Archaea, and the more complex Eukaryotes, which include multicellular organisms such as fungi, plants, animals1. However, the origin of these complex eukaryotic cell types has been the subject of debate ever since. In particular, the evolutionary relationships between Eukaryotes and Archaea have become a hot topic with several studies proposing Eukaryotes are not a separate domain but rather emerged from within the Archaea.
These discussions have been fuelled by recent genomics insights into uncultured microbial lineages known as microbial dark matter. The recovery of a genome from the Deep Sea Archaeal Group (DSAG), Lokiarchaeum, has been proposed as the missing link between “Prokaryotes” and Eukaryotes2,3. However, this proposal has divided the scientific community. Critics argue that the Lokiarchaeum genome could be contaminated with unidentified eukaryotic genes, or could have acquired such genes via horizontal gene transfer from eukaryotes.
To resolve the mystery surrounding the DSAG it is essential to increase its genomic coverage. This will allow to place the archaeal genomes into a taxonomic framework, clarify possible contamination issues, and to investigate their possible role as last common eukaryotic ancestor. Therefore, the overall goal of this Fellowship is to recover archaeal genomes with culture independent techniques and to investigate the highly controversial origin of eukaryotes, and thus all multicellular life, within the archaeal domain. In brief, I propose the following aims:
(1) Archaeal taxonomic framework: Overhauling the existing taxonomy of Archaea by reconciling traditional rRNA phylogenetics with genome-based phylogeny.
(2) Phylogenomic Placement of Eukaryotes: Screening Eukaryote genomes for nucleus-encoded marker genes with homologues in the archaeal domain. This will allow inclusion of the eukaryotic domain into the taxonomic framework, which will facilitate extensive phylogenomic testing of the 2D versus 3D hypothesis.
(3) Single-cell genomics optimisation: Establishing a new ultra-high throughput SCG workflow by combining state-of-the-art technologies with advanced microfluidics, and improving the recovery of single-cell genomes with a focus on archaeal lysis and coverage.
(4) Mining archaeal dark matter: Increasing the poor genomic coverage of archaeal candidate phyla via single-cell genomics with special emphasis on DSAG and the origin of Eukaryotes.
(5) Visualization of archaeal dark matter and possible eukaryotic features: Developing probes to visualize DSAG archaea via light microscopy combined with electron microscopy.