The intestinal microbiota is a critical determinant of mucosal homeostasis, yet the functional contributions of Archaea—which constitute up to 10% ...

Enceladus’s ocean is extremely alkaline and low on carbon dioxide, but one terrestrial extremophile made it work.

Cultures reveal conservation of cell structure, physical symbioses and anaerobiosis across Heimdallarchaeia (the archaeal lineage that branches closest to eukaryotes) and other Pro...

Cultures reveal conservation of cell structure, physical symbioses and anaerobiosis across Heimdallarchaeia (the archaeal lineage that branches closest to eukaryotes) and other Pro...

Temperature shapes the biochemistry of microbial proteins, and several amino acid compositional indices have been proposed to detect cold adaptation in microbial proteomes. Whether these indices capture cold adaptation in Archaea, which are abundant in cold marine environments such as the Arctic Ocean, has not been tested. We calculated six amino acid compositional indices (arginine to lysine ratio, acidic residue proportion, aliphatic index, aromaticity, grand average of hydropathicity, and proline residue proportion) across global protein families for 142 Marine Group I (MG-I; Thaumarchaeota) and 146 Euryarchaeota genomes from the Bacterial and Viral Bioinformatics Resource Center (BV-BRC), together with three MG-I metagenome-assembled genomes (MAGs) recovered from the Western Arctic Ocean. The Arctic MAGs fell within the range of index and phylogenetic distances of the wider MG-I population, and no signature of cold adaptation was detected. Instead, index values differed between the two main MG-I phylogenetic groups and between freshwater and marine genomes, and the Euryarchaeota formed five index-based clusters consistent with phylogeny. A group of 19 MG-I MAGs associated with sea sponges had significantly higher arginine to lysine ratios than other MG-I, differed in the usage of all amino acids except alanine and lysine, and had distinct codon usage and higher GC content; their anomalous placement in the MG-I phylogeny is consistent with long-branch attraction. These results indicate that amino acid compositional indices developed for Bacteria have limited power to detect cold adaptation in Archaea, but reveal strong proteomic signatures associated with host adaptation in sponge-associated Thaumarchaeota. ### Competing Interest Statement The authors have declared no competing interest. Natural Sciences and Engineering Research Council, https://ror.org/01h531d29, RGPIN-2022-05280 Canada Research Chairs, https://ror.org/0517h6h17 Digital Research Alliance of Canada, https://ror.org/010r6td27

Cultures reveal conservation of cell structure, physical symbioses and anaerobiosis across Heimdallarchaeia (the archaeal lineage that branches closest to eukaryotes) and other Pro...

The function of the glycyl radical enzyme (GRE) PFL2 from the hyperthermophilic archaeon Archaeoglobus fulgidus has remained unresolved since its discovery. Structural and sequence analyses initially ...

Cultures reveal conservation of cell structure, physical symbioses and anaerobiosis across Heimdallarchaeia (the archaeal lineage that branches closest to eukaryotes) and other Pro...

Tiny conductive particles in coastal sediments can help methane-producing microorganisms exchange electrons in a laboratory culture derived from Baltic Sea sediments. Researchers found that bacteria…

FEMS Microbiol Rev · 31 Oct 2026 — The fundamental biochemical and stereochemical difference in how cell membrane lipids are built between Archaea on one side, and Bacteria and Eukarya on the other is...

Methanogenic archaea drive global methane emissions, yet the molecular basis of their physiological flexibility is unclear. Archaeal adaptation is typically attributed to horizontal gene transfer, which is episodic and cannot explain rapid, reversible change. Here we show that direct tandem repeats (TRs) offer an intrinsic alternative. By screening 50,567 prokaryotic genomes, we find TR densities in Methanosarcina more than 30-fold above the prokaryotic average, paralleling Borg extrachromosomal elements. These TRs recur at conserved loci while sharing almost no sequence identity between strains, indicating independent origin, and evolve during routine cultivation. Methanogen TRs are transcribed, show ribosome occupancy, and lie near regulatory and cofactor-related genes, whilst being depleted around core energy-conserving and translational machinery. Genic TRs generate intrinsically disordered regions in proteins carrying nucleotide-binding, protein-protein interaction and cell-surface domains, and occur in structural and surface proteins of methanogen-infecting viruses. TRs are therefore an overlooked source of variability and adaptation potential in methanogens and their viruses. ### Competing Interest Statement The authors have declared no competing interest. Swiss National Science Foundation, https://ror.org/00yjd3n13, 226487