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学者姓名：赵艳琳
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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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The CHAB-I-5 cluster is a pelagic lineage that can comprise a significant proportion of all Roseobacters in surface oceans and has predicted roles in biogeochemical cycling via heterotrophy, aerobic anoxygenic photosynthesis (AAnP), CO oxidation, DMSP degradation, and other metabolisms. Though cultures of CHAB-I-5 have been reported, none have been explored and the best-known representative, strain SB2, was lost from culture after obtaining the genome sequence. We have isolated two new CHAB-I-5 representatives, strains US3C007 and FZCC0083, and assembled complete, circularized genomes with 98.7% and 92.5% average nucleotide identities with the SB2 genome. Comparison of these three with 49 other unique CHAB-I-5 metagenome-assembled and single-cell genomes indicated that the cluster represents a genus with two species, and we identified subtle differences in genomic content between the two species subclusters. Metagenomic recruitment from over fourteen hundred samples expanded their known global distribution and highlighted both isolated strains as representative members of the clade. FZCC0083 grew over twice as fast as US3C007 and over a wider range of temperatures. The axenic culture of US3C007 occurs as pleomorphic cells with most exhibiting a coccobacillus/vibrioid shape. We propose the name Candidatus Thalassovivens spotae, gen nov., sp. nov. for the type strain US3C007T (= ATCC TSD-433T = NCMA B160T).
Keyword ：
bacterioplankton bacterioplankton CHAB-I-5 CHAB-I-5 culturing culturing marine microbiology marine microbiology pangenomics pangenomics Roseobacter Roseobacter type strains type strains
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| GB/T 7714 | Lanclos, Victoria Celeste , Feng, Xiaoyuan , Cheng, Chuankai et al. New isolates refine the ecophysiology of the Roseobacter CHAB-I-5 lineage [J]. | ISME COMMUNICATIONS , 2025 , 5 (1) . |
| MLA | Lanclos, Victoria Celeste et al. "New isolates refine the ecophysiology of the Roseobacter CHAB-I-5 lineage" . | ISME COMMUNICATIONS 5 . 1 (2025) . |
| APA | Lanclos, Victoria Celeste , Feng, Xiaoyuan , Cheng, Chuankai , Yang, Mingyu , Hider, Cole J. , Coelho, Jordan T. et al. New isolates refine the ecophysiology of the Roseobacter CHAB-I-5 lineage . | ISME COMMUNICATIONS , 2025 , 5 (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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Phages play an essential role in controlling bacterial populations. Those infecting Pelagibacterales (SAR11), the dominant bacteria in surface oceans, have been studied in silico and by cultivation attempts. However, little is known about the quantity of phage-infected cells in the environment. Using fluorescence in situ hybridization techniques, we here show pelagiphage-infected SAR11 cells across multiple global ecosystems and present evidence for tight community control of pelagiphages on the SAR11 hosts in a case study. Up to 19% of SAR11 cells were phage-infected during a phytoplankton bloom, coinciding with a similar to 90% reduction in SAR11 cell abundance within 5 days. Frequently, a fraction of the infected SAR11 cells were devoid of detectable ribosomes, which appear to be a yet undescribed possible stage during pelagiphage infection. We dubbed such cells zombies and propose, among other possible explanations, a mechanism in which ribosomal RNA is used as a resource for the synthesis of new phage genomes. On a global scale, we detected phage-infected SAR11 and zombie cells in the Atlantic, Pacific, and Southern Oceans. Our findings illuminate the important impact of pelagiphages on SAR11 populations and unveil the presence of ribosome-deprived zombie cells as part of the infection cycle.
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| GB/T 7714 | Bruewer, Jan D. , Sidhu, Chandni , Zhao, Yanlin et al. Globally occurring pelagiphage infections create ribosome-deprived cells [J]. | NATURE COMMUNICATIONS , 2024 , 15 (1) . |
| MLA | Bruewer, Jan D. et al. "Globally occurring pelagiphage infections create ribosome-deprived cells" . | NATURE COMMUNICATIONS 15 . 1 (2024) . |
| APA | Bruewer, Jan D. , Sidhu, Chandni , Zhao, Yanlin , Eich, Andreas , Roessler, Leonard , Orellana, Luis H. et al. Globally occurring pelagiphage infections create ribosome-deprived cells . | NATURE COMMUNICATIONS , 2024 , 15 (1) . |
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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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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.
Keyword ：
biogeography biogeography CHAB-I-5 CHAB-I-5 genomics genomics metagenomic viral genomes metagenomic viral genomes novel phage genus novel phage genus phylogenetic analysis phylogenetic analysis roseophage roseophage
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| GB/T 7714 | Zhang, Zefeng , Wu, Zuqing , Liu, He et al. Genomic analysis and characterization of phages infecting the marine Roseobacter CHAB-I-5 lineage reveal a globally distributed and abundant phage genus [J]. | FRONTIERS IN MICROBIOLOGY , 2023 , 14 . |
| MLA | Zhang, Zefeng et al. "Genomic analysis and characterization of phages infecting the marine Roseobacter CHAB-I-5 lineage reveal a globally distributed and abundant phage genus" . | FRONTIERS IN MICROBIOLOGY 14 (2023) . |
| APA | Zhang, Zefeng , Wu, Zuqing , Liu, He , Yang, Mingyu , Wang, Rui , Zhao, Yanlin et al. Genomic analysis and characterization of phages infecting the marine Roseobacter CHAB-I-5 lineage reveal a globally distributed and abundant phage genus . | FRONTIERS IN MICROBIOLOGY , 2023 , 14 . |
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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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