Department of Microbial Ecology, University of Groningen, Nijenborgh 7, AG 9747, Groningen, The Netherlands.
Environ Microbiol. 2014 Mar;16(3):856-70. doi: 10.1111/1462-2920.12239. Epub 2013 Aug 27.
It has recently become feasible to study the basis and nature of evolutionary changes in bacteria in an experimental setting using defined media. However, assessment of adaptive changes in complex environments has been scarce. In an effort to describe the responses in such environments, we unravel, in a comparative approach, the transcriptional and genetic profiles of 19 Escherichia coli strains that evolved in Luria Bertani medium under three different oxygen regimes over 1000 generations. A positive relationship between upregulation of gene expression and the number of mutations was observed, suggesting that a number of metabolic pathways were activated. Phenotypic polymorphisms were observed in parallel cultures, of which some were related with mutations at the regulatory level. Non-parallel responses were observed at the intrapopulational level, which is indicative of diversifying selection. Parallel responses encompassed transcriptome diversity, and their effects were directly affected by differing genomic backgrounds. A fluctuating selective force produced higher phenotypic diversity compared with constant forces. This study demonstrates how phenotypic innovations may depend on the relationship between genomic changes and local ecological conditions. Using both comparative genomics and transcriptomics approaches, the results help elucidating various adaptive responses in cultures in unexplored complex environments.
最近，使用定义明确的培养基在实验环境中研究细菌进化变化的基础和性质已成为可能。然而，对复杂环境中适应性变化的评估却很少。为了描述这种环境中的反应，我们采用比较方法，解析了在 1000 代内于三种不同氧条件下在 LB 培养基中进化的 19 株大肠杆菌的转录组和遗传特征。观察到基因表达上调与突变数量之间存在正相关关系，表明许多代谢途径被激活。在平行培养物中观察到表型多态性，其中一些与调控水平的突变有关。在种群内观察到非平行反应，表明存在多样化选择。平行反应包含转录组多样性，其效果直接受到不同基因组背景的影响。波动的选择力与恒定的选择力相比产生了更高的表型多样性。这项研究表明了表型创新如何可能取决于基因组变化与局部生态条件之间的关系。使用比较基因组学和转录组学方法，结果有助于阐明在未知复杂环境中的培养物中的各种适应性反应。
