Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA.
Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061-0913, USA.
ISME J. 2022 Jun;16(6):1657-1667. doi: 10.1038/s41396-022-01214-x. Epub 2022 Mar 8.
Recent research has underscored the immense diversity and key biogeochemical roles of large DNA viruses in the ocean. Although they are important constituents of marine ecosystems, it is sometimes difficult to detect these viruses due to their large size and complex genomes. This is true for "jumbo" bacteriophages, which have genome sizes >200 kbp and large capsids reaching up to 0.45 µm in diameter. In this study, we sought to assess the genomic diversity and distribution of these bacteriophages in the ocean by generating and analyzing jumbo phage genomes from metagenomes. We recover 85 marine jumbo phages that ranged in size from 201 to 498 kilobases, and we examine their genetic similarities and biogeography together with a reference database of marine jumbo phage genomes. By analyzing Tara Oceans metagenomic data, we show that although most jumbo phages can be detected in a range of different size fractions, 17 of our bins tend to be found in those greater than 0.22 µm, potentially due to their large size. Our network-based analysis of gene-sharing patterns reveals that jumbo bacteriophages belong to five genome clusters that are typified by diverse replication strategies, genomic repertoires, and potential host ranges. Our analysis of jumbo phage distributions in the ocean reveals that depth is a major factor shaping their biogeography, with some phage genome clusters occurring preferentially in either surface or mesopelagic waters, respectively. Taken together, our findings indicate that jumbo phages are widespread community members in the ocean with complex genomic repertoires and ecological impacts that warrant further targeted investigation.
最近的研究强调了海洋中大型 DNA 病毒的巨大多样性和关键生物地球化学作用。尽管它们是海洋生态系统的重要组成部分,但由于它们的体积庞大和基因组复杂,有时很难检测到这些病毒。对于基因组大小>200 kbp 且衣壳直径可达 0.45 μm 的“巨型”噬菌体来说尤其如此。在这项研究中,我们通过从宏基因组中生成和分析巨型噬菌体基因组,来评估这些噬菌体在海洋中的基因组多样性和分布。我们共回收了 85 个海洋巨型噬菌体,其大小从 201 到 498 kb 不等,我们与海洋巨型噬菌体基因组的参考数据库一起检查了它们的遗传相似性和生物地理学。通过分析 Tara Oceans 宏基因组数据,我们表明,尽管大多数巨型噬菌体可以在一系列不同的大小范围内检测到,但我们的 17 个箱倾向于存在于大于 0.22 μm 的范围内,这可能是由于它们的体积较大。我们基于网络的基因共享模式分析表明,巨型噬菌体属于五个基因组群,其特征是具有不同的复制策略、基因组组成和潜在的宿主范围。我们对海洋中巨型噬菌体分布的分析表明,深度是塑造它们生物地理学的主要因素,一些噬菌体基因组群分别优先存在于表层或中层水域中。总之,我们的研究结果表明,巨型噬菌体是海洋中广泛存在的具有复杂基因组组成和生态影响的群落成员,值得进一步进行有针对性的研究。