Table_4_Genomic analysis and characterization of phages infecting the marine Roseobacter CHAB-I-5 lineage reveal a globally distributed and abundant phage genus.XLSX

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.

海洋噬菌体通过调控细菌的死亡、生理代谢与演化轨迹，在海洋生物地球化学循环中发挥关键作用。玫瑰杆菌类群是海洋中丰度颇高且功能重要的异养细菌类群，在碳、氮、硫、磷循环中扮演核心角色。CHAB-I-5演化支是最优势的玫瑰杆菌演化支之一，但目前仍大多未获得纯培养。由于缺乏可培养的CHAB-I-5菌株，目前尚无针对侵染该类群细菌的噬菌体的相关研究。本研究分离并测序了两株侵染CHAB-I-5菌株FZCC0083的新型噬菌体CRP-901与CRP-902。本研究通过宏基因组数据挖掘、比较基因组学、系统发育分析以及宏基因组读段比对，对以这两株噬菌体为代表的噬菌体类群的多样性、演化、分类学与生物地理学特征展开研究。这两株噬菌体相似度极高，平均核苷酸一致性达89.17%，共享77%的开放阅读框。研究团队从二者的基因组中鉴定出多个参与DNA复制与代谢、病毒粒子结构、DNA包装以及宿主裂解的功能基因。宏基因组挖掘共鉴定出24个与CRP-901、CRP-902亲缘关系紧密的宏基因组病毒基因组。基因组比较与系统发育分析结果显示，该类噬菌体与所有已知病毒均存在显著差异，代表一个全新的属级噬菌体类群（CRP-901型）。CRP-901型噬菌体不含DNA引物酶与DNA聚合酶基因，但拥有一种兼具引物酶与聚合酶活性的新型双功能DNA引物酶-聚合酶基因。读段比对分析表明，CRP-901型噬菌体在全球海洋中广泛分布，且在河口与极地水域丰度最高。该类噬菌体的丰度通常高于其他已知玫瑰杆菌噬菌体，在极地水域甚至高于多数远洋噬菌体。综上，本研究极大拓展了我们对玫瑰杆菌噬菌体遗传多样性、演化过程与分布模式的认知。分析结果表明，CRP-901型噬菌体是一类重要的新型海洋噬菌体类群，对玫瑰杆菌的生理与生态过程发挥关键调控作用。