Community, Distribution, and Ecological Roles of Estuarine Archaea DOI Creative Commons

Dayu Zou,

Hongbin Liu, Meng Li

et al.

Frontiers in Microbiology, Journal Year: 2020, Volume and Issue: 11

Published: Aug. 28, 2020

Archaea are diverse and ubiquitous prokaryotes present in both extreme moderate environments. Estuaries, serving as links between the land ocean, harbor numerous microbes that relatively highly active because of massive terrigenous input nutrients. account for a considerable portion estuarine microbial community. They play key roles biogeochemical cycles. Ammonia-oxidizing archaea (AOA) an abundant aquatic archaeal group estuaries, greatly contributing ammonia oxidation. Bathyarchaeota sediments, they may involve sedimentary organic matter degradation, acetogenesis, and, potentially, methane metabolism, based on genomics. Other groups also commonly detected estuaries worldwide. include Euryarchaeota, members DPANN Asgard archaea. Based biodiversity surveys 16S rRNA gene some functional genes, distribution abundance driven by physicochemical factors, such salinity oxygen concentration. Currently, increasing amount genomic information is becoming available advances sequencing technologies, especially AOA Bathyarchaeota, leading to better understanding their functions environmental adaptations. Here, we summarized current knowledge community composition major focusing Bathyarchaeota. We highlighted unique features potential adaptation strategies archaea, pointing out unknowns field scope future research.

Language: Английский

Expanded diversity of Asgard archaea and their relationships with eukaryotes DOI
Yang Liu, Kira S. Makarova, Wen-Cong Huang

et al.

Nature, Journal Year: 2021, Volume and Issue: 593(7860), P. 553 - 557

Published: April 28, 2021

Language: Английский

Citations

241
Ecological responses, adaptation and mechanisms of mangrove wetland ecosystem to global climate change and anthropogenic activities DOI
You‐Shao Wang,

Ji‐Dong Gu

International Biodeterioration & Biodegradation, Journal Year: 2021, Volume and Issue: 162, P. 105248 - 105248

Published: June 1, 2021

Language: Английский

Citations

179
Actin cytoskeleton and complex cell architecture in an Asgard archaeon DOI Creative Commons
Thiago Rodrigues-Oliveira, Florian Wollweber,

Rafael I. Ponce-Toledo

et al.

Nature, Journal Year: 2022, Volume and Issue: 613(7943), P. 332 - 339

Published: Dec. 21, 2022

Abstract Asgard archaea are considered to be the closest known relatives of eukaryotes. Their genomes contain hundreds eukaryotic signature proteins (ESPs), which inspired hypotheses on evolution cell 1–3 . A role ESPs in formation an elaborate cytoskeleton and complex cellular structures has been postulated 4–6 , but never visualized. Here we describe a highly enriched culture ‘ Candidatus Lokiarchaeum ossiferum’, member phylum, thrives anaerobically at 20 °C organic carbon sources. It divides every 7–14 days, reaches densities up 5 × 10 7 cells per ml significantly larger genome compared with single previously cultivated strain represent 5% its protein-coding genes, including four actin homologues. We imaged enrichment using cryo-electron tomography, identifying Ca L. ossiferum’ basis characteristic expansion segments their ribosomes. Cells exhibited coccoid bodies network branched protrusions frequent constrictions. The envelope consists membrane surface structures. long-range extends throughout bodies, twisted double-stranded architecture filaments is consistent F-actin. Immunostaining indicates that comprise Lokiactin—one most conserved archaea. propose actin-based predated emergence first eukaryotes was crucial feature phylum by scaffolding

Language: Английский

Citations

109
The Asgard archaeal origins of Arf family GTPases involved in eukaryotic organelle dynamics DOI
Romana Vargová,

Roxanne Chevreau,

Marine Alves

et al.

Nature Microbiology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 23, 2025

Language: Английский

Citations

2
Genomic and transcriptomic insights into methanogenesis potential of novel methanogens from mangrove sediments DOI Creative Commons
Cui‐Jing Zhang, Jie Pan, Yang Liu

et al.

Microbiome, Journal Year: 2020, Volume and Issue: 8(1)

Published: June 17, 2020

Methanogens are crucial to global methane budget and carbon cycling. from the phylum Euryarchaeota currently classified into one class seven orders, including two novel methanogen taxa, Methanofastidiosa Methanomassiliicoccales. The relative importance of methanogens production in natural environment is poorly understood.Here, we used a combined metagenomic metatranscriptomic approach investigate metabolic activity mangrove sediments Futian Nature Reserve, Shenzhen. We obtained 13 metagenome-assembled genomes (MAGs) representing (Methanofastidiosa) five orders (Methanomassiliicoccales, Methanomicrobiales, Methanobacteriales, Methanocellales, Methanosarcinales) methanogens, methanogens. Comprehensive annotation indicated presence an H2-dependent methylotrophic methanogenesis pathway Based on functional gene analysis, hydrogenotrophic dominant pathways sediments. MAG mapping revealed that Methanomicrobiales were most abundant Methanomassiliicoccales active analyzed sediment profile, suggesting their important roles production.Partial or near-complete Methanomassiliicoccales, environments recovered here for first time. presented findings highlight ecological complement knowledge how produced ecosystem. This study implies play vital role cycle. Video Abstract.

Language: Английский

Citations

93
Unique mobile elements and scalable gene flow at the prokaryote–eukaryote boundary revealed by circularized Asgard archaea genomes DOI Creative Commons
Fabai Wu, Daan R. Speth, Alon Philosof

et al.

Nature Microbiology, Journal Year: 2022, Volume and Issue: 7(2), P. 200 - 212

Published: Jan. 13, 2022

Eukaryotic genomes are known to have garnered innovations from both archaeal and bacterial domains but the sequence of events that led complex gene repertoire eukaryotes is largely unresolved. Here, through enrichment hydrothermal vent microorganisms, we recovered two circularized Heimdallarchaeum species belong an Asgard archaea clade phylogenetically closest eukaryotes. These reveal diverse mobile elements, including integrative viral genome bidirectionally replicates in a circular form aloposons, transposons encode 5,000 amino acid-sized proteins Otus Ephialtes. Heimdallaechaeal elements various genes bacteria bacteriophages, likely playing role shuffling functions across domains. The number archaea- bacteria-related follow strikingly different scaling laws archaea, exhibiting size-dependent ratio functional division resembling bacteria- archaea-derived Bacterial import has thus been continuous process unaltered by eukaryogenesis scaled up expansion. Our data further highlight importance viewing pan-Asgard context, which proposal conceptual framework, is, Heimdall nucleation-decentralized innovation-hierarchical model accounts for emergence eukaryotic complexity.

Language: Английский

Citations

54
Long-read assembled metagenomic approaches improve our understanding on metabolic potentials of microbial community in mangrove sediments DOI Creative Commons
Zhifeng Zhang,

Lirui Liu,

Yue-Ping Pan

et al.

Microbiome, Journal Year: 2023, Volume and Issue: 11(1)

Published: Aug. 23, 2023

Mangrove wetlands are coastal ecosystems with important ecological features and provide habitats for diverse microorganisms key roles in nutrient biogeochemical cycling. However, the overall metabolic potentials of microbial community mangrove sediment remained unanswered. In current study, profiles prokaryotic fungal communities sediments were investigated using metagenomic analysis based on PacBio single-molecule real time (SMRT) Illumina sequencing techniques.Comparing to short reads, incorporation long reads significantly contributed more contiguous assemblies, yielded than doubled high-quality metagenome-assembled genomes (MAGs), improved novelty MAGs. Further reconstruction recovered MAGs showed that prokaryotes potentially played an essential role carbon cycling sediment, displaying versatile potential degrading organic carbons, fermentation, autotrophy, fixation. fungi also functioned as a player cycling, involved degradation various carbohydrate peptide substrates. Notably, new candidate bacterial phylum named Candidatus Cosmopoliota ubiquitous distribution is proposed. Genomic revealed this capable utilizing types substrates, anaerobic fixation Wood-Ljungdahl (WL) pathway reverse tricarboxylic acid (rTCA) cycle.The study not only highlights advantages HiSeq-PacBio Hybrid assembly complete profiling environmental microbiomes but expands our understanding diversity distinct groups sediment. Video Abstract.

Language: Английский

Citations

23
Newly discovered Asgard archaea Hermodarchaeota potentially degrade alkanes and aromatics via alkyl/benzyl-succinate synthase and benzoyl-CoA pathway DOI Creative Commons
Jia-wei Zhang, Hongpo Dong, Lijun Hou

et al.

The ISME Journal, Journal Year: 2021, Volume and Issue: 15(6), P. 1826 - 1843

Published: Jan. 15, 2021

Asgard archaea are widely distributed in anaerobic environments. Previous studies revealed the potential capability of to utilize various organic substrates including proteins, carbohydrates, fatty acids, amino acids and hydrocarbons, suggesting that play an important role sediment carbon cycling. Here, we describe a previously unrecognized archaeal phylum, Hermodarchaeota, affiliated with superphylum. The genomes these were recovered from metagenomes generated mangrove sediments, found encode alkyl/benzyl-succinate synthases their activating enzymes similar those identified alkane-degrading sulfate-reducing bacteria. Hermodarchaeota also potentially involved alkyl-coenzyme A benzoyl-coenzyme oxidation, Wood-Ljungdahl pathway nitrate reduction. These results indicate members this phylum have strictly anaerobically degrade alkanes aromatic compounds, coupling reduction nitrate. By screening Sequence Read Archive, additional genes encoding 16S rRNA analogous metagenomic datasets wide range marine freshwater sediments. findings suggest capable degrading aromatics via formation alkyl/benzyl-substituted succinates ubiquitous

Language: Английский

Citations

53
Mythical origins of the actin cytoskeleton DOI Creative Commons
Caner Akıl, Yoshihito Kitaoku, Linh T. Tran

et al.

Current Opinion in Cell Biology, Journal Year: 2020, Volume and Issue: 68, P. 55 - 63

Published: Oct. 10, 2020

Language: Английский

Citations

51
Expanding Archaeal Diversity and Phylogeny: Past, Present, and Future DOI Open Access

Guillaume Tahon,

Patricia Geesink, Thijs J. G. Ettema

et al.

Annual Review of Microbiology, Journal Year: 2021, Volume and Issue: 75(1), P. 359 - 381

Published: Aug. 5, 2021

The discovery of the Archaea is a major scientific hallmark twentieth century. Since then, important features their cell biology, physiology, ecology, and diversity have been revealed. Over course some 40 years, known archaea has expanded from 2 to about 30 phyla comprising over 20,000 species. Most this archaeal revealed by environmental 16S rRNA gene amplicon sequencing surveys using broad range universal targeted primers. Of few primers that target large fraction diversity, all display bias against recently discovered lineages, which limits studies aiming survey overall diversity. Induced genomic exploration improved phylogenomics approaches, taxonomic classification frequently revised. Due computational limitations continued new stable phylogeny not yet within reach. Obtaining phylogenetic consensus should be high priority for research community.

Language: Английский

Citations

50