Baker Brett J, Hugenholtz Philip, Dawson Scott C, Banfield Jillian F
Department of Earth and Planetary Sciences, University of California at Berkeley, Berkeley, California 94720, USA.
Appl Environ Microbiol. 2003 Sep;69(9):5512-8. doi: 10.1128/AEM.69.9.5512-5518.2003.
During a molecular phylogenetic survey of extremely acidic (pH < 1), metal-rich acid mine drainage habitats in the Richmond Mine at Iron Mountain, Calif., we detected 16S rRNA gene sequences of a novel bacterial group belonging to the order Rickettsiales in the Alphaproteobacteria. The closest known relatives of this group (92% 16S rRNA gene sequence identity) are endosymbionts of the protist Acanthamoeba. Oligonucleotide 16S rRNA probes were designed and used to observe members of this group within acidophilic protists. To improve visualization of eukaryotic populations in the acid mine drainage samples, broad-specificity probes for eukaryotes were redesigned and combined to highlight this component of the acid mine drainage community. Approximately 4% of protists in the acid mine drainage samples contained endosymbionts. Measurements of internal pH of the protists showed that their cytosol is close to neutral, indicating that the endosymbionts may be neutrophilic. The endosymbionts had a conserved 273-nucleotide intervening sequence (IVS) in variable region V1 of their 16S rRNA genes. The IVS does not match any sequence in current databases, but the predicted secondary structure forms well-defined stem loops. IVSs are uncommon in rRNA genes and appear to be confined to bacteria living in close association with eukaryotes. Based on the phylogenetic novelty of the endosymbiont sequences and initial culture-independent characterization, we propose the name "Candidatus Captivus acidiprotistae." To our knowledge, this is the first report of an endosymbiotic relationship in an extremely acidic habitat.
在对加利福尼亚州铁山里士满矿中极度酸性（pH < 1）、富含金属的酸性矿山排水栖息地进行分子系统发育调查时，我们检测到了变形菌门立克次氏体目中一个新型细菌群的16S rRNA基因序列。该菌群最接近的已知亲缘种（16S rRNA基因序列同一性为92%）是原生生物棘阿米巴的内共生体。设计了寡核苷酸16S rRNA探针，并用于观察嗜酸原生生物中的该菌群成员。为了更好地观察酸性矿山排水样本中的真核生物种群，重新设计并组合了针对真核生物的广谱特异性探针，以突出酸性矿山排水群落的这一组成部分。酸性矿山排水样本中约4%的原生生物含有内共生体。对原生生物内部pH值的测量表明，它们的细胞质接近中性，这表明内共生体可能是嗜中性的。内共生体在其16S rRNA基因的可变区V1中有一个保守的273个核苷酸的间隔序列（IVS）。该IVS与当前数据库中的任何序列都不匹配，但预测的二级结构形成了明确的茎环。IVS在rRNA基因中并不常见，似乎仅限于与真核生物密切相关的细菌。基于内共生体序列的系统发育新颖性和初步的非培养特征描述，我们提出了“嗜酸原生生物候选俘获菌（Candidatus Captivus acidiprotistae）”这一名称。据我们所知，这是关于极端酸性栖息地中内共生关系的首次报道。
