SGER: A Method to Genomic Sequence Uncultured Marine Phage

当发现海洋噬菌体(感染细菌的病毒)以非常多的数量(每升约1010种)存在时，我们对海洋环境的理解发生了根本改变。自这一观察以来，海洋微生物生态学家试图将噬菌体纳入微生物食物网的概念中。这项工作表明，在各种条件下，噬菌体占所有细菌通过裂解产生的12-600%。可观察到的大量噬菌体及其高产量使人们对世界海洋中的能量和营养循环的概念提出了质疑。对海洋中大量噬菌体的观察也提出了另外两个非常令人兴奋的问题：1)海洋环境中生活着什么类型的噬菌体？2)噬菌体如何影响海洋环境中的遗传转移(例如，转导或溶源转换)？现有证据表明，海洋噬菌体多样性是原核生物多样性的十倍，与原核生物一样，人们认为每个噬菌体在海洋环境中都有独特的生存和繁殖策略，这些策略将反映在每个噬菌体编码的基因中。噬菌体采用的生命策略将反过来帮助塑造海洋的MMFW和生物地球化学过程。目前的噬菌体表征方法依赖于噬菌体形态、基因组大小和宿主范围。然而，这些方法对环境样本的适用性极其有限，主要是因为大多数宿主是不可培养的。阿扎姆博士和罗威尔博士将试图通过对未培养噬菌体的基因组测序来绕过这个问题。这将分三步完成。首先，噬菌体基因组将使用脉冲场凝胶相互分离。其次，随机扩增的鸟枪库(RASL)将从PF-Gel分离的条带中构建。最后，将对鸟枪库进行测序。

Our understanding of the marine environment was fundamentally changed when it was shown that marine phage (viruses that infect bacteria) are present in extraordinary numbers (ca.1010 per liter). Since this observation, marine microbial ecologists have attempted to incorporate phage into the microbial food web concepts. This work has shown that under various conditions phage account for 12-600% of all bacterial production via lysis. The high number of observable phage and their high production rates have called into question concepts of energy and nutrient cycles in the world's oceans. The observation of large numbers of phage in the ocean also raised two other extremely exciting questions: 1) What type of phage inhabit the marine environment?, and 2) How might phage affect genetic transfer (e.g., transduction or lysogenic conversion) in the marine environment?. Available evidence suggests that marine phage diversity is ten times as great as prokaryotic diversity and like their prokaryotic counterparts, it is believed that each phage will have a unique strategy for surviving and multiplying in the marine environment and these strategies will be reflected in the genes that each phage encodes. The life strategies adopted by phage will in turn help shape the MMFW and the biogeochemical processes of the ocean.Current methods of phage characterization rely on phage morphology, genome size, and host range. However, these approaches are extremely limited in their applicability to environmental samples, primarily because the majority of host are not culturable. Drs. Azam and Rohwer ill attempt to circumvent this problem by sequencing the genomes of uncultured phage. This will be accomplished in three steps. First, phage genomes will be separated from each other using pulse field gels. Second, randomly amplified shotgun libraries (RASLs) will be constructed from the bands isolated from the PF-gels. Finally, the shotgun libraries will be sequenced.