Why and how to use the SeqCode

mLife, Journal Year: 2024, Volume and Issue: 3(1), P. 1 - 13

Published: Feb. 7, 2024

Abstract The SeqCode, formally called the Code of Nomenclature Prokaryotes Described from Sequence Data, is a new code nomenclature in which genome sequences are nomenclatural types for names prokaryotic species. While similar to International (ICNP) structure and rules priority, it does not require deposition type strains international culture collections. Thus, allows formation permanent uncultured prokaryotes whose nearly complete have been obtained directly environmental DNA as well other that cannot be deposited Because diversity greatly exceeds readily culturable prokaryotes, SeqCode only suitable naming majority start date was January 1, 2022, online Registry ( https://seqco.de/ ) created ensure valid publication names. recognizes all validly published under ICNP before 2022. After date, compete with priority. As result, species can one name, either or ICNP, enabling effective communication creation unified taxonomies cultured prokaryotes. administered by Committee, comprised Community elected administrative components. Anyone an interest systematics encouraged join participate development this resource.

Language: Английский

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Distribution and Environmental Preference of Potential Mercury Methylators in Paddy Soils across China

Environmental Science & Technology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 17, 2025

The neurotoxin methylmercury (MeHg) is produced mainly from the transformation of inorganic Hg by microorganisms carrying hgcAB gene pair. Paddy soils are known to harbor diverse microbial communities exhibiting varying abilities in methylating Hg, but their distribution and environmental drivers remain unknown at a large spatial scale. Using hgcA amplicon sequencing, this study examined Hg-methylating major rice-producing paddy across transect ∼3600 km an altitude ∼1300 m China. Results showed that hgcA+ OTU richness was higher tropical subtropical compared temperate zones. Geobacteraceae, Smithellaceae, Methanoregulaceae were identified as dominant families associated with MeHg production, collectively accounting for up 77% total sequences. Hierarchical partitioning analyses revealed pH main driver genes Geobacteraceae (14.8%) (16.3%), while accounted 21.4% Smithellaceae. Based on these preferences, machine-learning algorithm used predict families, thereby providing novel insights into important determinants improved prediction production

Language: Английский

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Reconstructing Early Microbial Life

Annual Review of Microbiology, Journal Year: 2024, Volume and Issue: 78(1), P. 463 - 492

Published: Aug. 21, 2024

For more than 3.5 billion years, life experienced dramatic environmental extremes on Earth. These include shifts from oxygen-less to overoxygenated atmospheres and cycling between hothouse conditions global glaciations. Meanwhile, an ecological revolution took place. Earth evolved one dominated by microbial containing the plants animals that are most familiar today. Many key cellular features early in history of life, collectively defining nature our biosphere underpinning human survival. Recent advances molecular biology bioinformatics have greatly improved understanding evolution across deep time. However, incorporation genetics, population biology, evolutionary approaches into study Precambrian biota remains a significant challenge. This review synthesizes current knowledge with emphasis ancient metabolisms. It also outlines foundations emerging interdisciplinary area integrates microbiology, paleobiology, synthetic reconstruct biological innovations.

Language: Английский

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Phenotypic and genomic characterization of Bathyarchaeum tardum gen. nov., sp. nov., a cultivated representative of the archaeal class Bathyarchaeia

Frontiers in Microbiology, Journal Year: 2023, Volume and Issue: 14

Published: Aug. 22, 2023

Bathyarchaeia are widespread in various anoxic ecosystems and considered one of the most abundant microbial groups on earth. There only a few reports laboratory cultivation , none representatives this class has been isolated pure culture. Here, we report sustainable archaeon (strain M17C Ts ) enriched from anaerobic sediment coastal lake. The cells strain were small non-motile cocci, 0.4–0.7 μm diameter. cytoplasmic membrane was surrounded by an S-layer covered with outermost electron-dense sheath. Strain is strictly mesophile. It grows at 10–45°C (optimum 37°C), pH 6.0–10.0 8.0), NaCl concentrations 0–60 g l −1 20 ). Growth occurred presence methoxylated aromatic compounds (3,4-dimethoxybenzoate vanillate) together complex proteinaceous substrates. Dimethyl sulfoxide nitrate stimulated growth. phylogenomic analysis placed to BIN-L-1 genus-level lineage BA1 family-level B26-1 order-level (former subgroup-8) within . complete genome had size 2.15 Mb DNA G + C content 38.1%. Based position phenotypic genomic properties, propose assign new species novel genus Bathyarchaeum tardum gen. nov., sp. nov. This first sustainably cultivated representative We under SeqCode sequence (CP122380) as nomenclatural type which should be for proposed family Bathyarchaeaceae order Bathyarchaeales

Language: Английский

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Process stability in anaerobic Digestion: Unveiling microbial signatures of full-scale reactor performance

Chemical Engineering Journal, Journal Year: 2024, Volume and Issue: 497, P. 154962 - 154962

Published: Aug. 23, 2024

Language: Английский

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Widespread Bathyarchaeia encode a novel methyltransferase utilizing lignin‐derived aromatics

mLife, Journal Year: 2023, Volume and Issue: 2(3), P. 272 - 282

Published: Sept. 1, 2023

Abstract Lignin degradation is a major process in the global carbon cycle across both terrestrial and marine ecosystems. Bathyarchaeia , which are among most abundant microorganisms sediment, have been proposed to mediate anaerobic lignin degradation. However, mechanism of bathyarchaeial remains unclear. Here, we report an enrichment culture named Candidatus Baizosediminiarchaeum ligniniphilus DL1YTT001 ( Ca . B. ligniniphilus), from coastal sediments that can grow with as sole organic source under mesophilic anoxic conditions. possesses highly expresses novel methyltransferase 1 (MT1, mtgB ) for transferring methoxyl groups monomers cob(I)alamin. MtgBs no homology known microbial methyltransferases present only lineages. Heterologous expression gene confirmed O ‐demethylation activity. The genes were identified metagenomic data sets wide range sediments, they expressed East China Sea. These findings suggest capable via their specific methyltransferases, ubiquitous sediments.

Language: Английский

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Process exploration of domestication, start-up and rapid recovery strategies for anaerobic digestion of sole corn stover: Methane production efficiency and dominant microbial responses

Journal of Cleaner Production, Journal Year: 2024, Volume and Issue: 480, P. 144116 - 144116

Published: Oct. 30, 2024

Language: Английский

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Unveiling the life of archaea in sediments: Diversity, metabolic potentials, and ecological roles

iMetaOmics., Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 28, 2025

Abstract The domain Archaea was initially characterized as extremophiles upon its proposal. Recent significant discoveries have redrawn our views of archaeal biology, encompassing the identification mesophilic groups, expansion diversity and metabolic capabilities, elucidation evolutionary relationships among archaea, bacteria, eukaryotes. are ubiquitous constitute a substantial fraction microbial biomass within sediments. Therefore, comprehending their ecological roles is paramount for understanding contributions to global geochemical cycles. In this review, we summarize archaea across various sediment ecosystems, from terrestrial inland deep‐sea environments, utilizing representative genomes supported by Genome Taxonomy Database, which encompasses habitats such hot springs, salt lakes, freshwater rivers, mangroves, estuaries, coastal regions, seafloor sediments, cold seeps, hydrothermal vents. Furthermore, integrate analyses with recent studies highlight potentials, novel enzymatic functions, related carbon, nitrogen, sulfur cycles different lineages. Finally, discuss research hotspots achievements in studies, while projecting future exploration directions. expanding capacities broadened perspective on tree life underscored critical impacts ecosystems.

Language: Английский

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Persistent functional and taxonomic groups dominate an 8,000-year sedimentary sequence from Lake Cadagno, Switzerland

Frontiers in Microbiology, Journal Year: 2025, Volume and Issue: 16

Published: Feb. 3, 2025

Most of our knowledge deep sedimentary life comes from marine environments; however, despite their relatively small volume, lacustrine sediments constitute one the largest global carbon sinks and are largely unexplored. Here, we reconstruct microbial functional taxonomic composition an 8,000-year Holocene succession meromictic Lake Cadagno (Switzerland) using shotgun metagenomics 16S rRNA gene amplicon sequencing. While younger (<1,000 years) dominated by typical anaerobic surface bacterial taxa ( Deltaproteobacteria, Acidobacteria , Firmicutes) older layers with lower organic matter concentrations reduced terminal electron acceptor availability previously identified as “persistent populations” within anoxic Candidatus Bathyarchaeia, Chloroflexi Atribacteria ). Despite these dramatic changes in community sediment geochemistry throughout core, higher-order categories metabolic marker abundances remain consistent indicate a capable fixation, fermentation, dissimilatory sulfate reduction nitrate to ammonium. As conservation pathways through compositions helps preserve pathway connectivity required for nutrient cycling, hypothesize that persistence groups enable communities persist amidst changing environmental conditions.

Language: Английский

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Oxidative adaptations in prokaryotes imply the oxygenic photosynthesis before the crown group Cyanobacteria

PNAS Nexus, Journal Year: 2025, Volume and Issue: 4(2)

Published: Feb. 1, 2025

Abstract The metabolic transition from anaerobic to aerobic in prokaryotes reflects adaptations oxidative stress. Methanogen, one of the earliest life forms on Earth, has evolved into three major groups within Euryarchaeota, exhibiting different phylogenetic affiliations and characters. In comparison with other strictly methanogenic groups, Class II methanogens possess a better capability adapt limited oxygen pressure. Cyanobacteria is considered first only prokaryote evolving oxygenic photosynthesis responsible for Great Oxidation Event Earth. However, connection between evolutionary stress remains elusive. Here, through gene encoding structural maintenance chromosomes (SMC) protein, which was horizontally transferred ancient last common ancestor crown-group Cyanobacteria, we demonstrate that origin extant undoubtedly posterior occurrence oxygen-tolerant methanogens. addition, found certain prokaryotic lineages had tolerance mechanisms against before Cyanobacteria. contradiction predating implies existence more biological oxygenesis. We propose these potential organisms might represent extinct phototrophs emerge during Paleoarchean, contributing tree facilitating dispersal reaction centers across bacterial domain.

Language: Английский

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