Microbial ecology articles within Nature Communications

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  • Article
    | Open Access

    “Factors influencing soil microbiota functioning remain understudied. Here, the authors describe bacterial and fungal diversity across Europe and along a gradient of land-use perturbation, observing that the occurrence of pathogens, symbionts and saprotrophs varied among cropland, woodland and grassland.”

    • Maëva Labouyrie
    • , Cristiano Ballabio
    •  & Alberto Orgiazzi

  • Article
    | Open Access

    Bacterial symbionts of the Endozoicomonadaceae family are frequently found in marine animals but are poorly understood. Using data from the Tara Pacific expedition, this study of Endozoicomonadaceae ecology at an ocean basin-scale reveals that corals across the Pacific Ocean have different host-symbiont association strategies that are determined at the bacterial lineage level.

    • Corentin Hochart
    • , Lucas Paoli
    •  & Pierre E. Galand

  • Article
    | Open Access

    Using data from the Tara Pacific expedition, this study reports the biogeography and the diversity of microbiomes collected from corals, fish and plankton in 99 reefs across the Pacific Ocean. The large richness of Pacific Ocean reef microorganisms, when extrapolated to all fish and corals of the Pacific, represents the current estimated total prokaryotic diversity for the entire Earth.

    • Pierre E. Galand
    • , Hans-Joachim Ruscheweyh
    •  & Serge Planes

  • Article
    | Open Access

    Microbes often produce molecules (termed siderophores) that bind iron and then are taken up using specific receptors for iron acquisition. Here, the authors show that a compound produced by Bacillus subtilis plays a more complex role, by modulating iron availability and conferring protection against oxidative stress during inter-species competition.

    • Vincent Charron-Lamoureux
    • , Lounès Haroune
    •  & Pascale B. Beauregard

  • Article
    | Open Access

    Antibiotics impact the gut microbiota in complex ways. Here, employing ecological models of resource competition, Newton et al. elucidate species coexistence patterns under resource competition and species-specific death rates, providing a model to predict microbiota dynamics under deleterious perturbations.

    • Daniel P. Newton
    • , Po-Yi Ho
    •  & Kerwyn Casey Huang

  • Article
    | Open Access

    Here, Wang et al. use metagenomic sequencing to explore the impact of antibiotic treatment for Helicobacter pylori on the gut virome community in infected patients, showing that recurrent treatment leads to a lower virus community diversity and altered virus-bacteria interactions, compared with treatment naive patients.

    • Lingling Wang
    • , Haobin Yao
    •  & Wai K. Leung

  • Article
    | Open Access

    Phenological shifts driven by climate change are well-studied in plants and aboveground animals, but scarcely in belowground biota. Here, the authors show that soil warming causes phenological mismatches between plants, soil microbes and soil microarthropods in an alpine meadow.

    • Rui Yin
    • , Wenkuan Qin
    •  & Biao Zhu

  • Article
    | Open Access

    Cable bacteria are centimeter-long filamentous microbes that conduct electrons via internal wires, thus coupling sulfide oxidation between sediment layers. Here, Bjerg et al. show that the anoxic part of oxygen-respiring cable bacteria attracts swarms of other bacteria, which appear to transfer electrons to cable bacteria via soluble metabolites.

    • Jesper J. Bjerg
    • , Jamie J. M. Lustermans
    •  & Andreas Schramm

  • Article
    | Open Access

    This study investigates the average genome size of planktonic prokaryotes across tropical and polar oceans and down to the hadal realm. Using hundreds of metagenomes of marine microorganisms, genome size was found to be highest in the perennially cold polar ocean, suggesting that environmental factors influence genome size selection and the ecological strategies of marine microbes.

    • David K. Ngugi
    • , Silvia G. Acinas
    •  & Carlos M. Duarte

  • Article
    | Open Access

    Modelling diverse ecological phenomena across scales with a single mathematical framework is challenging. Here, the authors draw on density functional theory to develop a framework that bridges between mechanistic theories at fine scales and statistical models at large scales.

    • Martin-I. Trappe
    •  & Ryan A. Chisholm

  • Article
    | Open Access

    Temperature shapes the adaptation and composition of microbiomes, but whether their enzymes drive the thermal response remains unknown. Using an analysis of seven enzyme classes from worldwide marine microbiome data, this study shows that enzyme thermal properties explain microbial thermal plasticity and they are both finely tuned by the thermal variability of the environment.

    • Ramona Marasco
    • , Marco Fusi
    •  & Daniele Daffonchio

  • Article
    | Open Access

    Understanding the interactions between plants and microorganisms can inform microbiome management to enhance crop productivity and resilience to stress. Here, Howe et al. use metagenomics and metatranscriptomics to study changes in the leaf microbiome of perennial crops over two growing seasons.

    • Adina Howe
    • , Nejc Stopnisek
    •  & Ashley Shade

  • Article
    | Open Access

    Genome mining for biosynthetic gene clusters (BGCs) can be used for the discovery of new compounds of biotechnological interest. Here, the authors use metagenomics and metatranscriptomics to identify diverse BGCs in free-living and particle-associated microbial communities through the stratified water column of the Cariaco Basin, Venezuela.

    • David Geller-McGrath
    • , Paraskevi Mara
    •  & Maria Pachiadaki

  • Article
    | Open Access

    Microbial ecological strategies are expected to be phylogenetically conserved, but plasticity and acclimation to environmental change may complicate the picture. Here, the authors show that shifts in soil bacterial ecological strategies deviate from phylogenetic-based predictions after acclimation to long-term warming and CO2 enrichment.

    • Yang Ruan
    • , Yakov Kuzyakov
    •  & Ning Ling

  • Article
    | Open Access

    Fitness landscapes largely shape the dynamics of evolution, but it is unclear how they shift upon ecological diversification. By engineering genome-wide knockout libraries of a nascent bacterial community, Ascensao et al. show how ecological and epistatic patterns combine to shape adaptive landscapes.

    • Joao A. Ascensao
    • , Kelly M. Wetmore
    •  & Oskar Hallatschek

  • Article
    | Open Access

    The archetypal supergreenhouse Cretaceous Earth had an active cryosphere with permafrost in plateau deserts. A modern analogue is the aeolian–permafrost system from the Qiongkuai Lebashi Lake area, Xinjiang Uygur Autonomous Region, China.

    • Juan Pedro Rodríguez-López
    • , Chihua Wu
    •  & Chao Ma

  • Article
    | Open Access

    Over several years, this study examines how biotic interactions and warming affect the entire marine prokaryotic community at a location off the coast of Southern California. Analyses show that free-living and particle-associated prokaryotes were strongly predicted by phytoplankton and viral communities, and El Niño warming shifted cyanobacteria from cold-water ecotypes to warm-water ecotypes.

    • Yi-Chun Yeh
    •  & Jed A. Fuhrman

  • Article
    | Open Access

    Rhizosphere microbiota can influence plant pathogen interactions. Here the authors use field- and lab-based approaches to show that rhizosphere bacteria and fungi of healthy tomatoes can enhance tomato resistance against Fusarium wilt disease and formulate synthetic microbial communities that could help to control soil-borne disease.

    • Xin Zhou
    • , Jinting Wang
    •  & Lei Cai

  • Article
    | Open Access

    Bacteria can deliver toxic effector proteins into the cytosol of neighboring cells. Here, the authors show that Yersinia pseudotuberculosis secretes an effector that modulates gene expression in neighboring cells of the same species and inhibits the growth of other competitors.

    • Dandan Wang
    • , Lingfang Zhu
    •  & Xihui Shen

  • Article
    | Open Access

    Our understanding of microbial diversity and physiology in marine sediments is limited. Here, Gong et al. analyze thousands of metagenome-assembled genomes (MAGs) from coastal and deep-sea sediments, and identify MAGs belonging to new bacterial phyla that seem able to mediate key steps in sedimentary biogeochemistry.

    • Xianzhe Gong
    • , Álvaro Rodríguez del Río
    •  & Brett J. Baker

  • Article
    | Open Access

    Understanding the emergence, evolution, and transmission of antibiotic resistance genes (ARGs) is essential to combat antimicrobial resistance. Here, Munk et al. analyse ARGs in hundreds of sewage samples from 101 countries and describe regional patterns, diverse genetic environments of common ARGs, and ARG-specific transmission patterns.

    • Patrick Munk
    • , Christian Brinch
    •  & Frank M. Aarestrup

  • Article
    | Open Access

    In this study, the microbiota of multiple body sites from 101 marine fish species from Southern California were sampled and analysed. The authors compared diversity measures while also establishing a method to estimate microbial biomass. Body site is shown to be the strongest driver of microbial diversity and patterns of phylosymbiosis are observed across the gill, skin and hindgut.

    • Jeremiah J. Minich
    • , Andreas Härer
    •  & Eric E. Allen

  • Article
    | Open Access

    The mechanisms underlying methane production in oxygenated waters of oceans and lakes are unclear. Here, Perez-Coronel and Beman show that aerobic methane production in freshwater incubation experiments is associated with (bacterio)chlorophyll metabolism and photosynthesis, and with Proteobacterial degradation of methylphosphonate.

    • Elisabet Perez-Coronel
    •  & J. Michael Beman

  • Article
    | Open Access

    Soil viral communities remain understudied. Here, Liao et al. retrieve a catalogue of around sixty thousand vOTUs through a systematic viromic pipeline, and uncover the response of soil viral communities to anthropogenic land use changes.

    • Hu Liao
    • , Hu Li
    •  & Jian-Qiang Su

  • Article
    | Open Access

    Here, Nishijima et al. perform a large-scale analysis of the human gut virome in the Japanese 4D cohort of 4198 deeply phenotyped individuals, revealing thousands of bacteriophage genomes, virus-bacteria interactions, and describing associations with various host and environmental factors.

    • Suguru Nishijima
    • , Naoyoshi Nagata
    •  & Masahira Hattori

  • 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

    Some bacteria act as pathogens or predators of other bacteria, but their impact in natural settings is often unclear. Here, Bethany et al. describe a new type of obligate, intracellular predatory bacterium of widespread distribution that preys on soil cyanobacteria in biocrusts and thus severely impacts biocrust productivity.

    • Julie Bethany
    • , Shannon Lynn Johnson
    •  & Ferran Garcia-Pichel

  • Article
    | Open Access

    Communities of microbes play important roles in natural environments and hold great potential for deploying division-of-labor strategies in synthetic biology and bioproduction. Here, in a community of two competing E. coli strains, the authors show that the relative abundances of the strains can be stabilized and steered dynamically with remarkable precision by coupling the cells to an automated computer-controlled feedback-loop.

    • Joaquín Gutiérrez Mena
    • , Sant Kumar
    •  & Mustafa Khammash

  • Article
    | Open Access

    Soil microbial carbon is central to soil functions and services, but its spatial-temporal dynamics are unclear. Here the authors show global trends in soil microbial carbon, which suggests a global decrease in soil microbial carbon, mostly driven by temperature increases in northern areas.

    • Guillaume Patoine
    • , Nico Eisenhauer
    •  & Carlos A. Guerra

  • Article
    | Open Access

    Using CRISPR-Cas9 mediated-knockout and overexpression analyses, this study shows that a trypsin in the diatom Phaeodactylum tricornutum promotes phosphorus uptake and inhibits nitrogen uptake but its expression is downregulated under nitrogen stress and upregulated under phosphorus stress. Together, the findings suggest this trypsin is a coordinate regulator of nutrient homeostasis.

    • Yanchun You
    • , Xueqiong Sun
    •  & Senjie Lin

  • Article
    | Open Access

    Trace metals have been an important ingredient for life throughout Earth’s history. Here, the authors show that a member of an elusive archaeal lineage (Caldarchaeales or Aigarchaeota) requires tungsten for growth, and provide evidence that tungsten-dependent metabolism played a role in the origin and evolution of this lineage.

    • Steffen Buessecker
    • , Marike Palmer
    •  & Jeremy A. Dodsworth

  • Article
    | Open Access

    It is unknown what circumstances promote particular bacterial defenses against bacterial viruses (phages). Almeida & Hoikkala et al. show that mucin, derived from mucus, greatly accelerates CRISPR-Cas defenses against phage in an opportunistic pathogen.

    • Gabriel Magno de Freitas Almeida
    • , Ville Hoikkala
    •  & Lotta-Riina Sundberg

  • Article
    | Open Access

    The cryosphere includes those parts of Earth where water or soil is frozen, such as snow, ice, glaciers and permafrost soils. Here, the authors present a global inventory of cryospheric microbial communities and their genetic repertoires.

    • Massimo Bourquin
    • , Susheel Bhanu Busi
    •  & Tom J. Battin

  • Article
    | Open Access

    In this study, the concept of dynamic character displacement among interacting bacterial species from leaf-colonizing families was empirically tested using a proteomics approach. A phenotypic shift towards the utilization of alternative carbon sources was observed during coexistence, thereby minimizing niche overlap.

    • Lucas Hemmerle
    • , Benjamin A. Maier
    •  & Julia A. Vorholt

  • Article
    | Open Access

    The biogeography of viral communities in extreme environments remains understudied. Here, the authors use metagenomic sequencing on 90 acid mine drainage sediments sampled across Southern China, showing the predominant effects of prokaryotic communities and the influence of environmental variables on viral taxonomy and function.

    • Shaoming Gao
    • , David Paez-Espino
    •  & Linan Huang

  • Article
    | Open Access

    Microbial communities are responsible for biological wastewater treatment. Here, Dueholm et al. generate more than 5 million high-quality, full-length 16S rRNA gene sequences from wastewater treatment plants across the world to construct a database with a comprehensive taxonomy, providing insights into diversity and function of these microbial communities.

    • Morten Kam Dahl Dueholm
    • , Marta Nierychlo
    •  & Per Halkjær Nielsen

  • Article
    | Open Access

    The V-shaped Challenger Deep in the Mariana Trench is the deepest part of the world’s oceans. Using 586 prokaryotic metagenome-assembled genomes and metatranscriptomic data, this study explores metabolic capabilities and activities of microorganisms involved in elemental cycling in hadal sediments, and reveals the different distribution of processes between its bottom-axis and slope.

    • Ying-Li Zhou
    • , Paraskevi Mara
    •  & Yong Wang

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