Research articles

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  • CRISPR–Cas systems in bacteria and archaea have multifaceted evolutionary relationships with mobile genetic elements (MGEs), including viruses, plasmids and transposons. CRISPR–Cas systems or their components have also been recruited by MGEs on many independent occasions. In this Analysis article, Koonin and colleagues investigate and substantially expand the range of CRISPR–Cas components carried by MGEs.

    • Guilhem Faure
    • Sergey A. Shmakov
    • Eugene V. Koonin
    Analysis
  • In this Analysis article, Flemming and Wuertz calculate the total number of bacteria and archaea on Earth and estimate the fraction that lives in biofilms. They propose that biofilms are the most prominent and influential type of microbial life.

    • Hans-Curt Flemming
    • Stefan Wuertz
    Analysis
  • Candidate phyla radiation (CPR) bacteria and DPANN archaea are massive radiations of organisms recently identified. In this Analysis, Castelle et al. explore the metabolic potential of CPR and DPANN radiation, focusing in particular on metabolic gaps and unexpected biological features that are unusual outside of these groups.

    • Cindy J. Castelle
    • Christopher T. Brown
    • Jillian F. Banfield
    Analysis
  • Class 2 CRISPR–Cas systems are characterized by effector modules that consist of a single multidomain protein. In this Analysis, using a computational pipeline, the authors discover three novel families of class 2 effectors that correspond to three new CRISPR–Cas subtypes and present a comprehensive census of class 2 systems that are encoded in complete and draft bacterial and archaeal genomes.

    • Sergey Shmakov
    • Aaron Smargon
    • Eugene V. Koonin
    Analysis
  • CRISPR–Cas systems provide bacteria and archaea with adaptive immunity to invading foreign DNA. In an Analysis article, Koonin and colleagues update a previous classification of these systems to incorporate the large volume of genomic data generated in recent years.

    • Kira S. Makarova
    • Yuri I. Wolf
    • Eugene V. Koonin
    Analysis
  • 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.

    • Pablo Yarza
    • Pelin Yilmaz
    • Ramon Rosselló-Móra
    Analysis
  • Weitz and colleagues use a biophysical scaling model of intact virus particles to quantify differences in the elemental stoichiometry of marine viruses compared with their microbial hosts. They propose that, under certain circumstances, marine virus populations could make a previously unrecognised and important contribution to the reservoir and cycling of oceanic phosphorus.

    • Luis F. Jover
    • T. Chad Effler
    • Joshua S. Weitz
    Analysis
  • 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.

    • Laura Villanueva
    • Jaap S. Sinninghe Damsté
    • Stefan Schouten
    Analysis
  • The human genome encodes very few enzymes involved in the digestion of complex polysaccharides, and this deficit is compensated for by the myriad of carbohydrate-active enzymes (CAZymes) encoded by members of the gut microbiome. In this Analysis article, Henrissat and colleagues characterize the CAZymes present in a representative human mini-microbiome.

    • Abdessamad El Kaoutari
    • Fabrice Armougom
    • Bernard Henrissat
    Analysis
  • In this Analysis article, Morris and Schmidt report the results of surveys searching for high-affinity terminal oxidase genes in sequenced bacterial genomes and shotgun metagenomes. They find that bacteria with the potential to respire under microoxic conditions are phylogenetically diverse and intriguingly widespread in nature, and go on to highlight the importance of microaerobic metabolism in host-associated bacteria.

    • Rachel L. Morris
    • Thomas M. Schmidt
    Analysis
  • Like larger organisms, microorganisms display distinct distributions in space and time. Martiny, Hanson and colleagues propose that four processes — selection, drift, dispersal and mutation — can shape such microbial biogeographic patterns, and analyse the literature to assess the evidence for their importance in shaping one pattern, the distance–decay relationship.

    • China A. Hanson
    • Jed A. Fuhrman
    • Jennifer B. H. Martiny
    Analysis
  • Many bacteria in a variety of niches contain cellulases. Such microorganisms are primarily considered to be saprophytic, but recent evidence suggests that cellulases are also present in non-saprophytes. By examining the genomes of 1,500 bacteria, Henrissat and colleagues confirm this observation and reveal unusual roles for some cellulases.

    • Felix Mba Medie
    • Gideon J. Davies
    • Bernard Henrissat
    Analysis
  • Recombination can be an important evolutionary force for RNA viruses, but the rate of recombination varies greatly between different RNA viruses. In this Analysis article, Simon-Loriere and Holmes describe the mechanisms of recombination for RNA viruses and the role of these mechanisms in viral evolution.

    • Etienne Simon-Loriere
    • Edward C. Holmes
    Analysis
  • Horizontal gene transfer introduces into an organism genes that were not vertically transmitted from the parent organism, and therefore has the potential to interfere with phylogenetic analyses. In this Analysis article, Andam and Gogarten describe homeoalleles (alleles in bacteria and archaea that encode proteins with similar function but that have different phylogenetic origins) and their effect on phylogenetic analyses.

    • Cheryl P. Andam
    • J. Peter Gogarten
    Analysis
  • In this Analysis article, Makarova and colleagues provide an overview of the cell division and membrane budding systems of the Archaea. They show that at least four different systems regulate these processes, providing insight into the evolutionary history of archaeal and eukaryotic cells.

    • Kira S. Makarova
    • Natalya Yutin
    • Eugene V. Koonin
    Analysis
  • The identification of genomic islands in bacterial genomes is becoming increasingly important. In this Analysis article, Fiona Brinkman and colleagues look at the limitations and benefits of the major computational methods that are available for genomic island prediction.

    • Morgan G. I. Langille
    • William W. L. Hsiao
    • Fiona S. L. Brinkman
    Analysis
  • In this Analysis, Kirchman and colleagues compare microbial processes in the western Arctic Ocean and other polar waters with low-latitude oceans to attempt to understand the role of heterotrophic bacteria in oceanic biogeochemical cycles. This may further our understanding of the changes that could occur as these waters warm.

    • David L. Kirchman
    • Xosé Anxelu G. Morán
    • Hugh Ducklow
    Analysis
  • The vast resource of viral genome sequences has been exploited to carry out a genomic comparison and phylogenetic analysis of the picorna-like superfamily. The authors conclude that the diverse groups of picorna-like viruses probably evolved in a 'Big Bang' that came after the evolution of the main groups of eukaryotes.

    • Eugene V. Koonin
    • Yuri I. Wolf
    • Valerian V. Dolja
    Analysis
  • Ley, Gordon and colleagues have analysed and compared published sequences of bacterial communities from humans with both free-living communities and those that are associated with diverse animals. They conclude that gut-associated microbiotas are profoundly different from other free-living microbiotas, and call for widespread sampling of the human gut microbiota to study how different cultures, lifestyles and technologies are impacting on the biodiversity within these fascinating communities.

    • Ruth E. Ley
    • Catherine A. Lozupone
    • Jeffrey I. Gordon
    Analysis
  • The archaeal domain comprises two phyla, the Euryarchaeota and the Crenarchaeota. Phylogenetic and genomic analyses now show that mesophilic crenarchaeota should not be considered as crenarchaeota. Based on this, the authors advocate the creation of a third archaeal phylum, which they propose to name Thaumarchaeota (from the Greek 'thaumas', meaning wonder).

    • Céline Brochier-Armanet
    • Bastien Boussau
    • Patrick Forterre
    Analysis