Microbiology articles within Nature Communications

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  • Article
    | Open Access

    Turnover of sediment organic matter contributes to global carbon cycling, yet the microorganisms involved are largely unknown. Castelleet al.reveal that an aquifer sediment core hosts a ‘zoo’ of organisms, including representatives of a previously undescribed phylum (Zixibacteria).

    • Cindy J. Castelle
    • , Laura A. Hug
    •  & Jillian F. Banfield

  • Article
    | Open Access

    Horizontal gene transfer of mobile genetic elements contributes to bacterial evolution and emergence of new pathogens. Here the authors demonstrate that the highly diverse structure of wall teichoic acid polymers governs horizontal gene transfer among Gram-positive pathogens, even across long phylogenetic distances.

    • Volker Winstel
    • , Chunguang Liang
    •  & Guoqing Xia

  • Article |

    Viral vectors can be used both to map and manipulate neural circuits in vivo; however, their use is limited by weak expression levels, especially when expression of more than one protein is required. Here, the authors overcome this limitation using deletion-mutant rabies viruses.

    • Ian R. Wickersham
    • , Heather A. Sullivan
    •  & H. Sebastian Seung

  • Article |

    Sequencing whole microbial genomes has become standard practice and methods to examine their phylogenetic relationships need to match the increasing demand. Segata et al. present a new computational pipeline that allows fast and accurate taxonomic assignment of microbial species.

    • Nicola Segata
    • , Daniela Börnigen
    •  & Curtis Huttenhower

  • Article |

    Actin normally polymerizes into filaments in a cooperative manner, with nucleation and elongation phases. Skillman et al. show that actin from the protozoan parasite Toxoplasma gondiipolymerizes in an isodesmic manner, without any evidence of nucleation, resulting in filaments that are very short and unstable.

    • Kristen M. Skillman
    • , Christopher I. Ma
    •  & L. David Sibley

  • Article |

    The potential evolutionary advantage associated with genome segmentation in multipartite viruses is not well established. Here Sicard et al. demonstrate that genome segmentation can allow a differential regulation of the copy number of each gene in a multipartite plant nanovirus during host infection.

    • Anne Sicard
    • , Michel Yvon
    •  & Stéphane Blanc

  • Article
    | Open Access

    Phytophthora infestanscaused the potato famine in the nineteenth century. Martinet al. sequence the nuclear genomes of five archival samples of the pathogen and compare these to extant specimens allowing the reconstruction of the evolutionary history of P. infestans.

    • Michael D. Martin
    • , Enrico Cappellini
    •  & M. Thomas P. Gilbert

  • Article
    | Open Access

    Bacterial infections can influence disease outcome in influenza infection; however, the mechanisms mediating these complex interactions remain unclear. Wang et al. reveal how infection with a component of the airway microbiota enhances survival during influenza infection via induction of anti-inflammatory macrophages.

    • Jian Wang
    • , Fengqi Li
    •  & Zhigang Tian

  • Article
    | Open Access

    RamR is an important multidrug-resistance factor, however, its structure and the molecules to which it responds are hitherto unknown. Here, the authors report the crystal structures of RamR complexed with multiple drugs, revealing significant flexibility in its substrate-recognition region.

    • Suguru Yamasaki
    • , Eiji Nikaido
    •  & Kunihiko Nishino

  • Article |

    Debates on the formation of banded iron formations (BIFs) in ancient iron-rich oceans are dominated by contradictions between biological and non-biological iron cycling. This study provides environmental evidence that directly implicates photosynthetic iron-oxidizing microorganisms in vast-scale BIF deposition.

    • Ernest Chi Fru
    • , Magnus Ivarsson
    •  & Marco Stampanoni

  • Article |

    A role of toxin–antitoxin systems in global regulation of bacterial gene expression has been proposed. Bukowski et al. now demonstrate that a novel toxin–antitoxin system from S. aureusencodes an endoribonuclease that regulates virulence gene expression by targeting translation.

    • Michal Bukowski
    • , Robert Lyzen
    •  & Benedykt Wladyka

  • Article |

    Red algae form one of the most ancient eukaryotic lineages, and have undergone multiple symbioses. Here, Price et al. report the first genome sequence for a mesophilic red alga, and reveal significant differences between these organisms and hyperthermopilic algae.

    • Debashish Bhattacharya
    • , Dana C. Price
    •  & Hwan Su Yoon

  • Article |

    The spatial and temporal organization of bacterial chromosomes is important for many cellular functions. Using high-precision measurements of fluorescently labelled chromosomal loci, Javer et al.demonstrate variation in the dynamics of different chromosomal sites, which may either be due to differential organization of the chromosome or spatial variation in molecular noise.

    • Avelino Javer
    • , Zhicheng Long
    •  & Marco Cosentino Lagomarsino

  • Article
    | Open Access

    Deep subsurface formations are potential sites for carbon capture and storage but how subsurface microbial communities may respond to this is not clear. Here, Mayumi et al. construct microcosms and show that increasing CO2partial pressure via carbon capture and storage more than doubles the rate of methanogenesis.

    • Daisuke Mayumi
    • , Jan Dolfing
    •  & Yoichi Kamagata

  • Article |

    Erm methyltransferases confer antimicrobial drug resistance and their expression is induced by macrolides. Gupta et al.show that Erm-catalysed modification of rRNA affects synthesis of some proteins and reduces cell fitness, explaining why expression of Erm is deleterious in the absence of antibiotics.

    • Pulkit Gupta
    • , Shanmugapriya Sothiselvam
    •  & Alexander S. Mankin

  • Article |

    Influenza A viruses spread through contact, large and small respiratory droplets (aerosols), but the relative importance of these modes of transmission is unclear. Cowling et al. model data from community trials of face masks and hand hygiene and find that aerosol transmission accounts for half of influenza occurrences.

    • Benjamin J. Cowling
    • , Dennis K. M. Ip
    •  & James Mark Simmerman

  • Article
    | Open Access

    Transmission-blocking interventions aim to interrupt progression of Plasmodium parasites from the vertebrate host to the mosquito. Blagborough et al. demonstrate that only partially reducing transmission can be sufficient to eliminate experimental Plasmodiuminfection in successive mosquito and mice populations when biting rates are low.

    • A. M. Blagborough
    • , T. S. Churcher
    •  & R. E. Sinden

  • Article |

    With paleovirology it is possible to identify ancient endogenous viral elements within eukaryotic genomes. Here Suh and colleagues report a genomic record of hepatitis endogenizations through bird’s evolution; they find a complete hepatitis genome sequence, the first discovery of a Mesozoic paleovirus genome.

    • Alexander Suh
    • , Jürgen Brosius
    •  & Jan Ole Kriegs

  • Article |

    The identification of hosts of blood-sucking insects is important for studying ecological factors that affect pathogen distribution. Önder et al. report a proteomics-based methodology for the analysis of blood remnants in ticks that identifies the host species from which the tick has fed up to 6 months earlier.

    • Özlem Önder
    • , Wenguang Shao
    •  & Dustin Brisson

  • Article
    | Open Access

    The coffee ring effect is commonly observed in drying droplets containing suspended matter leading to a deposition at the droplet edge. Sempels et al. show that self-generated biosurfactants in living bacterial systems reverse the coffee ring effect and result in a homogeneous deposition.

    • Wouter Sempels
    • , Raf De Dier
    •  & Jan Vermant

  • Article
    | Open Access

    Cyanobacterial symbionts of marine diatoms can localize intracellularly or externally to their host partners. Here Hilton et al. describe the genomes of two diazotroph cyanobacterial symbionts of diatoms and show that the location of the symbiont affects expression of nitrogen assimilation genes.

    • Jason A. Hilton
    • , Rachel A. Foster
    •  & Tracy A. Villareal

  • Article |

    Detecting and phenotyping Mycobacterium tuberculosis, especially in resource-limited settings, is important for global tuberculosis control. Here Liong et al. report a point-of-care diagnostic platform based on magnetic barcoding and nuclear magnetic resonance for the detection of mycobacterial nucleic acids.

    • Monty Liong
    • , Anh N. Hoang
    •  & Ralph Weissleder

  • Article |

    Light-driven proton-pumping rhodopsins are widely distributed in microorganisms and convert sunlight energy into proton gradients. Inoue et al. report the discovery of a light-driven sodium ion pump from marine bacteria.

    • Keiichi Inoue
    • , Hikaru Ono
    •  & Hideki Kandori

  • Article |

    The number of human infections caused by the primate malaria parasite P. knowlesi is increasing. Lim et al. demonstrate that host specificity is due to the preference of the parasite for young blood cells, and that the parasite can adapt to proliferate in human blood containing a range of differently aged cells.

    • Caeul Lim
    • , Elsa Hansen
    •  & Manoj T. Duraisingh

  • Article |

    The hepatitis C virus RNA genome is translated via an internal ribosome entry site. Pérard et al. present an atomic model of this site, and using molecular dynamics simulations, identify conformational flexibility that may underlie its function during translation initiation.

    • Julien Pérard
    • , Cédric Leyrat
    •  & Marc Jamin

  • Article |

    Bacterial type III secretion systems (T3SS) improve the delivery of vaccine antigens and antigen-specific immune responses but require the use of live vaccines. Carleton et al. report the assembly of a functional T3SS in replication-incompetent bacterial minicells that can deliver vaccine antigens in vitro and in vivo.

    • Heather A. Carleton
    • , María Lara-Tejero
    •  & Jorge E. Galán

  • Article |

    Shigella triggers an increase in intracellular calcium during invasion of host cells. Here the authors show that increased actin polymerization at the invasion site slows the diffusion of signalling mediators, thus sustaining localized calcium influx at invasion sites.

    • Guy Tran Van Nhieu
    • , Bing Kai Liu
    •  & Laurent Combettes

  • Article
    | Open Access

    The factors that modulate growth rate of the human malaria parasite Plasmodium falciparum remain poorly understood. Here Scherf and collaborators demonstrate that the Plasmodiumsirtuin PfSir2a regulates the transcription of ribosomal DNA, thereby modulating parasite proliferation rate and virulence.

    • Liliana Mancio-Silva
    • , Jose Juan Lopez-Rubio
    •  & Artur Scherf

  • Article |

    The recognition of viruses by synthetic materials is historically difficult. Here, a templating procedure using silica nanoparticles coated with organosilanes is used to form virus-imprinted particles, possessing both shape and chemical imprints, capable of virus recognition at picomolar concentrations.

    • Alessandro Cumbo
    • , Bernard Lorber
    •  & Patrick Shahgaldian

  • Article
    | Open Access

    Bacterial cell wall peptidoglycan is essential for viability and shape determination. Using high-resolution microscopy, Foster and colleagues elucidate the peptidoglycan architecture and insertion pattern in Escherichia coliand other Gram-negative bacteria, and propose a new model for cell wall elongation.

    • Robert D. Turner
    • , Alexander F. Hurd
    •  & Simon J. Foster

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