Diverse, Abundant, and Novel Viruses Infecting the Marine Roseobacter RCA Lineage
Diverse, Abundant, and Novel Viruses Infecting the Marine Roseobacter RCA Lineage
复制标题
感染海洋玫瑰杆菌 RCA 谱系的多种、丰富的新型病毒
DOI：
10.1128/msystems.00494-19
复制
发表时间：
2019-11-01
期刊：
影响因子：
6.4
通讯作者：
Zhao, Yanlin
中科院分区：
文献类型：
--
作者：
Zhang, Zefeng;Chen, Feng;Zhao, Yanlin
海洋蔷薇属的RCA谱系代表了海洋微生物群落中生长缓慢但占主导地位的组成部分之一。虽然已经鉴定了几十种噬菌体，但没有报道感染RCA菌株的噬菌体。在这项研究中，我们报告了第一个RCA噬菌体基因组，并研究了它们的分布模式和相对丰度与其他重要的海洋噬菌体群相比。发现四个RCA噬菌体群中的两个分别与先前报道的SAR 116噬菌体HMO-2011和Cobavirus组玫瑰噬菌体密切相关。其余两组在基因组内容上是新的。我们的研究还表明，RCA病毒广泛分布，并在海洋病毒数据集中表现出高丰度。总而言之，我们的研究结果大大拓宽了我们对RCA的理解，并强调了RCA在海洋病毒圈中的生态和进化重要性。摘要许多主要的海洋细菌谱系，如SAR 11、原绿球藻、SAR 116和几种玫瑰球菌谱系，都具有丰富的、相对生长缓慢的、基因组精简的成员。感染SAR 11和SAR 116的细菌的分离证明了这些细菌在海洋病毒圈中的优势。然而，还没有从另一个丰富的海洋细菌群Roseastern RCA谱系中的细菌中分离出细菌。在这项研究中，七个RCA病毒感染三种不同的RCA菌株进行了分离和鉴定。所有7个RCA病毒都属于短尾病毒科，基因组大小为39.6至58.1 kb。有趣的是，三种RCA噬菌体（CRP-1、CRP-2和CRP-3）显示出与SAR 116噬菌体HMO-2011相似的基因组内容和结构，SAR 116噬菌体HMO-2011代表海洋中最丰富的已知病毒群之一。CRP-1、CRP-2、CRP-3和HMO-2011之间的高度同源性导致RCA β对HMO-2011型组的优势有贡献。CRP-4和CRP-5在基因内容和组织方面与Cobavirus组噬菌体相似。剩余的两个RCA噬菌体，CRP-6和CRP-7，与已知的噬菌体显示有限的基因组相似性，并代表两个新的噬菌体群。宏基因组片段募集分析表明，这些RCA噬菌体群在海洋中比大多数现有的海洋玫瑰噬菌体群丰富得多。这些RCA噬菌体的表征大大扩展了我们对海洋噬菌体的基因组多样性和进化的理解，并表明迫切需要从丰富但“不可培养”的细菌中分离噬菌体。海洋蔷薇属的RCA谱系代表了海洋微生物群落中生长缓慢但占主导地位的组成部分之一。虽然已经鉴定了几十种噬菌体，但没有报道感染RCA菌株的噬菌体。在这项研究中，我们报告了第一个RCA噬菌体基因组，并研究了它们的分布模式和相对丰度与其他重要的海洋噬菌体群相比。发现四个RCA噬菌体群中的两个分别与先前报道的SAR 116噬菌体HMO-2011和Cobavirus组玫瑰噬菌体密切相关。其余两组在基因组内容上是新的。我们的研究还表明，RCA噬菌体分布广泛，并且在海洋病毒数据集中表现出高丰度。总而言之，我们的研究结果大大拓宽了我们对RCA的理解，并强调了RCA在海洋病毒圈中的生态和进化重要性。
The RCA lineage of the marine Roseobacter group represents one of the slow-growing but dominant components of marine microbial communities. Although dozens of roseophages have been characterized, no phages infecting RCA strains have been reported. In this study, we reported on the first RCA phage genomes and investigated their distribution pattern and relative abundance in comparison with other important marine phage groups. Two of the four RCA phage groups were found closely related to previously reported SAR116 phage HMO-2011 and Cobavirus group roseophages, respectively. The remaining two groups are novel in the genome contents. Our study also revealed that RCA phages are widely distributed and exhibit high abundance in marine viromic data sets. Altogether, our findings have greatly broadened our understanding of RCA phages and emphasize the ecological and evolutionary importance of RCA phages in the marine virosphere. ABSTRACT Many major marine bacterial lineages such as SAR11, Prochlorococcus, SAR116, and several Roseobacter lineages have members that are abundant, relatively slow-growing, and genome streamlined. The isolation of phages that infect SAR11 and SAR116 have demonstrated the dominance of these phages in the marine virosphere. However, no phages have been isolated from bacteria in the Roseobacter RCA lineage, another abundant group of marine bacteria. In this study, seven RCA phages that infect three different RCA strains were isolated and characterized. All seven RCA phages belong to the Podoviridae family and have genome sizes ranging from 39.6 to 58.1 kb. Interestingly, three RCA phages (CRP-1, CRP-2, and CRP-3) show similar genomic content and architecture as SAR116 phage HMO-2011, which represents one of the most abundant known viral groups in the ocean. The high degree of homology among CRP-1, CRP-2, CRP-3, and HMO-2011 resulted in the contribution of RCA phages to the dominance of the HMO-2011-type group. CRP-4 and CRP-5 are similar to the Cobavirus group roseophages in terms of gene content and organization. The remaining two RCA phages, CRP-6 and CRP-7, show limited genomic similarity with known phages and represent two new phage groups. Metagenomic fragment recruitment analyses reveal that these RCA phage groups are much more abundant in the ocean than most existing marine roseophage groups. The characterization of these RCA phages has greatly expanded our understanding of the genomic diversity and evolution of marine roseophages and suggests the critical need for isolating phages from the abundant but “unculturable” bacteria. IMPORTANCE The RCA lineage of the marine Roseobacter group represents one of the slow-growing but dominant components of marine microbial communities. Although dozens of roseophages have been characterized, no phages infecting RCA strains have been reported. In this study, we reported on the first RCA phage genomes and investigated their distribution pattern and relative abundance in comparison with other important marine phage groups. Two of the four RCA phage groups were found closely related to previously reported SAR116 phage HMO-2011 and Cobavirus group roseophages, respectively. The remaining two groups are novel in the genome contents. Our study also revealed that RCA phages are widely distributed and exhibit high abundance in marine viromic data sets. Altogether, our findings have greatly broadened our understanding of RCA phages and emphasize the ecological and evolutionary importance of RCA phages in the marine virosphere.