Peculiar morphology of Asgard archaeal cells close to the prokaryote-eukaryote boundary

Abstract

The emergence of complex eukaryotic cells from prokaryotic ancestors is a major enigma in the history of life. Current data suggest that Asgard archaea are the closest prokaryotic relatives of eukaryotes and have a genetic potential for cellular complexity, suggesting their key role in the evolution of eukaryotes. The Asgard archaeal order Hodarchaeales was recently proposed as the sister lineage of eukaryotes with a unique set of eukaryotic signature proteins. However, there is no microscopic evidence to show the cellular structure of these closest known archaeal relatives of eukaryotes. Here, we retrieved Hodarchaeales-affiliated full-length 16S rRNA sequences from marine sediments (Aarhus Bay, Denmark), representing 0.1% of the relative rRNA read abundance in sequence libraries, and designed new oligonucleotide probes specifically targeting their cells. We then employed catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) and imaged the labeled cells by super-resolution microscopy with appropriate controls. Hodarchaeales-affiliated cells were characterized by an elongated cell body connected to a rounded expansion at one pole with a confined central DNA localization. They were conspicuously large, with an average length of 3 µm, ranging from 1.5 to 5.2 µm. The average width was 1.1-0.8 µm in the round expansion and the cell body, respectively. The remarkable size and morphology of the detected Hodarchaeales-related cells suggest a potential for complex eukaryote-like cellular architecture in these as-yet-uncultivated Asgard archaea, which could represent a key transitional stage in eukaryogenesis.IMPORTANCEAsgard archaea played a pivotal role in the evolution of complex cellular life, as recent data revealed their close relationship to eukaryotes in the Tree of Life and a genetic repertoire suggesting intricate cellular organization. This suggests that the key elements of eukaryotic cellular complexity originated in Asgard archaea. However, visual evidence to show their cellular structure and morphological diversity remains scarce, leaving an open question of how the genetic potential for cellular complexity translates into phenotype. In this study, we report the remarkable size and unusual shape of yet-uncultivated Asgard archaeal cells, which are close to the prokaryote-eukaryote boundary. Our findings suggest a previously unknown complex cellular structure in the closest archaeal relatives of eukaryotes and could contribute to our understanding of the evolution of complex life forms.

Keywords: Asgard archaea; Hodarchaeales; cellular complexity; eukaryogenesis; fluorescence microscopy; in situ hybridization; marine sediments.

Fig 1

Phylogenetic analysis of Hodarchaeales-related 16S rRNA sequences retrieved from Aarhus Bay sediments. Maximum likelihood phylogeny of two Hodarchaeales-affiliated operational taxonomic units (red) and related Asgard archaeal 16S rRNA sequences is shown. Specificities of FISH probes are highlighted in green and red. 16S rRNA sequence of the metagenome-assembled genome CSMAG_1182 is marked with green. Hodarchaeales sequences are depicted with the bold tree branch. Nanoarchaeota sequences (gray) are used as the outgroup. Lavender circles indicate nodes receiving >95% bootstrap support (100 replications). The scale bar shows 10% nucleotide sequence divergence.

Fig 2

Visualization of Hodarchaeales-related cells in Aarhus Bay sediments using CARD-FISH. Probe names and dyes are depicted for each panel. Three representative images for the morphotypes with short (3–1.5 µm, A–C) and long (3–5 µm, D–F) cell lengths are shown. The cells were imaged in a super-resolution confocal laser scanning microscope. Maximum intensity projection of the acquired z-stack images is depicted. Z-stack images used in maximum intensity projections are shown in Fig. S1. Control experiments are included in Fig. S4. Images represent dual-labeled Hodarchaeales-related cells (n = 40) in four individual experiments. The scale bar is 1 µm.