Environmental microbiology articles within Nature Communications

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  • 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

  • Article
    | Open Access

    Cheese fermentation and flavour formation are the result of complex biochemical reactions driven by the activity of multiple microorganisms. Here, the authors identify microbial interactions as a mechanism underlying flavour formation in Cheddar cheese.

    • Chrats Melkonian
    • , Francisco Zorrilla
    •  & Ahmad A. Zeidan

  • Article
    | Open Access

    The bark is the outermost defense of trees against microbial attack, largely due to toxicity of extractive compounds. Here, Ristinmaa et al. study microbial community dynamics and chemical changes during degradation of spruce bark over six months, showing that the microbial degradation of extractive compounds, such as resin acids, has a major role in shaping the microbial community.

    • Amanda Sörensen Ristinmaa
    • , Albert Tafur Rangel
    •  & Johan Larsbrink

  • Article
    | Open Access

    Crop rotation helps preventing pathogen infestations compared to monocultures, which may be partly due to root-associated microbes. Here, the authors show that rhizosphere microbiomes in monocultures are less able to suppress fungal pathogens compared to crop rotations, and that inoculating certain microbes can mitigate it.

    • Yanyan Zhou
    • , Zhen Yang
    •  & Xiaogang Li

  • Article
    | Open Access

    The ability of marine bacteria to direct their movement in response to chemical gradients influences inter-species interactions, nutrient turnover, and ecosystem productivity. Here, Clerc et al. show that marine bacteria are strongly attracted to algal polysaccharides, and this chemotactic behaviour is enhanced by dimethylsulfoniopropionate (DMSP), a ubiquitous algal metabolite.

    • Estelle E. Clerc
    • , Jean-Baptiste Raina
    •  & Roman Stocker

  • 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

    Engineering ammonium excretion diazotrophs suffers from severe penalties to the bacteria. Here, the authors utilize a thermo-sensitive glutamine synthetase-based regulatory switch that permits diurnal changes in diazotrophic lifestyle, coincident with seasonal temperatures for cereal cultivation.

    • Yuqian Tang
    • , Debin Qin
    •  & Yi-Ping Wang

  • 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

    Soil conceals a vast realm of unexplored microbes, often referred to as the “microbial dark matter.” This hidden universe boasts a rich tapestry of microbial and genetic biodiversity. Here, the authors introduce the SMAG catalogue, comprising of 40,039 metagenome-assembled genomes from 3304 soil metagenomes, and uncovering 21,077 species-level genome bins.

    • Bin Ma
    • , Caiyu Lu
    •  & Jianming Xu

  • Article
    | Open Access

    Most clinical isolates of the pathogenic yeast Candida orthopsilosis are hybrids of two parental lineages, only one of which has been identified. Here, del Olmo et al. show that C. orthopsilosis strains isolated from warm seawater are hybrids closely related to clinical isolates, and identify the missing parental lineage, thus providing a more complete view of the genomic evolution of this species.

    • Valentina del Olmo
    • , Verónica Mixão
    •  & Toni Gabaldón

  • Article
    | Open Access

    Phytopathogenic fungi threaten global food security but their global diversity and biogeography are underexplored. Using more than 20,000 globally distributed samples, this study builds a global atlas of phytopathogenic fungi, and predicts that that their diversity and invasion potential will increase globally by the end of this century, especially in forest and cropland ecosystems.

    • Pengfa Li
    • , Leho Tedersoo
    •  & Jiandong Jiang

  • Article
    | Open Access

    Here, the authors provide evidence that marine viruses spread via aerosolization and rain through the natural water cycle. Hosts from the first centimeters of the marine water column show signs of immunity against rain viruses. Those have DNA adaptations facilitating their stay in the air.

    • Janina Rahlff
    • , Sarah P. Esser
    •  & Alexander J. Probst

  • 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

    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

    Common methods for water disinfection involve oxidation or irradiation, and are often associated with a high carbon footprint and formation of toxic byproducts. Here, the authors describe a nano-structured material that is highly effective at killing bacteria in water through a hydrodynamic mechanism driven by mild water flow, in the absence of additional energy supply.

    • Lu Peng
    • , Haojie Zhu
    •  & Hong-Ying Hu

  • 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

    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

    The material-based evolution of organisms has attracted broad interdisciplinary interest, however, the fabrication of material-integrated organelles remains inadequately exploited. Here the authors engineer a bioartificial organism by integrating a semiartificial and specific virus-scavenging organelle to scavenge pathogenic waterborne viruses.

    • Huixin Li
    • , Yanpeng Xu
    •  & Ruikang Tang

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