Rainey P B, Bailey M J, Thompson I P
Institute of Virology and Environmental Microbiology, Oxford, UK.
Microbiology (Reading). 1994 Sep;140 ( Pt 9):2315-31. doi: 10.1099/13500872-140-9-2315.
A sample of 30 fluorescent pseudomonads isolated from the phyllosphere of sugar beet throughout a single growing season and shown to be closely related on the basis of fatty acid methyl ester (FAME) analysis was subjected to detailed phenotypic and genotypic characterization. Phenotypic traits were assessed on the basis of biochemical properties, assimilation of sole carbon sources, FAME analysis, organic pyrolysate content (MS-pyrolysis), and total cellular protein profiles. With the exception of total cellular protein profiles, numerical analysis of the data revealed two main clusters, each of which was divided into several subclusters. Numerical analysis of total cellular protein data failed to differentiate isolates into two main clusters, but nevertheless grouped isolates into six subclusters. On the basis of biochemical and carbon source assimilation profiles, 19 isolates were identified as Pseudomonas fluorescens biovar V, eight isolates as P. fluorescens biovar III and three isolates as P. syringae pathovar syringae. In general, all methods of phenotypic analysis grouped isolates according to time of sampling and leaf type. Genome analysis was undertaken by pulsed-field gel electrophoresis (PFGE) of PacI, SpeI, SwaI and XbaI macrorestriction fragments and revealed the presence of eight distinct genomic (clonal) groups. These groups correlated closely with the clusters generated by numerical analysis of phenotypic data, but there was no correlation between macrorestriction fragment profile and isolate identification; in fact the variation in macrorestriction fragment patterns within P. fluorescens biovars was as great as the variation detected between biovars, and between P. fluorescens and P. syringae. Statistical evaluation of macrorestriction fragment patterns revealed two examples of recent strain divergence: one was due to the presence of a 400 kbp plasmid within one isolate of a collection of nine otherwise genomically identical isolates, and the other was observed between two phenotypically similar isolates sampled 220 d apart. Genetic variation was expressed in terms of nucleotide diversity (pi) and pairwise comparisons yielded values ranging from 0.0029 to 0.1517. The mean intrapopulation genetic variation was high (0.0993), but limited genetic variation was detected among isolates sampled on each occasion. Taken together this suggests a population comprised of a variety of apparently distantly related clones (genomic groups), each adapted to local conditions. Genome sizes were estimated from the sum of SpeI restriction fragments and ranged from 4.2 to 5.5 Mbp. Examination of the distribution of XbaI, SpeI, SwaI and PacI restriction endonuclease sites showed that the distribution of SpeI sites differed significantly from the expected (random) distribution.
在一个生长季中从甜菜叶际分离出30株荧光假单胞菌，基于脂肪酸甲酯（FAME）分析显示它们密切相关，对其进行了详细的表型和基因型特征分析。根据生化特性、唯一碳源同化、FAME分析、有机热解产物含量（MS-热解）和全细胞蛋白质谱评估表型特征。除全细胞蛋白质谱外，数据的数值分析揭示了两个主要聚类，每个聚类又分为几个亚聚类。全细胞蛋白质数据的数值分析未能将分离株分为两个主要聚类，但仍将分离株分为六个亚聚类。根据生化和碳源同化谱，19株分离株被鉴定为荧光假单胞菌生物变种V，8株为荧光假单胞菌生物变种III，3株为丁香假单胞菌丁香致病变种。总体而言，所有表型分析方法都根据采样时间和叶片类型对分离株进行了分组。通过对PacI、SpeI、SwaI和XbaI酶切大片段进行脉冲场凝胶电泳（PFGE）进行基因组分析，结果显示存在八个不同的基因组（克隆）组。这些组与表型数据的数值分析所产生的聚类密切相关，但酶切大片段图谱与分离株鉴定之间没有相关性；事实上，荧光假单胞菌生物变种内酶切大片段模式的变异与生物变种之间以及荧光假单胞菌和丁香假单胞菌之间检测到的变异一样大。对酶切大片段模式的统计评估揭示了两个近期菌株分化的例子：一个是由于在一组九个基因组相同的分离株中的一个分离株中存在一个400 kbp的质粒，另一个是在相隔220天采样的两个表型相似的分离株之间观察到的。遗传变异以核苷酸多样性（pi）表示，成对比较产生的值范围为0.0029至0.1517。种群内平均遗传变异较高（0.0993），但在每次采样的分离株中检测到的遗传变异有限。综合来看，这表明该种群由各种明显远缘相关的克隆（基因组组）组成，每个克隆都适应于当地条件。根据SpeI酶切片段的总和估计基因组大小，范围为4.2至5.5 Mbp。对XbaI、SpeI、SwaI和PacI限制性内切酶位点分布的检查表明，SpeI位点的分布与预期（随机）分布有显著差异。
