Archaea articles within Nature Communications

Featured

  • Article
    | Open Access

    The symbiont Ca. Nanohaloarchaeum antarcticus is dependent on its host Halorubrum lacusprofundi for lipids due to a lack of certain biosynthetic genes. Here, the authors characterize the lipidome dynamics of this symbiotic relationship.

    • Su Ding
    • , Joshua N. Hamm
    •  & Anja Spang

  • Article
    | Open Access

    CRISPR arrays form the physical memory of prokaryotic adaptive immune systems by incorporating viral DNA sequences as spacers. Here, Blombach et al. show that transcription factor Cbp1 recruits chromatin protein Cren7 at CRISPR arrays, forming ‘chimeric’ chromatin-like structures that regulate expression of long CRISPR arrays in Sulfolobales archaea.

    • Fabian Blombach
    • , Michal Sýkora
    •  & Finn Werner

  • Article
    | Open Access

    Anaerobic methanotrophic (ANME) archaea are uncultivated microbes that oxidize the greenhouse gas methane and engage in extracellular electron transfer with other microbes, metal oxides, and electrodes. Here, Ouboter et al. observe strong methane-dependent current associated with high enrichment of ANME archaea on the anode, and provide insights into the mechanisms underlying extracellular electron transfer.

    • Heleen T. Ouboter
    • , Rob Mesman
    •  & Cornelia U. Welte

  • Article
    | Open Access

    Key cellular processes, such as cell-shape determination, are poorly understood in archaea. Here, Schiller et al. study the model archaeon Haloferax volcanii, which forms rods and disks, and identify a diverse set of proteins important for these processes, including a new actin homolog that plays a role in the formation of disk-shaped cells.

    • Heather Schiller
    • , Yirui Hong
    •  & Mechthild Pohlschroder

  • Article
    | Open Access

    The archaeal ancestor of eukaryotes belonged to the phylum Asgardarchaeota, or Asgard archaea. Here, the authors use ancestral sequence reconstruction and experimentally determine the optimal GDP-binding temperature of a translation elongation factor from ancient and extant Asgard archaea, to infer optimal growth temperatures for eukaryotes’ ancestors.

    • Zhongyi Lu
    • , Runyue Xia
    •  & Meng Li

  • Article
    | Open Access

    NAD serves as a 5′-terminal cap for bacterial and eukaryotic transcripts, and can be degraded at high temperatures to generate ADP-ribose (ADPR). Here, Gomes-Filho et al. identify NAD-RNAs in thermophilic and mesophilic archaea and provide insights into NAD- and ADPR-mediated turnover of RNAs in these organisms.

    • José Vicente Gomes-Filho
    • , Ruth Breuer
    •  & Lennart Randau

  • Article
    | Open Access

    The timing of cellular evolution is poorly constrained. Here, the authors used improved molecular dating approaches to study the evolution of the ATP synthase in light of a dated tree of life thereby providing an absolute timescale for cellular evolution including eukaryotic origins.

    • Tara A. Mahendrarajah
    • , Edmund R. R. Moody
    •  & Anja Spang

  • Article
    | Open Access

    Non-ammonia oxidising Thaumarachaeota lineages are common in acidic soils, but their evolution is unclear. Here, the authors assemble 15 genomes from deeply rooted Thaumarachaeota in topsoils and subsoils, investigating evolutionary divergence in the family Gagatemarchaeaceae.

    • Paul O. Sheridan
    • , Yiyu Meng
    •  & Cécile Gubry-Rangin

  • Article
    | Open Access

    Bacteria of the genus Streptomyces have complex life cycles involving cellular differentiation and multicellular structures that have never been observed in archaea. Here, the authors show that several halophilic archaea display a life cycle resembling that of Streptomyces bacteria, undergoing cellular differentiation into mycelia and spores.

    • Shu-Kun Tang
    • , Xiao-Yang Zhi
    •  & Ping Xu

  • Article
    | Open Access

    Asgard archaea include the closest known archaeal relatives of eukaryotes. Here, the authors provide evidence that eukaryotic and Asgard thymidylate synthases (required for DNA synthesis) may have a bacterial origin, and additional lateral transfer of bacterial genes may have shaped the metabolism of Asgard archaea.

    • Jonathan Filée
    • , Hubert F. Becker
    •  & Hannu Myllykallio

  • Article
    | Open Access

    Bacteria can exchange DNA through extracellular appendages (‘mating pili’) in a process known as conjugation. Here, Beltran et al. determine atomic structures by cryo-electron microscopy of a bacterial conjugative pilus and two archaeal pili, showing that the archaeal pili are homologous to bacterial mating pili.

    • Leticia C. Beltran
    • , Virginija Cvirkaite-Krupovic
    •  & Mart Krupovic

  • Article
    | Open Access

    Many eukaryotic and archaeal tRNAs carry a modified adenosine (t6A) that is synthesized by the KEOPS complex, which is composed of four subunits. A fifth subunit (Gon7) is found only in fungi and metazoa. Here the authors show that archaea also possess a fifth subunit, which is structurally and functionally similar to eukaryotic Gon7.

    • Marie-Claire Daugeron
    • , Sophia Missoury
    •  & Tamara Basta

  • Article
    | Open Access

    Pili are filamentous appendages on the surface of bacteria and archaea, and play roles in multiple processes such as adhesion, motility and horizontal gene transfer. Here, Gaines et al. describe the structure of a new type of pilus, termed ‘thread’, from the model archaeaon Sulfolobus acidocaldarius.

    • Matthew C. Gaines
    • , Michail N. Isupov
    •  & Bertram Daum

  • Article
    | Open Access

    Anaerobic methanotrophic (ANME) archaea obtain energy from the breakdown of methane. Here, Schoelmerich et al. describe large plasmids associated with ANME archaea of the Methanoperedens genus in enrichment cultures and other natural anoxic environments, opening the way for development of genetic vectors for research on these poorly understood organisms.

    • Marie C. Schoelmerich
    • , Heleen T. Ouboter
    •  & Jillian F. Banfield

  • Article
    | Open Access

    Sexual reproduction in eukaryotes involves gamete fusion, mediated by fusogenic proteins. Here, the authors identify fusogenic protein homologs encoded within mobile genetic elements in archaeal genomes, solve the crystal structure of one of the proteins, and show that its ectopic expression can fuse mammalian cells, suggesting potential roles in cell-cell fusion and gene exchange.

    • David Moi
    • , Shunsuke Nishio
    •  & Benjamin Podbilewicz

  • Article
    | Open Access

    Trace metals have been an important ingredient for life throughout Earth’s history. Here, the authors show that a member of an elusive archaeal lineage (Caldarchaeales or Aigarchaeota) requires tungsten for growth, and provide evidence that tungsten-dependent metabolism played a role in the origin and evolution of this lineage.

    • Steffen Buessecker
    • , Marike Palmer
    •  & Jeremy A. Dodsworth

  • Article
    | Open Access

    Here, by analyzing 250 species of animals covering a large taxonomic spectrum, the authors show that archaea are common constituent of the animal gut throughout the animal kingdom, and identify six main genera/families of gut archaea revealing their abundance and diversity to be driven by host diet, evolutionary history and physiology.

    • Courtney M. Thomas
    • , Elie Desmond-Le Quéméner
    •  & Guillaume Borrel

  • Article
    | Open Access

    The Micrarchaeota lineage includes poorly characterized archaea with reduced genomes that likely depend on host interactions for survival. Here, the authors report a stable co-culture of a member of the Micrarchaeota and its host, and use multi-omic and physiological analyses to shed light on this symbiosis.

    • Susanne Krause
    • , Sabrina Gfrerer
    •  & Johannes Gescher

  • Article
    | Open Access

    The archaellum is a molecular machine used by archaea to swim, consisting of an intracellular motor that drives the rotation of an extracellular filament composed of multiple copies of proteins named archaellins. Here, the authors use electron cryo-microscopy to elucidate the structure of an archaellum, and find that the filament is composed of two alternating archaellins.

    • Lavinia Gambelli
    • , Michail N. Isupov
    •  & Bertram Daum

  • Article
    | Open Access

    DNA primases initiate a short primer before handing off to DNA polymerases to continue replication. Here the authors reveal a unique ability of archaeal primases to first synthesize RNA before stochastically incorporating a deoxyribonucleotide and further extending the primer as DNA.

    • Mark D. Greci
    • , Joseph D. Dooher
    •  & Stephen D. Bell

  • Article
    | Open Access

    Understanding the structural basis for the inhibition of archaeal eukaryotic-like RNA polymerases (RNAPs) during virus infection is of interest for drug design. Here, the authors present the cryo-EM structures of apo Sulfolobus acidocaldarius RNAP and the RNAP complex structures with two regulatory factors, RIP and TFS4 that inhibit transcription and discuss their inhibitory mechanisms.

    • Simona Pilotto
    • , Thomas Fouqueau
    •  & Finn Werner

  • Article
    | Open Access

    Transcription in archaea is known to be regulated through the recruitment of RNA polymerase to promoters. Here, the authors show that the archaeon Saccharolobus solfataricus regulates transcription globally through a rate-limiting promoter-proximal elongation step.

    • Fabian Blombach
    • , Thomas Fouqueau
    •  & Finn Werner

  • Article
    | Open Access

    The biology of the archaeal phylum Woesearchaeota is poorly understood due to the lack of cultured isolates. Here, the authors analyze datasets of Woesearchaeota 16 S rRNA gene sequences and metagenome-assembled genomes to infer global distribution patterns, ecological preferences and metabolic capabilities.

    • Wen-Cong Huang
    • , Yang Liu
    •  & Meng Li

  • Article
    | Open Access

    Encapsulins are microbial protein compartments that sequester specific enzymes and are formed by self-assembly of a viral-like capsid protein. Here, Andreas and Giessen carry out a large-scale computational analysis of prokaryotic genomes to present a curated set of over 6,000 encapsulin-like systems, and present hypotheses about their potential biological functions.

    • Michael P. Andreas
    •  & Tobias W. Giessen

  • Article
    | Open Access

    In most bacteria, cell division depends on tubulin homolog FtsZ and other proteins, such as SepF. Cell division in many archaea also depends on FtsZ. Here, Nußbaum et al. show that a SepF homolog plays important roles in cell division in Haloferax volcanii, a halophilic archaeon that has two FtsZ homologs.

    • Phillip Nußbaum
    • , Maren Gerstner
    •  & Sonja-Verena Albers

  • Article
    | Open Access

    Most archaea divide by binary fission using an FtsZ-based system that is poorly understood. Here, the authors combine structural, cellular, and evolutionary analyses to show that the SepF protein acts as the FtsZ anchor in the archaeon Methanobrevibacter smithii.

    • Nika Pende
    • , Adrià Sogues
    •  & Simonetta Gribaldo

  • Article
    | Open Access

    Geothermal environments are hotspots for carbon cycling. Here, De Anda et al. reconstruct archaeal genomes from terrestrial and deep-sea geothermal sediments, and propose the classification of these microbes as a new phylum, ‘Brockarchaeota’, with unique metabolic capabilities including non-methanogenic anaerobic methylotrophy.

    • Valerie De Anda
    • , Lin-Xing Chen
    •  & Brett J. Baker

  • Article
    | Open Access

    A study of the first genomes of the marine Hikarchaeia, the closest known relatives of Haloarchaea, is presented. Their inclusion in ancestral reconstructions unveils an intermediate stage in the evolutionary transition from ancestral anaerobic methanogens to modern day aerobic halophiles.

    • Joran Martijn
    • , Max E. Schön
    •  & Thijs J. G. Ettema

  • Article
    | Open Access

    Ammonia-oxidising archaea of the phylum Thaumarchaeota are important organisms in the nitrogen cycle. Using 12 new genomes, this study finds evidence that Nitrososphaerales evolution was marked by lateral gene transfer followed by gene duplication.

    • Paul O. Sheridan
    • , Sebastien Raguideau
    •  & Cécile Gubry-Rangin

  • Article
    | Open Access

    The evolutionary relationships within Archaea remain unresolved. Here, the authors used genomic approaches to study the Undinarchaeota, a previously uncharacterized clade of DPANN, shed light on their position in an updated archaeal phylogeny and illuminate the history of archaeal genome evolution.

    • Nina Dombrowski
    • , Tom A. Williams
    •  & Anja Spang

  • Article
    | Open Access

    While archaeal proteomics advanced rapidly, a comprehensive proteome database for archaea is lacking. Therefore, the authors here launch the Archaeal Proteome Project, a community-effort providing insights into archaeal cell biology via the combined reanalysis of Haloferax volcanii proteomics data.

    • Stefan Schulze
    • , Zachary Adams
    •  & Mechthild Pohlschroder

  • Article
    | Open Access

    Here, the authors investigate the diversity and dynamics of the CRISPRome in the hyperthermophilic archaea of the order Sulfolobales, and find the most abundant spacers to come from mini-CRISPR arrays of archaeal viruses, which might represent a strategy for superinfection exclusion and promotion of archaeal virus speciation.

    • Sofia Medvedeva
    • , Ying Liu
    •  & Mart Krupovic

  • Article
    | Open Access

    The S-layer is a proteinaceous envelope often found in bacterial and archaeal cells. Here, the authors use CRISPR-based technology to silence slaB, encoding the S-layer membrane anchor, to show that an intact S-layer is important for cell division and virus susceptibility in the archaeon Sulfolobus solfataricus.

    • Isabelle Anna Zink
    • , Kevin Pfeifer
    •  & Christa Schleper

  • Article
    | Open Access

    Methane metabolism by some lineages of Archaea contributes to the cycling of carbon on Earth. Here, the authors show high diversity of methyl-coenzyme M reductase (Mcr), a key enzyme associated with archaeal methane/alkane metabolism, in hot spring Archaea, and investigate their ecological roles and evolution.

    • Zheng-Shuang Hua
    • , Yu-Lin Wang
    •  & Wen-Jun Li

  • Article
    | Open Access

    Microbial communities of plant leaf surfaces are ecologically important, but how they assemble and vary in time is unclear. Here, the authors identify core leaf microbiomes and seasonal patterns for two biofuel crops and show with source-sink models that soil is a reservoir of phyllosphere diversity.

    • Keara L. Grady
    • , Jackson W. Sorensen
    •  & Ashley Shade

  • Article
    | Open Access

    Archaea and bacteria often have gene pairs with overlapping stop and start codons, suggesting translational coupling. Here, Huber et al. analyse overlapping gene pairs from 720 genomes, and validate translational coupling via termination-reinitiation for 14 gene pairs in Haloferax volcanii and Escherichia coli.

    • Madeleine Huber
    • , Guilhem Faure
    •  & Jörg Soppa

  • Article
    | Open Access

    Natural gas reservoirs in the oceanic subsurface sustain complex communities of anaerobic microbes. Here, Seitz et al. describe a previously unknown archaeal phylum, Helarchaeota, belonging to the Asgard superphylum and with the potential for oxidation of hydrothermally generated short-chain hydrocarbons.

    • Kiley W. Seitz
    • , Nina Dombrowski
    •  & Brett J. Baker

  • Article
    | Open Access

    The prokaryote defence system Dnd relies on phosphorothioation (PT) of DNA backbone to distinguish between self and non-self DNA. Here, Xiong et al. describe a previously uncharacterized PT-based antiviral system that is independent of the canonical Dnd and is widespread in Archaea and Bacteria.

    • Lei Xiong
    • , Siyi Liu
    •  & Shi Chen

  • Article
    | Open Access

    Cofactor F420 plays crucial roles in bacterial and archaeal metabolism, but its biosynthetic pathway is not fully understood. Here, the authors present the structure of one of the enzymes and provide experimental evidence for a substantial revision of the pathway, including the identification of a new intermediate.

    • Ghader Bashiri
    • , James Antoney
    •  & Colin J. Jackson

Browse broader subjects

Browse narrower subjects

Browse Archaea across other nature.com journals