Microbial Dark Matter
A major outcome of the current environmental genomics revolution is our increasing awareness of the vastness of microbial diversity that extends beyond what has been revealed by traditional microbial cultivation. This diversity represents an enormous genetic reservoir that has been called "microbial dark matter". Because "dark matter groups" are typically outnumbered, achieving even a shallow understanding of the activities and ecological roles of these organisms is difficult. We have made significant advances into the "microbial dark matter" problem by combining focused single-cell genomics and metagenomics efforts. The central goal of this project is to assemble nearly-complete genomes from novel phylum- and class-level groups of Bacteria and Archaea and use modern genomics approaches to address questions about basic biology (e.g. DNA replication, transcription, translation, cell division) and evolution (e.g. gene sequence and gene content phylogenetics, evidence of horizontal gene transfer).
This work is possible through collaborations with many labs, including Tanja Woyke at DOE's Joint Genome Institute, Steve Quake at Stanford, and Wes Swingley at Northern Illinois and generous funding from the National Science Foundation (NSF) and the National Aeronautics and Space Administration (NASA).
This work is intended to make major advancements in microbial diversity exploration, especially major groups of microorganisms that are present in many ecosystems. We anticipate that this research will allow us to better understand the roles of microorganisms in nature and to understand why some groups of important microorganisms have defied more than 125 years of microbial cultivation studies.
July 2013, Nature paper featured on BBCJuly 2013, Press release by UNLV
July 2013, Single-cell genomics work on Science Daily
July 2013, "Microbial dark matter" research on PBS
June 2013, Hedlund lab work on phylum Atribacteria on Phys.org
November 2011, Single-cell and metagenomics work featured by NASA
September 2011, "Microbial dark matter" research featured in Science
A Hotspot for Novel Microorganisms
Great Boiling Spring, Nevada, a spring that is particularly rich in biological dark matter.