A main objective of the proposal was to Genomic explore the diversity of the Asgard archaea: As part of WP1 we obtained several samples of mostly anaerobic sediments that were screened using 16S rRNA primers to capture the microbial diversity that was present. We found that marine sediments from Aarhus Bay generally contained the highest diversity and relative abundances, and we decided to focus on these sediments for follow up analyses. This choice was also practical, as it was relatively easy to obtain samples via our collaborators at Aarhus University (Denmark).
Next, we used genome-resolved metagenomics of Asgard archaeain order to study their genomic content, and to perform phylogenomic analyses. We chose a number of samples that were enriched in Asgard archaea for metagenomic sequencing (WP2). Using deep sequencing with both short and long read technologies, we managed to generate several high quality draft Asgard archaeal genomes (MAGs) that were included in follow up phylogenomic analyses. Part of this work was published in scientific journals (e.g. Eme et al 2023, Nature; Tamarit et al 2022, Nature Microbiology).
Subsequently, we used the generated genomic data of Asgard archaea, supplemented with publicly available data, to build a phylogenomic dataset that was analysed to determine the phylogenetic position of eukaryotes in the tree of life. Using a variety of phylogenomic approaches we established that eukaryotes are embedded within the Heimdallarchaeia, as a sister group of the Hodarchaeales. Furthermore, we used ancestral reconstruction analyses to trace the evolution of gene content across the Asgard archaea, including the lineage leading towards the eukaryotes. We found that the Asgard archaeal ancestor of eukaryotes (LAECA, see DoA) likely was an mesophilic, anaerobic heterotroph, and that the evolution of its gene content potentially showed traces of eukaryotic like-processes (e.g. elevated gene duplication rates). The results of these analyses were published in the scientific journal Nature (Eme et al, 2023, Nature).
Next, we aimed to establish an in situ cultivation approach to detect potential syntrophic interactions between Asgard archaea and their anticipated syntrophic partners. Rather then the original plan, in which we planned to use hydrogel beads and which turned out challenging, we decided to focus on developing a microfluidics-based cultivation approach, alongside more traditional enrichment cultivation techniques. The microfluidics-based cultivation approach was established up to a proof of principle stage, and will be further optimized, after which it will be published. Using traditional enrichment cultivation techniques, we managed to obtain several enrichments of Asgard archaeal lineages. The established cultivation approach also resulted in the enrichment of a novel methanogenic lineage outside of the Euryarchaeota (Wu et al, 2024, Nature).
Finally, we managed to obtain preliminary 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. We are sill in the process of optimising these analyses, which are extremely challenging due to the slow growth speed of these organisms. Yet, we hope to conclude and publish the results of these analyses within the coming years.
