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| Open AccessFunctional and evolutionary significance of unknown genes from uncultivated taxa
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
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Article
| Open AccessBiosynthetic potential of the global ocean microbiome
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
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Article |
Chemotaxis shapes the microscale organization of the ocean’s microbiome
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
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Article
| Open AccessTerrestrial-type nitrogen-fixing symbiosis between seagrass and a marine bacterium
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
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Article |
Structure of Geobacter pili reveals secretory rather than nanowire behaviour
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
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Article |
Bacterial chemolithoautotrophy via manganese oxidation
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
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Article
| Open AccessClades of huge phages from across Earth’s ecosystems
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
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Article
| Open AccessGiant virus diversity and host interactions through global metagenomics
Analysis of metagenomics data revealed that large and giant viruses are globally widely distributed and are associated with most major eukaryotic lineages.
- Frederik Schulz
- , Simon Roux
- & Tanja Woyke
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Article |
Light-driven anaerobic microbial oxidation of manganese
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
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Article
| Open AccessNew insights from uncultivated genomes of the global human gut microbiome
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
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Letter |
Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis
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
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Letter
| Open AccessAtmospheric trace gases support primary production in Antarctic desert surface soil
Metagenomic and biochemical analyses of soil samples from Antarctic desert regions provides evidence that bacteria in these soils derive carbon and energy from atmospheric CO, H2 and CO2.
- Mukan Ji
- , Chris Greening
- & Belinda C. Ferrari
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Article
| Open AccessA communal catalogue reveals Earth’s multiscale microbial diversity
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
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Letter |
Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle
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
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Article |
Thermophilic archaea activate butane via alkyl-coenzyme M formation
Anaerobic archaea enriched in thermophilic microbial consortia completely degrade butane by modifying mechanisms which were hitherto thought to be specific to methane metabolism.
- Rafael Laso-Pérez
- , Gunter Wegener
- & Florin Musat
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Letter |
Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses
The assembly and analysis of complete genomes and large genomic fragments have tripled the number of known ocean viruses and uncovered the potentially important roles they play in nitrogen and sulfur cycling.
- Simon Roux
- , Jennifer R. Brum
- & Matthew B. Sullivan
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Article |
SAR11 bacteria linked to ocean anoxia and nitrogen loss
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
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Letter |
Environmental Breviatea harbour mutualistic Arcobacter epibionts
The cultivation of Lenisia limosa, a newly discovered breviate protist, symbiotically colonized by relatives of the animal-associated bacterium Arcobacter.
- Emmo Hamann
- , Harald Gruber-Vodicka
- & Marc Strous
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Letter |
Complete nitrification by a single microorganism
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
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Article |
Complete nitrification by Nitrospira bacteria
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
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Letter |
Intercellular wiring enables electron transfer between methanotrophic archaea and bacteria
Marine anaerobic methanotrophic archaea and sulfate-reducing bacteria connect by pili-like nanowires, suggesting that direct interspecies exchange of electrons could be a fundamental mechanism in the anaerobic oxidation of methane.
- Gunter Wegener
- , Viola Krukenberg
- & Antje Boetius
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Article |
Single cell activity reveals direct electron transfer in methanotrophic consortia
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
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Letter |
Cyanate as an energy source for nitrifiers
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
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Letter |
Unusual biology across a group comprising more than 15% of domain Bacteria
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
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Letter |
Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes
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
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Letter |
Viral tagging reveals discrete populations in Synechococcus viral genome sequence space
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
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Letter |
Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage
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
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Brief Communications Arising |
Giovannoni et al. reply
- Stephen Giovannoni
- , Ben Temperton
- & Yanlin Zhao
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Brief Communications Arising |
SAR11 viruses and defensive host strains
- Selina Våge
- , Julia E. Storesund
- & T. Frede Thingstad
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Letter |
Gene expression in the deep biosphere
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
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Letter |
Predominant archaea in marine sediments degrade detrital proteins
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
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News |
There are fewer microbes out there than you think
New estimate reduces the number of microbes on Earth by around half.
- Kathryn Lougheed
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Letter |
Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota
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
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News |
China third country to be hit by ‘brown tide’
Scientists identify causative species of algal bloom.
- Jane Qiu
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News |
US beef tests cook up a storm
Critics question benefits of broader E. coli screening.
- Helen Shen
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Research Highlights |
Seal corpses shelter Antarctic microbes
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Editorial |
Contaminated food for thought
If it is to deal effectively with outbreaks of infectious diseases, Germany must streamline its convoluted systems for reporting and communication.
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News |
Subterranean worms from hell
New species of nematode discovered more than a kilometre underground.
- Nadia Drake
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News |
Antibiotic resistance shows up in India's drinking water
Discovery of NDM-1 outside hospital environment raises alarm.
- Naomi Lubick
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News |
Virus-eater discovered in Antarctic lake
First of the parasitic parasites to be discovered in a natural environment points to hidden diversity.
- Virginia Gewin
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News |
Dumped drugs lead to resistant microbes
A continual discharge of antibiotic-contaminated water has created a hotspot of bacterial antibiotic resistance in an Indian river.
- Naomi Lubick
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Feature |
Public health: Food-safety sentinels
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
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News Feature |
Microbiology: The new germ theory
What can microbiologists who study human bowels learn from those who study the bowels of Earth?
- Lizzie Buchen
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Research Highlights |
Microbiology: Bacteria for breakfast
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News |
Microbe carries minimalism to extremes
Heat-loving organisms survive on surprisingly meagre rations.
- Amy Maxmen
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News & Views |
Close relatives are bad news
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
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Research Highlights |
Microbiology: Hitching a ride
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News & Views |
Genetic pot luck
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