Breitbart Mya, Felts Ben, Kelley Scott, Mahaffy Joseph M, Nulton James, Salamon Peter, Rohwer Forest
Department of Biology, San Diego State University, San Diego, CA 92182-4614, USA.
Proc Biol Sci. 2004 Mar 22;271(1539):565-74. doi: 10.1098/rspb.2003.2628.
Viruses, most of which are phage, are extremely abundant in marine sediments, yet almost nothing is known about their identity or diversity. We present the metagenomic analysis of an uncultured near-shore marine-sediment viral community. Three-quarters of the sequences in the sample were not related to anything previously reported. Among the sequences that could be identified, the majority belonged to double-stranded DNA phage. Temperate phage were more common than lytic phage, suggesting that lysogeny may be an important lifestyle for sediment viruses. Comparisons between the sediment sample and previously sequenced seawater viral communities showed that certain phage phylogenetic groups were abundant in all marine viral communities, while other phage groups were under-represented or absent. This 'marineness' suggests that marine phage are derived from a common set of ancestors. Several independent mathematical models, based on the distribution of overlapping shotgun sequence fragments from the library, were used to show that the diversity of the viral community was extremely high, with at least 10(4) viral genotypes per kilogram of sediment and a Shannon index greater than 9 nats. Based on these observations we propose that marine-sediment viral communities are one of the largest unexplored reservoirs of sequence space on the planet.
病毒,其中大部分是噬菌体,在海洋沉积物中极其丰富,但关于它们的身份或多样性却几乎一无所知。我们展示了对一个未培养的近岸海洋沉积物病毒群落的宏基因组分析。样本中四分之三的序列与之前报道的任何序列都不相关。在可识别的序列中,大多数属于双链DNA噬菌体。温和噬菌体比裂解性噬菌体更常见,这表明溶原性可能是沉积物病毒的一种重要生存方式。沉积物样本与之前测序的海水病毒群落之间的比较表明,某些噬菌体系统发育组在所有海洋病毒群落中都很丰富,而其他噬菌体组则代表性不足或不存在。这种 “海洋特性” 表明海洋噬菌体源自一组共同的祖先。基于文库中重叠鸟枪法序列片段的分布,使用了几个独立的数学模型来表明病毒群落的多样性极高,每千克沉积物中至少有10⁴ 种病毒基因型,香农指数大于9纳特。基于这些观察结果,我们提出海洋沉积物病毒群落是地球上最大的未被探索的序列空间库之一。