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

Biogeography, Assembly Patterns, Driving Factors, and Interactions of Archaeal Community in Mangrove Sediments DOI
Zhifeng Zhang, Jie Pan,

Yue-Ping Pan

et al.

mSystems, Journal Year: 2021, Volume and Issue: 6(3)

Published: June 15, 2021

Archaea are a major part of Earth's life. They believed to play important roles in nutrient biogeochemical cycling the mangrove. However, only few studies on archaeal community mangroves have been reported. In particular, assembly processes and interaction patterns that impact communities not investigated date. Here, biogeography, patterns, driving factors seven representative across southeastern China were systematically analyzed. The analysis revealed is more diverse surface sediments than subsurface sediments, at low latitudes high latitudes, with

Language: Английский

Citations

45
Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota lineages DOI Creative Commons
Jiarui Sun, Paul N. Evans, Emma J. Gagen

et al.

ISME Communications, Journal Year: 2021, Volume and Issue: 1(1)

Published: June 28, 2021

Abstract Asgardarchaeota have been proposed as the closest living relatives to eukaryotes, and a total of 72 metagenome-assembled genomes (MAGs) representing six primary lineages in this archaeal phylum thus far described. These organisms are predicted be fermentative heterotrophs contributing carbon cycling sediment ecosystems. Here, we double genomic catalogue by obtaining 71 MAGs from range habitats around globe, including deep subsurface, brackish shallow lakes, geothermal spring sediments. Phylogenomic inferences followed taxonomic rank normalisation confirmed previously established classes revealed four additional lineages, two which were consistently recovered monophyletic classes. We therefore propose names Candidatus Sifarchaeia class nov. Ca. Jordarchaeia nov., derived gods Sif Jord Norse mythology. Metabolic inference suggests that both represent hetero-organotrophic acetogens, also ability utilise methyl groups such methylated amines, with acetate probable end product remnants methanogen-derived core metabolism. This inferred mode energy conservation is enhanced genetic code expansions, i.e., stop codon recoding, allowing incorporation rare 21st 22nd amino acids selenocysteine (Sec) pyrrolysine (Pyl). found Sec recoding all other classes, likely benefit increased catalytic activities Sec-containing enzymes. Pyl on hand, restricted Asgardarchaeota, making it first reported non-methanogenic lineage an complete machinery, providing members efficient mechanism for methylamine utilisation. Furthermore, identified enzymes biosynthesis ester-type lipids, characteristic bacteria newly described supporting hypothesis mixed ether-ester lipids shared feature among Asgardarchaeota.

Language: Английский

Citations

42
High-Level Diversity of Basal Fungal Lineages and the Control of Fungal Community Assembly by Stochastic Processes in Mangrove Sediments DOI
Zhifeng Zhang,

Yue-Ping Pan,

Yue Liu

et al.

Applied and Environmental Microbiology, Journal Year: 2021, Volume and Issue: 87(17)

Published: June 30, 2021

As key components of microbial community in mangroves, fungi have important ecological functions. However, the fungal mangroves on a large scale is generally elusive, and are declining rapidly due to climate change anthropogenic activities.

Language: Английский

Citations

41
Three families of Asgard archaeal viruses identified in metagenome-assembled genomes DOI
Sofia Medvedeva, Jiarui Sun, Natalya Yutin

et al.

Nature Microbiology, Journal Year: 2022, Volume and Issue: 7(7), P. 962 - 973

Published: June 27, 2022

Language: Английский

Citations

38
Microbial degradation of various types of dissolved organic matter in aquatic ecosystems and its influencing factors DOI
Meilian Chen, Jin Hur,

Ji‐Dong Gu

et al.

Science China Earth Sciences, Journal Year: 2023, Volume and Issue: 66(2), P. 169 - 189

Published: Jan. 4, 2023

Language: Английский

Citations

21
The symbiotic origin of the eukaryotic cell DOI Creative Commons
Purificación López-Garcı́a, David Moreira

Comptes Rendus Biologies, Journal Year: 2023, Volume and Issue: 346(G1), P. 55 - 73

Published: May 30, 2023

Eukaryogenesis represented a major evolutionary transition that led to the emergence of complex cells from simpler ancestors. For several decades, most accepted scenario involved evolution an independent lineage proto-eukaryotes endowed with endomembrane system, including nuclear compartment, developed cytoskeleton and phagocytosis, which engulfed alphaproteobacterial ancestor mitochondria. However, recent discovery by metagenomic cultural approaches Asgard archaea, harbour many genes in common eukaryotes are their closest relatives phylogenomic trees, rather supports scenarios based on symbiosis one Asgard-like archaeon or more bacteria at origin eukaryotic cell. Here, we review discoveries this conceptual shift, briefly evoking current models eukaryogenesis challenges ahead discriminate between them establish detailed, plausible accounts for traits those prokaryotic ancestors.L’eucaryogenèse représente une évolutive majeure qui conduit à l’émergence de cellules complexes partir d’ancêtres plus simples. Pendant plusieurs décennies, le scénario accepté impliquait l’évolution d’une lignée indépendante proto-eucaryotes dotée d’un système endomembranaire, comprenant un compartiment nucléaire, cytosquelette développé et la phagocytose, aurait permis d’incorporer l’ancêtre alphaprotéobactérien des mitochondries. Cependant, découverte récente par approches métagénomiques culturales archées Asgard, partagent nombreux gènes avec les eucaryotes sont leurs proches parents dans arbres phylogénomiques, soutient plutôt scénarios basés sur symbiose archée type ou bactéries l’origine cellule eucaryote. Nous passons ici en revue découvertes récentes ont ce changement conceptuel, évoquant brièvement modèles actuels d’eucaryogenèse, défis pour discriminer entre ces derniers établir détaillé rende compte ceux ancêtres procaryotes.

Citations

18
Potential for mercury methylation by Asgard archaea in mangrove sediments DOI Open Access
Cui‐Jing Zhang, Yu‐Rong Liu, Guihong Cha

et al.

The ISME Journal, Journal Year: 2023, Volume and Issue: 17(3), P. 478 - 485

Published: Jan. 13, 2023

Language: Английский

Citations

17
Candidatus List. Lists of names of prokaryotic Candidatus phyla DOI Open Access
Aharon Oren, Markus Göker

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Journal Year: 2023, Volume and Issue: 73(5)

Published: May 9, 2023

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher we support invest in the microbiology community, to benefit of everyone. This supports our principal goal develop, expand strengthen networks available members so that they can generate new knowledge about microbes ensure it is shared with other communities.

Language: Английский

Citations

17
Asgard archaea modulate potential methanogenesis substrates in wetland soil DOI Creative Commons
Luis E. Valentin-Alvarado, Kathryn E. Appler, Valerie De Anda

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: July 31, 2024

Abstract The roles of Asgard archaea in eukaryogenesis and marine biogeochemical cycles are well studied, yet their contributions soil ecosystems remain unknown. Of particular interest archaeal to methane cycling wetland soils. To investigate this, we reconstructed two complete genomes for soil-associated Atabeyarchaeia, a new lineage, genome Freyarchaeia, predicted metabolism situ. Metatranscriptomics reveals expression genes [NiFe]-hydrogenases, pyruvate oxidation carbon fixation via the Wood-Ljungdahl pathway. Also expressed encoding enzymes amino acid metabolism, anaerobic aldehyde oxidation, hydrogen peroxide detoxification carbohydrate breakdown acetate formate. Overall, include non-methanogenic acetogens, highlighting potential role terrestrial environments.

Language: Английский

Citations

6
Insights into the evolution of regulated actin dynamics via characterization of primitive gelsolin/cofilin proteins from Asgard archaea DOI Creative Commons
Caner Akıl, Linh T. Tran, Magali Orhant‐Prioux

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2020, Volume and Issue: 117(33), P. 19904 - 19913

Published: Aug. 3, 2020

Asgard archaea genomes contain potential eukaryotic-like genes that provide intriguing insight for the evolution of eukaryotes. The eukaryotic actin polymerization/depolymerization cycle is critical providing force and structure in many processes, including membrane remodeling. In general, encode two classes actin-regulating proteins from sequence analysis, profilins gelsolins. were demonstrated to regulate filament nucleation. Here, we identify severing, capping, annealing bundling, monomer sequestration activities by gelsolin Thorarchaeota (Thor), which complete a depolymerization cycle, indicate complex cytoskeleton regulation organisms. Thor gelsolins have homologs other comprise one or copies prototypical domain. This appears be record an initial preeukaryotic gene duplication event, since are generally three six domains. X-ray structures these with mammalian revealed similar interactions first domain human cofilin actin. two-domain, but not one-domain, calcium-binding sites, manifested calcium-controlled activities. Expression two-domain cells enhanced disassembly on ionomycin-triggered calcium release. functional demonstration, at cellular level, provides evidence cytoskeleton, indicating calcium-regulated predates eukaryotes, dynamic bundled filaments responsible shaping filopodia microvilli. By correlation, hypothesize formation protrusions observed Lokiarchaeota cell bodies may involve gelsolin-regulated structures.

Language: Английский

Citations

49