Microorganisms (Bacteria, Archaea, and viruses) are key mediators in nearly all of the planet’s elemental cycles. However, our understanding of the ecological roles of many groups of microbes has been hampered by low-resolution analytical approaches to studying the staggering diversity present in nature. As a result the tree of life is full of branches, which remain undiscovered, and those, which have only been identified in single-gene sequencing surveys. This is a fundamental gap in our understanding of biology. Filling in the genomic gaps in the tree of life will provide a rich context to understand the evolution of life on the planet and will provide us with a genetic understanding of how microbial communities drive biogeochemical cycles.
Recent advances in DNA sequencing technologies and computational analyses have made it possible to reconstruct the genomes and transcriptomes of uncultured natural populations. The Baker lab has been involved in the development and implementation of environmental omics since the beginning. I was involved in the first metaproteomic study of a microbial community and have been using these approaches to track fine-scale evolutionary processes. Using these techniques we have discovered deeply branching, novel groups of microbes.
The Baker laboratory has reconstructed the genomes of hundreds of widespread, uncultured sediment microbes to understand how ecological roles are partitioned in these microbial communities. Many of the genomes belong to phyla which have no previous genomic representation. Several of these branches belong to microbes that are closely related to eukaryotes. These genomes have provided rich insights into the origin of eukaryotes.