Projects

Microbial organisms are not only the most diverse and abundant living entities on Earth but also the ones encompassing the largest part of life’s evolutionary radiation. Large-scale sequencing of environmental DNA showed that only a minute fraction of microbial diversity has been described and that the ‘uncultivated majority’ holds cues regarding the dawn of life and its evolution. Recent developments in sequencing technologies and bioinformatics stimulated a new ‘gold rush’ in microbial exploration by offering the means to scrutinize the microbial world through circumventing the cultivation-based bottleneck (via cultivation-independent genomics). The current technology-driven rise in genomic sampling of uncultivated prokaryotic (Bacteria and Archaea) lineages altered our

understanding of the ‘tree of life’ and brought to light unprecedented leads regarding the identity of our protoeukaryotic ancestry. Although it is generally accepted that the protoeukaryotic ancestor emerged through a symbiosis between two organisms belonging to the Archaea and Bacteria domains of life, little is known about the identity of the bacterial partner (which gave rise to mitochondria) and the evolutionary trajectories that it took after symbiogenesis. In the present Ambizione proposal I envisioned a research framework that will tackle synergistically the evolutionary history of mitochondria (i.e. the eukaryotic bacterial reminiscence) by making use of genomic data recovered from the current radiations of Eukarya and Bacteria. The project is conceived as an expansion of a prokaryote-centric view on microbial diversity and draws its essence from recent developments in sequencing technologies and phylogenomic approaches. Briefly, I will use cultivation-free approaches in order to sequence mitochondrial (mito-metagenomics) and bacterial (genome-resolved metagenomics) genomes recovered directly from aquatic environments. The mitochondrial genomic recovery will be centered on Protists (all eukaryotes that are not plants, fungi, or animals) since they encompass most of the evolutionary diversity and metabolic versatility within Eukarya and are highly underrepresented in genomic databases. The obtained genomic dataset will be used for improving the mitochondrial ‘perspective’ on the extant tree of life and uncovering evolutionary trajectories. The generated prokaryotic genomic dataset (together with the mitochondrial one) will be used to study the deep bacterial-mitochondria evolutionary history, in an attempt to identify the lineage from which the mitochondrial ancestor branched. While fundamental in nature, this research proposal is envisioned to generate knowledge that will span the fields of microbial ecology and evolutionary biology, due to its potential to offer information related to some of the most enigmatic events in the history of life: eukaryogenesis and eukaryotes diversification.