Suzuki M T, Rappé M S, Haimberger Z W, Winfield H, Adair N, Ströbel J, Giovannoni S J
College of Oceanic and Atmospheric Sciences, Oregon State University, Corvallis 97331, USA.
Appl Environ Microbiol. 1997 Mar;63(3):983-9. doi: 10.1128/aem.63.3.983-989.1997.
Numerous investigations applying the cloning and sequencing of rRNA genes (rDNAs) to the study of marine bacterioplankton diversity have shown that the sequences of genes cloned directly from environmental DNA do not correspond to the genes of cultured marine taxa. These results have been interpreted as support for the hypothesis that the most abundant heterotrophic marine bacterioplankton species are not readily culturable by commonly used methods. However, an alternative explanation is that marine bacterioplankton can be easily cultured but are not well represented in sequence databases. To further examine this question, we compared the small-subunit (SSU) rDNAs of 127 cellular clones isolated from a water sample collected off the Oregon coast to 58 bacterial SSU rDNAs cloned from environmental DNAs from the same water sample. The results revealed little overlap between partial SSU rDNA sequences from the cellular clones and the environmental clone library. An exception was the SSU rDNA sequence recovered from a cellular clone belonging to the Pseudomonas subgroup of the gamma subclass of the class Proteobacteria, which was related to a single gene cloned directly from the same water sample (OCS181) (similarity, 94.6%). In addition, partial SSU rDNA sequences from three of the cultured strains matched a novel rDNA clone related to the gamma subclass of the Proteobacteria found previously in an environmental clone library from marine aggregates (AGG53) (similarity, 94.3 to 99.6%). Our results support the hypothesis that many of the most abundant bacterioplankton species are not readily culturable by standard methods but also show that heterotrophic bacterioplankton that are culturable on media with high organic contents include many strains for which SSU rDNA sequences are not available in sequence databases.
众多将核糖体RNA基因（rDNA）克隆及测序应用于海洋细菌浮游生物多样性研究的调查表明，直接从环境DNA中克隆的基因序列与培养的海洋分类单元的基因不对应。这些结果被解释为支持以下假说：即最丰富的海洋异养细菌浮游生物物种难以通过常用方法培养。然而，另一种解释是海洋细菌浮游生物易于培养，但在序列数据库中代表性不足。为进一步研究这个问题，我们将从俄勒冈海岸采集的水样中分离出的127个细胞克隆的小亚基（SSU）rDNA与从同一水样的环境DNA中克隆的58个细菌SSU rDNA进行了比较。结果显示，细胞克隆的部分SSU rDNA序列与环境克隆文库之间几乎没有重叠。一个例外是从属于变形菌纲γ亚类假单胞菌亚组的细胞克隆中回收的SSU rDNA序列，它与直接从同一水样中克隆的单个基因（OCS181）相关（相似度为94.6%）。此外，三个培养菌株的部分SSU rDNA序列与先前在海洋聚集体环境克隆文库中发现的与变形菌纲γ亚类相关的一个新rDNA克隆匹配（相似度为94.3%至99.6%）。我们的结果支持以下假说：许多最丰富的细菌浮游生物物种难以通过标准方法培养，但也表明在高有机含量培养基上可培养的异养细菌浮游生物包括许多其SSU rDNA序列在序列数据库中不可用的菌株。
