Ramunas Stepanauskas, PhD

Research Program Website

Research Areas

Technology for Single-Cell Microbiology

Single-cell research technology offers tremendous opportunities in a wide array of microbial studies. Our recent technology developments include improved DNA amplification, scaled-up sequencing, and integrated analyses of cell’s genome and its phenotypic properties. Among other applications, this involves collaboration with NASA scientists, were life detection technologies with extreme sensitivity are required in order to detect minute levels of microbial contaminants in space missions.

Global Ocean Reference Genomes Database (GORG)

Microbial community omics tools - meta-genomics, -transcriptomics, -proteomics and -metabolomics – have become essential sources of information in investigations of ecosystem functioning, the impact and mitigation of global environmental changes, and the exploration for new, natural products for bioenergy and biotech applications. Yet, the majority of omics data obtained from marine and other environments remain not interpretable or misinterpreted, due to the lack of adequate databases of reference genomes. Our project addresses this challenge, by utilizing scaled-up single cell genomics and complementary approaches.

Deep Genealogy of Life

Microbial life emerged more than 3.5 billion years ago and still dominates biological diversity and biogeochemical impacts on our planet. The early evolutionary events that led to basal branches of the tree of life remain poorly understood, because many of these branches lack cultured representatives. We circumvent this challenge by analyzing genomic blueprints of the uncultured microbial groups using single cell genomics and complementary research tools. Our primary focus is on the subsurface environments, which remain under-explored and may constitute a refuge for cryptic microbial lineages over planetary time scales.

Horizontal gene transfer (HGT) in natural microbial communities

HGT enables fast adaptations to environmental changes but is often overlooked in studies of microbial ecology and biogeochemistry. The specific mechanisms, rates and consequences of HGT in nature remain poorly understood, largely due to methodological limitations. By employing scaled-up single cell genomics, my group examines how HGT and other microevolutionary processes shape microbial communities in the ocean and other environments.

Dark Ocean Carbon fixation

Water below the sunlit surface layer constitutes 90% of ocean volume and harbors one of the largest microbiomes on Earth. Surprisingly, microorganisms in the dark ocean fix a globally significant amount of inorganic carbon. My group studies which microbial lineages, metabolisms and energy sources are involved in this important, yet enigmatic process.

Bioprospecting of Uncultured Microorganisms

Uncultured microbial lineages constitute over 99% of global biological diversity and hold an enormous, untapped reservoir of biochemical capabilities. Single cell genomics, combined with single cell physiology, synthetic biology and other techniques, offers a powerful approach to tap into this reservoir for novel, environmentally responsible energy solutions, bioremediation, and natural products for nutritional and medicinal uses.

Select Publications

• Munson-McGee JH, Lindsay MR, Sintes E, Brown JM, D’Angelo T, Brown J, Lubelczyk LC, Tomko P, Emerson D, Orcutt BN, Poulton NJ, Herndl GJ, Stepanauskas R (2022) Decoupling of respiration rates and abundance in marine prokaryoplankton. Nature 612:764-770
• Pachiadaki MG, Brown JM, Brown J, Bezuidt O, Berube PM, Biller SJ, Poulton NJ, Burkart MD, La Clair JJ, Chisholm SW, Stepanauskas R (2019). Charting the complexity of the marine microbiome through single cell genomics. Cell 179:1623–1635.
• Pachiadaki MG, Sintes E, Bergauer K, Brown JM, Record NR, Swan BK, Mathyer ME, Hallam S Lopez-Garcia P, Takaki Y, Nunoura T, Woyke T, Herndl GJ, Stepanauskas R (2017) Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation. Science 358:1046–1051.
• Stepanauskas R, Fergusson EA, Brown J, Poulton NJ, Tupper B, Labonté JM, Becraft ED, Brown JM, Pachiadaki MJ, Povilaitis T, Thompson BP, Mascena CJ, Bellows WK, and Lubys A (2017) Improved genome recovery and integrated cell-size analyses of individual, uncultured microbial cells and viral particles. Nature Communications 8:84
• 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
• 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
• 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

For a complete list of publications go to

Orcid