Megataxonomy and global ecology of the virosphere

The ISME Journal, Journal Year: 2024, Volume and Issue: 18(1)

Published: Jan. 1, 2024

Nearly all organisms are hosts to multiple viruses that collectively appear be the most abundant biological entities in biosphere. With recent advances metagenomics and metatranscriptomics, known diversity of substantially expanded. Comparative analysis these using advanced computational methods culminated reconstruction evolution major groups enabled construction a virus megataxonomy, which has been formally adopted by International Committee on Taxonomy Viruses. This comprehensive taxonomy consists six realms, aspired monophyletic assembled based conservation hallmark proteins involved capsid structure formation or genome replication. The different taxa differ host range accordingly ecological niches. In this review article, we outline latest developments megataxonomy discoveries will likely lead reassessment some taxa, particular, split three current realms into two more independent realms. We then discuss correspondence between distribution among niches, as well abundance versus cells habitats. across environments appears primarily determined ranges, i.e. virome is shaped composition biome given habitat, itself affected abiotic factors.

Language: Английский

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Electron Transfer in the Biogeochemical Sulfur Cycle

Life, Journal Year: 2024, Volume and Issue: 14(5), P. 591 - 591

Published: May 6, 2024

Microorganisms are key players in the global biogeochemical sulfur cycle. Among them, some have garnered particular attention due to their electrical activity and ability perform extracellular electron transfer. A growing body of research has highlighted extensive phylogenetic metabolic diversity, revealing crucial roles ecological processes. In this review, we delve into transfer process between sulfate-reducing bacteria anaerobic alkane-oxidizing archaea, which facilitates growth within syntrophic communities. Furthermore, review phenomenon long-distance potential multicellular filamentous sulfur-oxidizing bacteria. These bacteria, with vast application prospects significance, play a pivotal role various Subsequently, discuss important pili/cytochrome for presented cutting-edge approaches exploring studying electroactive microorganisms. This provides comprehensive overview microorganisms participating By examining mechanisms, applied implications, offer novel insights microbial metabolism, thereby advancing applications development sustainable bioelectronics materials bioremediation technologies.

Language: Английский

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Unexpected scarcity of ANME archaea in hydrocarbon seeps within Monterey Bay

Biogeosciences, Journal Year: 2025, Volume and Issue: 22(2), P. 385 - 403

Published: Jan. 22, 2025

Abstract. Marine hydrocarbon seeps typically harbor a relatively predictable microbiome, including anaerobic methanotrophic (ANME) archaea. Here, we sampled two cold in Monterey Bay, CA – Clam Field and Extrovert Cliff which have been known for decades but never characterized microbiologically. Many aspects of these were typical worldwide, elevated methane sulfide concentrations, 13C-depleted dissolved inorganic carbon, the presence characteristic macrofauna. However, observed atypical microbial communities: extremely few ANME sequences detected either 16S rRNA or mcrA gene surveys at (< 0.1 % total community reads), even after 6 months incubation with laboratory, only slightly more recovered from 0.3 reads). At Field, lack transcription, methane-dependent sulfate reduction, linear porewater profile consistent low absent methanotrophy. Although reason scarcity archaea is still unclear, postulate that non-methane release excludes methanotrophs directly indirectly (e.g., through competitive interactions hydrocarbon-degrading bacteria). Our findings highlight potential without this critical biofilter therefore greater emissions sediments.

Language: Английский

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VITAP: a high precision tool for DNA and RNA viral classification based on meta-omic data

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: March 5, 2025

The rapid growth in the number of newly identified DNA and RNA viral sequences underscores need for an accurate comprehensive classification system all realms at different taxonomic levels. Here, we establish Viral Taxonomic Assignment Pipeline (VITAP), which addresses challenges by integrating alignment-based techniques with graphs, offering high precision classifying both providing confidence level each unit. This tool automatically updates its database sync latest references from International Committee on Taxonomy Viruses (ICTV), efficiently as short 1,000 base pairs to genus level. VITAP possesses good generalization capabilities, maintaining accuracy comparable other pipelines while achieving higher annotation rates across most phyla. Its application deep-sea viromes has led significant updates, diversity information viruses deep-sea. is available https://github.com/DrKaiyangZheng/VITAP . High-throughput sequencing retrieves diverse environments, but these can be difficult classify. here developed a assignment pipeline that classifies incomplete (as 1000-bp) down

Language: Английский

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Candidatus Alkanophaga archaea from Guaymas Basin hydrothermal vent sediment oxidize petroleum alkanes

Nature Microbiology, Journal Year: 2023, Volume and Issue: 8(7), P. 1199 - 1212

Published: June 1, 2023

Methanogenic and methanotrophic archaea produce consume the greenhouse gas methane, respectively, using reversible enzyme methyl-coenzyme M reductase (Mcr). Recently, Mcr variants that can activate multicarbon alkanes have been recovered from archaeal enrichment cultures. These enzymes, called alkyl-coenzyme (Acrs), are widespread in environment but remain poorly understood. Here we produced anoxic cultures degrading mid-chain petroleum n-alkanes between pentane (C

Language: Английский

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Widespread Horizontal Gene Transfer Among Animal Viruses

Published: June 5, 2024

The initial objective of this study was to shed light on the evolution small DNA tumor viruses by analyzing de novo assemblies publicly available deep sequencing datasets. survey generated a searchable database contig snapshots representing more than 100,000 Sequence Read Archive records. Using modern structure-aware search tools, we iteratively broadened include an increasingly wide range other virus families. analysis revealed surprisingly diverse chimeras involving different groups. In some instances, genes resembling known DNA-replication modules or virion protein operons were paired with unrecognizable sequences that structural predictions suggest may represent previously unknown replicases and novel architectures. Discrete clades emerging group called adintoviruses discovered in datasets humans primates. As proof concept, show is also useful for discovering RNA candidate archaeal phages. ancillary searches additional examples chimerization between observations support gene-centric taxonomic framework should be future virus-hunting efforts.

Language: Английский

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Metal-Driven Anaerobic Oxidation of Methane as an Important Methane Sink in Methanic Cold Seep Sediments

Microbiology Spectrum, Journal Year: 2023, Volume and Issue: 11(2)

Published: March 28, 2023

Anaerobic oxidation of methane (AOM) coupled with reduction metal oxides is supposed to be a globally important bioprocess in marine sediments. However, the responsible microorganisms and their contributions budget are not clear deep sea cold seep Here, we combined geochemistry, muti-omics, numerical modeling study metal-dependent AOM methanic sediments northern continental slope South China Sea. Geochemical data based on concentrations, carbon stable isotope, solid-phase sediment analysis, pore water measurements indicate occurrence anaerobic zone. The 16S rRNA gene transcript amplicons, along metagenomic metatranscriptomic suggest that diverse methanotrophic archaea (ANME) groups actively mediated zone either independently or syntrophy with, e.g., ETH-SRB1, as potential reducers. Modeling results estimated rates consumption via Fe-AOM Mn-AOM were both 0.3 μmol cm-2 year-1, which account for ~3% total CH4 removal Overall, our highlight metal-driven an sink IMPORTANCE Our findings provide comprehensive view uncovered mechanisms involved microorganisms. High amounts buried reactive Fe(III)/Mn(IV) minerals could available electron acceptors AOM. It metal-AOM at least contributes 3% from seep. Therefore, this research paper advances understanding role global cycle, especially sink.

Language: Английский

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Archaeal virus entry and egress

microLife, Journal Year: 2024, Volume and Issue: 5

Published: Jan. 1, 2024

Archaeal viruses display a high degree of structural and genomic diversity. Few details are known about the mechanisms by which these enter exit their host cells. Research on archaeal has lately made significant progress due to advances in genetic tools imaging techniques, such as cryo-electron tomography (cryo-ET). In recent years, steady output newly identified viral receptors egress offered first insight into how interact with cell envelope. As more entry unravelled, patterns starting emerge. This helps better understand interactions between envelope compare infection strategies other domains life. Here, we provide an overview developments field egress, shedding light onto most elusive part virosphere.

Language: Английский

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Deep-branching ANME-1c archaea grow at the upper temperature limit of anaerobic oxidation of methane

Frontiers in Microbiology, Journal Year: 2022, Volume and Issue: 13

Published: Sept. 23, 2022

In seafloor sediments, the anaerobic oxidation of methane (AOM) consumes most formed in anoxic layers, preventing this greenhouse gas from reaching water column and finally atmosphere. AOM is performed by syntrophic consortia specific methane-oxidizing archaea (ANME) sulfate-reducing bacteria (SRB). Cultures with diverse partners exist at temperatures between 12°C 60°C. Here, hydrothermally heated sediments Guaymas Basin, we cultured deep-branching ANME-1c that grow Thermodesulfobacteria 70°C. Like all ANME, oxidize using methanogenesis pathway reverse. As an uncommon feature, encode a nickel-iron hydrogenase. This hydrogenase has low expression during partner lack hydrogen-consuming hydrogenases. Therefore, it unlikely exchange hydrogen AOM. also does not consume for formation, disputing recent hypothesis on facultative methanogenesis. We hypothesize might have been present common ancestor ANME-1 but lost its central metabolic function archaea. For potential direct interspecies electron transfer (DIET), both express genes coding extracellular appendages multiheme cytochromes. pentaheme cytochrome high similarity to cytochromes other bacteria. associate specifically Thermodesulfobacteria, their co-occurrence so far only documented Gulf California. However, deep seafloor, sulfate-methane interphases appear up 80°C, suggesting these as habitats partnership Thermodesulfobacteria.

Language: Английский

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The Characteristics and Estimation of Greenhouse Gas Emissions from Urban Sewer Systems in Southern China

Sustainability, Journal Year: 2025, Volume and Issue: 17(6), P. 2504 - 2504

Published: March 12, 2025

Carbon emission fluxes in urban sewer systems and the microbial community structure sediments remain unclear. In this study, a system located southern China was utilized to investigate water quality characteristics. The results showed that chemical oxygen demand loss rates branch pipe sub-main were 27.1% 14.1%, respectively. estimated carbon flux by factor method. revealed total from 1.39 kg CO2-eq/m3 of methane dioxide 0.87 0.51 CO2-eq/m3, accounting for 62% 36.4%. analyzed 16S rRNA. indicated methanogenic archaea Methanobacterium, Methanosaeta, Methanobrevibacter. activity further assessed. This study confirmed main sources emissions are greenhouse gases system. furnishes novel insights control municipal sewage systems.

Language: Английский

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