Microbial ecology articles within Nature Communications

Featured

  • Article
    | Open Access

    Dimethylsulfoniopropionate (DMSP) is an osmolyte produced by marine microbes that plays an important role in nutrient cycling and atmospheric chemistry. Here the authors go to the Mariana Trench—the deepest point in the ocean—and find bacteria are key DMSP producers, and that DMSP has a role in protection against high pressure.

    • Yanfen Zheng
    • , Jinyan Wang
    •  & Xiao-Hua Zhang
  • Article
    | Open Access

    The blooming alga Emiliania huxleyi and its viruses are a model for density-dependent virulent dynamics. However, Knowles et al. show that this host–virus system exhibits temperate dynamics at natural host densities, in a manner dependent on host physiology.

    • Ben Knowles
    • , Juan A. Bonachela
    •  & Kay D. Bidle
  • Article
    | Open Access

    Ocean cold seeps are poorly understood relative to related systems like hydrothermal vents. Here the authors use high pressure bioreactors and microbial communities from a cold seep mud volcano and find a previously missing step of methane conversion to acetate that likely fuels heterotrophic communities.

    • Shanshan Yang
    • , Yongxin Lv
    •  & Yu Zhang
  • Article
    | Open Access

    Lipo-chitooligosaccharides (LCOs) are signaling molecules produced by certain bacteria and fungi that establish symbiotic relationships with plants. Here, the authors show that LCOs are produced also by many other, non-symbiotic fungi, and regulate fungal growth and development.

    • Tomás Allen Rush
    • , Virginie Puech-Pagès
    •  & Jean-Michel Ané
  • Article
    | Open Access

    The discovery of aerobic microbial communities in nutrient-poor sediments below the seafloor begs the question of the mechanisms for their persistence. Here the authors investigate subseafloor sediment in the South Pacific Gyre abyssal plain, showing that aerobic microbial life can be revived and retain metabolic potential even from 101.5 Ma-old sediment.

    • Yuki Morono
    • , Motoo Ito
    •  & Fumio Inagaki
  • Article
    | Open Access

    Microbial carbon use efficiency has an important role in soil C cycling. Here the authors test the interactive effects of temperature and moisture and manipulate microbial community composition in soil microcosms, showing a positive relationship between microbial diversity and CUE that is contingent on abiotic conditions.

    • Luiz A. Domeignoz-Horta
    • , Grace Pold
    •  & Kristen M. DeAngelis
  • Article
    | Open Access

    Early postnatal colonization has been described to be critical for the long-term microbiota composition and health. Here, via multi-omics approach, the authors investigate the impact of the developing host hepatic metabolism on the murine intestinal microbiota composition with comparative analysis at immediate postnatal period, early infancy and weaning and adulthood.

    • N. van Best
    • , U. Rolle-Kampczyk
    •  & M. W. Hornef
  • Article
    | Open Access

    Here, the authors present a theoretical framework based on community ecology and network science to investigate the efficacy of fecal microbiota transplantation in conditions associated with a disrupted gut microbiota, using the recurrent Clostridioides difficile infection as a prototype disease.

    • Yandong Xiao
    • , Marco Tulio Angulo
    •  & Yang-Yu Liu
  • Article
    | Open Access

    The ecological niche of host-associated microbes is defined by both abiotic and biotic dimensions. Here the authors analyse published data on fungal and oomycete pathogens of plants, demonstrating that specialization can evolve independently on abiotic and biotic axes and that interactions with host plants reduce thermal niche breadth.

    • Thomas M. Chaloner
    • , Sarah J. Gurr
    •  & Daniel P. Bebber
  • Article
    | Open Access

    Snow algae bloom along the coast of Antarctica and are likely to be biogeochemically important. Here, the authors produced the first map of such blooms, show that they are driven by warmer temperatures and proximity to birds and mammals, and are likely to increase given projected climate changes.

    • Andrew Gray
    • , Monika Krolikowski
    •  & Matthew P. Davey
  • Article
    | Open Access

    The spatial organisation of microbial communities is caused by the interplay of biotic and abiotic factors. Here the authors design a microfluidic platform to quantify the spatiotemporal parameters influencing diffusion-mediated interactions, and use this device to investigate information transmission and metabolic cross-feeding in synthetic microbial consortia.

    • Sonali Gupta
    • , Tyler D. Ross
    •  & Ophelia S. Venturelli
  • Article
    | Open Access

    Plastic pollution has infiltrated every ecosystem, but few studies have quantified the biogeochemical or ecological effects of plastic. Here the authors show that microplastics in ocean sediment can significantly alter microbial community structure and nitrogen cycling.

    • Meredith E. Seeley
    • , Bongkeun Song
    •  & Robert C. Hale
  • Article
    | Open Access

    Bioorthogonal non-canonical amino acid tagging (BONCAT) coupled with flow cytometry (FACS) has been utilized to profile active microbiome of environmental samples. Here, the authors combine BONCAT-FACS and 16 S rRNA sequencing to characterize the translational activity of bacterial communities within sputum derived from stable cystic fibrosis patients.

    • Talia D. Valentini
    • , Sarah K. Lucas
    •  & Ryan C. Hunter
  • Article
    | Open Access

    Microbial plant-soil feedbacks (PSF) are fundamentally important for plant diversity. The authors present a spatially explicit dynamic model that separates the effects of microbial mutualists and pathogens, thereby presenting a testable mechanistic framework to reconcile previously puzzling observations of the strength and direction of PSF with diversity maintenance.

    • John W. Schroeder
    • , Andrew Dobson
    •  & Edward Allen Herre
  • Article
    | Open Access

    Bacteria capable of anaerobic ammonium oxidation (anammox) produce half of the nitrogen gas in the atmosphere, but much of their physiology is still unknown. Here the authors show that anammox bacteria are capable of a novel mechanism of ammonium oxidation using extracellular electron transfer.

    • Dario R. Shaw
    • , Muhammad Ali
    •  & Pascal E. Saikaly
  • Article
    | Open Access

    DMSP is a ubiquitous organosulfur compound in the ocean that, once degraded by bacteria, plays key roles in global biogeochemical cycles and climate regulation. Here, the authors use single-cell measurements of transcription to investigate the intricate dynamics of bacterial DMSP degradation.

    • Cherry Gao
    • , Vicente I. Fernandez
    •  & Roman Stocker
  • Article
    | Open Access

    The amyloid protein TasA is a main component of the extracellular matrix in Bacillus subtilis biofilms. Here the authors show that, in addition to a structural function during biofilm assembly and interactions with plants, TasA contributes to the stabilization of membrane dynamics during stationary phase.

    • Jesús Cámara-Almirón
    • , Yurena Navarro
    •  & Diego Romero
  • Article
    | Open Access

    How complex microbial communities assemble through the animal’s life, and how predictable the assembly process is, remains poorly understood. Here, the authors profile the cow gut microbiome from birth to adulthood in animals born in C-section or natural birth and show that chance events early in life have a strong impact on microbiome development.

    • Ori Furman
    • , Liat Shenhav
    •  & Itzhak Mizrahi
  • Article
    | Open Access

    Nucleocytoplasmic large DNA viruses (NCLDV) exhibit a large genomic repertoire and complex evolutionary history. Here, the authors generate 501 metagenome-assembled genomes from diverse environments and show NCLDVs to harbor a wide range of potential metabolic capabilities.

    • Mohammad Moniruzzaman
    • , Carolina A. Martinez-Gutierrez
    •  & Frank O. Aylward
  • Article
    | Open Access

    Environments where antibiotics are used indiscriminately exhibit microbial communities that can represent hot-spots of resistance gene enrichment, which in turn could spread to humans. Here, the authors characterize how exposure to swine farms environment lead to temporal changes in the gut microbiome and resistome of healthy veterinary students.

    • Jian Sun
    • , Xiao-Ping Liao
    •  & Ya-Hong Liu
  • Article
    | Open Access

    A species’ ability to adapt to a new environment may be influenced by both intrinsic factors and extrinsic factors. Here, Scheuerl et al. show that bacterial adaptation to low pH depends on not only its genome size and initial level of adaptation, but also the diversity of the community.

    • Thomas Scheuerl
    • , Meirion Hopkins
    •  & Thomas Bell
  • Article
    | Open Access

    Microbes secrete a repertoire of extracellular proteins to serve various functions depending on the ecological context. Here the authors examine how bacterial community composition and habitat structure affect the extracellular proteins, showing that generalist species and those living in more structured environments produce more extracellular proteins, and that costs of production are lower in more diverse communities.

    • Marc Garcia-Garcera
    •  & Eduardo P. C. Rocha
  • Article
    | Open Access

    Cellular interactions are a major driver of microbial communities and shown highly variable in strength. Here the authors construct synthetic consortia and mathematical models to elucidate the role of interaction variability in driving ecosystem succession.

    • Feng Liu
    • , Junwen Mao
    •  & Ting Lu
  • Article
    | Open Access

    The relationship between the coral animal and symbiotic algae is essential to coral health, and researchers are turning to Exaiptasia, a model cnidarian system, to study this relationship mechanistically. Here the authors find that endosymbiotic algae become limited by nitrogen at high population densities and provide the host with high levels of fixed carbon.

    • Tingting Xiang
    • , Erik Lehnert
    •  & Arthur R. Grossman
  • Article
    | Open Access

    Fungal community assembly on crop plants is thought to be driven by deterministic selection exerted by the host. Here Gao et al. use a sorghum system to show that stochastic forces act on fungal community assembly in leaves and roots early in host development and when sorghum is drought stressed.

    • Cheng Gao
    • , Liliam Montoya
    •  & John W. Taylor
  • Article
    | Open Access

    The authors assemble and analyse previously generated mycobiome data linked to geographical locations across the world. They describe the distribution of fungal taxa and show that climate is an important driver of fungal biogeography and that fungal diversity appears to be concentrated at high latitudes.

    • Tomáš Větrovský
    • , Petr Kohout
    •  & Petr Baldrian
  • Article
    | Open Access

    Warmer temperatures could increase the growth and metabolic rates of microbes. Here, the authors assemble a dataset of thermal performance curves for over 400 bacteria and archaea, showing that metabolic rates are likely to increase under warming, with implications for global carbon cycling.

    • Thomas P. Smith
    • , Thomas J. H. Thomas
    •  & Samrāt Pawar
  • Article
    | Open Access

    There is ongoing interest in linking soil microbial diversity to ecosystem function. Here the authors manipulate the diversity and composition of microbial communities and show that complex microbial networks contribute more to ecosystem multifunctionality than simpler or low-diversity networks.

    • Cameron Wagg
    • , Klaus Schlaeppi
    •  & Marcel G. A. van der Heijden
  • Article
    | Open Access

    Microbes can establish mutualistic interactions with plants and insects. Here, Kim et al. show that Streptomyces bacteria can protect strawberry plants and honeybees from pathogens, can move into the plant vascular tissue from soil and from flowers, and are transferred among flowers by the pollinators.

    • Da-Ran Kim
    • , Gyeongjun Cho
    •  & Youn-Sig Kwak
  • Article
    | Open Access

    Methane metabolism by some lineages of Archaea contributes to the cycling of carbon on Earth. Here, the authors show high diversity of methyl-coenzyme M reductase (Mcr), a key enzyme associated with archaeal methane/alkane metabolism, in hot spring Archaea, and investigate their ecological roles and evolution.

    • Zheng-Shuang Hua
    • , Yu-Lin Wang
    •  & Wen-Jun Li
  • Article
    | Open Access

    Livestock play a role in maintaining antibiotic resistance reservoirs. Here, Liu et al. use metagenomics to study the dynamics of antibiotic resistance genes (ARGs) in the gut of dairy cattle during early life, showing that colostrum is a potential source of ARGs and ARG abundance declines during nursing covarying with dietary transition.

    • Jinxin Liu
    • , Diana H. Taft
    •  & David A. Mills
  • Article
    | Open Access

    Predator-prey coevolution is expected to hasten evolutionary rates, but this is difficult to test in long-lived species. Here, the authors report consequences of experimental coevolution between bacterial predators and prey, including accelerated molecular evolution and parallel genomic and phenotypic adaptation.

    • Ramith R. Nair
    • , Marie Vasse
    •  & Gregory J. Velicer
  • Article
    | Open Access

    Alkaline lakes have some of the highest productivity rates in freshwater ecosystems. Here the authors report amplicon, metagenome, and proteome sequencing from microbial mat communities of four alkaline lakes in Canada, and compare these lakes to central Asian soda lakes, revealing a shared core microbiome despite the geographical distance.

    • Jackie K. Zorz
    • , Christine Sharp
    •  & Marc Strous
  • Article
    | Open Access

    Anthropogenic CO2 emissions are causing ocean acidification, which can affect the physiology of some organisms. Here, Botté et al. use metagenomics to show differences in metabolic potential between sponge microbiomes sampled at a shallow volcanic CO2 seep and those from nearby control sites.

    • Emmanuelle S. Botté
    • , Shaun Nielsen
    •  & Nicole S. Webster
  • Article
    | Open Access

    Microbial communities of plant leaf surfaces are ecologically important, but how they assemble and vary in time is unclear. Here, the authors identify core leaf microbiomes and seasonal patterns for two biofuel crops and show with source-sink models that soil is a reservoir of phyllosphere diversity.

    • Keara L. Grady
    • , Jackson W. Sorensen
    •  & Ashley Shade
  • Article
    | Open Access

    It is thought that fungi protect themselves from predators by the production of toxic compounds. Here, Xu et al. show that a wide range of animal predators avoid feeding on Fusarium fungi, and this depends on fungal production of a bis-naphthopyrone pigment that is not toxic to the predators.

    • Yang Xu
    • , Maria Vinas
    •  & Petr Karlovsky
  • Article
    | Open Access

    Microbial respiration releases carbon from the soil. Here, the authors estimate bacterial carbon use efficiency in soils for over 200 species using constraint-based modeling, incorporate the values into an ecosystem model, and find that shifts in community composition may impact carbon storage.

    • Mustafa Saifuddin
    • , Jennifer M. Bhatnagar
    •  & Adrien C. Finzi
  • Review Article
    | Open Access

    Subseafloor microbial activities are central to global biogeochemical cycles, affecting Earth’s surface oxidation, ocean chemistry, and climate. Here the authors review present understanding of subseafloor microbes and their activities, identify research gaps, and recommend approaches to fill those gaps.

    • Steven D’Hondt
    • , Robert Pockalny
    •  & Arthur J. Spivack
  • Article
    | Open Access

    The flexibility of corals to associate with different bacteria in different environments has not been systematically investigated. Here, the authors study bacterial community dynamics for two coral species and show that bacterial community structure responds to environmental changes in a host-specific manner.

    • Maren Ziegler
    • , Carsten G. B. Grupstra
    •  & Christian R. Voolstra
  • Article
    | Open Access

    Standard DNA-based analyses of microbial communities cannot distinguish between active microbes and dead or dormant cells. Here, Couradeau et al. use BONCAT (bioorthogonal non-canonical amino acid tagging), flow cytometry, and 16S rRNA gene amplicon sequencing to identify active microbial cells in soils.

    • Estelle Couradeau
    • , Joelle Sasse
    •  & Trent R. Northen