Twelve previously unknown phage genera are ubiquitous in global oceans
Twelve previously unknown phage genera are ubiquitous in global oceans
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DOI：
10.1073/pnas.1305956110
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发表时间：
2013-07-30
影响因子：
11.1
通讯作者：
Sullivan, Matthew B.
中科院分区：
文献类型：
--
作者：
Holmfeldt, Karin;Solonenko, Natalie;Sullivan, Matthew B.
病毒是从海洋到人类的生态系统的基础，但我们研究它们的能力受到缺乏生态相关分离物的影响，导致“未知数”主导了独立于文化的调查。在这里，我们提出了31个基因组感染的水生细菌Cellulophaga baltica（拟杆菌）的多个菌株，以提供数据的代表性不足和环境丰富的细菌谱系。比较基因组学描绘了12个噬菌体群，（i）每个噬菌体群代表一个新的属，（ii）代表一个新的和四个众所周知的病毒家族。这种多样性与少数研究充分的海洋噬菌体系统形成对比，但与感染人类相关细菌的细菌的多样性相似。尽管所有12个Cellulophaga属都代表了新的属，但足状病毒和二十面体无尾ssDNA病毒是例外，其基因组是以前观察到的每种噬菌体类型的基因组的两倍。结构新奇也很重要，需要实验噬菌体蛋白质组学来识别83%的结构蛋白。在四个属中存在不常见的核苷酸代谢基因可能强调了清除富含营养物质的分子的重要性，正如以前在海洋环境中看到的那样。宏基因组招募分析表明，这些特定的Cellulophaga是罕见的，可能代表了罕见生物圈的噬菌体方面的第一次一瞥。然而，这些分析也揭示了这些噬菌体属是广泛存在的，在137个研究的宏基因组中有94%发生。总之，这种多样性和新颖的收集鉴定了一小部分但普遍存在的未知海洋病毒多样性，并提供了许多环境相关的噬菌体宿主系统的实验假设检验。
Viruses are fundamental to ecosystems ranging from oceans to humans, yet our ability to study them is bottlenecked by the lack of ecologically relevant isolates, resulting in "unknowns" dominating culture-independent surveys. Here we present genomes from 31 phages infecting multiple strains of the aquatic bacterium Cellulophaga baltica (Bacteroidetes) to provide data for an under-represented and environmentally abundant bacterial lineage. Comparative genomics delineated 12 phage groups that (i) each represent a new genus, and (ii) represent one novel and four well-known viral families. This diversity contrasts the few well-studied marine phage systems, but parallels the diversity of phages infecting human-associated bacteria. Although all 12 Cellulophaga phages represent new genera, the podoviruses and icosahedral, nontailed ssDNA phages were exceptional, with genomes up to twice as large as those previously observed for each phage type. Structural novelty was also substantial, requiring experimental phage proteomics to identify 83% of the structural proteins. The presence of uncommon nucleotide metabolism genes in four genera likely underscores the importance of scavenging nutrient-rich molecules as previously seen for phages in marine environments. Metagenomic recruitment analyses suggest that these particular Cellulophaga phages are rare and may represent a first glimpse into the phage side of the rare biosphere. However, these analyses also revealed that these phage genera are widespread, occurring in 94% of 137 investigated metagenomes. Together, this diverse and novel collection of phages identifies a small but ubiquitous fraction of unknown marine viral diversity and provides numerous environmentally relevant phage-host systems for experimental hypothesis testing.