Nunoura, Takuro

Abstract Many thermophiles that are abundant in high-temperature geothermal systems have never been cultivated and are poorly understood, including deeply branching Thermoproteota. Here, we describe the genome-guided cultivation of one such organism, Calditenuis ramacidaminiphagus, and show that it has evolved a heterotrophic metabolism focused on branched-chain amino acids (BCAAs). Initially, fluorescence in situ hybridization and nanoscale secondary ion mass spectrometry (FISH-nanoSIMS) showed that Cal. ramacidaminiphagus assimilated amino acids rapidly in casamino acid-amended enrichment cultures. Genome and metaproteome analyses showed a high abundance and expression of BCAA transporter genes, suggesting a BCAA-focused metabolism. This inference was supported by the subsequent enrichment of Cal. ramacidaminiphagus in BCAA-fed cultures, reaching 2.66×106 cells/mL and 48.7% of the community, whereas it was outcompeted when polar amino acids (PAAs) were included. Metabolic reconstruction and metaproteomics suggest that BCAAs are channeled into the mevalonate pathway for lipid biosynthesis and fuel ATP production through oxidative Stickland reactions and the TCA cycle, both coupled with aerobic respiration. Ancestral state reconstructions and phylogenetic analyses of 62 Caldarchaeales genomes revealed multiple horizontal transfers of BCAA transporters to the ancestor of the genus Calditenuis. Our study highlights the crucial role of BCAAs in the early evolution and niche of this genus, and suggests a high degree of resource partitioning even within low-diversity thermophilic communities.

Marine sediments are vast, underexplored habitats and represent one of the largest carbon deposits on our planet. Microbial communities drive nutrient cycling in these sediments, but the full extent of their taxonomic and metabolic diversity remains to be explored. Here, we analysed shallow coastal and deep subseafloor sediment cores from 0.01 to nearly 600 metres below the seafloor, in the Western Pacific Region. Applying metagenomics, we identified several taxonomic clusters across all samples, which mainly aligned with depth and sediment type. Inferring functional patterns provided insights into possible ecological roles of the main microbial taxa. These included Chloroflexota, the most abundant phylum across all samples, whereby the classes Dehalococcoida and Anaerolineae dominated deep-subsurface and most shallow coastal sediments, respectively. Thermoproteota and Asgardarchaeota were the most abundant phyla among Archaea, contributing to high relative abundances of Archaea reaching over 50% in some samples. We recovered high-quality metagenome-assembled genomes for all main prokaryotic lineages and proposed names for three phyla, i.e. Tangaroaeota phyl. nov. (former RBG-13-66-14), Ryujiniota phyl. nov. (former UBA6262) and Spongiamicota phyl. nov. (former UBA8248). Metabolic capabilities across all samples ranged from aerobic respiration and photosynthesis in the shallowest sediment layers to heterotrophic carbon utilization, sulphate reduction and methanogenesis in deeper anoxic sediments. We also identified taxa with the potential to be involved in nitrogen and sulphur cycling and heterotrophic carbon utilization. In summary, this study contributes to our understanding of the taxonomic and functional diversity in benthic prokaryotic communities across marine sediments in the Western Pacific Region.

Abstract Acidimicrobiia are widely distributed in nature and suggested to be autotrophic via the Calvin–Benson–Bassham (CBB) cycle. However, direct evidence of chemolithoautotrophy in Acidimicrobiia is lacking. Here, we report a chemolithoautotrophic enrichment from a saline lake, and the subsequent isolation and characterization of a chemolithoautotroph, Salinilacustristhrix flava EGI L10123T, which belongs to a new Acidimicrobiia family. Although strain EGI L10123T is autotrophic, neither its genome nor Acidimicrobiia metagenome-assembled genomes from the enrichment culture encode genes necessary for the CBB cycle. Instead, genomic, transcriptomic, enzymatic, and stable-isotope probing data hinted at the activity of the reversed oxidative TCA (roTCA) coupled with the oxidation of sulfide as the electron donor. Phylogenetic analysis and ancestral character reconstructions of Acidimicrobiia suggested that the essential CBB gene rbcL was acquired through multiple horizontal gene transfer events from diverse microbial taxa. In contrast, genes responsible for sulfide- or hydrogen-dependent roTCA carbon fixation were already present in the last common ancestor of extant Acidimicrobiia. These findings imply the possibility of roTCA carbon fixation in Acidimicrobiia and the ecological importance of Acidimicrobiia. Further research in the future is necessary to confirm whether these characteristics are truly widespread across the clade.

Abstract In the ongoing debates about eukaryogenesis—the series of evolutionary events leading to the emergence of the eukaryotic cell from prokaryotic ancestors—members of the Asgard archaea play a key part as the closest archaeal relatives of eukaryotes 1 . However, the nature and phylogenetic identity of the last common ancestor of Asgard archaea and eukaryotes remain unresolved 2–4 . Here we analyse distinct phylogenetic marker datasets of an expanded genomic sampling of Asgard archaea and evaluate competing evolutionary scenarios using state-of-the-art phylogenomic approaches. We find that eukaryotes are placed, with high confidence, as a well-nested clade within Asgard archaea and as a sister lineage to Hodarchaeales, a newly proposed order within Heimdallarchaeia. Using sophisticated gene tree and species tree reconciliation approaches, we show that analogous to the evolution of eukaryotic genomes, genome evolution in Asgard archaea involved significantly more gene duplication and fewer gene loss events compared with other archaea. Finally, we infer that the last common ancestor of Asgard archaea was probably a thermophilic chemolithotroph and that the lineage from which eukaryotes evolved adapted to mesophilic conditions and acquired the genetic potential to support a heterotrophic lifestyle. Our work provides key insights into the prokaryote-to-eukaryote transition and a platform for better understanding the emergence of cellular complexity in eukaryotic cells.