Colman Daniel R, Thomas Raquela, Maas Kendra R, Takacs-Vesbach Cristina D
Department of Biology, MSC03 2020, University of New Mexico, Albuquerque, NM, 87131-0001, USA,
Extremophiles. 2015 Mar;19(2):307-13. doi: 10.1007/s00792-014-0715-0. Epub 2014 Dec 5.
Recent metagenomic analyses of Yellowstone National Park (YNP) thermal spring communities suggested the presence of minor archaeal populations that simultaneous PCR-based assays using traditional 'universal' 16S rRNA gene primers failed to detect. Here we use metagenomics to identify PCR primers effective at detecting elusive members of the Archaea, assess their efficacy, and describe the diverse and novel archaeal community from a circum-neutral thermal spring from the Bechler region of YNP. We determined that a less commonly used PCR primer, Arch349F, captured more diversity in this spring than the widely used A21F primer. A search of the PCR primers against the RDP 16S rRNA gene database indicated that Arch349F also captured the largest percentage of Archaea, including 41 % more than A21F. Pyrosequencing using the Arch349F primer recovered all of the phylotypes present in the clone-based portion of the study and the metagenome of this spring in addition to several other populations of Archaea, some of which are phylogenetically novel. In contrast to the lack of amplification with traditional 16S rRNA gene primers, our comprehensive analyses suggested a diverse archaeal community in the Bechler spring, with implications for recently discovered groups such as the Geoarchaeota and other undescribed archaeal groups.
最近对黄石国家公园（YNP）温泉群落进行的宏基因组分析表明，存在一些少量的古菌种群，而使用传统“通用”16S rRNA基因引物进行的基于PCR的检测未能检测到这些种群。在此，我们利用宏基因组学来鉴定能有效检测难以捉摸的古菌类群的PCR引物，评估其有效性，并描述来自YNP贝奇勒地区一个中性温泉中多样且新颖的古菌群落。我们确定，一种较少使用的PCR引物Arch349F在该温泉中捕获到的多样性比广泛使用的A21F引物更多。将这些PCR引物与RDP 16S rRNA基因数据库进行比对搜索表明，Arch349F捕获到的古菌比例也最大，比A21F多41%。使用Arch349F引物进行的焦磷酸测序除了检测到该温泉克隆文库部分和宏基因组中存在的所有系统发育型外，还检测到了其他几个古菌种群，其中一些在系统发育上是新颖的。与使用传统16S rRNA基因引物无法扩增形成对比的是，我们的综合分析表明贝奇勒温泉中存在一个多样的古菌群落，这对最近发现的类群（如地古菌门）和其他未描述的古菌类群具有启示意义。
