Novel division level bacterial diversity in a Yellowstone hot spring
Novel division level bacterial diversity in a Yellowstone hot spring
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DOI：
10.1128/jb.180.2.366-376.1998
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发表时间：
1998-01-01
影响因子：
3.2
通讯作者：
Pace, NR
中科院分区：
文献类型：
--
作者：
Hugenholtz, P;Pitulle, C;Pace, NR
对黄石国家公园国家公园黑曜石池（OF）中的细菌群落进行了一项不依赖于培养的分子系统发育调查。M.巴恩斯河E. Fundyga，M. W. Jeffries和N. R. Page，Proc. Natl. Acad. Sci. USA 91：1609-1613 1994）。以OP沉积物DNA为模板，用通用保守引物或细菌特异引物，直接扩增并克隆了OP沉积物的小亚基rRNA基因。通过限制性片段长度多态性分析，在300多个克隆中鉴定出独特的rDNA类型，并确定了122个代表性的rDNA序列。发现这些代表54种不同的细菌序列类型或序列簇（大于或等于98%同一性）。大多数（70%）的序列类型隶属于14个以前公认的细菌部门（主要门，界），30%是不隶属于公认的细菌部门。非附属序列类型（由38个序列表示）名义上包括12个新的划分级别谱系，称为候选划分。几个OP序列几乎相同的培养化能无机营养的嗜热菌，包括氢氧化Calderobacterium和硫酸盐还原剂Thermoelasticfovibrio和Thermoelasticfobacterium，或属于一个特定类型的代谢，如氢氧化Aquificales和硫酸盐还原δ-变形菌的单系组合。这种生物的发生是一致的，与OP的化学成分（高还原铁和硫），并建议在这个温泉的初级生产力的石养基地，通过氢氧化和硫酸盐还原。出乎意料的是，在用通用引物制备的OP克隆文库中没有遇到古细菌序列。扩增的OP DNA与结构域特异性探针的杂交分析证实，所分析的社区rDNA从OP沉积物主要是细菌。这些结果大大扩展了我们对细菌多样性程度的认识，并对通常认为的细菌主导热液环境的观点提出了质疑。最后，对目前已知的细菌系统发育多样性的划分水平进行了整理和总结。
A culture-independent molecular phylogenetic survey was carried out for the bacterial community in Obsidian Pool (OF), a Yellowstone National Park hot spring previously shown to contain remarkable archaeal diversity (S. M. Barns, R. E. Fundyga, M. W. Jeffries, and N. R. Page, Proc. Natl. Acad. Sci. USA 91:1609-1613 1994). Small-subunit rRNA genes (rDNA) were amplified directly from OP sediment DNA by PCR with universally conserved or Bacteria-specific rDNA primers and cloned. Unique rDNA types among >300 clones were identified by restriction fragment length polymorphism, and 122 representative rDNA sequences were determined. These were found to represent 54 distinct bacterial sequence types or clusters (greater than or equal to 98% identity) of sequences. A majority (70%) of the sequence types were affiliated with 14 previously recognized bacterial divisions (main phyla; kingdoms); 30% were unaffiliated with recognized bacterial divisions. The unaffiliated sequence types (represented by 38 sequences) nominally comprise 12 novel, division level lineages termed candidate divisions. Several OP sequences were nearly identical to those of cultivated chemolithotrophic thermophiles, including the hydrogen oxidizing Calderobacterium and the sulfate reducers Thermodesulfovibrio and Thermodesulfobacterium, or belonged to monophyletic assemblages recognized for a particular type of metabolism, such as the hydrogen-oxidizing Aquificales and the sulfate-reducing delta-Proteobacteria. The occurrence of such organisms is consistent,vith the chemical composition of OP (high in reduced iron and sulfur) and suggests a lithotrophic base for primary productivity in this hot spring, through hydrogen oxidation and sulfate reduction. Unexpectedly, no archaeal sequences were encountered in OP clone libraries made with universal primers. Hybridization analysis of amplified OP DNA with domain-specific probes confirmed that the analyzed community rDNA from OP sediment was predominantly bacterial. These results expand substantially our knowledge of the extent of bacterial diversity and call into question the commonly held notion that Archaea dominate hydrothermal environments. Finally, the currently known extent of division level bacterial phylogenetic diversity is collated and summarized.