NSF: Go Life

Searching for Microbial Dark Matter at Kidd Creek

Searching for Microbial Dark Matter at Kidd Creek.

Current interpretations of Archean carbonaceous sediments suggest the emergence of first forms of life, presumably ancestors of modern bacteria and archaea, by 3.5 billion years ago, providing ample time for genetic diversification. About 1030 of these predominantly unicellular organisms currently occupy every known suitable environment and metabolic niche on Earth. The great majority of bacterial and archaeal phylogenetic groups have not yet been obtained in pure culture and we have only recently become aware of their presence, mainly through cultivation-independent surveys of 16S rRNA genes. However, 16S rRNA gene sequences alone have limited capacity to reveal biological features of this so-called "Microbial Dark Matter" or MDM. The recent development of robust protocols and infrastructure for single cell genomics has enabled, for the first time, routine recovery of genomic blueprints from uncultured taxonomic groups, providing rich information about their evolutionary histories, metabolic potential and ecological roles. This new capacity offers an unprecedented opportunity to fill a major knowledge gap, namely a robust reconstruction of the deep genealogy of the domains of Bacteria and Archaea. The goal of this project is a large-scale, but targeted microbial single cell genomics project to lay foundation for a major overhaul of the genealogy of Bacteria and Archaea domains and our understanding of the early evolution of life. Specifically, we will a) collect and screen over ~100 environmental samples around the globe from sites that are known to possess a high frequency and diversity of candidate phyla of Bacteria and Archaea, accompanied by geochemical and geospatial data; b) generate 12,600 single amplified genomes (SAGs) from 20 of these samples; c) genomically sequence 800 candidate division SAGs; d) use this data in phylogenomic and biochemical pathway reconstruction analyses to test the following general hypotheses:

  1. The extant number of major (phylum-level) evolutionary branches of Bacteria and Archaea is significantly greater than the current consensus.
  2. Extant cellular life forms three distinct domains: Bacteria, Archaea and Eukaryotes.
  3. The early evolution of Bacteria and Archaea followed a progression of bifurcating divergences rather than a single radiation from the last universal common ancestor.
  4. Inter-domain and inter-phylum horizontal gene transfer (HGT) had a significant impact on the early evolution of Bacteria and Archaea.
  5. Evolutionary divergence in the early history of Bacteria and Archaea co-occurred with the colonization of and adaptations to novel environments.
  6. The microbially-habitable subsurface is a reservoir for early evolutionary branches of Bacteria and Archaea.