Diversity of Bathyarchaeia viruses in metagenomes and virus-encoded CRISPR system components DOI Creative Commons
Changhai Duan, Yang Liu, Ying Liu

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Aug. 24, 2023

Abstract Bathyarchaeia represent a class of archaea common and abundant in sedimentary ecosystems. The virome so far has not been characterized. Here we report 56 metagenome-assembled genomes viruses identified metagenomes from different environments. Gene sharing network phylogenomic analyses led to the proposal four virus families, including realms Duplodnaviria Adnaviria , archaea-specific spindle-shaped viruses. Genomic uncovered diverse CRISPR elements these Viruses proposed family ‘ Fuxiviridae ’ harbor an atypical type IV-B CRISPR-Cas system Cas4 protein that might interfere with host immunity. Chiyouviridae encode Cas2-like endonuclease two mini-CRISPR arrays, one repeat identical array, potentially allowing recruit adaptation machinery acquire spacers could contribute competition other mobile genetic or inhibition defenses. These findings present outline offer glimpse into their counter-defense mechanisms.

Language: Английский

ICTV Virus Taxonomy Profile: Aoguangviridae 2023 DOI
Yifan Zhou, Yongjie Wang, Mart Krupovìč

et al.

Journal of General Virology, Journal Year: 2023, Volume and Issue: 104(11)

Published: Nov. 27, 2023

The family Aoguangviridae includes dsDNA viruses that have been associated with marine archaea. Currently, members of this virus are known through metagenomics. Virions predicted to consist an icosahedral capsid and a helical tail, characteristic in the class Caudoviricetes . Aoguangviruses some largest genomes among archaeal possess most components DNA replication machinery as well auxiliary functions. species Aobingvirus yangshanense Many unclassified relatives group, referred ‘magroviruses’, discovered by metagenomics globally distributed samples. This is summary International Committee on Taxonomy Viruses (ICTV) Report , which available at ictv.global/report/aoguangviridae

Language: Английский

Citations

2
New groups of highly divergent proteins in families as old as cellular life with important biological functions in the ocean DOI Creative Commons
Duncan Sussfeld, Romain Lannes, Eduardo Corel

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 8, 2024

Abstract Background Metagenomics has considerably broadened our knowledge of microbial diversity, unravelling fascinating adaptations and characterising multiple novel major taxonomic groups, e.g. CPR bacteria, DPANN Asgard archaea, viruses. Such findings profoundly reshaped the structure known tree life emphasised central role investigating uncultured organisms. However, despite significant progresses, a large portion proteins predicted from metagenomes remain today unannotated, both taxonomically functionally, across many biomes in particular oceanic waters, including at relatively lenient clustering thresholds. Results Here, we used an iterative, network-based approach for remote homology detection, to probe dataset 40 million ORFs marine environments. We assessed environmental diversity 53 gene families as old cellular life, broadly distributed Tree Life. About half them harboured clusters homologues that diverged significantly published complete genomes, with representatives all oceans. In particular, report detection clades new structural variants essential genes (SMC), divergent polymerase subunits forming deep-branching tree, variant DNA recombinases unknown origin ultra-small size fraction. Conclusions These results indicate may yet be unravelled even strongly conserved families. Protein sequence similarity network approaches, appear well-suited highlight potential sources biological novelty make better sense dark matter taxonomical scales.

Language: Английский

Citations

0
Metagenomic characterization of viruses and mobile genetic elements associated with the DPANN archaeal superphylum DOI
Zongzhi Wu, Shufeng Liu, Jinren Ni

et al.

Nature Microbiology, Journal Year: 2024, Volume and Issue: 9(12), P. 3362 - 3375

Published: Oct. 24, 2024

Language: Английский

Citations

0
Discovery and characterization of complete genomes of 38 head-tailed proviruses in four predominant phyla of archaea DOI Creative Commons
Tianqi Xu, Yimin Ni, Hailing Li

et al.

Microbiology Spectrum, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 15, 2024

Archaea play a significant role in natural ecosystems and the human body. Archaeal viruses exert considerable influence on structure composition of archaeal communities their associated ecological environments. The present study revealed complete genomes 38 head-tailed proviruses through comprehensive data mining. hosts these were identified as belonging to following four dominant phyla:

Language: Английский

Citations

0
Diverse viruses infect nitrifying archaea and bacteria communities in soil DOI Open Access
Sungeun Lee, Christina Hazard, Graeme W. Nicol

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Dec. 2, 2023

Abstract Soil virus communities are diverse and dynamic but contributions to specific processes, such as nitrification, largely uncharacterised. Chemolithoautotrophic nitrifiers perform this essential component of the nitrogen cycle established model groups for linking phylogeny, evolution ecophysiology due limited taxonomic functional diversity. Ammonia-oxidising bacteria (AOB) dominate first step ammonia oxidation at high supply rates, with ammonia-oxidising archaea (AOA) complete Nitrospira (comammox) often active lower rates or when AOB inactive, nitrite-oxidising (NOB) completing canonical nitrification. Here, diversity genome content dsDNA viruses infecting different nitrifier were characterised after in situ enrichment via differential host inhibition, a selective approach that alleviates competition non-inhibited populations determine relative activity. Microcosms incubated urea stimulate nitrification amended 1-octyne 3,4-dimethylpyrazole phosphate (AOB inhibited), acetylene (all oxidisers no inhibitor stimulated), virus-targeted metagenomes using databases genomes, reference (pro)viruses hallmark genes. Increases abundance consistent predicted inhibition profiles concomitant increases their viruses, represented by 200 viral operational units. These included 61 high-quality/complete genomes 35-173 kb length possessing minimal similarity validated families. Most AOA placed within unique lineage viromes enriched multicopper oxidase findings demonstrate focussed incubation studies facilitate characterisation host-virus interactions associated processes.

Language: Английский

Citations

1
Exploring the Archaeal Virosphere by Metagenomics DOI
Yifan Zhou, Yongjie Wang, David Prangishvili

et al.

Methods in molecular biology, Journal Year: 2023, Volume and Issue: unknown, P. 1 - 22

Published: Dec. 7, 2023

Language: Английский

Citations

1
Diversity of Bathyarchaeia viruses in metagenomes and virus-encoded CRISPR system components DOI Creative Commons
Changhai Duan, Yang Liu, Ying Liu

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Aug. 24, 2023

Abstract Bathyarchaeia represent a class of archaea common and abundant in sedimentary ecosystems. The virome so far has not been characterized. Here we report 56 metagenome-assembled genomes viruses identified metagenomes from different environments. Gene sharing network phylogenomic analyses led to the proposal four virus families, including realms Duplodnaviria Adnaviria , archaea-specific spindle-shaped viruses. Genomic uncovered diverse CRISPR elements these Viruses proposed family ‘ Fuxiviridae ’ harbor an atypical type IV-B CRISPR-Cas system Cas4 protein that might interfere with host immunity. Chiyouviridae encode Cas2-like endonuclease two mini-CRISPR arrays, one repeat identical array, potentially allowing recruit adaptation machinery acquire spacers could contribute competition other mobile genetic or inhibition defenses. These findings present outline offer glimpse into their counter-defense mechanisms.

Language: Английский

Citations

0