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Archaea and the tree of life

In 1977, Woese and Fox proposed the Archaea as a new domain of life and that the tree of life is divided into three branches — the Eukarya, Bacteria and Archaea. Although a three-domain tree was controversial to some, this study was soon accepted, and is widely regarded as one of the most important discoveries in biology of the past century. To mark 40 years of archaea research, this collection of articles from across the Nature group of journals explores the fundamental biology, evolution, metabolic versatility and ecological impact of archaea, and how the discovery of new species is reshaping the tree of life.

Reviews

The Archaea was recognized as a third domain of life 40 years ago. In this Review, Eme et 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.

Review Article | | Nature Reviews Microbiology

One of the most prominent features of archaea is the extraordinary diversity of their viruses. In this Review, Prangishvili et 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.

Review Article | | Nature Reviews Microbiology

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.

Review Article | | Nature Reviews Microbiology

In this Opinion article, López-García et 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.

Opinion | | Nature Reviews Microbiology

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.

Progress | | Nature Reviews Microbiology

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.

Analysis | | Nature Reviews Microbiology

Villanueva et 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.

Analysis | | Nature Reviews Microbiology

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.

Review Article | | Nature Reviews Microbiology

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.

Progress | | Nature Reviews Microbiology

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.

Opinion | | Nature Reviews Microbiology

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’.

Review Article | | Nature

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.

Review Article | | Nature Methods

News & Comment

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.

Genome Watch | | Nature Reviews Microbiology

Research

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.

Article | | Nature

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.

Article | | Nature

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.

Letter | open | | Nature Microbiology

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.

Brief Communication | | Nature Microbiology

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.

Article | open | | Nature Communications

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.

Article | open | | Nature Communications

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.

Article | open | | Nature Communications

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.

Article | open | | Nature Communications