Department of Crop and Soil Sciences, Cornell University, Ithaca, NY 14853, USA.
Appl Environ Microbiol. 2011 Jan;77(1):211-9. doi: 10.1128/AEM.01880-10. Epub 2010 Nov 12.
The intestinal microbe Escherichia coli is subject to fecal deposition in secondary habitats, where it persists transiently, allowing for the opportunity to colonize new hosts. Selection in the secondary habitat can be postulated, but its impact on the genomic diversity of E. coli is unknown. Environmental selective pressure on extrahost E. coli can be revealed by landscape genetic analysis, which examines the influences of dispersal processes, landscape features, and the environment on the spatiotemporal distribution of genes in natural populations. We conducted multilocus sequence analysis of 353 E. coli isolates from soil and fecal samples obtained in a recreational meadow to examine the ecological processes controlling their distributions. Soil isolates, as a group, were not genetically distinct from fecal isolates, with only 0.8% of genetic variation and no fixed mutations attributed to the isolate source. Analysis of the landscape genetic structure of E. coli populations showed a patchy spatial structure consistent with patterns of fecal deposition. Controlling for the spatial pattern made it possible to detect environmental gradients of pH, moisture, and organic matter corresponding to the genetic structure of E. coli in soil. Ecological distinctions among E. coli subpopulations (i.e., E. coli reference collection [ECOR] groups) contributed to variation in subpopulation distributions. Therefore, while fecal deposition is the major predictor of E. coli distributions on the field scale, selection imposed by the soil environment has a significant impact on E. coli population structure and potentially amplifies the occasional introduction of stress-tolerant strains to new host individuals by transmission through water or food.
肠道微生物大肠杆菌（Escherichia coli）会在次级生境中随着粪便沉积，在那里短暂生存，从而有机会定植于新宿主。可以推测次级生境中的选择作用，但它对大肠杆菌基因组多样性的影响尚不清楚。通过景观遗传分析可以揭示宿主外大肠杆菌（E. coli）所受到的环境选择压力，该分析方法研究了扩散过程、景观特征和环境对自然种群中基因时空分布的影响。我们对从休闲草地上采集的土壤和粪便样本中的 353 株大肠杆菌（E. coli）分离株进行了多位点序列分析，以研究控制其分布的生态过程。土壤分离株与粪便分离株在遗传上没有明显区别，群体间仅有 0.8%的遗传变异，且没有与分离株来源相关的固定突变。对大肠杆菌（E. coli）种群的景观遗传结构分析表明，存在斑块状的空间结构，这与粪便沉积的模式一致。通过控制空间模式，可以检测到与土壤中大肠杆菌（E. coli）遗传结构相对应的 pH 值、湿度和有机物的环境梯度。大肠杆菌（E. coli）亚种群（即大肠杆菌（E. coli）参考集[ECOR]群）之间的生态差异导致了亚种群分布的变化。因此，虽然粪便沉积是大肠杆菌（E. coli）在田间尺度上分布的主要预测因子，但土壤环境施加的选择对大肠杆菌（E. coli）种群结构有显著影响，并可能通过水或食物传播，偶尔将耐受应激的菌株引入新宿主个体。
