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

Clustered Regularly Interspaced Short Palindromic Repeat/CRISPR-Associated Protein and Its Utility All at Sea: Status, Challenges, and Prospects DOI Creative Commons
Jiashun Li,

Shuaishuai Wu,

Kaidian Zhang

et al.

Microorganisms, Journal Year: 2024, Volume and Issue: 12(1), P. 118 - 118

Published: Jan. 6, 2024

Initially discovered over 35 years ago in the bacterium Escherichia coli as a defense system against invasion of viral (or other exogenous) DNA into genome, CRISPR/Cas has ushered new era functional genetics and served versatile genetic tool all branches life science. revolutionized methodology gene knockout with simplicity rapidity, but it is also powerful for knock-in modification. In field marine biology ecology, this been instrumental characterization ‘dark’ genes documentation differentiation paralogs. Powerful is, challenges exist that have hindered advances some important lineages. This review examines status applications research assesses prospect quickly expanding deployment to address myriad fundamental biological oceanography questions.

Language: Английский

Citations

10
Hiding in plain sight: The discovery of complete genomes of 11 hypothetical spindle‐shaped viruses that putatively infect mesophilic ammonia‐oxidizing archaea DOI Creative Commons
Yimin Ni, Tianqi Xu, Shuling Yan

et al.

Environmental Microbiology Reports, Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 23, 2024

Abstract The genome of a putative Nitrosopumilaceae virus with hypothetical spindle‐shaped particle morphology was identified in the Yangshan Harbour metavirome from East China Sea through protein similarity comparison and structure analysis. This discovery accompanied by set 10 geographically dispersed close relatives found environmental datasets typical locations ammonia‐oxidizing archaeon distribution. Its host prediction supported iPHoP sequence similarity. predicted major capsid protein, together overall N ‐glycosylation site, transmembrane helices prediction, hydrophilicity profile, docking simulation proteins, indicate that these viruses resemble viruses. It suggests similarly assembled and, consequently, possibly newly discovered archaeal

Language: Английский

Citations

5
Insights Into Phylogeny, Diversity and Functional Potential of Poseidoniales Viruses DOI Creative Commons
Apoorva Prabhu, Julian Zaugg, Cheong Xin Chan

et al.

Environmental Microbiology, Journal Year: 2025, Volume and Issue: 27(1)

Published: Jan. 1, 2025

ABSTRACT Viruses infecting archaea play significant ecological roles in marine ecosystems through host infection and lysis, yet they have remained an underexplored component of the virosphere. In this study, we recovered 451 archaeal viruses from a subtropical estuary, identifying 63 that are associated with dominant order Poseidoniales (Marine Group II Archaea). Phylogenetic analyses subset complete nearly‐complete viral genomes assigned these to Magrovirales , lineage viruses, identified novel group distinct . Utilising demarcation criteria established for classification tailed propose two families within Magrovirales: Apasviridae (magrovirus A), comprising genera Agnivirus Savitrvirus, Krittikaviridae E) encompassing genus Velanvirus. Additionally, new order, named Adrikavirales, which includes Vyasavirus. Our detailed genomic characterisation lineages revealed genes involved assembly egress, such as those responsible creating holin rafts lyse cell membranes, feature predominantly known bacteriophages. Furthermore, broad spectrum auxiliary metabolic genes, suggesting can modulate metabolism. Collectively, our findings substantially enhance current understanding diversity functional potential viruses.

Language: Английский

Citations

0
Salinity as a key factor affects viral structure, function, and life strategies in lakes from arid and semi-arid regions DOI

Haojun Lei,

Nicolas Zhou, Jinhong Zhang

et al.

Journal of Hazardous Materials, Journal Year: 2025, Volume and Issue: unknown, P. 138075 - 138075

Published: March 1, 2025

Language: Английский

Citations

0
Marine Natural Products in Inflammation‐Related Diseases: Opportunities and Challenges DOI

Tao Zhang,

Zijun Ouyang,

Yueran Zhang

et al.

Medicinal Research Reviews, Journal Year: 2025, Volume and Issue: unknown

Published: April 9, 2025

ABSTRACT In recent decades, the potentiality of marine natural products (MNPs) in medical field has been increasingly recognized. Natural compounds derived from microorganisms, algae, and invertebrates have shown significant promise for treating inflammation‐related diseases. this review, we cover three primary sources MNPs their diverse unique chemical structures bioactivities. This review aims to summarize progress combating Moreover, functions mechanisms diseases, highlighting regulating inflammatory signaling pathways, cellular stress responses, gut microbiota, among others. Meanwhile, focus on key technologies scientific methods address current limitations challenges MNPs.

Language: Английский

Citations

0
Diversity of Bathyarchaeia viruses in metagenomes and virus-encoded CRISPR system components DOI Creative Commons
Changhai Duan, Yang Liu, Ying Liu

et al.

ISME Communications, Journal Year: 2024, Volume and Issue: 4(1)

Published: Jan. 1, 2024

Bathyarchaeia represent a class of archaea common and abundant in sedimentary ecosystems. 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 inhibit defenses. These findings present outline virome offer glimpse into their counter-defense mechanisms.

Language: Английский

Citations

3
Host range and cell recognition of archaeal viruses DOI Creative Commons
Emine Rabia Sensevdi, Zaloa Aguirre Sourrouille, Tessa E. F. Quax

et al.

Current Opinion in Microbiology, Journal Year: 2024, Volume and Issue: 77, P. 102423 - 102423

Published: Jan. 16, 2024

Archaea are members of a separate domain life that have unique properties, such as the composition their cell walls and structure lipid bilayers. Consequently, archaeal viruses face different challenges to infect host cells in comparison with bacteria eukaryotes. Despite significant impact on shaping microbial communities, our understanding infection processes remains limited. Several receptors used by recently been identified. The interactions between one determinants range viruses. Here, we review current literature ranges factors might width these ranges.

Language: Английский

Citations

2
Genomic Analysis and Taxonomic Characterization of Seven Bacteriophage Genomes Metagenomic-Assembled from the Dishui Lake DOI Creative Commons

H. Cai,

Yifan Zhou,

Xiefei Li

et al.

Viruses, Journal Year: 2023, Volume and Issue: 15(10), P. 2038 - 2038

Published: Sept. 30, 2023

Viruses in aquatic ecosystems exhibit remarkable abundance and diversity. However, scattered studies have been conducted to mine uncultured viruses identify them taxonomically lake water. Here, whole genomes (29–173 kbp) of seven dsDNA bacteriophages were discovered Dishui Lake, the largest artificial Shanghai. We analyzed their genomic signatures found a series viral auxiliary metabolic genes closely associated with protein synthesis host metabolism. Lake phages shared more uncultivated environmental than reference based on gene-sharing network classification. Phylogeny proteomes comparative genomics delineated three new genera within two known families Kyanoviridae Autographiviridae, four Caudoviricetes for these novel phages. Their potential hosts appeared be from dominant bacterial phyla Lake. Altogether, our study provides initial insights into composition diversity bacteriophage communities contributing valuable knowledge ongoing research roles played by freshwater ecosystems.

Language: Английский

Citations

4
Forty-nine metagenomic-assembled genomes from an aquatic virome expand Caudoviricetes by 45 potential new families and the newly uncovered Gossevirus of Bamfordvirae DOI
Yimin Ni, Ting Chu, Shuling Yan

et al.

Journal of General Virology, Journal Year: 2024, Volume and Issue: 105(3)

Published: March 6, 2024

Twenty complete genomes (29–63 kb) and 29 with an estimated completeness of over 90 % (30–90 were identified for novel dsDNA viruses in the Yangshan Harbor metavirome. These newly discovered contribute to expansion viral taxonomy by introducing 46 potential new families. Except one virus, all others belong class Caudoviricetes . The exception is a member recently characterized group known as Gossevirus. Fifteen predicted be temperate. hosts appear involved various aspects nitrogen cycle, including fixation, oxidation denitrification. Two have host Flavobacterium Tepidimonas fonticaldi , respectively, matching CRISPR spacers protospacers. Our findings provide overview characterizing identifying specific from Harbor. Gossevirus-like virus uncovered emphasizes need further comprehensive isolation investigation polinton-like viruses.

Language: Английский

Citations

1
Diversity, distribution, and functional potentials of magroviruses from marine and brackish waters DOI Creative Commons

Bu Xu,

Lu Fan, Wenxiu Wang

et al.

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

Published: April 21, 2023

Marine group II (MGII) archaea (Ca. Poseidoniales) are among the most abundant microbes in global oceanic surface waters and play an important role driving marine biogeochemical cycles. Magroviruses - viruses of MGII have been recently found to occur ubiquitously ocean. However, their diversity, distribution, potential ecological functions coastal zones especially brackish unknown. Here we obtained 234 non-redundant magroviral genomes from by using homology searches for viral signature proteins highlighting uncovered vast diversity this novel group. Phylogenetic analysis based on these magroviruses along with previously reported ones identified six taxonomic groups close evolutionary connection both haloviruses Group I archaea. were present abundantly open ocean samples some showing habitat specification others having broad spectrums distribution between different habitats. Genome annotation suggests they may be involved regulating multiple metabolic pathways Our results uncover overlooked potentials a major archaeal virial shed light cryptic history viruses.

Language: Английский

Citations

3