Microbial ecology articles within Nature Communications

Featured

  • 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

  • Article
    | Open Access

    Interference competition exemplified by antagonism remains controversial. Using comparative genomic analysis and antagonistic assessments, this study shows that the distribution profile of biosynthetic gene clusters within Bacillus genomes is consistent with their phylogenetic relationship and that congeneric antagonism among Bacillus strains is positively correlated with phylogenetic distance.

    • Liming Xia
    • , Youzhi Miao
    •  & Ruifu Zhang

  • Article
    | Open Access

    Understanding soil microbiota dynamics is key the development of soil-based sustainable agriculture and conservation strategies. This meta-analysis shows that bulk soil functions as a seed bank for the rhizosphere, which encompasses a rich microbiota adapted to dynamic conditions in hotpots.

    • Ning Ling
    • , Tingting Wang
    •  & Yakov Kuzyakov

  • 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

    Buffalo is an important livestock in Asia. Here, the authors present a comprehensive metagenomic analysis of the microbial communities present in different sites and compartments along the buffalo digestive tract.

    • Feng Tong
    • , Teng Wang
    •  & Qingyou Liu

  • Article
    | Open Access

    Bacteria often live in densely packed, spatially-structured communities; however, much of our understanding of their behavior stems from studies in liquid culture. Here, Monaco et al. show how spatial structure and quorum sensing modulate a cooperative behavior in colonies of Pseudomonas aeruginosa.

    • Hilary Monaco
    • , Kevin S. Liu
    •  & Joao B. Xavier

  • Article
    | Open Access

    Pollen can be a vehicle for viral spread among plants. Here, Fetters et al. apply viral metagenomics to characterize the pollen virome of a diverse set of wild plants, find known and previously un-known viruses and show that wild plant species harbor more viruses when surrounded by less natural vegetation and when they have traits that promote increased plant-pollinator vector interactions.

    • Andrea M. Fetters
    • , Paul G. Cantalupo
    •  & Tia-Lynn Ashman

  • Article
    | Open Access

    Microbial communities employ a variety of strategies to compete against competitors sharing their niche, for instance, by producing antibiotics. This study reveals that antibiotics produced by Bacillus subtilis act synergistically to eliminate phylogenetically distinct competitors and are regulated accordingly.

    • Harsh Maan
    • , Maxim Itkin
    •  & Ilana Kolodkin-Gal

  • Article
    | Open Access

    Understanding the interactions between bacteria and their viruses (phages) in natural communities is a major challenge. Here, the authors isolate and study large numbers of marine Vibrio bacteria and their phages, and find that lytic interactions are sparse and many phages are host-strain-specific, but nevertheless recombination between some phages is common.

    • Kathryn M. Kauffman
    • , William K. Chang
    •  & Libusha Kelly

  • Article
    | Open Access

    Cooperative mutualisms are widespread in many ecosystems but how they affect the ability of organisms to adapt to changing conditions was unclear. This study experimentally demonstrates that members of obligate cooperative mutualisms are less able to adapt evolutionarily to external selection pressures and are more likely to return to metabolic autonomy than their free-living counterparts.

    • Benedikt Pauli
    • , Leonardo Oña
    •  & Christian Kost

Browse broader subjects

Browse Microbial ecology across other nature.com journals