Head I M, Gray N D, Clarke K J, Pickup R W, Jones J G
Newcastle Research Group in Fossil Fuels and Environmental Geochemistry University of Newcastle upon Tyne, UK.
Microbiology (Reading). 1996 Sep;142 ( Pt 9):2341-54. doi: 10.1099/00221287-142-9-2341.
Achromatium oxaliferum is a large, morphologically conspicuous, sediment-dwelling bacterium. Nothing is known concerning its phylogeny and it has eluded all attempts at laboratory cultivation. The limited physiological description of A. oxaliferum has been based on morphological features of the bacterium such as the presence of intracellular sulphur inclusions. A. oxaliferum cells were purified from a wetland region close to Rydal Water (Cumbria, UK). Scanning and transmission electron microscopy revealed that a number of morphologically distinct A. oxaliferum cell-types, based on cell surface features and the size and abundance of calcite and sulphur inclusions within the cells, were present in a single sample of purified cells. PCR was used to amplify almost full-length 16S rRNA gene sequences from DNA extracted from A. oxaliferum cells directly purified from sediments. The PCR products were cloned and partial sequences (approx. 400 bp) were determined for seven of the clones. Three different sequence clusters were recovered from the clone libraries. A near full-length (1489 bp) 16S rRNA gene sequence was determined for a representative clone of the most dominant sequence-type (52% of the sequences). Comparative sequence analysis showed A. oxaliferum to form a deep branching lineage within the gamma-subdivision of the Proteobacteria. A. oxaliferum was related most closely to the Chromatium assemblage that includes sulphur-oxidizing symbiotic bacteria, purple sulphur bacteria, and sulphur- and iron-oxidizing thiobacilli. Phylogenetic inferences made using distance, parsimony and maximum likelihood methods all placed A. oxaliferum with this group of bacteria. Bootstrap support for a relationship with any particular lineage within the assemblage was weak. The seven clone sequences recovered from the A. oxaliferum cells however formed a monophyletic group well supported by bootstrap analysis (85-100% support depending on the analysis done). It was concluded that A. oxaliferum was related to organisms of the Chromatium assemblage but constituted a novel lineage within this group of bacteria. A. oxaliferum cells were confirmed as the source of the 16S rRNA sequence obtained, by the use of a fluorescently-labelled 16S rRNA-targeted oligonucleotide specific for the A. oxaliferum rRNA sequence.
草酸嗜盐菌是一种大型的、形态显著的、生活在沉积物中的细菌。关于其系统发育一无所知，并且所有实验室培养尝试均未成功。对草酸嗜盐菌有限的生理学描述是基于该细菌的形态特征，例如细胞内硫包涵体的存在。从靠近瑞德尔湖（英国坎布里亚郡）的湿地地区纯化出草酸嗜盐菌细胞。扫描电子显微镜和透射电子显微镜显示，基于细胞表面特征以及细胞内方解石和硫包涵体的大小和丰度，在单个纯化细胞样本中存在多种形态不同的草酸嗜盐菌细胞类型。使用聚合酶链反应（PCR）从直接从沉积物中纯化的草酸嗜盐菌细胞提取的DNA中扩增出几乎全长的16S核糖体RNA（rRNA）基因序列。将PCR产物克隆，并测定了其中7个克隆的部分序列（约400碱基对）。从克隆文库中获得了三个不同的序列簇。为最主要序列类型（占序列的52%）的一个代表性克隆测定了近乎全长（1489碱基对）的16S rRNA基因序列。比较序列分析表明，草酸嗜盐菌在变形菌门γ亚纲内形成一个深度分支的谱系。草酸嗜盐菌与包括硫氧化共生细菌、紫色硫细菌以及硫和铁氧化硫杆菌的嗜盐菌组合关系最为密切。使用距离法、简约法和最大似然法进行的系统发育推断均将草酸嗜盐菌置于这组细菌之中。对与该组合内任何特定谱系关系的自展支持较弱。然而从草酸嗜盐菌细胞中获得的7个克隆序列形成了一个单系群，自展分析对其有很好的支持（根据所做分析，支持率为85% - 100%）。得出的结论是，草酸嗜盐菌与嗜盐菌组合的生物有关，但在这组细菌中构成一个新的谱系。通过使用针对草酸嗜盐菌rRNA序列的荧光标记16S rRNA靶向寡核苷酸，证实了草酸嗜盐菌细胞是所获得的16S rRNA序列的来源。
