Microbial ecology articles within Nature Communications

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  • Article
    | Open Access

    Bacteria can exchange nutrients and macromolecules through tubular membranous structures called nanotubes. Here, the authors show that Bacillus subtilis can kill and prey on Bacillus megaterium by delivering a toxin and extracting nutrients in a nanotube-dependent manner.

    • Ofer Stempler
    • , Amit K. Baidya
    •  & Sigal Ben-Yehuda

  • Article
    | Open Access

    Cooperative behaviour among individuals provides a collective benefit, but is considered costly. Using Pseudomonas aeruginosa as a model system, the authors show that secretion of the siderophore pyoverdine only incurs a fitness cost and favours cheating when its building blocks carbon or nitrogen are growth-limiting.

    • D. Joseph Sexton
    •  & Martin Schuster

  • Article
    | Open Access

    The extent to which the ocean acts as a sink and source of airborne particles to the atmosphere is unresolved. Here, the authors report high microbial loads over the tropical Atlantic, Pacific and Indian oceans and propose islands as stepping stones for the transoceanic transport of terrestrial microbes..

    • Eva Mayol
    • , Jesús M. Arrieta
    •  & Carlos M. Duarte

  • Article
    | Open Access

    Single-cell genomics can be used to study uncultured microorganisms. Here, Stepanauskas et al. present a method combining improved multiple displacement amplification and FACS, to obtain genomic sequences and cell size information from uncultivated microbial cells and viral particles in environmental samples.

    • Ramunas Stepanauskas
    • , Elizabeth A. Fergusson
    •  & Arvydas Lubys

  • Article
    | Open Access

    Early-life microbiota alterations can affect infection susceptibility later in life, in animal models. Here, Knutie et al. show that manipulating the microbiota of tadpoles leads to increased susceptibility to parasitic infection in adult frogs, in the absence of substantial changes in the adults’ microbiota.

    • Sarah A. Knutie
    • , Christina L. Wilkinson
    •  & Jason R. Rohr

  • Article
    | Open Access

    Viruses play an important role in microbial communities but, due to limitations of available techniques, our understanding of viral diversity is limited. Here, the authors use SVGs and identify highly abundant viruses in marine communities that have been previously overlooked.

    • Francisco Martinez-Hernandez
    • , Oscar Fornas
    •  & Manuel Martinez-Garcia

  • Article
    | Open Access

    Multicellularity can arise by cells aggregating or remaining connected after cell division. Here, Driscoll and Travisano show that both mechanisms operate in experimentally evolved strains of the yeastKluyveromyces lactis, with transient aggregation facilitating the coexistence of unicellular and multicellular genotypes.

    • William W Driscoll
    •  & Michael Travisano

  • Article
    | Open Access

    Crystalline uraninite is believed to be the dominant form in uranium deposits. Here, the authors find that non-crystalline U(IV) generated through biologically mediated U(VI) reduction is the predominant U(IV)species in ore deposits, implying that biogenic processes are more important than previously thought.

    • Amrita Bhattacharyya
    • , Kate M. Campbell
    •  & Thomas Borch

  • Article
    | Open Access

    The use of anammox microbiomes to treat wastewater is an escalating biotechnology, yet the functional role heterotrophic bacteria play in these systems remains poorly understood. Here, Lawsonet al. use metagenomics and metatranscriptomics to reveal that heterotrophs degrade free peptides, while recycling nitrate to nitrite.

    • Christopher E. Lawson
    • , Sha Wu
    •  & Daniel R. Noguera

  • Article
    | Open Access

    Observations of recent or dynamic transitions between parasitism and mutualism are scarce. Here, Flórezet al. provide evidence that Burkholderia gladiolibacteria can protect the eggs of herbivorous beetles by producing antimicrobial compounds, while retaining their ancestral ability to infect plants.

    • Laura V. Flórez
    • , Kirstin Scherlach
    •  & Martin Kaltenpoth

  • Article
    | Open Access

    Coral-associated microbes could enhance the capacity of their host organism to respond to environmental change. Ziegler and colleagues use a reciprocal transplant experiment to show that microbiomes of heat-tolerant corals are more resilient to change than those of heat-sensitive corals.

    • Maren Ziegler
    • , Francois O. Seneca
    •  & Christian R. Voolstra

  • Article
    | Open Access

    Increased temperature and nutrient pollution are key features of anthropogenic change, but their dual effects on biodiversity remain unclear. Here Wanget al. conduct field experiments at two mountain elevation gradients to show that temperature and nutrients have independent and interactive effects on microbial diversity.

    • Jianjun Wang
    • , Feiyan Pan
    •  & Ji Shen

  • Article
    | Open Access

    Host-associated microbial communities can shift in structure or function when hosts change locations. Bletzet al. reciprocally transfer salamander larvae between pond and stream habitats to show that gut microbiomes shift in function, but not necessarily taxonomic identities, when hosts encounter a new environment.

    • Molly C. Bletz
    • , Daniel J. Goedbloed
    •  & Sebastian Steinfartz

  • Article
    | Open Access

    Cells of the yeast Saccharomyces cerevisiaecan mate with other cells of opposite mating type. Here, the authors show that the combination of a pheromone and a pheromone-degrading enzyme allows yeast cells to monitor relative mate abundance within a population and adjust their commitment to sexual reproduction.

    • Alvaro Banderas
    • , Mihaly Koltai
    •  & Victor Sourjik

  • Article
    | Open Access

    Though both the presence and traits of a species can influence the dynamics of its ecological community, the effects of these factors are difficult to disentangle. Here, Gómez et al. demonstrate in a microbial mesocosm that local adaptation of a focal species can influence the community as much as the presence of the focal species per se.

    • Pedro Gómez
    • , Steve Paterson
    •  & Angus Buckling

  • Article
    | Open Access

    Climate warming has a wide range of effects on biodiversity. Here, Zhou et al. show that although variation in environmental temperature is a primary driver of soil microbial biodiversity, microbes show much lower rates of turnover across temperature gradients than other major taxa.

    • Jizhong Zhou
    • , Ye Deng
    •  & James H. Brown

  • Article
    | Open Access

    The Arctic is melting at an unprecedented rate and key drivers are changes in snow and ice albedo. Here, the authors show that red pigmented snow algae play a crucial role in decreasing surface albedo and their patterns for diversity, pigmentation, and consequently albedo, are ubiquitous across the Arctic.

    • Stefanie Lutz
    • , Alexandre M. Anesio
    •  & Liane G. Benning

  • Article
    | Open Access

    Particles of organic matter in the ocean harbour microbial communities that digest and recycle essential nutrients. Here, Datta et al.use model marine particles to show that the attached bacterial communities undergo rapid, reproducible successions driven by ecological interactions.

    • Manoshi S. Datta
    • , Elzbieta Sliwerska
    •  & Otto X. Cordero

  • Article
    | Open Access

    Sponges are early-diverging marine organisms that establish complex symbioses with microorganisms. Here, Thomas et al.analyse the microbial communities associated with 81 species of sponges from around the world, shedding light on the ecological and evolutionary drivers of these host-microbe associations.

    • Torsten Thomas
    • , Lucas Moitinho-Silva
    •  & Nicole S. Webster

  • Article
    | Open Access

    Groundwater-surface water mixing zones link critical ecosystem domains, but attendant microbe-biogeochemistry-hydrology interactions are poorly known. Here, the authors show that groundwater-surface water mixing stimulates respiration, alters carbon composition, and shifts the ecology from stochastic to deterministic.

    • James C. Stegen
    • , James K. Fredrickson
    •  & Malak Tfaily

  • Article
    | Open Access

    ANaerobic AMMonium OXidation (ANAMMOX) combined with partial nitritation has been adopted for removal of ammonium from wastewater. Here, Speth et al. describe the bacterial metagenome of a partial-nitritation/anammox (PNA) reactor, and provide 23 draft genomes, 19 of which were previously uncharacterized/sequenced/cultivated.

    • Daan R. Speth
    • , Michiel H. in ’t Zandt
    •  & Mike S. M. Jetten

  • Article
    | Open Access

    The role of microbial diversity in ecosystems is less well understood than, for example, that of plant diversity. Analysing two independent data sets at a global and regional scale, Delgado-Baquerizo et al. show positive effects of soil diversity on multiple terrestrial ecosystem functions.

    • Manuel Delgado-Baquerizo
    • , Fernando T. Maestre
    •  & Brajesh K. Singh

  • Article
    | Open Access

    Horizontal gene transfer is central to microbial evolution. Here, the authors develop an eco-evolutionary model and show that migration can greatly promote horizontal gene transfer, which explains how ecologically-important loci can sweep through the species in a microbial community.

    • Rene Niehus
    • , Sara Mitri
    •  & Kevin R. Foster

  • Article
    | Open Access

    Wastewater treatment plants (WWTPs) are thought to play a central role in the dissemination of antibiotic resistance genes. Here, the authors identify novel antibiotic resistance genes in WWTPs and show that only a few of the most abundant resistance genes are found outside the WWTP environment.

    • Christian Munck
    • , Mads Albertsen
    •  & Morten O. A. Sommer

  • Article
    | Open Access

    The inner layer of the mucus that covers our intestine is nearly sterile. Here, the authors show in mice that the outer mucus layer constitutes a unique microbial niche hosting bacterial communities with distinct proliferation rates and resource utilization activities.

    • Hai Li
    • , Julien P. Limenitakis
    •  & Andrew J. Macpherson

  • Article
    | Open Access

    The coffee berry borer, the main insect pest of coffee, feeds and lives on the caffeine-rich beans despite caffeine’s toxic effects. Here Ceja-Navarro et al. show that certain microbes, including Pseudomonasspecies, mediate caffeine detoxification in the insect’s gut.

    • Javier A. Ceja-Navarro
    • , Fernando E. Vega
    •  & Eoin L. Brodie

  • Article
    | Open Access

    Certain soil fungi form specialized cellular structures or 'traps' to feed on nematodes, which in turn eat bacteria. Here, the authors show that urea released from bacteria induces trap formation in the fungi and this promotes nematode elimination.

    • Xin Wang
    • , Guo-Hong Li
    •  & Ke-Qin Zhang

  • Article
    | Open Access

    Within microbial communities, microorganisms adopt different lifestyle strategies to use the available resources. Here, the authors use an integrated ‘multi-omic’ approach to study niche breadth (generalist versus specialist lifestyles) in oleaginous microbial assemblages from an anoxic wastewater treatment tank.

    • Emilie E. L. Muller
    • , Nicolás Pinel
    •  & Paul Wilmes

  • Article
    | Open Access

    Understanding the factors determining pathogen host range is critical for human health. Here, the authors show that bacteria use cooperative secretions to modify their environment and to infect multiple host species, which suggests that cooperative secretions are key determinants of host range in bacteria.

    • Luke McNally
    • , Mafalda Viana
    •  & Sam P. Brown

  • Article
    | Open Access

    Intestinal microbes can have important effects on our health. Here, the authors analyse the gut microbiota composition in 1,000 western adults and find that certain bacteria are either abundant or nearly absent, and that these alternative states are associated with ageing and overweight.

    • Leo Lahti
    • , Jarkko Salojärvi
    •  & Willem M. de Vos

  • Article
    | Open Access

    Wolbachia bacteria live within the cells of many insect species, manipulating their hosts’ reproduction and immune responses. Here, the authors show that these microbes also infect wild populations of malaria-spreading Anopheles mosquitoes, supporting a potential use of Wolbachiato limit malaria transmission.

    • Francesco Baldini
    • , Nicola Segata
    •  & Flaminia Catteruccia

  • Article |

    Little is known about extracellular electron uptake by microbes. Here Bose et al. show that the anoxygenic photoautotroph Rhodopseudomonas palustrisTIE-1 accepts electrons from a poised electrode, which can be uncoupled from photosynthesis, and the pioABC system has a role in this uptake.

    • A. Bose
    • , E.J. Gardel
    •  & P.R. Girguis

  • Article |

    Microbial community function depends on metabolic interdependencies between individual species, some of which include electron transfer. Nagarajan et al. use genomic, transcriptomic and modelling approaches to describe the mechanisms supporting the syntrophic relationship between Geobacter metallireducens and Geobacter sulfurreducens.

    • Harish Nagarajan
    • , Mallory Embree
    •  & Karsten Zengler

  • Article |

    Persistence of cooperation requires limited spread of defectors, but it is unclear how evolutionary history affects the spread of these individuals. Here, Jousset et al.show that microbial cooperators can only inhibit defectors that are closely related to them, suggesting that evolutionary history can predict the stability of cooperation.

    • Alexandre Jousset
    • , Nico Eisenhauer
    •  & Stefan Scheu

  • Article |

    In microbial biogeography, little is known about processes involved in soil bacterial diversity turnover. By conducting a wide-scale investigation, this study shows that dispersal limitation and environmental selection of bacteria are not mutually exclusive, highlighting the importance of landscape diversity.

    • L. Ranjard
    • , S. Dequiedt
    •  & P. Lemanceau

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