Periodic Reporting for period 2 - PRO2EUK (Exploring Asgard archaea to illuminate the prokaryote-to-eukaryote transition)
Reporting period: 2020-12-01 to 2022-05-31
Cellular life on our planet is currently classified into three domains: Bacteria, Archaea and Eukarya. Whereas the cytological properties of Bacteria and Archaea are relatively simple, eukaryotes are characterized by a high degree of cellular complexity. The origin of the eukaryotic cell is regarded as one of the major evolutionary innovations in the history of life on our planet. Yet, the emergence of the complex and compartmentalized nature of eukaryotic cells represents a major conundrum in modern biology. The central aim of the present ERC project "PRO2EUK" is to provide new insights in the enigmatic origin and evolution of the eukaryotic cell.
The central question that is addressed in this ERC project ("How did complex (eukaryotic) life evolve?") is, in a broader context, relevant to uncovering our own origins. Humans are, together with other complex cellular life forms such as animals, plants, fungi etc, constitute the Eukarya. As such, by understanding how eukaryotic life evolved, this will also provide insights into the very beginning of the lineage in the tree fo life that eventually gave rise to the emergence of us, humans. So, eben though the central question is in essence a very fundamental one, it bears relevance to obtaining answers about our own origins - a recurring and hotly debated topic throughout human history.
The overall objectives of the present ERC project are as follows:
• To explore the diversity of the Asgard archaeal superphylum at the genomic level using a variety of cultivation-independent approaches. The obtained genomic data will form the basis for an in-depth investigation of the phylogenetic and genomic diversity of this poorly characterized group of archaea, revealing important details about their biology, metabolic capacity and ecological roles.
• To resolve the phylogenetic position of eukaryotes in the Tree of Life with respect to the improved taxonomic sampling of Asgard archaeal lineages and the use of state-of-the-art phylogenomics approaches. This analysis should reveal whether eukaryotes evolved from a particular Asgard lineage, or that eukaryotes represent a sister-group to the Asgard superphylum.
• To use state-of-the-art ancestral genome reconstruction algorithms to determine the genome content of the Asgard archaeal ancestor of eukaryotes, providing insights into its cell biology and physiology in light of eukaryogenesis.
• To perform innovative in situ culturing techniques to identify potential syntrophic interaction networks that comprise Asgard archaea. These results will be used to re-evaluate existing symbiogenic models to explain the origin of the eukaryotic cell.
• To obtain the first high-resolution images of Asgard archaeal cells using super-resolution microscopy and cryo-EM tomography techniques to provide insight in basic cell biological features of these archaea, and to infer cellular characteristics of the last common ancestor of archaea and eukaryotes.
The central question that is addressed in this ERC project ("How did complex (eukaryotic) life evolve?") is, in a broader context, relevant to uncovering our own origins. Humans are, together with other complex cellular life forms such as animals, plants, fungi etc, constitute the Eukarya. As such, by understanding how eukaryotic life evolved, this will also provide insights into the very beginning of the lineage in the tree fo life that eventually gave rise to the emergence of us, humans. So, eben though the central question is in essence a very fundamental one, it bears relevance to obtaining answers about our own origins - a recurring and hotly debated topic throughout human history.
The overall objectives of the present ERC project are as follows:
• To explore the diversity of the Asgard archaeal superphylum at the genomic level using a variety of cultivation-independent approaches. The obtained genomic data will form the basis for an in-depth investigation of the phylogenetic and genomic diversity of this poorly characterized group of archaea, revealing important details about their biology, metabolic capacity and ecological roles.
• To resolve the phylogenetic position of eukaryotes in the Tree of Life with respect to the improved taxonomic sampling of Asgard archaeal lineages and the use of state-of-the-art phylogenomics approaches. This analysis should reveal whether eukaryotes evolved from a particular Asgard lineage, or that eukaryotes represent a sister-group to the Asgard superphylum.
• To use state-of-the-art ancestral genome reconstruction algorithms to determine the genome content of the Asgard archaeal ancestor of eukaryotes, providing insights into its cell biology and physiology in light of eukaryogenesis.
• To perform innovative in situ culturing techniques to identify potential syntrophic interaction networks that comprise Asgard archaea. These results will be used to re-evaluate existing symbiogenic models to explain the origin of the eukaryotic cell.
• To obtain the first high-resolution images of Asgard archaeal cells using super-resolution microscopy and cryo-EM tomography techniques to provide insight in basic cell biological features of these archaea, and to infer cellular characteristics of the last common ancestor of archaea and eukaryotes.
WP1: Environmental samples have been collected from several locations (marine, hotspring and lake sediments), and screened for the presence of Asgard archaea. Several samples have been identified that contained high Asgard archaeal relative abundances.
WP2: Metagenomic data has been generated for several samples that were enriched with Asgard archaea, and genomes were obtained via metagenomic binning procedures. Using long-read sequencing technologies we managed to obtain a fully closed Asgard archaeal (Odinarchaeote) genome. A manuscript describing the complete Odinarchaeal genome has been submitted to Nature Microbiology, and this manuscript is currently under revision.
WP3: A phylogenomics workflow has been used to place the eukaryotes in the Tree of Life, in which an extended sampling of Asgard genomes have been included. This phylogenomics analyses resulted in pinpointing a new position of eukaryotes in the tree of life. Furthermore, we performed ancestral state reconstruction analyses in which Asgard archaeal ancestral genome content was determined. We found that, in contrast to most prokaryotes, Asgard archaea genomes evolve via elevated gene duplication rates rather than horizontal gene transfer events - a modus of genome evolution that is more in line with that of eukaryotes. A manuscript describing these findings has been submitted to Nature, and this manuscript is currently under revision.
WP4: We have established technology to perform micro-community profiling, using microfluidics technology. While this process is still being further developed, a proof of principle has been established by cultivating microbial communities in picoliter droplets, and we are also in the process of establishing this in hydrogel beads.
WP5: We have established and used several methods to enrich and visualise Asgard archaea from environmental samples. Thus far, using one of these methods, CARD-FISH, we have successfully managed to visualise Lokiarchaeota and Heimdallarchaeota from marine sediments (WP5).
WP2: Metagenomic data has been generated for several samples that were enriched with Asgard archaea, and genomes were obtained via metagenomic binning procedures. Using long-read sequencing technologies we managed to obtain a fully closed Asgard archaeal (Odinarchaeote) genome. A manuscript describing the complete Odinarchaeal genome has been submitted to Nature Microbiology, and this manuscript is currently under revision.
WP3: A phylogenomics workflow has been used to place the eukaryotes in the Tree of Life, in which an extended sampling of Asgard genomes have been included. This phylogenomics analyses resulted in pinpointing a new position of eukaryotes in the tree of life. Furthermore, we performed ancestral state reconstruction analyses in which Asgard archaeal ancestral genome content was determined. We found that, in contrast to most prokaryotes, Asgard archaea genomes evolve via elevated gene duplication rates rather than horizontal gene transfer events - a modus of genome evolution that is more in line with that of eukaryotes. A manuscript describing these findings has been submitted to Nature, and this manuscript is currently under revision.
WP4: We have established technology to perform micro-community profiling, using microfluidics technology. While this process is still being further developed, a proof of principle has been established by cultivating microbial communities in picoliter droplets, and we are also in the process of establishing this in hydrogel beads.
WP5: We have established and used several methods to enrich and visualise Asgard archaea from environmental samples. Thus far, using one of these methods, CARD-FISH, we have successfully managed to visualise Lokiarchaeota and Heimdallarchaeota from marine sediments (WP5).
Pinpointing the position of eukaryotes in the tree of life (achievement in WP2) using advanced phylogenomics approaches can be considered an achievement significantly beyond the state of the art. Phylogenomic analyses aiming to resolve ancient evolutionary events, such as the origin of eukaryotes, are extremely challenging. By expanding the genomic sampling of Asgard archaeal genome space, in combination with development of a new phylogenomics pipeline, helped us to determine a new position of eukaryotes in the tree of life. Still, as we are in the progress of expanding these these analyses with a yet further expanded dataset of Asgard archaeal genome data, the obtained results might actually be fune-tuned further, providing additional insights into the elusive origin of eukaryotes.
Beyond genomics and phylogeneomics, we managed to obtain the first images of Asgard archaeal cells that seemingly point at a certain level of cellular complexity (achievement in WP5). These images were however of limited resolution, which precludes us from making inferences about the cellular ultrastructure of Asgard archaea, and, by inference, of the last common ancestor of (Asgard) archaea and eukaryotes (LAECA). In case we would be able to obtain high resolution images of Asgard archaeal cells, this could potentially provide new insights about the cellular nature of LAECA, and in particular, about whether this ancestor already displayed a certain level of cellular complexity, or if this evolved later during eukaryotic evolution.
Beyond genomics and phylogeneomics, we managed to obtain the first images of Asgard archaeal cells that seemingly point at a certain level of cellular complexity (achievement in WP5). These images were however of limited resolution, which precludes us from making inferences about the cellular ultrastructure of Asgard archaea, and, by inference, of the last common ancestor of (Asgard) archaea and eukaryotes (LAECA). In case we would be able to obtain high resolution images of Asgard archaeal cells, this could potentially provide new insights about the cellular nature of LAECA, and in particular, about whether this ancestor already displayed a certain level of cellular complexity, or if this evolved later during eukaryotic evolution.