Featured
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| Open AccessA quantitative framework reveals ecological drivers of grassland microbial community assembly in response to warming
Studies of microbial community assembly mechanisms typically use metrics for turnover within the whole community. Here, the authors develop an alternative approach based on turnover within lineages and dissect mechanistic change in grassland bacterial assembly under experimental warming.
- Daliang Ning
- , Mengting Yuan
- & Jizhong Zhou
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Article
| Open AccessBacteria are important dimethylsulfoniopropionate producers in marine aphotic and high-pressure environments
Dimethylsulfoniopropionate (DMSP) is an osmolyte produced by marine microbes that plays an important role in nutrient cycling and atmospheric chemistry. Here the authors go to the Mariana Trench—the deepest point in the ocean—and find bacteria are key DMSP producers, and that DMSP has a role in protection against high pressure.
- Yanfen Zheng
- , Jinyan Wang
- & Xiao-Hua Zhang
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Article
| Open AccessTemperate infection in a virus–host system previously known for virulent dynamics
The blooming alga Emiliania huxleyi and its viruses are a model for density-dependent virulent dynamics. However, Knowles et al. show that this host–virus system exhibits temperate dynamics at natural host densities, in a manner dependent on host physiology.
- Ben Knowles
- , Juan A. Bonachela
- & Kay D. Bidle
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Article
| Open AccessGenomic and enzymatic evidence of acetogenesis by anaerobic methanotrophic archaea
Ocean cold seeps are poorly understood relative to related systems like hydrothermal vents. Here the authors use high pressure bioreactors and microbial communities from a cold seep mud volcano and find a previously missing step of methane conversion to acetate that likely fuels heterotrophic communities.
- Shanshan Yang
- , Yongxin Lv
- & Yu Zhang
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Article
| Open AccessLipo-chitooligosaccharides as regulatory signals of fungal growth and development
Lipo-chitooligosaccharides (LCOs) are signaling molecules produced by certain bacteria and fungi that establish symbiotic relationships with plants. Here, the authors show that LCOs are produced also by many other, non-symbiotic fungi, and regulate fungal growth and development.
- Tomás Allen Rush
- , Virginie Puech-Pagès
- & Jean-Michel Ané
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| Open AccessMicrobiota assembly, structure, and dynamics among Tsimane horticulturalists of the Bolivian Amazon
Selective and neutral forces shape human microbiota assembly in early life. Here, Sprockett et al. study microbial community assembly in 47 infant-mother pairs from the Tsimane, an indigenous Bolivian population, highlighting the importance of neutral forces during microbiota assembly.
- Daniel D. Sprockett
- , Melanie Martin
- & David A. Relman
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Article
| Open AccessAerobic microbial life persists in oxic marine sediment as old as 101.5 million years
The discovery of aerobic microbial communities in nutrient-poor sediments below the seafloor begs the question of the mechanisms for their persistence. Here the authors investigate subseafloor sediment in the South Pacific Gyre abyssal plain, showing that aerobic microbial life can be revived and retain metabolic potential even from 101.5 Ma-old sediment.
- Yuki Morono
- , Motoo Ito
- & Fumio Inagaki
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Article
| Open AccessMicrobial 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
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Article
| Open AccessBile acids drive the newborn’s gut microbiota maturation
Early postnatal colonization has been described to be critical for the long-term microbiota composition and health. Here, via multi-omics approach, the authors investigate the impact of the developing host hepatic metabolism on the murine intestinal microbiota composition with comparative analysis at immediate postnatal period, early infancy and weaning and adulthood.
- N. van Best
- , U. Rolle-Kampczyk
- & M. W. Hornef
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Article
| Open AccessAn ecological framework to understand the efficacy of fecal microbiota transplantation
Here, the authors present a theoretical framework based on community ecology and network science to investigate the efficacy of fecal microbiota transplantation in conditions associated with a disrupted gut microbiota, using the recurrent Clostridioides difficile infection as a prototype disease.
- Yandong Xiao
- , Marco Tulio Angulo
- & Yang-Yu Liu
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Article
| Open AccessMeta-analysis of the impacts of global change factors on soil microbial diversity and functionality
It is often assumed that various types of anthropogenic change reduce microbial diversity and function. Here, the authors do a meta-analysis showing that global change factors affect microbial diversity inconsistently; negative effects are most likely for global change factors that affect soil pH.
- Zhenghu Zhou
- , Chuankuan Wang
- & Yiqi Luo
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Article
| Open AccessBacterial symbionts support larval sap feeding and adult folivory in (semi-)aquatic reed beetles
Symbiotic microbes in insects can enable their hosts to access untapped nutritional resources. Here, the authors show that symbiotic bacteria in reed beetles can provide essential amino acids to sap-feeding larvae and help leaf-feeding adults to degrade pectin, respectively.
- Frank Reis
- , Roy Kirsch
- & Martin Kaltenpoth
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Article
| Open AccessGeometry and evolution of the ecological niche in plant-associated microbes
The ecological niche of host-associated microbes is defined by both abiotic and biotic dimensions. Here the authors analyse published data on fungal and oomycete pathogens of plants, demonstrating that specialization can evolve independently on abiotic and biotic axes and that interactions with host plants reduce thermal niche breadth.
- Thomas M. Chaloner
- , Sarah J. Gurr
- & Daniel P. Bebber
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Article
| Open AccessRemote sensing reveals Antarctic green snow algae as important terrestrial carbon sink
Snow algae bloom along the coast of Antarctica and are likely to be biogeochemically important. Here, the authors produced the first map of such blooms, show that they are driven by warmer temperatures and proximity to birds and mammals, and are likely to increase given projected climate changes.
- Andrew Gray
- , Monika Krolikowski
- & Matthew P. Davey
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Article
| Open AccessInvestigating the dynamics of microbial consortia in spatially structured environments
The spatial organisation of microbial communities is caused by the interplay of biotic and abiotic factors. Here the authors design a microfluidic platform to quantify the spatiotemporal parameters influencing diffusion-mediated interactions, and use this device to investigate information transmission and metabolic cross-feeding in synthetic microbial consortia.
- Sonali Gupta
- , Tyler D. Ross
- & Ophelia S. Venturelli
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Article
| Open AccessMicroplastics affect sedimentary microbial communities and nitrogen cycling
Plastic pollution has infiltrated every ecosystem, but few studies have quantified the biogeochemical or ecological effects of plastic. Here the authors show that microplastics in ocean sediment can significantly alter microbial community structure and nitrogen cycling.
- Meredith E. Seeley
- , Bongkeun Song
- & Robert C. Hale
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Article
| Open AccessBioorthogonal non-canonical amino acid tagging reveals translationally active subpopulations of the cystic fibrosis lung microbiota
Bioorthogonal non-canonical amino acid tagging (BONCAT) coupled with flow cytometry (FACS) has been utilized to profile active microbiome of environmental samples. Here, the authors combine BONCAT-FACS and 16 S rRNA sequencing to characterize the translational activity of bacterial communities within sputum derived from stable cystic fibrosis patients.
- Talia D. Valentini
- , Sarah K. Lucas
- & Ryan C. Hunter
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Article
| Open AccessMutualist and pathogen traits interact to affect plant community structure in a spatially explicit model
Microbial plant-soil feedbacks (PSF) are fundamentally important for plant diversity. The authors present a spatially explicit dynamic model that separates the effects of microbial mutualists and pathogens, thereby presenting a testable mechanistic framework to reconcile previously puzzling observations of the strength and direction of PSF with diversity maintenance.
- John W. Schroeder
- , Andrew Dobson
- & Edward Allen Herre
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Article
| Open AccessThe impact of antimalarial resistance on the genetic structure of Plasmodium falciparum in the DRC
The genome of the malaria parasite Plasmodium falciparum contains a record of past evolutionary forces. Here, using 2537 parasite sequences from the Democratic Republic of the Congo, the authors demonstrate how drug pressure and human movement have shaped the present-day parasite population.
- Robert Verity
- , Ozkan Aydemir
- & Jonathan J. Juliano
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Article
| Open AccessExtracellular electron transfer-dependent anaerobic oxidation of ammonium by anammox bacteria
Bacteria capable of anaerobic ammonium oxidation (anammox) produce half of the nitrogen gas in the atmosphere, but much of their physiology is still unknown. Here the authors show that anammox bacteria are capable of a novel mechanism of ammonium oxidation using extracellular electron transfer.
- Dario R. Shaw
- , Muhammad Ali
- & Pascal E. Saikaly
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Article
| Open AccessSingle-cell bacterial transcription measurements reveal the importance of dimethylsulfoniopropionate (DMSP) hotspots in ocean sulfur cycling
DMSP is a ubiquitous organosulfur compound in the ocean that, once degraded by bacteria, plays key roles in global biogeochemical cycles and climate regulation. Here, the authors use single-cell measurements of transcription to investigate the intricate dynamics of bacterial DMSP degradation.
- Cherry Gao
- , Vicente I. Fernandez
- & Roman Stocker
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Article
| Open AccessDual functionality of the amyloid protein TasA in Bacillus physiology and fitness on the phylloplane
The amyloid protein TasA is a main component of the extracellular matrix in Bacillus subtilis biofilms. Here the authors show that, in addition to a structural function during biofilm assembly and interactions with plants, TasA contributes to the stabilization of membrane dynamics during stationary phase.
- Jesús Cámara-Almirón
- , Yurena Navarro
- & Diego Romero
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Article
| Open AccessStochasticity constrained by deterministic effects of diet and age drive rumen microbiome assembly dynamics
How complex microbial communities assemble through the animal’s life, and how predictable the assembly process is, remains poorly understood. Here, the authors profile the cow gut microbiome from birth to adulthood in animals born in C-section or natural birth and show that chance events early in life have a strong impact on microbiome development.
- Ori Furman
- , Liat Shenhav
- & Itzhak Mizrahi
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Article
| Open AccessDynamic genome evolution and complex virocell metabolism of globally-distributed giant viruses
Nucleocytoplasmic large DNA viruses (NCLDV) exhibit a large genomic repertoire and complex evolutionary history. Here, the authors generate 501 metagenome-assembled genomes from diverse environments and show NCLDVs to harbor a wide range of potential metabolic capabilities.
- Mohammad Moniruzzaman
- , Carolina A. Martinez-Gutierrez
- & Frank O. Aylward
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Article
| Open AccessEnvironmental remodeling of human gut microbiota and antibiotic resistome in livestock farms
Environments where antibiotics are used indiscriminately exhibit microbial communities that can represent hot-spots of resistance gene enrichment, which in turn could spread to humans. Here, the authors characterize how exposure to swine farms environment lead to temporal changes in the gut microbiome and resistome of healthy veterinary students.
- Jian Sun
- , Xiao-Ping Liao
- & Ya-Hong Liu
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Article
| Open AccessBacterial adaptation is constrained in complex communities
A species’ ability to adapt to a new environment may be influenced by both intrinsic factors and extrinsic factors. Here, Scheuerl et al. show that bacterial adaptation to low pH depends on not only its genome size and initial level of adaptation, but also the diversity of the community.
- Thomas Scheuerl
- , Meirion Hopkins
- & Thomas Bell
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Article
| Open AccessCommunity diversity and habitat structure shape the repertoire of extracellular proteins in bacteria
Microbes secrete a repertoire of extracellular proteins to serve various functions depending on the ecological context. Here the authors examine how bacterial community composition and habitat structure affect the extracellular proteins, showing that generalist species and those living in more structured environments produce more extracellular proteins, and that costs of production are lower in more diverse communities.
- Marc Garcia-Garcera
- & Eduardo P. C. Rocha
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Article
| Open AccessVirulent coliphages in 1-year-old children fecal samples are fewer, but more infectious than temperate coliphages
The impact of bacteriophages in the human gut microbiome remains poorly understood. Here, the authors characterize coliphages isolated from a large cohort of 1-year-old infants and show that temperate coliphages dominate, while virulent ones have greater infectivity and broader host range.
- Aurélie Mathieu
- , Moïra Dion
- & Marie-Agnès Petit
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Article
| Open AccessInteraction variability shapes succession of synthetic microbial ecosystems
Cellular interactions are a major driver of microbial communities and shown highly variable in strength. Here the authors construct synthetic consortia and mathematical models to elucidate the role of interaction variability in driving ecosystem succession.
- Feng Liu
- , Junwen Mao
- & Ting Lu
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Article
| Open AccessA predator-prey interaction between a marine Pseudoalteromonas sp. and Gram-positive bacteria
Predator-prey interactions play important roles in the cycling of marine organic matter. Here the authors show that a Gram-negative bacterium isolated from marine sediments can kill and feed on Gram-positive bacteria by secreting a peptidoglycan-degrading enzyme.
- Bai-Lu Tang
- , Jie Yang
- & Yu-Zhong Zhang
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Article
| Open AccessSymbiont population control by host-symbiont metabolic interaction in Symbiodiniaceae-cnidarian associations
The relationship between the coral animal and symbiotic algae is essential to coral health, and researchers are turning to Exaiptasia, a model cnidarian system, to study this relationship mechanistically. Here the authors find that endosymbiotic algae become limited by nitrogen at high population densities and provide the host with high levels of fixed carbon.
- Tingting Xiang
- , Erik Lehnert
- & Arthur R. Grossman
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Article
| Open AccessSoil bacterial diversity mediated by microscale aqueous-phase processes across biomes
Numerous micro- and macro-scale factors influence soil microbial diversity. Here the authors create a model to demonstrate that fine scale soil moisture influences the carrying capacity of microbes, which then scales up to larger biogeographic patterns.
- Samuel Bickel
- & Dani Or
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Article
| Open AccessFungal community assembly in drought-stressed sorghum shows stochasticity, selection, and universal ecological dynamics
Fungal community assembly on crop plants is thought to be driven by deterministic selection exerted by the host. Here Gao et al. use a sorghum system to show that stochastic forces act on fungal community assembly in leaves and roots early in host development and when sorghum is drought stressed.
- Cheng Gao
- , Liliam Montoya
- & John W. Taylor
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Article
| Open AccessA meta-analysis of global fungal distribution reveals climate-driven patterns
The authors assemble and analyse previously generated mycobiome data linked to geographical locations across the world. They describe the distribution of fungal taxa and show that climate is an important driver of fungal biogeography and that fungal diversity appears to be concentrated at high latitudes.
- Tomáš Větrovský
- , Petr Kohout
- & Petr Baldrian
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Article
| Open AccessCommunity-level respiration of prokaryotic microbes may rise with global warming
Warmer temperatures could increase the growth and metabolic rates of microbes. Here, the authors assemble a dataset of thermal performance curves for over 400 bacteria and archaea, showing that metabolic rates are likely to increase under warming, with implications for global carbon cycling.
- Thomas P. Smith
- , Thomas J. H. Thomas
- & Samrāt Pawar
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Article
| Open AccessFungal-bacterial diversity and microbiome complexity predict ecosystem functioning
There is ongoing interest in linking soil microbial diversity to ecosystem function. Here the authors manipulate the diversity and composition of microbial communities and show that complex microbial networks contribute more to ecosystem multifunctionality than simpler or low-diversity networks.
- Cameron Wagg
- , Klaus Schlaeppi
- & Marcel G. A. van der Heijden
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Article
| Open AccessA mutualistic interaction between Streptomyces bacteria, strawberry plants and pollinating bees
Microbes can establish mutualistic interactions with plants and insects. Here, Kim et al. show that Streptomyces bacteria can protect strawberry plants and honeybees from pathogens, can move into the plant vascular tissue from soil and from flowers, and are transferred among flowers by the pollinators.
- Da-Ran Kim
- , Gyeongjun Cho
- & Youn-Sig Kwak
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Article
| Open AccessInsights into the ecological roles and evolution of methyl-coenzyme M reductase-containing hot spring Archaea
Methane metabolism by some lineages of Archaea contributes to the cycling of carbon on Earth. Here, the authors show high diversity of methyl-coenzyme M reductase (Mcr), a key enzyme associated with archaeal methane/alkane metabolism, in hot spring Archaea, and investigate their ecological roles and evolution.
- Zheng-Shuang Hua
- , Yu-Lin Wang
- & Wen-Jun Li
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Article
| Open AccessThe fecal resistome of dairy cattle is associated with diet during nursing
Livestock play a role in maintaining antibiotic resistance reservoirs. Here, Liu et al. use metagenomics to study the dynamics of antibiotic resistance genes (ARGs) in the gut of dairy cattle during early life, showing that colostrum is a potential source of ARGs and ARG abundance declines during nursing covarying with dietary transition.
- Jinxin Liu
- , Diana H. Taft
- & David A. Mills
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Article
| Open AccessBacterial predator-prey coevolution accelerates genome evolution and selects on virulence-associated prey defences
Predator-prey coevolution is expected to hasten evolutionary rates, but this is difficult to test in long-lived species. Here, the authors report consequences of experimental coevolution between bacterial predators and prey, including accelerated molecular evolution and parallel genomic and phenotypic adaptation.
- Ramith R. Nair
- , Marie Vasse
- & Gregory J. Velicer
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Article
| Open AccessA shared core microbiome in soda lakes separated by large distances
Alkaline lakes have some of the highest productivity rates in freshwater ecosystems. Here the authors report amplicon, metagenome, and proteome sequencing from microbial mat communities of four alkaline lakes in Canada, and compare these lakes to central Asian soda lakes, revealing a shared core microbiome despite the geographical distance.
- Jackie K. Zorz
- , Christine Sharp
- & Marc Strous
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Article
| Open AccessChanges in the metabolic potential of the sponge microbiome under ocean acidification
Anthropogenic CO2 emissions are causing ocean acidification, which can affect the physiology of some organisms. Here, Botté et al. use metagenomics to show differences in metabolic potential between sponge microbiomes sampled at a shallow volcanic CO2 seep and those from nearby control sites.
- Emmanuelle S. Botté
- , Shaun Nielsen
- & Nicole S. Webster
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Article
| Open AccessAssembly and seasonality of core phyllosphere microbiota on perennial biofuel crops
Microbial communities of plant leaf surfaces are ecologically important, but how they assemble and vary in time is unclear. Here, the authors identify core leaf microbiomes and seasonal patterns for two biofuel crops and show with source-sink models that soil is a reservoir of phyllosphere diversity.
- Keara L. Grady
- , Jackson W. Sorensen
- & Ashley Shade
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Article
| Open AccessBis-naphthopyrone pigments protect filamentous ascomycetes from a wide range of predators
It is thought that fungi protect themselves from predators by the production of toxic compounds. Here, Xu et al. show that a wide range of animal predators avoid feeding on Fusarium fungi, and this depends on fungal production of a bis-naphthopyrone pigment that is not toxic to the predators.
- Yang Xu
- , Maria Vinas
- & Petr Karlovsky
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Article
| Open AccessMicrobial carbon use efficiency predicted from genome-scale metabolic models
Microbial respiration releases carbon from the soil. Here, the authors estimate bacterial carbon use efficiency in soils for over 200 species using constraint-based modeling, incorporate the values into an ecosystem model, and find that shifts in community composition may impact carbon storage.
- Mustafa Saifuddin
- , Jennifer M. Bhatnagar
- & Adrien C. Finzi
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Article
| Open AccessManganese and iron deficiency in Southern Ocean Phaeocystis antarctica populations revealed through taxon-specific protein indicators
Low manganese availability could be a major control of phytoplankton growth in the Southern Ocean. Here the authors identify proteomic signatures of low manganese and iron availability in phytoplankton cultures and detect those signatures in Antarctic field samples.
- Miao Wu
- , J. Scott P. McCain
- & Erin M. Bertrand
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Review Article
| Open AccessSubseafloor life and its biogeochemical impacts
Subseafloor microbial activities are central to global biogeochemical cycles, affecting Earth’s surface oxidation, ocean chemistry, and climate. Here the authors review present understanding of subseafloor microbes and their activities, identify research gaps, and recommend approaches to fill those gaps.
- Steven D’Hondt
- , Robert Pockalny
- & Arthur J. Spivack
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Article
| Open AccessCoral bacterial community structure responds to environmental change in a host-specific manner
The flexibility of corals to associate with different bacteria in different environments has not been systematically investigated. Here, the authors study bacterial community dynamics for two coral species and show that bacterial community structure responds to environmental changes in a host-specific manner.
- Maren Ziegler
- , Carsten G. B. Grupstra
- & Christian R. Voolstra
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Article
| Open AccessProbing 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