Microbiology articles within Nature Communications

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  • Article |

    Microbes appear to play an important role in carbon sequestration. Here, the composition of microbial residues in a California grassland with elevated carbon dioxide, warming and nitrogen deposition reveals that warming and nitrogen deposition can both alter the fraction of carbon derived from microbes in soils.

    • Chao Liang
    •  & Teri C. Balser

  • Article |

    Humans tend to adopt one of a limited number of different bacterial community structures in the gut, known as enterotypes. Moeller et al.now show that these microbial fingerprints are conserved in chimpanzees, and that individuals can switch between enterotypes over periods of several years.

    • Andrew H. Moeller
    • , Patrick H. Degnan
    •  & Howard Ochman

  • Article |

    Large-scale sequencing techniques have helped to understand the genetic diversity of little-known microbial communities. These authors demonstrate a cheaper alternative to direct sequencing—the construction of virtual metagenomes using gel electrophoresis and related genome sequences.

    • Shujiro Okuda
    • , Yuki Tsuchiya
    •  & Hisao Morisaki

  • Article |

    The sulfation of protein tyrosine residues is a common post-translational modification in eukaryotes. Here, Han et al.show that the protein RaxST, produced by a plant bacterium, has tyrosine sulfotransferase activity, demonstrating for the first time tyrosine sulfation in prokaryotes.

    • Sang-Wook Han
    • , Sang-Won Lee
    •  & Pamela C. Ronald

  • Article |

    Microsporidia are widespread human parasites, but limited genome annotation has hampered efforts to understand their biology. Peyretailladeet al. use sequence motifs upstream of start codons to annotate or re-annotate microsporidian genomes and find new genes potentially involved in interactions with the host.

    • Eric Peyretaillade
    • , Nicolas Parisot
    •  & Pierre Peyret

  • Article |

    It has been proposed that phylogenetic diversity can be used as a proxy to estimate functional diversity and to predict ecosystem functioning. Here, the rapid evolutionary response of marine bacteria is used to study the positive effects of evolutionary history and species diversity on ecosystem productivity.

    • Dominique Gravel
    • , Thomas Bell
    •  & Nicolas Mouquet

  • Article
    | Open Access

    The ability of oleaginous fungi to produce lipids for biofuels remains untapped, in part due to a lack of genetic information required to engineer industrial strains. Zhuet al. present the genome of R. toruloides, and identify transcriptomic and proteomic changes associated with lipid production.

    • Zhiwei Zhu
    • , Sufang Zhang
    •  & Zongbao K. Zhao

  • Article
    | Open Access

    Sodium-gated ion channels open and close in response to the flow of ions. Here, McCusker et al.report the open structure of a sodium-gated ion channel pore from a bacterial homologue, and show, by comparison with the closed structure, that the movement of a C-terminal helix is sufficient to open the channel.

    • Emily C. McCusker
    • , Claire Bagnéris
    •  & B.A. Wallace

  • Article |

    Methane is an important anthropogenic greenhouse gas and is thought to be produced by industrial processes and prokaryotic methanogenic Archaea. In this study, the saprotrophic fungi,Basidiomycetes, is shown to produce methane in the absence of methanogenic Archaea.

    • Katharina Lenhart
    • , Michael Bunge
    •  & Frank Keppler

  • Article |

    Mechanosensitive channels are required to sense cell swelling in response to osmotic shock. Nakayamaet al.report that Msy1 and Msy2 are the fission yeast homologues of the bacterial mechanosensitive channel MscS, and are required for regulating intracellular calcium in response to cell swelling.

    • Yoshitaka Nakayama
    • , Kenjiro Yoshimura
    •  & Hidetoshi Iida

  • Article |

    The bacterial channel protein MscL opens in response to mechanical forces and could be exploited for vesicular-based drug delivery. Doerneret al. show that functional MscL can be expressed in mammalian cells and facilitate the controlled cellular uptake of relatively large, membrane-impermeable bioactive molecules.

    • Julia F. Doerner
    • , Sebastien Febvay
    •  & David E. Clapham

  • Article
    | Open Access

    The clustered regularly interspaced short palindromic repeats (CRISPR) system protects prokaryotes from foreign DNA. Here, bacteriophage DNA containing mutations that can circumvent this response are shown to be incorporated into the CRISPR locus, allowing bacteria to remember previous infections in an adaptive manner.

    • Kirill A. Datsenko
    • , Ksenia Pougach
    •  & Ekaterina Semenova

  • Article
    | Open Access

    Ganoderma lucidumis a macrofungus in traditional Chinese medicine known to produce different bioactive compounds. In this study, the genome ofG. lucidumis sequenced, making this organism a potential model system for future studies of secondary metabolic pathways and their regulation in medicinal fungi.

    • Shilin Chen
    • , Jiang Xu
    •  & Chao Sun

  • Article
    | Open Access

    Vascular plants with root systems evolved in the mid-Palaeozoic with symbiotic fungi. Fieldet al. show that in contrast to non-vascular plants lacking roots, the efficiency of plant–fungal symbiosis increased for vascular plants with root systems as carbon dioxide levels declined in the mid-Palaeozoic.

    • Katie J. Field
    • , Duncan D. Cameron
    •  & David J. Beerling

  • Article |

    Lamivudine treatment of hepatitis B is associated with drug-resistance mutations in the virus’ DNA polymerase. In this study, 11 patients with drug resistance are investigated and the primary mutation in the DNA polymerase shown to be essential but not sufficient for establishing drug resistance.

    • Hong Thai
    • , David S. Campo
    •  & Yury Khudyakov

  • Article |

    Microbial metabolism is usually considered to be phototrophic or chemotrophic. By showing that light-induced photoelectrons from metal oxide and metal sulfides can stimulate the growth of chemoautotrophic and heterotrophic bacteria, this study indicates that light may be involved in non-phototrophic microbial activity.

    • Anhuai Lu
    • , Yan Li
    •  & Hailiang Dong

  • Article |

    Graphene is characterized by unique physical properties that offer substantial promise, most notably for electronic applications. Mannooret al. present a wireless graphene-based sensor for detecting bacteria on a range of biological tissues.

    • Manu S. Mannoor
    • , Hu Tao
    •  & Michael C. McAlpine

  • Article |

    The treatment ofMycobacterium tuberculosis with drugs such as isoniazid often results in drug resistance, but the mechanisms leading to the resistance are not fully known. In this study, an M. tuberculosisstrain lacking the sigma factor I is shown to be resistant to isoniazid.

    • Jong-Hee Lee
    • , Nicole C. Ammerman
    •  & William R. Bishai

  • Article |

    It is unclear whether pathogens can advantageously exploit the host's immune response. UsingCandida albicans, the authors show that host IL-17A binds to the fungi and induces nutrient starvation and autophagy, which eventually leads to enhanced biofilm formation and resistance to the hosts' defence.

    • Teresa Zelante
    • , Rossana G. Iannitti
    •  & Luigina Romani

  • Article
    | Open Access

    GALgenes enhance their own transcription via the transcription factor Gal4p, and the number of Galp4 sites in a promoter is expected to strengthen the feedback. In this study, Hsuet al. show that instead the feedback loops are activated by genes that have frequent bursts of expression and fast RNA decay kinetics.

    • Chieh Hsu
    • , Simone Scherrer
    •  & Attila Becskei

  • Article
    | Open Access

    Myeloid cells are important in the response to severe infection by invasiveStreptococcusGroup A. In this study, a distinct population of immature myeloid cells with ring shaped nuclei that produce interferon-γ are shown to be important for protection of mice against the early stages of invasive infection.

    • Takayuki Matsumura
    • , Manabu Ato
    •  & Kazuo Kobayashi

  • Article
    | Open Access

    Epitopes presented by MHC-II molecules bind to T-cell receptors to activate CD4+ T cells. In this study, changes in the carboxy-terminal region of the influenza hemagglutinin epitope HA305-320alters the strength of binding to the T-cell receptor, thus modulating T-cell receptor usage and activation.

    • David K. Cole
    • , Kathleen Gallagher
    •  & Andrew Godkin

  • Article
    | Open Access

    The influenza A virus genome consists of eight RNA segments, which permits genetic reassortment and contributes to the emergence of novel strains with pandemic potential. Here, electron tomography is used to study the three-dimensional structure of ribonucleoprotein complexes within progeny virions.

    • Takeshi Noda
    • , Yukihiko Sugita
    •  & Yoshihiro Kawaoka

  • Article |

    Genome-scale metabolic models for bacterial species allow a systematic study of inter-species interactions. Here, competitive and cooperative potential is predicted between 6,903 pairs of species, to explore the role of these interactions in shaping coexistence patterns in natural communities.

    • Shiri Freilich
    • , Raphy Zarecki
    •  & Eytan Ruppin

  • Article |

    Herpesvirus glycoprotein D binds to nectin 1 and the herpes virus entry mediator protein on the surface of host cells. In this study, Zhanget al. report the crystal structure of glycoprotein D in complex with the immunoglobulin-like domains of nectin 1, which suggests that binding of glycoprotein D to nectin 1 prevents nectin 1 dimerization.

    • Na Zhang
    • , Jinghua Yan
    •  & George F Gao

  • Article
    | Open Access

    New approaches are required to combatPlasmodium falciparuminfection. In this proteome-wide study, 1305 phosphorylation sites are identified and 36 kinases are shown to have crucial roles in parasite survival, providing new insights into parasite biology and potential new drug targets for anti-malarial chemotherapy.

    • Lev Solyakov
    • , Jean Halbert
    •  & Christian Doerig

  • Article |

    The 30S ribosomal subunit ofEscherichia coliinhibits the RNA-degrading enzyme Ribonuclease T2. Using mutational studies and hybrid ribosomes, Kitahara and Miyazaki show that helix 41 of the 30S ribosomal subunit blocks the enzyme activity, suggesting that helix 41 is required for preventing RNase T2 toxicity.

    • Kei Kitahara
    •  & Kentaro Miyazaki

  • Article |

    Parasites such as malaria elicit an immune response in their host, causing cytokine levels to increase. In this study, a parasite housekeeping gene, tyrosyl-tRNA synthetase, is shown to bind to host macrophages and, once inside the cells, enhance the levels of proinflammatory cytokines.

    • Tarun Kumar Bhatt
    • , Sameena Khan
    •  & Amit Sharma

  • Article
    | Open Access

    The risk factors associated with both ischemic and haemorrhagic stroke are not fully understood. Here a certain strain of the bacteria,Streptococcus mutans, which expresses a collagen-binding protein, is shown to be associated with haemorrhagic stroke in both animal models and human patients.

    • Kazuhiko Nakano
    • , Kazuya Hokamura
    •  & Takashi Ooshima

  • Article
    | Open Access

    A bacterial export gate complex transports flagellar proteins across the cytoplasmic membrane, but the mechanism of this process is unclear. Here, the export gate complex is revealed as a proton–protein antiporter that uses separate components of the proton motive force for different steps of the export process.

    • Tohru Minamino
    • , Yusuke V. Morimoto
    •  & Keiichi Namba

  • Article
    | Open Access

    Group BStreptococcuscauses meningitis in newborn infants but how the bacterium crosses the blood-brain barrier is unknown. Here, the bacterial pili adhesion molecule, PilA, is shown to bind to collagen and promote binding of the bacteria to integrins expressed on the blood-brain endothelium.

    • Anirban Banerjee
    • , Brandon J. Kim
    •  & Kelly S. Doran

  • Article
    | Open Access

    The chronic disease schistosomiasis is caused by the blood flukeSchistosoma mansoni. By studying DNA modifications throughout the lifecycle of the pathogen, the authors identify DNA methylation as a factor in egg development and suggest that the epigenetic machinery responsible may be a therapeutic target.

    • Kathrin K. Geyer
    • , Carlos M. Rodríguez López
    •  & Karl F. Hoffmann

  • Article
    | Open Access

    Dissolved organic matter, the main form of aquatic organic carbon, supports the aquatic food web and regulates light penetration in lakes. This study probes the main influences on the optical properties of dissolved organic matter in a global dataset of alpine and remote lakes revealing latitudinal trends.

    • N. Mladenov
    • , R. Sommaruga
    •  & I. Reche

  • Article
    | Open Access

    Group-1 influenza A neuramidase proteins have a 150-cavity that can be targeted by drugs, but the 2009 H1N1 virus neuramidase is not thought to have a 150-cavity. Here, biophysical simulations show that the 2009 H1N1 neuramidase exists in solution with an open 150-cavity, which is stabilized by a salt bridge.

    • Rommie E. Amaro
    • , Robert V. Swift
    •  & Robin M. Bush

  • Article |

    Studying how pathogens enter polarized epithelial cells is important for understanding infection. Here, activation of chemokine receptors on the apical membrane of epithelial cells, is shown to engage Src family tyrosine signalling, resulting in relocation of the viral co-receptor αvβ3 to the apical membrane and adenovirus entry.

    • Verena Lütschg
    • , Karin Boucke
    •  & Urs F. Greber

  • Article |

    Phylogenetic analysis is used to identify transmission chains, but no software is available for the automated partition of large phylogenies. Prosperiet al. apply a new search algorithm to identify transmission clusters within the phylogeny of HIV-1gene sequences linking molecular and epidemiological data.

    • Mattia C.F. Prosperi
    • , Massimo Ciccozzi
    •  & Andrea De Luca

  • Article
    | Open Access

    Secondary metabolites are widely used in human health and nutrition, but extraction yields from plants are often low. Nakagawaet al. have engineered the metabolism of Escherichia colito develop a fermentation system that produces plant alkaloids from simple carbon sources.

    • Akira Nakagawa
    • , Hiromichi Minami
    •  & Hidehiko Kumagai

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