Ludwig W, Bauer S H, Bauer M, Held I, Kirchhof G, Schulze R, Huber I, Spring S, Hartmann A, Schleifer K H
Lehrstuhl für Mikrobiologie, Technische Universität München, Germany.
FEMS Microbiol Lett. 1997 Aug 1;153(1):181-90. doi: 10.1111/j.1574-6968.1997.tb10480.x.
16S rRNA gene libraries were prepared by polymerase chain reaction amplification and cloning from soil samples taken periodically from a field with genetically modified plants. Sequence analyses of the cloned rDNAs indicated that 140 of them clustered apart from known bacterial phyla. Based on 31 full sequences a new phylum could be defined. It includes Holophaga foetida, 'Geothrix fermentans' and Acidobacterium capsulatum as the only cultured species so far. Therefore, this line of descent was named the Holophagal Acidobacterium phylum. About 50 published partial sequences of cloned rDNAs retrieved from soil, freshwater sediments or activated sludge from different continents indicate the occurrence of further representatives of this phylum. Two specific hybridization probes were constructed for members of one of four subclusters. A careful data analysis revealed the importance and problems of identifying and dealing with artefacts such as chimeric structure when defining new phylogenetic groups based mainly upon cloned amplified rDNAs. For the first time, the presence of bacterial cells representing this group could be shown in soil, sediment, activated sludge and lake snow by in situ hybridization.
通过聚合酶链反应扩增和克隆，从定期采集的种植转基因植物的田间土壤样本中制备了16S rRNA基因文库。对克隆的rDNA进行序列分析表明，其中140个与已知细菌门类聚类不同。基于31个完整序列，可以定义一个新的门类。到目前为止，它包括恶臭全噬菌、“发酵土栖菌”和嗜酸胶囊菌作为仅有的已培养物种。因此，这条谱系被命名为全噬嗜酸杆菌门。从不同大陆的土壤、淡水沉积物或活性污泥中检索到的约50个已发表的克隆rDNA部分序列表明，该门类还有其他代表物种。针对四个亚簇之一的成员构建了两种特异性杂交探针。仔细的数据分析揭示了在主要基于克隆扩增的rDNA定义新的系统发育类群时，识别和处理嵌合结构等假象的重要性和问题。首次通过原位杂交在土壤、沉积物、活性污泥和湖雪中显示了代表该类群的细菌细胞的存在。
