Lu Zexun, Lapen David, Scott Andrew, Dang Angela, Topp Edward
Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario, Canada.
Appl Environ Microbiol. 2005 Oct;71(10):5992-8. doi: 10.1128/AEM.71.10.5992-5998.2005.
Repetitive extragenic palindromic PCR fingerprinting of Escherichia coli is one microbial source tracking approach for identifying the host source origin of fecal pollution in aquatic systems. The construction of robust known-source libraries is expensive and requires an informed sampling strategy. In many types of farming systems, waste is stored for several months before being released into the environment. In this study we analyzed, by means of repetitive extragenic palindromic PCR using the enterobacterial repetitive intergenic consensus primers and comparative analysis using the Bionumerics software, collections of E. coli obtained from a dairy farm and from a swine farm, both of which stored their waste as a slurry in holding tanks. In all fecal samples, obtained from either barns or holding tanks, the diversity of the E. coli populations was underrepresented by collections of 500 isolates. In both the dairy and the swine farms, the diversity of the E. coli community was greater in the manure holding tank than in the barn, when they were sampled on the same date. In both farms, a comparison of stored manure samples collected several months apart suggested that the community composition changed substantially in terms of the detected number, absolute identity, and relative abundance of genotypes. Comparison of E. coli populations obtained from 10 different locations in either holding tank suggested that spatial variability in the E. coli community should be accounted for when sampling. Overall, the diversity in E. coli populations in manure slurry storage facilities is significant and likely is problematic with respect to library construction for microbial source tracking applications.
大肠杆菌的重复基因外回文PCR指纹图谱是一种用于识别水生系统中粪便污染宿主来源的微生物源追踪方法。构建强大的已知来源文库成本高昂，且需要明智的采样策略。在许多类型的养殖系统中，粪便会储存数月后才排放到环境中。在本研究中，我们通过使用肠杆菌重复基因间共有引物进行重复基因外回文PCR，并使用Bionumerics软件进行比较分析，对从奶牛场和养猪场采集的大肠杆菌样本进行了分析，这两个养殖场都将粪便以泥浆形式储存在储存池中。在从畜舍或储存池获得的所有粪便样本中，500个分离株的集合未能充分代表大肠杆菌种群的多样性。在奶牛场和养猪场，当在同一天采样时，储存池中大肠杆菌群落的多样性均高于畜舍。在两个养殖场中，对相隔数月采集的储存粪便样本进行比较表明，就检测到的基因型数量、绝对同一性和相对丰度而言，群落组成发生了显著变化。对从储存池10个不同位置获得的大肠杆菌种群进行比较表明，采样时应考虑大肠杆菌群落的空间变异性。总体而言，粪便泥浆储存设施中大肠杆菌种群的多样性显著，这可能给微生物源追踪应用的文库构建带来问题。
