Extremophile deep-sea viral communities from hydrothermal vents: Structural and functional analysis

Castelán-Sánchez, Hugo G; López-Rosas, Itzel; García-Suástegui, Wendy Argelia; Peralta, Raúl; Dobson, Alan D. W.; Batista-García, Ramón Alberto; Dávila-Ramos, Sonia

doi:10.1016/j.margen.2019.03.001

Cited by 32 publications

(28 citation statements)

References 91 publications

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“…The results from the phylogenetic analysis using only one marker might not represent the acutal phylogenetic relationships among different viruses. In the future, the phylogenetic analysis using the whole viral genomes could provide more solid phylogenetic relationships among different viruses (Castelan-Sanchez et al, 2019).…”

Section: Resultsmentioning

confidence: 99%

Metagenomic Analysis of the Diversity of DNA Viruses in the Surface and Deep Sea of the South China Sea

Liang

Wang

et al. 2019

Front. Microbiol.

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A metagenomic analysis of the viral community from five surface and five deep sea water (>2000 m below the surface, mbs) samples collected from the central basin of the South China Sea and adjacent Northwest Pacific Ocean during July–August 2017 was conducted herein. We builded up a South China Sea DNA virome (SCSV) dataset of 29,967 viral Operational Taxonomic Units (vOTUs), which is comparable to the viral populations from the original Tara Ocean and Malaspina expeditions. The most abundant and widespread viral populations were from the uncultivated viruses annotated from the viral metagenomics. Only 74 and 37 vOTUs have similarity with the reported genomes from the cultivated viruses and the single-virus genomics, respectively. The community structures of deep sea viromes in the SCSV were generally different from the surface viromes. The carbon flux and nutrients (PO 4 and NOx) were related to the surface and deep sea viromes in the SCSV, respectively. In the SCSV, the annotated vOTUs could be affiliated to the cultivated viruses mainly including Pelagibacter (SAR11) phage HTVC010P, Prochlorococcus phages (P-GSP1, P-SSM4, and P-TIM68), Cyanophages (MED4-184 and MED4-117) and Mycobacterium phages (Sparky and Squirty). It indicated that phage infection to the SAR11 cluster may occur ubiquitously and has significant impacts on bathypelagic SAR11 communities in the deep sea. Meanwhile, as Prochlorococcus is prominently distributed in the euphotic ocean, the existence of their potential phages in the deep sea suggested the sedimentation mechanism might contribute to the formation of the deep sea viromes. Intriguingly, the presence of Mycobacterium phages only in the deep sea viromes, suggests inhabitance of endemic viral populations in the deep sea viromes in the SCSV. This study provided an insight of the viral community in the South China Sea and for the first time uncovered the deep sea viral diversity in the central basin of the South China Sea.

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Section: Resultsmentioning

confidence: 99%

Metagenomic Analysis of the Diversity of DNA Viruses in the Surface and Deep Sea of the South China Sea

Liang

Wang

et al. 2019

Front. Microbiol.

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“…Viruses are the most abundant entities in the biosphere and have the potential to infect all domains of life, producing diseases, influencing biogeochemical cycles, facilitating gene transfer, and affecting the course of microbial evolution. One important mechanism of viral impact on the diversity and function of microbial populations is through the incorporation of auxiliary metabolic genes (AMGs) [ 15 ], which may modulate cellular activity by expressing enzymes that participate in C, N, P and S metabolic pathways [ 16 , 17 , 18 , 19 ].…”

Section: Introductionmentioning

confidence: 99%

Virus and Potential Host Microbes from Viral-Enriched Metagenomic Characterization in the High-Altitude Wetland, Salar de Huasco, Chile

et al. 2020

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Salar de Huasco is a wetland in the Andes mountains, located 3800 m above sea level at the Chilean Altiplano. Here we present a study aimed at characterizing the viral fraction and the microbial communities through metagenomic analysis. Two ponds (H0 and H3) were examined in November 2015. Water samples were processed using tangential flow filtration to obtain metagenomes from which the DNA fraction of the sample was amplified and sequenced (HiSeq system, Illumina). The ponds were characterized by freshwater and the viral-like particles to picoplankton ratio was 12.1 and 2.3 for H0 and H3, respectively. A great number of unassigned viral sequences were found in H0 (55.8%) and H3 (32.8%), followed by the family Fuselloviridae 20.8% (H0) and other less relatively abundant groups such as Microviridae (H0, 11.7% and H3, 3.3%) and Inoviridae (H3, 2.7%). The dominant viral sequences in both metagenomes belong to the order Caudovirales, with Siphoviridae being the most important family, especially in H3 (32.7%). The most important bacteria phyla were Proteobacteria, Bacteroidetes and Firmicutes in both sites, followed by Cyanobacteria (H0). Genes encoding lysogenic and lytic enzymes (i.e., recombinases and integrases) were found in H0 and H3, indicating a potential for active viral replication at the time of sampling; this was supported by the presence of viral metabolic auxiliary genes at both sites (e.g., cysteine hydrolase). In total, our study indicates a great novelty of viral groups, differences in taxonomic diversity and replication pathways between sites, which contribute to a better understanding of how viruses balance the cycling of energy and matter in this extreme environment.

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“…13,17,43 . The BLASTp output was then imported into MEGAN v6.17.0 using the Lowest Common Ancestor (LCA) algorithm for taxonomic analysis44 .Abundance profiles RPKM (Reads per kilobase per million mapped reads) values were used to represent relative abundances of viruses and microorganisms.…”

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confidence: 99%

Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity

Li¹,

Pan

Wei

et al. 2020

Preprint

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In marine ecosystems, viruses exert control on the composition and metabolism of microbial communities, thus influencing overall biogeochemical cycling. Deep sea sediments associated with cold seeps are known to host taxonomically diverse microbial communities, but little is known about viruses infecting these microorganisms. Here, we probed metagenomes from seven geographically diverse cold seeps across global oceans, to assess viral diversity, virus-host interaction, and virus-encoded auxiliary metabolic genes (AMGs). Gene-sharing network comparisons with viruses inhabiting other ecosystems reveal that cold seep sediments harbour considerable unexplored viral diversity. Most cold seep viruses display high degrees of endemism with seep fluid flux being one of the main drivers of viral community composition. In silico predictions linked 14.2% of the viruses to microbial host populations, with many belonging to poorly understood candidate bacterial and archaeal phyla. Lysis was predicted to be a predominant viral lifestyle based on lineage-specific virus/host abundance ratios. Metabolic predictions of prokaryotic host genomes and viral AMGs suggest that viruses influence microbial hydrocarbon biodegradation at cold seeps, as well as other carbon, sulfur and nitrogen cycling via virus-induced mortality and/or metabolic augmentation. Overall, these findings reveal the global diversity and biogeography of cold seep viruses and indicate how viruses may manipulate seep microbial ecology and biogeochemistry.

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Extremophile deep-sea viral communities from hydrothermal vents: Structural and functional analysis

Cited by 32 publications

References 91 publications

Metagenomic Analysis of the Diversity of DNA Viruses in the Surface and Deep Sea of the South China Sea

Metagenomic Analysis of the Diversity of DNA Viruses in the Surface and Deep Sea of the South China Sea

Virus and Potential Host Microbes from Viral-Enriched Metagenomic Characterization in the High-Altitude Wetland, Salar de Huasco, Chile

Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity

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