“ Sifarchaeota ,” a Novel Asgard Phylum from Costa Rican Sediment Capable of Polysaccharide Degradation and Anaerobic Methylotrophy

Abstract

The Asgard superphylum is a deeply branching monophyletic group of Archaea, recently described as some of the closest relatives of the eukaryotic ancestor. The wide application of genomic analyses from metagenome sequencing has established six distinct phyla, whose genomes encode for diverse metabolic capacities and play important biogeochemical and ecological roles in marine sediments. Here, we describe two metagenome-assembled genomes (MAGs) recovered from deep marine sediments off Costa Rica margin, defining a novel lineage phylogenetically married to Thorarchaeota, as such we propose the name “Sifarchaeota” for this phylum. The two “Sifarchaeota” MAGs encode for an anaerobic pathway for methylotrophy enabling the utilization of C1-C3 compounds (methanol and methylamines) to synthesize acetyl CoA. The MAGs showed a remarkable saccharolytic capabilities compared to other Asgard lineages and encoded for diverse classes of carbohydrate active enzymes (CAZymes) targeting different mono-, di- and oligosaccharides. Comparative genomic analysis based on the full metabolic profiles of different Asgard lineages revealed the close relation between “Sifarchaeota” and Odinarchaeota MAGs, which suggested similar metabolic potentials and ecological roles. Furthermore, we identified multiple HGT events from different bacterial donors within “Sifarchaetoa” MAGs, which hypothetically expanded “Sifarchaeota” capacities for substrate utilization, energy production and niche adaptation. Importance The exploration of deep marine sediments has unearthed many new lineages of microbes. The finding of this novel phylum of Asgard archaea is important since understanding the diversity and evolution of Asgard archaea may inform also about the evolution of eukaryotic cells. The comparison of metabolic potentials of the Asgard archaea can help inform about selective pressures the lineages have faced during evolution.

Unique mobile elements and scalable gene flow at the prokaryote–eukaryote boundary revealed by circularized Asgard archaea genomes

“…The updated HMM file has been provided as a supplementary data file. The updated HMM was used to evaluate the 282 genomes reported in this study and in the literature 3,[6][7][8][9][10][11][12]16,23,26,[68][69][70][71][72][73][74][75][76][77] through (1) CheckM, which uses Prodigal for gene calling, and (2) the more up to date HMMER3.2.2 on our gene calls described above. The latter generally produced slightly higher completeness and redundancy values (Supplementary Tables 8 and 9).…”

Comparative Analysis of rRNA removal methods for RNA-seq Differential Expression in Halophilic Archaea

“…The rapid pace of discovery of new archaeal species [6,46] as well as the use of novel archaeal model organisms in lab will bring further challenges for transcriptomics experiments. However, the methods tested here provide sufficient flexibility to solve such challenges.…”

“…Accurate detection of lowly expressed transcripts is also important when using RNA-Seq to map the transcriptome [12,45], including in metatranscriptomic protocols [44]. The rapid pace of discovery of new archaeal species [6,46] as well as the use of novel archaeal model organisms in lab will bring further challenges for transcriptomics experiments. However, the methods tested here provide sufficient flexibility to solve such challenges.…”

A closed Candidatus Odinarchaeum genome exposes Asgard archaeal viruses

“…To assess the taxonomy of selected MAGs, all archaeal GTDB 44 representative sequences (as of August 2021) were retrieved and supplemented with Asgard archaeal sequences from the Hermod 45 , Sif 5 , Wukong 6 and Jord 7 groups. Together with query sequences, GToTree 46 v1.5.45 was then used to reconstruct a tree with parameters “-H Archaea -D -G 0.2”.…”

“…Asgard archaea are a diverse group of microorganisms that comprise the closest relatives of eukaryotes [1][2][3][4][5][6][7] . Their genomes were first explored over six years ago 8 , and much of their physiology and cell biology remains to be studied.…”