School of Environmental Science and Engineering International Environmental Research Center, Gwangju Institute of Science and Technology, Gwangju, Korea.
Environ Microbiol. 2011 Dec;13(12):3103-13. doi: 10.1111/j.1462-2920.2011.02541.x. Epub 2011 Aug 30.
Seasonal and spatial variation in the genotypic richness of 3480 Escherichia coli isolates obtained from the Yeongsan River basin in South Korea was investigated by using the horizontal fluorophore-enhanced rep-PCR (HFERP) DNA fingerprinting technique. The relationship between 60 E. coli isolates from each of 58 freshwater samples was determined by using multidimensional scaling (MDS) analysis and self-organized maps (SOMs). The MDS analysis, done based on HFERP DNA fingerprints, showed that E. coli isolates obtained in October through December clustered tightly, while those obtained in other sampling periods were more genetically diverse. However, site-specific E. coli genotypes were not observed. SOMs analysis, done using the 10 most frequently isolated E. coli genotypes, showed the occurrence of season-specific E. coli genotypes and the main SOMs clusters were most influenced by temperature, strain diversity and biochemical oxygen demand. Diversity among E. coli genotypes tended to decrease as water temperature decreased, and the numbers of E. coli genotypes observed in urban area were greater, more diverse and less dependent on water temperature than those obtained from agricultural areas. Taken together, our findings indicate that that an ecological approach needs to be considered in order to obtain a better understanding of E. coli community dynamics in the environment and that SOMs analysis is useful to visualize the multidimensional dependent variables that are influencing the types and dynamics of specific E. coli genotypes in the environment.
采用水平荧光增强重复聚合酶链反应（HFERP）DNA 指纹图谱技术，研究了从韩国荣山河流域获得的 3480 株大肠杆菌基因型丰富度的季节性和空间变化。通过多维尺度分析（MDS）和自组织映射（SOM）分析了来自 58 个淡水样本中每个样本的 60 个大肠杆菌分离株之间的关系。基于 HFERP DNA 指纹图谱的 MDS 分析表明，10 月至 12 月获得的大肠杆菌分离株聚类紧密，而其他采样期获得的分离株遗传多样性更高。然而，没有观察到特定地点的大肠杆菌基因型。使用最常分离的 10 种大肠杆菌基因型进行的 SOM 分析表明，出现了特定季节的大肠杆菌基因型，并且主要的 SOM 簇主要受温度、菌株多样性和生化需氧量的影响。随着水温的降低，大肠杆菌基因型之间的多样性趋于降低，而在城市地区观察到的大肠杆菌基因型数量比农业地区更多、更多样化，且对水温的依赖性更小。综上所述，我们的研究结果表明，需要采用生态方法来更好地了解环境中大肠杆菌群落的动态变化，而 SOM 分析有助于可视化影响环境中特定大肠杆菌基因型的类型和动态的多维因变量。
