Morphology, host range and phylogenetic diversity of Sphingomonas phages in the floodwater of a Japanese paddy field
Morphology, host range and phylogenetic diversity of Sphingomonas phages in the floodwater of a Japanese paddy field
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DOI：
10.1111/j.1747-0765.2008.00332.x
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发表时间：
2009-02-01
影响因子：
2
通讯作者：
Kimura, Makoto
中科院分区：
文献类型：
--
作者：
Nakayama, Natsuko;Tsuge, Takashi;Kimura, Makoto
鞘氨醇单胞菌属的相关属（鞘氨醇单胞菌属、鞘氨醇单胞菌属、新鞘氨醇单胞菌属和鞘氨醇单胞菌属）的成员在来自日本稻田的洪水的细菌分离物中占优势。分离了58株鞘氨醇单胞菌/新鞘氨醇杆菌噬菌体（SphingomonasNovosphingobiumbacteriophagens，Sphingobium），根据衣壳蛋白基因（g23）序列分析了它们的形态、宿主范围和系统发育多样性。所有这些病毒都是具有等长或伸长的二十面体衣壳和长的非收缩性尾的管蚜病毒。基因组为双链DNA，大小为40、60、100或160 kb。通过感染来自洪水的16种细菌分离物来检查噬菌体的宿主范围，这些细菌分离物属于鞘氨醇单胞菌属、新鞘氨醇菌属、鞘氨醇球菌属和紫杆菌属。宿主范围有很大的不同，并且在仅感染用于分离的宿主和感染属于鞘氨醇单胞菌属、新鞘氨醇菌属和卟啉杆菌属三个属的宿主之间变化。所有病毒都有g23，表明g23基因在肌尾病毒科和虹吸病毒科成员中普遍存在。每个g23序列都属于Fujii et al.（2008）提出的6个未表征的Paddy类群之一。g23序列是相同的，在核苷酸水平上的几个等轴和细长的衣壳与60和160 kb的基因组，和之间的一些pneumonia和克隆，从遥远的稻田检索。这表明g23在稻田中水平转移的现象普遍存在。g23序列与这些细菌的宿主范围无关。此外，一个更大程度的分歧g23从大肠杆菌噬菌体T4在稻田相比，海洋环境中估计从本研究。
Members of the Sphingomonas-related genera (Sphingomonas, Sphingobium, Novosphingobium and Sphingopyxis) are dominant in bacterial isolates from the floodwater of Japanese paddy fields. Fifty-eight Sphingomonas/Novosphingobium bacteriophages (phages) were isolated to elucidate their morphology, host range and phylogenetic diversity based on the capsid gene (g23) sequence. All of the phages were siphoviruses with isometric or elongated, icosahedral capsids and a long, non-contractile tail. The genomes were double-stranded DNA measuring either 40, 60, 100 or 160 kb. The host range of the phages was examined by infecting 16 bacterial isolates from the floodwater, belonging to Sphingomonas, Novosphingobium, Sphingopyxis and Porphyrobacter. The host range was widely different and varied between infection of only the host used for isolation and infection of hosts belonging to the three genera of Sphingomonas, Novosphingobium and Porphyrobacter. All phages had g23, indicating the ubiquity of the g23 gene among Myoviridae and Siphoviridae members. Every g23 sequence of the phages belonged to one of the six uncharacterized Paddy Groups proposed by Fujii et al. (2008). The g23 sequences were identical at the nucleotide level for several phages with isometric and elongated capsids with 60 and 160 kb genomes, and between some phages and the clones that were retrieved from distant paddy fields. This indicates the common occurrence of horizontal transfer of g23 in the paddy fields. The g23 sequence does not correlate with the host range of those phages. In addition, a larger degree of divergence of g23 from coliphage T4 in paddy fields compared to marine environments was estimated from the present study.