title: Population genetic analysis of Streptomyces albidoflavus reveals habitat barriers to homologous recombination in the diversification of streptomycetes.
abstract: 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.
authors.affiliation: State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China University of Chinese Academy of Sciences, Beijing, China.
authors.forename: Kun
authors.initials: K
authors.lastname: Cheng
authors.affiliation: State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Xiaoying
authors.initials: X
authors.lastname: Rong
authors.affiliation: Center for Research in Cell and Molecular Biology, University of Costa Rica, San José, Costa Rica Center for Research in Microscopic Structures, University of Costa Rica, San José, Costa Rica.
authors.forename: Adrián A
authors.initials: AA
authors.lastname: Pinto-Tomás
authors.affiliation: Center for Research in Cell and Molecular Biology, University of Costa Rica, San José, Costa Rica Center for Research in Microscopic Structures, University of Costa Rica, San José, Costa Rica.
authors.forename: Marcela
authors.initials: M
authors.lastname: Fernández-Villalobos
authors.affiliation: Center for Research in Cell and Molecular Biology, University of Costa Rica, San José, Costa Rica Center for Research in Microscopic Structures, University of Costa Rica, San José, Costa Rica.
authors.forename: Catalina
authors.initials: C
authors.lastname: Murillo-Cruz
authors.affiliation: State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China huangy@im.ac.cn.
authors.forename: Ying
authors.initials: Y
authors.lastname: Huang
mesh_terms: D000818:Animals; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D017753:Ecosystem; D051456:Gene Flow; D014644:Genetic Variation; D005828:Genetics, Population; D059765:Homologous Recombination; D007313:Insecta / Q000382:microbiology; D008969:Molecular Sequence Data; D058885:Multilocus Sequence Typing; D012623:Seawater / Q000382:microbiology; D012988:Soil Microbiology; D013302:Streptomyces / Q000235:genetics* / Q000302:isolation & purification
chemical_list: D004269:DNA, Bacterial