College of Marine Science, University of South Florida, 140 Seventh Avenue South, St Petersburg, FL 33701, USA.
ISME J. 2011 May;5(5):822-30. doi: 10.1038/ismej.2010.188. Epub 2010 Dec 2.
Knowledge of marine phages is highly biased toward double-stranded DNA (dsDNA) phages; however, recent metagenomic surveys have also identified single-stranded DNA (ssDNA) phages in the oceans. Here, we describe two complete ssDNA phage genomes that were reconstructed from a viral metagenome from 80 m depth at the Bermuda Atlantic Time-series Study (BATS) site in the northwestern Sargasso Sea and examine their spatial and temporal distributions. Both genomes (SARssφ1 and SARssφ2) exhibited similarity to known phages of the Microviridae family in terms of size, GC content, genome organization and protein sequence. PCR amplification of the replication initiation protein (Rep) gene revealed narrow and distinct depth distributions for the newly described ssDNA phages within the upper 200 m of the water column at the BATS site. Comparison of Rep gene sequences obtained from the BATS site over time revealed changes in the diversity of ssDNA phages over monthly time scales, although some nearly identical sequences were recovered from samples collected 4 years apart. Examination of ssDNA phage diversity along transects through the North Atlantic Ocean revealed a positive correlation between genetic distance and geographic distance between sampling sites. Together, the data suggest fundamental differences between the distribution of these ssDNA phages and the distribution of known marine dsDNA phages, possibly because of differences in host range, host distribution, virion stability, or viral evolution mechanisms and rates. Future work needs to elucidate the host ranges for oceanic ssDNA phages and determine their ecological roles in the marine ecosystem.
海洋噬菌体的知识主要偏向双链 DNA（dsDNA）噬菌体；然而，最近的宏基因组调查也在海洋中发现了单链 DNA（ssDNA）噬菌体。在这里，我们描述了两个完整的 ssDNA 噬菌体基因组，它们是从北大西洋时间序列研究（BATS）站点 80m 深处的病毒宏基因组中重建的，并研究了它们的时空分布。这两个基因组（SARssφ1 和 SARssφ2）在大小、GC 含量、基因组组织和蛋白质序列方面与已知的微病毒科噬菌体具有相似性。复制起始蛋白（Rep）基因的 PCR 扩增显示，新描述的 ssDNA 噬菌体在 BATS 站点水柱的上层 200m 范围内具有狭窄而独特的深度分布。对 BATS 站点随时间获得的 Rep 基因序列进行比较表明，尽管从相隔 4 年的样本中回收了一些几乎相同的序列，但 ssDNA 噬菌体的多样性在每月的时间尺度上发生了变化。对沿北大西洋航线的 ssDNA 噬菌体多样性的检查表明，遗传距离与采样点之间的地理距离之间存在正相关关系。这些数据表明，这些 ssDNA 噬菌体的分布与已知的海洋 dsDNA 噬菌体的分布存在根本差异，这可能是由于宿主范围、宿主分布、病毒粒子稳定性或病毒进化机制和速度的差异所致。未来的工作需要阐明海洋 ssDNA 噬菌体的宿主范围，并确定它们在海洋生态系统中的生态作用。
