New Grants Power Single-Cell Microbial Research

Bigelow Laboratory for Ocean Sciences was recently awarded nearly $3.5 million in funding from the National Science Foundation for pioneering research in environmental single-cell genomics that may unlock the biotechnology potential of untapped genetic resources.

The first award, from NSF’s Major Research Instrumentation program, provides $2.7M of funding to expand the capabilities of Bigelow Laboratory’s Single Cell Genomics Center. SCGC is the only facility in the world that offers open-access services and educational programs in microbial single cell genomics, a powerful technology to unlock the most fundamental unit in biology: the individual cell.

The grant was led by Senior Research Scientist, and SCGC Director, Ramunas Stepanauskas, alongside fellow senior research scientists David Emerson, Nicole Poulton, and John Burns, as well as the institute's two newest senior scientists, Julia Brown and Melody Lindsay.

“Most of life on our planet consists of tiny microorganisms. They are too small individually to be seen with the naked eye, but their numbers are so staggering that, together, they dominate many planetary-scale processes,” Stepanauskas said. “But most of these microbial cells refuse to grow in the lab and cannot be studied using older research tools. Single-cell genomics opens wide opportunities for deeper understanding of the microbial world that dominates our planet by studying it at relevant scales and recovering the incredibly rich information encoded in microbial DNA.”

For the last several years, the SCGC team has been advancing new approaches to link the genomic blueprint of individual cells with their functional characteristics, one of the most fundamental but challenging questions to answer in microbiology. The new award provides funding to enhance that novel analytical system and create new possibilities for both sequencing uncultivated microbial cells, which constitutes much of the diversity of life on Earth, and connecting that genetic information to physical traits.

Purchasing new equipment and integrating it into SCGC’s current workflow will reduce analytical costs, increase efficiency, and facilitate the development of new methods to analyze environmental and microbial DNA.

“The updated system will allow for the development of new methodologies,” said Vice President for Research Beth Orcutt. “It holds the potential to fundamentally change how species-based environmental research is conducted, inform the health of monitored populations, and enable new forecasting tools.”

SCGC’s increased capacity will also help open doors for research across the institute. That includes a new project, led by Melody Lindsay, to advance fundamental knowledge about some of the lesser-known branches on the Tree of Life. The work, which includes Stepanaukas, Poulton, and Emerson, was just awarded $750,000 in funding from the NSF Division of Environmental Biology.

This new project builds on previous discoveries of abundant, yet enigmatic microbes in marine sediments, described by Lindsay and others in a study earlier this year. It will help scientists better understand the evolutionary history of several groups of bacteria and disentangle how they function and contribute to global chemical cycles. These efforts will also shed light on the biotechnology potential of these microbes, and — thanks to SCGC’s advanced technology — contribute thousands of high-quality, single-cell genomes to databases that can be leveraged by microbiologists around the world.

“It’s exciting that we can further leverage new methodologies in pursuit of discovering fundamental rules for how this life evolves and functions, thanks to the combined technologies of SCGC and the Center for Aquatic Cytometry” Lindsay said.