Lab News

Single Cell-Genomics

Building on recent advances in DNA sequencing technology, microbiologists have stepped up efforts to understand whole microbial communities through deep phylogenetic surveys and metagenomic analyses. One major outcome of this environmental genomics revolution is our increasing awareness of the vastness of microbial diversity that extends well beyond what has been revealed by traditional microbial cultivation. This vast diversity represents an enormous genetic reservoir that has been called biological dark matter to call attention to our profound ignorance of these groups or, alternatively, the rare biosphere to emphasize that most novel groups are outnumbered in nature. Because dark matter groups are typically outnumbered, achieving even a shallow understanding of the activities and ecological roles of these organisms is profoundly difficult. We have overcome this problem by identifying geothermal springs in the US Great Basin (GB) that appear to be dominated by dark matter and by developing and successfully implementing a work flow to access dark matter genomes amplified from single cells isolated by using optical traps and custom-made microfluidic chips. 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). Emphasis will be put on understanding central metabolism (e.g. energy metabolism and biosynthetic pathways) to enable us to hypothesize the roles these organisms play in biogeochemical cycling of major elements (e.g. carbon and nitrogen).

This work is possible through collaborations with Steve Quake at Stanford, Jason Raymond at Arizona State, and Wes Swingley at UC Merced 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.