Expanding Archaeal Diversity and Phylogeny: Past, Present, and Future

Abstract

The discovery of the Archaea is a major scientific hallmark of the twentieth century. Since then, important features of their cell biology, physiology, ecology, and diversity have been revealed. Over the course of some 40 years, the diversity of known archaea has expanded from 2 to about 30 phyla comprising over 20,000 species. Most of this archaeal diversity has been revealed by environmental 16S rRNA amplicon sequencing surveys using a broad range of universal and targeted primers. Of the few primers that target a large fraction of known archaeal diversity, all display a bias against recently discovered lineages, which limits studies aiming to survey overall archaeal diversity. Induced by genomic exploration of archaeal diversity, and improved phylogenomics approaches, archaeal taxonomic classification has been frequently revised. Due to computational limitations and continued discovery of new lineages, a stable archaeal phylogeny is not yet within reach. Obtaining phylogenetic and taxonomic consensus of archaea should be a high priority for the archaeal research community. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Candidatus Nitrosopolaris, a genus of putative ammonia-oxidizing archaea with a polar/alpine distribution

“…Genome-resolved metagenomics has revolutionized our knowledge of archaeal diversity by giving us access to the genome of uncultured microorganisms at an unprecedented rate (Tahon et al ., 2021). In a recent metagenomic investigation of tundra soils in northern Finland (Pessi et al ., 2022, pre-print), we have manually binned and curated a MAG belonging to the genus “UBA10452”, an uncultured and largely uncharacterized lineage in the order Nitrososphaerales (“terrestrial group I.1b”) of the phylum Thaumarchaeota (Rinke et al ., 2021).…”

Editorial: Archaeal Ribosomes: Biogenesis, Structure and Function

“…Their study describes a core set of putative ribosome biogenesis factors widely conserved among archaea that may contribute to ribosome synthesis, although this is still to be proven experimentally. Notably, this study also reveals that the expansion of ribosome biogenesis factors characteristic of the eukaryotic pathway is not present in the Asgard archaea phylum which has been proposed to be more closely related to eukaryotes (Tahon et al, 2021). Altogether, this comprehensive study provides an important resource that will further help to functionally explore the archaeal ribosome biogenesis pathway and its evolution.…”

“…At the end of the 1970s, Carl Woese identified microorganisms that belong to a separate domain of life, the archaea (Fox et al, 1977 ; Albers et al, 2013 ). In the subsequent years, in-depth studies of the molecular and cellular biology of archaea, as well as of their physiology and environmental distribution, have revealed that archaea possess some very unique and distinctive biological traits (Albers et al, 2013 ; Tahon et al, 2021 ).…”

Looking through the Lens of the Ribosome Biogenesis Evolutionary History: Possible Implications for Archaeal Phylogeny and Eukaryogenesis

“… Archaeal diversity and their current phylogenetic relationship. A simplified archaeal phylogenetic tree based on Tahon et al (2021) is depicted. Archaea are divided into the Euryarchaea phylum, and the TACK, DPANN, Asgard superphyla.…”