2022 marks the JGI’s 25th anniversary. Over the next few months, we’ll be revisiting a number of notable achievements that showcase our collaborations and capabilities to enable great science that will help solve energy and environmental challenges.
Researchers are applying techniques such as single-cell genomics to extract genomic dark matter for sequencing and analysis from samples collected from around the world.
(Composition by Zosia Rostomian/Berkeley Lab)
In 2009, researchers at the JGI and the Bigelow Laboratory for Ocean Sciences described a novel technique to access high-quality genomic information using minute quantities of DNA derived from individual environmental cells. The proof of principle study built off earlier approaches and offered a way for researchers to study the planet’s microbial diversity, much of which remains unknown and uncultured in laboratories. Other firsts followed. The next year, the JGI team reported the first closed and finished genome derived from an uncultured bacterial single cell – a symbiont of the green sharpshooter. In 2012, single cells isolated from the microbes found in the oil plume from Deepwater Horizon oil spill led to a draft genome of the first deep-sea, oil-eating bacterium from a single cell. Several years later, the continuing single cell sequencing collaboration between the JGI and Bigelow Lab led to the identification of key microbial culprits in carbon fixation in the dark ocean. Combining single cell genomics and synthetic biology, a team studying microbial populations in oxygen minimum zones identified SAR11 bacteria as initiators of nitrogen loss in these waters.
Single cell genomics animation by Emma Schiappacasse,
former JGI Communications & Outreach intern now at Pixar
Top image: From a single bacterial cell (seen here in a glass capillary), researchers sequenced and assembled the first complete genome of an uncultured symbiont (Candidatus Sulcia muelleri DMIN). (Woyke T et al. (2010) One Bacterial Cell, One Complete Genome. PLoS ONE 5(4): e10314. https://doi.org/10.1371/journal.pone.0010314)
Bottom image: The single cell was isolated from the bacteriome of the green sharpshooter Draeculacephala minerva bacteriome. (Damon Tighe)
Perhaps most notably, JGI’s Microbial Program head Tanja Woyke and her colleagues harnessed the JGI’s single cell genomics capabilities to assemble, identify, and characterize more than 200 microbial genomes that were mapped to nearly 30 major previously uncharted branches of the tree of life. Used in tandem over the years, metagenomics and single cell genomics have afforded JGI users and the larger research community a means to access microbial lineages from a variety of environments. In 2017, the first New Lineages of Life (NeLLi) workshop was held, inviting the research community to discuss how to move from cataloging microbial diversity to experimental characterization and validation of the functional potential of these new lineages.
Relevant Links:
- JGI Release: DNA of Uncultured Organisms Sequenced Using Novel Single-Cell Approach
- JGI Primer, Spring 2010: JGI Reports First Whole Uncultured Genome
- JGI Release: Waves of Berkeley Lab Responders Deploy Omics to Track Deepwater Horizon Oil Spill Cleanup Microbes
- JGI Video: Scott Clingenpeel on single-cell genomics
- JGI Release: Boldly Illuminating Biology’s “Dark Matter”
- JGI Feature: Tanja Woyke Elected to American Academy of Microbiology
- JGI Release: Streamlining a Common Survival Strategy in Marine Microbes
- JGI Highlight: Examining a predominant Deepwater Horizon microbe
- JGI Highlight: Insights into carbon fixation in the dark ocean
- JGI Highlight: Solving Microbial “Dark Matter” With Single-Cell Genomics
- JGI Highlight: A Single-Cell Pipeline for Soil Samples
- JGI Highlight: Identifying the Microbial Culprits Initiating Oceanic Nitrogen Loss
- JGI Highlight: Expanding Fungal Diversity, One Cell at a Time
- JGI NeLLi 2021 Seminar Series