Article
|
Open Access
Featured
-
-
Article
| Open AccessGenetic diversity in terrestrial subsurface ecosystems impacted by geological degassing
Geological degassing can impact subsurface metabolism. Here, the authors describe microbial communities from a cold-water geyser are described and compared with other deep subsurface sites, finding a key role for an uncultivated archaeon.
- Till L. V. Bornemann
- , Panagiotis S. Adam
- & Alexander J. Probst
-
Article
| Open AccessThe role of methanotrophy in the microbial carbon metabolism of temperate lakes
Methane metabolism is considered of secondary importance in most lake food webs. Here the authors quantify the contribution of methanotrophs to C cycling in six lakes, finding evidence of a large role of methanotrophs due to their higher specific activity and larger cell size.
- Paula C. J. Reis
- , Shoji D. Thottathil
- & Yves T. Prairie
-
Article
| Open AccessNutrient supply controls the linkage between species abundance and ecological interactions in marine bacterial communities
Environmental and biotic factors control ecological communities. Here, the authors study community ribosomal rRNA gene copy number in coastal sediment and ocean bacterial communities, and in microcosm nutrient addition experiments, to propose a conceptual framework of how nutrient supply and ecological interactions shape the community.
- Tianjiao Dai
- , Donghui Wen
- & Yunfeng Yang
-
Article
| Open AccessGenetic determinants of endophytism in the Arabidopsis root mycobiome
Plant roots host diverse fungal communities that affect plant health. Here, Mesny et al. use comparative genomics and transcriptomics of fungal isolates from the Arabidopsis thaliana root mycobiota, together with root colonization assays, to identify genetic determinants of endophytism.
- Fantin Mesny
- , Shingo Miyauchi
- & Stéphane Hacquard
-
Article
| Open AccessSubstantial oxygen consumption by aerobic nitrite oxidation in oceanic oxygen minimum zones
Oxygen is fundamental for marine life, yet it is absent from large areas of the ocean. Here the authors demonstrate that microbial nitrite oxidation effectively consumes oxygen where oxygen concentrations are low, playing a pivotal role in these regions.
- J. M. Beman
- , S. M. Vargas
- & S. D. Wankel
-
Article
| Open AccessCross-feeding between intestinal pathobionts promotes their overgrowth during undernutrition
Malnourished children experience a high burden of intestinal pathogens that exacerbate growth stunting, and preventing this pathogen overgrowth has proved challenging. Here the authors show that diet-specific bacterial crossfeeding contributes to the overgrowth of intestinal pathogens during child malnutrition.
- K. E. Huus
- , T. T. Hoang
- & B. B. Finlay
-
Article
| Open AccessComplementary resource preferences spontaneously emerge in diauxic microbial communities
Many microbes grow diauxically, utilizing resources one at a time rather than simultaneously. This study developed a minimal model of diauxic microbial communities assembling in a serially diluted culture, providing testable predictions for the assembly of natural as well as synthetic communities of diauxically shifting microorganisms.
- Zihan Wang
- , Akshit Goyal
- & Sergei Maslov
-
Article
| Open AccessTemporal variability in quantitative human gut microbiome profiles and implications for clinical research
Here, the authors report quantitative daily gut microbiome variation of individual gut bacterial abundances in healthy individuals, linked to changes in transit time and diet, highlighting the potential need for multiple samplings for microbiome target identification and the development and application of reliable microbiome diagnostics.
- Doris Vandeputte
- , Lindsey De Commer
- & Jeroen Raes
-
Article
| Open AccessType VI secretion system mutations reduced competitive fitness of classical Vibrio cholerae biotype
The bacterium Vibrio cholerae has caused seven recorded cholera pandemics. The factors responsible for the decline of 6th pandemic classical biotype strains are not well understood. Here, Kostiuk et al. propose that classical strains underwent sequential mutations in type-six secretion system genes that disadvantaged them when confronted with 7th pandemic El Tor biotype strains.
- Benjamin Kostiuk
- , Francis J. Santoriello
- & Stefan Pukatzki
-
Article
| Open AccessThe origin and impeded dissemination of the DNA phosphorothioation system in prokaryotes
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 AccessDiurnal oscillations in gut bacterial load and composition eclipse seasonal and lifetime dynamics in wild meerkats
Circadian rhythms in gut microbiota composition are crucial for metabolic function, yet the extent to which they govern microbial dynamics in comparison to seasonal and lifetime processes remains unknown. This study of gut bacterial dynamics in wild meerkats over a 20-year period finds that diurnal oscillations in bacterial load and composition eclipse seasonal and lifetime dynamics.
- Alice Risely
- , Kerstin Wilhelm
- & Simone Sommer
-
Article
| Open AccessSpecific gut microbiome signatures and the associated pro-inflamatory functions are linked to pediatric allergy and acquisition of immune tolerance
Here, the authors profile the taxonomic composition and genetic potential of the gut microbiome of children with food or respiratory allergies and find that the gut metagenome of these patients is characterized by higher proinflammatory potential and reduced capacity of degrading complex polysaccharides, with Ruminococcus gnavus playing a central role.
- Francesca De Filippis
- , Lorella Paparo
- & Roberto Berni Canani
-
Article
| Open AccessDiverse sediment microbiota shape methane emission temperature sensitivity in Arctic lakes
Arctic lakes are strong and increasing sources of atmospheric methane, but extreme conditions and limited observations hinder robust understanding. Here the authors show that microbes in the middle of Arctic lakes have elevated methane producing potential, and are poised to release even more in the future.
- Joanne B. Emerson
- , Ruth K. Varner
- & Virginia I. Rich
-
Article
| Open AccessPersistence of plant-mediated microbial soil legacy effects in soil and inside roots
Legacies of past plant communities are likely to influence plant-soil interactions. Here, the authors report a reciprocal transplant experiment showing that soil microbial legacies shaped by previous plants persist for soil fungi and root endophytes but can be reversed by a next generation of plants for soil bacteria.
- S. Emilia Hannula
- , Robin Heinen
- & T. Martijn Bezemer
-
Article
| Open AccessCommunity and single cell analyses reveal complex predatory interactions between bacteria in high diversity systems
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 AccessThe biogeographic differentiation of algal microbiomes in the upper ocean from pole to pole
Latitudinal ecosystem boundaries in the global upper ocean may be driven by many factors. Here the authors investigate pole-to-pole eukaryotic phytoplankton metatranscriptomes, gene co-expression networks, and beta diversity, finding that geographic patterns are best explained by temperature gradients.
- Kara Martin
- , Katrin Schmidt
- & Thomas Mock
-
Article
| Open AccessProkaryotic viruses impact functional microorganisms in nutrient removal and carbon cycle in wastewater treatment plants
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 AccessAridity-driven shift in biodiversity–soil multifunctionality relationships
Biodiversity-ecosystem functioning relationships may vary with climate. Here, the authors study relationships of plant and soil microbial diversity with soil nutrient multifunctionality in 130 dryland sites in China, finding a shift towards greater importance of soil microbial diversity in arid conditions.
- Weigang Hu
- , Jinzhi Ran
- & Jianming Deng
-
Article
| Open AccessEcological memory of recurrent drought modifies soil processes via changes in soil microbial community
Legacies of past ecological disturbances are expected but challenging to demonstrate. Here the authors report a 10-year field experiment in a mountain grassland that shows ecological memory of soil microbial community and functioning in response to recurrent drought.
- Alberto Canarini
- , Hannes Schmidt
- & Andreas Richter
-
Article
| Open AccessComparative genomic analysis reveals metabolic flexibility of Woesearchaeota
The biology of the archaeal phylum Woesearchaeota is poorly understood due to the lack of cultured isolates. Here, the authors analyze datasets of Woesearchaeota 16 S rRNA gene sequences and metagenome-assembled genomes to infer global distribution patterns, ecological preferences and metabolic capabilities.
- Wen-Cong Huang
- , Yang Liu
- & Meng Li
-
Article
| Open AccessLytic archaeal viruses infect abundant primary producers in Earth’s crust
Little is known about viral-host interactions in the continental subsurface. Here, the authors use a combination of metagenomics, fluorescence in situ hybridization, and electron microscopy to show infections of abundant C-fixing subsurface archaea by lytic viruses.
- Janina Rahlff
- , Victoria Turzynski
- & Alexander J. Probst
-
Article
| Open AccessRapid ecosystem-scale consequences of acute deoxygenation on a Caribbean coral reef
How acute deoxygenation events affect tropical marine ecosystems remains poorly understood. This study integrates analyses of coral reef benthic communities with microbial community sequencing to show how a deoxygenation event rapidly altered a shallow tropical coral reef ecosystem in the Caribbean.
- Maggie D. Johnson
- , Jarrod J. Scott
- & Andrew H. Altieri
-
Article
| Open AccessEnergy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater
Ecological constraints on microbial niches in oligotrophic deep groundwaters remain elusive. This study provides support for the existence of a common core microbiome in two deep groundwater biomes of the Fennoscandian Shield using a genome-resolved, integrated omics analysis.
- Maliheh Mehrshad
- , Margarita Lopez-Fernandez
- & Mark Dopson
-
Article
| Open AccessPangenomics reveals alternative environmental lifestyles among chlamydiae
Chlamydiae are strictly intracellular bacteria that exist in a wide variety of environments but the diversity of the phylum is not well described. Here, the authors analyze 82 metagenome-assembled genomes, identify seven new families, and describe genomic signals of metabolic diversity.
- Stephan Köstlbacher
- , Astrid Collingro
- & Matthias Horn
-
Article
| Open AccessThe Great Oxygenation Event as a consequence of ecological dynamics modulated by planetary change
The Great Oxygenation Event (GOE) 2.4 billion years ago is believed to have been critical for the evolution of complex life. Here, Olejarz et al. propose a model suggesting that competition between major bacterial groups could have triggered the GOE in a feedback loop with geophysical processes.
- Jason Olejarz
- , Yoh Iwasa
- & Martin A. Nowak
-
Article
| Open AccessKin discrimination promotes horizontal gene transfer between unrelated strains in Bacillus subtilis
Genetically distinct swarms of the bacterium Bacillus subtilis attack each other, forming a boundary upon encounter. Here, the authors show that these swarm antagonisms promote transformation-mediated horizontal gene transfer between strains of low relatedness.
- Polonca Stefanic
- , Katarina Belcijan
- & Ines Mandic-Mulec
-
Article
| Open AccessNutrients cause consolidation of soil carbon flux to small proportion of bacterial community
The fate of soil carbon depends on microbial processes, but whether different microbial taxa have individualistic effects on carbon fluxes is unknown. Here the authors use 16 S amplicon sequencing and stable isotopes to show how taxonomic differences influence bacterial respiration and carbon cycling across four ecosystems.
- Bram W. Stone
- , Junhui Li
- & Bruce A. Hungate
-
Article
| Open AccessDesign of synthetic human gut microbiome assembly and butyrate production
Microbiomes designed with predictable functions could enable broad applications in health, agriculture and bioprocessing. Here the authors use a model-guided approach to design diverse synthetic human gut communities for production of the health-relevant metabolite butyrate.
- Ryan L. Clark
- , Bryce M. Connors
- & Ophelia S. Venturelli
-
Article
| Open AccessCommunity composition of microbial microcosms follows simple assembly rules at evolutionary timescales
Evolution affects microbial community composition, but it is still unknown how commonly compositions change, and how predictable such changes are. Using experimental evolution, Meroz et al. show that compositional changes typically occur within ~400 generations, and are predictable by a bottom-up approach.
- Nittay Meroz
- , Nesli Tovi
- & Jonathan Friedman
-
Article
| Open AccessReductive evolution and unique predatory mode in the CPR bacterium Vampirococcus lugosii
The Candidate Phyla Radiation (CPR) constitutes a large group of bacterial lineages with small cell sizes and limited biosynthetic capabilities. Here, Moreira et al. study the biology and genome of Vampirococcus lugosii, an epibiotic parasite of other bacteria, supporting parasitism as a common lifestyle of CPR bacteria.
- David Moreira
- , Yvan Zivanovic
- & Purificación López-García
-
Article
| Open AccessBrockarchaeota, a novel archaeal phylum with unique and versatile carbon cycling pathways
Geothermal environments are hotspots for carbon cycling. Here, De Anda et al. reconstruct archaeal genomes from terrestrial and deep-sea geothermal sediments, and propose the classification of these microbes as a new phylum, ‘Brockarchaeota’, with unique metabolic capabilities including non-methanogenic anaerobic methylotrophy.
- Valerie De Anda
- , Lin-Xing Chen
- & Brett J. Baker
-
Article
| Open AccessNon-additive microbial community responses to environmental complexity
How microbial community properties change under increasingly complex combinations of resources remains unclear. Here, the authors studied hundreds of synthetic consortia to identify the factors that govern how growth and taxonomic diversity scale with environmental complexity.
- Alan R. Pacheco
- , Melisa L. Osborne
- & Daniel Segrè
-
Article
| Open AccessDiet and gut microbiome enterotype are associated at the population level in African buffalo
There are stable relationships between diet and microbiome in humans and lab animals. A study on African buffalo finds that diet influences microbiome variation and enterotype formation. Three pathogens may associate with microbiome depending on host diet, suggesting nutrition impacts relationships between gut microbiome and host health.
- Claire E. Couch
- , Keaton Stagaman
- & Anna E. Jolles
-
Article
| Open AccessMetabolic pathways inferred from a bacterial marker gene illuminate ecological changes across South Pacific frontal boundaries
Extracting functional information from 16S rRNA data surveys would provide a valuable tool for large-scale functional ecology. Here, the authors use PICRUSt2 to infer metabolic functions from bacterial marker gene data across the South Pacific Ocean, and compare them with rate data, biomass estimators and predictions based on shotgun metagenomes.
- Eric J. Raes
- , Kristen Karsh
- & Anya M. Waite
-
Article
| Open AccessA prevalent and culturable microbiota links ecological balance to clinical stability of the human lung after transplantation
Here, the authors combine 16 S rRNA sequencing, culture and bioinformatics to profile the microbiome in 234 serial bronchoalveolar lavage samples from 64 lung transplant recipients collected over 49-months and identify distinct compositional states, termed pneumotypes, linked to current health status, and establish a collection of primary lung bacterial isolates, LuMiCol.
- Sudip Das
- , Eric Bernasconi
- & Laurent P. Nicod
-
Article
| Open AccessMetabolic 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 AccessPili allow dominant marine cyanobacteria to avoid sinking and evade predation
It was thought that marine cyanobacteria drifted randomly in the water column. Here the authors show that one in four picocyanobacteria encode a type IV pilus which allows these organisms to increase drag and retain optimal positions in the water column, as well as evade predation by grazers.
- Maria del Mar Aguilo-Ferretjans
- , Rafael Bosch
- & Joseph A. Christie-Oleza
-
Comment
| Open AccessSeeding the idea of encapsulating a representative synthetic metagenome in a single yeast cell
Synthetic metagenomics could potentially unravel the complexities of microbial ecosystems by revealing the simplicity of microbial communities captured in a single cell. Conceptionally, a yeast cell carrying a representative synthetic metagenome could uncover the complexity of multi-species interactions, illustrated here with wine ferments.
- Ignacio Belda
- , Thomas C. Williams
- & Isak S. Pretorius
-
Article
| Open AccessComplex yeast–bacteria interactions affect the yield of industrial ethanol fermentation
Industrial sugarcane ethanol fermentations are accomplished by a microbial community dominated by S. cerevisiae and co-occurring bacteria. Here, the authors investigate how microbial community composition contributes to community function and reveal the role of acetaldehyde in improving yeast growth rate and ethanol production.
- Felipe Senne de Oliveira Lino
- , Djordje Bajic
- & Morten Otto Alexander Sommer
-
Article
| Open AccessEcology-guided prediction of cross-feeding interactions in the human gut microbiome
Understanding a complex microbial ecosystem such as the human gut microbiome requires information about both microbial species and the metabolites they produce and secrete. Here, the authors propose an ecology-based computational method to predict hundreds of new experimentally untested cross-feeding interactions in the human gut microbiome.
- Akshit Goyal
- , Tong Wang
- & Sergei Maslov
-
Article
| Open AccessExpanded catalog of microbial genes and metagenome-assembled genomes from the pig gut microbiome
Here, the authors present a pig integrated gene catalog and metagenome-assembled genomes, which they construct from swine gut microbiomes spanning various ages, sexes, breeds, geographical locations, domestication, and gut locations by metagenomic sequencing, providing expanded resources for pig microbiome studies.
- Congying Chen
- , Yunyan Zhou
- & Lusheng Huang
-
Article
| Open AccessDroplet printing reveals the importance of micron-scale structure for bacterial ecology
The spatial arrangement of bacterial strains and species within microbial communities is considered crucial for their ecology. Here, Krishna Kumar et al. use a droplet-based printing method to arrange different bacterial genotypes across a sub-millimetre array, and show that micron-scale changes in spatial distributions can drive major shifts in ecology.
- Ravinash Krishna Kumar
- , Thomas A. Meiller-Legrand
- & Kevin R. Foster
-
Article
| Open AccessC-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 AccessAutomated design of synthetic microbial communities
In naturally occurring microbial systems, there is a positive relationship between species diversity and productivity of the community. Here the authors perform model selection to find potential amensal interactions that yield robust stable synthetic microbial consortia.
- Behzad D. Karkaria
- , Alex J. H. Fedorec
- & Chris P. Barnes
-
Article
| Open AccessLimitation by a shared mutualist promotes coexistence of multiple competing partners
Mutualists benefit their partners by providing resources that would be difficult to obtain independently. Here, the authors show in a bacterial community and with mathematical modeling how a mutualist can promote coexistence between competitors by providing them with different limiting resources.
- Sarah P. Hammarlund
- , Tomáš Gedeon
- & William R. Harcombe
-
Article
| Open AccessContact-independent killing mediated by a T6SS effector with intrinsic cell-entry properties
Bacteria can use type VI secretion systems (T6SSs) to inject toxic effector proteins into adjacent cells, in a contact-dependent manner. Here, the authors provide evidence of contact-independent killing by a T6SS effector that is secreted into the extracellular milieu and then taken up by other bacterial cells.
- Li Song
- , Junfeng Pan
- & Xihui Shen
-
Article
| Open AccessLongitudinal evaluation of fecal microbiota transplantation for ameliorating calf diarrhea and improving growth performance
Here, the authors report the results of a longitudinal multi-omics trial of the use of fecal microbiota transplantation (FMT) to ameliorate diarrhea and restore gut microbial composition in 57 growing calves, and find that oral FMT induces alterations in the gut microbiota correlate with the remission of diarrhea and improves the growth performance of the cattle.
- Hyun Sik Kim
- , Tae Woong Whon
- & Jin-Woo Bae
-
Matters Arising
| Open AccessVariables in the effect of land use on soil extrapore enzymatic activity and carbon stabilization
- Melanie M. Glenn
-
Article
| Open AccessOrganism body size structures the soil microbial and nematode community assembly at a continental and global scale
It is unclear whether body size affects community assembly mechanisms of soil biota. Here, the authors analyse soil microbial and nematode communities sampled along a 4000-km transect in China and global soil microbiome data to show that bacterial assembly is governed by high dispersal, whereas larger taxa are more influenced by deterministic processes.
- Lu Luan
- , Yuji Jiang
- & Bo Sun