Microbial ecology articles within Nature Communications

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  • 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

  • Article
    | Open Access

    Disease transmission is particularly complex at the human-livestock-wildlife interface. Here the authors sample E. coli from wild birds near households in Nairobi and show that antimicrobial resistance gene diversity is correlated with human and lifestock density, while virulence gene diversity is correlated with avian species richness.

    • J. M. Hassell
    • , M. J. Ward
    •  & E. M. Fèvre

  • Article
    | Open Access

    Developing a predictive understanding of bacterial community responses to environmental change is an ongoing challenge. Here, Isobe et al. reanalyze data on soil microbial responses to nitrogen addition across 5 continents, finding that responses are predictable based on phylogeny.

    • Kazuo Isobe
    • , Steven D. Allison
    •  & Jennifer B. H. Martiny

  • Article
    | Open Access

    Here, Maury et al. show that hypervirulent Listeria monocytogenes (Lm) clones associated to dairy products exhibit higher adaptation to the mammalian gut environment, while hypovirulent clones persist in food processing environment, suggesting a relationship between Lm pathogenic potential and niche adaptation.

    • Mylène M. Maury
    • , Hélène Bracq-Dieye
    •  & Marc Lecuit

  • Article
    | Open Access

    Soil fungi play essential roles in ecosystems worldwide. Here, the authors sequence and analyze 235 soil samples collected from across the globe, and identify dominant fungal taxa and their associated environmental attributes.

    • Eleonora Egidi
    • , Manuel Delgado-Baquerizo
    •  & Brajesh K. Singh

  • Article
    | Open Access

    Host phylogeny and diet are major explanatory factors of animal gut microbiome diversity, but our understanding of these associations is limited by a focus on captive animals and a narrow taxonomic scope. Here, the authors isolate evolutionary and ecological drivers of gut microbiomes from wild mammals, birds, reptiles, amphibians, and fish.

    • Nicholas D. Youngblut
    • , Georg H. Reischer
    •  & Andreas H. Farnleitner

  • Article
    | Open Access

    Environmental stress can affect the outcome of ecological competition. Here, the authors use theory and experiments with a synthetic microbial community to show that a tradeoff between growth rate and competitive ability determines which species prevails when the population faces variable mortality rates.

    • Clare I. Abreu
    • , Jonathan Friedman
    •  & Jeff Gore

  • Article
    | Open Access

    The drivers of coexistence between species with different growth rates are of interest in both ecology and applied microbial science. The authors show, via modelling, that species interactions moderated by consumption or degradation of chemicals can allow coexistence.

    • Lori Niehaus
    • , Ian Boland
    •  & Babak Momeni

  • Article
    | Open Access

    Ammonia-oxidizing bacteria and archaea are major producers of the gases nitrous oxide and nitric oxide. Here, Kits et al. show that a complete ammonia-oxidizing (comammox) bacterium emits nitrous oxide at levels that are comparable to those produced by ammonia-oxidizing archaea.

    • K. Dimitri Kits
    • , Man-Young Jung
    •  & Holger Daims

  • Article
    | Open Access

    Microbes structure biogeochemical cycles and food webs in the marine environment. Here, the authors sample coral reef-associated microbes across a 24-hour period, showing clear day–night patterns of microbial populations and thus calling for more studies to consider temporal variation in microbiomes at this scale.

    • Linda Wegley Kelly
    • , Craig E. Nelson
    •  & Forest Rohwer

  • Article
    | Open Access

    Here the authors holistically examine prokaryote communities associated with diverse coral reef hosts, including sponges, nudibranchs, sea cucumbers, and corals. The results show that sponges have a relatively low diversity of prokaryotes, most of which are shared across a wide range of host taxa rather than being sponge-specific.

    • Daniel F. R. Cleary
    • , Thomas Swierts
    •  & Nicole J. de Voogd

  • Article
    | Open Access

    Findings regarding the impacts of ocean acidification (OA) on the growth and N2 fixation of Trichodesmium are conflicted. Here, the authors find that Trichodesmium growth rates decrease under OA primarily due to reduced nitrogenase efficiency and OA under RCP 8.5 could reduce the N2 fixation potential of Trichodesmium by 27%.

    • Ya-Wei Luo
    • , Dalin Shi
    •  & Futing Zhang

  • Article
    | Open Access

    The effect of plant biodiversity on microbial function has been tested in limited studies and is likely to be context-dependent. In this meta-analysis of 106 prior studies comparing plant monocultures to mixtures, the authors find that plant diversity increases microbial biomass and respiration rates, an effect moderated by stand age.

    • Chen Chen
    • , Han Y. H. Chen
    •  & Zhiqun Huang

  • Article
    | Open Access

    Some microorganisms may be transferred across the food production chain and, potentially, colonize the human gut. Here, Milani et al. provide strain-level evidence supporting that dairy cattle-associated bacteria can be transferred to the human gut via consumption of Parmesan cheese.

    • Christian Milani
    • , Sabrina Duranti
    •  & Francesca Turroni

  • Article
    | Open Access

    Leaf-feeding insect microbiomes could be influenced by the soil, the plant, or a product of the two. Here, the authors conduct a series of experiments to show that an herbivorous insect predominantly acquires its microbiome from the soil rather than the plant, and that these insect microbiomes reflect soil legacies of earlier growing plants.

    • S. Emilia Hannula
    • , Feng Zhu
    •  & T. Martijn Bezemer

  • Article
    | Open Access

    Here, Sieradzki et al. use metatranscriptomics to study active community-wide viral infections at three coastal California sites throughout a year, identify potential viral hosts, and show that viruses can contribute a substantial amount to photosystem-II psbA expression.

    • Ella T. Sieradzki
    • , J. Cesar Ignacio-Espinoza
    •  & Jed A. Fuhrman

  • Article
    | Open Access

    It is unclear whether microbes and animals residing in soils follow similar distribution patterns. Here, the authors report richness and diversity of soil microbes and invertebrates across soil, vegetation, and land use gradients in Wales, showing that land use affects animals while soil traits affect microbes.

    • Paul B. L. George
    • , Delphine Lallias
    •  & Davey L. Jones

  • Article
    | Open Access

    Controlling microbial communities could help restore ecosystems and maintain healthy microbiota. Here, the authors introduce the notion of structural accessibility and develop a framework to identify minimal sets of driver species, manipulation of which could allow control of a microbial community.

    • Marco Tulio Angulo
    • , Claude H. Moog
    •  & Yang-Yu Liu

  • Article
    | Open Access

    Lurgi et al. analyse the distribution of microbial symbionts across many sponge species and reveal modules of non-random associations which are primarily driven by host features and microbial phylogenies, and less by the environment. Results also show that metabolic functions are distinct across modules.

    • Miguel Lurgi
    • , Torsten Thomas
    •  & Jose M. Montoya

  • Article
    | Open Access

    Viruses can encode genes that regulate the host's translational machinery to their advantage. Here, the authors show that viruses encode ribosomal proteins that can be incorporated into the host’s ribosome and may affect translation.

    • Carolina M. Mizuno
    • , Charlotte Guyomar
    •  & Mart Krupovic

  • Article
    | Open Access

    The pathogen Pseudomonas aeruginosa undergoes complex trait adaptation within cystic fibrosis patients. Here, Bartell, Sommer, and colleagues use statistical modeling of longitudinal isolates to characterize the joint genetic and phenotypic evolutionary trajectories of P. aeruginosa within hosts.

    • Jennifer A. Bartell
    • , Lea M. Sommer
    •  & Helle Krogh Johansen

  • Article
    | Open Access

    Recent efforts have been made to apply ecological theory on succession to understand the dynamics of human microbiomes throughout development. Here, Guittar et al. use a trait-based approach to show how microbial traits putatively related to dispersal and environmental tolerance shift in the infant microbiome over the first three years of life.

    • John Guittar
    • , Ashley Shade
    •  & Elena Litchman

  • Article
    | Open Access

    Previous surveys of global ocean microbial diversity have focused on planktonic microbes. Here, Zhang et al. use metagenomics to study biofilm-forming marine microbes, increasing the known microbial diversity in the oceans by more than 20% and revealing new biosynthetic gene clusters and CRISPR-Cas systems.

    • Weipeng Zhang
    • , Wei Ding
    •  & Pei-Yuan Qian

  • Article
    | Open Access

    The structure and distribution of strain-level diversity in host-associated bacterial communities is largely unexplored. Here, Ellegaard and Engel analyze strain level diversity of the honey bee gut microbiota, showing that bees from the same colony differ in strain but not phylotype composition.

    • Kirsten M. Ellegaard
    •  & Philipp Engel

  • Article
    | Open Access

    Biological complexity has impeded our ability to predict the dynamics of mutualistic interactions. Here, the authors deduce a general rule to predict outcomes of mutualistic systems and introduce an approach that permits making predictions even in the absence of knowledge of mechanistic details.

    • Feilun Wu
    • , Allison J. Lopatkin
    •  & Lingchong You

  • Article
    | Open Access

    Our knowledge of DNA methylation systems in prokaryotes is mostly limited to those of culturable microbes. Here, Hiraoka et al. analyse DNA methylation patterns in metagenomic data from a microbial community, revealing new methylated motifs and experimentally validating the methyltransferases’ specificities.

    • Satoshi Hiraoka
    • , Yusuke Okazaki
    •  & Wataru Iwasaki

  • Article
    | Open Access

    Numerous microbial symbionts, both commensal and pathogenic, are associated with honey bees. Here, the authors genomically characterize this ‘metagenome’ of the British honey bee, identifying a diversity of commensal microbes as well as known and putative pathogens

    • Tim Regan
    • , Mark W. Barnett
    •  & Tom C. Freeman

  • Article
    | Open Access

    Associations between corals and symbiotic microorganisms could be driven by the environment or shared evolutionary history. Here, the authors examine relationships between coral phylogenies and associated microbiomes, finding evidence of phylosymbiosis in microbes from coral skeleton and tissue, but not mucus.

    • F. Joseph Pollock
    • , Ryan McMinds
    •  & Jesse R. Zaneveld

  • Article
    | Open Access

    Research on plant root-associated microbial communities may help develop more efficient or sustainable crop production methods. Here the authors analyse the citrus rhizosphere microbiome, using both amplicon and deep shotgun metagenomic sequencing of samples collected across six continents.

    • Jin Xu
    • , Yunzeng Zhang
    •  & Nian Wang

  • Review Article
    | Open Access

    Facilitation is a well-known ecological interaction among free-living species, but symbionts residing in or on a host can also positively affect other symbiont species. Here, the authors review examples of facilitation among symbionts, revealing how facilitation theory can improve understanding of these interactions.

    • Flore Zélé
    • , Sara Magalhães
    •  & Alison B. Duncan

  • Article
    | Open Access

    Marine cyanophages infect oceanic cyanobacteria that are important contributors to global primary production. By using an experimental evolution approach, here the authors show that adaptation to sub-optimal cyanobacterial hosts result in genomic diversification of cyanophage populations.

    • Hagay Enav
    • , Shay Kirzner
    •  & Oded Béjà

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