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| Open AccessAuxin-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
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Article
| Open AccessHydrodynamic tearing of bacteria on nanotips for sustainable water disinfection
Common methods for water disinfection involve oxidation or irradiation, and are often associated with a high carbon footprint and formation of toxic byproducts. Here, the authors describe a nano-structured material that is highly effective at killing bacteria in water through a hydrodynamic mechanism driven by mild water flow, in the absence of additional energy supply.
- Lu Peng
- , Haojie Zhu
- & Hong-Ying Hu
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| Open AccessMyxobacteria 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
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Article
| Open AccessSingle-cell isotope tracing reveals functional guilds of bacteria associated with the diatom Phaeodactylum tricornutum
Bacterial remineralization of algal organic matter promotes algal growth but is rarely quantified. Here, Mayali et al. quantify bacterial incorporation of algal-derived organic carbon and nitrogen, and algal incorporation of remineralized carbon and nitrogen, for 15 bacterial co-cultures growing with the diatom Phaeodactylum tricornutum to identify functional guilds of metabolic interactions.
- Xavier Mayali
- , Ty J. Samo
- & Peter K. Weber
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| Open AccessGenome-resolved correlation mapping links microbial community structure to metabolic interactions driving methane production from wastewater
Anaerobic digestion of municipal mixed sludge is a microbial-mediated process that produces renewable natural gases such as methane. Here, Kieft et al. present the results of a two-year study of microbial community structure and function at a wastewater treatment plant, shedding light on metabolic interactions between microorganisms in relation with methane production.
- Brandon Kieft
- , Niko Finke
- & Steven J. Hallam
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Article
| Open AccessCultivation of marine bacteria of the SAR202 clade
Bacteria of the SAR202 clade are ubiquitously distributed in the ocean, but their biology is poorly understood due to the lack of cultivated isolates. Here, Lim et al. report the cultivation of marine SAR202 bacteria and provide insights into the physiology of these enigmatic microorganisms.
- Yeonjung Lim
- , Ji-Hui Seo
- & Jang-Cheon Cho
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Article
| Open AccessMaterial-engineered bioartificial microorganisms enabling efficient scavenging of waterborne viruses
The material-based evolution of organisms has attracted broad interdisciplinary interest, however, the fabrication of material-integrated organelles remains inadequately exploited. Here the authors engineer a bioartificial organism by integrating a semiartificial and specific virus-scavenging organelle to scavenge pathogenic waterborne viruses.
- Huixin Li
- , Yanpeng Xu
- & Ruikang Tang
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Article
| Open AccessCrystal 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
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Article
| Open AccessCharacterization of crAss-like phage isolates highlights Crassvirales genetic heterogeneity and worldwide distribution
Here, the authors report the isolation and genetic characterization of 25 unique crAss-like phages (termed “crAssBcn”) infecting Bacteroides intestinalis, and show that CrAssBcn phages are commonly found in fecal samples from people around the globe, indicating their wide distribution.
- María Dolores Ramos-Barbero
- , Clara Gómez-Gómez
- & Maite Muniesa
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Article
| Open AccessCooperative microbial interactions drive spatial segregation in porous environments
Cooperative interactions might be important in spatially structured microbial habitats. Here, the authors show that cooperative interactions between planktonic and biofilm-forming bacteria drive spatial segregation, and thereby enable species’ coexistence, in a microfluidic chip environment.
- Yichao Wu
- , Chengxia Fu
- & Peng Cai
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Article
| Open AccessImportant role of endogenous microbial symbionts of fish gills in the challenging but highly biodiverse Amazonian blackwaters
Amazonian blackwaters are acidic and physiologically-challenging, but are one of Earth’s most diversified ecosystems. This study revealed that fish survival in these hostile habitats depends on the colonization of their gills by endogenous blackwater Betaproteobacteria, with the potential to regulate host ionoregulatory processes.
- Sylvain François-Étienne
- , Leroux Nicolas
- & Derome Nicolas
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Article
| Open AccessA joint proteomic and genomic investigation provides insights into the mechanism of calcification in coccolithophores
Coccolithophorid algae are globally important for marine biogeochemical cycles, but the molecular basis of their biology is poorly understood. Using proteomics and a new genome, Skeffington et al. identify candidate proteins involved in calcification in Emiliania huxleyi.
- Alastair Skeffington
- , Axel Fischer
- & André Scheffel
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Article
| Open AccessHydrogen and dark oxygen drive microbial productivity in diverse groundwater ecosystems
Microbes in ancient groundwaters can be very diverse and productive. Some microbes seem to produce oxygen in the dark, which others use to consume the greenhouse gas methane. Their metabolisms are relevant for groundwater health and global change.
- S. Emil Ruff
- , Pauline Humez
- & Marc Strous
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| Open AccessTrajectories of freshwater microbial genomics and greenhouse gas saturation upon glacial retreat
Diverse microbial trajectories in carbon and nitrogen cycle processes represent a positive feedback loop of deglaciation on climate warming.
- Jing Wei
- , Laurent Fontaine
- & Alexander Eiler
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| Open AccessSimultaneous sulfide and methane oxidation by an extremophile
Aerobic methanotrophic bacteria oxidize methane in sulfide-rich environments, even though hydrogen sulfide (H2S) inhibits methane oxidation and aerobic respiration. Here, Schmitz et al. show that a single microorganism can oxidize methane and H2S simultaneously, and this is associated with upregulation of a sulfide-insensitive terminal oxidase.
- Rob A. Schmitz
- , Stijn H. Peeters
- & Arjan Pol
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| Open AccessHighly host-linked viromes in the built environment possess habitat-dependent diversity and functions for potential virus-host coevolution
Viruses in built environments raise public health concerns. By analyzing diverse samples, Du et al. provide evidence that virus–host interactions occur frequently in built environments and that viruses are integral members of built environment microbiomes.
- Shicong Du
- , Xinzhao Tong
- & Patrick K. H. Lee
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Article
| Open AccessRoles of adenine methylation in the physiology of Lacticaseibacillus paracasei
The bacterium Lacticaseibacillus paracasei is used in the food industry and as a probiotic. Here, the authors use multi-omics and high-throughput chromosome conformation capture analyses to investigate the roles of a type of DNA methylation (N6-methyladenine modification) in this organism.
- Jie Zhao
- , Meng Zhang
- & Wenyi Zhang
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Article
| Open AccessO2 partitioning of sulfur oxidizing bacteria drives acidity and thiosulfate distributions in mining waters
Microbial genomics is a widely under-utilized tool in mining in understanding water quality drivers. Here the authors show early acid generation and thiosulfate concentrations are driven by O2 dependent microbial sulfur oxidizing bacterial niches in a mine tailings impoundment
- Kelly J. Whaley-Martin
- , Lin-Xing Chen
- & Lesley A. Warren
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| Open AccessCable bacteria with electric connection to oxygen attract flocks of diverse bacteria
Cable bacteria are centimeter-long filamentous microbes that conduct electrons via internal wires, thus coupling sulfide oxidation between sediment layers. Here, Bjerg et al. show that the anoxic part of oxygen-respiring cable bacteria attracts swarms of other bacteria, which appear to transfer electrons to cable bacteria via soluble metabolites.
- Jesper J. Bjerg
- , Jamie J. M. Lustermans
- & Andreas Schramm
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| Open AccessIndoor air surveillance and factors associated with respiratory pathogen detection in community settings in Belgium
Surveillance of respiratory pathogens in air may improve understanding of indoor transmission risks but impacts of context-specific factors on pathogen abundance are not well understood. Here, the authors investigate factors associated with 29 respiratory pathogens through surveillance of 21 community settings in Belgium.
- Joren Raymenants
- , Caspar Geenen
- & Emmanuel André
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| Open AccessEnzyme adaptation to habitat thermal legacy shapes the thermal plasticity of marine microbiomes
Temperature shapes the adaptation and composition of microbiomes, but whether their enzymes drive the thermal response remains unknown. Using an analysis of seven enzyme classes from worldwide marine microbiome data, this study shows that enzyme thermal properties explain microbial thermal plasticity and they are both finely tuned by the thermal variability of the environment.
- Ramona Marasco
- , Marco Fusi
- & Daniele Daffonchio
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Article
| Open AccessStructural 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
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Article
| Open AccessDark 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
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Article
| Open AccessMacroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces
Here, the authors describe the geographies, hosts, substrates, and phylogenetic relationships for 1,794 Saccharomyces strains. They provide insight into the genetic and phenotypic diversity in the genus, not seen through prior work focused on the model species Saccharomyces cerevisiae.
- David Peris
- , Emily J. Ubbelohde
- & Chris Todd Hittinger
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Article
| Open AccessDiverse secondary metabolites are expressed in particle-associated and free-living microorganisms of the permanently anoxic Cariaco Basin
Genome mining for biosynthetic gene clusters (BGCs) can be used for the discovery of new compounds of biotechnological interest. Here, the authors use metagenomics and metatranscriptomics to identify diverse BGCs in free-living and particle-associated microbial communities through the stratified water column of the Cariaco Basin, Venezuela.
- David Geller-McGrath
- , Paraskevi Mara
- & Maria Pachiadaki
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Article
| Open AccessViral infection switches the balance between bacterial and eukaryotic recyclers of organic matter during coccolithophore blooms
Algal blooms are hotspots of marine primary production that play central roles in microbial ecology and global elemental cycling. Here, the authors show how bloom termination by viral infection can shift the balance between eukaryotic and prokaryotic recyclers of phytoplankton biomass.
- Flora Vincent
- , Matti Gralka
- & Assaf Vardi
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Article
| Open AccessElevated temperature and CO2 strongly affect the growth strategies of soil bacteria
Microbial ecological strategies are expected to be phylogenetically conserved, but plasticity and acclimation to environmental change may complicate the picture. Here, the authors show that shifts in soil bacterial ecological strategies deviate from phylogenetic-based predictions after acclimation to long-term warming and CO2 enrichment.
- Yang Ruan
- , Yakov Kuzyakov
- & Ning Ling
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Article
| Open AccessA widespread group of large plasmids in methanotrophic Methanoperedens archaea
Anaerobic methanotrophic (ANME) archaea obtain energy from the breakdown of methane. Here, Schoelmerich et al. describe large plasmids associated with ANME archaea of the Methanoperedens genus in enrichment cultures and other natural anoxic environments, opening the way for development of genetic vectors for research on these poorly understood organisms.
- Marie C. Schoelmerich
- , Heleen T. Ouboter
- & Jillian F. Banfield
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| Open AccessMultiple sources of aerobic methane production in aquatic ecosystems include bacterial photosynthesis
The mechanisms underlying methane production in oxygenated waters of oceans and lakes are unclear. Here, Perez-Coronel and Beman show that aerobic methane production in freshwater incubation experiments is associated with (bacterio)chlorophyll metabolism and photosynthesis, and with Proteobacterial degradation of methylphosphonate.
- Elisabet Perez-Coronel
- & J. Michael Beman
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Article
| Open AccessAnaerobic oxidation of propane coupled to nitrate reduction by a lineage within the class Symbiobacteriia
Anaerobic microorganisms can oxidize short-chain gaseous alkanes such as ethane, propane and butane using sulfate as electron acceptor. Here, the authors show that a bioreactor enrichment of a wastewater microbial community can perform anaerobic propane oxidation coupled to nitrate reduction.
- Mengxiong Wu
- , Jie Li
- & Jianhua Guo
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Article
| Open AccessPast 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
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Article
| Open AccessA pathway for chitin oxidation in marine bacteria
Lytic polysaccharide monooxygenases contribute to microbial degradation of chitin, but how the resulting oxidized chitooligosaccharides are utilized by microbes is unclear. Here, the authors describe a complete pathway for oxidative chitin utilization in marine bacteria.
- Wen-Xin Jiang
- , Ping-Yi Li
- & Yu-Zhong Zhang
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Article
| Open AccessA miniaturized bionic ocean-battery mimicking the structure of marine microbial ecosystems
Marine ecosystems are dominated by microbial communities. Inspired by the photoelectric conversion feature of the marine ecosystems, the authors design a four-species microbial community to mimic primary producer, primary degrader, and ultimate consumers, and show its ability to convert light into electricity for over one month.
- Huawei Zhu
- , Liru Xu
- & Yin Li
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Article
| Open AccessStructural 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
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| Open AccessStructure and activity of particulate methane monooxygenase arrays in methanotrophs
Particulate methane monooxygenase (pMMO) is the main enzyme used by methanotrophs. Here, the authors determined the native structure of pMMO by cryo-electron tomography, revealing lipid-stabilized features and a higher-order hexagonal array arrangement in intact cells.
- Yanan Zhu
- , Christopher W. Koo
- & Peijun Zhang
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Article
| Open AccessBiodiversity, environmental drivers, and sustainability of the global deep-sea sponge microbiome
This study presents a large-scale analysis of microbial diversity in deep-sea sponges. They show that sponge microbial abundance status, geographic distance, sponge phylogeny and the physical-biogeochemical environment drive microbiome composition, in descending order of relevance. The uniqueness of each deep-sea sponge ground stresses the need for their strategic preservation.
- Kathrin Busch
- , Beate M. Slaby
- & Ute Hentschel
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| Open AccessTerrigenous dissolved organic matter persists in the energy-limited deep groundwaters of the Fennoscandian Shield
Dissolved organic matter in the Fennoscandian Shield deep continental bedrock fracture waters of varying characteristics and ages carries a strong terrigenous signature, and only a small proportion of this potential energy source links to the deep biosphere microbial community.
- Helena Osterholz
- , Stephanie Turner
- & Mark Dopson
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Article
| Open AccessHigh 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
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Article
| Open AccessSARS-CoV-2 and other respiratory pathogens are detected in continuous air samples from congregate settings
Air surveillance offers a potential means of monitoring airborne pathogens without the need for individual sampling. Here, the authors perform continuous air sampling in 15 community settings in the US for 29 weeks and demonstrate its feasibility for routine detection of SARS-CoV-2 and other respiratory pathogens.
- Mitchell D. Ramuta
- , Christina M. Newman
- & Shelby L. O’Connor
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Article
| Open AccessPlastic pollution fosters more microbial growth in lakes than natural organic matter
Ultra-high resolution mass spectrometry revealed that plastic bags leach labile compounds. Bioassays performed in Scandinavian lakes indicated that these compounds are incorporated into biomass faster and more efficiently than natural organic matter.
- Eleanor A. Sheridan
- , Jérémy A. Fonvielle
- & Andrew J. Tanentzap
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Article
| Open AccessTrypsin is a coordinate regulator of N and P nutrients in marine phytoplankton
Using CRISPR-Cas9 mediated-knockout and overexpression analyses, this study shows that a trypsin in the diatom Phaeodactylum tricornutum promotes phosphorus uptake and inhibits nitrogen uptake but its expression is downregulated under nitrogen stress and upregulated under phosphorus stress. Together, the findings suggest this trypsin is a coordinate regulator of nutrient homeostasis.
- Yanchun You
- , Xueqiong Sun
- & Senjie Lin
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Article
| Open AccessSeparating natural from human enhanced methane emissions in headwater streams
The effects of fertiliser from intensive agriculture are well recognised, but not so well for fine-sediment. Here we show how widespread ingress of agriculturally derived fine-sediment since the 1940s markedly amplifies methane emissions from streams.
- Yizhu Zhu
- , J. Iwan Jones
- & Mark Trimmer
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Article
| Open AccessThe microbiome of cryospheric ecosystems
The cryosphere includes those parts of Earth where water or soil is frozen, such as snow, ice, glaciers and permafrost soils. Here, the authors present a global inventory of cryospheric microbial communities and their genetic repertoires.
- Massimo Bourquin
- , Susheel Bhanu Busi
- & Tom J. Battin
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Article
| Open AccessInsights into methionine S-methylation in diverse organisms
S-methyl methionine (SMM) is a key molecule in production of dimethylsulfoniopropionate (DMSP), an important marine anti-stress compound, with roles in global nutrient cycling. Here, the authors determine the mechanism of SMM synthesis and uncover unexpected roles for SMM in archaea, CPR bacteria and animals.
- Ming Peng
- , Chun-Yang Li
- & Yu-Zhong Zhang
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Article
| Open AccessGenomic and metabolic adaptations of biofilms to ecological windows of opportunity in glacier-fed streams
In glacier-fed streams, ecological windows of opportunity allow complex microbial biofilms to develop and transiently form the basis of the food web. Using metagenomics, this study reveals the metabolic strategies and key genomic underpinnings of adaptive traits that enable these biofilms to exploit environmental opportunities.
- Susheel Bhanu Busi
- , Massimo Bourquin
- & Tom J. Battin
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| Open AccessMiDAS 4: A global catalogue of full-length 16S rRNA gene sequences and taxonomy for studies of bacterial communities in wastewater treatment plants
Microbial communities are responsible for biological wastewater treatment. Here, Dueholm et al. generate more than 5 million high-quality, full-length 16S rRNA gene sequences from wastewater treatment plants across the world to construct a database with a comprehensive taxonomy, providing insights into diversity and function of these microbial communities.
- Morten Kam Dahl Dueholm
- , Marta Nierychlo
- & Per Halkjær Nielsen
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Article
| Open AccessAssessment of global health risk of antibiotic resistance genes
Antibiotic resistance genes (ARGs) have accelerated microbial threats to human health. Here, Zhang et al. analyze 4572 metagenomic samples to illustrate the global patterns of ARG distribution in diverse habitats. They quantitatively evaluate the health risk to humans of 2561 ARGs by integrating human accessibility, mobility, pathogenicity and clinical availability. With the machine learning, they map the antibiotic resistance threats in global marine habitats.
- Zhenyan Zhang
- , Qi Zhang
- & Haifeng Qian
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| Open AccessMicrobiomes in the Challenger Deep slope and bottom-axis sediments
The V-shaped Challenger Deep in the Mariana Trench is the deepest part of the world’s oceans. Using 586 prokaryotic metagenome-assembled genomes and metatranscriptomic data, this study explores metabolic capabilities and activities of microorganisms involved in elemental cycling in hadal sediments, and reveals the different distribution of processes between its bottom-axis and slope.
- Ying-Li Zhou
- , Paraskevi Mara
- & Yong Wang
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Article
| Open AccessStructure 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