Soil 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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    Although giant viruses are abundant in aquatic environments, less is known about giant viruses in soil. Here, the authors use permafrost metagenomics to reveal giant virus diversity and heterogeneity, as well as gene transfers between viruses from different families.

    • Sofia Rigou
    • , Sébastien Santini
    •  & Matthieu Legendre

  • 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

    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

    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

  • 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

    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

    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

    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

    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

    Research on plant root-associated microbial communities may help develop more efficient or sustainable crop production methods. Here the authors analyse the citrus rhizosphere microbiome, using both amplicon and deep shotgun metagenomic sequencing of samples collected across six continents.

    • Jin Xu
    • , Yunzeng Zhang
    •  & Nian Wang

  • Article
    | Open Access

    Land use intensification could modify microbial activity and thus ecosystem function. Here, Malik et al. sample microbes and carbon-related functions across a land use gradient, demonstrating that microbial biomass and carbon use efficiency are reduced in human-impacted near-neutral pH soils.

    • Ashish A. Malik
    • , Jeremy Puissant
    •  & Robert I. Griffiths

  • Article
    | Open Access

    Spatial organisation of bacteria could contribute to the persistence of anoxic hotspots in soils, however such processes are difficult to observe directly. Here, the authors develop an experimental platform mimicking resource gradients postulated in soil aggregates to assess bacterial spatial organisation.

    • Benedict Borer
    • , Robin Tecon
    •  & Dani Or

  • Article
    | Open Access

    Metagenomic sequencing provides a window into microbial community structure and metabolic potential. Here, Swenson et al. integrate metabolomics and shotgun sequencing to functionally link microbial community structure with environmental chemistry in biological soil crust (biocrust).

    • Tami L. Swenson
    • , Ulas Karaoz
    •  & Trent R. Northen

  • Article
    | Open Access

    The maintenance of bacterial and fungal activity is essential for ecosystem functioning, particularly in dry soils where the two phyla co-exist. Here, Worrich and colleagues show experimentally that mycelia traffic water and nutrients and thereby stimulate bacterial activity in stressful conditions.

    • Anja Worrich
    • , Hryhoriy Stryhanyuk
    •  & Lukas Y. Wick

  • Article
    | Open Access

    The endophytic fungusMetarhizium robertsiiis also an insect pathogen and can facilitate transfer of insect-derived nitrogen to host plants. Here, the authors show that carbon is transferred from plant to fungus suggesting a tripartite interaction where nitrogen is exchanged for photosynthate.

    • Scott W. Behie
    • , Camila C. Moreira
    •  & Michael J. Bidochka

  • Article
    | Open Access

    Climate warming has a wide range of effects on biodiversity. Here, Zhou et al. show that although variation in environmental temperature is a primary driver of soil microbial biodiversity, microbes show much lower rates of turnover across temperature gradients than other major taxa.

    • Jizhong Zhou
    • , Ye Deng
    •  & James H. Brown

  • Article
    | Open Access

    Atmospheric methane may be consumed by microorganisms in soil, but the mechanisms behind high-affinity methane oxidization remain poorly understood. Here, Jia et al. show that known methanotrophic bacteria are responsible for atmospheric methane uptake in periodically drained wetland ecosystems.

    • Yuanfeng Cai
    • , Yan Zheng
    •  & Zhongjun Jia

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