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学者姓名：张泽风
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Abstract ：
Marine viral communities harbor an astounding diversity of phages infecting diverse marine bacteria. The double-stranded DNA phage family Autographiviridae is among the most abundant phage families in the ocean. However, the current understanding of marine Autographiviridae phages is predominantly derived from isolates infecting cyanobacteria, SAR11, and Roseobacter. To achieve a more comprehensive understanding of the diversity, ecological traits, and functional profiles of this phage family, we recovered 1253 complete marine Autographiviridae uncultivated viral genomes (UViGs). Comparative genomic analysis showed that marine-derived Autographiviridae phages display genome synteny and share a conserved core of seven genes. The core gene-based phylogenomic analysis classified them into 14 groups, 6 of which were previously undescribed. These groups varied in G + C content, genome size, and presence of specific genes. Metagenomic recruitment analysis demonstrated that Autographiviridae phages are globally distributed and enriched in the upper ocean layers of tropical and temperate zones. The differential distribution patterns among these groups mirror the ecological niches of their potential hosts, emphasizing the top-down control these phages exert on their host populations. Collectively, our study substantially expands knowledge regarding the diversity, potential hosts, functional capacity, and ecological distribution of Autographiviridae phages in the ocean, emphasizing their ecological implications in marine environments.
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| GB/T 7714 | Du, Sen , Wu, Zuqing , Wu, Ying et al. Marine Autographiviridae phages exhibit high genetic diversity and global-scale biogeographic patterns [J]. | COMMUNICATIONS BIOLOGY , 2025 , 8 (1) . |
| MLA | Du, Sen et al. "Marine Autographiviridae phages exhibit high genetic diversity and global-scale biogeographic patterns" . | COMMUNICATIONS BIOLOGY 8 . 1 (2025) . |
| APA | Du, Sen , Wu, Zuqing , Wu, Ying , Yang, Mingyu , Deng, Chunmei , Zhang, Yahui et al. Marine Autographiviridae phages exhibit high genetic diversity and global-scale biogeographic patterns . | COMMUNICATIONS BIOLOGY , 2025 , 8 (1) . |
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Roseobacters are prevalent in marine environments and play a crucial role in global carbon and sulphur cycles. Although many roseophages that infect roseobacters have been characterized, those infecting members of the ecologically dominant pelagic Roseobacter cluster (PRC) remain largely unexplored due to the challenges of culturing these organisms. In this study, we isolated 7 phylogenetically related roseophages from 3 PRC lineages and retrieved 279 uncultured viral genomes (UViGs) related to these roseophages from marine environmental viral databases. Comparative genomic and phylogenetic analyses revealed that these roseophages and their related UViGs form a novel family- level phage group (designated the CRP- 822- type group) comprising at least five subgroups. These subgroups display distinct genomic features in terms of G+C content, amino acid usage and codon usage, suggesting host- range specialization. Host prediction suggests that subgroup V with low G+C content may infect the SAR86 clade, while the high G+C subgroup IV likely infects the high G+C KI89A clade. Finally, viromic read- mapping analyses revealed that CRP- 822- type phages are widely distributed across the global ocean and are adapted to diverse marine environments. All members of subgroup IV were more abundant in trade, westerlies and coastal regions with high temperatures. The other four subgroups exhibited more divergent biogeographic patterns, with some members more abundant in trade and westerlies ocean regions, whereas others dominated in polar or estuarine regions. Collectively, this study elucidates the genetic diversity and ecology of a previously unrecognized marine phage group that infects PRC roseobacters and other important marine bacteria.
Keyword ：
CHUG CHUG ecological distribution ecological distribution genome sequence genome sequence Roseobacter phage Roseobacter phage
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| GB/T 7714 | Wu, Zuqing , Wu, Ying , Deng, Chunmei et al. Novel roseophages provide insights into a genetically and ecologically diverse phage family [J]. | MICROBIAL GENOMICS , 2025 , 11 (11) . |
| MLA | Wu, Zuqing et al. "Novel roseophages provide insights into a genetically and ecologically diverse phage family" . | MICROBIAL GENOMICS 11 . 11 (2025) . |
| APA | Wu, Zuqing , Wu, Ying , Deng, Chunmei , Xiao, Hang , Wang, Sige , Ye, Songlin et al. Novel roseophages provide insights into a genetically and ecologically diverse phage family . | MICROBIAL GENOMICS , 2025 , 11 (11) . |
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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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| GB/T 7714 | Du, Sen , Wu, Ying , Ying, Hanqi et al. Genome sequences of the first Autographiviridae phages infecting marine Roseobacter [J]. | MICROBIAL GENOMICS , 2024 , 10 (4) . |
| MLA | Du, Sen et al. "Genome sequences of the first Autographiviridae phages infecting marine Roseobacter" . | MICROBIAL GENOMICS 10 . 4 (2024) . |
| APA | Du, Sen , Wu, Ying , Ying, Hanqi , Wu, Zuqing , Yang, Mingyu , Chen, Feng et al. Genome sequences of the first Autographiviridae phages infecting marine Roseobacter . | MICROBIAL GENOMICS , 2024 , 10 (4) . |
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Bacteriophages play an essential role in shaping the diversity and metabolism of bacterial communities. Marine Roseobacter group is an abundant heterotrophic bacterial group that is involved in many major element cycles, especially carbon and sulfur. Members of the Roseobacter CHUG (Clade Hidden and Underappreciated Globally) lineage are globally distributed and are activated in pelagic marine environments. In this study, we isolated and characterized a phage, CRP-810, that infects the CHUG strain FZCC0198. The genome of CRP-810 was dissimilar to those of other known phages. Additionally, 251 uncultured viral genomes (UViGs) closely related to CRP-810 were obtained from the uncultivated marine viral contig databases. Comparative genomic and phylogenetic analyses revealed that CRP-810 and these related UViGs exhibited conserved genome synteny, representing a new phage family with at least eight subgroups. Most of the CRP-810-type phages contain an integrase gene, and CRP-810 can be integrated into the host genome. Further analysis revealed that three CRP-810-type members were prophages found in the genomes of marine SAR11, Poseidonocella, and Sphingomonadaceae. Finally, viromic read-mapping analysis showed that CRP-810-type phages were globally distributed and displayed distinct biogeographic patterns related to temperature and latitude. Many members with a lower G + C content were mainly distributed in the trade station, whereas members with a higher G + C content were mainly distributed in polar and westerlies station, indicating that the niche differentiation of phages was subject to host adaptation. Collectively, these findings identify a novel phage family and expand our understanding of phylogenetic diversity, evolution, and biogeography of marine phages.
Keyword ：
CHUG lineage CHUG lineage CHUG phages CHUG phages ecological distribution ecological distribution genome sequence genome sequence Roseobacter Roseobacter
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| GB/T 7714 | Wu, Zuqing , Guo, Luyuan , Wu, Ying et al. Novel phage infecting the Roseobacter CHUG lineage reveals a diverse and globally distributed phage family [J]. | MSPHERE , 2024 , 9 (7) . |
| MLA | Wu, Zuqing et al. "Novel phage infecting the Roseobacter CHUG lineage reveals a diverse and globally distributed phage family" . | MSPHERE 9 . 7 (2024) . |
| APA | Wu, Zuqing , Guo, Luyuan , Wu, Ying , Yang, Mingyu , Du, Sen , Shao, Jiabing et al. Novel phage infecting the Roseobacter CHUG lineage reveals a diverse and globally distributed phage family . | MSPHERE , 2024 , 9 (7) . |
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Small single-stranded DNA phages of the Microviridae family are diverse and prevalent in oceans. Our understanding of Microviridae phages that infect the ecologically important marine Roseobacter is currently limited, comprising few isolates. Here, we report six roseophages that infect Roseobacter RCA strains. Genomic and phylogenetic analyses revealed that they were new members of the previously identified subfamily Occultatumvirinae. Additionally, 232 marine uncultivated virus genomes (UViGs) affiliated to Occultatumvirinae were obtained from environmental genome datasets. Phylogenomic analysis revealed that marine Occultatumvirinae phages could be further grouped into 11 subgroups. Moreover, meta-omics based read-mapping analysis showed that Occultatumvirinae phages were globally distributed, with two low G + C subgroups showing the most prevalent distribution. Furthermore, one phage in subgroup 2 was found to be extremely ubiquitous. Overall, this study expands our understanding of the diversity and ecology of the Occultatumvirinae microviruses in the ocean and highlights their ecological impacts. Six roseophages that infect Roseobacter RCA are described as new Occultatumvirinae, to which further 232 marine uncultivated virus genomes obtained from environmental genome datasets could be assigned; these are globally distributed in 11 subgroups.
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| GB/T 7714 | Wu, Ying , Wu, Zuqing , Guo, Luyuan et al. Diversity and distribution of a prevalent Microviridae group across the global oceans [J]. | COMMUNICATIONS BIOLOGY , 2024 , 7 (1) . |
| MLA | Wu, Ying et al. "Diversity and distribution of a prevalent Microviridae group across the global oceans" . | COMMUNICATIONS BIOLOGY 7 . 1 (2024) . |
| APA | Wu, Ying , Wu, Zuqing , Guo, Luyuan , Shao, Jiabing , Xiao, Hang , Yang, Mingyu et al. Diversity and distribution of a prevalent Microviridae group across the global oceans . | COMMUNICATIONS BIOLOGY , 2024 , 7 (1) . |
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The marine methylotrophic OM43 clade is considered an important bacterial group in coastal microbial communities. OM43 bacteria, which are closely related to phytoplankton blooms, have small cell sizes and streamlined genomes. Bacteriophages profoundly shape the evolutionary trajectories, population dynamics, and physiology of microbes. The prevalence and diversity of several phages that infect OM43 bacteria have been reported. In this study, we isolated and sequenced two novel OM43 phages, MEP401 and MEP402. These phages share 90% of their open reading frames (ORFs) and are distinct from other known phage isolates. Furthermore, a total of 99 metagenomic viral genomes (MVGs) closely related to MEP401 and MEP402 were identified. Phylogenomic analyses suggest that MEP401, MEP402, and these identified MVGs belong to a novel subfamily in the family Zobellviridae and that they can be separated into two groups. Group I MVGs show conserved whole-genome synteny with MEP401, while group II MVGs possess the MEP401-type DNA replication module and a distinct type of morphogenesis and packaging module, suggesting that genomic recombination occurred between phages. Most members in these two groups were predicted to infect OM43 bacteria. Metagenomic read-mapping analysis revealed that the phages in these two groups are globally ubiquitous and display distinct biogeographic distributions, with some phages being predominant in cold regions, some exclusively detected in estuarine stations, and others displaying wider distributions. This study expands our knowledge of the diversity and ecology of a novel phage lineage that infects OM43 bacteria by describing their genomic diversity and global distribution patterns. IMPORTANCEOM43 phages that infect marine OM43 bacteria are important for host mortality, community structure, and physiological functions. In this study, two OM43 phages were isolated and characterized. Metagenomic viral genome (MVG) retrieval using these two OM43 phages as baits led to the identification of two phage groups of a new subfamily in the family Zobellviridae. We found that group I MVGs share similar genomic content and arrangement with MEP401 and MEP402, whereas group II MVGs only possess the MEP401-type DNA replication module. Metagenomic mapping analysis suggests that members in these two groups are globally ubiquitous with distinct distribution patterns. This study provides important insights into the genomic diversity and biogeography of the OM43 phages in the global ocean. OM43 phages that infect marine OM43 bacteria are important for host mortality, community structure, and physiological functions. In this study, two OM43 phages were isolated and characterized. Metagenomic viral genome (MVG) retrieval using these two OM43 phages as baits led to the identification of two phage groups of a new subfamily in the family Zobellviridae. We found that group I MVGs share similar genomic content and arrangement with MEP401 and MEP402, whereas group II MVGs only possess the MEP401-type DNA replication module. Metagenomic mapping analysis suggests that members in these two groups are globally ubiquitous with distinct distribution patterns. This study provides important insights into the genomic diversity and biogeography of the OM43 phages in the global ocean.
Keyword ：
comparative genomics comparative genomics novel phage groups novel phage groups OM43 clade OM43 clade OM43 phages OM43 phages
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| GB/T 7714 | Yang, Mingyu , Du, Sen , Zhang, Zefeng et al. Genomic diversity and biogeographic distributions of a novel lineage of bacteriophages that infect marine OM43 bacteria [J]. | MICROBIOLOGY SPECTRUM , 2023 , 11 (5) . |
| MLA | Yang, Mingyu et al. "Genomic diversity and biogeographic distributions of a novel lineage of bacteriophages that infect marine OM43 bacteria" . | MICROBIOLOGY SPECTRUM 11 . 5 (2023) . |
| APA | Yang, Mingyu , Du, Sen , Zhang, Zefeng , Xia, Qian , Liu, He , Qin, Fang et al. Genomic diversity and biogeographic distributions of a novel lineage of bacteriophages that infect marine OM43 bacteria . | MICROBIOLOGY SPECTRUM , 2023 , 11 (5) . |
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Viruses play critical roles in influencing biogeochemical cycles and adjusting host mortality, population structure, physiology, and evolution in the ocean. Marine viral communities are composed of numerous genetically distinct subfamily/genus-level viral groups. Among currently identified viral groups, the HMO-2011-type group is known to be dominant and broadly distributed. However, only four HMO-2011-type cultivated representatives that infect marine SAR116 and Roseobacter strains have been reported to date, and the genetic diversity, potential hosts, and ecology of this group remain poorly elucidated. Here, we present the genomes of seven HMO-2011-type phages that were isolated using four Roseobacter strains and one SAR11 strain, as well as additional 207 HMO-2011-type metagenomic viral genomes (MVGs) identified from various marine viromes. Phylogenomic and shared-gene analyses revealed that the HMO-2011-type group is a subfamily-level group comprising at least 10 discernible genus-level subgroups. Moreover, >2000 HMO-2011-type DNA polymerase sequences were identified, and the DNA polymerase phylogeny also revealed that the HMO-2011-type group contains diverse subgroups and is globally distributed. Metagenomic read-mapping results further showed that most HMO-2011-type phages are prevalent in global oceans and display distinct geographic distributions, with the distribution of most HMO-2011-type phages being associated with temperature. Lastly, we found that members in subgroup IX, represented by pelagiphage HTVC033P, were among the most abundant HMO-2011-type phages, which implies that SAR11 bacteria are crucial hosts for this viral group. In summary, our findings substantially expand current knowledge regarding the phylogenetic diversity, evolution, and distribution of HMO-2011-type phages, highlighting HMO-2011-type phages as major ecological agents that can infect certain key bacterial groups.
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| GB/T 7714 | Qin, Fang , Du, Sen , Zhang, Zefeng et al. Newly identified HMO-2011-type phages reveal genomic diversity and biogeographic distributions of this marine viral group [J]. | ISME JOURNAL , 2022 , 16 (5) : 1363-1375 . |
| MLA | Qin, Fang et al. "Newly identified HMO-2011-type phages reveal genomic diversity and biogeographic distributions of this marine viral group" . | ISME JOURNAL 16 . 5 (2022) : 1363-1375 . |
| APA | Qin, Fang , Du, Sen , Zhang, Zefeng , Ying, Hanqi , Wu, Ying , Zhao, Guiyuan et al. Newly identified HMO-2011-type phages reveal genomic diversity and biogeographic distributions of this marine viral group . | ISME JOURNAL , 2022 , 16 (5) , 1363-1375 . |
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Viruses are the most abundant living entities in marine ecosystems, playing critical roles in altering the structure and function of microbial communities and driving ocean biogeochemistry. Phages that infect Roseobacter clade-affiliated (RCA) cluster strains are an important component of marine viral communities. Here, we characterize the genome sequences of two new RCA phages, CRP-9 and CRP-13, which infect RCA strain FZCC0023. Genomic analysis reveals that CRP-9 and CRP-13 represent a novel evolutionary lineage of marine phages. They both have a DNA replication module most similar to those in Cobavirus group phages. In contrast, their morphogenesis and packaging modules are distinct from those in cobaviruses but homologous to those in HMO-2011-type phages. The genomic architecture of CRP-9 and CRP-13 suggests a genomic recombination event between distinct phage groups. Metagenomic data sets were examined for metagenome-assembled viral genomes (MAVGs) with similar recombinant genome architectures. Fifteen CRP-9-type MAVGs were identified from marine viromes. Additionally, 158 MAVGs were identified containing HMO-2011-type morphogenesis and packaging modules with other types of DNA replication genes, providing more evidence that recombination between different phage groups is a major driver of phage evolution. Altogether, this study significantly expands the understanding of diversity and evolution of marine roseophages. Meanwhile, the analysis of these novel RCA phages and MAVGs highlights the critical role of recombination in shaping phage diversity. These phage sequences are valuable resources for inferring the evolutionary connection of distinct phage groups. IMPORTANCE Diversity and evolution of phages that infect the relatively slow-growing but dominant Roseobacter lineages are largely unknown. In this study, RCA phages CRP-9 and CRP-13 have been isolated on a Roseobacter RCA strain and shown to have a unique genomic architecture, which appears to be the result of a recombination event. CRP-9 and CRP-13 have a DNA replication module most similar to those in Cobavirus group phages and morphogenesis and packaging modules most similar to those in HMO-2011-type phages. HMO-2011-type morphogenesis and packaging modules are found in combination with distinct types of DNA replication genes, suggesting compatibility with various DNA replication modules. Altogether, this study contributes toward a better understanding of marine viral diversity and evolution.
Keyword ：
comparative genomics comparative genomics functional module functional module phage evolution phage evolution RCA phages RCA phages Roseobacter RCA lineage Roseobacter RCA lineage
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| GB/T 7714 | Zhai, Zhiqiang , Zhang, Zefeng , Zhao, Guiyuan et al. Genomic Characterization of Two Novel RCA Phages Reveals New Insights into the Diversity and Evolution of Marine Viruses [J]. | MICROBIOLOGY SPECTRUM , 2021 , 9 (2) . |
| MLA | Zhai, Zhiqiang et al. "Genomic Characterization of Two Novel RCA Phages Reveals New Insights into the Diversity and Evolution of Marine Viruses" . | MICROBIOLOGY SPECTRUM 9 . 2 (2021) . |
| APA | Zhai, Zhiqiang , Zhang, Zefeng , Zhao, Guiyuan , Liu, Xinxin , Qin, Fang , Zhao, Yanlin . Genomic Characterization of Two Novel RCA Phages Reveals New Insights into the Diversity and Evolution of Marine Viruses . | MICROBIOLOGY SPECTRUM , 2021 , 9 (2) . |
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SAR11 bacteria dominate ocean surface bacterioplankton communities, and play an important role in marine carbon and nutrient cycling. The biology and ecology of SAR11 are impacted by SAR11 phages (pelagiphages) that are highly diverse and abundant in the ocean. Among the currently known pelagiphages, HTVC010P represents an extremely abundant but under- studied phage group in the ocean. In this study, we have isolated seven new HTVC010P- type pelagiphages, and recovered 77 nearly full- length HTVC010P- type metagenomic viral genomes from marine metagenomes. Comparative genomic and phylogenomic analyses showed that HTVC010P- type pelagiphages display genome synteny and can be clustered into two major subgroups, with subgroup I consisting of strictly lytic phages and subgroup II mostly consisting of phages with potential lysogenic life cycles. All but one member of the subgroup II contain an integrase gene. Site- specific integration of subgroup II HTVC010P- type pelagiphage was either verified experimentally or identified by in silico genomic sequence analyses, which revealed that various SAR11 tRNA genes can serve as the integration sites of HTVC010P- type pelagiphages. Moreover, HTVC010P- type pelagiphage integration was confirmed by the detection of several Global Ocean Survey (GOS) fragments that contain hybrid phage-host integration sites. Metagenomic recruitment analysis revealed that these HTVC010P- type phages were globally distributed and most lytic subgroup I members exhibited higher relative abundance. Altogether, this study significantly expands our knowledge about the genetic diversity, life strategies and ecology of HTVC010P- type pelagiphages.
Keyword ：
distribution patterns distribution patterns genomic diversity genomic diversity life strategies life strategies metagenomic viral genomes metagenomic viral genomes pelagiphages pelagiphages SAR11 SAR11
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| GB/T 7714 | Du, Sen , Qin, Fang , Zhang, Zefeng et al. Genomic diversity, life strategies and ecology of marine HTVC010P-type pelagiphages [J]. | MICROBIAL GENOMICS , 2021 , 7 (7) . |
| MLA | Du, Sen et al. "Genomic diversity, life strategies and ecology of marine HTVC010P-type pelagiphages" . | MICROBIAL GENOMICS 7 . 7 (2021) . |
| APA | Du, Sen , Qin, Fang , Zhang, Zefeng , Tian, Zhen , Yang, Mingyu , Liu, Xinxin et al. Genomic diversity, life strategies and ecology of marine HTVC010P-type pelagiphages . | MICROBIAL GENOMICS , 2021 , 7 (7) . |
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Bacteriophages have a significant impact on the structure and function of marine microbial communities. Phages of some major bacterial lineages have recently been shown to dominate the marine viral communities. However, phages that infect many important bacterial clades still remained unexplored. Members of the marine OM43 clade are methylotrophs that play important roles in C1 metabolism. OM43 phages (phages that infect the OM43 bacteria) represent an understudied viral group with only one known isolate. In this study, we describe the genomic characterization and biogeography of an OM43 phage that infects the strain HTCC2181, designated MEP301. MEP301 has a genome size of 34,774 bp. We found that MEP301 is genetically distinct from other known phage isolates and only displays significant sequence similarity with some metagenomic viral genomes (MVGs). A total of 12 MEP301-type MVGs were identified from metagenomic datasets. Comparative genomic and phylogenetic analyses revealed that MEP301-type phages can be separated into two subgroups (subgroup I and subgroup II). We also performed a metagenomic recruitment analysis to determine the relative abundance of reads mapped to these MEP301-type phages, which suggested that subgroup I MEP301-type phages are present predominantly in the cold upper waters with lower salinity. Notably, subgroup II phages have an inverse different distribution pattern, implying that they may infect hosts from a distinct OM43 subcluster. Our study has expanded the knowledge about the genomic diversity of marine OM43 phages and identified a new phage group that is widespread in the ocean.
Keyword ：
distribution patterns distribution patterns genomics genomics metagenomic viral genomes metagenomic viral genomes OM43 OM43 OM43 phage OM43 phage
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| GB/T 7714 | Yang, Mingyu , Xia, Qian , Du, Sen et al. Genomic Characterization and Distribution Pattern of a Novel Marine OM43 Phage [J]. | FRONTIERS IN MICROBIOLOGY , 2021 , 12 . |
| MLA | Yang, Mingyu et al. "Genomic Characterization and Distribution Pattern of a Novel Marine OM43 Phage" . | FRONTIERS IN MICROBIOLOGY 12 (2021) . |
| APA | Yang, Mingyu , Xia, Qian , Du, Sen , Zhang, Zefeng , Qin, Fang , Zhao, Yanlin . Genomic Characterization and Distribution Pattern of a Novel Marine OM43 Phage . | FRONTIERS IN MICROBIOLOGY , 2021 , 12 . |
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