Cheng Kun, Rong Xiaoying, Pinto-Tomás Adrián A, Fernández-Villalobos Marcela, Murillo-Cruz Catalina, Huang Ying
State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China University of Chinese Academy of Sciences, Beijing, China.
State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
Appl Environ Microbiol. 2015 Feb;81(3):966-75. doi: 10.1128/AEM.02925-14. Epub 2014 Nov 21.
Examining the population structure and the influence of recombination and ecology on microbial populations makes great sense for understanding microbial evolution and speciation. Streptomycetes are a diverse group of bacteria that are widely distributed in nature and a rich source of useful bioactive compounds; however, they are rarely subjected to population genetic investigations. In this study, we applied a five-gene-based multilocus sequence analysis (MLSA) scheme to 41 strains of Streptomyces albidoflavus derived from diverse sources, mainly insects, sea, and soil. Frequent recombination was detected in S. albidoflavus, supported by multiple lines of evidence from the pairwise homoplasy index (Φw) test, phylogenetic discordance, the Shimodaira-Hasegawa (SH) test, and network analysis, underpinning the predominance of homologous recombination within Streptomyces species. A strong habitat signal was also observed in both phylogenetic and Structure 2.3.3 analyses, indicating the importance of ecological difference in shaping the population structure. Moreover, all three habitat-associated groups, particularly the entomic group, demonstrated significantly reduced levels of gene flow with one another, generally revealing habitat barriers to recombination. Therefore, a combined effect of homologous recombination and ecology is inferred for S. albidoflavus, where dynamic evolution is at least partly balanced by the extent that differential distributions of strains among habitats limit genetic exchange. Our study stresses the significance of ecology in microbial speciation and reveals the coexistence of homologous recombination and ecological divergence in the evolution of streptomycetes.
研究种群结构以及重组和生态对微生物种群的影响，对于理解微生物进化和物种形成具有重要意义。链霉菌是一类多样的细菌，广泛分布于自然界，是有用生物活性化合物的丰富来源；然而，它们很少受到种群遗传学研究。在本研究中，我们对41株来自不同来源（主要是昆虫、海洋和土壤）的白黄链霉菌菌株应用了基于五个基因的多位点序列分析（MLSA）方案。通过成对同塑性指数（Φw）测试、系统发育不一致性、Shimodaira-Hasegawa（SH）测试和网络分析等多方面证据支持，在白黄链霉菌中检测到频繁的重组，这突出了链霉菌物种内同源重组的主导地位。在系统发育分析和Structure 2.3.3分析中也观察到强烈的栖息地信号，表明生态差异在塑造种群结构中的重要性。此外，所有三个与栖息地相关的群体，特别是昆虫群体，彼此之间的基因流动水平显著降低，总体上揭示了重组的栖息地障碍。因此，推断白黄链霉菌存在同源重组和生态的联合效应，其中动态进化至少部分地由菌株在不同栖息地的差异分布限制基因交换的程度所平衡。我们的研究强调了生态在微生物物种形成中的重要性，并揭示了链霉菌进化过程中同源重组和生态分化的共存。
