Symbiosis articles within Nature Communications

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  • Article
    | Open Access

    This study provides insights into the functional roles of microbial symbionts within the reef-building coral Acropora kenti. The findings reveal molecular mechanisms underpinning coral health and adaptation to local environmental stressors, which may support host resilience in the face of anthropogenic climate change and pollution.

    • Lauren F. Messer
    • , David G. Bourne
    •  & Gene W. Tyson

  • Article
    | Open Access

    Here, Rühlemann et al. analyze the gut microbiome of wild-living African great apes (Gorillas, Bonobos, Chimpanzees) in comparison to that of humans, identifying host specific patterns and shared evolutionary conserved traits disrupted in humans.

    • M. C. Rühlemann
    • , C. Bang
    •  & A. Franke

  • Article
    | Open Access

    The deep ocean is increasingly subjected to human-induced environmental change, but little is known about species-specific responses to stressors, including those from deep sea mining. This study shows that elevated temperatures and simulated sediment plumes cause physiological stress in a cosmopolitan deep-sea jellyfish, confirming the detrimental impact of seabed mining.

    • Vanessa I. Stenvers
    • , Helena Hauss
    •  & Henk-Jan T. Hoving

  • Article
    | Open Access

    The mechanisms regulating fungal-algal interactions during the formation of lichen symbioses are not clear. Here, Wang et al. establish conditions conducive to symbiotic interactions and lichen differentiation using a fungus amenable to genetic manipulation, showing the importance of a MAP kinase in lichen development.

    • Yanyan Wang
    • , Rong Li
    •  & Jin-Rong Xu

  • Article
    | Open Access

    A new study reveals that bacterial partners supply essential metabolites to the vital microalgal symbionts of corals, including metabolites that boost symbiont growth. This breakthrough increases our understanding of coral microbial ecology and also opens the door to innovative ways of protecting coral reefs.

    • Jennifer L. Matthews
    • , Abeeha Khalil
    •  & Jean-Baptiste Raina

  • Article
    | Open Access

    The rhizosheath, or the soil layer closely attached to roots, can help plants tolerate drought. Here, the authors show that rhizosheath formation in barley is promoted by soil bacteria that produce indole-3-acetic acid, a common auxin.

    • Feiyun Xu
    • , Hanpeng Liao
    •  & Weifeng Xu

  • Article
    | Open Access

    Metagenomic data and network analyses are often used to predict microbial interactions in complex communities, but these predictions are rarely explored experimentally. Here, Hessler et al. combine experiments with metagenome-informed, microbial consortia-based network analyses to identify interactions in microbial consortia grown under dozens of conditions.

    • Tomas Hessler
    • , Robert J. Huddy
    •  & Jillian F. Banfield

  • Article
    | Open Access

    Bacterial symbionts, such as Wolbachia species, can manipulate the sexual development and reproduction of their insect hosts. Here, the authors identify a Wolbachia protein that interacts with a host masculinization factor and leads to male killing in lepidopteran insects.

    • Susumu Katsuma
    • , Kanako Hirota
    •  & Takashi Kiuchi

  • Article
    | Open Access

    This study presents a large-scale analysis of microbial diversity in deep-sea sponges. They show that sponge microbial abundance status, geographic distance, sponge phylogeny and the physical-biogeochemical environment drive microbiome composition, in descending order of relevance. The uniqueness of each deep-sea sponge ground stresses the need for their strategic preservation.

    • Kathrin Busch
    • , Beate M. Slaby
    •  & Ute Hentschel

  • Article
    | Open Access

    The bacterial genus Rickettsia includes vector-borne pathogens and arthropod symbionts that are close relatives of symbionts of microeukaryotes classified under the genus ‘Candidatus Megaira’. Here, Davison et al. clarify the evolutionary relationships between these organisms by assembling 28 genomes of understudied species, and propose that a distinct clade known as Torix Rickettsia should be considered a separate genus.

    • Helen R. Davison
    • , Jack Pilgrim
    •  & Stefanos Siozios

  • Article
    | Open Access

    The Micrarchaeota lineage includes poorly characterized archaea with reduced genomes that likely depend on host interactions for survival. Here, the authors report a stable co-culture of a member of the Micrarchaeota and its host, and use multi-omic and physiological analyses to shed light on this symbiosis.

    • Susanne Krause
    • , Sabrina Gfrerer
    •  & Johannes Gescher

  • Article
    | Open Access

    Nitrogen depletion in the ocean provides a favourable niche for nitrogen-fixing cyanobacteria, which can form symbioses with eukaryotic algae. This study reports the discovery of two distinct marine pennate diatom–diazotroph symbioses, which had previously only been observed in freshwater environments and represent an overlooked but widespread source of bioavailable nitrogen in marine habitats.

    • Christopher R. Schvarcz
    • , Samuel T. Wilson
    •  & Grieg F. Steward

  • Article
    | Open Access

    This study reports the discovery of dense sponge gardens across the peaks of permanently ice-covered, extinct volcanic seamounts of the Langseth Ridge and on the remnants of a now extinct seep ecosystem. Using approaches to sample and infer food and energy sources to this ice-covered community, the authors suggest that the sponges use refractory organic matter trapped in the extinct seep community on which they sit.

    • T. M. Morganti
    • , B. M. Slaby
    •  & A. Boetius

  • Article
    | Open Access

    Mucosal antibodies maintain gut homeostasis, and may influence gut health through modulation of microbiota composition. Here the authors use a CD19-deficient mouse model with deficient B-cell immune responses to uncover an association between humoral immunodeficiency, dysbiosis, and perturbations to bile acid homeostasis in the gut in the context of glute-sensitive enteropathy.

    • Ahmed Dawood Mohammed
    • , Zahraa Mohammed
    •  & Jason L. Kubinak

  • Article
    | Open Access

    Malnourished children experience a high burden of intestinal pathogens that exacerbate growth stunting, and preventing this pathogen overgrowth has proved challenging. Here the authors show that diet-specific bacterial crossfeeding contributes to the overgrowth of intestinal pathogens during child malnutrition.

    • K. E. Huus
    • , T. T. Hoang
    •  & B. B. Finlay

  • Article
    | Open Access

    Here, the authors report quantitative daily gut microbiome variation of individual gut bacterial abundances in healthy individuals, linked to changes in transit time and diet, highlighting the potential need for multiple samplings for microbiome target identification and the development and application of reliable microbiome diagnostics.

    • Doris Vandeputte
    • , Lindsey De Commer
    •  & Jeroen Raes

  • Article
    | Open Access

    Insect acquisition of insecticide resistance represents a serious problem for agriculture. Here, authors reveal an insect symbiotic bacteria that degrades insecticide fenitrothion into a non-insecticidal but bactericidal compound, which is subsequently excreted by the insect host.

    • Yuya Sato
    • , Seonghan Jang
    •  & Yoshitomo Kikuchi

  • Perspective
    | Open Access

    The microbiome is becoming recognized as a key determinant of host phenotype. Here, Henry et al. present a framework for building our understanding of how the microbiome also influences host evolution, review empirical examples and research approaches, and highlight emerging questions.

    • Lucas P. Henry
    • , Marjolein Bruijning
    •  & Julien F. Ayroles

  • Article
    | Open Access

    Chlamydiae are strictly intracellular bacteria that exist in a wide variety of environments but the diversity of the phylum is not well described. Here, the authors analyze 82 metagenome-assembled genomes, identify seven new families, and describe genomic signals of metabolic diversity.

    • Stephan Köstlbacher
    • , Astrid Collingro
    •  & Matthias Horn

  • Article
    | Open Access

    Human gut bacteria can degrade arabinoxylans, polysaccharides found in dietary fiber. Here, Pereira et al. identify a bacterial gene cluster encoding esterases for degradation of complex arabinoxylans. The action of these enzymes results in accumulation of ferulic acid, a phenolic compound with antioxidative and immunomodulatory properties.

    • Gabriel V. Pereira
    • , Ahmed M. Abdel-Hamid
    •  & Isaac Cann

  • 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

    The gut microbiota can alter the effects of anticancer fluoropyrimidines such as 5-fluorodeoxyuridine (FUdR) in the model organism C. elegans. Here, the authors show that these effects are further affected by diet, and dietary thymidine and serine increase FUdR toxicity in C. elegans via different mechanisms.

    • Wenfan Ke
    • , James A. Saba
    •  & Eyleen J. O’Rourke

  • Article
    | Open Access

    Ceramides are a type of sphingolipid (SL) that have been shown to play a role in several metabolic disorders. Here, the authors investigate the effect of SL-production by gut Bacteroides on host SL homeostasis and show that microbiome-derived SLs enter host circulation and alter ceramide production.

    • Elizabeth L. Johnson
    • , Stacey L. Heaver
    •  & Ruth E. Ley

  • Article
    | Open Access

    Here, the authors established and characterized the mouse gut microbial biobank (mGMB), which includes 244 strains and 126 species that enlarges previous mouse intestinal bacterial collections and represents a resource for studies using mouse models to investigate microbiome-associated health and disease.

    • Chang Liu
    • , Nan Zhou
    •  & Shuang-Jiang Liu

  • Article
    | Open Access

    Photosynthesis generates reactive oxygen species that can damage cells. Here, the authors show that unicellular predators of photosynthetic prey have shared responses to photosynthetic oxidative stress and these may also have been important for the evolution of endosymbiosis.

    • Akihiro Uzuka
    • , Yusuke Kobayashi
    •  & Shin-ya Miyagishima

  • 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

    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

    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

    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

    Acromyrmex ants cultivate fungus gardens that can be parasitized by Escovopsis sp., leading to colony collapse. Here, Heine et al. identify two secondary metabolites produced by Escovopsis that accumulate in Acromyrmex tissue, reduce behavioural defenses and suppress symbiotic Pseudonocardia bacteria.

    • Daniel Heine
    • , Neil A. Holmes
    •  & Barrie Wilkinson

  • Article
    | Open Access

    The mucus layer is an important physical niche within the gut which harbours a distinct microbial community. Here the authors show that specific carbohydrate-binding modules associated with bacterial carbohydrate-active enzymes are mucus adhesins that target regions of the distal colon rich in sialomucins.

    • C. David Owen
    • , Louise E. Tailford
    •  & Nathalie Juge

  • Article
    | Open Access

    Certain neuropeptides, in addition to their neuromodulatory functions, display antibacterial activities of unclear significance. Here, the authors show that a secreted neuropeptide modulates the distribution of bacterial communities on the body surface during development of the model organism Hydra.

    • René Augustin
    • , Katja Schröder
    •  & Thomas C. G. Bosch

  • Article
    | Open Access

    Environmental factors often outweigh host heritable factors in structuring host-associated microbiomes. Here, Bowen et al. show that host lineage is crucial for determination of rhizosphere bacterial communities in Phragmites australis, a globally distributed invasive plant.

    • Jennifer L. Bowen
    • , Patrick J. Kearns
    •  & Laura A. Meyerson

  • Article
    | Open Access

    Hosts vary in how dependent they are on their beneficial symbionts. Here, Fisher and colleagues analyse the results of symbiont-removal experiments from 106 symbioses in a phylogenetic context and show that host dependence is associated with symbiont transmission mode, function, and genome size.

    • Roberta M. Fisher
    • , Lee M. Henry
    •  & Stuart A. West

  • 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

    Both host diet and phylogeny have been argued to shape mammalian microbiome communities. Here, the authors show that diet predicts the presence of ancient bacterial lineages in the microbiome, but that co-speciation between more recent bacterial lineages and their hosts may drive associations between microbiome composition and phylogeny.

    • Mathieu Groussin
    • , Florent Mazel
    •  & Eric J. Alm

  • Article
    | Open Access

    Direct interspecies electron transfer has been shown in methane-producing communities, but it is unknown how widespread this mechanism is. Here, Haet al. show that anoxygenic photosynthesis can be driven by direct electron transfer from a heterotrophic partner bacterium.

    • Phuc T. Ha
    • , Stephen R. Lindemann
    •  & Haluk Beyenal

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