Microbiology Spectrum, Год журнала: 2024, Номер unknown
Опубликована: Ноя. 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:
Язык: Английский
Nature Communications, Год журнала: 2024, Номер 15(1)
Опубликована: Сен. 27, 2024
Язык: Английский
Процитировано
10
The ISME Journal, Год журнала: 2024, Номер 18(1)
Опубликована: Янв. 1, 2024
The microbiomes in macroalgal holobionts play vital roles regulating growth and ocean carbon cycling. However, the virospheres remain largely underexplored, representing a critical knowledge gap. Here we unveil that holobiont of kelp (Saccharina japonica) harbors highly specific unique epiphytic/endophytic viral species, with novelty (99.7% unknown) surpassing even extreme marine habitats (e.g. deep-sea hadal zones), indicating virospheres, despite being closest to us, are among least understood. These viruses potentially maintain microbiome equilibrium for health via lytic-lysogenic infections expression folate biosynthesis genes. In-situ mesocosm cultivation metagenomic mining revealed profoundly reshaped surrounding seawater sediment virus-prokaryote pairings through changing environmental conditions virus-host migrations. Some epiphytic could infect autochthonous bacteria after deposition. Moreover, presence ample auxiliary metabolic genes polysaccharide laminarin) degradation underscores underappreciated influence on This study provides key insights into understanding previously overlooked ecological significance within macroalgae-prokaryotes-virus tripartite relationship.
Язык: Английский
Процитировано
6
Virus Evolution, Год журнала: 2024, Номер 10(1)
Опубликована: Янв. 1, 2024
Abstract The transition between lytic and lysogenic life cycles is the most important feature of life-history temperate viruses. To explain this transition, an optimal model offered based a discrete-time formulation phage/bacteria population dynamics that features infection bacteria by Poisson sampling virions from environment. time step viral latency period. In model, density-dependent absorption onto bacterial surface produces virus/bacteria coexistence density dependence in growth not needed. formula for phases termed ‘fitness switch’. According to virus switches when its grows faster as prophage than produced lysis infected cells, conversely switch lytic. A benefits bacterium it infects automatically incurs lower fitness upon exiting genome, resulting becoming locked into genome what here ‘prophage lock’. qualitatively predicts ecogeographic rule environmental enrichment leads microbialization with concomitant increase lysogeny, fluctuating conditions promote virus-mediated horizontal gene transfer, prophage-containing can integrate microbiome eukaryotic host forming functionally integrated tripartite holobiont. These predictions accord more ‘Piggyback-the-Winner’ hypothesis ‘Kill-the-Winner’ ecology.
Язык: Английский
Процитировано
4
LWT, Год журнала: 2025, Номер unknown, С. 117334 - 117334
Опубликована: Янв. 1, 2025
Язык: Английский
Процитировано
0
Environmental Microbiome, Год журнала: 2025, Номер 20(1)
Опубликована: Янв. 13, 2025
Abstract Background Viruses that infect prokaryotes (phages) constitute the most abundant group of biological agents, playing pivotal roles in microbial systems. They are known to impact community dynamics, ecology, and evolution. Efforts document diversity, host range, infection effects bacteriophage on cell metabolism extremely underexplored. Phages classified as virulent or temperate based their life cycles. Temperate phages adopt lysogenic mode infection, where genome integrates into forming a prophage. Prophages enable viral replication without lysis, often contribute novel beneficial traits genome. Current phage research predominantly focuses lytic phages, leaving significant gap knowledge regarding prophages, including biology, ecological roles. Results Here we develop describe Prophage-DB, database proteins, associated metadata will serve resource for genomics ecology. To create database, identified characterized prophages from genomes three largest publicly available databases. We applied several state-of-the-art tools our pipeline annotate these viruses, cluster them, taxonomically classify detect respective auxiliary metabolic genes. In total, identify characterize over 350,000 35,000 Our prophage is highly representative statistical results contains diverse set archaeal bacterial hosts which show wide environmental distribution. Conclusion Given particularly overlooked merit increased attention due vital implications microbiomes hosts, created Prophage-DB advance understanding through comprehensive characterization genomes. propose valuable advancing research, offering insights taxonomy, relationships, genes,
Язык: Английский
Процитировано
0
Water Research, Год журнала: 2025, Номер 274, С. 123140 - 123140
Опубликована: Янв. 13, 2025
Язык: Английский
Процитировано
0
Science Bulletin, Год журнала: 2025, Номер unknown
Опубликована: Март 1, 2025
Язык: Английский
Процитировано
0
ISME Communications, Год журнала: 2024, Номер 4(1)
Опубликована: Янв. 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.
Язык: Английский
Процитировано
3
Microbiology Spectrum, Год журнала: 2024, Номер 12(7)
Опубликована: Июнь 11, 2024
The diversity of birds in most parts the world is very high, and thus, they may carry different types highly differentiated unknown viruses. Thanks to advanced sequencing technologies, studies on bird-associated viruses have increased over past few years. In this study, a large-scale viral metagenomics survey was performed cloacal swabs 2,990 from nine provinces Chinese mainland. To detect undescribed RNA birds, more than 1,800 sequences sharing relatively low (<60%) amino acid sequence identity with best match GenBank database were screened. Potentially novel related vertebrates been identified, several potential recombination signals found. Additionally, hundreds plants, fungi, insects detected, including previously Furthermore, we investigated novelty, functionality, classification phages examined study. These occupied topological positions evolutionary trees certain extent might form putative families, genera, or species, thus providing information fill phylogenetic gaps findings provided new insights into viruses, but interactions among these remain require further investigation.IMPORTANCEStudying mammals crucial due their impact human health global ecosystem. Many such as influenza coronaviruses, shown cross species barrier cause zoonotic diseases. study involving at least 82 identified distant relationships known some which are rare birds. highlights scope data predict disease risks monitor threats wildlife, livestock, health. This can aid development strategies for prevention control.
Язык: Английский
Процитировано
2
bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown
Опубликована: Июль 16, 2024
Viruses that infect prokaryotes (phages) constitute the most abundant group of biological agents, playing pivotal roles in microbial systems. They are known to impact community dynamics, ecology, and evolution. Efforts document diversity, host range, infection effects bacteriophage on cell metabolism extremely underexplored. Phages classified as virulent or temperate based their life cycles. Temperate phages adopt lysogenic mode infection, where genome integrates into forming a prophage. Prophages enable viral replication without lysis, often contribute novel beneficial traits genome. Current phage research predominantly focuses lytic phages, leaving significant gap knowledge regarding prophages, including biology, ecological roles.
Язык: Английский
Процитировано
1