Environmental microbiology articles within Nature Communications

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  • Article
    | Open Access

    Biosensors are powerful tools for quantification of a wide range of molecules but require extensive engineering for each analyte. Here, the authors engineered a robust environmental bacterium for sensing a diverse set of chemicals, such as lactate and PET degradation products, via growth-coupling

    • Javier M. Hernández-Sancho
    • , Arnaud Boudigou
    •  & Pablo I. Nikel

  • Article
    | Open Access

    The expansion and intensification of agriculture has led to a loss of soil carbon. Here the authors show that increasing plant diversity within an agricultural soil increases positive associations within the soil microbial community, which increases carbon use efficiency.

    • Luiz A. Domeignoz-Horta
    • , Seraina L. Cappelli
    •  & Anna-Liisa Laine

  • Article
    | Open Access

    Artificial selection is a promising way to improve microbial community functions. Here, Arias-Sánchez et al. evaluate a method inspired by genetic algorithms to select small bacterial communities of known species composition based on their degradation of an industrial pollutant.

    • Flor I. Arias-Sánchez
    • , Björn Vessman
    •  & Sara Mitri

  • Article
    | Open Access

    Life may have originated in a hydrothermal habitat, but the extent that contemporary thermophilic microbes and their environments reflect those on early Earth is unclear. Here, Colman et al. evaluate covariation in microbial taxonomy, metabolism and phylogeny as a function of hot spring geochemistry, suggesting moderately acidic springs as early Earth analogs.

    • Daniel R. Colman
    • , Lisa M. Keller
    •  & Eric S. Boyd

  • Article
    | Open Access

    This study analyzes a global dataset of soil metagenomes to explore environmental drivers of growth potential, a fundamental aspect of bacterial life history. The authors show that growth potential, estimated from codon usage statistics, was highest in forested biomes and lowest in arid latitudes, which indicates that bacterial productivity generally reflects ecosystem productivity globally.

    • Ernest D. Osburn
    • , Steven G. McBride
    •  & Michael S. Strickland

  • Article
    | Open Access

    Research on permafrost microbial communities is crucial for predicting the response of permafrost ecosystems to climate change. Here, Kang et al. provide insights into the structure and functional potential of permafrost microbial communities by analyzing 16S rRNA gene sequence data and metagenomic data obtained from an ∼1000 km transect on the Tibetan Plateau.

    • Luyao Kang
    • , Yutong Song
    •  & Yuanhe Yang

  • Article
    | Open Access

    Anaerobic digesters play an important role in biodegradation. In the MiDAS 5 project, the authors use global 16S rRNA sequencing to expand the microbial reference database, improving taxonomic classification and revealing how environmental factors and geography shape microbial communities in anaerobic digesters.

    • Morten Kam Dahl Dueholm
    • , Kasper Skytte Andersen
    •  & Per Halkjær Nielsen

  • Article
    | Open Access

    The occurrence of aerobic methane-oxidizing bacteria in anoxic environments is puzzling, as oxygen is thought to be required for methane oxidation. Here, Schorn et al. show that the methane assimilation activity of these bacteria is similar under hypoxic and anoxic conditions in a stratified lake, and the bacteria use fermentation-based methanotrophy as well as denitrification under anoxic conditions.

    • Sina Schorn
    • , Jon S. Graf
    •  & Jana Milucka

  • Article
    | Open Access

    Several groups of archaea, such as the order Methanocellales, are characterised by their ability to produce methane. Here, Suzuki et al. identify a Methanocellales archaeon that lacks essential methanogenesis genes and seems to be instead a CO2-reducing, electron-fueled acetogen.

    • Shino Suzuki
    • , Shun’ichi Ishii
    •  & Kenneth H. Nealson

  • Article
    | Open Access

    Aerobic methanotrophic bacteria are considered strict aerobes but are often highly abundant in hypoxic or anoxic environments. Here, the authors show that acidophilic methanotrophs can respire nitrous oxide and grow anaerobically on diverse non-methane substrates, including methanol, C-C substrates, and hydrogen.

    • Samuel Imisi Awala
    • , Joo-Han Gwak
    •  & Sung-Keun Rhee

  • Article
    | Open Access

    Microbial reduction of nitrous oxide to dinitrogen is considered negligible under acidic conditions. However, Guang He et al. show that a co-culture of two bacterial species derived from acidic tropical forest soil can reduce nitrous oxide at pH 4.5.

    • Guang He
    • , Gao Chen
    •  & Frank E. Löffler

  • Article
    | Open Access

    Phytoplankton blooms provoke bacterioplankton blooms, from which bacterial biomass (necromass) is released via zooplankton grazing and viral lysis. Here, Beidler et al. show that the bacterial biomass, including alpha-glucan polysaccharides generated from the consumption of algal organic matter, is reused by microbes in vitro and during a diatom-dominated bloom.

    • Irena Beidler
    • , Nicola Steinke
    •  & Thomas Schweder

  • Article
    | Open Access

    Carbohydrate binding modules (CBMs) are non-catalytic domains found within multi-modular carbohydrate-active enzymes like glycoside hydrolases. Here, the authors show the crystal structures of two CBM family 92 members, which use three different surface binding sites to bind to β-glucans.

    • Meng-Shu Hao
    • , Scott Mazurkewich
    •  & Lauren S. McKee

  • Article
    | Open Access

    Metagenomic taxonomic profiling usually relies either on reads or assembled contigs/MAGs. Here, authors present RAT, a tool that integrates taxonomic signals from reads, contigs, and MAGs into one profile with high precision and sensitivity. RAT provides a comprehensive view of the microbiome.

    • Ernestina Hauptfeld
    • , Nikolaos Pappas
    •  & F. A. Bastiaan von Meijenfeldt

  • Article
    | Open Access

    Prompt physiological reactivation after rainfall pulses may be key for microbial survival in arid ecosystems. Here, the authors use stable isotope tracers, single-cell NanoSIMS and metatranscriptomics to shed light on how desert biocrust microbial communities respond to rewetting.

    • Stefanie Imminger
    • , Dimitri V. Meier
    •  & Dagmar Woebken

  • Article
    | Open Access

    Little is known about viral communities in deep-sea seamounts. In this study, the authors performed metagenomic and virome analysis from sediments in the western Pacific Ocean and characterize the diversity, distribution and potential ecological roles of viruses in deep-sea seamount sediments.

    • Meishun Yu
    • , Menghui Zhang
    •  & Min Jin

  • Article
    | Open Access

    Here, the authors analyze the plasmidome in 3,467 human gut microbiome samples across continents and disease states, revealing that plasmid dispersal in the human gut is predominantly neutral, but becomes more selective in inflammatory diseases, shedding light on microbial evolution in health and disease.

    • Alvah Zorea
    • , David Pellow
    •  & Itzhak Mizrahi

  • Article
    | Open Access

    The microbial valorisation of greenhouse gases could offer promising approaches climate change mitigation. Here, authors demonstrate the coupling of methane oxidation and carbon dioxide reduction by microbial consortia, facilitated by the redox cycling of iron minerals.

    • Yue Zheng
    • , Huan Wang
    •  & Feng Zhao

  • Article
    | Open Access

    Soil viruses could have a disproportionate role in ecosystem functioning. Here, the authors combine multiple data and approaches to explore diversity and distribution of P-acquisition genes encoded by soil bacteriophages, suggesting the importance of viral auxiliary metabolism for nutrient cycling.

    • Jie-Liang Liang
    • , Shi-wei Feng
    •  & Jin-tian Li

  • Article
    | Open Access

    Fungi have the potential to produce sustainable foods for a growing population, but current products are based on a small number of strains with inherent limitations. Here, the authors develop genetic tools for an edible fungus and engineer its nutritional value and sensory appeal for alternative meat applications.

    • Vayu Maini Rekdal
    • , Casper R. B. van der Luijt
    •  & Jay D. Keasling

  • Article
    | Open Access

    Bacteria have evolved numerous innate and adaptive defence mechanisms. Here, Beavogui et al characterise the impact of biogeography, genetic mobility, and clustering in defense islands, on the defence systems of soil, marine, and human gut bacterial populations genomes.

    • Angelina Beavogui
    • , Auriane Lacroix
    •  & Pedro H. Oliveira

  • Article
    | Open Access

    The relative importance of the various mechanisms that can drive microbial speciation is poorly understood. Here, Stanojković et al. explore the diversification of the soil cyanobacterium Microcoleus, showing that this genus represents a global speciation continuum of at least 12 lineages, with lineage divergence driven by selection, geographical distance, and the environment.

    • Aleksandar Stanojković
    • , Svatopluk Skoupý
    •  & Petr Dvořák

  • Article
    | Open Access

    This study shows that a multitrophic community model jointly recapitulates diel rhythms in abundances of Prochlorococcus picocyanobacteria, as well as viral infection, viral abundances and grazer abundances. Model-data integration implies that grazing predominantly controls Prochlorococcus abundances in surface waters of the North Pacific Subtropical Gyre, despite high viral densities.

    • Stephen J. Beckett
    • , David Demory
    •  & Joshua S. Weitz

  • Article
    | Open Access

    The role of viruses in environmental methane cycling is still largely unclear. Here, Zhong et al. analyse metagenomics data to identify auxiliary metabolic genes related to methane metabolism within viral contigs. They found that the potential viral impacts on methane production and oxidation varies by habitat.

    • Zhi-Ping Zhong
    • , Jingjie Du
    •  & Matthew B. Sullivan

  • Article
    | Open Access

    The soil microbiome communicates with plant roots using a chemical language. Here, using p-coumaroyl-homoserine lactone as the synthetic communication signal, the authors demonstrate programmable microbe-to-plant communication from the sender in the soil bacteria to a receiver in the plant.

    • Alice Boo
    • , Tyler Toth
    •  & Christopher A. Voigt

  • Article
    | Open Access

    Herbicides used in terrestrial environments pollute coastal ecosystems. Here, the authors analyse the presence of 32 herbicides at 661 bays and gulfs worldwide from 1990 to 2022, showing how under current herbicide stress, phytoplankton primary productivity was inhibited by more than 5% at 25%.

    • Liqiang Yang
    • , Xiaotong He
    •  & Yongyu Zhang

  • Article
    | Open Access

    The Tibetan Plateau is the largest plateau in the world and hosts a variety of aquatic ecosystems. Here, the authors present a gene and genome catalogue of Tibetan Plateau aquatic microbiomes, greatly expanding known taxonomic and functional diversity for the region and giving insights into its microbial biogeography.

    • Mingyue Cheng
    • , Shuai Luo
    •  & Kang Ning

  • Article
    | Open Access

    It is unclear whether microbes can efficiently degrade biodegradable plastics in the extreme environmental conditions of the seafloor. Here, Omura et al. show that biodegradable plastics can be degraded by the action of microorganisms on the deep-sea floor, although with much less efficiency than in coastal settings.

    • Taku Omura
    • , Noriyuki Isobe
    •  & Tadahisa Iwata

  • Article
    | Open Access

    Phage satellites are bacterial genetic elements that co-opt phage machinery for their own dissemination. Here, Barcia-Cruz et al. identify a family of satellites, named PICMIs, that are characterized by reduced gene content and are broadly distributed in marine bacteria of the family Vibrionaceae.

    • Rubén Barcia-Cruz
    • , David Goudenège
    •  & Frédérique Le Roux

  • Article
    | Open Access

    What a microbial strain is and how many strains make up a natural bacterial population remain elusive concepts. Here, Viver et al. analyse Salinibacter ruber isolates and metagenomes from two solar salterns, revealing gaps within the species sequence space that they use to define and quantify sub-species categories, such as genomovars and strains, that co-exist in a saltern pond.

    • Tomeu Viver
    • , Roth E. Conrad
    •  & Ramon Rossello-Mora

  • Article
    | Open Access

    Pores and channels within complex porous structures, such as the soil or the human gut, influence fluid flow and thus bacterial colonization. Here, Scheidweiler et al. study bacterial colonization of a model complex porous structure and show how the interactions between fluid flow, microscale structure, chemotaxis, and gradients of a quorum-sensing signaling molecule control the heterogenous accumulation of bacterial biomass.

    • David Scheidweiler
    • , Ankur Deep Bordoloi
    •  & Pietro de Anna

  • Article
    | Open Access

    This study investigates the dynamic associations among microbes in the world’s tropical and subtropical oceans. It reveals that potential interactions vary with ocean depth and location, with most surface associations not persisting in deeper waters. The results contribute to understanding the ocean microbiome in the context of global change.

    • Ina M. Deutschmann
    • , Erwan Delage
    •  & Ramiro Logares

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