Journal 8:1440-1451.
  • Kminek G, Conley C, Allen CC, Bartlett DH, Beaty DW, Benning LG, Bhartia R, Boston PJ, Duchaine C, Farmer JD, Flynn GJ, Glavin DP, Gorby Y, Hallsworth JE, Mogul R, Moser D, Buford Price P, Pukall R, Fernandez-Remolar D, Smith CL, Stedman K, Steele A, Stepanauskas R, Sun H, Vago JL, Voytek MA, Weiss PS, Westall F. 2014. Report of the workshop for life detection in samples from Mars. Life Sciences in Space Research 2:1-5.
  • Kashtan N, Roggensack SE, Rodrigue S, Thompson JW, Biller SJ, Coe A, Ding H, Marttinen P, Malmstrom R, Stocker R, Follows MJ, Stepanauskas R, Chisholm SW. 2014. Single cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus. Science 344:416-420
  • Swan BK, Chaffin M, Martinez-Garcia M, Morrison HG, Field EK, Poulton NJ, Masland DEP, Harris C, Sczyrba A, Chain PSG, Koren S, Woyke T, Stepanauskas R. 2014. Genomic and Metabolic Diversity of Marine Group I Thaumarchaeota in the Mesopelagic of Two Subtropical Gyres. PLoS ONE 9:e95380
  • Rinke C, Lee J, Nath N, Goudeau D, Thompson B, Poulton N, Ferguson E, Malmstrom R, Stepanauskas R, Woyke T. 2014. Obtaining genomes from uncultivated environmental microorganisms. Nature Protocols 9:1038-1048.
  • Wilkins MJ, Kennedy DW, Castelle CS, Field EK, Stepanauskas R, Fredrickson JK, Konopka AE. 2014. Single-cell genomics reveal metabolic strategies for growth and survival in an oligotrophic aquifer. Microbiology 160:362–372.
  • Luo H, Swan BK, Stepanauskas R, Hughes AL, Moran MA. 2014. Comparing Effective Population Sizes of Dominant Marine Alphaproteobacteria Lineages. Environmental Microbiology Reports 6:167-172.
  • Luo H, Tolar BB, Swan BK, Zhang CL, Stepanauskas R, Ann Moran M, Hollibaugh JT. 2014. Single-cell genomics shedding light on marine Thaumarchaeota diversification. The ISME Journal, 8:732-736.
  • Wasmund K, Schreiber L, Lloyd KG, Petersen DG, Schramm A, Stepanauskas R, Jørgensen BB, Adrian L. 2014. Genome sequencing of a single cell of the widely distributed marine subsurface Dehalococcoidia, phylum Chloroflexi. The ISME Journal 8: 383-397.

2013

  • Zaremba-Niedzwiedzka K, Viklund J, Zhao W, Ast J, Sczyrba A, Woyke T, McMahon KD, Bertilsson S, Stepanauskas R, Andersson SGE. 2013. Single cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade. Genome Biology 14:R130.
  • Nurk S, Bankevich A, Antipov D, Gurevich AA, Korobeynikov A, Lapidus A, Prjibelski AD, Pyshkin A, Sirotkin A, Sirotkin Y, Stepanauskas R, Clingenpeel SR, Woyke T, McLean JS, Lasken R, Tesler G, Alekseyev MA, Pevzner PA. 2013. Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. Journal of Computational Biology 20:714-737.
  • Garrity GM, Banfield J, Eisen J, van der Lelie N, McMahon T, Rusch D, Delong E, Moran MA, Currie C, Furhman J, Hallam S, Hugenholtz P, Moran N, Nelson K, Roberts R, Stepanauskas R. 2013. Prokaryotic super program advisory committee DOE joint genome institute, Walnut Creek, CA, March 27, 2012. Standards in Genomic Sciences 8:3.
  • 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.
  • 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.
  • 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.
  • Zhaxybayeva O, Stepanauskas R, Mohan NR, Papke RT. 2013. Cell sorting analysis of geographically separated hypersaline environments. Extremophiles 17:265-75.
  • Nurk S, Bankevich A, Antipov D, Gurevich A, Korobeynikov A, Lapidus A, Prjibelsky A, Pyshkin A, Sirotkin A, Sirotkin Y, Stepanauskas R, McLean J, Lasken R, Clingenpeel SR, Woyke T, Tesler G, Alekseyev MA, Pevzner PA. 2013. Assembling genomes and mini-metagenomes from highly chimeric reads. Lecture Notes in Computer Science 7821 LNBI , pp. 158-170.
  • Garcia LG, McMahon KD, Martinez-Garcia M, Srivastava A, Sczyrba A, Stepanauskas R, Grossart HP, Woyke T, Warnecke F. 2013. Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton. The ISME Journal 7:137-147.

2012

  • Stepanauskas, R. 2012. Single cell genomics: An individual look at microbes. Current Opinion in Microbiology, 15:613–620.
  • 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.
  • 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.
  • 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.

2011

  • 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.
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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

Pre-2011

  • 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
  • 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
  • Jorgensen NOG, Stepanauskas R. 2009. Biomass of pelagic fungi in Baltic rivers. Hydrobiologia 623:105-112
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • Baker BJ, Wright MS, Stepanauskas R, McArthur JV.2006. Co-selection of antibiotic and metal resistance. TRENDS In Microbiology 14:176-182
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • Stepanauskas R, Laudon H, Jorgensen NOG. 2000. High DON bioavailability in boreal streams during a spring flood. Limnology and Oceanography 45:1298-1307
  • 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
  • Stepanauskas R, Leonardson L, Tranvik LJ. 1999. Bioavailability of wetland-derived DON to freshwater and marine bacterioplankton. Limnology and Oceanography 44:1477-1485
  • 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
  • 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
  • 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
  • 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