11:30 AM - 12:15 PM
[O01-02] The origin of “imperfect” us eukaryotes as seen from marine sediment archaea
★Invited Papers
Keywords:Origin of eukaryotes, Archaea, Syntrophy, Marine sediment, Amino acids
The origin of the eukaryotes remains a major enigma in biology. Current data suggest that eukaryotes may have emerged from an archaeal lineage known as “Asgard” archaea. Despite the eukaryote-like genomic features found in these archaea, the evolutionary transition from archaea to eukaryotes remains unclear due to the lack of cultured representatives and corresponding physiological insight. In this presentation, we will introduce the isolation procedure, the unique physiological properties of the first cultured representative of Asgrad archaea isolated deep marine sediment, and a new model for eukaryogenesis.
To effectively cultivate deep marine sediment microorganisms including Asgard archaea, we applied a two-stage approach: enrichment/activation of indigenous microorganisms by using a continuous-flow down-flow hanging sponge (DHS) bioreactor and subsequent selective batch cultivation. We anaerobically incubated deep-sea methane-seep sediment collected from the Nankai Trough, Japan, and fed with methane as the main energy source for more than 2,000 days at 10°C. As phylogenetically diverse uncultured microorganisms including Asgard archaea members were increasingly enriched over time, we transitioned towards further enrichment and isolation in glass tubes/vials with simple substrates and selective compounds (e.g., antibiotics). One culture amended with casamino acids and antibiotics contained a small population of a novel archaeon (designated strain MK-D1) belonging to the “Candidatus phylum Lokiarchaeota” of the Asgard archaea. Through successive in vitro cultivation combined with qPCR- and iTag-based cell density and community composition monitoring, we obtained a pure co-culture of the target archaeon and methanogenic archaeon Methanogenium– 12 years after the first sampling of deep-sea sediment.
The MK-D1 cells are small cocci (approximately 550 nm in diameter) and generally form aggregates surrounded extracellular polymer substances. Electron microscopic observations revealed that the cells contain no visible organelle-like inclusions, although eukaryote-like intracellular complexes have been proposed for Asgard archaea in previous metagenomic-based studies. Instead, MK-D1 is morphologically complex and unique protrusions that are long and often branching. The MK-D1 cells also produce many membrane vesicles. Strain MK-D1 is an extremely slow-growing, anaerobic archaeon that degrades amino acids/peptides syntrophically with sulfate-reducing bacteria and methanogenic archaea via interspecies hydrogen (and/or formate) transfer. The strain was also predicted to lack various biosynthetic machinery and depend on the above partners for biosynthesis. A survey of the publicly available Asgard archaea genomes reveals that most also encode amino acids catabolism and H2 metabolism and lack many biosynthetic pathways. Exhaustive comparative genomics revealed several genes related to amino acids catabolism and fermentative metabolism conserved across the phylum. In total, we provide the first evidence that Asgard archaea are capable of syntrophic amino acids degradation, dependent on symbiotic interactions for both catabolism and anabolism (e.g., H2, formate, and metabolite transfer), and conserve related metabolic features across the superphylum, suggesting that the Asgard archaea ancestor possessed such capacities.
Based on the MK-D1’s physiological and genomic properties, and reasoned interpretations of the existing literature, we propose a new hypothetical model for eukaryogenesis, termed the “Entangle-Engulf-Endogenize (E3) model”.
To effectively cultivate deep marine sediment microorganisms including Asgard archaea, we applied a two-stage approach: enrichment/activation of indigenous microorganisms by using a continuous-flow down-flow hanging sponge (DHS) bioreactor and subsequent selective batch cultivation. We anaerobically incubated deep-sea methane-seep sediment collected from the Nankai Trough, Japan, and fed with methane as the main energy source for more than 2,000 days at 10°C. As phylogenetically diverse uncultured microorganisms including Asgard archaea members were increasingly enriched over time, we transitioned towards further enrichment and isolation in glass tubes/vials with simple substrates and selective compounds (e.g., antibiotics). One culture amended with casamino acids and antibiotics contained a small population of a novel archaeon (designated strain MK-D1) belonging to the “Candidatus phylum Lokiarchaeota” of the Asgard archaea. Through successive in vitro cultivation combined with qPCR- and iTag-based cell density and community composition monitoring, we obtained a pure co-culture of the target archaeon and methanogenic archaeon Methanogenium– 12 years after the first sampling of deep-sea sediment.
The MK-D1 cells are small cocci (approximately 550 nm in diameter) and generally form aggregates surrounded extracellular polymer substances. Electron microscopic observations revealed that the cells contain no visible organelle-like inclusions, although eukaryote-like intracellular complexes have been proposed for Asgard archaea in previous metagenomic-based studies. Instead, MK-D1 is morphologically complex and unique protrusions that are long and often branching. The MK-D1 cells also produce many membrane vesicles. Strain MK-D1 is an extremely slow-growing, anaerobic archaeon that degrades amino acids/peptides syntrophically with sulfate-reducing bacteria and methanogenic archaea via interspecies hydrogen (and/or formate) transfer. The strain was also predicted to lack various biosynthetic machinery and depend on the above partners for biosynthesis. A survey of the publicly available Asgard archaea genomes reveals that most also encode amino acids catabolism and H2 metabolism and lack many biosynthetic pathways. Exhaustive comparative genomics revealed several genes related to amino acids catabolism and fermentative metabolism conserved across the phylum. In total, we provide the first evidence that Asgard archaea are capable of syntrophic amino acids degradation, dependent on symbiotic interactions for both catabolism and anabolism (e.g., H2, formate, and metabolite transfer), and conserve related metabolic features across the superphylum, suggesting that the Asgard archaea ancestor possessed such capacities.
Based on the MK-D1’s physiological and genomic properties, and reasoned interpretations of the existing literature, we propose a new hypothetical model for eukaryogenesis, termed the “Entangle-Engulf-Endogenize (E3) model”.