Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formation

被引:106
作者
Simmons, Sheri L. [1 ]
DiBartolo, Genevieve [1 ]
Denef, Vincent J. [1 ]
Goltsman, Daniela S. Aliaga [1 ]
Thelen, Michael P. [2 ]
Banfield, Jillian F. [1 ]
机构
[1] Univ Calif Berkeley, Dept Earth & Planetary Sci, Berkeley, CA 94720 USA
[2] Lawrence Livermore Natl Lab, Chem Directorate, Livermore, CA USA
基金
美国国家科学基金会;
关键词
D O I
10.1371/journal.pbio.0060177
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Deeply sampled community genomic (metagenomic) datasets enable comprehensive analysis of heterogeneity in natural microbial populations. In this study, we used sequence data obtained from the dominant member of a low-diversity natural chemoautotrophic microbial community to determine how coexisting closely related individuals differ from each other in terms of gene sequence and gene content, and to uncover evidence of evolutionary processes that occur over short timescales. DNA sequence obtained from an acid mine drainage biofilm was reconstructed, taking into account the effects of strain variation, to generate a nearly complete genome tiling path for a Leptospirillum group II species closely related to L. ferriphilum (sampling depth similar to 20x). The population is dominated by one sequence type, yet we detected evidence for relatively abundant variants (>99.5% sequence identity to the dominant type) at multiple loci, and a few rare variants. Blocks of other Leptospirillum group II types (similar to 94% sequence identity) have recombined into one or more variants. Variant blocks of both types are more numerous near the origin of replication. Heterogeneity in genetic potential within the population arises from localized variation in gene content, typically focused in integrated plasmid/phage-like regions. Some laterally transferred gene blocks encode physiologically important genes, including quorum-sensing genes of the LuxIR system. Overall, results suggest inter-and intrapopulation genetic exchange involving distinct parental genome types and implicate gain and loss of phage and plasmid genes in recent evolution of this Leptospirillum group II population. Population genetic analyses of single nucleotide polymorphisms indicate variation between closely related strains is not maintained by positive selection, suggesting that these regions do not represent adaptive differences between strains. Thus, the most likely explanation for the observed patterns of polymorphism is divergence of ancestral strains due to geographic isolation, followed by mixing and subsequent recombination.
引用
收藏
页码:1427 / 1442
页数:16
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