Archaea and the tree of life

The Archaea was recognized as a third domain of life 40 years ago. In this Review, Emeet al. outline a brief history of the changing shape of the tree of life and examine how the recent discovery of diverse archaeal lineages has changed our understanding of the evolutionary relationships between the three domains of life and the origin of the eukaryotic cell.

One of the most prominent features of archaea is the extraordinary diversity of their viruses. In this Review, Prangishviliet al. summarize their morphological diversity, the molecular biology of their life cycles and virus–host interactions, and discuss their evolution and their role in the global virosphere.

Archaea are highly diverse microorganisms that inhabit various environments. This evolutionary flexibility and adaptability has been supported by abundant horizontal gene transfer. In this Review, Albers and colleagues discuss the mechanisms and consequences of archaeal DNA transfer.

In this Opinion article, López-Garcíaet al. describe recent archaeal phylogenomic data relating to the massive acquisition of bacterial genes by horizontal gene transfer. They argue that the findings presented suggest that the import of these bacterial genes was crucial for the adaptation of archaea to mesophilic lifestyles.

The archaeal genome is organized by either eukaryotic-like histone proteins or bacterial-like architectural proteins. Dame and colleagues discuss the interplay between chromatin proteins and components of the basal and regulatory transcription machinery, and describe how these factors cooperate in nucleoid structuring and gene regulation.

The vast increase in the number of 16S ribosomal RNA gene sequences that are now available has led to an urgent need to implement taxonomic boundaries and classification principles that can apply to both cultured and uncultured microorganisms. In this Analysis article, the authors use 16S rRNA gene sequence identities to propose rational taxonomic boundaries for high taxa of bacteria and archaea and suggest a rationale for the circumscription of uncultured taxa that is compatible with the taxonomy of cultured bacteria and archaea.

Villanuevaet al. analyse the relationship between archaeal membrane lipids and the enzymes that are involved in their biosynthesis and conclude that our current understanding of the archaeal membrane lipid biosynthesis pathway needs some reconsideration. On the basis of amino acid sequence analysis, they present an alternative biosynthetic pathway that involves a 'multiple key, multiple lock' mechanism.

Bernander and Lindås provide an overview of recent studies that have enhanced our understanding of the archaeal cell cycle. They discuss the multiple-origin mode of DNA replication, the archaeal replisome, the identification of a genome segregation machinery, the first cytoskeletal structure and the discovery of a novel cell division system.

N-glycosylation was first reported in archaea almost 40 years ago. However, as Jerry Eichler describes in this Progress article, it is only recently, with the ready availability of archaeal genome sequences and new and improved molecular tools, that we have begun to make major advances in our understanding of this crucial post-translational modification.

The evolution of monoderm and diderm cell envelopes, and thus of Gram-positive and Gram-negative bacteria, is a long-standing question. In this Opinion article, Tocheva, Ortega and Jensen propose, based on recent electron cryotomography data, a new model that places sporulation at the heart of bacterial evolution.

Accumulating evidence that the eukaryotic nuclear lineage originated from within the Archaea provides support for a tree containing only two primary domains of life—the Achaea and Bacteria—over the currently accepted ‘three-domains tree’.

This review outlines experimental considerations, advances and challenges in microbial single-cell genome sequencing and discusses the applications and scientific questions that this approach enabled.

This issue marks the 40th anniversary of the publication of the landmark article by Carl Woese and George Fox in which they proposed the Archaea as a third domain of life.

In this Essay, Alberset al. discuss the remarkable achievements of two leaders of the archaeal research field: the late Carl Woese and the late Wolfram Zillig. They highlight how the discoveries of these two researchers have inspired the current and upcoming generations of microbiologists.

This month's Genome Watch highlights how metagenomics is continuing to reveal the diversity of microorganisms in the environment and how it is challenging and expanding our understanding of how life evolved on Earth.

This study provides insights into the archaeal ancestor of eukaryotes and the primal stages of eukaryogenesis.

A new large-scale genomics study reports a vastly expanded tree of life that is based on genomic data from over 3,000 species, including many uncultivated and poorly characterized prokaryotes.

This work describes the Asgard superphylum, an assemblage of diverse archaea that comprises Odinarchaeota, Heimdallarchaeota, Lokiarchaeota and Thorarchaeota, offering insights into the earliest days of eukaryotic cells and their complex features.

This study identifies a clade of archaea that is the immediate sister group of eukaryotes in phylogenetic analyses, and that also has a repertoire of proteins otherwise characteristic of eukaryotes—proteins that would have provided the first eukaryotes with a ‘starter kit’ for the genomic and cellular complexity characteristic of the eukaryotic cell.

Anaerobic archaea enriched in thermophilic microbial consortia completely degrade butane by modifying mechanisms which were hitherto thought to be specific to methane metabolism.

An update to the ‘tree of life’ has revealed a dominance of bacterial diversity in many ecosystems and extensive evolution in some branches of the tree. It also highlights how few organisms we have been able to cultivate for further investigation.

A phylogenetic approach was used to illuminate the physiology of the last universal common ancestor, supporting the theory that LUCA was an H₂-dependent autotroph in a hydrothermal setting rich in hydrogen, carbon dioxide and iron.

Diversity-generating retroelements are abundant in the reduced genomes of bacteria and archaea belonging to the CPR and DPANN phyla, driving hypervariability on proteins involved in signalling, transcriptional regulation, attachment and defence.

Significant gaps in our characterization of microbial diversity remain; this meta-analysis of amplicon-based rRNA studies shows that they miss approximately 10% of environmental microbial sequences, most belonging to the candidate phyla radiation.

The recovery of 7,903 bacterial and archaeal metagenome-assembled genomes increases the phylogenetic diversity represented by public genome repositories and provides the first representatives from 20 candidate phyla.

Methanonatronarchaeia are a distinct class-level lineage of extremely halophilic methanogens, which lack features of classical methanogenesis and have a high intracellular concentration of potassium, suggesting potassium-based osmoprotection.

Genomic reconstruction from hot spring sediment metagenomes show that 'Hadesarchaea' have streamlined yet metabolically versatile genomes, with genes involved in CO and H₂ oxidation, with potential coupling to nitrite reduction to ammonia.

Genetic evidence demonstrates that some Bathyarchaeota lineages are capable of homoacetogenesis, a metabolism so far restricted to the Bacteria.

The Verstraetearchaeota encode divergent methyl-coenzyme M reductase genes, which are required for methylotrophic methanogenesis, increasing methanogen diversity and the complexity of the global methane cycle.

Comparative genomic analyses suggest that Lokiarchaeota, the closest known prokaryotic relative of eukaryotes, are hydrogen dependent, supporting the ‘hydrogen hypothesis’ for the origin of eukaryotic cells.

An archaeal plasmid that can be transported in membrane vesicles, similar to a virus, and encodes proteins that can insert into host membranes and membrane vesicles, provides insights into the evolutionary link between plasmids and viruses.

3D tracking of quantum dots, cross-kymography and computational modelling reveals a left-hand corkscrew motion of the H. salinarum archaellum, with a right-handed helical structure and a motor efficiency of 6–10%.

A cryoEM structure of the archaeal flagella, the archaellum, shows distinct features from related bacterial structures.

Termination sequencing reveals that several archaeal genes contain multiple consecutive-terminators, which results in the generation of alternative 3′ UTR isoforms during transcription, similar to what is observed in eukaryotes.

A transcriptional analysis of Methanocaldococcus jannaschii identifies Spt4/5 as a general elongation factor in Archaea with two modes of recruitment to the RNA polymerase.

Crystal structures of the Argonaute protein from the archaeon Methanocaldococcus jannaschii (MjAgo) in its apo state and bound to a guide DNA elucidate the molecular mechanisms that drive DNA-guided DNA silencing in Archaea.

In addition to canonical guide-dependent endonuclease activity, the Argonaute protein from the archaeon Methanocaldococcus jannaschii (MjAgo) is capable of guide-independent DNA cleavage, enabling MjAgo to process plasmids and genomic DNA.

Metagenomic and microbial sequence data are made easier to interpret with the addition of 1,003 genomes to the Genomic Encyclopedia of Bacteria and Archaea.

Many microbial lineages have not yet been cultured, which hampers our understanding of their physiology. Here, Wurch et al. use single-cell genomics to infer cultivation conditions for the isolation of a tiny ectosymbiotic nanoarchaeon and its crenarchaeota host from a geothermal spring.

The contribution of marine archaea to the ocean's carbon cycle is unclear. Here, Li et al. analyse the genomes and transcriptomes from five deep-sea archaeal groups to reveal their metabolic characteristics, suggesting a crucial role in modulating the carbon cycle in deep oceans.

Diversity-generating retroelements (DGRs) are genetic elements that introduce sequence variation within target genes in bacteria and their viruses. Here, Paul et al. report the discovery of DGRs in an archaeal virus and in two archaea from marine and terrestrial subsurface environments, respectively.

Although not photosynthetic, some archaea possess RuBisCO, one of the enzymes characteristic of the photosynthetic Calvin-Benson cycle, but apparently lack another one, phosphoribulokinase (PRK). Here the authors describe a carbon metabolic pathway in methanogenic archaea, involving RuBisCO and PRK.

In the absence of complete genomes, the metabolic capabilities of uncultured ARMAN-like archaea have been uncertain. Here, Golyshina et al. apply an enrichment culture technique and find that the ungapped genome of the ARMAN-like archaeon Mia14 has lost key metabolic pathways, suggesting dependence on the host archaeon Cuniculiplasma divulgatum.

Small archaeal ubiquitin-like modifiers (SAMPs) have been hypothesized to be part of an ancestral version of the ubiquitin-proteasome system. Here, Anjum et al. identify a SAMP homologous to the eukaryotic ubiquitin-related modifier-1 and show that it is processed by the 20S core proteasome in S. acidocaldarius.

The Critical Assessment of Metagenome Interpretation (CAMI) community initiative presents results from its first challenge, a rigorous benchmarking of software for metagenome assembly, binning and taxonomic profiling.