Virioplankton assemblages from challenger deep, the deepest place in the oceans

Gao, Chen; Liang, Yantao; Jiang, Yong; Páez-Espino, David; Han, Meiaoxue; Gu, Chengxiang; Wang, Meiwen; Yang, Yumei; Liu, Fengjiao; Yang, Qiaoqiao; Gong, Zheng; Zhang, Xinran; Luo, Zhixiang; He, Hui; Guo, Cui; Shao, Hongbing; Zhou, Chun; Shi, Yang; Yu, Xin; Xing, Jinyan; Tang, Xuexi; Qin, Qi‐Long; Zhang, Yuzhong; He, Jianfeng; Jiao, Nianzhi; McMinn, Andrew; Tian, Jie; Suttle, Curtis A.; Wang, Min

doi:10.1016/j.isci.2022.104680

Cited by 18 publications

(15 citation statements)

References 124 publications

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“…The relative abundance of the Autographiviridae roseophages was estimated using a viromic read-mapping analysis. A total of 220 marine viromic datasets, including Global Ocean Viromes 2.0[ 13 ], Pearl River estuary virome [ 57 ], Mariana Trench virome [ 58 ], Eastern Tropical North Pacific virome [ 59 ], Delaware Bay and Chesapeake Bay viromes [ 60 ], Black Sea virome [ 61 ], Red Sea virome [ 62 ] and South China Sea DNA virome [ 63 ], were used for viromic read-mapping analysis.…”

Section: Methodsmentioning

confidence: 99%

Genome sequences of the first Autographiviridae phages infecting marine Roseobacter

Du,

Wu,

Ying

et al. 2024

Microbial Genomics

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The ubiquitous and abundant marine phages play critical roles in shaping the composition and function of bacterial communities, impacting biogeochemical cycling in marine ecosystems. Autographiviridae is among the most abundant and ubiquitous phage families in the ocean. However, studies on the diversity and ecology of Autographiviridae phages in marine environments are restricted to isolates that infect SAR11 bacteria and cyanobacteria. In this study, ten new roseophages that infect marine Roseobacter strains were isolated from coastal waters. These new roseophages have a genome size ranging from 38 917 to 42 634 bp and G+C content of 44.6–50 %. Comparative genomics showed that they are similar to known Autographiviridae phages regarding gene content and architecture, thus representing the first Autographiviridae roseophages. Phylogenomic analysis based on concatenated conserved genes showed that the ten roseophages form three distinct subgroups within the Autographiviridae, and sequence analysis revealed that they belong to eight new genera. Finally, viromic read-mapping showed that these new Autographiviridae phages are widely distributed in global oceans, mostly inhabiting polar and estuarine locations. This study has expanded the current understanding of the genomic diversity, evolution and ecology of Autographiviridae phages and roseophages. We suggest that Autographiviridae phages play important roles in the mortality and community structure of roseobacters, and have broad ecological applications.

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Section: Methodsmentioning

confidence: 99%

Genome sequences of the first Autographiviridae phages infecting marine Roseobacter

Du,

Wu,

Ying

et al. 2024

Microbial Genomics

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“…A total of 258 marine virome datasets were used for metagenomic read-mapping to assess the relative abundance of phages, including Global Ocean Viromes (v2.0; Gregory et al, 2019 ), Pearl River estuary virome ( Xu et al, 2022 ), Mariana Trench virome ( Gao et al, 2022 ), Eastern Tropical North Pacific virome ( Jurgensen et al, 2022 ), viromes of the Delaware Bay and Chesapeake Bay ( Sun et al, 2021 ), Black Sea virome ( Jaiani et al, 2020 ), Red Sea virome ( Hevroni et al, 2020 ), South China Sea DNA virome ( Liang et al, 2019 ), Pacific Ocean Virome ( Hurwitz and Sullivan, 2013 ), Scripps Pier Virome ( Hurwitz et al, 2013 ), and India Ocean Virome ( Williamson et al, 2012 ; listed in Supplementary Table 3 ). Duplicate sequences of the 24 MVGs were removed using CD-HIT v4.8.1 (-c 0.95 -aS 0.8), and the longest sequences of each species cluster were retained for read-mapping analysis.…”

Section: Methodsmentioning

confidence: 99%

Genomic analysis and characterization of phages infecting the marine Roseobacter CHAB-I-5 lineage reveal a globally distributed and abundant phage genus

Zhang

et al. 2023

Front. Microbiol.

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Marine phages play an important role in marine biogeochemical cycles by regulating the death, physiological metabolism, and evolutionary trajectory of bacteria. The Roseobacter group is an abundant and important heterotrophic bacterial group in the ocean, and plays an important role in carbon, nitrogen, sulfur and phosphorus cycling. The CHAB-I-5 lineage is one of the most dominant Roseobacter lineages, but remains largely uncultured. Phages infecting CHAB-I-5 bacteria have not yet been investigated due to the lack of culturable CHAB-I-5 strains. In this study, we isolated and sequenced two new phages (CRP-901 and CRP-902) infecting the CHAB-I-5 strain FZCC0083. We applied metagenomic data mining, comparative genomics, phylogenetic analysis, and metagenomic read-mapping to investigate the diversity, evolution, taxonomy, and biogeography of the phage group represented by the two phages. The two phages are highly similar, with an average nucleotide identity of 89.17%, and sharing 77% of their open reading frames. We identified several genes involved in DNA replication and metabolism, virion structure, DNA packing, and host lysis from their genomes. Metagenomic mining identified 24 metagenomic viral genomes closely related to CRP-901 and CRP-902. Genomic comparison and phylogenetic analysis demonstrated that these phages are distinct from other known viruses, representing a novel genus-level phage group (CRP-901-type). The CRP-901-type phages do not contain DNA primase and DNA polymerase genes, but possess a novel bifunctional DNA primase-polymerase gene with both primase and polymerase activities. Read-mapping analysis showed that the CRP-901-type phages are widespread across the world’s oceans and are most abundant in estuarine and polar waters. Their abundance is generally higher than other known roseophages and even higher than most pelagiphages in the polar region. In summary, this study has greatly expanded our understanding of the genetic diversity, evolution, and distribution of roseophages. Our analysis suggests that the CRP-901-type phage is an important and novel marine phage group that plays important roles in the physiology and ecology of roseobacters.

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“…These bacteria and archaea, which are chemolithoautotrophic, use sulfur, nitrate, and heavy metals as energy sources [8,[18][19][20] and may even have developed morphological adaptions to the seamount environment [21]. Notably, viruses have been demonstrated to manipulate the mortality of microorganisms, releasing labile organic matter, and expressing vAMGs that can rewire host metabolism [6,8,22]. However, the community composition, diversity and ecological roles of viral assemblages inhabiting seamount sediments are still unknown.…”

Section: Introductionmentioning

confidence: 99%

Diversity and ecological potentials of viral assemblages from the seamount sediments of the Northwest Pacific Ocean

Chen,

Gao,

Liu

et al. 2024

Preprint

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Viruses are the most abundant life forms in the sea, influencing the community structure and metabolism of host cells as well as biogeochemical cycles. However, the diversity and ecological roles of viruses within seamount ecosystems, natural microbiota havens characterized by high biodiversity, remain unknown. Here, the first seamount viral genome (SMVG) dataset, based on a metagenomic analysis of twelve seamount sediment samples collected from the seamount regions of the Northwest Pacific Ocean, is established. A total of 78,069 viral operational taxonomic units (vOTUs) were found, spanning 18 viral classes and 63 viral families. The detection of sixteen viral auxiliary metabolic genes (vAMGs) suggests that viruses may participate in both the complex metabolic dynamics associated with sediment microbial communities and also biogeochemical cycles, including carbon, sulfur, metal, heme, and cobalamin cycling. vAMGs involved in the metabolism of heme, cobalamin and metals, in particular, are more often detected in seamount sediments than in trenches, cool seeps, and hydrothermal vents. This investigation of the viral communities in these seamount sediments provides new insights into the high diversity and ecological potential of the viruses and establishes a foundation for the future study of benthic viruses from deep-sea seamounts.

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Virioplankton assemblages from challenger deep, the deepest place in the oceans

Cited by 18 publications

References 124 publications

Genome sequences of the first Autographiviridae phages infecting marine Roseobacter

Genome sequences of the first Autographiviridae phages infecting marine Roseobacter

Genomic analysis and characterization of phages infecting the marine Roseobacter CHAB-I-5 lineage reveal a globally distributed and abundant phage genus

Diversity and ecological potentials of viral assemblages from the seamount sediments of the Northwest Pacific Ocean

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