Featured
-
-
Article
| Open Access
Plant diversity drives positive microbial associations in the rhizosphere enhancing carbon use efficiency in agricultural soils
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
Determining how oxygen legacy affects trajectories of soil denitrifier community dynamics and N2O emissions
A soil history of constant oxygen exposure enhances N2O reduction rates under anoxia compared to a history of long or short anoxic pulses, highlighting the importance of knowing the oxygen legacy of a soil for accurate N2O emission predictions.
- Louise B. Sennett
- , Constance A. Roco
- & Åsa Frostegård
-
Article
| Open Access
Global patterns in the growth potential of soil bacterial communities
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
The lactonase BxdA mediates metabolic specialisation of maize root bacteria to benzoxazinoids
Maize root bacteria were investigated for how they cope with the antimicrobial root exudates of their host plant. A gene cluster was identified, allowing the bacteria to metabolise these compounds and to specialize on the exudates of their host.
- Lisa Thoenen
- , Marco Kreuzer
- & Klaus Schlaeppi
-
Article
| Open Access
Metagenomic insights into microbial community structure and metabolism in alpine permafrost on the Tibetan Plateau
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
Sulfur oxidation and reduction are coupled to nitrogen fixation in the roots of the salt marsh foundation plant Spartina alterniflora
The mechanisms underlying plant-microbe interactions in coastal ecosystems are little explored. Here, the authors use multi-omics and biogeochemical measurements to investigate the saltmarsh cordgrass root microbiome and its role in coupling nitrogen fixation and sulfur cycling.
- J. L. Rolando
- , M. Kolton
- & J. E. Kostka
-
Article
| Open Access
Purines enrich root-associated Pseudomonas and improve wild soybean growth under salt stress
Root-associated microbiota confers benefits to plant in responding to environmental stress. Here, the authors show that wild soybean secretes purines under salt stress, reshapes the microbiota and recruits Pseudomonas.
- Yanfen Zheng
- , Xuwen Cao
- & Cheng-Sheng Zhang
-
Article
| Open Access
Structural and biochemical analysis of family 92 carbohydrate-binding modules uncovers multivalent binding to β-glucans
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
Survival and rapid resuscitation permit limited productivity in desert microbial communities
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
Trace gas oxidation sustains energy needs of a thermophilic archaeon at suboptimal temperatures
Diverse bacteria can use the low levels of hydrogen and carbon monoxide present in the air as energy sources for growth and survival. Here, Leung et al. show that ability is also found in thermophilic archaea of the order Sulfolobales.
- Pok Man Leung
- , Rhys Grinter
- & Chris Greening
-
Article
| Open Access
Unveiling unique microbial nitrogen cycling and nitrification driver in coastal Antarctica
This study reveals a unique microbial nitrogen cycling process in Antarctica’s coastal regions, with nitrification playing a significant role. The research notably identifies comammox Nitrospira clade B as a key driver of this process.
- Ping Han
- , Xiufeng Tang
- & Guitao Shi
-
Article
| Open Access
Hidden diversity and potential ecological function of phosphorus acquisition genes in widespread terrestrial bacteriophages
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
Widespread extracellular electron transfer pathways for charging microbial cytochrome OmcS nanowires via periplasmic cytochromes PpcABCDE
How do cells put electrons to rest? Using a minimal pathway to get rid of excess metabolic electrons, diverse environmentally important microbes overcome large spatial, kinetic, and thermodynamic barriers in order to survive in extreme anoxic conditions.
- Pilar C. Portela
- , Catharine C. Shipps
- & Nikhil S. Malvankar
-
Article
| Open Access
The global speciation continuum of the cyanobacterium Microcoleus
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
Synthetic microbe-to-plant communication channels
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
Spatial structure, chemotaxis and quorum sensing shape bacterial biomass accumulation in complex porous media
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 and native microbiome inoculation restore soil capacity to suppress a root disease
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
Metagenomic profiles of archaea and bacteria within thermal and geochemical gradients of the Guaymas Basin deep subsurface
The authors study microbial communities in hydrothermally heated, subseafloor sediment layers. They find that microbial abundance and diversity decrease with sediment depth and temperature, and provide evidence for the existence of a specialized deep, hot biosphere.
- Paraskevi Mara
- , David Geller-McGrath
- & Andreas Teske
-
Article
| Open Access
Hi-C metagenome sequencing reveals soil phage–host interactions
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
Diurnal switches in diazotrophic lifestyle increase nitrogen contribution to cereals
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 genome size and gene functional diversity negatively correlate with taxonomic diversity along a pH gradient
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
A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources
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
Oxygen respiration and polysaccharide degradation by a sulfate-reducing acidobacterium
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
Microbial growth under drought is confined to distinct taxa and modified by potential future climate conditions
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
A subset of viruses thrives following microbial resuscitation during rewetting of a seasonally dry California grassland soil
Rewetting of seasonally dry soils induces dramatic shifts in viral biomass and diversity. Combining stable isotope probing, metagenomics, and viromics Nicolas et al. provide evidence that viral lysis contributes to microbial turnover and the associated CO2 efflux.
- Alexa M. Nicolas
- , Ella T. Sieradzki
- & Steven J. Blazewicz
-
Article
| Open Access
Auxin-producing bacteria promote barley rhizosheath formation
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
Myxobacteria restrain Phytophthora invasion by scavenging thiamine in soybean rhizosphere via outer membrane vesicle-secreted thiaminase I
The plant pathogen Phytophthora sojae requires exogenous thiamine for growth. Here, Li et al. show that soil myxobacteria inhibit Phytophthora’s growth by scavenging thiamine through the secretion a thiaminase via outer membrane vesicles.
- Chengyao Xia
- , Yuqiang Zhao
- & Zhongli Cui
-
Article
| Open Access
Crystal structures of herbicide-detoxifying esterase reveal a lid loop affecting substrate binding and activity
The esterase SulE, which detoxifies and hydrolyses a variety of sulfonylurea herbicides, is increasingly of interest in efforts to eliminate environmental contamination of sulfonylurea herbicides and engineer herbicide-tolerant crops. Here, the SulE is structurally and mechanistically characterised.
- Bin Liu
- , Weiwu Wang
- & Jian He
-
Article
| Open Access
Structural remodelling of the carbon–phosphorus lyase machinery by a dual ABC ATPase
Here, authors analyse the structural organisation of the large carbon-phosphorus lyase enzyme from bacteria using electron microscopy and discover that it contains two ATP-binding cassette dimers of PhnK and PhnL and opens upon ATP hydrolysis.
- Søren K. Amstrup
- , Sui Ching Ong
- & Ditlev E. Brodersen
-
Article
| Open Access
Dark microbiome and extremely low organics in Atacama fossil delta unveil Mars life detection limits
Unique microorganisms of a fossil river delta in the Atacama Desert unveil the current limits of life detection on Mars.
- Armando Azua-Bustos
- , Alberto G. Fairén
- & Elizabeth Rampe
-
Article
| Open Access
Past and present giant viruses diversity explored through permafrost metagenomics
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
Structural characterization of a soil viral auxiliary metabolic gene product – a functional chitosanase
Metagenomics is revealing auxiliary metabolic genes (AMGs) in soil viral genomes. Here, authors solve the crystal structure for a soil viral AMG product, free and ligand bound, and show the protein can decompose chitin, a common carbon polymer.
- Ruonan Wu
- , Clyde A. Smith
- & Janet K. Jansson
-
Article
| Open Access
High impact of bacterial predation on cyanobacteria in soil biocrusts
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
Structure and function of the soil microbiome underlying N2O emissions from global wetlands
The wetland soil microbiome has a major impact on greenhouse gas emissions. Here the authors characterize how a group of archaea contribute to N2O emissions and find that climate and land use changes could promote these organisms.
- Mohammad Bahram
- , Mikk Espenberg
- & Ülo Mander
-
Article
| Open Access
Shared features and reciprocal complementation of the Chlamydomonas and Arabidopsis microbiota
Plants and algae associate with microbial communities that affect their growth and development. Here, the authors characterize the microbiota associated with a unicellular alga in soil, revealing extensive taxonomic and functional overlap with the root microbiota of land plants.
- Paloma Durán
- , José Flores-Uribe
- & Ruben Garrido-Oter
-
Article
| Open Access
Genome-resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics
Advances in omics provide a tool to understand mechanisms for plant–microbial interactions under stress. Here the authors apply genome-resolved metagenomics to investigate sorghum and its microbiome responses to drought, identifying an unexpected role of iron metabolism.
- Ling Xu
- , Zhaobin Dong
- & Devin Coleman-Derr
-
Article
| Open Access
Decrypting bacterial polyphenol metabolism in an anoxic wetland soil
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
Metabolic capabilities mute positive response to direct and indirect impacts of warming throughout the soil profile
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
C-STABILITY an innovative modeling framework to leverage the continuous representation of organic matter
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
A bacterial endophyte exploits chemotropism of a fungal pathogen for plant colonization
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 diversity drives carbon use efficiency in a model soil
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
Genome-scale metabolic reconstruction of the symbiosis between a leguminous plant and a nitrogen-fixing bacterium
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
Cable bacteria reduce methane emissions from rice-vegetated soils
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
Uncovering the biosynthetic potential of rare metagenomic DNA using co-occurrence network analysis of targeted sequences
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
Probing the active fraction of soil microbiomes using BONCAT-FACS
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
Phylogenetic conservation of bacterial responses to soil nitrogen addition across continents
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
A few Ascomycota taxa dominate soil fungal communities worldwide
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
The structure and function of the global citrus rhizosphere microbiome
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 driven change in soil pH affects microbial carbon cycling processes
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
Number and dissimilarity of global change factors influences soil properties and functions