Featured
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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 |
Amphibians acquire resistance to live and dead fungus overcoming fungal immunosuppression
The fungal pathogen Batrachochytrium dendrobatidis has been implicated in the decline of a large number of amphibian species; here it is shown that frogs can learn to avoid the pathogen, acquire resistance to it and be immunized against it using dead pathogen, findings that potentially offer a way in which resistant populations could be reintroduced into areas that have seen catastrophic declines.
- Taegan A. McMahon
- , Brittany F. Sears
- & Jason R. Rohr
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Letter |
Bacterial phylogeny structures soil resistomes across habitats
Functional metagenomic selections for resistance to 18 antibiotics in 18 different soils reveal that bacterial community composition is the primary determinant of soil antibiotic resistance gene content.
- Kevin J. Forsberg
- , Sanket Patel
- & Gautam Dantas
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Letter |
Trace-gas metabolic versatility of the facultative methanotroph Methylocella silvestris
Distinct groups of microorganisms have been thought to grow on methane and on short-chain alkanes; now, the methanotroph Methylocella silvestris is shown to express two distinct soluble di-iron centre monooxygenases that allow it to use either methane or propane as a carbon and energy source.
- Andrew T. Crombie
- & J. Colin Murrell
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Letter |
Reconciliation of the carbon budget in the ocean’s twilight zone
The discrepancy between the components of the oceanic carbon budget — export of carbon from the surface and its conversion into carbon dioxide by water-column biota at depth — is reconciled using field data and a steady-state model which indicates that synergy between microbes and zooplankton is an important factor.
- Sarah L. C. Giering
- , Richard Sanders
- & Daniel J. Mayor
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Letter |
Nitrogen losses in anoxic marine sediments driven by Thioploca–anammox bacterial consortia
A novel symbiotic consortium is described between two chemolithotrophic bacteria — anaerobic ammonium-oxidizing (anammox) bacteria and the nitrate-sequestering sulphur-oxidizing Thioploca species — in anoxic sediments of the Soledad basin at the Mexican Pacific margin.
- M. G. Prokopenko
- , M. B. Hirst
- & D. M. Sigman
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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 |
Diverse type VI secretion phospholipases are functionally plastic antibacterial effectors
A functionally diverse superfamily of bacterial phospholipase enzymes that mediate antagonisitc interactions as effectors of the type VI secretion system is uncovered; these enzymes degrade the bacterial membrane, representing a novel mechanism of bacterial competition.
- Alistair B. Russell
- , Michele LeRoux
- & Joseph D. Mougous
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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 |
Life abounds in Antarctic lake sealed under ice
Lake Vida's cold brine has yielded a bounty of microbes.
- Quirin Schiermeier
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Research Highlights |
Populations cooperate
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Research Highlights |
Ecosystems compete
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Review Article |
Diversity, stability and resilience of the human gut microbiota
- Catherine A. Lozupone
- , Jesse I. Stombaugh
- & Rob Knight
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Review Article |
Functional interactions between the gut microbiota and host metabolism
- Valentina Tremaroli
- & Fredrik Bäckhed
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Review Article |
Reciprocal interactions of the intestinal microbiota and immune system
- Craig L. Maynard
- , Charles O. Elson
- & Casey T. Weaver
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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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Article |
Human gut microbiome viewed across age and geography
The human gut microbiome from a large cohort of more than 500 indivduals living on three continents with three distinct cultures is analysed, emphasizing the effect of host age, diet and environment on the composition and functional repertoire of fecal microbiota.
- Tanya Yatsunenko
- , Federico E. Rey
- & Jeffrey I. Gordon
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Research Highlights |
Seal corpses shelter Antarctic microbes
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Letter |
Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw
- Rachel Mackelprang
- , Mark P. Waldrop
- & Janet K. Jansson
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Research Highlights |
Reefs wrecked by shipwrecks
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Research Highlights |
Russian doll-style symbiosis
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News & Views |
Arms race in a drop of sea water
Marine cyanobacteria can shrug off viral assault by inactivating the genes involved in virus attachment. But this strategy has a cost: it may affect cell fitness or even favour infection by other viruses. See Article p.604
- Frédéric Partensky
- & Laurence Garczarek
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Article |
Genomic island variability facilitates Prochlorococcus–virus coexistence
- Sarit Avrani
- , Omri Wurtzel
- & Debbie Lindell
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News |
Critics weigh in on arsenic life
Field needs independent experiments to prove or disprove the work, researchers say.
- Erika Check Hayden
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Letter |
Metabolic trade-offs and the maintenance of the fittest and the flattest
- Robert E. Beardmore
- , Ivana Gudelj
- & Laurence D. Hurst
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News |
Slime moulds prosper on the microfarm
Soil-dwelling amoebae harvest and transport their food.
- Geoff Marsh
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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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Letter |
Early oxygenation of the terrestrial environment during the Mesoproterozoic
It is thought that rises in atmospheric oxygen concentrations occurred about 2.3 and 0.8 billion years ago, with the latter implicated in the subsequent evolutionary expansion of complex biota. Sulphur isotope fractionation data from an ancient sedimentary succession in Scotland now suggest that the terrestrial environment was already sufficiently oxygenated to support a biota adapted to an oxygen-rich atmosphere about 1.2 billion years ago.
- John Parnell
- , Adrian J. Boyce
- & Sam Spinks
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Research Highlights |
Ecology: Hunt for pathogen's home
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Research Highlights |
Microbial ecology: Sated snakes
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Research Highlights |
Microbial ecology: Bacterial pest killer
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Letter |
Stoichiometric control of organic carbon–nitrate relationships from soils to the sea
The accumulation of nitrate in freshwater and coastal marine ecosystems is one of the consequences of the worldwide production of artificial fertilizers. Here it is shown that nitrate accumulation in ecosystems shows consistent and negative nonlinear correlations with organic carbon availability, along a continuum from soils, through freshwater systems and coastal margins, to the open ocean. This pattern can be explained by carbon:nitrate ratios, which influence nitrate accumulation by regulating microbial processes.
- Philip G. Taylor
- & Alan R. Townsend
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News |
Hostile volcanic lake teems with life
Microbes thriving in salty, alkali waters containing arsenic.
- Ana Belluscio
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News |
Methane-eating microbes make their own oxygen
Bacteria may have survived on Earth without plants, thanks to unique metabolism.
- Amanda Leigh Mascarelli
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Letter |
Electric currents couple spatially separated biogeochemical processes in marine sediment
It has been previously demonstrated that some microbes are capable of extracellular electron transport through so–called nanowires or electron shuttles. Here it is demonstrated that this may be a significant process in the marine sediment.
- Lars Peter Nielsen
- , Nils Risgaard-Petersen
- & Mikio Sayama
A microbial ecosystem beneath the West Antarctic ice sheet