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Carbon Fixation in Dark Ocean


Photo by NASA

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.

Photo by R. Stepanauskas

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.

Photo by R. Stepanauskas

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

Dark Ocean Carbon fixation

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.

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.

Bioprospecting of Uncultured Microorganisms

Photo by NOAA

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.

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Photo from Shutterstock

Art by Glynn Gorick

Stepanauskas' Research Interests

I see the individuality of microbial cells as a major, unresolved enigma and a key to future improvements in our understanding of microbial ecology, evolution, biotechnology potential and impact on human health. Unicellular bacteria, archaea and eukaryotes constitute the oldest, the most abundant, and the most diverse forms of life on our planet. Yet, the extent, impact and underlying mechanisms of microbial diversity remain poorly understood, primarily due to technical challenges and paucity of unifying concepts that focus on discrete organisms  - individual cells. My research group develops new technologies for single cell microbiology and utilizes them, along with other research tools, to address a wide array of questions in fundamental and applied microbiology.

Apart from my research program, I also direct Bigelow Laboratory Single Cell Genomics Center.

For information about Bigelow Laboratory Single Cell Genomics Center, click here



+1.207.315.2567, ext 308 (office)

+1.207.380.4688 (mobile)

Ramunas Stepanauskas

Bigelow Laboratory for Ocean Sciences

60 Bigelow Drive

East Boothbay

Maine 04544


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