Microbial ecology articles within Nature

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  • Article
    | Open Access

    Cultivation of a new anoxygenic phototrophic bacterium from Boreal Shield lake water—representing a transition form in the evolution of photosynthesis—offers insights into how the major modes of phototrophy diversified.

    • J. M. Tsuji
    • , N. A. Shaw
    •  & J. D. Neufeld

  • Article |

    Recent resurgences of highly pathogenic avian influenza H5 viruses have different origins and virus ecologies as their epicentres shift and viruses evolve, with changes indicating increased adaptation among domestic birds.

    • Ruopeng Xie
    • , Kimberly M. Edwards
    •  & Vijaykrishna Dhanasekaran

  • Article
    | Open Access

    An assessment of variations in phytoplankton nutrient limitation in the tropical Pacific over the past two decades finds that phytoplankton iron limitation is more stable in response to ENSO dynamics than models predict.

    • Thomas J. Browning
    • , Mak A. Saito
    •  & Alessandro Tagliabue

  • Article |

    Provora is an ancient supergroup of microbial predators that are genetically, morphologically and behaviourally distinct from other eukaryotes, and comprise two divergent clades of predators—Nebulidia and Nibbleridia—that differ fundamentally in ultrastructure, behaviour and gene content.

    • Denis V. Tikhonenkov
    • , Kirill V. Mikhailov
    •  & Patrick J. Keeling

  • Article |

    Changes in climate and land use will lead to species aggregating in new combinations at high elevations, in biodiversity hotspots and in areas of high human population density in Asia and Africa, driving the cross-species transmission of animal-associated viruses.

    • Colin J. Carlson
    • , Gregory F. Albery
    •  & Shweta Bansal

  • Article |

    A bacterial enzyme is characterized and demonstrated to have Ni2+-dependent activity and high specificity for free guanidine enabling the bacteria to use guanidine as the sole nitrogen source for growth.

    • D. Funck
    • , M. Sinn
    •  & J. S. Hartig

  • Article |

    A survey of species-level genes from 13,174 publicly available metagenomes shows that most species-level genes are specific to a single habitat, encode a small number of protein families and are under low positive (adaptive) pressure.

    • Luis Pedro Coelho
    • , Renato Alves
    •  & Peer Bork

  • Article
    | Open Access

    The N2-fixing symbiont ‘Candidatus Celerinatantimonas neptuna’ lives inside the root tissue of the seagrass Posidonia oceanica, providing ammonia and amino acids to its host in exchange for sugars and enabling highly productive seagrass meadows to thrive in the nitrogen-limited Mediterranean Sea.

    • Wiebke Mohr
    • , Nadine Lehnen
    •  & Marcel M. M. Kuypers

  • Article
    | Open Access

    ‘Candidatus Azoamicus ciliaticola’ transfers energy to its ciliate host in the form of ATP and enables this host to breathe nitrate, demonstrating that eukaryotes with remnant mitochondria can secondarily acquire energy-providing endosymbionts.

    • Jon S. Graf
    • , Sina Schorn
    •  & Jana Milucka

  • Article |

    Absolute microbial abundances delineate longitudinal dynamics of bacteria, fungi and archaea in the infant gut microbiome, uncovering drivers of microbiome development masked by relative abundances and revealing notable parallels to macroscopic ecosystem assemblies.

    • Chitong Rao
    • , Katharine Z. Coyte
    •  & Seth Rakoff-Nahoum

  • Article |

    Ruhugu virus and rustrela virus are the first close relatives of rubella virus, providing insights into the zoonotic origin of rubella virus and the epidemiology and evolution of all three viruses.

    • Andrew J. Bennett
    • , Adrian C. Paskey
    •  & Tony L. Goldberg

  • Article |

    Reduced abundance of immune-stimulating gut bacteria ameliorated the inflammatory and autoimmune phenotypes of mice with mutations in C9orf72, which in the human orthologue are linked to amyotrophic lateral sclerosis and frontotemporal dementia.

    • Aaron Burberry
    • , Michael F. Wells
    •  & Kevin Eggan

  • Article |

    Analyses of microbial communities that live 10–750 m below the seafloor at Atlantis Bank, Indian Ocean, provide insights into how these microorganisms survive by coupling energy sources to organic and inorganic carbon resources.

    • Jiangtao Li
    • , Paraskevi Mara
    •  & Virginia P. Edgcomb

  • Article |

    Marine Proteobacteria use the β-hydroxyaspartate cycle to assimilate glycolate, which is secreted by algae on a petagram scale, providing evidence of a previously undescribed trophic interaction between autotrophic phytoplankton and heterotrophic bacterioplankton.

    • Lennart Schada von Borzyskowski
    • , Francesca Severi
    •  & Tobias J. Erb

  • Article |

    The human placenta does not have a microbiota, suggesting that bacterial infection of the placenta is not a common cause of adverse pregnancy outcome, but group B Streptococcus is found in approximately 5% of placental samples.

    • Marcus C. de Goffau
    • , Susanne Lager
    •  & Gordon C. S. Smith

  • Article |

    The authors systematically characterize structural variation in the genomes of gut microbiota and show that they are associated with bacterial fitness and with host risk factors, and that examining genes coded in these regions facilitates investigation of mechanisms that may underlie these associations.

    • David Zeevi
    • , Tal Korem
    •  & Eran Segal

  • Article |

    Lipopeptides secreted by Bacillus bacteria block quorum sensing by Staphylococcus aureus and thereby inhibit the growth of this opportunistic pathogen in the gut, suggesting why people in rural Thailand who are colonized by Bacillus are not also colonized by S. aureus.

    • Pipat Piewngam
    • , Yue Zheng
    •  & Michael Otto

  • Letter |

    Metagenomic, chemical and biomass analyses of topsoil samples from around the world reveal spatial and environmental trends in microbial community composition and genetic diversity.

    • Mohammad Bahram
    • , Falk Hildebrand
    •  & Peer Bork

  • Letter |

    Metagenomic and soil microcosm analyses identify abundant biosynthetic gene clusters in genomes of microorganisms from a northern Californian grassland ecosystem that provide a potential source for the future development of bacterial natural products.

    • Alexander Crits-Christoph
    • , Spencer Diamond
    •  & Jillian F. Banfield

  • Article |

    Analyses of data from 137 forest plots across 20 European countries show that ectomycorrhizal fungal diversity is strongly influenced by environmental and host species factors and provide thresholds to inform ecosystem assessment tools

    • Sietse van der Linde
    • , Laura M. Suz
    •  & Martin I. Bidartondo

  • Letter |

    Members of a family of marine dsDNA non-tailed bacterial viruses have short, 10-kb genomes, infect a broader range of hosts than tailed viruses and belong to the double jelly roll capsid lineage of viruses, which are associated with diverse bacterial and archaeal hosts.

    • Kathryn M. Kauffman
    • , Fatima A. Hussain
    •  & Martin F. Polz

  • Article |

    Two hypervirulent ribotypes of the enteric pathogen Clostridium difficile, RT027 and RT078, have independently acquired unique mechanisms to metabolize low concentrations of the disaccharide trehalose, suggesting a correlation between the emergence of these ribotypes and the widespread adoption of trehalose in the human diet.

    • J. Collins
    • , C. Robinson
    •  & R. A. Britton

  • Letter |

    Nutrient amendment experiments at the boundary of the South Atlantic gyre reveal extensive regions in which nitrogen and iron are co-limiting, with other micronutrients also approaching co-deficiency; such limitations potentially increase phytoplankton community diversity.

    • Thomas J. Browning
    • , Eric P. Achterberg
    •  & C. Mark Moore

  • Letter |

    A pure culture of the complete nitrifier Nitrospira inopinata shows a high affinity for ammonia, low maximum rate of ammonia oxidation, high growth yield compared to canonical nitrifiers and genomic potential for alternative metabolisms, probably reflecting an important role in nitrification in oligotrophic environments.

    • K. Dimitri Kits
    • , Christopher J. Sedlacek
    •  & Michael Wagner

  • Letter |

    A tree biodiversity and ecosystem function experiment shows that leaf bacterial diversity is positively related to plant community productivity, and explains a portion of the variation in productivity that would otherwise be attributed to plant diversity and functional traits.

    • Isabelle Laforest-Lapointe
    • , Alain Paquette
    •  & Steven W. Kembel

  • Letter |

    The authors investigated the disease ecology of the fast-spreading fungal pathogen Batrachochytrium salamandrivorans in fire salamanders; on the basis of their research, they call for Europe-wide monitoring systems and conservation strategies for threatened species.

    • Gwij Stegen
    • , Frank Pasmans
    •  & An Martel

  • Letter |

    Using a metagenomic approach, three types of CRISPR–Cas systems have been discovered in uncultivated bacterial and archaeal hosts from a variety of different environments.

    • David Burstein
    • , Lucas B. Harrington
    •  & Jillian F. Banfield

  • Article |

    An integrated computational approach that explores the viral content of more than 3,000 metagenomic samples collected globally highlights the existing global viral diversity, increases the known number of viral genes by an order of magnitude, and provides detailed insights into viral distribution across diverse ecosystems and into virus–host interactions.

    • David Paez-Espino
    • , Emiley A. Eloe-Fadrosh
    •  & Nikos C. Kyrpides

  • Letter |

    A new computational method to characterize the dynamics of human-associated microbial communities is applied to data from two large-scale metagenomic studies, and suggests that gut and mouth microbiomes of healthy individuals are subjected to universal (that is, host-independent) dynamics, whereas skin microbiomes are shaped by the host environment; the method paves the way to designing general microbiome-based therapies.

    • Amir Bashan
    • , Travis E. Gibson
    •  & Yang-Yu Liu

  • Article |

    An analysis of bacterial community structure and antibiotic resistance gene content of interconnected human faecal and environmental samples from two low-income communities in Latin America was carried out using a combination of functional metagenomics, 16S sequencing and shotgun sequencing; resistomes across habitats are generally structured along ecological gradients, but key resistance genes can cross these boundaries, and the authors assessed the usefulness of excreta management protocols in the prevention of resistance gene dissemination.

    • Erica C. Pehrsson
    • , Pablo Tsukayama
    •  & Gautam Dantas

  • Article |

    An analysis of 24 coral reef viromes challenges the view that lytic phage are believed to predominate when the density of their hosts increase and shows instead that lysogeny is more important at high host densities; the authors also show that this model is consistent with predator–prey dynamics in a range of other ecosystems, such as animal-associated, sediment and soil systems.

    • B. Knowles
    • , C. B. Silveira
    •  & F. Rohwer

  • Letter |

    In mice on a low microbiota-accessible carbohydrate (MAC) diet, the diversity of the gut microbiota is depleted, and the effect is transferred and compounded over generations; this phenotype is only reversed after supplementation of the missing taxa via faecal microbiota transplantation, suggesting dietary intervention alone may by insufficient at managing diseases characterized by a dysbiotic microbiota.

    • Erica D. Sonnenburg
    • , Samuel A. Smits
    •  & Justin L. Sonnenburg

  • Article |

    The anaerobic oxidation of methane in marine sediments is performed by consortia of methane-oxidizing archaea and sulfate-reducing bacteria; an examination of the role of interspecies spatial positioning on single cell activity reveals that interspecies electron transfer may overcome the requirement for close spatial proximity, a proposition supported by large multi-haem cytochromes in ANME-2 genomes as well as redox-active electron microscopy staining.

    • Shawn E. McGlynn
    • , Grayson L. Chadwick
    •  & Victoria J. Orphan

  • Letter |

    The abundance of key microbial lineages can be used to predict atmospherically relevant patterns in methane isotopes and the proportion of carbon metabolized to methane during permafrost thaw, suggesting that microbial ecology may be important in ecosystem-scale responses to global change.

    • Carmody K. McCalley
    • , Ben J. Woodcroft
    •  & Scott R. Saleska

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