Environmental microbiology articles within Nature Communications

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  • Article
    | Open Access

    The host range of bacteriophages defines their impact on bacterial ecology and diversity. Here, Göller et al. isolate 94 staphylococcal phages from wastewater and determine their host range on 117 staphylococci from 29 species, revealing a predominant multi-species host range and thus great potential for horizontal gene transfer.

    • Pauline C. Göller
    • , Tabea Elsener
    •  & Elena Gómez-Sanz

  • Article
    | Open Access

    Phosphorothioate (PT) modification by the dnd gene cluster is the first identified DNA backbone modification and has been shown to constitute a multifunctional epigenetic system. Despite a variety of advantages for hosting dnd systems, these systems are surprisingly distributed sporadically among contemporary microbial genomes. To address this ecological paradox, Jian et al. systematically investigated the occurrence and phylogeny of dnd systems in prokaryotes, and provided evidence to suggest that dnd systems have originated in ancient Cyanobacteria (probably Nostocales) after the Great Oxygenation Event.

    • Huahua Jian
    • , Guanpeng Xu
    •  & Xiang Xiao

  • Article
    | Open Access

    Studying the role of predator–prey interactions in food-web stability and species coexistence in the environment is arduous. Here, Cohen et al. use a combination of community and single-cell analyses to show that bacterial predators can regulate prey populations in the species-rich environments of wastewater treatment plants.

    • Yossi Cohen
    • , Zohar Pasternak
    •  & Edouard Jurkevitch

  • Article
    | Open Access

    Activated sludge (AS) systems in wastewater treatment plants (WWTPs) contain high concentration of viruses. Here, the authors apply a systematic metagenomic pipeline and retrieve a catalogue of around 50,000 prokaryotic viruses from samples of six WWTPs, revealing a large and uncharacterized viral diversity in AS communities.

    • Yiqiang Chen
    • , Yulin Wang
    •  & Tong Zhang

  • Article
    | Open Access

    Over the past century, the Western Antarctic Peninsula has experienced rapid warming and a substantial loss of sea ice with important implications for plankton biodiversity and carbon cycling. Using a 5-year DNA metabarcoding dataset, this study assesses how interannual variability in sea-ice conditions impacts biodiversity and biological carbon fluxes in this region.

    • Yajuan Lin
    • , Carly Moreno
    •  & Nicolas Cassar

  • Article
    | Open Access

    N2 fixation was key to the expansion of life on Earth, but which organisms fixed N2 and if Mo-nitrogenase was functional in the low Mo early ocean is unknown. Here, the authors show that purple sulfur bacteria fix N2 using Mo-nitrogenase in a Proterozoic ocean analogue, despite low Mo conditions.

    • Miriam Philippi
    • , Katharina Kitzinger
    •  & Marcel M. M. Kuypers

  • Article
    | Open Access

    Nitrogen fixation by diazotrophs is critical for marine primary production. Using Tara Oceans datasets, this study combines a quantitative image analysis pipeline with metagenomic mining to provide an improved global overview of diazotroph abundance, diversity and distribution.

    • Juan José Pierella Karlusich
    • , Eric Pelletier
    •  & Rachel A. Foster

  • Article
    | Open Access

    Here the authors use microfluidics and single-cell microscopy to quantify the growth dynamics of individual E. coli cells exposed to nutrient fluctuations with periods as short as 30 seconds, finding that nutrient fluctuations reduce growth rates up to 50% compared to a steady nutrient delivery of equal average concentration, implying that temporal variability is an important parameter in bacterial growth.

    • Jen Nguyen
    • , Vicente Fernandez
    •  & Roman Stocker

  • Article
    | Open Access

    Here, the authors report a large-scale comparative analysis of <30,000 Diversity-Generating Retroelements (DGRs) across ~9000 metagenomes (representing diverse taxa and biomes), to identify patterns in terms of prevalence and activity. Combined with examination of longitudinal data on <100 metagenomes part of time series, they demonstrate that DGRs are broadly and consistently active, implying an important role in microbiota ecology and evolution.

    • Simon Roux
    • , Blair G. Paul
    •  & Emiley A. Eloe-Fadrosh

  • Article
    | Open Access

    It is thought that polyphenols inhibit organic matter decomposition in soils devoid of oxygen. Here the authors use metabolomics and genome-resolved metaproteomics to provide experimental evidence of polyphenol biodegradation and maintained soil microbial community metabolism despite anoxia.

    • Bridget B. McGivern
    • , Malak M. Tfaily
    •  & Kelly C. Wrighton

  • Article
    | Open Access

    There is much uncertainty on the response of soil microbial communities to warming, particularly in the subsoil. Here, the authors investigate microbial community and metabolism response to 4.5 years of whole-profile soil warming, finding depth-dependent effects and elevated subsoil microbial respiration.

    • Nicholas C. Dove
    • , Margaret S. Torn
    •  & Neslihan Taş

  • Article
    | Open Access

    Cyanobacterial photosynthesis is thought to have oxygenated Earth’s atmosphere during the Great Oxidation Event, but these organisms had to overcome the toxic effects of iron. Here the authors simulate Archaean conditions in Cyanobacterial cultures and find that gas exchange and rust formation alleviated iron toxicity.

    • A. J. Herrmann
    • , J. Sorwat
    •  & M. M. Gehringer

  • Article
    | Open Access

    Microbes play key roles in wastewater treatment. Here, Singleton et al. use long-read and short-read sequencing to recover 1083 high-quality metagenome-assembled genomes from 23 wastewater treatment plants, and combine this information with amplicon data, Raman microspectroscopy and FISH to reveal functionally important lineages.

    • Caitlin M. Singleton
    • , Francesca Petriglieri
    •  & Mads Albertsen

  • Article
    | Open Access

    Soil organic matter (SOM) is a huge sink of carbon, but the varied flux dynamics are challenging to predict. Here, the authors present a new model with the complexities of SOM cycling, including parameters for substrate accessibility, microbe diversity, and enzymatic substrate depolymerization.

    • Julien Sainte-Marie
    • , Matthieu Barrandon
    •  & Delphine Derrien

  • Comment
    | Open Access

    Many newly-discovered microbial phyla have been studied solely by cultivation-independent techniques such as metagenomics. Much of their biology thus remains elusive, because the organisms have not yet been isolated and grown in the lab. Katayama et al. lift the curtain on some intriguing biology by cultivating and studying bacteria from the elusive OP9 phylum (Atribacterota).

    • Muriel C. F. van Teeseling
    •  & Christian Jogler

  • Article
    | Open Access

    Herold et al. present an integrated meta-omics framework to investigate how mixed microbial communities, such as oleaginous bacterial populations in biological wastewater treatment plants, respond with distinct adaptation strategies to disturbances. They show that community resistance and resilience are a function of phenotypic plasticity and niche complementarity.

    • Malte Herold
    • , Susana Martínez Arbas
    •  & Paul Wilmes

  • Article
    | Open Access

    Soil-borne fungal pathogens use chemotropism and extracellular pH alkalinisation to reach and penetrate plant roots. Here, Palmieri et al. show that soil endophytic bacteria swim along fungal hyphae to colonize plant roots and protect host plants by modulating the pH of the rhizosphere.

    • Davide Palmieri
    • , Stefania Vitale
    •  & David Turrà

  • Article
    | Open Access

    Dimethylsulfoniopropionate (DMSP) is an osmolyte produced by marine microbes that plays an important role in nutrient cycling and atmospheric chemistry. Here the authors go to the Mariana Trench—the deepest point in the ocean—and find bacteria are key DMSP producers, and that DMSP has a role in protection against high pressure.

    • Yanfen Zheng
    • , Jinyan Wang
    •  & Xiao-Hua Zhang

  • Article
    | Open Access

    Successful application of microbial community for bioproduction relies on the selection of appropriate heterotroph and phototroph partners. Here, the authors construct community metabolic models to guide strain selection and experimentally validate metabolic exchanges that sustain the heterotrophs in minimal media.

    • Cristal Zuñiga
    • , Tingting Li
    •  & Karsten Zengler

  • Article
    | Open Access

    The discovery of aerobic microbial communities in nutrient-poor sediments below the seafloor begs the question of the mechanisms for their persistence. Here the authors investigate subseafloor sediment in the South Pacific Gyre abyssal plain, showing that aerobic microbial life can be revived and retain metabolic potential even from 101.5 Ma-old sediment.

    • Yuki Morono
    • , Motoo Ito
    •  & Fumio Inagaki

  • Article
    | Open Access

    Microbial carbon use efficiency has an important role in soil C cycling. Here the authors test the interactive effects of temperature and moisture and manipulate microbial community composition in soil microcosms, showing a positive relationship between microbial diversity and CUE that is contingent on abiotic conditions.

    • Luiz A. Domeignoz-Horta
    • , Grace Pold
    •  & Kristen M. DeAngelis

  • Article
    | Open Access

    Here, the authors sample air and surfaces in hospital rooms of COVID-19 patients, detect SARS-CoV-2 RNA in air samples of two of three tested airborne infection isolation rooms, and find surface contamination in 66.7% of tested rooms during the first week of illness and 20% beyond the first week of illness.

    • Po Ying Chia
    • , Kristen Kelli Coleman
    •  & Daniela Moses

  • Article
    | Open Access

    The association between leguminous plants and rhizobial bacteria is a paradigmatic example of a symbiosis driven by metabolic exchanges. Here, diCenzo et al. report the reconstruction and modelling of a genome-scale metabolic network of the plant Medicago truncatula nodulated by the bacterium Sinorhizobium meliloti.

    • George C. diCenzo
    • , Michelangelo Tesi
    •  & Marco Fondi

  • Article
    | Open Access

    Bacteria capable of anaerobic ammonium oxidation (anammox) produce half of the nitrogen gas in the atmosphere, but much of their physiology is still unknown. Here the authors show that anammox bacteria are capable of a novel mechanism of ammonium oxidation using extracellular electron transfer.

    • Dario R. Shaw
    • , Muhammad Ali
    •  & Pascal E. Saikaly

  • Article
    | Open Access

    Rice paddies are a major source of the Earth’s atmospheric methane, making these important food crops potent contributors to greenhouse gas emissions. Here the authors show that inoculation of paddies with a particular bacterium could significantly curb methane production.

    • Vincent V. Scholz
    • , Rainer U. Meckenstock
    •  & Nils Risgaard-Petersen

  • Article
    | Open Access

    Ammonia oxidizing archaea and Nitrospinae are the main known nitrifiers in the ocean, but the much greater abundance of the former is puzzling. Here, the authors show that differences in mortality, rather than thermodynamics, cell size or biomass yield, explain the discrepancy, without the need to invoke yet undiscovered, abundant nitrite oxidizers.

    • Katharina Kitzinger
    • , Hannah K. Marchant
    •  & Marcel M. M. Kuypers

  • Article
    | Open Access

    Alkaline lakes have some of the highest productivity rates in freshwater ecosystems. Here the authors report amplicon, metagenome, and proteome sequencing from microbial mat communities of four alkaline lakes in Canada, and compare these lakes to central Asian soda lakes, revealing a shared core microbiome despite the geographical distance.

    • Jackie K. Zorz
    • , Christine Sharp
    •  & Marc Strous

  • Article
    | Open Access

    Anthropogenic CO2 emissions are causing ocean acidification, which can affect the physiology of some organisms. Here, Botté et al. use metagenomics to show differences in metabolic potential between sponge microbiomes sampled at a shallow volcanic CO2 seep and those from nearby control sites.

    • Emmanuelle S. Botté
    • , Shaun Nielsen
    •  & Nicole S. Webster

  • Article
    | Open Access

    Microbial communities of plant leaf surfaces are ecologically important, but how they assemble and vary in time is unclear. Here, the authors identify core leaf microbiomes and seasonal patterns for two biofuel crops and show with source-sink models that soil is a reservoir of phyllosphere diversity.

    • Keara L. Grady
    • , Jackson W. Sorensen
    •  & Ashley Shade

  • Article
    | Open Access

    The International Space Station is a unique habitat for humans and microbes. Here, Mora et al. analyze microbial communities from several areas aboard, finding similarities with those of ground-based indoor environments, as well as adaptations towards biofilm formation but not necessarily relevant to human health.

    • Maximilian Mora
    • , Lisa Wink
    •  & Christine Moissl-Eichinger

  • Article
    | Open Access

    Soil microorganisms are a rich source of bioactive molecules. Here, the authors present a targeted sequencing workflow that reconstructs the clustered organization of biosynthetic domains in metagenomic libraries from amplicon data, thus guiding the discovery of novel metabolites from rare members of the soil microbiome.

    • Vincent Libis
    • , Niv Antonovsky
    •  & Sean F. Brady

  • Article
    | Open Access

    Standard DNA-based analyses of microbial communities cannot distinguish between active microbes and dead or dormant cells. Here, Couradeau et al. use BONCAT (bioorthogonal non-canonical amino acid tagging), flow cytometry, and 16S rRNA gene amplicon sequencing to identify active microbial cells in soils.

    • Estelle Couradeau
    • , Joelle Sasse
    •  & Trent R. Northen

  • Article
    | Open Access

    Developing a predictive understanding of bacterial community responses to environmental change is an ongoing challenge. Here, Isobe et al. reanalyze data on soil microbial responses to nitrogen addition across 5 continents, finding that responses are predictable based on phylogeny.

    • Kazuo Isobe
    • , Steven D. Allison
    •  & Jennifer B. H. Martiny

  • Article
    | Open Access

    Soil fungi play essential roles in ecosystems worldwide. Here, the authors sequence and analyze 235 soil samples collected from across the globe, and identify dominant fungal taxa and their associated environmental attributes.

    • Eleonora Egidi
    • , Manuel Delgado-Baquerizo
    •  & Brajesh K. Singh

  • Article
    | Open Access

    Ammonia-oxidizing bacteria and archaea are major producers of the gases nitrous oxide and nitric oxide. Here, Kits et al. show that a complete ammonia-oxidizing (comammox) bacterium emits nitrous oxide at levels that are comparable to those produced by ammonia-oxidizing archaea.

    • K. Dimitri Kits
    • , Man-Young Jung
    •  & Holger Daims

  • Article
    | Open Access

    Pseudomonas and Bacillus can promote plant growth but their mutual interactions are unclear. Here, the authors show that the extracellular matrix protects Bacillus colonies from infiltration by Pseudomonas cells, while the Pseudomonas type VI secretion system stimulates Bacillus sporulation.

    • Carlos Molina-Santiago
    • , John R. Pearson
    •  & Diego Romero

  • Article
    | Open Access

    The prokaryote defence system Dnd relies on phosphorothioation (PT) of DNA backbone to distinguish between self and non-self DNA. Here, Xiong et al. describe a previously uncharacterized PT-based antiviral system that is independent of the canonical Dnd and is widespread in Archaea and Bacteria.

    • Lei Xiong
    • , Siyi Liu
    •  & Shi Chen

  • Article
    | Open Access

    Some microorganisms may be transferred across the food production chain and, potentially, colonize the human gut. Here, Milani et al. provide strain-level evidence supporting that dairy cattle-associated bacteria can be transferred to the human gut via consumption of Parmesan cheese.

    • Christian Milani
    • , Sabrina Duranti
    •  & Francesca Turroni

  • Article
    | Open Access

    Anammox bacteria couple nitrite reduction to ammonium oxidation, with nitric oxide (NO) and hydrazine as intermediates, and produce N2 and nitrate. Here, Hu et al. show that an anammox bacterium can grow in the absence of nitrite by coupling ammonium oxidation to NO reduction, producing only N2.

    • Ziye Hu
    • , Hans J. C. T. Wessels
    •  & Boran Kartal

  • Article
    | Open Access

    Obtaining data on antimicrobial resistance (AMR) from healthy human populations is difficult. Here, Hendriksen et al. use metagenomic analysis to obtain AMR data from untreated sewage from 79 sites in 60 countries, finding correlations with socio-economic, health and environmental factors.

    • Rene S. Hendriksen
    • , Patrick Munk
    •  & Frank M. Aarestrup

  • Article
    | Open Access

    The environmental microbiota can have important implications for our well-being. Here, the authors describe the composition of microbiomes from diverse buildings, including samples from clinical environments, and show that cleaner environments are associated with a loss of microbial diversity and an increase in genes associated with antibiotic resistance.

    • Alexander Mahnert
    • , Christine Moissl-Eichinger
    •  & Gabriele Berg

  • Article
    | Open Access

    Previous surveys of global ocean microbial diversity have focused on planktonic microbes. Here, Zhang et al. use metagenomics to study biofilm-forming marine microbes, increasing the known microbial diversity in the oceans by more than 20% and revealing new biosynthetic gene clusters and CRISPR-Cas systems.

    • Weipeng Zhang
    • , Wei Ding
    •  & Pei-Yuan Qian

  • Article
    | Open Access

    Our knowledge of DNA methylation systems in prokaryotes is mostly limited to those of culturable microbes. Here, Hiraoka et al. analyse DNA methylation patterns in metagenomic data from a microbial community, revealing new methylated motifs and experimentally validating the methyltransferases’ specificities.

    • Satoshi Hiraoka
    • , Yusuke Okazaki
    •  & Wataru Iwasaki

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