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| Open AccessLand conversion to agriculture induces taxonomic homogenization of soil microbial communities globally
Agricultural land-use change affects belowground biodiversity. Here, the authors compare soil microbial communities from natural ecosystems and agricultural systems, finding that agricultural conversion leads to taxonomic and functional homogenisation.
- Ziheng Peng
- , Xun Qian
- & Shuo Jiao
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Article
| Open AccessComposition and metabolism of microbial communities in soil pores
The work proposes the concept of distinct micro-habitats within an intact soil matrix and describes composition and metabolic pathways of their bacterial inhabitants, as a first step towards a generalizable C processing-focused classification of soil micro-environmental conditions.
- Zheng Li
- , Alexandra N. Kravchenko
- & Evgenia Blagodatskaya
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Article
| Open AccessMetabolic coupling between soil aerobic methanotrophs and denitrifiers in rice paddy fields
Microbial denitrification in rice paddy fields reduces N use efficiency. Here, the authors use field samples from major rice producing areas in China and identify microbial taxa involved in the metabolic couplings between aerobic CH4 oxidation and denitrification in rice paddy fields.
- Kang-Hua Chen
- , Jiao Feng
- & Yu-Rong Liu
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Article
| Open AccessFreshwater genome-reduced bacteria exhibit pervasive episodes of adaptive stasis
Here, by applying evolutionary genomics approaches to metagenomics data of lake microbiomes, the authors reveal that freshwater species with small genomes face extended periods with their niche adaptation capabilities frozen.
- Lucas Serra Moncadas
- , Cyrill Hofer
- & Adrian-Stefan Andrei
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| Open AccessTowards establishing a fungal economics spectrum in soil saprobic fungi
Challenges in obtaining empirical trait data hinder the development of trait-based frameworks for soil microbes. Here, the authors analyse traits of saprobic fungal isolates from a grassland site to propose a fungal economics spectrum, suggesting a general trait framework for soil fungi.
- Tessa Camenzind
- , Carlos A. Aguilar-Trigueros
- & Matthias C. Rillig
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Article
| Open AccessSurvival 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
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Article
| Open AccessDiversity and potential host-interactions of viruses inhabiting deep-sea seamount sediments
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
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| Open AccessAll-inclusive nitrifiers in Antarctic soils
Multidisciplinary culture-dependent and -independent techniques elucidate the unique microbial nitrogen cycle in nutrient-poor coastal Antarctica soils and reveal the contribution of novel key microbes to their nitrogen budget.
- Maximiliano Ortiz
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Article
| Open AccessPlasmids in the human gut reveal neutral dispersal and recombination that is overpowered by inflammatory diseases
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
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Article
| Open AccessLegume rhizodeposition promotes nitrogen fixation by soil microbiota under crop diversification
Sustainability in agriculture can be improved harnessing biological N2 fixation in legumes. Here, the authors combine different crops with peanut plants finding that maize and oilseed rape are the most successful combinations which have potential to enhance rhizosphere microbiota N2 fixation.
- Mengjie Qiao
- , Ruibo Sun
- & Yan Chen
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Article
| Open AccessA genome-centric view of the role of the Acropora kenti microbiome in coral health and resilience
This study provides insights into the functional roles of microbial symbionts within the reef-building coral Acropora kenti. The findings reveal molecular mechanisms underpinning coral health and adaptation to local environmental stressors, which may support host resilience in the face of anthropogenic climate change and pollution.
- Lauren F. Messer
- , David G. Bourne
- & Gene W. Tyson
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Article
| Open AccessHidden 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
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Article
| Open AccessAnaerobic fungi in the tortoise alimentary tract illuminate early stages of host-fungal symbiosis and Neocallimastigomycota evolution
Here, Pratt et al identify a community of deep-branching anaerobic fungi in tortoise feces. Multiple characteristics underpinning their success in tortoise, as opposed to scarcity in mammalian alimentary tracts, are presented.
- Carrie J. Pratt
- , Casey H. Meili
- & Noha H. Youssef
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Article
| Open AccessIntermediate soil acidification induces highest nitrous oxide emissions
Intermediate soil acidification alters the denitrifier community composition and induces high nitrous oxide (N2O) emissions, which contributes to the observed acceleration of N2O emissions from global soils
- Yunpeng Qiu
- , Yi Zhang
- & Shuijin Hu
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Article
| Open AccessNiche availability and competitive loss by facilitation control proliferation of bacterial strains intended for soil microbiome interventions
Bioremediation via microbial inoculation often performs poorly in real-world conditions. Here, the authors show that bacterial inoculants may fail to establish in complex soil microbiomes because they open new niches that facilitate growth of resident microbes.
- Senka Čaušević
- , Manupriyam Dubey
- & Jan Roelof van der Meer
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Article
| Open AccessHigh hydrostatic pressure stimulates microbial nitrate reduction in hadal trench sediments under oxic conditions
Hadal trenches are the deepest oceanic ecosystems, with water depth over 6000 m, and are among the least explored habitats on Earth. This research demonstrates that high hydrostatic pressure enhances denitrification activity under oxic conditions, potentially making hadal trenches fixed nitrogen loss hotpots.
- Na Yang
- , Yongxin Lv
- & Yu Zhang
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Article
| Open AccessData-driven prediction of colonization outcomes for complex microbial communities
Predicting the colonization of exogenous species in complex communities is a challenge in ecology. Here, the authors propose a data-driven approach to predict colonization outcomes and perform validation experiments in human gut microbial communities.
- Lu Wu
- , Xu-Wen Wang
- & Lei Dai
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Article
| Open AccessFungal community composition predicts forest carbon storage at a continental scale
Soil microbial diversity and composition is thought to play a major role in elemental cycling. Here, the authors analyse a large dataset of soil microbiome and carbon data from European forests and find that soil fungal community composition is a strong predictor of carbon storage.
- Mark A. Anthony
- , Leho Tedersoo
- & Colin Averill
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Article
| Open AccessBet hedging in a unicellular microalga
Bet hedging is an evolutionary strategy facilitating survival in randomly fluctuating environments. Here, the authors report bet hedging in the unicellular microalga Haematococcus pluvialis, undergoing reversible diversification into mobile and non-mobile cells.
- Si Tang
- , Yaqing Liu
- & Zhonghua Cai
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Article
| Open AccessViral potential to modulate microbial methane metabolism varies by habitat
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
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Article
| Open AccessDynamic root microbiome sustains soybean productivity under unbalanced fertilization
Root-associated microbiomes contribute to plant growth and health. Here, the authors unveil the quantitative development of the root microbiome under unbalanced fertilization and highlight a key microbial cluster for soybean productivity.
- Mingxing Wang
- , An-Hui Ge
- & Ertao Wang
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Article
| Open AccessEnhancing phosphate-solubilising microbial communities through artificial selection
Phosphate-solubilising microorganisms can contribute to reduce the use of P fertiliser. Here, the authors use two artificial selection methods, environmental perturbation and propagation, to build phosphate-solubilising communities that retain P-solubilising capacity in hydroponic systems.
- Lena Faller
- , Marcio F. A. Leite
- & Eiko E. Kuramae
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Article
| Open AccessDuplicated antibiotic resistance genes reveal ongoing selection and horizontal gene transfer in bacteria
Mobile genetic elements can promote the duplication of antibiotic resistance genes which may in turn accelerate the evolution of resistance to new drugs. Here, the authors show that duplicated antibiotic resistance genes are enriched in bacterial isolates from environments associated with rampant antibiotic use.
- Rohan Maddamsetti
- , Yi Yao
- & Lingchong You
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Article
| Open AccessA genome and gene catalog of the aquatic microbiomes of the Tibetan Plateau
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
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Article
| Open AccessEco-evolutionary dynamics of gut phageome in wild gibbons (Hoolock tianxing) with seasonal diet variations
The significance of gut phageome for wild animals with seasonal diets remains unexplored. Here, the authors use complementary metagenomics to analyze the phage-host dynamics and its implications for diet variations in wild skywalker hoolock gibbons.
- Shao-Ming Gao
- , Han-Lan Fei
- & Peng-Fei Fan
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Article
| Open AccessExperimental warming accelerates positive soil priming in a temperate grassland ecosystem
Soil priming could release large amounts of soil C into the atmosphere. Here the authors show that experimental warming boosts soil priming and CO2 emissions in grasslands potentially due to microbial changes. Model accuracy could be improved by incorporating these mechanisms.
- Xuanyu Tao
- , Zhifeng Yang
- & Jizhong Zhou
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Article
| Open AccessMicrobiome convergence enables siderophore-secreting-rhizobacteria to improve iron nutrition and yield of peanut intercropped with maize
Intercropping has the potential to improve plant nutrition and crop yield. Here, the authors intercrop peanut and maize and show that Pseudomonas secreted siderophore pyoverdine play an important role in plant iron nutrition.
- Nanqi Wang
- , Tianqi Wang
- & Yuanmei Zuo
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Article
| Open AccessHorizontal gene transfer is predicted to overcome the diversity limit of competing microbial species
Combining theoretical derivation and numerical simulations, this study predicts an ecological mechanism for maintaining microbial coexistence via dynamic neutrality enabled by horizontal gene transfer. This mechanism allows the emergence of microbial diversity beyond the limit predicted by previous theories.
- Shiben Zhu
- , Juken Hong
- & Teng Wang
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Article
| Open AccessHost- plasmid network structure in wastewater is linked to antimicrobial resistance genes
Authors apply theory and microbial ecology modelling to a wastewater sample, and show that antimicrobial resistance carrying plasmids interact with a higher number and more diverse range of bacteria than plasmids that do not carry resistance genes.
- Alice Risely
- , Arthur Newbury
- & Dirk Sanders
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Article
| Open AccessTowards estimating the number of strains that make up a natural bacterial population
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
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Article
| Open AccessDefining the biogeographical map and potential bacterial translocation of microbiome in human ‘surface organs’
Given that the human body is composed of many microbial niches, and there have been few reports on the biogeography of the microbiome, the authors analyse the intra-individual inter-organ and intra-organ microbiome of seven surface organs of deceased individuals.
- Jun-Jun She
- , Wei-Xin Liu
- & Jun Yu
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Article
| Open AccessVESPA: an optimized protocol for accurate metabarcoding-based characterization of vertebrate eukaryotic endosymbiont and parasite assemblages
DNA sequencing methods for characterizing microbial communities are well developed for bacteria, archaea and fungi, but less so for eukaryotic parasites and commensals. Here, the authors present an optimized and validated metabarcoding protocol for host-associated eukaryotic communities.
- Leah A. Owens
- , Sagan Friant
- & Tony L. Goldberg
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Article
| Open AccessMicrobially mediated mechanisms underlie soil carbon accrual by conservation agriculture under decade-long warming
Agricultural soil C dynamics under climate change are difficult to predict. Here, the authors report that experimental warming increases soil organic C stocks in conservation agriculture but not in conventional agriculture, which appears driven by soil microbial responses to no tillage and C inputs from the crops.
- Jing Tian
- , Jennifer A. J. Dungait
- & Jizhong Zhou
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Article
| Open AccessFunctional host-specific adaptation of the intestinal microbiome in hominids
Here, Rühlemann et al. analyze the gut microbiome of wild-living African great apes (Gorillas, Bonobos, Chimpanzees) in comparison to that of humans, identifying host specific patterns and shared evolutionary conserved traits disrupted in humans.
- M. C. Rühlemann
- , C. Bang
- & A. Franke
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Article
| Open AccessBiotic homogenization, lower soil fungal diversity and fewer rare taxa in arable soils across Europe
How arable farming affects soil fungal biogeography is poorly understood. Here, the authors find that prevalent fungal groups become more abundant, whereas rare groups become fewer or absent in arable lands across Europe, suggesting a biotic homogenization due to arable farming.
- Samiran Banerjee
- , Cheng Zhao
- & Marcel G. A. van der Heijden
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| Open AccessSpatial 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
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Article
| Open AccessEffects of plant tissue permeability on invasion and population bottlenecks of a phytopathogen
Bottleneck effects of plant barriers on pathogenic invasions remain unclear. Using a random barcoding approach, this study investigates how plant root permeability limits the invasion and population bottlenecks of a phytopathogenic Ralstonia.
- Gaofei Jiang
- , Yuling Zhang
- & Zhong Wei
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Article
| Open AccessLand management shapes drought responses of dominant soil microbial taxa across grasslands
Soil microbial communities are affected by climate extremes. Here, the authors impose experimental drought across 30 UK grasslands showing that bacteria and fungi exhibit drought resistance but that intensive management has a negative impact on fungi drought resilience.
- J. M. Lavallee
- , M. Chomel
- & R. D. Bardgett
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Article
| Open AccessOptogenetic spatial patterning of cooperation in yeast populations
Microbial communities are the siege of complex metabolic interactions including cooperation and competition. Here, the authors report the utilization of optogenetics and spatial light-patterning to activate the expression of the invertase SUC2 at selected locations and selectively switch cooperation and competition roles of the yeast cells.
- Matthias Le Bec
- , Sylvain Pouzet
- & Pascal Hersen
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Article
| Open AccessPervasive associations between dark septate endophytic fungi with tree root and soil microbiomes across Europe
While mycorrhizal-plant interactions are widely studied, other root symbionts may also be ecologically important. Here, the authors show that dark septate endophytes are a strong predictor of rhizosphere and associated soil microbiomes in broad-leaved tree across Europe.
- Tarquin Netherway
- , Jan Bengtsson
- & Mohammad Bahram
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Article
| Open AccessTargeted treatment of injured nestmates with antimicrobial compounds in an ant society
Infected wounds pose a major mortality risk in animals and are common in predatory ants. Here, the authors show that M. analis ants apply antimicrobial compounds produced in the metapleural glands to treat infected wounds and reduce nestmate mortality.
- Erik. T. Frank
- , Lucie Kesner
- & Laurent Keller
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Article
| Open AccessMetallic micronutrients are associated with the structure and function of the soil microbiome
Soil micronutrients may be important for belowground biota and associated functions. Here, the authors identify the relationships between metallic micronutrients and soil microbial communities and functions across 180 sites, and validate them in a soil incubation experiment.
- Zhongmin Dai
- , Xu Guo
- & Jianming Xu
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Article
| Open AccessViruses under the Antarctic Ice Shelf are active and potentially involved in global nutrient cycles
The diversity and impact of viruses in remote marine environments are less well understood. In this study, the authors analyse an -omics dataset to gain insights into the genomics and potential role of endemic viruses infecting ecologically important microbes inhabiting the ocean cavity beneath the Ross Ice Shelf.
- Javier Lopez-Simon
- , Marina Vila-Nistal
- & Manuel Martinez-Garcia
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Article
| Open AccessIdentification of inulin-responsive bacteria in the gut microbiota via multi-modal activity-based sorting
Here, Riva et al. employ a multi-modal approach to identify gut microbes stimulated by the popular dietary supplement inulin and reveal that inulin binding and metabolic stimulation are widespread in the microbiome, making the framework a suitable way to study key microbes that perform specific functions in the microbiome.
- Alessandra Riva
- , Hamid Rasoulimehrabani
- & David Berry
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Article
| Open AccessPhyloecology of nitrate ammonifiers and their importance relative to denitrifiers in global terrestrial biomes
Nitrate ammonifiers are poorly known despite their importance for soil nitrogen retention. This study shows that they are phylogenetically diverse and globally distributed across terrestrial biomes and that the outcome of the competition with denitrifiers is controlled by soil nitrate.
- Aurélien Saghaï
- , Grace Pold
- & Sara Hallin
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Article
| Open AccessCrop 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
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Article
| Open AccessStrong chemotaxis by marine bacteria towards polysaccharides is enhanced by the abundant organosulfur compound DMSP
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
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Article
| Open AccessIdentifying microbiota community patterns important for plant protection using synthetic communities and machine learning
The authors investigate microbiota properties for plant protection using synthetic communities and machine learning approaches. They identify strains that reduce pathogen colonization despite variation in microbiota composition.
- Barbara Emmenegger
- , Julien Massoni
- & Julia A. Vorholt
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Article
| Open AccessA computational framework for resolving the microbiome diversity conundrum
The microbiome is thought to be important for its host’s wellbeing, but it varies much among individuals. We offer a solution to this conundrum, showing that factors like the form of microbes’ contribution to hosts’ fitness and host population size may be preventing natural selection from operating effectively.
- Itay Daybog
- & Oren Kolodny