Microbial ecology articles within Nature Communications

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  • Article
    | Open Access

    The microbiome is thought to be important for its host’s wellbeing, but it varies much among individuals. We offer a solution to this conundrum, showing that factors like the form of microbes’ contribution to hosts’ fitness and host population size may be preventing natural selection from operating effectively.

    • Itay Daybog
    •  & Oren Kolodny

  • Article
    | Open Access

    This study uses high-throughput chromosome conformation capture (Hi-C) to identify phage–host relationships in soil. By coupling Hi-C with DNA and RNA sequencing, the authors demonstrate the impact of soil drying on phage–host interactions and the downstream effects on abundances and interspecies interactions within bacterial communities.

    • Ruonan Wu
    • , Michelle R. Davison
    •  & Kirsten S. Hofmockel

  • Article
    | Open Access

    Many microorganisms are auxotrophic, that is, unable to synthesize the compounds they require for growth. Here, Ramoneda et al. predict amino acid biosynthetic capabilities of over 26,000 bacterial genomes using a metabolic pathway model validated with empirical data, and identify ecological contexts in which auxotrophy can be a successful strategy.

    • Josep Ramoneda
    • , Thomas B. N. Jensen
    •  & Noah Fierer

  • Article
    | Open Access

    Bacterial functional diversity does not necessarily correlate with taxonomic diversity because average genome size may vary by community. Here, Wang et al. investigate bacterial communities along a natural pH gradient in forest soils, and find that average genome size and functional diversity decrease, whereas taxonomic diversity increases, as soil pH rises from acid to neutral.

    • Cong Wang
    • , Qing-Yi Yu
    •  & Cheng Gao

  • Article
    | Open Access

    Microbial degradation of organic matter in landfills generates methane, a potent greenhouse gas. Here, Grégoire et al. use metagenomic approaches to study microbial methane cycling in waste landfilled over 39 years, highlighting the importance of specific microbial lineages and methane oxidation in the absence of oxygen.

    • Daniel S. Grégoire
    • , Nikhil A. George
    •  & Laura A. Hug

  • Article
    | Open Access

    Here, Lou et al. apply metagenomics and microbiome cultivation to infant fecal samples and uncover co-existing members encoding extracellular fucosidases that initiate 2’-fucosyllactose (2’FL) breakdown and can promote extensive growth of Bifidobacterium breve.

    • Yue Clare Lou
    • , Benjamin E. Rubin
    •  & Jillian F. Banfield

  • Article
    | Open Access

    Non-ammonia oxidising Thaumarachaeota lineages are common in acidic soils, but their evolution is unclear. Here, the authors assemble 15 genomes from deeply rooted Thaumarachaeota in topsoils and subsoils, investigating evolutionary divergence in the family Gagatemarchaeaceae.

    • Paul O. Sheridan
    • , Yiyu Meng
    •  & Cécile Gubry-Rangin

  • Article
    | Open Access

    Coastal upwelling regions are among the most productive marine ecosystems but may be threatened by amplified ocean acidification. Here the authors show from community to molecular levels that phytoplankton in an upwelling region respond to short-term acidification exposure with iron uptake pathways and strategies that reduce cellular iron demand.

    • Robert H. Lampe
    • , Tyler H. Coale
    •  & Andrew E. Allen

  • Article
    | Open Access

    Photosymbioses enable efficient nutrient recycling between heterotrophic and phototrophic organisms. This study shows that nutrient cycling in a cnidarian-algal symbiosis is regulated through resource competition between symbiotic partners. Mutualistic interactions can therefore emerge from mutual exploitation in nutrient–exchange symbioses.

    • Nils Rädecker
    • , Stéphane Escrig
    •  & Anders Meibom

  • Article
    | Open Access

    Gut microbes rely on nutrient exchange for survival, but these cross-feeding interactions remain poorly characterized. Here, Marcelino et al. present a metabolite-exchange scoring system derived from metagenome-scale metabolic models, designed to identify the potential microbial cross-feeding interactions most affected in human diseases.

    • Vanessa R. Marcelino
    • , Caitlin Welsh
    •  & Samuel C. Forster

  • Article
    | Open Access

    Photosynthesis is thought to be restricted to a few bacterial and eukaryotic phyla. Here, Li et al. provide evidence of photosynthetic abilities in uncultivated bacteria within the phylum Myxococcota, suggesting that some of these organisms may combine predatory and photosynthetic abilities.

    • Liuyang Li
    • , Danyue Huang
    •  & Yinzhao Wang

  • Article
    | Open Access

    This study examines the biogeography and functional gene repertoires of marine eukaryote-infecting large and giant DNA viruses. It shows a clear divide in the viral communities between polar and nonpolar environments, with recurrent evolutionary adaptations to the polar environment likely driven by alterations of their genomic functions.

    • Lingjie Meng
    • , Tom O. Delmont
    •  & Hiroyuki Ogata

  • Article
    | Open Access

    Sulfate-reducing microorganisms are common in anoxic environments and represent an important link between the sulfur and carbon cycles. Here, Dyksma & Pester show that microbial sulfate reduction and aerobic respiration are not mutually exclusive in the same organism, sulfate reducers can mineralize organic polymers, and anaerobic mineralization of complex organic matter is not necessarily a multi-step process.

    • Stefan Dyksma
    •  & Michael Pester

  • Article
    | Open Access

    Modelling a planktonic ecosystem in the ocean is challenging as it is embedded in a patch of water that is continuously moving, stretching, and diluting. This study introduces a new theoretical framework to account for such aspects, tracking a patch of water hosting a drifting ecosystem, along with its physical, environmental and biochemical features.

    • Enrico Ser-Giacomi
    • , Ricardo Martinez-Garcia
    •  & Michael J. Follows

  • Article
    | Open Access

    Viruses are ubiquitous in the oceans, exhibiting high abundance and diversity. Here, Yi et al. present a systematic catalogue and analysis of genomic sequences from marine prokaryotes and their proviruses, thus contributing to a better understanding of the ecology of these microorganisms.

    • Yi Yi
    • , Shunzhang Liu
    •  & Huahua Jian

  • Article
    | Open Access

    Climate change increases the frequency and intensity of drought events, affecting soil functions driven by microorganisms. Here, Metze et al. develop a method to estimate microbial growth rates in dry soils, and provide insights into the response of active microbes to drought today and in potential future climate conditions (high temperatures and CO2 levels).

    • Dennis Metze
    • , Jörg Schnecker
    •  & Andreas Richter

  • 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

    Bacterial remineralization of algal organic matter promotes algal growth but is rarely quantified. Here, Mayali et al. quantify bacterial incorporation of algal-derived organic carbon and nitrogen, and algal incorporation of remineralized carbon and nitrogen, for 15 bacterial co-cultures growing with the diatom Phaeodactylum tricornutum to identify functional guilds of metabolic interactions.

    • Xavier Mayali
    • , Ty J. Samo
    •  & Peter K. Weber

  • Article
    | Open Access

    Soil microbial respiration responses to warming have important implications for biogeochemical feedbacks. Here, using data from temperature gradients, the authors show that the rate of thermal adaptation of soil microbial respiration is lower than the rate of warming despite large community changes.

    • Charlotte J. Alster
    • , Allycia van de Laar
    •  & Louis A. Schipper

  • Article
    | Open Access

    Abiotic stress is thought to promote microbial mutualism, although there is a paucity of research in this area. Here, Zhao et al. study microbial communities in a quasi-natural composting system, where temperature variation (20°C−70°C) is the main abiotic stress, showing how high temperature favours mutualism and reduces competition at both the community and species levels.

    • Yuxiang Zhao
    • , Zishu Liu
    •  & Baolan Hu

  • Article
    | Open Access

    Anaerobic digestion of municipal mixed sludge is a microbial-mediated process that produces renewable natural gases such as methane. Here, Kieft et al. present the results of a two-year study of microbial community structure and function at a wastewater treatment plant, shedding light on metabolic interactions between microorganisms in relation with methane production.

    • Brandon Kieft
    • , Niko Finke
    •  & Steven J. Hallam

  • Article
    | Open Access

    Bacteria of the SAR202 clade are ubiquitously distributed in the ocean, but their biology is poorly understood due to the lack of cultivated isolates. Here, Lim et al. report the cultivation of marine SAR202 bacteria and provide insights into the physiology of these enigmatic microorganisms.

    • Yeonjung Lim
    • , Ji-Hui Seo
    •  & Jang-Cheon Cho

  • Article
    | Open Access

    Nutrient limitation is a key constraint on ocean productivity. Here, by analysing a compilation of field experiments spanning the global ocean, this study shows that increasing the number of different nutrients supplied significantly increases net phytoplankton growth, suggesting multiple nutrients are often approaching co-limiting levels.

    • Thomas J. Browning
    •  & C. Mark Moore

  • Perspective
    | Open Access

    The ecology and evolution of eukaryotic microbes in extreme environments are poorly understood. In this Perspective, Rappaport and Oliverio summarize data from over 80 studies of protists in extreme environments and identify lineages of particular interest as targets for future research.

    • Hannah B. Rappaport
    •  & Angela M. Oliverio

  • Article
    | Open Access

    Root exudates can either promote or impede the formation of stable, mineral-associated soil organic carbon (MAOC). Yet, carbon stabilisation in MAOC is decoupled from changes in the total soil carbon pool, i.e., carbon sequestration.

    • Guopeng Liang
    • , John Stark
    •  & Bonnie Grace Waring

  • 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

    Cooperative interactions might be important in spatially structured microbial habitats. Here, the authors show that cooperative interactions between planktonic and biofilm-forming bacteria drive spatial segregation, and thereby enable species’ coexistence, in a microfluidic chip environment.

    • Yichao Wu
    • , Chengxia Fu
    •  & Peng Cai

  • Article
    | Open Access

    Amazonian blackwaters are acidic and physiologically-challenging, but are one of Earth’s most diversified ecosystems. This study revealed that fish survival in these hostile habitats depends on the colonization of their gills by endogenous blackwater Betaproteobacteria, with the potential to regulate host ionoregulatory processes.

    • Sylvain François-Étienne
    • , Leroux Nicolas
    •  & Derome Nicolas

  • Article
    | Open Access

    Keystone taxa in ecological communities are native taxa that have an especially important role in the stability of their ecosystem. This study introduces a novel method for detecting keystones in microbial communities by comparing data with and without specific species.

    • Guy Amit
    •  & Amir Bashan

  • Article
    | Open Access

    Previous, a long-term evolution experiment in E.coli resulted in spontaneous emergence of ecotypes that coexisted for more than 14,000 generations. Here, the authors show that the emergence and persistence of this phenomenon results from two interacting trade-offs, rooted in biochemical constraints.

    • Avik Mukherjee
    • , Jade Ealy
    •  & Markus Basan

  • Article
    | Open Access

    Anaerobic gut fungi are a functionally important component of mammalian herbivores’ microbiomes. Here, the authors surveys anaerobic gut fungi in 34 species of ruminants and hindgut fermenters, assessing their patterns and identifying 56 novel genera.

    • Casey H. Meili
    • , Adrienne L. Jones
    •  & Mostafa S. Elshahed

  • Article
    | Open Access

    Soil microbial networks play a crucial role in plant community stability. This study shows that decoupled prokaryote and fungal networks in dry grassland soil support plant community stability over time, while coupled networks in abandoned agricultural soil are associated to instability.

    • Dina in ‘t Zandt
    • , Zuzana Kolaříková
    •  & Zuzana Münzbergová

  • Article
    | Open Access

    Plasmids are the main vector by which antibiotic resistance is transferred between bacterial cells within surface-associated communities. Here, Ma et al. show that plasmid spread peaks at intermediate antibiotic administration times, when the intermixing of plasmid donors and potential recipients is maximal.

    • Yinyin Ma
    • , Josep Ramoneda
    •  & David R. Johnson

  • Article
    | Open Access

    Drivers responsible for plant microbiome variation between sites remain elusive. Here, the authors test how soil nutrient addition and herbivore exclusion affect plant microbiota in grasslands worldwide, showing that microbiota diversity responded to environmental variation similarly across sites.

    • Eric W. Seabloom
    • , Maria C. Caldeira
    •  & Elizabeth T. Borer

  • 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

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