Viruses in deep-sea cold seep sediments harbor diverse survival mechanisms and remain genetically conserved within species

Peng, Yongyi; Zhang, Lu; Pan, Donald; Shi, Ling-Dong; Zhao, Zhao; Liu, Qing; Zhang, Chuwen; Li, Jiwei; Hubert, Casey R.J.; Dong, Xiyang

doi:10.1101/2023.03.12.532262

Cited by 4 publications

(4 citation statements)

References 97 publications

(154 reference statements)

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“…The geNomad v1.3.3 pipeline [72] was used for the taxonomic assignment of the vOTUs following the taxonomy contained in ICTV's VMR number 19 [73]. Representative viral genomes from each vOTU were clustered into VCs using vConTACT2 v0.11.3 [74] with parameters: '-pcs-mode MCL -vcs-mode ClusterONE -rel-mode Diamond -db ProkaryoticViralRefSeq85-ICTV'.…”

Section: Viral Taxonomic Assignment and Clusteringmentioning

confidence: 99%

Spatial heterogeneity of viral communities across the gastrointestinal tracts of ruminants

Zhang,

Li,

Peng

et al. 2024

Preprint

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Background: The gastrointestinal tract (GIT) microbiome of ruminants significantly influences their nutrition metabolism and health. Current understanding is extensive for bacterial and archaeal communities, but limited for viral communities within the GIT. Results: We created the Ruminant Gastrointestinal Virome Catalogue (RGVC), which includes 43,981 non-redundant viral Operational Taxonomic Units (vOTUs), with 89.3% newly identified, derived from 370 samples across 10 GIT regions in seven ruminant species. The composition of viral communities is mainly influenced by the GIT regions rather than by the ruminant species. We identified 4,603 putative prokaryotic hosts across 31 bacterial and three archaeal classes for 5,954 viruses, along with significant variations across GIT regions and a strong correlation between hosts and their associated viruses. Lysogeny, constituting 45.6% of survival strategies, was more prevalent than the lytic cycle (4.08%), and the abundances of these viruses varied regionally. The lysogenic viruses encoded 1,805 auxiliary metabolic genes (AMGs) that play key roles in carbohydrates, amino acids, and other metabolisms in their hosts. The variation in AMG abundance across regions highlights the distinct viral communities and the varied virus-host interactions within the GIT. Conclusion: This study offers a comprehensive view of the spatial heterogeneity of viral communities in the ruminant GIT and indicates that this diversity is driven by the interaction of lysogenic viruses with their prokaryotic hosts through AMGs. These findings set the stage for future research into the ecological and nutritional impacts of the ruminant virome, with the potential to uncover novel roles and mechanisms in various GIT regions.

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Section: Viral Taxonomic Assignment and Clusteringmentioning

confidence: 99%

Spatial heterogeneity of viral communities across the gastrointestinal tracts of ruminants

Zhang,

Li,

Peng

et al. 2024

Preprint

Self Cite

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“…The remaining vOTUs were assigned based on their completeness as assessed by CheckV. Viral genomes with completeness were labeled as 'Lytic', while others were considered 'Unknown' [73].…”

Section: Phylogenetic and Functional Analysis Of Host Magsmentioning

confidence: 99%

Spatial heterogeneity of viral communities across the gastrointestinal tracts of ruminants

Wang

2024

Preprint

View full text Add to dashboard Cite

The gastrointestinal tract (GIT) microbiome of ruminants significantly influences their nutrition metabolism and health. Current understanding is extensive for bacterial and archaeal communities, but limited for viral communities within the GIT. To address this, we created the Ruminant Gastrointestinal Virome Catalogue (RGVC), which includes 43,981 non-redundant viral Operational Taxonomic Units (vOTUs), with 89.3% newly identified, derived from 370 samples across 10 GIT regions in seven ruminant species. The composition of viral communities is mainly influenced by the GIT regions rather than by the ruminant species. We identified 4,603 putative prokaryotic hosts across 31 bacterial and three archaeal classes for 5,954 viruses, along with significant variations across GIT regions and a strong correlation between hosts and their associated viruses. Lysogeny, constituting 45.6% of survival strategies, was more prevalent than the lytic cycle (4.08%), and the abundances of these viruses varied regionally. The lysogenic viruses encoded 1,805 auxiliary metabolic genes (AMGs) that play key roles in carbohydrates, amino acids, and other metabolisms in their hosts. The variation in AMG abundance across regions highlights the distinct viral communities and the varied virus-host interactions within the GIT. Overall, this study offers a comprehensive view of the spatial heterogeneity of viral communities in the ruminant GIT and indicates that this diversity is driven by the interaction of lysogenic viruses with their prokaryotic hosts through AMGs. These findings set the stage for future research into the ecological and nutritional impacts of the ruminant virome, with the potential to uncover novel roles and mechanisms in various GIT regions.

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“…Because of the dynamic processes of seepages and chemosynthetic transformations, cold seeps are hotspots of biomass and diversity in the deep sea (4), harboring compositionally and functionally unique microbial communities (5,6). Nevertheless, extensive competition for resources and space in these sediments exerts strong eco-evolutionary pressures (7)(8)(9). Thus, microbes use a plethora of strategies to adapt to these unique environments.…”

Section: Introductionmentioning

confidence: 99%

A vast repertoire of secondary metabolites potentially influences community dynamics and biogeochemical processes in cold seeps

Dong,

Zhang,

et al. 2024

Sci. Adv.

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In deep-sea cold seeps, microbial communities thrive on the geological seepage of hydrocarbons and inorganic compounds, differing from photosynthetically driven ecosystems. However, their biosynthetic capabilities remain largely unexplored. Here, we analyzed 81 metagenomes, 33 metatranscriptomes, and 7 metabolomes derived from nine different cold seep areas to investigate their secondary metabolites. Cold seep microbiomes encode diverse and abundant biosynthetic gene clusters (BGCs). Most BGCs are affiliated with understudied bacteria and archaea, including key mediators of methane and sulfur cycling. The BGCs encode diverse antimicrobial compounds that potentially shape community dynamics and various metabolites predicted to influence biogeochemical cycling. BGCs from key players are widely distributed and highly expressed, with their abundance and expression levels varying with sediment depth. Sediment metabolomics reveals unique natural products, highlighting uncharted chemical potential and confirming BGC activity in these sediments. Overall, these results demonstrate that cold seep sediments serve as a reservoir of hidden natural products and sheds light on microbial adaptation in chemosynthetically driven ecosystems.

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Viruses in deep-sea cold seep sediments harbor diverse survival mechanisms and remain genetically conserved within species

Cited by 4 publications

References 97 publications

Spatial heterogeneity of viral communities across the gastrointestinal tracts of ruminants

Spatial heterogeneity of viral communities across the gastrointestinal tracts of ruminants

Spatial heterogeneity of viral communities across the gastrointestinal tracts of ruminants

A vast repertoire of secondary metabolites potentially influences community dynamics and biogeochemical processes in cold seeps

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