Environmental microbiology articles within Nature

Featured

  • 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
    | Open Access

    We analysed 149,842 environmental genomes from multiple habitats and compiled a curated catalogue of 404,085 functionally and evolutionarily significant novel gene families exclusive to uncultivated prokaryotic taxa spanning multiple species.

    • Álvaro Rodríguez del Río
    • , Joaquín Giner-Lamia
    •  & Jaime Huerta-Cepas

  • Article
    | Open Access

    Global ocean microbiome survey reveals the bacterial family ‘Candidatus Eudoremicrobiaceae’, which includes some of the most biosynthetically diverse microorganisms in the ocean environment.

    • Lucas Paoli
    • , Hans-Joachim Ruscheweyh
    •  & Shinichi Sunagawa

  • Article |

    In situ experiments have demonstrated chemotaxis of marine bacteria and archaea towards specific phytoplankton-derived dissolved organic matter, which leads to microscale partitioning of biogeochemical transformation in the ocean.

    • Jean-Baptiste Raina
    • , Bennett S. Lambert
    •  & Justin R. Seymour

  • 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 |

    Structural, functional and localization studies reveal that Geobacter sulfurreducens pili cannot behave as microbial nanowires, instead functioning in a similar way to secretion pseudopili to export cytochrome nanowires that are essential for extracellular electron transfer.

    • Yangqi Gu
    • , Vishok Srikanth
    •  & Nikhil S. Malvankar

  • Article |

    A co-culture of two newly identified microorganisms—‘Candidatus Manganitrophus noduliformans’ and Ramlibacter lithotrophicus—exhibits exponential growth that is dependent on manganese(II) oxidation, demonstrating the viability of this metabolism for supporting life.

    • Hang Yu
    •  & Jared R. Leadbetter

  • Article
    | Open Access

    Genomic analyses of major clades of huge phages sampled from across Earth’s ecosystems show that they have diverse genetic inventories, including a variety of CRISPR–Cas systems and translation-relevant genes.

    • Basem Al-Shayeb
    • , Rohan Sachdeva
    •  & Jillian F. Banfield

  • Article |

    Anoxygenic photosynthetic microorganisms can biomineralize manganese oxides without molecular oxygen being present and without high-potential photosynthetic reaction centres, which sheds doubt on proposed dates for the origins of oxygenic photosynthetic metabolism.

    • Mirna Daye
    • , Vanja Klepac-Ceraj
    •  & Tanja Bosak

  • Article
    | Open Access

    Draft prokaryotic genomes from faecal metagenomes of diverse human populations enrich our understanding of the human gut microbiome by identifying over two thousand new species-level taxa that have numerous disease associations.

    • Stephen Nayfach
    • , Zhou Jason Shi
    •  & Nikos C. Kyrpides

  • 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
    | Open Access

    As phase 1 of the Earth Microbiome Project, analysis of 16S ribosomal RNA sequences from more than 27,000 environmental samples delivers a global picture of the basic structure and drivers of microbial distribution.

    • Luke R. Thompson
    • , Jon G. Sanders
    •  & Hongxia Zhao

  • 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

  • Article |

    Bacteria of the SAR11 clade constitute up to one half of all marine microbes and are thought to require oxygen for growth; here, a subgroup of SAR11 bacteria are shown to thrive in ocean oxygen minimum zones and to encode abundant respiratory nitrate reductases.

    • Despina Tsementzi
    • , Jieying Wu
    •  & Frank J. Stewart

  • Letter |

    Until now, the oxidation steps necessary for complete nitrification had always been observed to occur in two separate microorganisms in a cross-feeding interaction; here, together with the study by Daims et al., van Kessel et al. report the enrichment and characterization of Nitrospira species that encode all of the enzymes necessary to catalyse complete nitrification, a phenotype referred to as ‘comammox’ (for complete ammonia oxidation).

    • Maartje A. H. J. van Kessel
    • , Daan R. Speth
    •  & Sebastian Lücker

  • Article |

    Until now, the oxidation steps necessary for complete nitrification have always been observed to occur in two separate microorganisms in a cross-feeding interaction; here, together with the study by van Kessel et al., Daims et al. report the enrichment and characterization of Nitrospira species that encode all of the enzymes necessary to catalyse complete nitrification, a phenotype referred to as “comammox” (for complete ammonia oxidation).

    • Holger Daims
    • , Elena V. Lebedeva
    •  & Michael Wagner

  • 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 ammonia-oxidizing archaeon Nitrososphaera gargensis can utilize cyanate as the only source of energy for growth due to the presence of a cyanase enzyme, and cyanase-encoding nitrite-oxidizing bacteria can work together with cyanase-negative ammonia oxidizers to collectively grow on cyanate via reciprocal feeding; cyanases are widespread in the environment according to metagenomic data sets, pointing to the potential importance of cyanate in the nitrogen cycle.

    • Marton Palatinszky
    • , Craig Herbold
    •  & Michael Wagner

  • Letter |

    More than 15% of the bacterial domain consists of a radiation of phyla about which very little is known; here, metagenomics is used to reconstruct 8 complete and 789 draft genomes from more than 35 of these phyla, revealing a shared evolutionary history, metabolic limitations, and unusual ribosome compositions.

    • Christopher T. Brown
    • , Laura A. Hug
    •  & Jillian F. Banfield

  • Letter |

    A multi-omics approach, integrating metagenomics, metatranscriptomics and metaproteomics, determines the phylogenetic composition of the microbial community and assesses its functional potential and activity along a thaw transition from intact permafrost to thermokast bog.

    • Jenni Hultman
    • , Mark P. Waldrop
    •  & Janet K. Jansson

  • Letter |

    The metagenome of uncultured, Pacific Ocean viruses linked to a ubiquitous cyanobacteria is characterized using viral-tagging, revealing discrete populations in viral sequence space that includes previously cultivated populations and new populations missed in isolate-based studies.

    • Li Deng
    • , J. Cesar Ignacio-Espinoza
    •  & Matthew B. Sullivan

  • Letter |

    An anaerobic methanotroph (ANME-2d) can perform nitrate-driven anaerobic oxidation of methane through reverse methanogenesis, using nitrate as the terminal electron acceptor, and nitrite produced by ANME-2d is reduced to dinitrogen gas through a syntrophic relationship with an anaerobic ammonium-oxidizing bacterium.

    • Mohamed F. Haroon
    • , Shihu Hu
    •  & Gene W. Tyson

  • Letter |

    Gene expression of microbes in anaerobic sediment from the Peru Margin at depths up to 159 metres below the sea floor is analysed: anaerobic metabolism of amino acids, carbohydrates and lipids are seen to be the dominant metabolic processes, and genes associated with cell division are found to be correlated with microbial cell concentration, suggesting that ongoing cell division contributes to biomass turnover.

    • William D. Orsi
    • , Virginia P. Edgcomb
    •  & Jennifer F. Biddle

  • Letter |

    Miscellaneous crenarchaeotal group (MCG) and marine benthic group-D (MBG-D) are among the most numerous archaea in sea-floor sediments; single-cell genomics reveals that these archaea belong to new branches of the archaeal tree and probably have a role in protein remineralization in anoxic marine sediments.

    • Karen G. Lloyd
    • , Lars Schreiber
    •  & Bo Barker Jørgensen

  • Letter |

    Roots of land plants are populated by a specific microbiota capable of modulating plant growth and development; here large-scale sequencing analysis shows that the bacterial community inhabiting Arabidopsis roots is influenced by soil type and plant genotype, and that plant cell-wall features serve as colonization cue for a subcommunity of the root microbiota.

    • Davide Bulgarelli
    • , Matthias Rott
    •  & Paul Schulze-Lefert

  • Editorial |

    If it is to deal effectively with outbreaks of infectious diseases, Germany must streamline its convoluted systems for reporting and communication.

  • News |

    A continual discharge of antibiotic-contaminated water has created a hotspot of bacterial antibiotic resistance in an Indian river.

    • Naomi Lubick

  • Feature |

    Disease outbreaks in recent years have revealed the vulnerability of food supplies. But they offer opportunities for those interested in waging war on microbes.

    • Laura Cassiday

  • News Feature |

    What can microbiologists who study human bowels learn from those who study the bowels of Earth?

    • Lizzie Buchen

  • News & Views |

    In tropical rainforests, tree seedlings growing close to their parent are more likely to die. This mortality, caused by soil organisms, helps to explain the coexistence and relative abundance of species.

    • Owen T. Lewis

  • News & Views |

    Without the trillions of microbes that inhabit our gut, we can't fully benefit from the components of our diet. But cultural differences in diet may, in part, dictate what food our gut microbiota can digest.

    • Justin L. Sonnenburg

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