Population Genomic Analysis of Strain Variation in Leptospirillum Group II Bacteria Involved in Acid Mine Drainage Formation

Abstract

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 ∼20×). 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 (∼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. Communities of microbes in nature consist of a large number of distinct individuals. The variation in DNA sequence between these individuals contains a record of the evolutionary processes that have shaped each community. In most environments, however, the high number of distinct species makes obtaining information about the nature of this variation difficult or impossible. We obtained large amounts of sequence data for a natural community in an acid mine drainage system consisting of only a few species. This enabled us to reconstruct the genome of the dominant bacterium (Leptospirillum group II) and obtain detailed information about sequence variation between individuals, including differences in both gene content and gene sequence. Our analysis shows extensive recombination between closely related populations, as well as fewer instances of recombination between more distantly related individuals. Additionally, viruses and plasmids account for high variability in gene content between individuals. We conclude that sequence-level variation in this population is maintained through neutral processes (migration, recombination, and genetic drift) rather than natural selection. This suggests that closely related strains of the Leptospirillum group II population may not be ecologically distinct.